BIOL371 Microbiology Lecture 9 PDF

BIOL371: Microbiology Lecture 9 – Mechanisms of microbial evolution 1 Topics of today 1. 2. 3. 4. 5. The evolutionary process Experimental evolution Gene families, duplications, and deletions Horizontal gene transfer The evolution of microbial genomes Materials covered:  Chapters 13.6-13.12 ...

BIOL371: Microbiology Lecture 9 – Mechanisms of microbial evolution 1 Topics of today 1. 2. 3. 4. 5. The evolutionary process Experimental evolution Gene families, duplications, and deletions Horizontal gene transfer The evolution of microbial genomes Materials covered:  Chapters 13.6-13.12  Figures 13.13-13.23, 13.26, 13.32  Table 13.2 2 Origins of genetic diversity  Evolution: a change in allele (alternative gene version) frequencies in a population over time  Origins of Genetic Diversity  Mutations: random changes in DNA sequence over time  drive evolutionary process  Most mutations are neutral or deleterious; some are beneficial  Several forms including substitutions, deletions, insertions, duplications  Recombination breaks and rejoins DNA segments to make new combinations of genetic material  can re-assort genetic material already present  required for integration of acquired DNA  can be classified as homologous (requiring short flanking segments of similar sequence) or nonhomologous (does not require high similarity) 3 Evolutionary selection  Evolutionary selection is defined by fitness (ability of an organism to produce progeny and contribute to genetic makeup of future generations)  Most mutations are neutral (no effect) and accumulate over time  Deleterious mutations decrease fitness and are removed by natural selection over time  Beneficial mutations increase fitness and are favored by natural selection (e.g., antibiotic resistance during therapy)  Mutations occur by chance; environment selects for advantageous mutations 4 Genetic drift  Genetic drift: random process that can cause gene frequencies to change over time, resulting in evolution in the absence of natural selection  Some populations have more offspring by chance  Most powerful in small populations and those experiencing frequent “bottleneck” events (severe reduction in population size followed by regrowth from remaining cells, such as pathogens) 5 Origins of microbial species  Species can encompass a variety of strains with different traits  Sequence changes can be used as a molecular clock to estimate time since a species diverged  Major assumptions are that nucleotide changes accumulate in proportion to time, are generally neutral and do not interfere with function, and are random  Examples: E. coli harmless K-12 and O157:H7 pathogen diverged ~4.5 millions years ago; E. coli and Salmonella enterica diverged ~100-140 million years ago 6 Experimental evolution  Experimental evolution uses experiments with microbes to investigate evolutionary processes  Possible because of rapid growth and preservation through freezing  Evolutionary events can be observed relatively quickly  Loss-of-function mutations – relatively easy to obtain  Deleterious mutations in any region of the gene can lead to loss of function  Gain-of-function mutations – rare  Requires precise mutations that lead to functional (structural) change without losing function 7 Selection in a population of phototrophic purple bacteria  Rhodobacter capsulatus: phototrophic purple bacterium, photopigments are required for harvesting light  Random mutations can result in reduced levels of photopigments  A deleterious mutation in the light, loss of mutant  A beneficial mutation due to energy savings (wild-type cells continue to make bacteriochlorophyll and carotenoids), takes over the population due to fitness 8 Long term experimental evolution in E. coli  Running since 1988, tracing the evolution of 12 parallel lines for >60,000 generations  Grown aerobically on defined media with glucose as sole carbon source and citrate as buffering agent  Ancestral and evolved strains marked with neutral marker to distinguish them  Dramatic increase in fitness over the first 500 generations, then slowed down 9 Gain-of-function mutation after 31,5000 generations  E. coli cannot utilize citrate  Citrate was present in the long-term evolution experiment as a pH buffer  Random accumulation of mutations allowed for the evolution of the ability to use citrate  This occurred in only one of the 12 evolving populations (a chance event) and provided a selective advantage once it occurred 10 Gene duplication in evolution  After a gene is duplicated, one copy is free to evolve new function while the other copy continues with the original function  Gnome analysis suggests the genome of the budding yeast Saccharomyces cerevisiae had undergone whole genome duplication followed by extensive deletion 11 Genome evolution: gene families Homologs  Homologs: Genes descended from a common ancestral sequence  Orthologs: sequences that have diverged due to a speciation event  Paralogs: homologous sequences that share a common ancestor due to one or more gene duplication events  Gene families: groups of gene homologs Why do we care? Well, if we know the function of a protein in one organism, we can usually predict the function of homologs in other organisms Note: error in Figure 13.16 of the Textbook; the top level should be homologs instead of paralogs. 12 Gene deletions in microbial genome dynamics  Gene deletions play an important role in microbial genome dynamics  Occur more often than insertions/duplications  Nonessential/non-functional genes deleted over time  Maintain small size of microbial genomes  Deletions drive tiny genomes in obligate intracellular symbionts and intracellular pathogens  Metabolites available in host cytoplasm  Deletions removing biosynthetic genes might have little effect on fitness  Also eliminate redundant functions (e.g., mitochondria, chloroplasts) 13 Deletions and the evolution of interdependence  In nature, microorganisms grow in communities, so deletion preventing production of essential nutrient may not be lethal if nutrient is available elsewhere  Can increase fitness but promote interdependency  Microbes that grow in pure culture without growth factor additions preserve all essential functions but are at a disadvantage compared to a community 14 Horizontal gene transfer      Impacts microbial evolution Allows transfer of DNA between distant branches of evolutionary tree If no fitness benefit, deleted over time Mechanisms: transformation, transduction, conjugation Involvement of mobile genetic elements: transposons, insertion sequences, plasmids 15 Comparative genomics reveal diversity within species  Whole genome sequencing and comparison  Microbial genomes are highly diverse and dynamic  Microbial species consists of individual strains differing in composition 16 The Pan and Core genome concept for species  Core genome: genes shared by all strains of a species  Pan genome: core genome plus genes not shared by all strains  Species can have major differences in genome size, gene content, functional traits 17 Chromosomal and pathogenicity islands of E. coli  Chromosomal islands: entire genetic pathways (e.g., pollution-degradation pathways) can be acquired as blocks via horizontal gen transfer  Often flanked by repeats, implying transposition  Base composition and codon bias differ from genome  Core genome of E. coli is 1976 genes  Average E. coli genome is 4721 genes  E. coli K-12 strain and two pathogenic strains share 39% of genes  Pathogenicity islands: genes associated with pathogenicity (e.g., virulent factor) are clustered in blocks 18 Systematics  Systematics: the study of the diversity of organisms and their relationships  link phylogeny with taxonomy, in which organisms are characterized, named, and grouped based on natural (evolutionary) relationships  Species are fundamental units of diversity  For plants and animals, species has a special status  Biological species concept: a species is an interbreeding population that is reproductively isolated from other such populations  This is problematic in describing bacteria and archaea  A microbial species is a taxonomic category that defines a population of individuals that  Is monophyletic (descended from common ancestor)  Is genomically coherent  Is phenotypically coherent  Can be clearly distinguised from other species 19 The polyphasic approach to taxonomy  The objective is to reach a consensus classification by integrating multiple forms of data and information into a classification that presents a minimum number of contradictions  The polyphasic approach to taxonomy uses three methods:  Phenotypic (morphological, metabolic, physiological, chemical characteristics) analysis  Genotypic (genome) analysis  Phylogenetic (evolutionary) analysis 20 Phenotypic analysis Category Characteristics Morphology Colony morphology; Gram reaction; cell size and shape; pattern of flagellation; presence of spores, inclusion bodies (e.g., P H B, Super a glycogen, or polyphosphate granules, gas vesicles, magnetosomes); capsules, S-layers, or slime layers; stalks or appendages; fruiting body formation Motility Nonmotile; gliding motility; swimming (flagellar) motility; swarming; motile by gas vesicles Metabolism Mechanism of energy conservation (phototroph, chemoorganotroph, chemolithotroph); utilization of individual carbon, nitrogen, or sulfur compounds; fermentation of sugars; nitrogen fixation; growth factor requirements Physiology Temperature, pH, and salt ranges for growth; response to oxygen (aerobic, facultative, anaerobic); presence of catalase or oxidase; production of extracellular enzymes Cell lipid chemistry Fatty acids; polar lipids; respiratory quinones Cell wall chemistry Presence or absence of peptidoglycan; amino acid composition of cross-links; presence or absence of cross-link interbridge Other traits Pigments; luminescence; antibiotic sensitivity; serotype; production of unique compounds, for example, antibiotics Problem: phenotypic characteristics of a strain are generally highly dependent on growth conditions, thus care must be taken in using them in systematic analyses 21 Molecular phylogeny  Phylogenetic trees: Diagrams depicting evolutionary history  Difference in nucleotide sequence between two homologous genes is a function of number of mutations accumulated since they shared a common ancestor  Differences in DNA sequences can be used to infer relationships  SSU (small subunit) ribosomal RNA (rRNA) genes highly conserved and easily sequenced and analyzed  Can amplify SSU rRNA genes from environmental samples or to sequence or using metagenomics 22 Taxonomic assignment based on rRNA gene sequencing  Sequence the SSU rRNA gene and align the sequence to SSU rRNA genes of other species  Strains that exhibit >97% SSU rRNA sequence identity are considered to belong to the same species 23 Multilocus sequence analysis  DNA sequences of proteinencoding genes accumulate mutations faster than rRNA genes, thus distinguishing species that cannot be resolved by rRNA sequences  Multilocus sequence analysis can distinguish at species level  Use highly conserved genes; e.g., recA  Use single-copy gene: compare only orthologs, not paralogs  Use as many genes as available 24 Genome analysis  Use of entire genomes increasingly common as sequencing improves and cost declines  Analyses of content: presence/absence of genes  Synteny: order of genes  GC content  Can reconstruct metabolic/physiological characteristics with genome data  Average nucleotide identity: most commonly used metric for estimating overall relatedness by aligning ~1,000 bp fragments and calculating average nucleotide identity  >96% average nucleotide identity – same species  <93% average nucleotide identity –different species 25