Bioinformatics%20and%20Evolutionary%20Genomics%20The%20tree%20of%20life%20/%20HGT%20,%20origin%20of%20eukaryotes

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Bioinformatics and Evolutionary GenomicsThe
tree of life / HGT , origin of eukaryotes
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LUCA
three kingdoms
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How to root the tree of life?1 Find paralogs
that duplicated before the LUCA
6 found so far
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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
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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

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HGT
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HGT
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HGT
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HGT
10
HGT frequently observed when many genome
sequences became available
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HGT Tree of Life (ToL)
b
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Transition prokaryotes to eukaryotes big
transition

• The prekaryote
• No more intermediates
• How to look before the event horizon?

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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
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rRNA tree
Mitochondria have their own mini genome
16S Ribosomal RNA
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Identifying eukaryotic proteins with an
alpha-proteobacterial origin based on their
phylogeny
A
B
Alpha-proteobacterial proteins with the rest of
the bacteria and archaea
Eukaryotic alpha-proteobacteria in the
same branch
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Detecting eukaryotic genes of alpha-proteobacteria
l ancestry
GENOME
6 alpha-proteobacteria (22 500 genes)
6 alpha-proteobacteria 9 eukaryotes 56
BacteriaArchaea
TREE SCANNING
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Proto-mitochondrial metabolism
- Catabolism of fatty acids, glycerol and amino
acids.- Some pathways are not mitochondrial.

non-mitoch..
mitochondrial
not in yeast/human
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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)
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303
59
293
10
Huh et al., Nature 2003 (green fluorescent
genomics)
527
755
Human mitochondrial proteome
Eric Schon, Methods Cell Biol 2001
508
113
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From endosymbiont to organell, not only loss and
gain of proteins but also retargeting
Modern mitochondria
Gabaldon and Huynen, Science 2004
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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)

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what about all other cellular innovations that
set eukaryotes apart from prokaryotes?
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the prekaryote-LECA transition
Makarova NAR 2005
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Duplication more prevalent in pre-eukaryotes that
in archaea or bacteria
Makarova NAR 2005
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duplications e.g. small GTPases
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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)

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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

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Animals

• Most primitive sponges
• Quite a number of genome sequences (of dubious
  completeness)

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Fungi

• Many complete genomes
• Broad, Genolevures
• Microsporidium (E. cuniculi)
• Mushrooms are Basidomyctes
• Together with animals ophistokonts

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Amoebozoa

• Few genomes
• Entamoeba histolytica
• Dictyostelium discoideum

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Archaeplastida

• Second bacterial endosymbiosis event
  cyanobacteria
• Green algae, red algae, plants
• 5 genomes

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Chromalveoates

• Secondary endosymbios plastids
• Very different species
• (diatoms (also commonly referred to as algae),
  oomycetes, paramecium, alvealotes,
  dinoflagelates)
• Quite some genomes (10)

B
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Excavata

• Weird parasites (Giardia, Trypanosome, Leismania)
• But also Naegleria gruberi amoeboflagelate

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Rhizaria

• Amoeboids amoeboflagellates
• produce shells which make up the vast majority
  of protozoan fossils.
• No genomes (yet)

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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