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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 1January 2009

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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 worldOrigin(s) of life

LUCA: last universal common ancestor

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Discovery in 1977 of the three domains of life

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SAB : similarity score between fragments of 2 rRNA molecules.

SAB scores are high within each of the 3 groups and low between groups.

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Search of the root of the universal phylogeny

E: eucaryotes; B: bacteria; A: archeaLUCA: Last Universal Common Ancestor

Ancestralduplication

Ancestralduplication

Ancestralduplication

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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.

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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 ?

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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

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Conservation of gene order between mitochondria and -proteobacteria

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The gene-richest mitochondrial genome known as of today.

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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 ?

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Phylogenetic analysis of small subunit ribosomal RNA

Cavalier-Smith & Chao (1996) J Mol Evol 43:551

Amitochondrialeucaryotes:« Archezoa »

Mitochondrialsymbiosis?

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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

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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

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Phylogenetic analysis of -tubulin

Edlind et al. (1996) Mol. Phyl. Evol. 5:359.

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

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Is it possible to reconcile ribosomal RNAs, tubulins and RNA polymerases ?

Amitochondrialeucaryotes

MICROSPORIDIA ?

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The Long Branch Attraction artifact [ Felsenstein (1978) Syst Zool 27:401 ]

Philippe et al. (2000) Proc. Royal Soc. Lond. B 267:1213.

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Distance-based analysis of 42 Distance-based analysis of 42 LSU rRNA sequences from LSU rRNA sequences from microsporidia and other microsporidia and other eukaryotes.eukaryotes.

Distances were corrected for Distances were corrected for site-to-site rate variation.site-to-site rate variation.

So this analysis uses a more So this analysis uses a more realistic model of molecular realistic model of molecular evolution.evolution.

Van de Peer et al. (2000) Gene 246:1Van de Peer et al. (2000) Gene 246:1

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Conclusion at this stage:

The nice correspondence, for microsporidia, between

- absence of mitochondriaand- early origin among eucaryotes

does not hold anymore.

23from Roger & Silberman (2002) Nature 418:827.

Diversity of (anaerobe) ‘amitochondrial’ protists• no detectable‘mitochondrial’ organelle (microsporidia, diplomonads, Entamoeba,…)• hydrogenosomes: genomeless organelles producing ATP and H2 (some ciliates, anaerobe fungi, Parabasalia (ex: Trichomonas))

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transfer to nucleusloss

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.

25Mycoplasma genitalium

Mycoplasma sp.

Aeropyrum

PyrococcusMethanobacterium

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100100

Bacillus

DeinococcusAquifex

ArchaeoglobusLactobacillus

ThermotogaHelicobacter

Anabaena spAnabaena azollae

Azotobacter vinelandii

Azotobacter chroococcumAzospirillum100

Enterobacter

Klebsiella

100

100RhizobiumRhodobacter sphaeroides

Rhodobacter capsulatus

100

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97

100

100

100

69

99

HaemophilusEscherichia

Synechocystis

Rickettsia

ZygomonasArabidopsis-mt37

Encephalitozoon

Schizosaccharomyces-mt

Saccharomyces-mtCandida maltosa-mt

Candida albicans-mt

100100

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Caenorhabditis-mt

Mus-mtHomo-mt100

86

100

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85

38

100

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59

84

55

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75

48

100

0.2 subst./site

Discovery in the genome of microsporidion Encephalitozoon cuniculi of several genes of mitochondrial evolutionary originExample: IscS gene

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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.

27Vivarès et al. (2002) Current Opinion in Microbiology 5:499.

The microsporidian mitosome predicted by genome analysis: evolutionarily, it derives from a mitochondrion

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Detection of double- membraned organelles by anti-HSP70 antibodies

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Clark & Roger (1995) PNAS 92:6518.

mitosome Identification by cellular mapping of the CPN60 protein in Entamoeba histolyticaTovar et al. (1999) Mol. Microbiol. 32:1013.

The mitosome of the amitochondrial parasite Entamoeba histolyticaPhylogeny of CPN60

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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.

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double membrane

Immunofluorescence mapping of IscS and IscU in Giardia trophozoites.

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The missing link between mitochondrion and hydrogenosome

14,027 bp fragment of the hydrogenosomal genome

Discovery [Akhmanova et al. (1998) Nature 396:527]

and partialsequencing 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).

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Phylogenetic analyses of 2 hydrogenosomal genome genes

12S (SSU) rRNAnad7 (s.u. 49 kDa complex I)

Boxma et al. (2005) Nature 434:74.

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Amitochondrialeukaryotes« Archezoa »

Death of the concept of primitively amitochondrial eucaryotes

Mitochondrialsymbiosis

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Eukaryotic distribution of mitochondrial-derived organelles

Roger & Silberman (2002) Nature 418:827.

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Evolutionary history of the chloroplastic endosymbiosis

- what was the donor organism ?

- was the endosymbiosis unique or repeated ?

- what eukaryotic lineages received it ?

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50 plastid proteins

143 nuclear proteins

Demonstration of the unique origin of primary photosynthetic eukaryotes

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Model of primary chloroplastic endosymbiosis

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Secondary chloroplastic endosymbiosis

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Secondary chloroplastic endosymbiosis in the cryptophyte Guillardia theta

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Euglenozoa

Chlorarachniophytes

?

GlaucophytesRhodophytesGreen plants

Primary endosymbiosis

Dinoflagellates

Apicomplexa

HeterokontsCryptophytes

Haptophytes

Secondaryendosymbioses

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Glaucophytes

Euglenozoa

Chlorarachniophytes

Dinoflagellates

RhodophytesGreen plants

Apicomplexa

HeterokontsCryptophytes

Haptophytes

Secondaryendosymbioses

DinoflagellatesDinoflagellatesEuglenozoa

ChlorarachniophytesSecondary plastid

replacement(Lepidodinium)

Tertiaryendosymbioses

Karenia

Kryptoperidinium

Dinophysis

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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.

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Bacterial domain phylogeny.

In the « classical » vision, a natural division in phyla exists.

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Archaeal domain phylogeny.

Recent discovery of a new phylum.

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

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

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Eukaryotic domain phylogeny.

Emerging consensus for the identification of five super- phyla.

Relationships between them remain very uncertain.

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Models of the origin of the eukaryotic cell

- the fusion hypotheses

- how to test these hypotheses

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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).

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Models of the origin by fusion of the eukaryotic cella-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.

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Homogeneous model Heterogeneous model

“The archaebacterial origin of eukaryotes.”

Recent evidence for a link between eukaryotes and a specific archaeal lineage