Biology 322 Course Notes 12/13/2013 1:42:00 PM Topic One The Origins of Life Introduction to the Origin of Life Formation of Earth Stable hydrosphere prebiotic chemistry pre-RNA world RNA world First DNA/protein life Last Universal Common Ancestor (LUCA) o RNA primers – Replication of the lagging DNA strand initiates with a DNA primer. o Telomerase RNA – Needed at the ends of linear chromosomes. Splicing and RNA Processing o snRNA – Involved in splicing. o snoRNA – Posttranscriptional processing of rRNA. * shows that RNA has many catalytic activities and enzyme function.
Transcript
Biology 322 Course Notes 12/13/2013 1:42:00 PM
Topic One
The Origins of Life
Introduction to the Origin of Life
Formation of Earth Stable hydrosphere prebiotic chemistry pre-RNA world RNA world First DNA/protein life Last Universal Common
Ancestor (LUCA)
Miller-Urey experiments showed that it was possible to synthesize basic molecules from the theorized environmental conditions of early earth.
It was also proven that the four nucleobases could be formed.
All the necessary components (sugar, nucelobases, phosphates) for the formation of RNA are present and it is possible to obtain RNA from early
Earth. Although it is possible, it is not proven.
Clay may have played an important role in creating long strands of RNA. This is because they allow the molecules to concentrate in the layers and link up
similar to modern RNA.
o Clay acted as a catalyst, facilitating the natural alignment of the RNA
components.
o Thus, the ribonucelotide chain is capable of being formed.
Replicase – catalyzes that synthesis of the complimentary strand. o The additional activities that RNA can perform is more evidence of an
RNA world.
Ribosome – the cellular machinery that catalyzes the growth of a peptide chain.
o It is made of RNA, reads RNA, and synthesizes protein.
o Provides evidence that the RNA world came first.
Modern RNA Roles
Translation o mRNA – Product of DNA transcription.
o tRNA – Involved in translation of the genetic code.
o rRNA – Serves as part of a ribosomal subunit.
DNA Replication o RNA primers – Replication of the lagging DNA strand initiates with a
DNA primer.
o Telomerase RNA – Needed at the ends of linear chromosomes.
Splicing and RNA Processing o snRNA – Involved in splicing.
o snoRNA – Posttranscriptional processing of rRNA.
* shows that RNA has many catalytic activities and enzyme function.
Ribozymes
An RNA molecule capable of performing specific biochemical reactions, similar to
protein enzymes. Types:
Self-splicing introns – some introns splice themselves by an autocatalytic process.
Ribonuclease P – creates the 5’ end of bacterial tRNAs.
Ribosomal RNA – the peptidyl transferase activity required for peptide bond formation during protein synthesis.
The Lipid Envelope
Placing a replicase in a vesicle protects it from replicating everything around it.
In a membrane, it only has access to itself.
Inner aqueous compartment of a phospholipid bilayer provides this.
One theory of the development of the lipid envelope is through geysers. They release, forming mini protocells. When they are in a solution, these molecules
form an envelope spontaneously.
The Protocell
Self replicating – able to divide.
Molecules clay chain incorporated into a lipid bilayer (lipids formed in geysers).
One theory: Assisted reproduction via hot/cold environments o At the warm side of the “pond”, the RNA is warmed and denaturation
occurs, membranes grow, and daughter cells separate. On the cold side,
the single RNA strands act as a template on which new nucleotides
formed base pairs.
So Far….
Pre-RNA world o Prebiotic pool of random sequences.
o Prebiological compounds.
o Alternative genetic system, such as RNA/DNA analogs or
informational polymers using metal ions for catalytic activity.
Transition o RNA catalyzes its own replication.
o Fidelity of replication improved.
o Genome length reaches about 100 nucleotides.
RNA World o RNA as the only genetically encoded compound.
o Evolution based on RNA replication via Watson Crick base pairing.
o Translation arises.
DNA replaces RNA
o DNA copy made by RNA.
o Protein world evolves.
Or
o Protein world evolves.
o NTPs dNTPs DNA copy made by proteins.
DNA World
RNA world is the core to many things tRNA, catalytic RNA.
Evolution promotes better cell: RNA Proteins DNA
DNA is more stable, can encode more information, leading to more stable genetic material.
Deoxyribonucleotide requires a reductase in order to be formed from a ribonucleotide.
DNA can self-replicate, but not efficiently. A polymerase makes it more efficient.
Longer exposure of DNA to UV light lead to longer polymers.
Journey to the Modern Cell
1. Evolution Starts
The first protocell is just a sac of water and RNA and requires an external
stimulus (such as cycles of heat and cole) to reproduce.
2. RNA Catalysts
Ribozymes – folded RNA molecules analogous to protein-based enzymes –
arise and take on such jobs as speeding up reproduction and strengthening
the protocell’s membrane. The protocells then begin reproducing on their
own.
3. Metabolism Begins
Other ribozymes catalyze metabolism – chains of chemical reactions that
enable protocells to tap into nutrients from the environment.
4. Proteins Appear
Complex systems of RNA catalysts begin to translate strings of RNA letters
(genes) into chains of amino acids (proteins). Proteins later prove to be more
efficient catalysts and able to carry out a variety of tasks.
5. Proteins Take Over
Proteins take on a wide range of tasks within the cell. Protein-based catalysts,
or enzymes, gradually replace most ribozymes.
6. The Birth of DNA
Other enzymes begin to make DNA. Thanks to its superior stability, DNA
takes on the role of the primary genetic molecule. RNA’s main role is not to
act as a bridge between DNA and protein.
7. Bacterial World
Organisms resembling modern bacteria adapt to living virtually everywhere
on Earth and rule unopposed for billions of years until some of them begin to
evolve into more complex organisms.
Last Universal Common Ancestor (LUCA)
Genetic code confirms that there was a last universal common ancestor.
Three letter genetic code uses A, C, T, G for DNA and A, C, U, G for RNA.
Genetic code is shared by all forms of life.
No reason for this specific code – random survival.
There are variations to the code and they are relatively rare. It happened later in life and only a few codons are involved.
Trees of Life
Haekel’s Tree of Life was the first to show a relationship. o No systematic system.
o Qualitative – based on his own judgment.
Whittaker’s Five Kingdom Tree shows a false linear classification. The plantae, fungi, and animalia groups are distinguished by their nutrition.
The current rooted tree of life with three domains was hypothesized first in the 1980’s.
o Based on RNA sequence.
o Archaea are so different from bacteria that they branched elsewhere.
Modern Tree of Life o Dynamic interaction between branches w/ mixed genes due to LGT.
Protein translation o Ribosomes made up of RNA and proteins – 16S/18S rRNA.
o Charged tRNAs used – Many ribosomal proteins.
Transcription o At least a three subunit DNA-dependent RNA polymerase – rpoA
DNA Replication o DNA was the genetic material – Pol1-type exonuclease.
DNA Recombination o RecA
Protein insertion in membranes o SecY & FtsY
Phylogenetic Trees
Can be based on one gene, multiple genes, or a genome.
Ancestral Trait – The trait evolved in the common ancestor of a group of organisms; it was present in the common ancestor the of the species.
Derived Trait – The trait is not present in the common ancestor of a set of different species.
Homologous – The trait is present in a common ancestor of two species. o Example: human hand and bat wing, photosynthesis is cyanobacteria
and chloroplasts.
Analogous – The trait evolved independently among two species. o Example: bird and insect wings, capture of light by chlorophyll and
rhodopsins.
Trees are rooted based on the principle of parsimony. That is, the lease number of assumptions is generally correct.
Terms to Explain Trees o Branches
o Nodes (speciation events)
o Internodes (ancestors)
Orthologs – diverge due to species lineages separating (common ancestor).
Paralogs – genes evolve in parallel within species after a duplication.
Long Branch Attraction – a methodological artifact that can cause phylogenetic trees to inaccurately portray evolutionary history. It causes
errors in phylogenetic reconstruction. Famous example is microsporidia.
Lateral Gene Transfer – many LGT’s can create a network within the tree.
Convergent Evolution – the evolution of two similar traits, such as the coloration of different animals.
Monophyly – all members of the group share a common ancestor. That is, it consists of an ancestral species and all its descendants.
Polyphyly – a group consisting of one or more homoplasies (convergent evolution events). Example: grouping of warm blooded species places
mammals and birds together. However, the most recent common ancestor
was cold-blooded.
Paraphyly – consists of all the descendants of the last common ancestor of the group minus a small number of monophyletic groups to the descendants.
Example: the group of reptiles is paraphyletic with respect to mammals and
birds.
Two Cell Membranes
Bacterial/Eukaryotic o Ester link
o Fatty acids
Archaeal * o Ether link
o Isoprenoid
* Still hydrophobic, but has different properties.
The heads are stereoisomers of each other, but are formed through completely different pathways, with the same precursor.
Current theory is that LUCA had a heterochiral membrane and could make fatty acids and isoprenoids. Enzymes were later developed with a specific
stereochemistry. The membrane was mixed at the point of LUCA, but
eventually one of the pathways was lost. This is the split between isoprenoids
and fatty acids.
Major Inventions of Archaea
Halobacteria – can survive in high salt and can make energy from sunlight.
Most species of Euryarchaeota (except Halobacteria) are methanogens and not extreme thermophiles
Crenarchaeota – can survive at high temperatures and/or high acidity.
Major Inventions of Bacteria
Aquificae – grow in cold environments.
Thermotogae – grow in hot environments.
Deinococcus-Thermus – resistant to radiation.
Chloroflexi – photosynthetic.
Chlorobi – anaerobic phototrophs (use sulfur compounds as source of electrons).
Thermophilic Ancestor?
Species close to the root of LUCA are thermophilic.
Likely due to long branch attraction.
Ability to live at high temperatures evolves relatively quickly.
Need to change amino acid composition to include more Hydrogen Bonds.
Energy Metabolism
Chart o Phototrophs – use light as the energy source.
Photoautotrophs – use carbon dioxide.
Photoheterotrophs – use organic carbon.
o Chemotrophs – use chemical compounds as the energy source.
Chemolithotrophs – use inorganic chemicals.
Chemolithoautotrophs use carbon dioxide.
Mixotrophs use organic carbon.
Chemoorganotrophs – use organic chemicals.
Trinomial Nomenclature: o Carbon, energy, and electrons are the three requirements.
o Eight types
Photolithoautotrophs
Photolithoheterotrophs
Photoorganoautotrophs
Photoorganoheterotroph
Chemolithoautotroph
Chemolithoheterotroph
Chemoorganoautotroph
Chemoorganoheterotroph
Key Points: o Heterotroph – organic compounds.
o Autotroph – carbon dioxide.
o Chemolithotrophy – only found in prokaryotes, uses inorganic
compounds.
o Chemoorganotroph – uses organic compounds.
o Methanogeneis is found only in some Archaea.
o Photosynthesis is unique to bacteria – cyanobacteria.
o Two types of phototrophy:
One. Oxygenic
Produces oxygen.
Electrons for ETC come from water.
Two. Anoxygenic.
Does not produce oxygen.
Electrons come from sources other than H2O.
Oxygenic Photosynthesis o Reaction Centre One – can catalyze the oxidation of hydrogen and
highly reduced electron donors – likely the first to evolve.
o Reaction Centre Two – Does not work well with very reduced
substrates like hydrogen, has higher affinity for sulfur or water.
o The Origin of Oxygenic Photosynthesis (Know This!):
1. Procyanobacteria invent RC1 – possibly to protect from UV
radiation.
2. They become able to use RC1 in photosynthesis with highly
reduced substrates as electron donors.
3. This creates a depletion of reduced substrates.
4. This creates evolutionary pressure for the invention of RC2 –
specialized in using more oxidized substrates.
5. Procyanobacteria evolve the ability to split water and make
oxygen using a combination of RC1 and RC2.
6. Levels of atmospheric oxygen increase as a result of oxygenic
photosynthesis.
7. This further depletes reduced substrates and increased the
advantage of accessing water for electrons.
The Evolution of Eukaryotes
Two Main Hypotheses: 1. Hydrogen Hypothesis
Can use CO2 to form methane.
Integrate hydrogen producing symbiotic cell to produce more
H2 and, thus, more energy.
More parsimonious (?)
2. Syntrophy Hypothesis
Methane-feeding symbiont is incorporated to eliminate waste
products from the cell.
o In both cases, the symbiont becomes the mitochondria.
DNA Structure o Histones are found only in Eukaryotes.
Evolution of the Nucleus o Karyogenic Hypothesis – cell creates membrane.
o Endokaryotic Hypothesis – membrane imported into gram negative
bacterium to create a protoeukaryote.
Acquisition of Organelles
Mitochondria o A single event in which the ancestor of all eukaryotes engulfed an
alphaproteobacteria is at the origin of mitochondria in eukaryotes.
o This alphaproteobacteria was, over time, enslaved by its host to
become a mitochondrion.
o Mitochondria are organelles responsible for generating energy through
respiration.
o Types of Mitochondria:
Fully functional – mitochondria with genome.
Relic – partial genome, function unknown.
Hydrogenosomes – no genome, generate energy by oxidation of
pyruvate.
Complete loss – no mitochondria present.
o Share an ancestor with alphaproteobacteria.
o Primary amitochondriate never had a mitochondria – doesn’t exist
today.
o Secondary amitochondriate lost it’s mitochondria – does exist.
o Bacteria would have lived in the cytoplasm for an extended period of
time until a successful replacement event occurred.
o Mitochondria have a single origin, but have been lost or degenerated
many times.
Plastids o A single event in which the ancestor of Archaeplastida engulfed a
cyanobacteria is at the origin of photosynthesis in eukaryotes.
o It was, over time, enslaved, to become a plastid.
o Plastids are organelles responsible for photosynthesis, storage of
products like starch, and for the synthesis of pigments.
o They can differentiate and redifferentiate between these and other
forms.
o All plastids are derived from pro-plastids.
o Found throughout tree of life.
o One origin, many transfers.
Endosymbiosis Summary a. Amitochondriate eukaryotic ancestor.
b. Development of the nucleus.
c. Alphaproteobacteria.
d. Mitochondriate eukaryotes.
e. Cyanobacteria.
f. Ancestor of green algae, red algae, glaucophytes, and land plants.
g. Secondary endosymbiosis.
h. Secondary loss of plastid.
i. Tertiary endosymbiosis.
Evolution
Three things required for evolution: 1. Genetic Diversity.
2. Replication.
3. Drift and Selection.
Mutation – all intracellular processes creating genetic changes.
Lateral transfer – all processes allowing penetration of DNA in the cells and its integration in the genome.
o Intergenomic homologous recombination.
o Intergenomic heterologous recombination.
o Extrachromosomal maintenance.
Mutation
Any heritable change in DNA sequence.
Only changes in the DNA sequence of a genome considered to have been inherited from a progenitor are considered mutations.
Includes base pair substitutions, insertions, deletions, chromosomal rearrangement, gene duplication, etc.
Base Pair Substitutions o Can be synonymous (silent) – codon encodes for the same amino acid.
o Non-synonymous – codon encodes for a different amino acid
(missense) or creates a stop codon (nonsense).
o Also called single nucleotide polymorphisms.
Gene Duplication o A section of DNA is duplicated.
o Selective pressure if there is improved function.
Chromosomal Rearrangement o Fastest type of mutation.
o Moves in front of stronger or weaker promoters.
o Impacts strength of gene expression.
Dotplots show similarity between two strains. o A diagonal line indicates high similarity.
o A diagonal line in the opposite direction indicates an inversion.
o Breaks indicate and island.
o Can also be used to view changes in gene order. An inversion creates an
“X” pattern. This is particularly relevant for bacterial and archael,
which has two origins of replication.
Ribosomal protein operons are the most highly conserved.
Genomes are not growing in size.
Acquisition of foreign genetic elements are offset by the loss of native genes. If the gene is no longer beneficial, then there is selective pressure for gene loss.
Mutation occurs at the individual level and at the population level. Selection and natural drift determine the abundance of specific mutations in a
population. A mutation isn’t significant unless it enters the population and the
genome.
Lateral Gene Transfer
When genetic material from other cells is involved in changing the DNA sequence of a genome, the process can be termed lateral gene transfer.
This process consists of two main steps: 1. Foreign DNA penetrates the cellular envelope in one of three ways:
transformation, conjugation, or transduction.
Conjugation – physical connection between the two cells. In
halophilic Archaea, cell fusions occur and an intercytoplasmic
bridge is formed between two cells, allowing the exchange of
DNA. Also, pili induce DNA exchange.
Transduction – transfer without physical contact between two
cells. A viral vector, such as a phage, introduces new genetic
material to the host cell. A gene transfer agent (phage-like
particle) can be released without lysing the host and become
encoded; DNA remains protected. Likewise, cell vesicles (bleb)
can come out of a cell and contain DNA, proteins, or toxins.
Transformation – a naturally competent cell is exposed to DNA
in the environment and takes up the DNA, which combines with
the chromosome. Calcium or lightening can induce competence
by making pores in the cell membrane.
It have been three hypothesized DNA uptake system reasons:
a. DNA for genetic diversity – acquisition of potential useful
genetic information.
b. DNA repair – environmental DNA might serve as a
template for DNA damage.
c. DNA as food – DNA can be use as a source of carbon,
nitrogen, and phosphorous.
2. Integration into the new host genome is required, which can be
achieved by either homologous recombination, heterologous
recombination, or extrachromosomal maintenance and replication.
When DNA comes in, it must become single stranded.
DNA must have a minimum level of similarity to the outgoing
gene.
Integron – has promotor ready for new DNA. Assists in
heterologous recombination, with no sequence similarity
required between donor and recipient.
Replication
Tree branches represent the sum of lateral transfers and mutations.
Replication and recombination are seen as tightly interconnected.
The primary role of homologous recombination at the cellular level is now appreciated to be the completion of DNA replication, rather than the
exchange of genetic information.
The same system is responsible for ensuring the accuracy of DNA replication and limiting homologous recombination.
No mobile genetic element is purely extra-chromosomal.
Extra-chromosomal element segregation is often coupled to chromosomal segregation.
Mutability
Constitutive Mutators o Always on.
o Permanently increased mutation rates.
o Bacteria have a mutation rate of one nucleotide per 300 generations.
o Due to defects in mismatch repair system, changes in DNA polymerase,
and changes in other proteins involved in DNA replication.
Inducible Mutators o Requires trigger to be turned on.
o SOS Response – DNA damage causes LexA protein to be broken down
and induces umuDC, recA, and uvrA genes.
Induces error-prone polymerases.
Activates conjugative elements.
Induces movement of transposons and pathogenicity islands.
Triggers bacteriophages.
Activates integrons.
Topic Two 12/13/2013 1:42:00 PM
Taxonomy of Bacteria and Archaea
Diversity
The diversity of bacteria has been highly underestimated.
Taxonomy uses the following categorization method: o Life Domain Kingdom Phylum Class Order Family
Genus Species Subspecies
Species – the basic unit of classification.
Species concept – a framework to understand how and why a observer can sort organisms into species; that is, what kind of unit do we think the term
species embraces, and what characteristics are shared between all members of
a species.
Species definition – a more practical outline of how to assign isolates to a named species or identify a new species.
o Biological – interbreeding natural populations.
o Ecological – lineages occupying an adaptive zone.
o Phylogenetic – biological entity forming a diagnosable monophyletic.
Different species concepts can yield different, incompatible groups.
All these groups are valid and contain information on different biological aspects of organisms.
Morphospecies – a species distinguished from others by its morphology.
Taxospecies – species are based on numerical taxonomy, a battery of biochemical tests that can be assigned a value. This isn’t commonly used
because it is expensive, time consuming, and LGT confuses results.
Genomospecies – strains with approximately 70% or greater DNA-DNA relatedness and with 5 degrees or less delta Tm. Genomospecies should not be
names unless they can be differentiated on the basis of some phenotypic
feature.
Ribosomal RNA o 16S rRNA
o Universal – present in both eukaryotes and prokaryotes.
o Functionality is conserved.
o Slow and fast evolving regions.
o Encodes an RNA molecule, not a protein.
o Abundant in microbial cells.
o 16S rRNA sequence identity of less than 97% between strains indicate
that they represent different species, but at 97% or higher 16S rRNA
sequence identity, DNA relatedness must be used to determine
whether strains belong to different species.
o Drawbacks:
Limited resolution at fine phylogenetic scale.
Multiple copies present.
Intragenomic heterogeneity.
Does not represent whole genome.
Example: comparison of 16S rRNA sequence similarity
vs. DNA-DNA hybridization shows a narrow window.
Multi-locus Sequencing o Select dispersed genes throughout chromosome. Generally, 3-8 protein
coding housekeeping genes are selected.
o They are regularly spaced across the genome, occur in a single copy,
and targets a single genera or species.
o Uses the allelic mismatches of a small number of genes. Statistically,
seven genes is a good amount.
o Single locus variants – two isolates differing at a single allele.
o Sequence types – a unique set of alleles, when the strings are identical.
o If there is more than one base pair different, then there is a >95%
chance that it is due to recombination.
Average Nucleotide Identity o ANI is the Average Nucleotide Identity of all protein-coding genes
shared by two bacteria (core genome comparison).
o Offers greater resolution than either MLST or 16S rRNA sequencing.
o Limitation: only looks at genes from the core.
o Correlates well with DNA hybridization.
o Core Genome Phylogeny – concatenated phylogeny based on all
protein-coding genes shared by two organisms (core genomes).
o Provides higher resolution.
o Genome Composition
Expressed as a % of conserved genes between two organisms.
Calculated by: # of genes in core genome / # of genes in whole
genome.
How to Measure Similarity Between 2 Organisms o Average nucleotide identity – evolutionary relatedness.
o Gene content similarity – ecological relatedness.
o Evolutionary relatedness should be coupled to ecological relatedness.
Polyphasic Taxonomy
Concept – a taxonomy that assembles and assimilates many levels of information, from molecular to ecological, and incorporates several distinct,
and separable, portions of information extractable from a nonhomogeneous
system to yield a multidimensional taxonomy.
Definition – a species is a group of strains sharing at least 70% total genome DNA-DNA hybridization and less than 5% delta Tm. Phenotypic features
should agree with this genotypic definition and should override the
“phylogenetic” species concept only in a few exceptional cases. Total genome
DNA-DNA hybridization values are the key parameter in this species
delineation.
Topic Three – Part A 12/13/2013 1:42:00 PM
Bacteria
Cell Wall
Gram-positive (Actinobacteria & Firmicutes): o Cell wall is 20-80 nm thick.
o One-layer cell wall.
o >50% peptidoglycan content.
o Consists of a plasma layer with an outer peptidoglycan layer.
Gram-negative (All other bacteria): o Cell wall is 10 nm thick.
o Two-layer cell wall.
o 10-20% peptidoglycan content.
o 58% lipid and lipoprotein content.
o Consists of a central peptidoglycan layer, with periplasmic space and
an outer membrane made of lipopolysaccharide and protein.
Vibrio
Genus of gram-negative bacteria with a curved rod shape.
Typically found in saltwater.
Facultative anaerobes.
Vibrio coralliilitycus bleaches coral.
Vibrio cholera secrete the cholera toxin, which causes diarrhea.
In general, obligate intracellular bacteria have smaller genomes, few repears, and many pseudogenes. This is a universal trend.
Smallest Genomes o Buchnera aphidicola – 816 Kb.
Lives in specialized aphid cells.
Cannot repair DNA.
No lipopolysaccharides.
Overproduces amino acids.
o Sulcia muelleri (246 Kb) and Baumannia cicadellinicola (640 Kb)
Leafhopper symbionts.
Missing essential DNA replication genes.
Sulcia supplies amino acids. Baumannia supplies vitamins and
cofactors.
Chlamydia
Obligate intracellular parasites.
Most common bacterial sexually transmitted infections in humans.
Found in the form of an elementary body and a reticulate body.
The elementary body is the non-replicating infections particle that is released when infected cells rupture. It is responsible for the bacteria’s ability to spread
person-to-person. It is analogous to a spore.
The reticulate body is an intracytoplasmatic form, highly involved in the process of replication and growth of these bacteria. After division, the
reticulate body transforms back to the elementary form and is released by the
cell in exocytosis.
Mycoplasma & Phytoplasma
Lack a cell wall.
Unaffected by common antibiotics.
Mycoplasma genitalium – 480 proteins. A very minimal prokaryotic genome. o Theorized that the minimum number of proteins necessary is 240.
Rickettsia
Non motile, gram-negative, non-sporeforming.
Obligate intracellular parasites.
Depend on entry, growth, and replication within the cytoplasm of eukaryotic host cells.
Pelagibacter
Free living organism with the smallest genome.
Atypical photosynthesis: o Uses proteo-rhodopsin.
o Organe/Red colour.
o Rhodopsin changes shape, releasing protons and creating a gradient.
Can remotely sense objects and hunt prey in coordinated attack (social behavior).
Deinococcus
Can withstand an enormous amount of radiation – 10 000 Grays.
Highly pigmented.
Multiple chromosomes.
Extremely active DNA repair system.
Four cytosolic compartments in each cell.
In Deinococcus, recA binds to double stranded DNA and repairs with single stranded DNA – doesn’t let the damage get too bad.
Resistance to radiation likely evolved to reduce the impact of desiccation (or another challenge that required a high rate of DNA repair).
Believed to have evolved independently many times, along with some cases of LGT.
Shigella
Destroys epithelial cells.
Human pathogen, which destroys epithelial cells that form the intestinal musoca through the secretion of a toxin.
Can result in dysentery and death.
Part of the E. coli species and only differentiated through a virulence phenotype.
All Shigella are pathogenic.
Plasmid and two genomic islands in Shigella encode virulence functions.
Thermotogales
Has an outer polysaccharide layer – “toga”
Can survive in high and low temperature environments.
Caulobacter
Alpha proteobacteria.
Related to Rickettsia.
Common ancestor with mitochondria.
Asymmetric division. During the cell cycle, it finds a site, grows a stalk, a flagella, and replicates chromosomes. Two different daughter cells are
produced.
Bacillus
Is able to form a highly resistant spore.
Asymmetrical division – FtsZ creates a division between mother cell and prospore.
Occurs as bacteria age due to nutrient deprivation. It is only triggered due to nutrient limitations.
Generally, all spore forming bacteria are gram positive. It is too complex to laterally transfer, so it is more likely that it occurred at some point in
evolution and some would have lost it.
Paenibaallus o Clusters at end.
o Complex swarming behavior.
o High social IQ.
Helicobacter
Found inside patients with gastric ulcers.
Performs chemotaxis through mucus toward the epithelial cells in the stomach, as the pH is higher than inside the stomach.
Pathogenicity is due to the Caf pathogenicity island. This island encodes several virulence determinants, including type IV secretion system.
The bacteria works by creating a microenvironment with a higher pH. The H. pylori accumulate and produce toxins that can penetrate the endothelial cells.
Bdellovibrio
Pokes a hole in the membrane of its prey and eat the cytoplasm.
Collides with them at high speeds.
Attaches to prey and then enters the periplasmic space.
Bdellovibrio uses hydrolytic enzymes to break down the host cell molecules, which it uses to form a filament.
Life cycle takes up to three hours and produces approximately 3-6 progeny cells.
Streptomyces
Source of antibiotics for humans.
Complex life cycle – five steps. o Germinating spore.
o Underground hypha – vegetative mycelium.
o Aerial growth – aerial hypha.
o Spore chains.
o Spore.
Can form colonies characterized by “fuzzy” outer ridge.
Shows that bacteria are capable of advanced life cycles.
Multiple spores are released at once.
Asymmetric division.
Regulation of the life cycle is a complex process.
Genes code for different modules of amino acids, so it is relatively easy to change the sequence. Thus, changing the product.
Cyanobacteria
Photosynthetic cells.
Consists of groups of cyanobacteria.
Microcolonies of other bacteria accumulate at the surface of cyanobacteria clusters – they reduce the oxygen content. This is necessary because oxygen
inhibits the fixation of nitrogen.
Can form spores when nutrient availability is low.
Cyanobacteria are connected via tunnels.
Again, complex regulation.
Topic Three – Part B 12/13/2013 1:42:00 PM
Archaea
Chlorobium
Green sulfur bacteria.
Oxidize sulfur.
Anaerobic methanogen.
Symbiotic relationship with a non-photosynthetic bacteria.
Desulfovibrio
Gram negative.
Found in bogs.
Form symbiotic relationship with anaerobic methanogen.
Difficult to cultivate.
Oxidizes methane.
Requires sulfate-reducing bacteria.
Bacterial-Archaeal Consortium – symbiotic relationship between a bacteria and an Archaea.
o Capable of combination reactions.
o Can produce energy.
o E.g. ANME-1/ANME-2 and Desulfovibrio.
Possible to use formate, convert it to CO2 and then produce
CH4 via complex processes.
Didn’t believe it was possible until now.
Thermoplasmatales
Acidophile – grow optimally at a pH below 2.
Do not contain a cell wall (generally).
Facultative anaerobe.
Motile.
Live in hot springs and coal waste piles.
Can change shape due to a lack of cell wall.
Share a lot of genes with Sulfolobales, even though they are very distant evolutionarily. Shows the significance of lateral gene transfer.
Halobacteriales
Survive in high salt concentrations.
An extremophile.
Found in hypersaline lakes or solar salterns.
Contain carotenoid pigments – lead to pink and red colourations.
Phototaxis via rhodopsin pigments. When light is detected, energy is produced and chlorine is pumped out.
o Rhodopsin presence is due to LGT.
Aerobic metabolism of haloarchaea is likely from bacteria.
Haloquadratum walsbyi o Square cell shape.
o Difficult to cultivate due to slow doubling time.
o Extremely high salt conditions.
o Very large.
o Have a large gas vacuole to control buoyancy.
o Strict aerobe.
o Optimal growth is 37 degrees Celsius and high salt concentration.
Genomic Islands o Part of a genome that has evidence of horizontal origins.
o Can code for a variety of functions.
o Can be complex genes, such as photosynthesis.
o Gas vesicle is likely carried on a plasmid.
o Passed on via LGT.
o The gas vesicle island can be transferred from Archaea to bacteria. It
allows for movement towards light, O2, and potentially more nutrients.
Ignicoccus
Live in hydrothermal vents.
Reduce elemental sulfur to hydrogen sulfide using molecular hydrogen as the donor.
Has a symbiosis with (or parasitism by) nanoarchaea.
Nanoarchaea must be in contact with Ignococcus in order to survive.
Can’t grow by itself.
Topic Four 12/13/2013 1:42:00 PM
Phylogenetics
Basic Steps
1. Choose genes of interest.
2. Identify homologs.
3. Align sequence.
o Generally done by computer.
o Perform BLAST.
4. Calculate gene tree.
o Parsimony.
o Distance.
o Maximum likelihood.
OTU
Operational taxonomic unit.
Terminal nodes in a phylogenetic tree.
Common definition: all genes sharing a given % identity in their DNA sequence.
Substitution Matrix
Relative likelihood of changing from one form into the other.
Programs calculate this – based off work of other scientists.
Generally, the higher a value, the more likely they are to be observed in nature.
Exploring Tree Space
Parsimony analysis.
Neighbor joining.
Subtree pruning and regrafting.
Problems with Trees
Long-branch attraction.
Homoplasy – the presence of identical character states that did not arise through shared descent.
Bootstrapping
Comparison of how close two items are.
100 is the highest.
Higher value = better tree.
Rooting a Tree
Root at the most divergent ancestor.
Arbitrary rooting.
Most distantly related species.
Concatenated Alignment
Separate alignments of individual genes are combined into mega alignments.
The alignments are stitched together, keeping individual species separate.
The idea is that more sites provide more mutations and this yields more information.
Molecular Homology
Homolog – genes that are descended from a common ancestor.
Ortholog – Homologous genes that have diverged from each other after speciation events.
Paralog – Homologous genes that have diverged from each other after gene duplication events (e.g. beta and gamma globin).
Xenolog – Homologous genes that have diverged from each other after lateral gene transfer events.
Positional Homology – specific amino acid or nucleotide positions in different proteins or genes that have a common ancestor; frequently represented by
sequence alignments.
Steps in Phylogenetics:
1. Choose the gene of interest.
2. Identify homologues.
3. Align sequence.
4. Calculate gene tree.
5. Overlay known functions onto tree.
6. Infer likely function of genes of interest.
7. Actual evolution (always assumed to be unknown)
Eukaryotic Cells 12/13/2013 1:42:00 PM
Eukaryotic Cells
Eukaryotes
Most eukaryotes are unicellular.
There exists a lot of diversity.
There are six supergroups.
Brown algae are as similar as they are to humans as they are to green algae.
20% of the world’s primary productivity comes from diatoms.
Hacrobia (CCTH) group has enormous algal blooms.
The Six Supergroups
1. Amebozoa
2. Opistokonts
3. Archaeplastids
4. Excavata
5. SAR (stramenophiles, alveolates, rhizaria)
6. CCTH or Hacrobia (Cryptomonads, Centrohelids, Telonemids, and
Hapthophytes).
Opisthokonts
Include fungi, insects, mammals.
Both unicellular and multicellular.
Have only one rear-facing flagellum.
The closest relatives to animals are choanoflagellates: sponges contain cells that are virtually identical to them.
Choanoflagellates o Small, unicellular.
o One of the closest unicellular species to humans.
o Actin-based microvilli.
o Flagellated to generate current.
Capsaspora o Filose amoeboid cell.
o Found in snails.
o Independent lineage from choanoflagellates.
o More basal relative of humans.
Ichthyosporids o All are either commensals or parasites.
o They are all associated with animals.
o Trophic stages are all large, multinucleated cells that contain many
vacuoles.
o Always have a chitin wall.
o Important pathogens of fish.
Fungi o Morphologically diverse.
o Generally characterized by a chitin wall and lack of flagella.
o Saccharomycotina:
Yeasts.
Medically and economically relevant.
o Microsporidia
Pathogens of species such as silkworms and bees.
Biological control agent against locusts.
Role as human pathogen increasing as a result of increasing
HIV/AIDS. 38% of AIDS patients with diarrhea have
microsporidia infections.
o Chytridiomycota
Fungi with flagellum.
Can be symbiotic (mammals) or a pathogen (amphibians).
Cryptomycota o Either fungi or a sister group.
o Include Rozellids.
o Have a flagellum.
o Do not have a chitin wall.
Nucleariids o Filose amoebae.
o Discoid mitochondrial cristae (different mitochondria).
o Basal relative of fungi.
Amoebozoans
Move through bulk cytoplasmic shifts.
Form cell processes called pseudopodia.
All amoebae are united by possession of tubular pseudopodia, unidirectional (monoaxial) cytoplasmic streaming.
Giant amoebae o Include amoeba, chaos, etc.
o Can be seen with the naked eye – enormous.
o Amoeba has one single polygenomic nucleus.
o Chaos is multinucleated, essentially a plasmodium.
Plasmodium o Acellular, multinucleate mass, often enclosed by a slime sheath.
o Often brightly coloured.
o Typically a network of vein-like strands of protoplasm.
o Synchronous nuclear division.
o Can be seen with the naked eye.
Flabellinida/Discosea o Flattened cell shape.
o Poly-axial cytoplasmic movement.
Acanthapodida o Acanthamoeba castellani
Common in soil and water.
Often an opportunistic pathogen that can invade the cornea and
cause eye infections.
o Balamuthia
Pathogenic.
Causes amoebic encephalitis in animals.
Rare but almost always fatal.
Closely related to Acanthamoeba.
Mycetozoans (slime molds) o Often classified with fungus because of overall appearance, production
of spores, and the sharing of habitats.
o However, slime molds are not saprophytic like fungi, they are real
predators of bacteria (do not feed like fungus).
Have pseudopodia to eat bacteria.
o Pseudopodia of the amoeboid stages are often filose.
o Slime molds can have amoeboid, amoeboflagellate, or plasmodial
trophic stages. This is how the group is typically divided:
Myxogastrids/myxomycetes (plasmodial slime molds)
One cell with many nuclei.
Protostelids
Dictyostelids
Trophic stages are generally amoebao, seldomly
uniflagellate amoeboflagellates.
Never form plasmodia.
Archaemoebae o Entamoeba
Inhabits the intestinal mucosa of humans and other mammals.
E. histolytica causes disease in humans.
Causes approx. 70 000 deaths per year.
o Mastigamoeba
Free-living, anaerobic amoeba.
Found in anoxic sediments.
Archaeplastids
Descendents of an ancestral host cell that took up a cyanobacterial endosymbiont (primary endosymbiosis).
Many endosymbiont genes were transferred from the plastid to the ancestral host lineage.
Process is called Endosymbiosis Gene Transfer.
o If EGT is shared by the hosts, then it is most likely that the event
occurred prior to the divergence of the lineages.
Divided into three main classification:
Viridiplantae o Includes land plants and algae.
o Split occurred 750-1200 million years ago into streptophytes and
chlorophytes.
o Micromonas
Might be the smallest eukaryote.
One flagellum.
Possibly the most common eukaryote in marine plankton.
o Volvox
Very large, motile colonies.
Between 500 and several thousand individual cells in the
periphery of a mucilaginous shell.
Colony has polar organization – cells near the front have more
eyespots and daughter colonies develop from the rear.
Glaucophytes o Also called claucocystophytes.
o All occur in fresh water.
o Contain blue-green plastids often called cyanelles.
o Fundamentally biflagellated but in some species, the flagella are either
reduced and hidden under a thick cell wall or only appear in certain life
stages.
Rhodoplantae o Large group.
o Lack flagella and flagellar roots in all life history stages.
o Red plastids (but not every species is red in colour).
o Most forms are multicellular.
o Cyanidiophytes
Unicellular.
Thick, proteinaceous cell walls.
Often on single cup-shaped plastid.
Inhabit extreme environments, such as acidic hotsprings.
Colour more similar to cyanobacteria (i.e. not red).
o Bangiomorpha pubescens
Oldest multicellular eukaryotic fossil that people trust.
1200 MYA
Very similar to examples of modern red algae.
Excavata
Various taxa possessing a ventral feeding groove.
Lack “classical” mitochondria.
Discoba (Kinetoplastids, Diplonemids, Euglenids, Hereolobosea, Jakobids). o Euglenozoa
Some free-living.
Some pathogens.
Nagana
Wasting disease in cattle, horses, camels, etc.
Transmitted by the tsetse fly.
Common in sub-Saharan Africa.
Most wildlife are resistant, as well as some recent breeds
of cattle.
Impacted African history significantly. Prevented cavalry,
knights, messengers, etc. from entering Africa. Currently,
it prevents the use of grassland for food production.
Sleeping Sickness
Fatal disease caused by T. brucei.
Transmitted by the tsetse fly.
Damages the vascular, immune, and central nervous
system, inflammation of the brain.
Pigs, cattle, and antelope are reservoirs.
Jakobids
Free-living bi-flagellates with a ventral groove.
Reclinomonas americana
Two flagella.
Ventral groove.
Pedicel attaches to surface and it is sessile. Heterolobosea
Naegleria fowleri
Amoeba free-living in warm bodies of fresh water.
Enters the body of humans through the nose.
Infects neural tissue.
Rare disease.
Almost always fatal.
Metamonads (Oxymonads, Parabasalids, Retortamonads, Diplomonads) o Defined by conspicuous Golgi and cytoskeletal apparatus.
o Hydrogenosome, not mitochondria.
o Flagella, no groove.
o Almost entirely parasitic/symbiotic.
o Human and veterinary importance.
o Anaerobic/microaerophillic.
o T. vaginalis
Part of the parabasalids group.
Common human parasite that infects the genital tract of up to
3.5% of the total world population.
Can increase the risk of infection or cancer.
o Hypermastigotes
Obligate symbionts of termites and wood-eating cockroaches.
Anaerobes.
Very large cells.
Many rows of flagella with basal bodies arranged
perpendicularly to the parabasals.
o Diplomonads
Small group.
Many species have two karyomastigonts. They resemble double
organisms.
Highly diverged.
Many are parasitic (e.g. Beaver Fever)
Hacrobians (CCTH)
Recently concatenated phylogeny unites haptophytes and crytophytes with two previously unplaced groups – telonemids and centrohelids.
Haptophytes o Not a large group, but ecologically important.
o Mostly marine – very few freshwater.
o Third major group of primary producer in the ocean after diatoms and
dinoflagellates.
o Play a large role in the sulfur cycle. Produces dimethylsulfate (DMS) by
removing the phosphate atom in DMS-P. DMS forms clouds in the
atmosphere. This can cool the earth in localized areas.
o Blooms in the ocean.
Cryptomonads o Photosynthetic (mostly)
o Red plastid. Name means “hidden single cells”.
o Very inconspicuous – small and delicate.
o Usually free living, but some mucus encapsulated forms exist.
o Very common in cold waters at high latitudes.
o Can tolerate very low levels of light – found deep in lakes and oceans.
o Some have lost photosynthesis – since they are heterotrophic,
maintaining photosynthesis might not have been an advantage.
Telonemids o Small and non-photosynthetic.
o Have two posterior flagella.
Centrohelid heliozoans o Rounded body with stiff axopodia (phagocytic pseudopodia containing
microtubules).
o Axopodia supported internally by interlinked microtubules arranged in
hexagonal patterns.
SAR (Stramenophile, Alveolates, Rhizaria)
Rhizaria o United by the presence of filose or reticulate pseudopodia.
o Huge diversity of size and body type.
o Taxonomy is unstable at the moment.
o Are poorly understood because they are the least studied. They have
great ecological importance because of their abundance in the ocean.
o Three main groups:
Cercozoa
Diverse group, includes photosynthetic flagellates
(chlorarachniophytes – green algae), heterotrophic
flagellates, or organisms covered in shells.
Foraminiferans
Name: hole bearers
Leeuwenhoek initially thought they were cephalopods.
Some protists in this group can be up to 25 cm long.
Generally marine.
Can literally pave the sea floor – living sands.
About a quarter of the world’s calcium carbonate is
produced by forams.
Nummulites – fossil forams. Members of this group are
the main components of the rock used to make the
pyramids.
Radiozoa
Always planktonic.
Always marine.
Exist at all depths, including the deep sea.
Stramenophiles o Name: straw hairs – refers to the typical tripartite mastigonemes of the
group. Mastigonemes reverse the thrust of the flagellum; the beating
anterior flagellum pulls cells forward.
o Also called heterokonts – name means different flagella. One flagella is
generally long and forward directed and the other is short and typically
towards the rear.
o Generally well supported as a group.
o Very diverse and ecologically important.
o Diatoms
One of the largest protist groups.
Ubiquitous in marine and freshwater environments.
20% of primary production globally.
Name means “two parts”
Have a glass wall that has the shape of a box with an overlapping
lid (frustule).
Diatomite – mined marine sediments used for a variety of
purposes. Alfred Noble invented dynamite in 1866.
o Brown Algae
No unicellular species.
Range in size from microscopic filaments to giant kelps.
Can be huge primary producers in costal areas.
o Oomycetes
Cause of the potato famine in Ireland.
Potatoes came from N. America to Ireland in 1590.
Became a staple food.
Likely that the oomycete Phytophthora infestans came from N.
America.
1845 – wet, cool summer.
Potato blight spread across the country.
The disease was established and resulted in a massive famine.
Killed approximately 1 million people.
Many emigrated to the USA.
Ireland population went form 8.1 million to 4.4 million.
P. infestans was the first organism proven to be the cause of
disease.
They look like a fungus and kill like a fungus. However, they are
not a fungus.
Likely the result of a massive LGT event.
Alveolates o Alveolae are flattened vesicles that lie immediately under the plasma
membrane.
o Common feature of all alveolates, but are present in other groups, such
as haptophytes and glaucophytes.
o Three major groups:
o Ciliates
Best known for having many small flagella.
Two types of nuclei
Micronuclei – usually diploid and are transcriptionally
