Download Eukaryogenesis, endosymbiosis, LECA (HGT) RAL evoluzon? RAL

04/06/14 Human S. cerevisiae Bony Fish SHARKS! (Chondrichthyes) Lamprey Ciona Lancelet (amphioxus) WGD hemichordates protostomes Cnididaria, trichoplax Eukaryogenesis, endosymbiosis, LECA (HGT) sponge Zygomycota monosiga filasporea Chytridiomycota nucleariidae 04/06/14 1 RalGEF subcluster of RasGEF tree Ral subcluster of Ras tree RAL evoluQon? Animal RAS Fungal RAS Animal RAL B. dendroba+dis R. oryzae P. blakesleeanus Animal invenQon and wrong tree ( “consensus” in the RAS field) OR old duplicaQon and loss RAL evoluQon? Animal RAS Fungal RAS Animal RAL ToL & 3 kingdoms Early branching fungi RAL Old duplicaQon and loss. No more OR. More data indeed in this case IS beZer 1 04/06/14 Eocyte hypothesis First EukaryoQc Common Ancestor (FECA) / proto eukaryote Latest trees suggest eocyte (2 kingdoms, not 3) Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):
20356-­‐61. Epub 2008 Dec 10. The archaebacterial origin of eukaryotes. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. Timing of alpha-­‐proteobacterial endosymbiosis relaQve to bacterial radiaQons? NB in this tree the Source of mito arrow is incorrect Mol Phylogenet Evol. 2013 Oct;69(1):17-­‐38. doi: 10.1016/j.ympev.2013.05.006. Epub 2013 May 22. The effects of model choice and mi<ga<ng bias on the ribosomal tree of life. Lasek-­‐Nesselquist E1, Gogarten JP. Timing of alpha-­‐proteobacterial endosymbiosis relaQve to bacterial radiaQons? First came: Emergence of proteobacteria, emergence of alpha proteobacteria within the proteobacteria and many speciaQons within the alpha-­‐
proteobacteria I think this fits beZer with eocyte than with 3 kingdoms Ophistokont tyrosyl-­‐tRNA synthetase falls INSIDE a bacterial genus! Ophistokonts Mol Biol Evol. 2005 Nov;22(11):
2142-­‐6. The presence of a haloarchaeal type tyrosyl-­‐tRNA synthetase marks the opisthokonts as monophyle<c. Huang J, Xu Y, Gogarten JP. 2 04/06/14 Late origin of eukaryotes? •  Proto eukaryote not ancient as bacterial and archael radiaQons, endosymbiosis was amer many bacterial radiaQons, leca was thus also amer these radiaQons, supported by ophistokonts (supposedly “short” amer LECA) being within archaeal genus •  Proto-­‐eukaryote sQll seems to have had a long way to go to a eukaryote:, “feca-­‐2-­‐leca” •  Nature of proto-­‐eukaryote? Novel archaea has operon with UBQ system •  Insights into the evoluQon of Archaea and eukaryoQc 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, HaZori M, Kanai A, Atomi H, Takai K, Takami H. Nucleic Acids Res. 2011 Apr;39(8):
3204-­‐23 The gene cluster of the Ub-like protein modifier system in C. subterraneum. ,
eukaryotic “type” ubiquitin
Nunoura T et al. Nucl. Acids Res. 2011;39:3204-3223
© The Author(s) 2010. Published by Oxford University Press.
In eukaryoQc and bacterial cells, spaQal organizaQon is dependent upon cytoskeletal filaments AcQn is a main eukaryoQc cytoskeletal element, cell shape determinaQon, mechanical force generaQon and cytokinesis Archaeal cytoskeleton of crenacQn which forms helical structures within Pyrobaculum calidifon+s cells, as shown by in situ immunostaining 1:1 Orthologous to eukaryoQc acQn with limited phylogeneQc dsitrubuQon in archaea Examples of subpopulaQon of cells displaying centrally located band-­‐
like structures. Cytokinesis? 3 04/06/14 EukaryoQc features in archaea are present in subclade of archaea where also now the ToL places the eukaryotes Proto-­‐eukaryote is gepng more complex as more archaeal diversity is sequenced and bioinformaQcally and biochemically characterized Eukaryogenesis: FECA to LECA •  Endosymbiosis •  DuplicaQon Similarity in membrane “topology” between a mitochondria and a eukaryo<c cell that eats a bacterium: the double membrane topology DNA
Mitchondria have their own chromosome … but this chromosome is circular and not enveloped in a “nucleus” prokaryotes Circular chromosomes, no organelles eukaryotes Linear chromosomes organelles “Theory of endosymbiosis” “Theory of endosymbiosis” hZp://en.wikipedia.org/wiki/Phagocytosis hZp://home.nc.rr.com/ambiient/site/mtdna.htm 4 04/06/14 Identifying eukaryotic proteins with an alphaproteobacterial origin based on their phylogeny
Phylogenetic trees
• Mitochondrial chromosome, genes, rRNA • Similarity according to an established model of sequence change. Determine how organisms / genes are related: tree • Tree: eukaryoQc mitochondria cluster within bacteria, within alpha -­‐proteobacteria, next to rickeZsia, obligate intracellular parasites of eukaryoQc cells Eukaryotic + alpha-proteobacteria Alpha-proteobacterial proteins with
in the same branch
the rest of the bacteria and archaea
Benchmarking? Detecting eukaryotic genes of alpha-proteobacterial ancestry
GENOME 6 alpha-­‐proteobacteria (22 500 genes) GENOMES 6 alpha-­‐proteobacteria 9 eukaryotes 56 Bacteria+Archaea SELECTION OF HOMOLOGS LIST 1.  “a control” 2.  ML works! ALIGNMENTS AND TREE TREE SCANNING PHYLOME ReconstrucQon of the Proto-­‐mitochondrial Cell The majority of the proto-­‐mitochondrial proteome is not mitochondrial (anymore) 566 Gabaldon & Huynen Science 2003 alpha-­‐prot. Yeast mitochondrial proteome: Eric Schon, Methods Cell Biol 2001 (manually curated) 35 293 303 59 10 Huh et al., Nature 2003 (green fluorescent genomics) 527 Human mitochondrial proteome: 755 Eric Schon, Methods Cell Biol 2001 113 508 5 04/06/14 From endosymbiont to organell, not only loss
and gain of proteins but also “retargeting”:
proteins loss FECA/eocyte to LECA DuplicaQons InvenQons re-­‐targeQng ~65% of the alpha-­‐
proteobacteria derived set is not mitochondrial. Ancestor Modern mitochondria ~16% of the mitochondrial yeast proteins are of alpha-­‐
proteobacterial origin. gain t Nucleic Acids Res. 2005 Aug 16;33(14):4626-­‐38 Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryo<c cell. Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV. Gabaldon and Huynen, Science 2004 Not just the gtpases, also their acQvaQng proteins: Rap/Ral/RheB GAP tree: events from before the LECA duplicaQons: e.g. small GTPases 100
99
31 13
RapGAP (animals(LSE), fungi, dicty)
PHYSOJ14061 Phytophthora sojae 142624
PHYINF15173 Phytophthora infestans PITG 15173
RalGAPB (oomycetes, dicty, naegleria, fungi, animals))
23
8
RalGAPA (dicty, naegleria, fungi, animals)
RheBGAP (TSC2, oomycetes, diatoms, red algea, animals, fungi, dicty, tetrahymena)
24
Dupl of RAS superfamily gave rise to families of Rho, Ras, Rab and ARF which in turn gave rise to e.g. in the case of RAS, RheB, Ral, RasA RasB etc, 0.5
bacteria InterpreQng the tree: Horizontal Gene Transfer ( HGT ) ToL & 3 kingdoms Bacteria Eukarya Archaea 6 04/06/14 HGT between eukaryotes Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15258-­‐63. Horizontal gene transfer facilitated the evoluQon of plant parasiQc 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 hZp://www.amjbot.org/content/91/10/1481/F2.large.jpg 7 04/06/14 Serial / secondary endosymbiosis (EGT, gene transfer, protein re-­‐targeQng Serial / secondary endosymbiosis e.g. Tree of 1,6-­‐bisphosphatase . hZp://www.amjbot.org/content/91/10/1481/F2.large.jpg 8