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On the nature of the last common universal ancestor David Moreira [email protected] CNRS - Université Paris-Sud • A historical approach • A robot portrait of the last common ancestor "Phylogeny studies the relationships among organisms to understand their evolution" Two historical periods: “before the evolutionary theory” “after the evolutionary theory” The ancestor of phylogeny: classification Linné, 1707-1778 Hierarchical system with three kingdoms: animals, plants, and minerals. Augier, 1801 The beginings of evolutionary theory • Species can transform ("evolve") • The different species are related • They share a basic structural unit: the cell Theodor Schwann (1810-1882) : ‘Cell theory’: all living beings are composed of cells Charles Darwin (1859) : ‘Probably all the organic beings which have ever lived on this earth have descended from some primordial form, into which life was first breathed’ Ernst Haeckel (1834-1919) : First ‘universal phylogeny’ La phylogénie moléculaire Carl Woese (70’s) : la révolution ‘woesienne’ Eucarya Archaea Bacteria Grec kainos, qui signifie récent et koinos, qui signifie commun) La phylogénie moléculaire Carl Woese (70’s) : la révolution ‘woesienne’ Eucarya Archaea Bacteria Grec kainos, qui signifie récent et koinos, qui signifie commun) LAST COMMON ANCESTOR Molecular biology (1950…) Molecular biology All living beings share similar biochemical traits ‘What is true for Escherichia coli is true for elephants’ (Jacques Monod) Molecular biology Proteins (ATPases, ribosomal, etc) Membrane - Lipids Last common Genetic material - DNA Ribosomes Polysaccharides ancestor? The last common ancestor and the origin of life LCA Prebiotic chemistry Origin of life Present life s ge u ro s a s ld o e b e u u m o lg s A e m n ta b e s la sti de E i m m A i p Sl éto K in glena s i ne Eu n ad o ne s m n adi ho o c i m r lo T Dip ridie s o sp o r c i M St r Champignons am én op il es C i D lié i A no s pi fl co a g m el pl lé èx s es Comparative genomics Animaux Plantes lf Su Bacteria Bacteria Ch le ba olo la ale s rmo to g The A qu i fi ca le s cto my es ce ( s n so o n uf r du e) s a te pro le s Archaea Archaea o e rm h le s T s ca c a le co m o s a erm mop l es Th bal er lo g h o T h ae A rc Halobactériaceae Me M th et an ha om no i cr ba ob ia ct le s ér ia le s s le ra Ve rt py no ha Pl an et M my Protéobactéries di ale c hè t es s Bac te ro i d e s V e rte s d u sou fre Cianobactéries GC L ow GC es gh siti v o i p H m G ra / us cus m er oc Th noc ei D Sp i ro Eucarya UNIVERSAL GENES = ANCESTRAL GENES ANCESTRAL GENES = THOSE FOUND IN ARCHAEA AND BACTERIA Comparative genomics: ancestral genes Archaea and bacteria share many caracters but... only ~60 genes are shared by all species • rRNAs et ribosomal proteins : protein synthesis with a very evolved molecular machinery • RNA polymerase: RNA synthesis similar to that of contemporary cells • Membrane ATPase: ATP synthesis using a H+ gradient Ö presence of a cell membrane? Comparative genomics: ancestral genes ~60 genes are not enough to assure a cell metabolism, even the simplest one Certain genes are lost in certain species (parasites…) Less strict criteria are necessary • Comparison of groups of species instead of individual species • Looking for gene families instead of specific individual genes 500-600 ancestral genes Comparative genomics: ancestral genes • >500 genes : genome size comparable to that of many small prokaryotes • Capacity to code for a complex metabolism but many caracteristics of this ancestral metabolism remain controversial… Genomes may help to find the good answer The lipid problem: Had the last common ancestor a lipid membrane? Phospholipid structure phosphate (PO43-) Hydrocarbon chain glycerol (C3) — Hydrocarbon chain (C14-C20) Koga et al. 1998 Martin & Russell 2003 Had the last common ancestor a lipid membrane? • G1PDH et G3PDH belong to two ancestral enzymatic superfamilies • Most of the enzymes involved in synthesis and degradation of fatty acids and isopreénoids are also ancestral Pereto et al. 2003 Lombard et al. 2013 Had the last common ancestor a lipid membrane? It had the enzymes to synthesize glycerol, fatty acids, and isoprenoids : It had a lipid membrane The ancestral genome : DNA or RNA? • Many proteins involved in RNA metabolism are universal • Few proteins involved in DNA replication and repair are conserved between bacteria and archaea The last common ancestor synthesized RNA but not DNA? Had it a RNA genome? Mushegian & Koonin 1996 Leipe et al. 1999 Koonin & Martin 2005 Forterre 2006 Glansdorff, Xu & Labedan 2008 The origin of DNA and its replication BACTERIA Forterre, 1999 ARCHAEA Forterre, 2006 RNA EUCARYA Villareal, 2003 Forterre, 2006 The origin of DNA and its replication HOWEVER : • No known virus has all the genes needed for the synthesis and replication of DNA. All viruses depend on the machineries of the infected cells. • Genes involved in DNA synthesis and replication have been transferred from the host cells towards the viruses that infect them. No evidence to support that viruses have "invented" DNA The origin of DNA and its replication • Some DNA replication and repair enzymes are ancestral: Evidence for a DNA genome in the last common ancestor? • RNA genomes have a maximum size of 35-50 kb, this is the ‘Eigen limit’ which is due to: • High error frequency during RNA replication • High mutation rate Incompatible with a genome of >500 genes inferred for the last common ancestor It likely had a DNA genome The question of temperature : Was the last common ancestor hyperthermophilic? St r am én op il es C i D lié A in o s pi fl co a g m el pl lé èx s es The question of temperature : Was the last common ancestor hyperthermophilic? Champignons Animaux Plantes Bacteria si ti v es l es myd ia Ch l a es hè t i roc s Sp de re f ro i cte sou u po sd am ba ct é Ba Gr no r te Ve C ia ri e s Lo w GC Hi g h GC le ba olo f l Su Th s g o to m r e o rm a te pro le s Archaea le s s c ca o a le oc sm a m l r e op le s Th e rm lo ba g o Th h ae A rc Halobactériaceae Me M th et an ha om no i cr ba ob ia ct le s ér ia le s s le ra Aq le i ca u if s e Th py no ha es to myc P la n c u nd (n o s ) rt e V e ou f re s ro té ob ac té ri e s Eucarya et M Thermus / Deino coccus P s ge u ro s a s ld o e b e u u o m lg s A e m n ta b e s la sti de E A mi il m p S éto K in glena es u adi n E n o ne s hom n adi Tric Diplo mo ie s p o rid s o r c Mi s ale Stetter 1996 am én op il es C i D lié A in o s pi fl co a g m el pl lé èx s es St r Champignons Animaux Plantes Bacteria si ti v es l es myd ia Ch l a es hè t i roc s Sp de re f ro i cte sou u po ri e s Lo w GC Hi g h GC Th e rmo to g ale s s a te pro le s Archaea o e rm h le s T ca le s c c o a s ma o pl es e rm bal Th he rmo lo g o T h ae A rc Halobactériaceae Me M th et an ha om no i cr ba ob ia ct le s ér ia le s s le ra es ? py no ha an Pl yc m o t c ro té ob ac té ri e s et M Th ermus / De ino coccus (n on du les V e rte s fica so u fre) A qui P Eucarya a le lo b o f l Su sd am ba ct é Ba Gr no r te Ve C ia s ge u ro s ba s e u ld o e u m g o l s A e m n ta b e s la sti de E i m m A i p Sl éto K in glena s i ne Eu n ad o es m adi n ho Tric Diplo mo n ridie s o sp o r c i M Brochier & Philippe 2002 Adaptations of bacteria and archaea to high temperatures are not exactly the same, so probably they have not been inherited from a hyperthermophilic last common ancestor. However, it may have been mesophilic or thermophilic A mesophilic last common ancestor? Boussau et al., 2008 A thermophilic last common ancestor? Nature, 2008 A thermophilic last common ancestor? Earth was warmer during the Archaean period Age (Gyr) Robert & Chaussidon, 2006 But… Hren et al. (2009) have found a temperature ~40°C colder! Metabolism (C et energy) Very difficult to study : the genes involved have been very frequently transferred between distant lineages Metabolism (C et energy) • A membrane ATPase was used to synthesize ATP with a proton gradient across the membrane • Very likely a heterotrophic metabolism, metabolism with simple glycolysis and fermentation pathways • Oxygen respiration? respiration Very controversial, a possible source of oxygen before the evolution of oxygenic photosynthesis remains unknown Conclusion: a very complex ancestor Proteins (ATPases, ribosomal, etc) Membrane - Lipids Genetic material - DNA Ribosomes Polysaccharides Rapid evolution between the origin of life and the last common ancestor Conclusions - Phylogeny and genomics allow the study of the caracteristics of ancestral species - The last common ancestor was a complex organism - Several basic molecular functions of cells have not significantly changed for billions of years (no permanent "complexification" is observed)