The Origins of Life and Precambrian EvolutionQuestionsCartoon of the tree of life (Fig. 16.1)What is “alive”?Molecules as living thingsProtein vs. nucleic acidThe RNA world hypothesisRibozyme from Tetrahymena themophila: a self-splicing intron between adjacent rRNA genes (Fig. 16.2 a)The catalysis performed by the Tetrahymena ribozyme in vitro (Fig. 16.2 b)The case for an RNA-based system as an early life formCan RNA evolve? – experimental evolution of RNA (Beaudry and Joyce 1992)Test tube evolution of RNA (Beaudry and Joyce 1992) (Fig. 16.4)Slide 13Genotypic changes in an evolving RNA population (Beaudry and Joyce 1992) (Fig. 16.5b)Toward self-replicating RNA moleculesLaboratory evolution of the ability of catalyze the joining of adjacent nucleotides (phosphoester bond) (Bartel and Szostak 1993)Test-tube selection scheme for identifying ribozymes that can link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 a,b)Test-tube selection scheme for identifying ribozymes that can link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 c,d)Test-tube selection scheme for identifying ribozymes that can link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 e)Evolution of catalytic ability in a laboratory population of ribozymes (Bartel and Szostak 1993) ( Fig. 16.7)RNA world – summaryPre-biotic synthesis of organic molecules: the Miller – Urey experiments (1953)The Oparin – Haldane model (Fig. 16.12): “the prebiotic soup”Criticisms of Miller – Urey and Oparin – HaldaneExtra-terrestrial origins?When was life first present on Earth?The history of large impacts on Earth and Moon (Sleep et al. 1989) (Fig. 16.11)What was the most recent common ancestor of all extant organisms?The phylogeny of everythingSmall-subunit rRNA phylogeny (Woese 1996) (Fig. 16.18): Three-domain classificationThe tree of life – old style (Fig. 16.17): five-kingdom classificationThree-domain classification system: Bacteria, Archaea, EucaryaWhat was the most recent common ancestor like?Different genes give different universal phylogenies – 1 (Fig. 16.22 a,b)Different genes give different universal phylogenies – 2 (Fig. 16.22 c,d)Horizontal gene transferEvidence for horizontal gene transfer of the HMGCoA reductase gene into an archaean (Doolittle and Lodgson 1998) (Fig. 16.23)The cenancestor was not a single species, but a community (Fig. 16.26)The latest possible date for the root of the tree of lifeThe origin of mitochondria and chloroplastsPlacement of mitochondria and chloroplasts on the universal tree based on small-subunit rRNA genes (Giovannoni et al. 1988) (Fig. 16.30)1The Origins of Life and Precambrian EvolutionChapter 162Questions•What was the first living thing?•Where did it come from?•What was the last common ancestor of today’s organisms and when did it live?•What is the shape of the tree of life?•How did the last common ancestor’s descendants evolve into today’s organisms?3Cartoon of the tree of life (Fig. 16.1)4What is “alive”?•Living things have:–the ability to replicate or reproduce, together with the ability to store and transmit heritable information – to have a “genotype”–the ability to express that information – to have a “phenotype”–the ability to evolve – to make changes in the heritable material and to have those changes “tested” in order to distinguish valuable ones from detrimental ones5Molecules as living things•In principle, a molecule could be alive by our definition:–If it had the ability to copy itself using raw materials in its environment, and if errors in copying led to differences in the speed of self-replication or in chemical stability–In this case, the “genotype” is the chemical structure of the molecule, and the “phenotype” is the speed of self- replication or stability of the molecule6Protein vs. nucleic acid•Proteins possess the enzymatic function that would presumably be necessary for a self-replicating molecule – but there is no evidence that proteins can propagate themselves•Nucleic acids possess, in principle, the ability to direct their self-replication via complementary base-pairing – but until about 20 years ago were not known to possess any enzymatic function7The RNA world hypothesis•Catalytic RNA molecules were a transitional form between non-living matter and the earliest cells•In the early 1980’s it was discovered independently by Sidney Altman and Thomas Cech that some RNA molecules had enzymatic activity – specifically, they could form and break the phosphoester bonds that link adjacent nucleotides in nucleic acids – ribozymes•This enzymatic function would be essential if nucleic acids were the first self-replicating things8Ribozyme from Tetrahymena themophila: a self-splicing intron between adjacent rRNA genes(Fig. 16.2 a)9The catalysis performed by the Tetrahymena ribozyme in vitro (Fig. 16.2 b)10The case for an RNA-based system as an early life form•Existence of catalytic RNA•RNA is a core component of the apparatus for translating genetic information into proteins – rRNA a component of ribosomes (probably the component that actually catalyzes protein synthesis), and tRNA “adapters” also required for protein synthesis•Ribonucleoside triphosphates (ATP, GTP) are the basic energy currency of all cells and are components of electron-transfer cofactors such as NAD (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide)11Can RNA evolve? – experimental evolution of RNA(Beaudry and Joyce 1992)•Select for the ability of Tetrahymena ribozyme to catalye the cutting of a DNA oligonucleotide and attachment of a fragment to its 3’ end12Test tube evolution of RNA (Beaudry and Joyce 1992) (Fig. 16.4)13Can RNA evolve? – experimental evolution of RNA(Beaudry and Joyce 1992)•Experiment was seeded with a large population of randomly mutated ribozymes•After 10 “generations” the catalytic ability of the average RNA in the population had improved by a factor of 30•Most of the improvement in catalytic ability was attributable to mutations at 4 locations•Many additional experiments with natural and synthetic RNA have produced ribozymes that can catalyze reactions such as phosphorylation, peptide bond formation, and carbon-carbon bond formation.•BUT, a crucial piece is missing from the experiment that we have just described – self-replication14Genotypic changes in an evolving RNA population (Beaudry and Joyce 1992) (Fig.