Amsterdam 2004 - Universiteit Utrecht

Amsterdam 2004 - Universiteit Utrecht

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 alpha-proteobacterial origin based on their phylogeny Eukaryotic + alphaproteobacteria in the same

Alpha-proteobacterial proteins with the rest of the bacteria and archaea tecting eukaryotic genes of alpha-proteobacterial ances 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. on-mitoch.. mitochondrial not in

yeast/human The majority of the proto-mitochondrial proteome is not mitochondrial (anymore) 566 Yeast mitochondrial proteome: Eric Schon, Methods Cell Biol 2001

(manually curated) Gabaldon & Huynen Science 2003 alpha-prot. 35 293 59

303 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

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