The Origins of Life and Precambrian Evolution

1. The Origins of Life and Precambrian Evolution Chapter 16

2. Questions • 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?

3. Cartoon of the tree of life (Fig. 16.1)

4. What 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 ones

5. Molecules 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 molecule

6. Protein 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 function

7. The 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 things

8. Ribozyme from Tetrahymena themophila: a self-splicing intron between adjacent rRNA genes(Fig. 16.2 a)

9. The catalysis performed by the Tetrahymena ribozyme in vitro (Fig. 16.2 b)

10. The 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)

11. Can 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’ end

12. Test tube evolution of RNA (Beaudry and Joyce 1992) (Fig. 16.4)

13. Can 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-replication

14. Genotypic changes in an evolving RNA population (Beaudry and Joyce 1992) (Fig. 16.5b)

15. Toward self-replicating RNA molecules • So far, we do not have a self-replicating RNA molecule (or a self-replicating system of RNA molecules) • If we can produce such a thing (perhaps by selective “breeding” experiments in the laboratory) then, by one definition at least, we will have succeeding in creating life (although obviously not complex cells)

16. Laboratory evolution of the ability of catalyze the joining of adjacent nucleotides (phosphoester bond) (Bartel and Szostak 1993) • Variable population of synthetic RNA molecules selected for ability to catalyze joining of nucleotides • This is not self-replication, but a necessary function of a self-replicating RNA molecule • Experiment still depends on the use of replicating enzymes to “reproduce” the “successful” RNA molecules after each “generation”

17. Test-tube selection scheme for identifying ribozymes that can link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 a,b)

18. Test-tube selection scheme for identifying ribozymes that can link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 c,d)

19. Test-tube selection scheme for identifying ribozymes that can link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 e)

20. Evolution of catalytic ability in a laboratory population of ribozymes (Bartel and Szostak 1993) ( Fig. 16.7)

21. RNA world – summary • RNA molecules possess at least some of the necessary properties of living systems • the sequence of nucleotides provides a heritable information storage mechanism (= genotype) • Catalytic ability is a variable, heritable phenotype upon which selection can act • Natural or synthetic ribozymes possess a variety of enzymatic activities, including the ability to join nucleotides together to make short (40 - 50 bp) polynucleotide strands • However, so far, no one has succeeded in producing an RNA molecule that can copy itself • Even if that is achieved, it still leaves the question of how the first RNA molecules were made

22. Pre-biotic synthesis of organic molecules:the Miller – Urey experiments (1953) • Water vapor + methane + ammonia + hydrogen + electric spark = amino acids (glycine, alanine) • Similar experiments by others have yielded other organic compounds, including nitrogenous bases (from ammonia and hydrogen cyanide) and ribose (from formaldehyde)

23. The Oparin – Haldane model (Fig. 16.12):“the prebiotic soup”

24. Criticisms of Miller – Ureyand Oparin – Haldane • Earth’s early atmosphere may not have been composed of methane and ammonia, but rather carbon dioxide and nitrogen, which would not have been favorable for formation of the necessary organic molecules (although aldehydes could be formed from carbon dioxide) • Formation and stabilization of polymers of basic buiding blocks (such as amino acids) in the aqueous prebiotic soup also appears to present difficulties (mineral “scaffolding”?) • Still a long way from biological polymers to “cells”

25. Extra-terrestrial origins? • Meteorites are sources of amino acids, at least some of which survive impact • The Panspermia hypothesis • Life originated elsewhere in the solar system and was carried here on meteorites that originated from other planets or moons, or possibly life originated outside the solar system • McKay et al. (1996): meteroite from Mars contained globules of carbonate + magnetite, iron sulfide, and polycyclic aromatic hydrocarbons: and a suggestion of microfossils that resemble bacteria • Many (most?) are not convinced that the Martian rock provides evidence of life – the compounds that were present can also be formed by abiotic processes • In any event, the Panspermia hypotheis merely shifts the problem of the origin of life to somewhere else at some other time

26. When was life first present on Earth? • Radiometric dating of meteorites suggests that the solar system, including Earth, is about 4.5 to 4.6 billion years old • Sedimentary rocks from Greenland, and dated at 3.7 billion years, contain microscopic graphite globules that have a 12C/13C isotopic ratio that is characteristic of molecules produced by biological processes • This may be about the oldest evidence of life that we are likely to find, because conditions much before that might have been unsuitable for life, or would have obliterated earlier origins of life

27. The history of large impacts on Earth and Moon (Sleep et al. 1989) (Fig. 16.11) Red boxes represent lunar impacts; blue boxes terrestrial impacts (some of which are hypothetical. Dashed line represents impact energy sufficient to vaporize the global ocean. A = Archaean spherule beds; V = Vredevort; S = Sudbury; M = Manicougan; K/T = Cretaceous-Tertiary impact crater (Yucatan)

28. What was the most recent common ancestor of all extant organisms? • Regardless of the origin of organic molecules, and whether or not an RNA world was an intermediate step in the evolution of life, the evidence that all present day life forms share a common ancestor is compelling • All life forms (except some viruses) use DNA and proteins, and all use them in the same way (same 20 amino acids, same genetic code) • The oldest cellular fossils (which resemble bacteria) are 3.4 billion years old

29. The phylogeny of everything • Carl Woese (and others) • We need a highly conserved molecule that has recognizable similarities across all life forms • Small subunit ribosomal RNA • all organisms have ribosomes • all use ribosomes in the same way (translation) • all ribosomes are composed of RNA + protein • all ribosomes have similar structure, being composed of small and large subunits

30. Small-subunit rRNA phylogeny (Woese 1996) (Fig. 16.18):Three-domain classification

31. The tree of life – old style (Fig. 16.17):five-kingdom classification

32. Three-domain classification system:Bacteria, Archaea, Eucarya • Archaea (archaebacteria) more closely related to eukaryotes than they are to “true” Bacteria • Archaea composed of two (or three) kingdoms • Protista must be abandoned as a kingdom (paraphyletic) or must include animals, plants, and fungi. • Animals, plants, and fungi do appear as natural, monophyletic groups (with removal of slime molds from fungi)

33. What was the most recent common ancestor like? • Highly evolved and biologically sophisticated – perhaps similar to modern bacteria • All living organisms store genetic information as DNA and have similar transcription and translation machinery • DNA polymerases are relatively similar across domains • All organisms have DNA-dependent RNA polymerases that show strong similarities across all domains

34. Different genes give different universal phylogenies – 1 (Fig. 16.22 a,b)

35. Different genes give different universal phylogenies – 2 (Fig. 16.22 c,d)

36. Horizontal gene transfer • Inconsistencies among genes for the universal phylogeny have led to the suggestion that taxa have exchanged genes horizontally • Bacteria are known to be able to take up DNA from their environment and to incorporate that DNA into their genomes (transformation, etc.) • 18% of E. coli genes estimated to have arrived by horizontal gene transfer in last 100 million years (Lawrence and Ochman 1998)

37. Evidence for horizontal gene transfer of the HMGCoA reductase gene into an archaean (Doolittle and Lodgson 1998) (Fig. 16.23)

38. The cenancestor was not a single species, but a community (Fig. 16.26)

39. The latest possible date for the root of the tree of life • Oldest known probable eukaryotic fossils (algae) are 1.85 – 2.1 billion years old • Fossil cyanobacteria also suggest that the root is more than 2 billion years old • The most recent date for the root of the tree of all living organisms is between 3.4 and 2 billion years ago

40. The origin of mitochondria and chloroplasts • The mitochondria and chloroplasts of eukaryotic cell have their own genomes • Analysis of small-subunit rRNA genes suggests that both organelles are derived from bacteria which have become obligate endosymbionts

41. Placement of mitochondria and chloroplasts on the universal tree based on small-subunit rRNA genes(Giovannoni et al. 1988) (Fig. 16.30)