Lec 11 PDF - Microbial Evolution and Systematics

PowerPoint® Lecture Presentations CHAPTER 13 Microbial Evolution and Systematics © 2018 Pearson Education, Inc. Origins of Life • Early geological evidence of life • 3.4 billion years ago • Stromatolites 2 Origin of cellular life • The Earth is ~4.5 billion years old • Cellular life is bel...

PowerPoint® Lecture Presentations CHAPTER 13 Microbial Evolution and Systematics © 2018 Pearson Education, Inc. Origins of Life • Early geological evidence of life • 3.4 billion years ago • Stromatolites 2 Origin of cellular life • The Earth is ~4.5 billion years old • Cellular life is believed to have evolved ~4 billion years ago • Hostile conditions on Earth’s surface: anoxic, extremely hot, high levels of UV radiation • Organic precursors to living cells can form spontaneously under certain conditions • Set the stage for the origin of life Scanning electron micrograph of microfossil rod-shaped bacteria from 3.45 billion year old rocks Evidence of Life • Stromatolites • Isotope ratios • Limestone depleted of 13CO2 • Microfossils Cyanobacteria Filamentous Prokaryotes Algae 4 Eventually, lipid bilayers took the place of mineral compartments, allowing the first cells to disperse to new habitats. Subsurface origin hypothesis • Hypothesis that life originated at hydrothermal springs on ocean floor • Less hostile and more stable conditions than Earth’s surface • Steady and abundant supply of energy • Reduced inorganic compounds, e.g. H2 and H2S • Formation of critical molecules and compartmentalized structures  emergence of life Compartments allow coupling of energetic reactions to molecular replication. Mound: precipitates of clay, metal sulfides, silica, and carbonates Ocean water (< 20ºC, containing metals, CO2, and PO42–) Mineral pores form first biological compartments . Amino acids Nitrogen bases Sugars Nutrients in hot hydrothermal water Ocean crust Models for Early Life • Prebiotic soup • Small organic molecules arise abiotically • Created by lightning • Can replicate in laboratory • Found on other planets • Lipids spontaneously organize into micelles 6 Self-replicating systems • First self-replicating systems may have been RNA-based • = RNA world theory • Ribonucleotides are a component of certain essential cofactors and molecules (ATP, NADH, coenzyme A) • RNA can bind small molecules (e.g., ATP, amino acids, other nucleotides) • RNA has catalytic activity • RNA may have once had the ability to catalyze its own synthesis • Eventually: • Proteins took over most of catalytic activities • DNA, a more stable molecule, became genetic repository • Three-part systems (DNA, RNA, and protein) evolved and became universal among cells Origin of cellular life Prebiotic chemistry Early cellular life Precellular life 4.3–3.8 bya 3.8–3.7 bya RNA A Protein mRNA A UGC GACU G UU T GGAG G C AG CU G C GAC AG C U G AT TA GC CG C DNA CG G TA A GC C AU T CG G T AU AU T CG G C GC TA A GC C AU T CG G T A G C G C G C C G TA CG AT GC CG Biological building blocks - Amino acids - Nucleosides - Sugars Evolutionary diversification LUCA Bacteria Archaea HGT between cells RNA world Protein synthesis DNA Lipid bilayers - Catalytic RNA - Self-replicating RNA - RNA-templated translation - Replication - Transcription - Cellular compartments - Early cells likely had high rates of HGT Divergence of Bacteria and Archaea - Components of DNA replication, transcription, and translation all in place Earliest Molecules - RNA • original molecule must have fulfilled protein and hereditary function • ribozymes • RNA molecules that form peptide bonds • perform cellular work and replication • earliest cells may have been RNA surrounded by liposomes Metabolic diversification • Following origin of cells, microbial life began diversifying to exploit various resources on Earth • Metabolism was exclusively anaerobic until evolution of cyanobacteria • Earliest life believed to use H2 as electron donor and S0 as electron acceptor = Chemolithotrophs • Abundant in early earth • Requires relatively few enzymes to yield energy • CO2 likely major source of carbon = autotrophs • Over time, organic compounds would have accumulated, providing conditions for evolution of chemoorganotrophic bacteria Photosynthesis and the Oxidation of Earth • Anoxygenic phototrophs evolved ~3.5 BYA • Used H2S as electron donor • ~3 BYA, cyanobacteria developed a photosystem that could use H2O instead of H2S, generating O2 • In absence of O2, all Earth’s iron would be in reduced form Fe2+ • Red oceans! • Only after abundant Fe2+ was consumed could O2 accumulate in the atmosphere • By 2.4 billion years ago, O2 concentrations raised to 0.0001%; initiation of the Great Oxidation Event • Reached current levels (~21%) ~600 – 900 MYA Oxidation of Earth • Bacteria and archaea unable to adopt to oxic change were increasingly restricted to anoxic habitats • Oxic environment also allowed for evolution of new metabolic schemes • O2 respiration = energetic advantage due to high reduction potential of O2/H2O • UV radiation converted some O2 to O3 (ozone), forming an ozone shield • Strongly absorbs UV radiation • Rendered Earth’s surface more hospitable • New habitats & evolution of greater diversity The Species Concept in Microbiology • No universally accepted concept of species for prokaryotes! • Biological species concept not meaningful • Phylogenetic species concept is best alternative • Prokaryotic species = group of strains that are genetically cohesive and share a unique recent common ancestor based on DNA sequences of multiple genes • Current criteria for strains to be same species: • 70% or greater DNA–DNA hybridization • 97% or greater 16S rRNA gene sequence identity • Over 10,000 species of Bacteria & Archaea formally recognized Evolutionary Chronometers: Who’s related To Whom? -evolutionary distance can be measured by comparing nucleotide sequences Dr. Carl Woese (1978) © 2008 W.W. Norton & Company, Inc. MICROBIOLOGY 1/e 15 Molecular Clocks • Assume neutral/silent mutations accumulate steadily • Constant rate per generation • Sequence differences are proportional to number of generations since divergence • Best to compare conserved sequences • Gene for small subunit rRNA • Adjustments to rate • Conservation of sequences needed for function 16 Choosing the right chronometer -universally distributed -functionally homologous -ribosomal RNA -evolutionary relationships implicated by degree of similarity -amplify using PCR and primers © 2008 W.W. Norton & Company, Inc. MICROBIOLOGY 1/e 17 16S rRNA comparison • Small subunit rRNA genes are used in phylogenetic analysis • Found in the genomes of all organisms, functionally constant, adequate length, slow rate of change • If a long time has elapsed since two species diverged, their genes tend to be more different than closely related species A phylogenetic distance map from the 16S ribosomal RNA sequence -evolutionary distance as non-identical nucleotides -corrected to account for back mutation -computer analysis or “best fit” 19 Microbial Phylogeny • 3 Domains • Archaea • Bacteria • Eukaryotes • No root to tree? • No outgroup! ? 20 Horizontal Gene Transfer • Acquisition of DNA from another cell • Not as common as vertical transfer • DNA passed from parent to child • More frequent in microbes • Plasmid transfer • Transposable elements • Bacteriophages/transduction 21 Horizontal Gene Transfer • Complicates determination of phylogeny • Many genes derived from other species • “Informational” genes usually not transferred • Interact with many cellular components  “Operational” genes transferred Function independently of other cell components  Bring added functions to recipient  Confer selective advantage  22 Horizontal Gene Transfer • Pathogenicity islands • Large set of genes grouped together • Transferred as a unit • Confer ability to invade eukaryotic host • Example: E. coli O157:H7  Several groups of genes not found in other E. coli strains 23 Identifying strains • 16S rRNA are not always useful for distinguishing between closely related species • Sequences of other highly conserved protein-coding genes may be used • To distinguish between strains, multilocus sequence typing (MLST) is used • Several different "housekeeping genes" are sequenced • Can distinguish between very closely related strains • Widely used in clinical microbiology and in epidemiology studies tracking virulent strains Bacterial chromosome Various "housekeeping" genes Analyze alleles. New isolate or clinical sample Isolate DNA. Amplify 6–7 target genes. Sequence. Compare with other strains and generate tree. Strains 1–5 New strain Strain 6 Strain 7 Microbial Genomes are dynamic • Dramatic differences in genome size and gene content between strains of a single species Genome 1 Genome 2 Pan Core • Genes placed in two classes: • Core genome: Shared by all members of a species • Pan genome: Core genome + genes not shared by all members • Analysis of 20 strains of E coli: • Avg. 4721 genes (4068 – 5379) • Core genome = 1976 genes • Pan genome = 17,838 • Deletions occur frequently • Reduced genome size = selective advantage Genome 3 Pan genome Core genome Symbiosis • Microbes interact with other organisms • Mutualism • Parasitism • Interacting organisms coevolve • Rhizobium and mutualist plant hosts • Parasites and hosts • Parasites lose functions provided by hosts 26 Endosymbionts • Many organisms live inside another • Intestinal flora • Some live intracellularly • Paramecium and Chlorella • Paramecium shields algae • Algae provide nutrients • Paramecium can digest algae if necessary 27 Endosymbiotic Origin of Eukaryotes • Oxygen also spurred evolution of organelle-containing eukaryotic microorganisms • Oldest eukaryotic microfossils ~2 billion years old • Endosymbiotic hypothesis states that mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell • Mitochondria: Respiring bacterium • Chloroplasts: Cyanobacterium-like organism • Evidence: • Mitochondria and chloroplasts both contain circular genomes • Ribosomes are prokaryotic size (70S) • 16S rRNA sequence is characteristic of Bacteria Origin of eukaryotes • Exact origin remains unresolved Bacteria Eukarya Animals Ancestor of chloroplast Archaea Bacteria Plants Nucleus formed Ancestor of mitochondrion Eukaryotes began as nucleus-bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis Eukarya Animals Ancestor of chloroplast Archaea Plants Nucleus formed Engulfment of a H2-producing cell of Bacteria by a H2-consuming cell of Archaea A species of archaea engulfed an H2consuming bacterium, which gave rise to mitochondria. The eukaryotic nucleus developed later. Mitochondria and Chloroplasts • Organelles were bacteria • Own circular genome • Double membrane • Electron transport components • Behave like endosymbiotic organisms • Reproduce independently • Lost functions to host 30 Mitochondria and Chloroplasts • Chloroplast: Cyanobacterium • Photosynthesis components similar • rRNA similarities • Mitochondria: Rickettsia (a-Proteobacterium) • Electron transport components • rRNA similarities 31 -plasmids and/or other DNA can be transferred by conjugation, transformation or transduction to other bacterial species.