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reading: Chapters 3, 5
Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees.
Textbook General Morphology 1866 Traces all of life to Moneren (Monera).Linear progress from Monera to Man.
Ernst Haeckel
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Yet another version of Haeckel’s tree of life
All eukaryotes descended from prokaryotes, culminating in man.
Prokaryotes not all that interesting.
Zuckerkandl & Pauling
Pauling: 1954 Nobel Prize,nature of the chemical bond
Series of papers in 1962-1965:
Mutations form the basis for disease.Disease has a molecular basis.Studying diseases that involve different forms of hemoglobin.
Showed that:a. if you knew the genetic code, you could trace the mutations
that caused diseaseb. there is buried history in protein (or gene) sequences (hold information)c. approximate time of the existence of an ancestral sequenced. can infer the probable sequence of the ancestor (AACGTTC)e. can infer “the lines of descent along which given changes in amino-
acid sequence occurred”
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Thermus thermophilus GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UGSynechocystis PCC 6301 GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UGMicrococcus luteus GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UUFlexibacterium sp. GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UUAgrobacterium tumefaciens GAC-ACGUGAA-AUCCUGUUC-GAACAU-GGGGAG--ACCA-CUC-U-CCA-AG-CCUA-AGUAC-UC-G-UGEscherichia coli GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UGPseudomonas cepacia GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UGAquifex aeolicus GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UUChloroflexus aurantiacus GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU
treereconstruction/inferencealgorithm
DNA extraction
clone
sequence
cells/culture
time
Overall Scheme for Constructing a Phylogenetic Tree
phylogeny -development of a raceor species
Example How to Construct a Phylogenetic Tree
Count the number ofdifferences. Correct for
multiple mutations.
Construct a Tree that Best Explains the Distances Observed
1. chose which taxa2. tabulate traits3. identify synapomorphies
= shared derived traits4. build up a cladogram
= tree showing evolutionary relationships
good introductory resource:www.ucmp.berkeley.edu
TABLE 2 limbs scales amniote feathers hair placenta bloodfrog 4 N N N N N Coldalligator 4 Y Y N N N Coldduck 4 Y Y Y N N Warmcat 4 N Y N Y Y Warmopossum 4 N Y N Y N Warm
Can also Build a Tree using Cladistics
cladistics - reconstructing trees usingshared, derived traits
The Importance of Having A Phylogenetic Tree
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The Importance of Having A Phylogenetic Tree, cont.
Tree of Life
Constructed by aligning a gene sequence common to all organisms.Common gene: ribosomal RNA gene.Three major lineages - these are called domains.Root is where the last common ancestor gave rise to the three domains.Root is placed at the base of the bacterial domain.
Ribosome
Synthesizes Proteins in the CellLarge complex made of RNA and small proteinsRNA catalyzes the reaction to make proteinsRNAs called ribosomal RNAs
Archaea are more closely related to Eukaryotes than to Bacteria
At first this was a big surprise - expected Bacteria and Archaea to be more similar to the exclusion of Eukaryotes
1989: Rooting the Tree of Life
three studies:Gogarten et al. ATPasesIwabe et al. tRNA synthetasesBaldauf et al. elongation factors
The Bacterial Domain
At least 18 divisions - major lineages.Some divisions have never been cultured!Some have unique characteristics (e.g., the Cyanobacteria).Most lack unique characteristics.One major group Proteobacteria - have a large variety of different
physiologies
Bacterial tree is notwell resolved atpresent
The Bacterial Domain, cont.
Early lineages are hyperthermophiles.Deinococcus branches somewhat deep.E. coli is a member of the Proteobacteria, branches late.Cyanobacteria also branch late.Bacillus & Clostridium members of the Low G+C Gram Positive Bacteria.Are several lineages of photosynthetic phyla.
Are Five Phyla ContainPhotosynthetic Taxa:Green Non-Sulfur BacteriaGreen Sulfur BacteriaCyanobacteriaLow G+C Gram Positives (Heliobacillus)Proteobacteria
Key Characteristics of Bacteria
1. Cell walls made of a similar polymer (peptidoglycan)2. Lipids are made of similar compounds (fatty acids with ester linkages)3. RNA polymerase (enzyme that makes mRNA copies of genes)
made of 4 different proteins (’)4. Signature sequences tell RNA polymerase where to start making
RNA 5. All proteins begin with a modified amino acid formyl-Methionine
The Archaeal Domain
Two major well-studied phyla are Euryarchaeota and Crenarchaeota.Two new phyla are Korarchaeota (no pure cultures yet) and
Nanoarchaeota (is a symbiont of a Crenarchaeote). Not clear where these lineages branch.
Most of the early branches are hyperthermophilic.
Obsidian Pool, Yellowstone,home of Korarchaeota
Crenarchaeota
All cultured species are hyperthermophilic.Many inhabit “extreme environments”:hyperthermophiles- very high T lovingthermoacidophiles - high T acid lovingMany have short branches - evolve slowly.
(should, in principle, be good models for early life on Earth)Great deal of uncultured mesophiles (moderate T loving) everywhere - 30% of
biomass in the open oceans.Mesophiles have long branches - evolving more rapidly.Mesophilic lineages are peripheral.
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red cells are Archaeagreen are Bacteria
marine hydrothermal vent
terrestrial acidic hot spring
Euryarchaeota
Physiologically diverse group.Inhabit many extreme environments:
acidophiles- acid lovingthermoacidophileshalophiles- salt lovingalkaliphiles- alkaline lovinghyperthermophiles
Many lineages are methanogens - generate methane,are strict anaerobes (can only grow without O2)
Methanogens found in diverse habitats:swamps, deep-sea hydrothermal vents, animal intestines, cow rumen, rice paddies,oil wells
Key Characteristics of Archaea
1. Cell walls are different than bacteria (pseudopeptidoglycan)2. Lipids different from bacteria (isoprenoids with ether linkages)3. RNA polymerase more complex than bacteria -
8 or more proteins (eukaryotes have 8-10)4. RNA polymerase needs “help” from other proteins to begin
making mRNA copies of genes (called transcription factors -are similar to eukaryotes)
5. Signature sequences also tell RNA polymerase where to start making RNA, but are unique (TATA boxes - similar to eukaryotes)
6. All proteins begin with the regular amino acid Methionine7. The number of ribosomal proteins are different from bacteria.
Archaea and Bacteria Share Many Characteristics
1. Genes are often linked together in the chromosome2. Have circular chromosomes (eukaryotes have linear chromosomes)3. Genomes are small (eukaryote genomes are huge)4. Both have ribosomes that are small (eukaryotes have larger ribosomes)5. Both metabolically diverse (eukaryotes are not)6. Lack nucleus
…. many more ….
EukaryotesProkaryotes- lack nucleus/nucleiEukaryote (“true nucleus”)are much more complexDNA containing organelles (“little organs”)
nucleusmitochondrion - respirationchloroplast - photosynthesis }were once free-living prokaryotes
often have multiple chromosomes(linear chromosomes)lots more geneslots of “junk DNA” in their genes
Eukaryotes are Typically Larger than Prokaryotes
reading: none
Lecture 17. Why Do You Need to Construct a Tree for Prokaryotes? Trees as
Frameworks
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Cassini Spacecraft found older terrainsand major fractures on moon Enceladus
Course crystalline ice which will degrade overtime.
Must be < 1000 years old!Organic compounds found in the fractures.Must be heated - required T > 100K (-173˚C)Erupting jets of water observed.Cause of eruptions not known….
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Mystery of Enceladus
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