(eukaryotic) tree of life, eukaryogenesis,...
TRANSCRIPT
3112013 1
(eukaryotic) Tree of Life eukaryogenesis LECA
bull Counting back from human (and S cerevisiae) ldquocrucialrdquo ldquoearly branchingrdquo genomes
bull Eukaryotic supergroups (quick) bull Three kingdoms or two nature of the first
eukaryote bull From FECA to LECA duplications bull From FECA to LECA enodsymbiosis
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Ciona
Lancelet (amphioxus) Allowed mapping vertebrate WGD
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
Cnididaria trichoplax
httpwwwtrichoplaxcommediafilesl15jpg httpgenomejgi-psforgTriad1TrichoplaxSEM_Sagasserjpg httpuploadwikimediaorgwikipediaenthumbff7Exodigestion_in_Trichoplax_adhaerensjpg380px-Exodigestion_in_Trichoplax_adhaerensjp
protostomes hemicorhdates
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
bull Counting back from human (and S cerevisiae) ldquocrucialrdquo ldquoearly branchingrdquo genomes
bull Eukaryotic supergroups (quick) bull Three kingdoms or two nature of the first
eukaryote bull From FECA to LECA duplications bull From FECA to LECA enodsymbiosis
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Ciona
Lancelet (amphioxus) Allowed mapping vertebrate WGD
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
Cnididaria trichoplax
httpwwwtrichoplaxcommediafilesl15jpg httpgenomejgi-psforgTriad1TrichoplaxSEM_Sagasserjpg httpuploadwikimediaorgwikipediaenthumbff7Exodigestion_in_Trichoplax_adhaerensjpg380px-Exodigestion_in_Trichoplax_adhaerensjp
protostomes hemicorhdates
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Ciona
Lancelet (amphioxus) Allowed mapping vertebrate WGD
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
Cnididaria trichoplax
httpwwwtrichoplaxcommediafilesl15jpg httpgenomejgi-psforgTriad1TrichoplaxSEM_Sagasserjpg httpuploadwikimediaorgwikipediaenthumbff7Exodigestion_in_Trichoplax_adhaerensjpg380px-Exodigestion_in_Trichoplax_adhaerensjp
protostomes hemicorhdates
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Crucial genomes fill gaps Human S cerevisiae Bony Fish
SHARKS (Chondrichthyes)
Lamprey
Ciona
Lancelet (amphioxus) Allowed mapping vertebrate WGD
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
Cnididaria trichoplax
httpwwwtrichoplaxcommediafilesl15jpg httpgenomejgi-psforgTriad1TrichoplaxSEM_Sagasserjpg httpuploadwikimediaorgwikipediaenthumbff7Exodigestion_in_Trichoplax_adhaerensjpg380px-Exodigestion_in_Trichoplax_adhaerensjp
protostomes hemicorhdates
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
Cnididaria trichoplax
httpwwwtrichoplaxcommediafilesl15jpg httpgenomejgi-psforgTriad1TrichoplaxSEM_Sagasserjpg httpuploadwikimediaorgwikipediaenthumbff7Exodigestion_in_Trichoplax_adhaerensjpg380px-Exodigestion_in_Trichoplax_adhaerensjp
protostomes hemicorhdates
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemicorhdates
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Monosiga brevicollis choanoflagelates single celled colonial protists with a
collar and flagellum to filter feed
httpusersrcncomjkimballmaultranetBiologyPagesCchoanoflagellatesgif
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Monosiga brevicolis
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y Letunic I Marr M Pincus D Putnam N Rokas A Wright KJ Zuzow R Dirks W Good M Goodstein D Lemons D Li W Lyons JB Morris A Nichols S Richter DJ Salamov A Sequencing JG Bork P Lim WA Manning G Miller WT McGinnis W Shapiro H Tjian R Grigoriev IV Rokhsar D Nature 2008 Feb 14451(7180)783-8
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Human S cerevisiae
Bony Fish SHARKS (Chondrichthyes)
Lamprey
Ciona Lancelet (amphioxus) WGD
protostomes Cnididaria trichoplax
sponge
monosiga
hemichordates
filasporea
nucleariidae
Chytridiomycota
Zygomycota
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
RAL evolution
Animal RAS Fungal RAS Animal RAL
Animal invention and wrong tree ( ldquoconsensusrdquo in the RAS field) OR old duplication and loss
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree
B dendrobatidis R oryzae
P blakesleeanus
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
RAL evolution
Animal RAS Fungal RAS Animal RAL
Old duplication and loss No more OR
Early branching fungi RAL
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Is the asymmetry (comb) real
bull Part is perspective (protostomes) bull Part is sampling bull Part is real
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
many genomes many more underway
bull Diversity at many levels bull Allow needed for different questions bull Reveals more old diversity re duplicates or
OGs
bull Fun biology (not directly applicable but helps to remember the names and relationships of the weird beasties) (a good taxonomy button like in jackhmmer also helps)
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
UN
IKON
TS OPHISTOKONTS
AMOEBOZOA
EXCAVATA
BIKON
TS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
~6 Supergroups
bull Current sampling hugely biased gtgt 300 ophistokonts 1 rhizaria 5() excavates
bull Phylogenetic cellular protein diversity staggering as compared to eg human-fruitfly
bull Especially relevant for ldquoevolutionary cell biologyrdquo
bull Mini project one of each (super)group fungi animals plantae alveolates amoebozoa stramenopiles
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Early branching key genomes in supergroups gives beautiful stories
MPS1 parallel loss of TPR
domain
Tromer kops in press
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
UNIKONTS OPHISTOONTS
AMOEBOZOA
EXCAVATA
BIKONTS
ALVEOLATES
STRAMENOPILES
PLANTAE
RHIZARIA
ROOT UNKNOWN
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
ToL amp 3 kingdoms
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Eocyte hypothesis
First Eukaryotic Common Ancestor (FECA) proto eukaryote
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Proc Natl Acad Sci U S A 2008 Dec 23105(51)20356-61 Epub 2008 Dec 10 The archaebacterial origin of eukaryotes Cox CJ Foster PG Hirt RP Harris SR Embley TM
Latest trees suggest eocyte
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
Source of mito arrow is incorrect
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
First came Emergence of proteobacteria emergence of alpha proteobacteria within the proteobacteria and many speciations within the alpha-proteobacteria I think this fits better with eocyte than with 3 kingdoms
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Mol Biol Evol 2005 Nov22(11)2142-6 The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic Huang J Xu Y Gogarten JP
Ophistokont tyrosyl-tRNA
synthetase falls INSIDE a
bacterial genus
Ophistokonts
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Late origin of eukaryotes
bull Proto eukaryote not ancient as bacterial and archael radiations endosymbiosis was after many bacterial radiations leca was thus also after these radiations supported by ophistokonts (supposedly ldquoshortrdquo after LECA) being within archaeal genus
bull Proto-eukaryote still seems to have had a long way to go to a eukaryote ldquofeca-2-lecardquo
bull Nature of proto-eukaryote
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Novel archaea has operon with UBQ system
bull Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura T Takaki Y Kakuta J Nishi S Sugahara J Kazama H Chee GJ Hattori M Kanai A Atomi H Takai K Takami H Nucleic Acids Res 2011 Apr39(8)3204-23
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
The gene cluster of the Ub-like protein modifier system in C subterraneum eukaryotic ldquotyperdquo ubiquitin
Nunoura T et al Nucl Acids Res 2011393204-3223
copy The Author(s) 2010 Published by Oxford University Press
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
11 Orthologous to eukaryotic actin with limited phylogenetic dsitrubution in archaea
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
In eukaryotic and bacterial cells spatial organization is dependent upon cytoskeletal filaments Actin is a main eukaryotic cytoskeletal element cell shape determination mechanical force generation and cytokinesis Archaeal cytoskeleton of crenactin which forms helical structures within Pyrobaculum calidifontis cells as shown by in situ immunostaining
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Examples of subpopulation of cells displaying centrally located band-like structures Cytokinesis
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
SMC proteins represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Arcadin 2 cytokinesis
Molecular Microbiology Volume 80 Issue 4 pages 1052-1061 6 APR 2011 DOI 101111j1365-2958201107635x httponlinelibrarywileycomdoi101111j1365-2958201107635xfullf8
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Eukaryotic features in archaea are present in
subclade of archaea where also now the
ToL places the eukaryotes
Proto-eukaryote is
getting more complex as more archaeal
diversity is sequenced and bioinformatically
and biochemically characterized
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Eukaryogenesis FECA to LECA
bull Endosymbiosis
bull Duplication
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
httpenwikipediaorgwikiPhagocytosis
ldquoTheory of endosymbiosisrdquo
Similarity in membrane ldquotopologyrdquo between a mitochondria and a eukaryotic cell that eats a bacterium the double membrane topology
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
DNA
Mitchondria have their own chromosome
hellip but this chromosome is circular and not enveloped in a ldquonucleusrdquo
prokaryotes eukaryotes Circular chromosomes no organelles
Linear chromosomes organelles
ldquoTheory of endosymbiosisrdquo
httphomencrrcomambiientsitemtdnahtm
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Phylogenetic trees
bullMitochondrial chromosome genes rRNA
bullSimilarity according to an established model of sequence change Determine how organisms genes are related tree
bullTree eukaryotic mitochondria cluster within bacteria within alpha -proteobacteria next to rickettsia obligate intracellular parasites of eukaryotic cells
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
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
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
PHYLOME
SELECTION OF HOMOLOGS
ALIGNMENTS AND TREE
GENOME
GENOMES
TREE SCANNING
LIST
Detecting eukaryotic genes of alpha-proteobacterial ancestry
6 alpha-proteobacteria 9 eukaryotes 56 Bacteria+Archaea
6 alpha-proteobacteria (22 500 genes)
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Benchmarking
1 ldquoa controlrdquo 2 ML works
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Reconstruction of the Proto-mitochondrial Cell
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Eric Schon Methods Cell Biol 2001 (manually curated)
Huh et al Nature 2003 (green fluorescent genomics)
566
527
303
Gabaldon amp Huynen Science 2003 alpha-prot
10
59
35
293
Yeast mitochondrial proteome
Human mitochondrial proteome
Eric Schon Methods Cell Biol 2001
755
508
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 ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
t
proteins loss
gain
re-targeting
Ancestor Modern mitochondria
From endosymbiont to organell not only loss and gain of proteins but also ldquoretargetingrdquo
~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
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Fecaeocyte to LECA
Nucleic Acids Res 2005 Aug 1633(14)4626-38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell Makarova KS Wolf YI Mekhedov SL Mirkin BG Koonin EV
Duplications Inventions
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
duplications eg small GTPases
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Not just the gtpases also their activating proteins RapRalRheB GAP
tree events from before the LECA
RapGAP (animals(LSE) fungi dicty)
PHYSOJ14061 Phytophthora sojae 142624 PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes dicty naegleria fungi animals))
RalGAPA (dicty naegleria fungi animals)
RheBGAP (TSC2 oomycetes diatoms red algea animals fungi dicty tetrahymena
99
13
823
31
100
24
05
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
bull Adaptor protein (AP) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another
bull Evolution of specificity in the eukaryotic endomembrane systemDacks JB Peden AA Field MC Int J Biochem Cell Biol 2009 Feb41(2)330-40
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Adaptor proteins arose via feca-2-leca duplications
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Fig 3 Organelle evolution driven by gene duplication of the identity-encoding machinery (A) An initial endomembraneous compartment is shown with an as-yet undifferentiated set of identity-encoding machinery shown The segmented circle indicate
Neo or sub functionalization hellip for membrane identity
Parallels discussion for protein Complexes eg zipper model
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes
(Eugene V Koonin)
~4000 genes The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK Prochnik SE Ginger ML Dacks JB Carpenter ML Field MC Kuo A Paredez A Chapman J Pham J Shu S Neupane R Cipriano M Mancuso J Tu H Salamov A Lindquist E Shapiro H Lucas S Grigoriev IV Cande WZ Fulton C Rokhsar DS Dawson SC Cell 2010 Mar 5140(5)631-42
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Signalling complexity
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Euk ToL Orthology complications
bull HGT between eukaryotes bull Parallel HGT from bacteria
bull Serial secondary endosymbiosis
bull (tertriary endosymbiosis)
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
HGT between eukaryotes Proc Natl Acad Sci U S A 2011 Sep 13108(37)15258-63 Horizontal gene transfer facilitated the evolution of plant
parasitic mechanisms in the oomycetes Richards TA Soanes DM Jones MD Vasieva O Leonard G Paszkiewicz K Foster PG Hall N Talbot NJ
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
HGT from bacteria
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Parallel HGT from bacteria
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Serial secondary endosymbiosis
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
httpwwwamjbotorgcontent91101481F2largejpg
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-
A good KOG database would
bull How should it relate to COGrsquos ndash to endosymbiosis origin vs archael origin ndash Fusions and duplications (Big bang) during feca to leca
bull (How) should it deal with serial endosymbiosis bull (How) should it deal with HGT between euks bull (How) should it deal with parallel HGT from bacs
to euks
- (eukaryotic) Tree of Life eukaryogenesis LECA
- Crucial genomes fill gaps
- Crucial genomes fill gaps
- Slide Number 5
- Slide Number 6
- Monosiga brevicollis choanoflagelates single celled colonial protists with a collar and flagellum to filter feed
- Monosiga brevicolis
- Slide Number 9
- RAL evolution
- Slide Number 11
- RAL evolution
- Is the asymmetry (comb) real
- many genomes many more underway
- Slide Number 15
- ~6 Supergroups
- MPS1 parallel loss of TPR domain
- Slide Number 18
- ToL amp 3 kingdoms
- Eocyte hypothesis
- Latest trees suggest eocyte
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Timing of alpha-proteobacterial endosymbiosis relative to bacterial radiations
- Ophistokont tyrosyl-tRNA synthetase falls INSIDE a bacterial genus
- Late origin of eukaryotes
- Novel archaea has operon with UBQ system
- Slide Number 27
- Slide Number 28
- Slide Number 29
- Slide Number 30
- Slide Number 31
- Arcadin 2 cytokinesis
- Eukaryotic features in archaea are present in subclade of archaea where also now the ToL places the eukaryotesProto-eukaryote is getting more complex as more archaeal diversity is sequenced and bioinformatically and biochemically characterized
- Eukaryogenesis FECA to LECA
- Slide Number 35
- Slide Number 36
- Slide Number 37
- Slide Number 38
- Slide Number 39
- Benchmarking
- Slide Number 41
- Slide Number 42
- Slide Number 43
- Fecaeocyte to LECA
- duplications eg small GTPases
- Not just the gtpases also their activating proteins RapRalRheB GAP tree events from before the LECA
- Slide Number 47
- Adaptor proteins arose via feca-2-leca duplications
- Neo or sub functionalization hellip for membrane identity
- LECA ldquogenome of edenrdquo ldquoThe Incredible Expanding Ancestor of Eukaryotes(Eugene V Koonin)
- Signalling complexity
- Slide Number 52
- Euk ToL Orthology complications
- HGT between eukaryotes
- Slide Number 55
- HGT from bacteria
- Parallel HGT from bacteria
- Serial secondary endosymbiosis
- Serial secondary endosymbiosis (EGT) and gene transfer to the nucleus
- Serial secondary endosymbiosis (EGT gene transfer protein re-targeting
- Serial secondary endosymbiosis eg Tree of 16-bisphosphatase
- A good KOG database would
-