Microbial Evolution
Microbial Evolution -
First micro-organisms about 3.5 billion years ago. Likely cyanobacteria.
Taxonomy -
The science of defining groups of biological organisms on the basis of shared characteristics and giving names to these groups. Aristotle started grouping the life on earth. Grouping based of visual components. Andrea Cesalpino, grouped based of structure. Hierarchical classification scheme o Domain Kingdom Phylum Class Order Family Genus Species o Binomial naming system: Genus, Species.
Phylogeny -
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The study of evolutionary relationships among groups of organisms. Features required to compare life: o A feature present in all living organisms (Highly conserved) o But has variation between organisms. The ribosomal small subunit: (SSU) o Why base phylogenetic on the SSU rRNA gene? ▪ Provides sufficient sequence information (variable and invariant regions) to permit statistically significant comparisons between homologues. ▪ Highly abundant in the cell and the quantity reflects the capacity of an organism to make protein and therefore do work. ▪ SSU rRNA is also the subject of large curated databases. Bacteria species definition: o Because bacteria reproduce asexually, every individual bacterium is its one species. o Members of the same bacterial species: ▪ Share phenotypic characteristics ▪ Have >70% total genome similarity ▪ Have >97% sequence identity in the 16S rRNA gene. But, just because two cells belong to the same species doesn’t mean they are identical. Micro-organisms are present in all kingdoms of life.
Bacterial Phyla -
In 1987 Carl Woese listed 11 bacterial phyla. Now there are more than 11 phyla, due to culture independent methods. A couple of common phyla: o Thermophiles: deeply branching phyla. E.g. Aquificae, Thermotagae, Chloroflexi (Use light, but doesn’t make oxygen so not photosynthetic). o Firmicutes (low G+C, gram positive): most abundant. E.g. Staphylococcus, bacillus, clostridium. o High G+C (Gram positive): actinobacteria, e.g. Streptomyces, found in soil and produce antibiotics.
o o
Photosynthetic (gram negative): Cyanobacteria, chlorobi. Major contribution to oxygenic atmosphere. Proteobacteria (gram negative): Divided in 5 subcategories, beta, gamma, alpha, epsilon, and delta. E.coli and salmonella in gamma.
Adaptive Radiation -
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Organisms diversify from a common ancestor o Often driven by environmental changes. Requires both o Genetic diversity o Selection pressure Organisms selected for fitness in new environment. Can lead to speciation. Applicable to both whole organisms and genes. Infer relationship by looking at DNA sequence, and calculate random probability of differences. Homologous sequences share non-random levels of sequence identity.
Mechanisms of gene evolution -
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Introduced by: o Replication and repair errors o Mutagenic agents (UV, oxidative stress, chemicals) Basic mechanisms for gene change o Point mutations (mispairing) (SNPs) o Insertion/Deletions of bases (strand slippage, when DNA puckers) o Duplication o Inversion.
Experimental Evolution -
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Ways to study evolution o Looking at fossils (paleontology) o Compare extant species (E.g. 16S rRNA trees) o Experimental evolution (plant and animal breeding and microbe) The long-term evolution experiment (Richard Lenski) o E.coli fast growing. o Every day, sub culturing E.coli over 20 years. o Looking at how the E.coli population changes over time. o Cryogenic store each generation. o Monitor changes in fitness. o Monitor mutations o Monitor reproducibility of evolution. Results: o Steady accumulation of mutations: 45 mutations (14 conserved across experiments) ▪ 29 SNPs/ 16 indels. o Steady (but declining) increase in fitness.
o o
▪ Mutations with greatest benefit emerge early. Over 20K generations E.coli was selected for incremental increase in fitness. Over 30K generations, E.coli evolved the ability to eat Vitamin C (citrate), allowing them to grow to a much higher biomass. This is from a duplication event. ▪ Usually the cit transporter is under the control of a promoter that is inactive in the presence of O2. ▪ Gene duplication places citT under Prna control: thus aerobic expression. ▪ Further duplications increase citrate transport & fitness
Lateral Gene transfer -
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Quantum leaps in microbial evolution. Lateral gene transfer has played a key role in evolution of many pathogenic bacteria Transfer of foreign genetic information between microorganisms. Boundaries for transfer dictated by: o Transfer method o Properties of the DNA transferred. Diversity of phenotypes transferred: o Methanogenisis o Antibiotic resistance o Virulence genes o Toxins. 3 basic mechanisms: o Transformation: direct insertion. o Transduction: by bacteriophage. o Conjugation: bacteria bacteria transfer
Plasmids -
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Replicate autonomously. Encode non-essential (accessory) functions Can be transferred by conjugation – Self transmissible – Mobilizable May exist in different host bacteria o Broad host range: replicate well in any host. o Narrow host range: only replicate in some host. Carry diverse range of accessory functions
Bacterial virulence and plasmid -
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Bacillus anthracis (anthrax) o Bacillus cereus (food poisoning) o They differ by 2 plasmids: ▪ pXO1 – anthrax toxin ▪ pOX2 Yersinia pestis (plague) o Different complement of plasmids, that encode virulence genes.
Bacteriophage and lateral gene transfer -
Bacterial viruses are phage. Incredible diversity of types. Estimated at >1031 – 10M per cm3 – 10-100 fold more that prokaryotes Obligate parasite: Requires bacteria for replication Two life cycles o Lytic (explodes bacterium to release phage) o Lysogenic (integrates into bacterial chromosome)
Bacteriophage and virulence -
Encode many important virulence genes Transfer virulence genes through Generalized Transduction Bacteriophage carry toxins in important human pathogens
Gene loss -
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If lateral gene transfer provides genetic diversity for adaption, why aren’t bacterial genomes HUGE? Deletion bias in (asexual) bacterial genomes Pressures on the genome to reduce size o Genetic drift and neutral selection of genes (Use it or lose it) ▪ Accumulation of mutations occur. o Negative selection of genes within a new environment Rapid changes in environmental niche (specialization) precipitate changes in the genome o Accumulation of pseudogenes (genes with STOP mutations) o Gene loss Many bacteria that have adopted a pathogenic lifestyle (host restriction) show evidence of genome reduction. Salmonella: diverged from E.coli through LGT. o Has a broad host range. o Each host, has a specialize type of salmonella. o Allows reduction of genome. o Accumulation of many pseudogenes - 4.5% of all genes. o Accumulation of pseudogenes suggests recent niche adaption – Gene deletion hasn’t kept pace. Streptococcus thermophiles o Originally found in salvia. As Strep. Salivarius. o Humans use saliva to culture dairy products. o Due to new specific environment, the bacteria has accumulated 10% pseudogenes.
First micro-organisms about 3.5 billion years ago. Likely cyanobacteria.
Taxonomy -
The science of defining groups of biological organisms on the basis of shared characteristics and giving names to these groups. Aristotle started grouping the life on earth. Grouping based of visual components. Andrea Cesalpino, grouped based of structure. Hierarchical classification scheme o Domain Kingdom Phylum Class Order Family Genus Species o Binomial naming system: Genus, Species.
Phylogeny -
-
-
-
The study of evolutionary relationships among groups of organisms. Features required to compare life: o A feature present in all living organisms (Highly conserved) o But has variation between organisms. The ribosomal small subunit: (SSU) o Why base phylogenetic on the SSU rRNA gene? ▪ Provides sufficient sequence information (variable and invariant regions) to permit statistically significant comparisons between homologues. ▪ Highly abundant in the cell and the quantity reflects the capacity of an organism to make protein and therefore do work. ▪ SSU rRNA is also the subject of large curated databases. Bacteria species definition: o Because bacteria reproduce asexually, every individual bacterium is its one species. o Members of the same bacterial species: ▪ Share phenotypic characteristics ▪ Have >70% total genome similarity ▪ Have >97% sequence identity in the 16S rRNA gene. But, just because two cells belong to the same species doesn’t mean they are identical. Micro-organisms are present in all kingdoms of life.
Bacterial Phyla -
In 1987 Carl Woese listed 11 bacterial phyla. Now there are more than 11 phyla, due to culture independent methods. A couple of common phyla: o Thermophiles: deeply branching phyla. E.g. Aquificae, Thermotagae, Chloroflexi (Use light, but doesn’t make oxygen so not photosynthetic). o Firmicutes (low G+C, gram positive): most abundant. E.g. Staphylococcus, bacillus, clostridium. o High G+C (Gram positive): actinobacteria, e.g. Streptomyces, found in soil and produce antibiotics.
o o
Photosynthetic (gram negative): Cyanobacteria, chlorobi. Major contribution to oxygenic atmosphere. Proteobacteria (gram negative): Divided in 5 subcategories, beta, gamma, alpha, epsilon, and delta. E.coli and salmonella in gamma.
Adaptive Radiation -
-
Organisms diversify from a common ancestor o Often driven by environmental changes. Requires both o Genetic diversity o Selection pressure Organisms selected for fitness in new environment. Can lead to speciation. Applicable to both whole organisms and genes. Infer relationship by looking at DNA sequence, and calculate random probability of differences. Homologous sequences share non-random levels of sequence identity.
Mechanisms of gene evolution -
-
Introduced by: o Replication and repair errors o Mutagenic agents (UV, oxidative stress, chemicals) Basic mechanisms for gene change o Point mutations (mispairing) (SNPs) o Insertion/Deletions of bases (strand slippage, when DNA puckers) o Duplication o Inversion.
Experimental Evolution -
-
-
Ways to study evolution o Looking at fossils (paleontology) o Compare extant species (E.g. 16S rRNA trees) o Experimental evolution (plant and animal breeding and microbe) The long-term evolution experiment (Richard Lenski) o E.coli fast growing. o Every day, sub culturing E.coli over 20 years. o Looking at how the E.coli population changes over time. o Cryogenic store each generation. o Monitor changes in fitness. o Monitor mutations o Monitor reproducibility of evolution. Results: o Steady accumulation of mutations: 45 mutations (14 conserved across experiments) ▪ 29 SNPs/ 16 indels. o Steady (but declining) increase in fitness.
o o
▪ Mutations with greatest benefit emerge early. Over 20K generations E.coli was selected for incremental increase in fitness. Over 30K generations, E.coli evolved the ability to eat Vitamin C (citrate), allowing them to grow to a much higher biomass. This is from a duplication event. ▪ Usually the cit transporter is under the control of a promoter that is inactive in the presence of O2. ▪ Gene duplication places citT under Prna control: thus aerobic expression. ▪ Further duplications increase citrate transport & fitness
Lateral Gene transfer -
-
-
Quantum leaps in microbial evolution. Lateral gene transfer has played a key role in evolution of many pathogenic bacteria Transfer of foreign genetic information between microorganisms. Boundaries for transfer dictated by: o Transfer method o Properties of the DNA transferred. Diversity of phenotypes transferred: o Methanogenisis o Antibiotic resistance o Virulence genes o Toxins. 3 basic mechanisms: o Transformation: direct insertion. o Transduction: by bacteriophage. o Conjugation: bacteria bacteria transfer
Plasmids -
-
Replicate autonomously. Encode non-essential (accessory) functions Can be transferred by conjugation – Self transmissible – Mobilizable May exist in different host bacteria o Broad host range: replicate well in any host. o Narrow host range: only replicate in some host. Carry diverse range of accessory functions
Bacterial virulence and plasmid -
-
Bacillus anthracis (anthrax) o Bacillus cereus (food poisoning) o They differ by 2 plasmids: ▪ pXO1 – anthrax toxin ▪ pOX2 Yersinia pestis (plague) o Different complement of plasmids, that encode virulence genes.
Bacteriophage and lateral gene transfer -
Bacterial viruses are phage. Incredible diversity of types. Estimated at >1031 – 10M per cm3 – 10-100 fold more that prokaryotes Obligate parasite: Requires bacteria for replication Two life cycles o Lytic (explodes bacterium to release phage) o Lysogenic (integrates into bacterial chromosome)
Bacteriophage and virulence -
Encode many important virulence genes Transfer virulence genes through Generalized Transduction Bacteriophage carry toxins in important human pathogens
Gene loss -
-
-
-
If lateral gene transfer provides genetic diversity for adaption, why aren’t bacterial genomes HUGE? Deletion bias in (asexual) bacterial genomes Pressures on the genome to reduce size o Genetic drift and neutral selection of genes (Use it or lose it) ▪ Accumulation of mutations occur. o Negative selection of genes within a new environment Rapid changes in environmental niche (specialization) precipitate changes in the genome o Accumulation of pseudogenes (genes with STOP mutations) o Gene loss Many bacteria that have adopted a pathogenic lifestyle (host restriction) show evidence of genome reduction. Salmonella: diverged from E.coli through LGT. o Has a broad host range. o Each host, has a specialize type of salmonella. o Allows reduction of genome. o Accumulation of many pseudogenes - 4.5% of all genes. o Accumulation of pseudogenes suggests recent niche adaption – Gene deletion hasn’t kept pace. Streptococcus thermophiles o Originally found in salvia. As Strep. Salivarius. o Humans use saliva to culture dairy products. o Due to new specific environment, the bacteria has accumulated 10% pseudogenes.
