Download Amsterdam 2004

Bioinformatics and Evolutionary
Genomics
The tree of life / HGT , origin of
eukaryotes
LUCA
“three kingdoms”
How to root the tree of life?
1: Find paralogs that duplicated before the
LUCA
6 found so far
How to root the tree of life? 2: Make a tree of
paralogs that duplicated before the LUCA
Griblado 1998 J Mol Evol
Griblado 1998 J Mol Evol
How ta make a tree of life?
Issue: Horizontal Gene Transfer (HGT)
• As opposed to
normal vertical
inheritance
• Inheritance from
somewhere else
than parents
• AKA lateral gene
transfer
HGT
Ec1
Rp1 Bs1 Mg1
Ct1
Af1
HGT
Ec1
Rp1 Bs1 Mg1
Ct1
Af1
HGT
Bs2 Mg2
Ec1
Rp1 Bs1 Mg1
Ct1
Af1
HGT
Bs2 Mg2
Ec1
Rp1
Ct1
Af1
HGT: frequently observed when many
genome sequences became available
HGT & Tree of Life (ToL)
b
Transition prokaryotes to eukaryotes: big
transition
• The prekaryote
• No more intermediates
• How to look before the event horizon?
Endo symbiosis of alpha proteo-bacteria gave
rise to mitochondria
• Mitochondrial DNA in the mitochondria
• Hydrogenosomes shown to be derived from
mitochondria
• Many proteins active in present-day mitochondria
are coded for by proteins of eukaryotic invention,
archaeal descent
• Many proteins of alpha-protein ancestor active in
in other parts of the cell
B
rRNA tree
Mitochondria have
their own mini genome
16S Ribosomal RNA
Identifying eukaryotic proteins with an alphaproteobacterial origin based on their phylogeny
Eukaryotic + alphaproteobacteria
in the same branch
Alpha-proteobacterial proteins
with the rest of the bacteria
and archaea
Detecting eukaryotic genes of alpha-proteobacterial ancestry
GENOME
6 alpha-proteobacteria (22 500 genes)
6 alpha-proteobacteria
GENOMES 9 eukaryotes
56 Bacteria+Archaea
SELECTION OF HOMOLOGS,
(Smith&Waterman)
LIST
ALIGNMENTS AND TREE
(Clustalx, Kimura+Dayhoff)
TREE SCANNING
PHYLOME
Proto-mitochondrial metabolism:
- Catabolism of fatty acids, glycerol and amino acids.
- Some pathways are not mitochondrial.
non-mitoch..
mitochondrial
not in
yeast/human
The majority of the proto-mitochondrial proteome is not mitochondrial (anymore)
566
Gabaldon & Huynen
Science 2003
alpha-prot.
Yeast mitochondrial proteome:
Eric Schon,
Methods Cell Biol 2001
(manually curated)
35
293
303
59
10
Huh et al., Nature 2003
(green fluorescent genomics) 527
Human mitochondrial proteome:755
Eric Schon,
Methods Cell Biol 2001
113
508
From endosymbiont to organell, not only loss
and gain of proteins but also “retargeting”:
proteins
loss
re-targeting
~65% of the alphaproteobacteria derived set is
not mitochondrial.
Ancestor
Modern mitochondria
~16% of the mitochondrial
yeast proteins are of alphaproteobacterial origin.
gain
t
Gabaldon and Huynen, Science 2004
“When” did the mitochondria invade the
eukaryotes?
• Genes from alpha-proteobacterial descent
present in genomes in mitochondria-less
organisms (cf. toni)
• All eukaryotes have or had a mitochondria/alpha
proteobacterial symbiont
• It thus happened before the last common
ancestor of all eukaryotes
• But then still “when”? (b)
what about all other cellular innovations
that set eukaryotes apart from
prokaryotes?
the prekaryote-LECA transition
Makarova NAR 2005
Duplication more prevalent in preeukaryotes that in archaea or bacteria
Makarova NAR 2005
duplications: e.g.
small GTPases
Thus all these duplications & endosymbios
order?
• Unknown but all before eluca
• According to the theory of endocytosis as a late
thing for the prekaryote, after many of the
eukaryotic inventions: to be tested involvement of
genes of alpha-prot origin in crucial (cellular) euk
processes?
(nuclear import)
Eukaryotic tree of life?
• The divisions:
– Ophistokonts (animals, fungi, microsporidia)
– Amoebozoa (Dicty)
– Chromalveolata Paramecium, Plasmodium but
also diatoms
– Archaeplastida
– Excavata
– Rhizaria
• Historically: crown-group eukaryotes vs protists
• What is a complete genome; draft genomes
Animals
• Most primitive: sponges
• Quite a number of genome sequences (of
dubious completeness)
Fungi
•
•
•
•
Many complete genomes
Broad, Genolevures
Microsporidium (E. cuniculi)
Mushrooms are
Basidomyctes
• Together with animals:
ophistokonts
Amoebozoa
• Few genomes
– Entamoeba histolytica
– Dictyostelium discoideum
Archaeplastida
• Second bacterial endosymbiosis event:
cyanobacteria
• Green algae, red algae, plants
• ~5 genomes
Chromalveoates
• Secondary endosymbios: plastids
• Very different species
• (diatoms (also commonly referred to as algae),
oomycetes, paramecium, alvealotes,
dinoflagelates)
• Quite some genomes (~10)
B
Excavata
• Weird parasites (Giardia, Trypanosome,
Leismania)
• But also: Naegleria gruberi: amoeboflagelate
Rhizaria
• Amoeboids + amoeboflagellates
• produce shells which make up the vast majority
of protozoan fossils.
• No genomes (yet)
How are eukaryotes related ???
• Historically: crown-group eykaryotes vs protists
but now molecular evidence
• Two hypothesis:
– In or just after excavata
– Inbetween ophistokonts/amoebozoa vs the
rest (unikont vs bikont), myosins
• Rhizaria?
• phagotrophic origin of eukaryotes: an amoebe
with flagella?
b