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

How ta make a tree of life? Issue: Horizontal Gene Transfer (HGT) As opposed to normal vertical inheritanceAs opposed to normal vertical inheritance Inheritance from somewhere else than parentsInheritance from somewhere else than parents AKA lateral gene transferAKA lateral gene transfer As opposed to normal vertical inheritanceAs opposed to normal vertical inheritance Inheritance from somewhere else than parentsInheritance from somewhere else than parents AKA lateral gene transferAKA lateral gene transfer

HGTHGT Bs1 Mg1 Ec1 Ct1 Rp1 Af1

HGTHGT Bs1 Mg1 Ec1 Ct1 Rp1 Af1

HGTHGT Bs2 Mg2 Bs1 Mg1 Ec1 Ct1 Rp1 Af1

HGTHGT Bs2 Mg2 Ec1 Ct1 Rp1 Af1

HGT: frequently observed when many genome sequences became available

HGT & Tree of Life (ToL) b

Transition prokaryotes to eukaryotes: big transition The prekaryoteThe prekaryote No more intermediatesNo more intermediates How to look before the event horizon?How to look before the event horizon? The prekaryoteThe prekaryote No more intermediatesNo more intermediates How to look before the event horizon?How to look before the event horizon?

Endo symbiosis of alpha proteo-bacteria gave rise to mitochondria Mitochondrial DNA in the mitochondriaMitochondrial DNA in the mitochondria Hydrogenosomes shown to be derived from mitochondriaHydrogenosomes shown to be derived from mitochondria Many proteins active in present-day mitochondria are coded for by proteins of eukaryotic invention, archaeal descentMany 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 cellMany proteins of alpha-protein ancestor active in in other parts of the cell Mitochondrial DNA in the mitochondriaMitochondrial DNA in the mitochondria Hydrogenosomes shown to be derived from mitochondriaHydrogenosomes shown to be derived from mitochondria Many proteins active in present-day mitochondria are coded for by proteins of eukaryotic invention, archaeal descentMany 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 cellMany proteins of alpha-protein ancestor active in in other parts of the cell B

rRNA tree 16S Ribosomal RNA Mitochondria have their own mini genome

Alpha-proteobacterial proteins with the rest of the bacteria and archaea Eukaryotic + alpha- proteobacteria in the same branch Identifying eukaryotic proteins with an alpha- proteobacterial origin based on their phylogeny

PHYLOME SELECTION OF HOMOLOGS, (Smith&Waterman) ALIGNMENTS AND TREE (Clustalx, Kimura+Dayhoff) GENOME GENOMES TREE SCANNING LIST Detecting eukaryotic genes of alpha-proteobacterial ancestry 6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea 6 alpha-proteobacteria ( genes)

- Catabolism of fatty acids, glycerol and amino acids. - Some pathways are not mitochondrial. Proto-mitochondrial metabolism: non-mitoch.. mitochondrial not in yeast/human

Eric Schon, Methods Cell Biol 2001 (manually curated) Huh et al., Nature 2003 (green fluorescent genomics) Gabaldon & Huynen Science 2003 alpha-prot Yeast mitochondrial proteome: Human mitochondrial proteome: Eric Schon, Methods Cell Biol The majority of the proto-mitochondrial proteome is not mitochondrial (anymore) 113

t proteins loss gain re-targeting Ancestor Modern mitochondria From endosymbiont to organell, not only loss and gain of proteins but also “retargeting”: ~16% of the mitochondrial yeast proteins are of alpha- proteobacterial origin. ~65% of the alpha- proteobacteria derived set is not mitochondrial. 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)Genes from alpha-proteobacterial descent present in genomes in mitochondria-less organisms (cf. toni) All eukaryotes have or had a mitochondria/alpha proteobacterial symbiontAll eukaryotes have or had a mitochondria/alpha proteobacterial symbiont It thus happened before the last common ancestor of all eukaryotesIt thus happened before the last common ancestor of all eukaryotes But then still “when”? (b)But then still “when”? (b) Genes from alpha-proteobacterial descent present in genomes in mitochondria-less organisms (cf. toni)Genes from alpha-proteobacterial descent present in genomes in mitochondria-less organisms (cf. toni) All eukaryotes have or had a mitochondria/alpha proteobacterial symbiontAll eukaryotes have or had a mitochondria/alpha proteobacterial symbiont It thus happened before the last common ancestor of all eukaryotesIt thus happened before the last common ancestor of all eukaryotes But then still “when”? (b)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 pre- eukaryotes that in archaea or bacteria Makarova NAR 2005

duplications: e.g. small GTPases

Thus all these duplications & endosymbios order? Unknown but all before elucaUnknown 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?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) Unknown but all before elucaUnknown 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?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:The divisions: –Ophistokonts (animals, fungi, microsporidia) –Amoebozoa (Dicty) –Chromalveolata Paramecium, Plasmodium but also diatoms –Archaeplastida –Excavata –Rhizaria Historically: crown-group eukaryotes vs protistsHistorically: crown-group eukaryotes vs protists What is a complete genome; draft genomesWhat is a complete genome; draft genomes The divisions:The divisions: –Ophistokonts (animals, fungi, microsporidia) –Amoebozoa (Dicty) –Chromalveolata Paramecium, Plasmodium but also diatoms –Archaeplastida –Excavata –Rhizaria Historically: crown-group eukaryotes vs protistsHistorically: crown-group eukaryotes vs protists What is a complete genome; draft genomesWhat is a complete genome; draft genomes

AnimalsAnimals Most primitive: spongesMost primitive: sponges Quite a number of genome sequences (of dubious completeness)Quite a number of genome sequences (of dubious completeness) Most primitive: spongesMost primitive: sponges Quite a number of genome sequences (of dubious completeness)Quite a number of genome sequences (of dubious completeness)

FungiFungi Many complete genomesMany complete genomes Broad, GenolevuresBroad, Genolevures Microsporidium (E. cuniculi)Microsporidium (E. cuniculi) Mushrooms are BasidomyctesMushrooms are Basidomyctes Together with animals: ophistokontsTogether with animals: ophistokonts Many complete genomesMany complete genomes Broad, GenolevuresBroad, Genolevures Microsporidium (E. cuniculi)Microsporidium (E. cuniculi) Mushrooms are BasidomyctesMushrooms are Basidomyctes Together with animals: ophistokontsTogether with animals: ophistokonts

AmoebozoaAmoebozoa Few genomesFew genomes –Entamoeba histolytica –Dictyostelium discoideum Few genomesFew genomes –Entamoeba histolytica –Dictyostelium discoideum

ArchaeplastidaArchaeplastida Second bacterial endosymbiosis event: cyanobacteriaSecond bacterial endosymbiosis event: cyanobacteria Green algae, red algae, plantsGreen algae, red algae, plants ~5 genomes~5 genomes Second bacterial endosymbiosis event: cyanobacteriaSecond bacterial endosymbiosis event: cyanobacteria Green algae, red algae, plantsGreen algae, red algae, plants ~5 genomes~5 genomes

ChromalveoatesChromalveoates Secondary endosymbios: plastidsSecondary endosymbios: plastids Very different speciesVery different species (diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, dinoflagelates)(diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, dinoflagelates) Quite some genomes (~10)Quite some genomes (~10) Secondary endosymbios: plastidsSecondary endosymbios: plastids Very different speciesVery different species (diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, dinoflagelates)(diatoms (also commonly referred to as algae), oomycetes, paramecium, alvealotes, dinoflagelates) Quite some genomes (~10)Quite some genomes (~10) B

ExcavataExcavata Weird parasites (Giardia, Trypanosome, Leismania)Weird parasites (Giardia, Trypanosome, Leismania) But also: Naegleria gruberi: amoeboflagelateBut also: Naegleria gruberi: amoeboflagelate Weird parasites (Giardia, Trypanosome, Leismania)Weird parasites (Giardia, Trypanosome, Leismania) But also: Naegleria gruberi: amoeboflagelateBut also: Naegleria gruberi: amoeboflagelate

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

How are eukaryotes related ??? Historically: crown-group eykaryotes vs protists but now molecular evidenceHistorically: crown-group eykaryotes vs protists but now molecular evidence Two hypothesis:Two hypothesis: –In or just after excavata –Inbetween ophistokonts/amoebozoa vs the rest (unikont vs bikont), myosins Rhizaria?Rhizaria? phagotrophic origin of eukaryotes: an amoebe with flagella?phagotrophic origin of eukaryotes: an amoebe with flagella? Historically: crown-group eykaryotes vs protists but now molecular evidenceHistorically: crown-group eykaryotes vs protists but now molecular evidence Two hypothesis:Two hypothesis: –In or just after excavata –Inbetween ophistokonts/amoebozoa vs the rest (unikont vs bikont), myosins Rhizaria?Rhizaria? phagotrophic origin of eukaryotes: an amoebe with flagella?phagotrophic origin of eukaryotes: an amoebe with flagella? b