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1 Recent discoveries about the molecular evolution of the three domains of life (Bacteria, Archaea, Eukaryota) Manolo Gouy Laboratoire de Biométrie & Biologie.

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Presentation on theme: "1 Recent discoveries about the molecular evolution of the three domains of life (Bacteria, Archaea, Eukaryota) Manolo Gouy Laboratoire de Biométrie & Biologie."— Presentation transcript:

1 1 Recent discoveries about the molecular evolution of the three domains of life (Bacteria, Archaea, Eukaryota) Manolo Gouy Laboratoire de Biométrie & Biologie Evolutive - CNRS / Univ. Lyon 1 January 2009

2 2 the 3 domains of life LUCA First cell Today First age : Pre-cellular world Second age : Pre-luca cellular world Third age : Post-luca cellular world Origin(s) of life LUCA: last universal common ancestor

3 3 Discovery in 1977 of the three domains of life

4 4 S AB : similarity score between fragments of 2 rRNA molecules. S AB scores are high within each of the 3 groups and low between groups.

5 5

6 6 Search of the root of the universal phylogeny E: eucaryotes; B: bacteria; A: archea LUCA: Last Universal Common Ancestor Ancestral duplication Ancestral duplication Ancestral duplication

7 7

8 8 Current hypotheses about the origin of the three domains 1)The most widely accepted one, based of analyses of a few pre-LUCA gene duplicates. 2)Iconoclastic hypothesis proposed by some authors: the prokaryotic state (simple) is seen as resulting from a simplification rather than as ancestral. 4)The eukaryotic cell is seen as resulting from an archae + bacterium fusion. Several scenarios have been proposed.

9 9 Evolutionary history of the mitochondrial endosymbiosis - what was the donor organism ? - was the endosymbiosis unique or repeated ? - when did it occur ? what eukaryotic lineages received it ?

10 10 The unique endosymbiotic origin of mitochondria from an ancestral  -proteobacterium Concatenation of amino acid sequences of respiratory chain proteins apocytochrome b (Cob) and cytochrome oxidase subunits 1 to 3 (Cox1-3).  -proteobacteria mitochondria

11 11 Conservation of gene order between mitochondria and  -proteobacteria

12 12 The gene-richest mitochondrial genome known as of today.

13 13 Evolutionary history of the mitochondrial endosymbiosis - what was the donor organism ? - was the endosymbiosis unique or repeated ? - when did it occur ? what eukaryotic lineages received it ?

14 14 Phylogenetic analysis of small subunit ribosomal RNA Cavalier-Smith & Chao (1996) J Mol Evol 43:551 Amitochondrial eucaryotes: « Archezoa » Mitochondrial symbiosis?

15 15 Tom Cavalier-Smith (1987) Nature 326:332 “It is a widespread fallacy that mitochondria are found in all eukaryotic cells.” “It is not the mitochondria, but the nucleus, endomembrane system and cytoskeleton that are the true hallmarks of the eukaryote cell.” “The idea that some protozoa are the living relics of the earliest phase of eukaryote cell evolution and diverged from our ancestors before the symbiotic origin of mitochondria is given strong support by DNA sequence studies.” Eucaryotes from before the birth of mitochondria

16 16 spore polar tube sporoplasm (nucleus + cytoplasm) spore of Nosema algerae (Undeen 1997) Microsporidia > 1000 species unicellular eukaryotes of very small size obligate intracellular parasites amitochondriate, aperoxysomal evolutionary origin subject of much debate

17 17 Phylogenetic analysis of  -tubulin Edlind et al. (1996) Mol. Phyl. Evol. 5:359.

18 18 Phylogenetic analysis of RNA polymerase II large subunit Hirt et al. (1999) Proc.Natl.Acad.Sci. USA 96:580

19 19 Is it possible to reconcile ribosomal RNAs, tubulins and RNA polymerases ? Amitochondrial eucaryotes MICROSPORIDIA ?

20 20 The Long Branch Attraction artifact [ Felsenstein (1978) Syst Zool 27:401 ] Philippe et al. (2000) Proc. Royal Soc. Lond. B 267:1213.

21 21 Distance-based analysis of 42 LSU rRNA sequences from microsporidia and other eukaryotes. Distances were corrected for site-to-site rate variation. So this analysis uses a more realistic model of molecular evolution. Van de Peer et al. (2000) Gene 246:1

22 22 Conclusion at this stage: The nice correspondence, for microsporidia, between - absence of mitochondria and - early origin among eucaryotes does not hold anymore.

23 23 from Roger & Silberman (2002) Nature 418:827. Diversity of (anaerobe) ‘amitochondrial’ protists no detectable‘mitochondrial’ organelle (microsporidia, diplomonads, Entamoeba,…) hydrogenosomes: genomeless organelles producing ATP and H 2 (some ciliates, anaerobe fungi, Parabasalia (ex: Trichomonas) )

24 24 transfer to nucleus loss stay Ancestral  -proteobacterial endosymbiont Gene shuffling during evolution of mitochondria A gene of mitochondrial evolutionary origin can be carried by the nuclear genome of a eucaryote.

25 25 Mycoplasma genitalium Mycoplasma sp. Discovery in the genome of microsporidion Encephalitozoon cuniculi of several genes of mitochondrial evolutionary origin Example: IscS gene

26 26 Identification of 6 putative proteins that are closer to their mitochondrial or bacterial than to their eukaryotic homologues. These E. cuniculi proteins are very probably of mitochondrial evolutionary origin. Yeast homologues of these 6 E. cuniculi proteins :  ATM1 (mitochondrial transporter )  ISU1 et ISU2  NFS1 (IscS cysteine desulfurase)  SSQ1 (Heat Shock Protein 70 homologue)  YAH1  PDB1 (pyruvate dehydrogenase E1 component  subunit) 5 of them are involved in the assembly of Fe-S clusters, co-factors of several mitochondrial and cytoplasmic enzymes. Katinka et al. (2001) Nature 414:450.

27 27 Vivarès et al. (2002) Current Opinion in Microbiology 5:499. The microsporidian mitosome predicted by genome analysis: evolutionarily, it derives from a mitochondrion

28 28 Detection of double- membraned organelles by anti-HSP70 antibodies

29 29 Clark & Roger (1995) PNAS 92:6518. mitosome Identification by cellular mapping of the CPN60 protein in Entamoeba histolytica Tovar et al. (1999) Mol. Microbiol. 32:1013. The mitosome of the amitochondrial parasite Entamoeba histolytica Phylogeny of CPN60

30 30 The mitosome of the amitochondrial parasite Giardia intestinalis Identification in Giardia of genes coding for mitochondrially targeted proteins in other eukaryotes : Cpn60, Hsp70, IscS (cysteine desulfurase) One example: IscS Tachezy et al. (2001) Mol. Biol. Evol. 18:1919.

31 31 double membrane Immunofluorescence mapping of IscS and IscU in Giardia trophozoites.

32 32 The missing link between mitochondrion and hydrogenosome 14,027 bp fragment of the hydrogenosomal genome Discovery [Akhmanova et al. (1998) Nature 396:527] and partial sequencing of the hydrogenosomal genome of the ciliate Nyctothermus ovalis - Several putative proteins of the hydrogenosomal genome group with their mitochondrial homologues of aerobic ciliate. - Identification of several nuclear genes coding for components of the mitochondrial proteome (pyruvate dehydrogenase, complex II).

33 33 Phylogenetic analyses of 2 hydrogenosomal genome genes 12S (SSU) rRNAnad7 (s.u. 49 kDa complex I) Boxma et al. (2005) Nature 434:74.

34 34 Amitochondrial eukaryotes « Archezoa » Death of the concept of primitively amitochondrial eucaryotes Mitochondrial symbiosis

35 35 Eukaryotic distribution of mitochondrial-derived organelles Roger & Silberman (2002) Nature 418:827.

36 36 Evolutionary history of the chloroplastic endosymbiosis - what was the donor organism ? - was the endosymbiosis unique or repeated ? - what eukaryotic lineages received it ?

37 37

38 38 50 plastid proteins 143 nuclear proteins Demonstration of the unique origin of primary photosynthetic eukaryotes

39 39 Model of primary chloroplastic endosymbiosis

40 40 Secondary chloroplastic endosymbiosis

41 41 Secondary chloroplastic endosymbiosis in the cryptophyte Guillardia theta

42 42 Euglenozoa Chlorarachniophytes ? GlaucophytesRhodophytes Green plants Primary endosymbiosis Dinoflagellates Apicomplexa Heterokonts Cryptophytes Haptophytes Secondary endosymbioses

43 43 Glaucophytes Euglenozoa Chlorarachniophytes Dinoflagellates Rhodophytes Green plants Apicomplexa Heterokonts Cryptophytes Haptophytes Secondary endosymbioses Dinoflagellates Euglenozoa Chlorarachniophytes Secondary plastid replacement (Lepidodinium) Tertiary endosymbioses Karenia Kryptoperidinium Dinophysis

44 44 State of the art about phylogenetic knowledge at the scale of each domain of the tree of life - Much debate for bacterial and archeal domains. Is the concept of phylogenetic tree adequate ? - Eukaryotic domain phylogeny : after much confusion, some structure begins to emerge.

45 45 Bacterial domain phylogeny. In the « classical » vision, a natural division in phyla exists.

46 46 Archaeal domain phylogeny. Recent discovery of a new phylum.

47 47 Standard model of the tree of life natural division in phyla or kingdoms

48 48 Alternative model: horizontal gene transfers between prokaryotes are so frequent that the notion of natural phyla does not apply.

49 49 Eukaryotic domain phylogeny. Emerging consensus for the identification of five super- phyla. Relationships between them remain very uncertain.

50 50 Models of the origin of the eukaryotic cell - the fusion hypotheses - how to test these hypotheses

51 51 A Two-step scenario - creation by an bacteria/archaea fusion of an amitochondrial eukaryotic cell then - endosymbiosis with an  -proteobacterium B Simultaneous creation of the eukaryotic nucleus and of the mitochondrion. The bacterial partner is always an  - proteobactérium. The archaeal partner varies according to theories (here a methanogen).

52 52 Models of the origin by fusion of the eukaryotic cell a-d: 2-step models e-g: mitochondrial origin = eukaryotic cell creation These hypotheses are testable: each predict similarities between part of the eukaryotic genome and some bacteria, and between the rest of this genome and some archaea.

53 53

54 54 Homogeneous modelHeterogeneous model “The archaebacterial origin of eukaryotes.” Recent evidence for a link between eukaryotes and a specific archaeal lineage


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