Transcript endosymbiosis

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
1
Today
the 3 domains of life
LUCA
First cell
Origin(s) of life
Third age : Post-luca cellular world
Second age : Pre-luca cellular world
First age : Pre-cellular world
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
Ancestral
duplication
Ancestral
duplication
Ancestral
duplication
E: eucaryotes; B: bacteria; A: archea
LUCA: Last Universal Common Ancestor
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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
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fusion. Several scenarios have been proposed.
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
-proteobacteria
mitochondria
Concatenation of amino acid sequences of respiratory chain proteins
apocytochrome b (Cob) and cytochrome oxidase subunits 1 to 3 (Cox1-3).
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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
Mitochondrial
symbiosis?
Amitochondrial
eucaryotes:
« Archezoa »
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Cavalier-Smith & Chao (1996) J Mol Evol 43:551
Eucaryotes from before the birth of mitochondria
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.”
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Microsporidia
spore
polar tube
sporoplasm
(nucleus + cytoplasm)
spore of Nosema algerae (Undeen 1997)
• > 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 b-tubulin
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Edlind et al. (1996) Mol. Phyl. Evol. 5:359.
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 ?
MICROSPORIDIA ?
Amitochondrial
eucaryotes
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The Long Branch Attraction artifact
[ Felsenstein (1978) Syst Zool 27:401 ]
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Philippe et al. (2000) Proc. Royal Soc. Lond. B 267:1213.
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.
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Van de Peer et al. (2000) Gene 246:1
Conclusion at this stage:
The nice correspondence, for microsporidia, between
- absence of mitochondria
and
- early origin among eucaryotes
does not hold anymore.
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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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from Roger & Silberman (2002) Nature 418:827.
Gene shuffling during evolution of mitochondria
Ancestral -proteobacterial
endosymbiont
transfer
to nucleus
loss
stay
A gene of mitochondrial evolutionary origin can be carried by
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the nuclear genome of a eucaryote.
Discovery in the genome of microsporidion Encephalitozoon cuniculi
of several genes of mitochondrial evolutionary origin
Example: IscS gene
Homo-mt
Mus-mt
Caenorhabditis-mt
100 Candida albicans-mt
85
100
Candida maltosa-mt
99
Saccharomyces-mt
38
Schizosaccharomyces-mt
86
Encephalitozoon
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Arabidopsis-mt
Zygomonas
37
84
Rickettsia
37
Synechocystis
Escherichia
100
Haemophilus
100
Rhodobacter capsulatus
97
Rhodobacter sphaeroides
Rhizobium
100
100
Klebsiella
Enterobacter
Azospirillum
100
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Azotobacter chroococcum
100
Azotobacter vinelandii
100
99
Anabaena azollae
Anabaena sp
100
Helicobacter
Thermotoga
Lactobacillus
69
Archaeoglobus
Aquifex
Deinococcus
Bacillus
Methanobacterium
Pyrococcus
Mycoplasma sp.
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100
Mycoplasma genitalium
Aeropyrum
100
0.2 subst./site
55
48
48
59
75
100
100
100
100
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 b subunit)
5 of them are involved in the assembly of Fe-S clusters, co-factors of
several mitochondrial and cytoplasmic enzymes.
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Katinka et al. (2001) Nature 414:450.
The microsporidian mitosome predicted by genome analysis:
evolutionarily, it derives from a mitochondrion
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Vivarès et al. (2002) Current Opinion in Microbiology 5:499.
Detection of doublemembraned organelles by
anti-HSP70 antibodies
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The mitosome of the amitochondrial parasite Entamoeba histolytica
Phylogeny of CPN60
mitosome Identification
by cellular mapping of
the CPN60 protein in
Entamoeba histolytica
Tovar et al. (1999)
Mol. Microbiol. 32:1013.
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Clark & Roger (1995) PNAS 92:6518.
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
Discovery [Akhmanova et al. (1998)
Nature 396:527] and partial
sequencing of the
hydrogenosomal genome of the
ciliate Nyctothermus ovalis
14,027 bp fragment of the hydrogenosomal genome
- 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 32
II).
Phylogenetic analyses of 2 hydrogenosomal genome genes
nad7 (s.u. 49 kDa complex I)
12S (SSU) rRNA
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Boxma et al. (2005) Nature 434:74.
Death of the concept of primitively amitochondrial eucaryotes
Mitochondrial
symbiosis
Amitochondrial
eukaryotes
« Archezoa »
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Eukaryotic distribution of mitochondrial-derived organelles
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Roger & Silberman (2002) Nature 418:827.
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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Demonstration of the unique origin of primary photosynthetic eukaryotes
50 plastid proteins
143 nuclear proteins
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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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Primary endosymbiosis
Green plants
Rhodophytes
Glaucophytes
?
Euglenozoa
Dinoflagellates
Heterokonts
Cryptophytes
Apicomplexa
Chlorarachniophytes
Secondary
endosymbioses
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Haptophytes
Green plants
Rhodophytes
Glaucophytes
Secondary
endosymbioses
Euglenozoa
Euglenozoa
Dinoflagellates
Dinoflagellates
Dinoflagellates
Heterokonts
Cryptophytes
Apicomplexa
Chlorarachniophytes
Chlorarachniophytes
Secondary plastid
replacement
Karenia (Lepidodinium)
Kryptoperidinium
Haptophytes
Dinophysis
Tertiary
endosymbioses
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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 superphyla.
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 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.
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Homogeneous model
Heterogeneous model
Recent
evidence
for a link
between
eukaryotes
and a
specific
archaeal
lineage
“The archaebacterial origin
of eukaryotes.”
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