The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull Counting back from human (and S cerevisiae) ldquocrucialrdquo ldquoearly branchingrdquo genomes
bull Eukaryotic supergroups (quick) bull Three kingdoms or two nature of the first
eukaryote bull From FECA to LECA duplications bull From FECA to LECA enodsymbiosis
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Presenter
Presentation Notes
hellip and depend upon your question13
Crucial genomes fill gaps Human S cerevisiae Bony Fish
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Presenter
Presentation Notes
hellip and depend upon your question13
Crucial genomes fill gaps Human S cerevisiae Bony Fish
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Crucial genomes fill gaps Human S cerevisiae Bony Fish
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Presenter
Presentation Notes
hellip and depend upon your question13
Monosiga brevicollis choanoflagelates single celled colonial protists with a
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Monosiga brevicollis choanoflagelates single celled colonial protists with a
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
Presenter
Presentation Notes
hellip and depend upon your question13Chytrids = fungi with flagellar motility13
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
Presenter
Presentation Notes
To get relations we made a tree it is too big too show Hence we annotated the tree in terms of speciations and duplications And hence we obtain orthologies and hence rasGEF repertoire of ancestral genomes Here I show what I mean when I say duplications speciations and ancestral repertoires The tree I on the left is rasgef Bootstrap values are quite low So we go to the ras tree And we find the same thing so our confidence is somewhat improved
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Presenter
Presentation Notes
Could make same story for all supergroups hellip13
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
Presenter
Presentation Notes
Root is unknown Lack of time vs 13Mitochondria are primitive lac of mito is derived13A lot of diversity Lack of genomes I plan to be able to use those genomes as they come available to study evolution of pathways and complexes13Secondary enodymbiosis Relevant for eg michael seidl but also plasmodium malaria13MRP leshmania13Lack of appreciation for enormous eukaryotic diversity
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
ToL amp 3 kingdoms
Presenter
Presentation Notes
Mainly relevant all the LGT hellip that is currently the paradigm means LUCA as such might not exists But LECA stil does
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Presenter
Presentation Notes
Current theory but I have seen it change now quite often so although the article might say something else it could still be ldquotruerdquo or at the very least you should have an idea of which pieces of evidence lead us to believe it is this way and which pieces of the puzzle lead us to believe it is the other way hellip
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
Presenter
Presentation Notes
The gene cluster of the Ub-like protein modifier system in C subterraneum CDSs without gene annotation encode hypothetical proteins CDSs rpn11l (CSUB_C1473) ubl (CSUB_C1474) e2l (CSUB_C1475) e1l (CSUB_C1476) and srfp (CSUB_C1477) encode eukaryotic RPN11 Ubl E2l and E1l and small RING finger protein respectively1313Rpn11 is component of proteosome that removes ubiquitin of captured target13Srfp zou E3 kunnen zijn 13
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
131313In situ immunostainings with anti‐Arcadin‐2 antibodiesA In situ immunofluorescence microscopy of exponentially growing P calidifontis cells stained with anti‐Arcadin‐2 antibodies (green) B Double staining with anti‐Arcadin‐2 antibodies (green) and the DNA‐specific DAPI dye (blue) C Short cells displaying a single fluorescence focus at the extreme end1313copy This slide is made available for non-commercial use only Please note that permission may be required for re-use of images in which the copyright is owned by a third party
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
Presenter
Presentation Notes
Theory of endosymbiosis is dus de theorie dat een bacterie dat een primitieve eukaryoot een bacterie als endosymbiont opnam13En dat die symbiose permanent is geworden13A clue hellip13
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Presenter
Presentation Notes
Zorsquon mitochondria is dus zrsquon eigen mini cel hellip
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
Presenter
Presentation Notes
Eukaryotic nucleur rRNA does not cluster within alphaproteobacteria it clusters on its own Separate from normal bacteria and archaeabacteria
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Alpha-proteobacterial proteins with the rest of the bacteria and archaea
Eukaryotic + alpha-proteobacteria in the same branch
Identifying eukaryotic proteins with an alpha-proteobacterial origin based on their phylogeny
Presenter
Presentation Notes
Hoe doen we dat concept 11313We zoeken bomen type A13En niet bomen type B
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
De pijplijn13Methode1313Die genomen haal je gewoon van het web die zijn publiek
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Reconstruction of the Proto-mitochondrial Cell
Presenter
Presentation Notes
Reconstuctie 131315 miljard redelijk onzeker hellip1313En terug naar onze vraag zo zag ie er dus uit hellip basis voor een discussie over het waarom en waarvoor
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
113
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~16 of the mitochondrial yeast proteins are of alpha-proteobacterial origin
~65 of the alpha-proteobacteria derived set is not mitochondrial
Gabaldon and Huynen Science 2004
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
Presenter
Presentation Notes
Who sais current wisdom is absolute hellip
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
duplications eg small GTPases
Presenter
Presentation Notes
As an example of these massive duplications hellip13Figure 3 Origins of eukaryotic endomembranes mitosis the nucleus and phagocytosis A A prekaryote with a soft surface first13developed a tubular secretory endomembrane system The small GTPase cenancestor induced membrane tubule formation from the13plasma membrane by recruiting microtubule motors B With the advent of vesicle trafficking and membrane recycling the tubular13endomembranes became independent of the plasma membrane Ancestral ArfSar1 regulated secretion to digest surface-bound bacteria13extracellularly and SRb refined the targeting of ribosomes to the secretory membranes Food initially was ingested diffusely all over the cell13cortex and later at defined sites by fluid-phase endocytosis Other cells could not yet be internalised C DNA was attached to the plasma13membrane and was segregated by a bacterial-like mechanism With the origin of Ran a microtubule-based apparatus evolved to stabilise13chromosome segregation Since microtubules were recruited for DNA segregation endomembranes dispersed during mitosis which13facilitated their segregation D After the perfection of mitosis DNA could be liberated from the plasma membrane The nuclear membrane13originated from the secretory membranes Ran played a central role in the evolution of this novel compartment and in the parallel development13of the nuclear transport system The latest common ancestor of the Rab Rho and Ras families regulated phagocytosis The GTPase13was activated by a cell surface receptor and co-ordinated changes in the actin cytoskeleton with membrane targeting and fusion1313
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Not just the gtpases also their activating proteins RapRalRheB GAP
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
Presenter
Presentation Notes
AND a very convenient way to simplify the tree ie the only way to make sense of the data And orthology definition
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
Presenter
Presentation Notes
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicates a group of subunits that are part of extensive paralagous families (Rabs SNAREs etcetera) while the central hexagon is a non-paralagous factor (eg tethering complexes) (B) Gene duplication and sequence divergence of individual components of the identity-encoding machinery would produce new members of these protein families that could potentially associate with new organelles (C) The various protein factors within the identity-encoding machinery would undergo gene duplication and co-evolution as part of a gradual process and with replacement of different components not occurring in a synchronous manner The process would eventually create a novel identity-encoding machine that would control trafficking for a novel transport step This new identity would be reinforced by the inability to interact with accessory factors (yellow hexagon) and acquisition of novel factors (purple hexagon) (D) Gradual subunit replacement of an identity-encoding machine would produce new endomembranous organelles with several iterations giving rise to the observed complexity of organelles in the membrane-trafficking system as well as possibly other non-endosymbiotically derived compartments The concept of the identity-encoding machinery is virtualmdasha single complex does not appear to encode specificity as discussed in the text
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
Presenter
Presentation Notes
(C) Schematic ML phylogeny of fructose-16-bisphosphatase an enzyme with cytosolic and plastidic isoforms that unites Plantae (plastid-targeted protein) and shows an example of a protein affected by EGT The plastidic gene has been transferred from red algae to chromalveolates that contain a red algalndashderived plastid presumably through EGT (marked by the filled red circle) The full tree is shown in fig S2 (D) Schematic ML phylogeny of a gene encoding a thiamine pyrophosphate (TPP)ndashdependent pyruvate decarboxylase family protein involved in alcohol fermentation RAxML bootstrap support values are shown at the nodes of the trees in panels (C) and (D) in which glaucophytes red algae green algae and chromalveolates are in purple red green and brown respectively
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
Presenter
Presentation Notes
REPEAT LARGE SCALE ORTHOLOGY SCHEMES AND HOW THEY WOULD DEAL WITH THIS hellip
(eukaryotic) Tree of Life eukaryogenesis LECA
Crucial genomes fill gaps
Crucial genomes fill gaps
Slide Number 5
Slide Number 6
Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
Monosiga brevicolis
Slide Number 9
RAL evolution
Slide Number 11
RAL evolution
Is the asymmetry (comb) real
many genomes many more underway
Slide Number 15
~6 Supergroups
MPS1 parallel loss of TPR domain
Slide Number 18
ToL amp 3 kingdoms
Eocyte hypothesis
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
Late origin of eukaryotes
Novel archaea has operon with UBQ system
Slide Number 27
Slide Number 28
Slide Number 29
Slide Number 30
Slide Number 31
Arcadin 2 cytokinesis
Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
Eukaryogenesis FECA to LECA
Slide Number 35
Slide Number 36
Slide Number 37
Slide Number 38
Slide Number 39
Benchmarking
Slide Number 41
Slide Number 42
Slide Number 43
Fecaeocyte to LECA
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
Slide Number 47
Adaptor proteins arose via feca-2-leca duplications
Neo or sub functionalization hellip for membrane identity
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
Signalling complexity
Slide Number 52
Euk ToL Orthology complications
HGT between eukaryotes
Slide Number 55
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
