MCBL121 Lecture 2 - Biogenesis & Diversity PDF

BIOL/MCBL 121 INTRODUCTORY MICROBIOLOGY Lecture 2 Biogenesis, Evolution, and Diversity Copyright Ansel Hsiao 2021 Objectives • Describe the basic differences between models of abiogenesis and expansion in pool of biological molecules available • Explain what 16S is, how it is used as a molecular...

BIOL/MCBL 121 INTRODUCTORY MICROBIOLOGY Lecture 2 Biogenesis, Evolution, and Diversity Copyright Ansel Hsiao 2021 Objectives • Describe the basic differences between models of abiogenesis and expansion in pool of biological molecules available • Explain what 16S is, how it is used as a molecular clock for bacterial evolution, and why it is suited for this • Describe the endosymbiont theory for the evolution of mitochondria and chloroplasts Copyright Ansel Hsiao 2021 Origins of Life • The earliest forms of life for which we have clear fossil evidence are bacterial communities called stromatolites. • Bulbous masses of sedimentary layers of limestone (CaCO3) that are 3.4 billion years old Copyright Ansel Hsiao 2021 Origins of Life • Before the first cells could evolve, fundamental conditions were required including: • Essential elements: To compose organic molecules • Continual source of energy: Mainly nuclear fusion reactions within the sun • Temperature range permitting liquid water: Otherwise metabolic reactions cease Copyright Ansel Hsiao 2021 The Prebiotic Soup • Small organic molecules arise abiotically from simple reduced chemicals sparked by lightning – generation of organic building blocks • These produced complex macromolecules that eventually acquired the apparatus for self-replication and membrane compartmentalization. Copyright Ansel Hsiao 2021 Miller-Urey Experiment • Simulated chemical and energy conditions though to be present on early Earth • Sterilized to prevent contamination • Began with hydrogen, ammonia, methane, and water • Produced glycine, alanine, some other amino acids and AA derivatives • Subsequent similar experiments generated nucleic acids from hydrogen cyanide and ammonia Copyright Ansel Hsiao 2021 The Origin of Life • Early organic molecules are made • Now what? Copyright Ansel Hsiao 2021 Biological Information Flow Energy Copyright Ansel Hsiao 2021 Biological Information Flow Information Structure and Activity Copyright Ansel Hsiao 2021 Biological Information Flow Replication Transcription Information DNA (genes) Translation RNA Copyright Ansel Hsiao 2021 Protein Structure and Activity The Origin of Life • Neither model fully explains how we go from a subset of critical biological molecules to a functional cell with a replicating genome to pass on information from generation to generation • Once cells with genetic information (genomes) form, how can we measure evolutionary change? Copyright Ansel Hsiao 2021 Molecular Clock/Evolutionary Chronometer • The molecular clock is the temporal information contained in a macromolecular sequence • Based on the acquisition of new random mutations in each round of DNA replication • mutation – changes in genetic sequence Copyright Ansel Hsiao 2021 Molecular Clock/Evolutionary Chronometer • The molecular clock is the temporal information contained in a macromolecular sequence • Based on the acquisition of new random mutations in each round of DNA replication Copyright Ansel Hsiao 2021 Molecular Clock/Evolutionary Chronometer • Must be able to align molecules to determine genetic relatedness • Universal molecule found in all organisms • Has conserved functions in all organisms • Strictly vertically transferred (generation to generation) • Can’t be picked up from the environment or different cells • Constant substitution rate – sequence divergence proportional to time (slow evolving) Copyright Ansel Hsiao 2021 Molecular Clocks • Genes that show the most consistent measures of evolutionary time encode components of the transcription and translation apparatus • Ribosomal RNA and proteins, tRNA, and RNA polymerase • The most widely used molecular clock is the gene encoding the small subunit rRNA (SSU rRNA) • 16S rRNA (bacteria) or 18S rRNA (eukaryotes) • Use of a molecular clock requires the alignment of homologous (similar) sequences in divergent species or strains Copyright Ansel Hsiao 2021 Molecular Clocks • Prokaryotes: 70S ribosome • 50S + 30S • 30S has 16S rRNA • 16S rRNA (18S rRNA) • ~ 1.5 kb in length Copyright Ansel Hsiao 2021 Molecular Clocks • Can be aligned (gene) • Strictly vertically transferred • Universal molecule – translation • Conserved function - translation • Constant substitution rate – sequence divergence proportional to time (slow evolving) Copyright Ansel Hsiao 2021 RNA Structure • RNA bases can base-pair within the same molecule (secondary structure) • Structural basis for independent activity • Base pairing determines structure • As long as function is necessary, sequences that contribute to base pairing will be conserved Copyright Ansel Hsiao 2021 Translation • Ribosome-binding site (RBS aka ShineDalgarno sequence) on mRNA allows binding to 30s subunit • Shine-Dalgarno site is complementary to sequence at the 3’ end of the 16sRNA • Ribosomes are in all cells, and machinery is conserved Copyright Ansel Hsiao 2021 Molecular Clocks • 16S rRNA (18S rRNA) • ~ 1.5 kb in length • Conserved regions across all life forms – allow correct alignment • Variable regions specific to species, genus, phylum, or domain – used as chronometer Copyright Ansel Hsiao 2021 Carl Woese • In 1977, Carl Woese was studying recently discovered prokaryotes that live in hot springs and produce methane • Analysis of the 16S rRNA of these organisms revealed that these prokaryotes were a distinct form of life Copyright Ansel Hsiao 2021 Three domains of life Copyright Ansel Hsiao 2021 Phylogenetics • Study of evolutionary relationships among biological individuals (species, groups of organisms, genetic sequences) • Involves the construction of trees (phylogeny(ies)) to show evolutionary relationships Copyright Ansel Hsiao 2021 Phylogenetics Copyright Ansel Hsiao 2021 Phylogenetics • Modern phylogenetics is computational and molecular, versus narrative and based on gross morphology • Phylogenetics can be done on any sequence (DNA or protein), but in terms of bacterial species relationships are often done with 16S rRNA genes Copyright Ansel Hsiao 2021 Phylogenetics • Sequence alignment – find the most similar sequences and work backwards Copyright Ansel Hsiao 2021 Phylogenetics • Can construct phylogenetic trees that show inferred evolutionary relationships between sequences Copyright Ansel Hsiao 2021 Diversity • Most biodiversity is microbial (bacteria and archaea) • Microbes are found in all environments with life Copyright Ansel Hsiao 2021 Jill Banfield, UC Berkeley, and Laura Hug, University of Waterloo Archaea differ from Bacteria and Eukaryotes • Archaea are not bacteria • • • • Similar size, shape Different cell wall and membrane lipid biochemistry Different basic metabolism Ribosomes more similar to eukaryotes • Archaea and bacteria share 16S RNA sequences in the ribosome • Accumulation of mutations in these sequences can be used to distinguish microbial species Copyright Ansel Hsiao 2021 Evolution of Eukaryotes • How did eukaryotes arise? • DNA similar to archaeal DNA • Mitochondrial, chloroplast DNA similar to bacterial DNA • Endosymbiont theory: • • • • Mitochondria WERE bacteria Chloroplasts WERE cyanobacteria Infected or eaten by other species Ended up living together inside Copyright Ansel Hsiao 2021 Endosymbiosis • Endosymbionts are microbes livings symbiotically inside a larger organism • Endosymbiotic bacteria known as rhizobia induce the roots of legumes to form special nodules to facilitate bacterial nitrogen fixation • Endosymbiotic microbes make essential nutritional contributions to host animals Copyright Ansel Hsiao 2021 Endosymbiont Theory • The old five-kingdom system was modified dramatically by Lynn Margulis (1938–2011) • She proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes • Mitochondria behave like endosymbiotic organisms: • • • • Live inside of another organism Reproduce independently Contain their own circular genomes and prokaryotic-like ribosomes (with 16S) Extreme reductive evolution Copyright Ansel Hsiao 2021 Endosymbiont Theory • The endosymbiosis theory was highly controversial • It implied a polyphyletic ancestry of living species, instead of the long-held assumption that species evolve only by divergence from a common ancestor (monophyletic ancestry) Copyright Ansel Hsiao 2021