Microbial Genomics Microbial Genomics Michael J. Stanhope, Michael - PowerPoint PPT Presentation

Microbial Genomics Microbial Genomics Michael J. Stanhope, Michael J. Stanhope, Pop. Med. Diagnostic Sci Pop. Med. Diagnostic Sci. . Fleischmann et al. 1995. Science 269: 496

Outline Outline � Introduction � Introduction � Microbial diversity � Microbial diversity � Universal Tree of Life � Universal Tree of Life � Bacterial genome size � Bacterial genome size � Core and pan genomes � Core and pan genomes � Horizontal Gene Transfer (HGT) � Horizontal Gene Transfer (HGT) � Mechanisms of HGT � Mechanisms of HGT � Detecting HGT � Detecting HGT � Comparative genomics of � Comparative genomics of Streptococcus Streptococcus � Comment on genome sequencing technology � Comment on genome sequencing technology � E.g. of 454 bacterial genome sequence � E.g. of 454 bacterial genome sequence � Applications of microbial genomics � Applications of microbial genomics

Introduction Introduction � Microbial diversity � Microbial diversity

Microbial diversity Microbial diversity � Superficial inspection, bacteria and Superficial inspection, bacteria and � archaea hardly seem diverse hardly seem diverse archaea http://www.ucmp.berkeley.edu/archaea/archaeamm.html

Microbial diversity Microbial diversity � But metabolic diversity great, particularly � But metabolic diversity great, particularly energy generating energy generating � Even within a species; e.g. Even within a species; e.g. E . coli : E . coli : � � Fermentation or respiration; respire aerobically or Fermentation or respiration; respire aerobically or � anaerobically; glucose or lactose as sole carbon source anaerobically ; glucose or lactose as sole carbon source – transforming sugar into amino acids, vitamins, – transforming sugar into amino acids, vitamins, nucleotides nucleotides

Microbial diversity Microbial diversity � Energy generating metabolism in bacteria: Energy generating metabolism in bacteria: � � Alcohol fermentation Alcohol fermentation � � Lactic acid fermentation Lactic acid fermentation present in eukaryotes present in eukaryotes & prokaryotes & prokaryotes � � Aerobic respiration Aerobic respiration � � Oxygenic photosynthesis Oxygenic photosynthesis � � Anaerobic degradation of carbohydrates through the Anaerobic degradation of carbohydrates through the Embden Embden- - � Meyerhof pathway. Meyerhof pathway. � Other fermentation pathways e.g. Other fermentation pathways e.g. phosphoketolase phosphoketolase pathway pathway � � Anaerobic respiration Anaerobic respiration � � Lithotrophy Lithotrophy ( (inorganics inorganics as source of energy) as source of energy) � � Anoxygenic Anoxygenic photosynthesis photosynthesis � � Methanogenesis Methanogenesis (H (H 2 as energy source and produces methane) 2 as energy source and produces methane) � � Light driven Light driven nonphotosynthetic nonphotosynthetic photophosphorylation photophosphorylation �

Microbial diversity Microbial diversity � prokaryotic cells on Earth = 6 X 10 prokaryotic cells on Earth = 6 X 10 30 30 � � Prokaryotic cellular carbon = 60 Prokaryotic cellular carbon = 60- -100% of estimated 100% of estimated � carbon in terrestrial and marine plants. carbon in terrestrial and marine plants. � Abundant in environments where eukaryotes are rare Abundant in environments where eukaryotes are rare � � How many species? How many species? � � Definition of species? Definition of species? � � Lack diagnostic morphological characteristics Lack diagnostic morphological characteristics � � Exchange genetic material in unique and unusual ways Exchange genetic material in unique and unusual ways � � Same species = 70% DNA Same species = 70% DNA- -DNA hybridization DNA hybridization � � Underestimating prokaryotic diversity Underestimating prokaryotic diversity � � Practical limitations in counting Practical limitations in counting � � 1% cultivable 1% cultivable �

Introduction Introduction � Universal Tree � Universal Tree

Universal Tree of Life Universal Tree of Life � 1980 1980’ ’s Carl s Carl Woese Woese, , phylogenetic phylogenetic analysis of all analysis of all � forms of cellular life; ssrRNA ssrRNA forms of cellular life; � Found in all cells Found in all cells � � Present in thousands of copies and easy to isolate Present in thousands of copies and easy to isolate � � Complementary to sequence of gene Complementary to sequence of gene � � Sequence can be compared to reveal similarity and Sequence can be compared to reveal similarity and � differences differences � Defined three cellular domains of life: Defined three cellular domains of life: � � Eukaryotes Eukaryotes � � Eubacteria Eubacteria (Bacteria) (Bacteria) � � Archaeabacteria Archaeabacteria ( (Archaea Archaea) ) �

Pace, NR. 1997. Science 276:734

http://whyfiles.org/022critters/archaea.html

Genome Size Genome Size

Genome size Genome size � 405 complete bacterial genomes on NCBI 405 complete bacterial genomes on NCBI � ruddii (159,662) (159,662) – – Burkholderia � Carsonella Carsonella ruddii Burkholderia � xenovorans (9.73 Mb) (9.73 Mb) xenovorans � Genome size / ecological niche Genome size / ecological niche � � Smaller genomes, Smaller genomes, endocellular endocellular parasites or parasites or � symbionts symbionts

Genome size Genome size � Mutually obligate Mutually obligate � endosymbiotic endosymbiotic associations with associations with animal hosts animal hosts � bacteriocytes bacteriocytes � Distel and Cavanaugh. 1994. J. Bact. 4:1932.

Genome size Genome size Nakabachi et al. 2006. Science 314:267

Genome size Genome size � Free living bacteria, genome size correlates with Free living bacteria, genome size correlates with � species metabolism & width of ecological niche species metabolism & width of ecological niche � Pathogenic species, narrow range of hosts, small Pathogenic species, narrow range of hosts, small � genomes; e.g. Helicobacter, genomes; e.g. Helicobacter, Streptococcus Streptococcus � Anaerobic bacteria, restricted metabolism, e.g. Anaerobic bacteria, restricted metabolism, e.g. � methanogens, small genomes. , small genomes. methanogens � Aerobic organisms, and opportunistic pathogens, Aerobic organisms, and opportunistic pathogens, � higher diversity of genome size; e.g. Pseudomonas Pseudomonas (6 (6 higher diversity of genome size; e.g. Mb) Mb)

pan and core genomes pan and core genomes � Core Core � � Genes present in all strains Genes present in all strains � � Pan (from Greek meaning whole) Pan (from Greek meaning whole) � � Dispensable genome composed of genes Dispensable genome composed of genes � absent from one or more strains and genes absent from one or more strains and genes unique to particular strains unique to particular strains

Bacteria chromosomes Bacteria chromosomes � Most, single circular chromosome, but Most, single circular chromosome, but � exceptions: exceptions: � E.g. E.g. Streptomyces , Borrelia , Agrobacterium , Streptomyces , Borrelia , Agrobacterium , � linear chromosomes linear chromosomes � Linear plasmids Linear plasmids – – e.g. e.g. Klebsiella , Escherichia , Klebsiella , Escherichia , � Thiobacillus Thiobacillus � Linearity: enhances genomic plasticity? Linearity: enhances genomic plasticity? � � Multichromosome Multichromosome spp spp.; e.g. some .; e.g. some � proteobacteria with free living, opportunistic with free living, opportunistic proteobacteria lifestyle lifestyle

Horizontal Gene Transfer Horizontal Gene Transfer

Horizontal Gene Transfer Horizontal Gene Transfer � Genetic exchanges between different evolutionary Genetic exchanges between different evolutionary � lineages lineages � 1944 Avery et al., DNA can be absorbed by 1944 Avery et al., DNA can be absorbed by � microorganisms (Studies on the chemical nature of the substance inducing microorganisms (Studies on the chemical nature of the substance inducing transformations of transformations of pneumococcal pneumococcal types. J. Exp. Med.79:137) types. J. Exp. Med.79:137) � Extent or degree is much debated Extent or degree is much debated �

Mechanisms of HGT Mechanisms of HGT http://fig.cox.miami.edu/Faculty/Dana/bacfun.jpg

Detecting HGT Detecting HGT � Phylogenetics Phylogenetics � � Gene tree that differs significantly from Gene tree that differs significantly from � species tree species tree � Compare all gene trees; gene trees that are Compare all gene trees; gene trees that are � significantly different from majority are significantly different from majority are putative LGT putative LGT

Detecting HGT Detecting HGT

Detecting HGT Detecting HGT � Best sequence match detection (BLAST) Best sequence match detection (BLAST) � � Rapid, but of limited use, since sequence Rapid, but of limited use, since sequence � similarity not necessarily correlated with similarity not necessarily correlated with evolutionary history. evolutionary history.