Midterm #1 Flashcards
What are the characteristics of cells that point to LUCA?
- DNA as genetic material
- A,C,T,G and A,C,U,G for DNA and RNA bases
- Three letter genetic code
- Lipoprotein membranes in cell envelope
- 20 core amino acids compose proteins
- Translation: small subunit RNA, large subunit RNA, ribosomal proteins, tRNA
- Transcription: RNA polymerase
- Membrane transport systems: ABC transporters
What indications do we have that archaea are more closely related to eukarya than they are to bacteria?
- Archaea and eukarya share more fundamental similarities
- E.g., sensitivity to antibiotics means archaea and eukarya have similar ribosomes
- E.g., more similar RNA polymerase
- Transcription and translation
In terms of energy metabolism, what are the different types of energy sources?
- Light (photo)
- Chemicals (chemo)
In terms of energy metabolism, what are the different types of electron donors?
- Inorganic compounds (litho)
- Organic compounds (organo)
In terms of energy metabolism, what are the different sources of carbon?
- Inorganic (mostly carbon dioxide) (autotroph)
- Organic (heterotroph)
Which photosynthetic reaction centres are in the following organisms?
- Heliobacillus
- Chloroflexi
- Purple bacteria
- Chlorobi
- Cyanobacteria
- Heliobacillus = RC1
- Chloroflexi = RC2
- Purple bacteria = RC2
- Chlorobi = RC1
- Cyanobacteria = RC1, RC2, chlorophyll
Describe the differences between reaction centre 1 and reaction centre 2
- RC1 = Capacity to catalyze oxidation of hydrogen and highly reduced electron donors, likely first one to evolve
- RC2 = Does not work with very reduced substrates like hydrogen, has higher affinity for sulfur or water
What are orthologs? What are paralogs?
- Orthologs = same gene in two different species (separated by speciation event)
- Paralogs = One cell has two copies of a gene (separated by duplication event)
Difference in bacteria/eukaryote membrane and archaea membrane
- Bacteria/eukaryote: Ester-linked, G3P, fatty acids, bilayer
- Archaea: Ether-linked, G1P, isoprenoid, can form monolayer
What are the two types of phototrophy?
- Oxygenic: Produces oxygen (oxygen is terminal electron acceptor); electrons from ETC come from water
- Anoxygenic: No oxygen production; electrons come from sources other than water
What are the two types of base pair substitutions?
- Synonymous (silent): Codes for same amino acid
- Non-synonymous: Codes for different amino acid (missense) or codes for stop codon (nonsense)
In base pair substitutions, what are transitions and transversions?
- Transitions: Interchanges of 2-ring purines or one-ring pyrimidines
- Transversions: Interchanges of purines and pyrimidines
What are the three ways to exchange DNA during lateral gene transfer?
- Conjugation
- Transduction
- Transformation
What are the two main steps involved in lateral gene transfer?
- Foreign DNA must penetrate cellular envelope via transformation, conjugation, or transduction
- Integration into the host genome via homologous recombination, heterologous recombination, of extrachromosomal maintenance and repair
Describe conjugation and the different ways it can occur
- Exchange DNA through cellular contact
- Bacterial donor with conjugative plasmid forms a connection with neighbouring cell (pilus)
- DNA is sent through pilus and a complementary strand of the plasmid is made
- Genomic material essentially “hitchhikes” on plasmid
- In thermoacidophilic archaea, a UV inducible pilus promotes DNA exchange (stress inducible evolution)
Describe transduction and the three ways that it can occur
- Exchange of DNA through a vesicle
- Gene transfer agent can be used (phage-like particles that release without lysing the host)
- DNA can be transported in cell vesicles (bud from cell membrane and transfers its contents when it finds another cell membrane)
- Phage (this is the most common - transports DNA between two cells in protected vesicle)
Describe transformation and the necessary qualities of cells for this to occur
- Uptake of “naked”/free DNA
- Cells take up free DNA and insert it into their cytoplasm. This free DNA recombines with the chromosome
- Cell needs to be naturally competent (needs a mechanism to uptake DNA from the environment - can take up DNA for food, repair, or genetic diversity)
- Cells can also be artificially competent (pores made in membrane via lightning or calcium)
What are the four types of lateral gene transfer?
- Novel acquisition (Gene x –> selection for function x –> novel adaptation)
- Loss and regain (X function not needed –> gene lost –> X function needed again –> X function supplied by Y gene)
- Homologous replacement (Antibiotic pressure –> Resistant form of X –> Possible recombination (2 gene copies) –> Loss of old X + hybrid copy) (gene is essential in this case)
- Analogous replacement (Gene with the same function but a different protein sequence)
What are the two ways that DNA can get into chromosomes? What are the differences between these?
- Homologous recombination: Requires sequence similarity (RecA will only bind similar sequences - only mechanism to do this)
- Heterologous recombination: Does not require sequence similarity (uses a phage or integron to transfer DNA - many different mechanisms)
What are some examples of the interdependence of replication, recombination, and mutation?
- Repairs stalled replication forks (homologous recombination)
- Replication is required for many heterologous recombination events
- Many mutations are caused by biosynthetic errors during DNA replication
- Every type of mutation can occur during DNA replication
- Same system is responsible for ensuring the accuracy of DNA replication and limiting homologous recombination (e.g., mismatch repair system)
- No mobile genetic element is purely extra-chromosomal (integrons, lytic phages etc.)
- Extra-chromosomal elements segregation is often coupled to chromosomal segregation (plasmids)
What is constitutive mutability? What does it lead to?
- Permanently increase mutation rates
- Leads to: Defects in mismatch repair system; changes in DNA polymerase (rare); changes in other proteins involved in DNA replication
The mismatch only recognizes strands of DNA that are what?
- Methylated
- Non-methylated strands are destroyed
Give two examples of inducible mutability
- The SOS response: Stress bacteria activates SOS system, leads to LexA being turned off and no longer regulating other genes, makes cell a temporary mutator by increasing homologous recombination etc…cell mutates fast = stress-induced mutation
- The Growth Advantage in Stationary Phase (GASP) response: Specific to starvation, cells maintained at low concentrations, induction of Pol IV (mutate to cope with starving)
What are the three species concepts?
- Biological (biospecies): Interbreeding natural populations (LGT in bacteria); recombination to mutation ration > 1; higher the ratio, greater the recombination
- Ecological (ecospecies): Lineage occupying an adaptive zone (same niche); e.g., grouping by pathogenecity
- Phylogenetic (phylospecies): Biological species forming a diagnosable monophyletic; take all genes that bacteria have in common and make phylogenetic tree based on ALL this information
Species definition: Morphospecies
- Based on shape/movement
Species definition: Taxospecies
- Based on numerical taxonomy (battery of biochemical tests) - see how culture reacts
Species definition: Genomospecies
- “Strains with around 70% or greater DNA-DNA relatedness and with 5C or less change in melting temperature”
Species definition: ribosomal rRNA (+ advantages and disadvantages?)
- Small ribosomal subunit (higher than 97% sequence identity + DNA relatedness to be the same species)
- Advantages: Universal, functionally conserved, slow and fast evolving regions, encodes an RNA molecule (not a protein), abundant in cells
- Disadvantages: Limited resolution at fine phylogenetic scale, multiple copies, intragenomic heterogeneity, does not represent the whole genome
MLSA and MLST?
- Multi-locus sequence typing: Genotypic characterization of prokaryotes at infraspecific level (allelic mismatches of a small number of housekeeping genes to recognize distinct strains)
- Multi-locus sequence analysis: Genotypic characterization of more diverse groups of prokaryotes using sequences of multiple protein-coding genes (uses cocatenated phylogenetic tree - puts genes together like one big gene and see how closely related strains are)
In MLST, what are sequence types and single-locus variants (in allelic profiles)?
- Sequence type (ST) = Unique set of alleles. Two bacteria with a single allele that is different (even if due to a single point mutation) belong to different sequence types
- Single-locus variants (SLVs) = Two isolates differing at a single allele
Recombination to mutation ratios: = 1 ; > 1 ; < 1 ?
- = 1 : 50% mutation; 50% recombination
- > 1 : Recombination causes more change that mutation
- < 1 : Mutation causes more change than recombination
Species definition: Whole genome
- “Core” set of genes found in all strains of species
- “Auxilliary” set of genes found in different subset of all strains
Species definition: Average Nucleotide Identity
- Average nucleotide identity of all protein-coding genes shared by two different bacteria (core genome comparison). Greater resolution that 16S rRNA sequencing and MLST
- Species with 95% ANI correlate very well with DNA:DNA hybridization (70%) (much easier to get ANI)
Species definition: Core genome phylogeny
- Concatenated phylogeny based on all protein-coding genes shared by two organisms
- All genes the have in common put onto phylogenetic tree
Species definition: Genome composition
- Express as a % of conserved genes between two organisms
- Calculated by # genes in core genome / # genes in whole genome
- Gene content similarity / conserved DNA
- Does not correlate well with ANI
What does high ANI and high gene content similarity reflect in bacterial populations?
- High ANI = evolutionary relatedness
- High gene content similarity = ecological relatedness
What is a polyphasic taxonomy?
- Assembles and assimilates many levels of information and incorporates many distinct portions of information to yield a multi-dimensional taxonomy
- 95% 16S rRNA, 70% gene content, 95% ANI and phenotypic features that agree with genotypic definition
Vibrio sp.
- V. coralliilitycus (bleaches corals - regulated by temperature)
- V. fischeri (found in squids, creates light to match light of moon to mask shadow)
- V. cholera (toxin makes cells lose water)
Different intracellular parasites and symbionts?
- Mycoplasma, Sulcia, Chlamydia, Proteobacteria, Rickettsia, Buchnera, Baumannia
Buchnera aphidicola
- Obligate symbiont
- Very small genome
- Lives in specialized aphid cells
- Overproduces amino acids from sugars (can’t repair DNA, no lipopolysaccharides)
Sulcia muelleri and Baumannia cicadellinicola
- Leafhopper symbionts
- Sulcia supplies amino acids
- Baumannia supplies vitamins and cofactors
Chlamydia
- Obligate intracellular parasite
- Requires host eukaryotic cell to replicate (elementary bodies (can’t replicate) infect host, form into reticular bodies (can replicate), binary fission, transformed back into elementary body, released)
Mycoplasma and Cytoplasma
- “Gracilicutes” = thin cell wall, little peptidoglycan, gram negative
- “Firmacutes” = thicker cell wall, more peptidoglycan, gram positive
- “Mollicutes” = no cell wall
Rickettsia
- Closely related to mitochondria
- Requires animal host cell to be able to replicate (can only replicate in host cytosol)
Pelagibacter ubique
- Alphaproteobacteria
- 50% of cells in temperate water
- Photosynthetic (important in carbon cycle) - not a normal photosynthetic apparatus though, proteorhodopsin based phototrophy
- Very small genome for free-living bacteria
- Carotenoid pigments
Myxobacteria (deltaproteobacterium) - Sorangium cellulosum
- Very large genome because it encodes complex behaviour
- Forms very complex structures
- Complex, multicellular structures with different cell types in bacteria = cellular differentiation (fruiting bodies!)
- Independently evolved in bacteria and eukarya
- Can remotely sense objects and hunts prey in coordinated fashion
Deinococcus radiodurans
- Highly pigmented
- 4 chromosomes (condensed nucleoid maintains structure after irradiation)
- Active DNA repair systems
- High levels of manganese
- Keeps DNA double stranded
- Convergent evolution with other radiation resistant species (but not lateral gene transfer because it is not the same gene encoding this)
Shigella
- Human pathogen (destroys epithelial cells that form intestinal mucosa)
- Releases toxin
- Only differentiated from E. coli because of a virulent phenotype (acquired plasmid that allowed it to be pathogenic to humans - lateral gene transfer)
- Gained functions by losing genes (Evolution by loss)
Thermotoga
- Heterotrophs that live at a variety of temperatures
- Complex trait that has evolved from convergent evolution
- No isolates
- Low temp = mesothermotoga
Caulobacter - Caulobacter crescentus
- Alphaproteobacteria
- Cellular differentiation (stalk and flagella) = derived trait
- Complex life cycle
- Asymmetrical division (also found in Bacillus subtilis)
Bacillus
- Model system for sporulation
- Triggered by lack of food (no other environmental stress)
Paenibacillus
- Complex social behaviour
- Form vortexes (leave high density areas)
- Cell to cell signaling
Helicobacter pylori
- Epsilon proteobacteria
- Gastric ulcer patients
- Chemotaxis through mucous toward epithelial cells in stomach (higher pH)
- Pathogenecity from Cag pathogenecity island (type IV secretion systems inject toxins; cagA encodes protein that disrupts host cell activity)
Bdellovibrio and Daptobacter
- Predatory bacteria
- Kill other bacteria
- Likely convergent evolution between the two
Streptomyces
- Actinobacteria
- Filamentous bacteria with linear chromosomes
- Hyphae is reproductive structure
- Produces multiple spores for reproduction (different from Bacillus spores)
- Incredible secondary metabolite producers - source of many antibiotics today
Cyanobacteria
- Evolve spores (independent of Bacillus)
- Some can fix nitrogen (heterocysts) = cellular differentiation and complex behaviour
- Connections between cells…multicellular?
Symbiotic relationship between ANME-2 and Desulfovibrio?
- Methane-oxidizing archaea (produces energy)
- Sulfate-reducing bacteria (“breathe” sulfate)
Thermoplasma
- Facultative anaerobe
- Grows best at 55-60C and pH 0.5-4
- Can change shape
- No cell wall, just a cell membrane
Haloarchaea (Haloquadratum walsbyi)
- Survives at 5M salt concentration
- Proteorhodopsin - creates a proton gradient and uses phototaxis
- H. walsbyi: Square cell shape, hard to cultivate, strict aerobe, gas vesicles made out of protein to help it float (non-motile)
Ignicoccus (and nanoarchaea)
- Lives at high pressure, high temperature (hydrothermal vents)
- Nanoarchaea = small archaea that attaches itself to Ignicoccus (so divergent that no primers can amplify it)
