Skip to main content
SpringerLink
Log in

The falsifiability of the models for the origin of eukaryotes

  • Review
  • Published:
Current Genetics Aims and scope Submit manuscript

Abstract

One group of hypotheses suggests archaeal and/or bacterial ancestry of eukaryotes, while the second group suggests that the ancestor of eukaryotes was different. Especially, the followers of the first group of hypotheses should ask the following: is the replacement of archaeal lipids by bacterial (or vice versa) possible? Do the phylogenies support the origin of one domain from another (or the others)? Can we consider the nutritional mode to resolve the problems of cell origin(s)? Is there any evidence that the ancestor of eukaryotes was intron-free? Would the symbiosis of α-proteobacterial ancestors of mitochondria be successful in an asexual host? Is there evidence that the last universal common ancestor (LUCA) or the last eukaryotic common ancestor was bounded by one membrane only? With respect to the current knowledge about cells and their molecular components, the answer to most of these questions is: No! A model for the origins of domains is briefly presented which cannot be assigned as false through the current scientific data, and is rather consistent with the assumption that eukaryotes are direct descendants of neither archaea nor bacteria. It is proposed that the domain Bacteria arose the first, and that the last common ancestor of Archaea and Eukarya was a pre-cell or a progenote similar to LUCA. The pre-karyote (the host entity for α-proteobacterial ancestors of mitochondria) was probably bounded by two membranes, possessed spliceosomal introns and spliceosomes, was sexual, and α-proteobacterial ancestors of mitochondria were most likely parasites of the pre-karyote periplasm (intermembrane space).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

Abbreviations

LACA:

Last archaeal common ancestor

LBCA:

Last bacterial common ancestor

LCAAE:

Last common ancestor of Archaea and Eukarya

LECA:

Last eukaryotic common ancestor

LUCA:

Last universal common ancestor

RNP:

Ribonucleoprotein

References

  • Adams KL, Daley DO, Whelan J, Palmer JD (2002) Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts. Plant Cell 14:931–943

    PubMed  CAS  Google Scholar 

  • Allen CA, Jackson AP, Rigden DJ, Willis AC, Ferguson AC, Ginger ML (2008) Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems? FEBS J 275:2385–2402

    PubMed  CAS  Google Scholar 

  • Amos LA, van den Ent F, Löwe J (2004) Structural/functional homology between the bacterial and eukaryotic cytoskeletons. Curr Opin Cell Biol 16:24–31

    PubMed  CAS  Google Scholar 

  • Andersson SGE, Kurland CG (1999) Origins of mitochondria and hydrogenosomes. Curr Opin Microbiol 2:535–541

    PubMed  CAS  Google Scholar 

  • Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UCM, Podowski RM, Naslund AK, Eriksson AS, Winkler HH, Kurland CG (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133–140

    PubMed  CAS  Google Scholar 

  • Andersson SGE, Alsmark C, Canbäck B, Davids W, Frank C, Karlberg O, Klasson L, Antoine-Legault B, Mira A, Tamas I (2002) Comparative genomics of microbial pathogens and symbionts. Bioinformatics 18:S17

    PubMed  Google Scholar 

  • Andersson SGE, Karlberg O, Canback B, Kurland CG (2003) On the origin of mitochondria: a genomics perspective. Phil Trans R Soc Lond B 358:165–179

    CAS  Google Scholar 

  • Archetti M (2003) A selfish origin for recombination. J Theor Biol 223:335–346

    PubMed  CAS  Google Scholar 

  • Asai T, Zaporojets D, Squires C, Squires CL (1999) An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci USA 96:1971–1976

    PubMed  CAS  Google Scholar 

  • Baluška F, Volkmann D, Barlow PW (2004) Eukaryotic cells and their cell bodies: cell theory revised. Ann Botany 94:9–32

    Google Scholar 

  • Bapteste E, Brochier C (2004) On the conceptual difficulties in rooting the tree of life. Trends Microbiol 12:9–13

    PubMed  CAS  Google Scholar 

  • Bapteste E, Charlebois RL, McLeod D, Brochier C (2005) The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure. Genome Biol 6:R85

    PubMed  Google Scholar 

  • Basu MK, Rogozin IB, Deusch O, Dagan T, Martin W, Koonin EV (2008) Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues. Mol Biol Evol 25:111–119

    PubMed  CAS  Google Scholar 

  • Baurén G, Wieslander L (1994) Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76:183–192

    PubMed  Google Scholar 

  • Berg OG, Kurland CG (2000) Why mitochondrial genes are most often found in nuclei. Mol Biol Evol 17:951–961

    PubMed  CAS  Google Scholar 

  • Bernstein H, Byers GS, Michod RE (1981) Evolution of sexual reproduction: importance of DNA repair, complementation and variation. Am Nat 117:537–549

    CAS  Google Scholar 

  • Beyer AL, Osheim YN (1988) Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev 2:754–765

    PubMed  CAS  Google Scholar 

  • Blobel G (1980) Intracellular topogenesis. Proc Natl Acad Sci USA 77:1496–1500

    PubMed  CAS  Google Scholar 

  • Bonen L (2008) Cis- and trans-splicing of group II introns in plant mitochondria. Mitochondrion 8:26–34

    PubMed  CAS  Google Scholar 

  • Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008a) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6:245–252

    PubMed  CAS  Google Scholar 

  • Brochier-Armanet C, Gribaldo S, Forterre P (2008b) A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya. Biol Direct 3:54

    PubMed  Google Scholar 

  • Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol 14:1–8

    Google Scholar 

  • Brunelle SA, van Dolah FM (2011) Post-transcriptional regulation of S-phase genes in the dinoflagellate, Karenia brevis. J Eukaryot Microbiol 58:373–382

    PubMed  CAS  Google Scholar 

  • Canbäck B, Andersson SGE, Kurland CG (2002) The global phylogeny of glycolytic enzymes. Proc Natl Acad Sci USA 99:6097–6102

    PubMed  Google Scholar 

  • Cavalier-Smith T (1987) The origin of eukaryotic and archaebacterial cells. Ann N Y Acad Sci 503:17–54

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (1991) Intron phylogeny: a new hypothesis. Trends Gen 7:145–148

    CAS  Google Scholar 

  • Cavalier-Smith T (2000) Membrane heredity and early chloroplast evolution. Trends Plant Sci 5:174–182

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (2001) Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of genetic code, the first cells, and photosynthesis. J Mol Evol 53:555–595

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (2002a) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (2002b) Origin of the machinery of recombination and sex. Heredity 88:125–141

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (2002c) The phagotrophic origin of eukaryotes and the phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 52:297–354

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (2003) Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote–eukaryote chimaeras (meta-algae). Phil Trans R Soc Lond B 358:109–134

    CAS  Google Scholar 

  • Cavalier-Smith T (2006) Rooting the tree of life by transition analyses. Biol Direct 1:19

    Google Scholar 

  • Cavalier-Smith T (2009) Predation and eukaryote cell origins. Int J Biochem Cell Biol 41:307–322

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (2010a) Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biol Lett 6:342–345

    PubMed  Google Scholar 

  • Cavalier-Smith T (2010b) Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 5:7

    PubMed  Google Scholar 

  • Cech TR (2011) The RNA world in context. Cold Spring Harb Perspect Biol (in press). doi:10.1101/cshperspect.a006742

  • Chalamcharla VR, Curcio MJ, Belfort M (2010) Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry. Genes Dev 24:827–836

    PubMed  CAS  Google Scholar 

  • Chia N, Cann I, Olsen GJ (2010) Evolution of DNA replication protein complexes in eukaryotes and Archaea. PLoS One 5:e10688

    Google Scholar 

  • Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287

    PubMed  CAS  Google Scholar 

  • Coetzee JN, Sirgel FA, Lecastsas G (1979) Genetic recombination in fused sphaeroplasts of Providencia alcalifaciens. J Gen Microbiol 114:313–322

    PubMed  CAS  Google Scholar 

  • Collins L, Penny D (2005) Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 22:1053–1066

    PubMed  CAS  Google Scholar 

  • Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM (2008) The archaeabacterial origin of eukaryotes. Proc Natl Acad Sci USA 105:20356–20361

    PubMed  CAS  Google Scholar 

  • Cramer P (2006) Molecular biology. Self-correcting messages. Science 313:447–448

    PubMed  CAS  Google Scholar 

  • Dacks JB, Field MC (2007) Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode. J Cell Sci 120:2977–2985

    PubMed  CAS  Google Scholar 

  • Dacks JB, Poon PP, Field MC (2008) Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution. Proc Natl Acad Sci USA 105:588–593

    PubMed  CAS  Google Scholar 

  • Dacks JB, Peden AA, Field MC (2009) Evolution of specificity in the eukaryotic endomembrane system. Int J Biochem Cell Biol 41:330–340

    PubMed  CAS  Google Scholar 

  • Dagan T, Martin W (2007) Testing hypothesis without considering prediction. BioEssays 29:500–503

    PubMed  Google Scholar 

  • Dai L, Zimmerly S (2003) ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs. RNA 9:14–19

    PubMed  CAS  Google Scholar 

  • Darnell JE (1978) Implications of RNA–RNA splicing in evolution of eukaryotic cells. Science 202:1257–1260

    PubMed  CAS  Google Scholar 

  • Davidov Y, Jurkevitch E (2009) Predation between prokaryotes and the origin of eukaryotes. Bioessay 31:748–757

    CAS  Google Scholar 

  • Davidov Y, Huchon D, Koval SF, Jurkevitch E (2006) A new α-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory. Environ Microbiol 8:2179–2188

    PubMed  CAS  Google Scholar 

  • Davis R, Singh H, Botka C, Hardwick M, Meanawy AE, Villanueva J (1994) RNA trans-splicing in Fasciola hepatica: identification of a spliced leader SL RNA and SL sequences on mRNAs. J Biol Chem 269:20026–20030

    PubMed  CAS  Google Scholar 

  • de Duve C (2007) Origin of eukaryotes: a reappraisal. Nat Rev Genet 8:395–403

    PubMed  Google Scholar 

  • de Nooijer S, Holland BR, Penny D (2009) The emergence of predators in early life: there was no Garden of Eden. PLoS One 4:e5507

    PubMed  Google Scholar 

  • Derelle R, Momose T, Manuel M, Da Silva C, Wincker P, Houliston E (2010) Convergent origins and rapid evolution of spliced leader trans-splicing in metazoa: insights from the ctenophora and hydrozoa. RNA 16:696–707

    PubMed  CAS  Google Scholar 

  • Desmond E, Brochier-Armanet C, Forterre P, Gribaldo S (2011) On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes. Res Microbiol 162:53–70

    PubMed  CAS  Google Scholar 

  • Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP (2004) Components of coated vesicles and nuclear pore complexes share a common molecular architecture. Plos Biol 2:e380

    PubMed  Google Scholar 

  • Di Giulio M (2007) The universal ancestor and the ancestors of Archaea and Bacteria were anaerobes whereas the ancestor of the Eukarya domain was an aerobe. J Evol Biol 20:543–548

    PubMed  CAS  Google Scholar 

  • Di Giulio M (2011) The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes. J Mol Evol 72:119–126

    PubMed  CAS  Google Scholar 

  • Doolittle WF (1978) Genes in pieces: were they ever together? Nature 272:581–582

    Google Scholar 

  • Doolittle WF (1991) The origin of introns. Curr Biol 1:145–146

    PubMed  CAS  Google Scholar 

  • Doolittle RF (2000) Searching for the common ancestor. Res Microbiol 151:85–89

    PubMed  CAS  Google Scholar 

  • Doolittle WF, Lukeš J, Archibald JM, Keeling PJ, Gray MW (2011) Comment on “Does constructive neutral evolution play an important role in the origin of cellular complexity?”. Bioessays 33:427–429

    PubMed  Google Scholar 

  • Douris V, Telford MJ, Averof M (2010) Evidence for multiple independent origins of trans-splicing in Metazoa. Mol Biol Evol 27:684–693

    PubMed  CAS  Google Scholar 

  • Edgell DR, Doolittle WF (1997) Archaea and the origin(s) of DNA replication proteins. Cell 89:995–998

    PubMed  CAS  Google Scholar 

  • Embley TM, Martin W (2006) Eukaryotic evolution, changes and challenges. Nature 440:623–630

    PubMed  CAS  Google Scholar 

  • Esser C, Ahmadinejad N, Wiegand C, Route C, Sebastiani F, Gelius-Dietrich G, Hentze K, Kretschmann E, Richly E, Leister D, Bryant D, Steel MA, Lockhart PJ, Penny D, Martin W (2004) A genome phylogeny for mitochondria among α-proteobacteria and predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21:1643–1660

    PubMed  CAS  Google Scholar 

  • Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410

    Google Scholar 

  • Field MC, Dacks JB (2009) First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes. Curr Opin Cell Biol 21:4–13

    PubMed  CAS  Google Scholar 

  • Fisher RA (1930) The genetical theory of natural selection. Oxford University Press, Oxford

    Google Scholar 

  • Flegontov P, Gray MW, Burger G, Lukeš J (2011) Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa? Curr Genet 57:225–232

    PubMed  CAS  Google Scholar 

  • Fodor K, Alfoldi L (1976) Fusion of protoplasts of Bacillus megatherium. Proc Natl Acad Sci USA 73:2147–2150

    PubMed  CAS  Google Scholar 

  • Forterre P (1995) Thermoreduction, a hypothesis for the origin of prokaryotes. C R Acad Sci Paris Life Sci 318:414–422

    Google Scholar 

  • Forterre P (1999) Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol Microbiol 33:457–465

    PubMed  CAS  Google Scholar 

  • Forterre P (2002) The origin of DNA genomes and DNA replication proteins. Curr Opin Microbiol 5:525–532

    PubMed  CAS  Google Scholar 

  • Forterre P (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci USA 103:3669–3674

    PubMed  CAS  Google Scholar 

  • Forterre P, Philippe H (1999) Where is the root of the universal tree of life? Bioessays 21:871–879

    PubMed  CAS  Google Scholar 

  • Foster PG, Cox CJ, Embley TM (2009) The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil Trans R Soc Lond B Biol Sci 364:2197–2207

    Google Scholar 

  • Fournier GP, Gogarten JP (2010) Rooting the ribosomal tree of life. Mol Biol Evol 27:1792–1801

    PubMed  CAS  Google Scholar 

  • Fuerst JA (2005) Intracellular compartmentation in Planctomycetes. Annu Rev Microbiol 59:299–328

    PubMed  CAS  Google Scholar 

  • Fuerst JA, Sagulenko E (2010) Protein uptake by bacteria: an endocytosis-like process in the planctomycete Gemmata obscuriglobus. Commun Integr Biol 3:572–575

    PubMed  Google Scholar 

  • Fuerst JA, Sagulenko E (2011) Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 9:403–413

    PubMed  CAS  Google Scholar 

  • Gabaldón T, Huynen MA (2004) Shaping the mitochondrial proteome. Biochim Biophys Acta 1659:212–220

    PubMed  Google Scholar 

  • Ganot P, Kallesoe T, Reinhardt R, Chourrout D, Thompson E (2004) Spliced-leader RNA trans-splicing in a chordate, Oikopleura dioica, with compact genome. Mol Cell Biol 24:7795–7805

    PubMed  CAS  Google Scholar 

  • Gilbert W (1978) Why genes in pieces? Nature 271:501

    PubMed  CAS  Google Scholar 

  • Glansdorff N, Xu Y, Labedan B (2008) The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 3:29

    PubMed  Google Scholar 

  • Glansdorff N, Xu Y, Labedan B (2009) The conflict between horizontal gene transfer and the safeguard of identity: origin of meiotic sexuality. J Mol Evol 69:470–480

    PubMed  CAS  Google Scholar 

  • Glanz S, Kück U (2009) Trans-splicing of organelle introns—a detour to continuous RNAs. Bioessays 3:921–934

    Google Scholar 

  • Godoy PD, Nogueira-Junior LA, Paes LS, Cornejo A, Martins RM, Silber AM, Schenkman S, Elias MC (2009) Trypanosome prereplication machinery contains a single functional Orc1/Cdc6 protein, which is typical of archaea. Eukaryot Cell 8:1592–1603

    PubMed  CAS  Google Scholar 

  • Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF, Poole RJ, Date T, Oshimaii T, Konishiii J, Dendaii K, Yoshidaii M (1989) Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86:6661–6665

    PubMed  CAS  Google Scholar 

  • Gould SB, Waller RF, McFadden GI (2008) Plastid evolution. Ann Rev Plant Biol 59:491–517

    CAS  Google Scholar 

  • Gratia JP (2007) Spontaneous zygogenesis a wide-ranging mating process in bacteria. Res Microbiol 158:671–678

    PubMed  CAS  Google Scholar 

  • Gratia JP, Thiry M (2003) Spontaneous zygogenesis in Escherichia coli, a form of true sexuality in prokaryotes. Microbiology 149:2571–2584

    PubMed  CAS  Google Scholar 

  • Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Nature 283:1476–1481

    CAS  Google Scholar 

  • Gray MW, Lukeš J, Archibald JM, Keeling PJ, Doolitle WF (2010) Cell biology. Irremediable complexity? Science 12:920–921

    Google Scholar 

  • Gribaldo S, Brochier C (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol 160:513–521

    PubMed  CAS  Google Scholar 

  • Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C (2010) The origin of eukaryotes and their relation with Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol 8:743–751

    PubMed  CAS  Google Scholar 

  • Griffiths G (2007) Cell evolution and the problem of membrane topology. Nat Rev Mol Cell Biol 8:1018–1024

    PubMed  CAS  Google Scholar 

  • Gupta RS (1998) Life’s third domain (Archaea): an established fact or endangered paradigm? Theor Popul Biol 54:91–104

    PubMed  CAS  Google Scholar 

  • Gupta RS (2011) Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Antonie Van Leeuwenhoek 100:171–182

    PubMed  CAS  Google Scholar 

  • Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci USA 106:3859–3864

    PubMed  CAS  Google Scholar 

  • Harris JK, Kelley ST, Spiegelman GB, Pace NR (2003) The genetic core of the Universal Ancestor. Genome Res 13:407–412

    PubMed  CAS  Google Scholar 

  • Hartman H, Fedorov A (2002) The origin of the eukaryotic cell: a genomic investigation. Proc Natl Acad Sci USA 99:1420–1425

    PubMed  CAS  Google Scholar 

  • Hartman H, Favaretto P, Smith TF (2006) The archaeal origins of the eukaryotic translational system. Archaea 2:1–9

    PubMed  CAS  Google Scholar 

  • Hastings KEM (2005) SL trans-splicing: easy come or easy go? Trends Genet 21:240–247

    PubMed  CAS  Google Scholar 

  • Hickey DA (1982) Selfish DNA: a sexually-transmitted nuclear parasite. Genetics 101:519–531

    PubMed  CAS  Google Scholar 

  • Hopwood DA, Wright HM, Bibb MJ, Cohen SN (1977) Genetic recombination through protoplast fusion in Streptomyces. Nature 268:171–174

    PubMed  CAS  Google Scholar 

  • Horiike T, Hamada K, Kanaya S, Shinozawa T (2001) Origin of nucleic acid cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nat Cell Biol 3:210–214

    PubMed  CAS  Google Scholar 

  • Horiike T, Hamada K, Miyata D, Shinozawa T (2004) The origin of eukaryotes is suggested as the symbiosis of Pyrococcus into γ-proteobacteria by phylogenetic tree based on gene content. J Mol Evol 59:606–619

    PubMed  CAS  Google Scholar 

  • Houliston E, Momose T, Manuel M (2010) Clytia hemispherica: a jellyfish cousin joins the laboratory. Trends Genet 26:159–167

    PubMed  CAS  Google Scholar 

  • Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86:9355–9359

    PubMed  CAS  Google Scholar 

  • Jacobs J, Glanz S, Bunse-Grassmann A, Kruse O, Kück U (2010) RNA trans-splicing: identification of components of a putative chloroplast spliceosome. Eur J Cell Biol 89:932–939

    PubMed  CAS  Google Scholar 

  • Jahn U, Gallenberger M, Paper W, Junglas B, Eisenreich W, Stetter KO, Rachel R, Huber H (2008) Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea. J Bacteriol 190:1743–1750

    PubMed  CAS  Google Scholar 

  • Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801–3806

    PubMed  CAS  Google Scholar 

  • Jalasvuori M, Bamford JKH (2008) Structural co-evolution of viruses and cells in the primordial world. Orig Life Evol Biosph 38:165–181

    PubMed  Google Scholar 

  • Jeffares DC, Poole AM, Penny D (1998) Relics from RNA world. J Mol Evol 46:18–36

    PubMed  CAS  Google Scholar 

  • Jeffares DC, Mourier T, Penny D (2006) The biology of intron gain and loss. Trends Genet 22:16–22

    PubMed  CAS  Google Scholar 

  • Jékely G (2003) Small GTPases and the evolution of the eukaryotic cell. Bioessays 25:1129–1138

    PubMed  Google Scholar 

  • Jékely G (2006) Did the last common ancestor have a biological membrane? Biol Direct 1:35

    Google Scholar 

  • Jékely G (2007a) Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms. Biol Direct 2:3

    PubMed  Google Scholar 

  • Jékely G (2007b) Origin of eukaryotic endomembranes—a critical evaluation of different model scenarios. Adv Exp Med Biol 607:38–51

    PubMed  Google Scholar 

  • Kaganer VM, Möhwald H, Dutta P (1999) Structure and phase transitions in Langmuir monolayers. Rev Mod Phys 71:779–819

    CAS  Google Scholar 

  • Kandler O (1994a) The early diversification of life. In: Bengtson S (ed) Nobel Symposium 84. Early Life on Earth. Columbia University Press, New York, pp 152–160

    Google Scholar 

  • Kandler O (1994b) Cell wall biochemistry in Archaea and its phylogenetic implications. J Biol Phys 20:165–169

    CAS  Google Scholar 

  • Kandler O (1998) The early diversification of life and the origin of the three domains: a proposal. In: Wiegel J, Adams MWW (eds) Thermophiles: the keys to molecular evolution and the origin of life. Taylor & Francis, London, pp 19–28

    Google Scholar 

  • Karlberg O, Canbäck B, Kurland CG, Andersson SGE (2000) The dual origin of the yeast mitochondrial proteome. Yeast 17:170–187

    PubMed  CAS  Google Scholar 

  • Keeling PJ (2009) Chromalveolates and the evolution of plastids by secondary endosymbiosis. J Eukaryot Microbiol 56:1–8

    PubMed  CAS  Google Scholar 

  • Kelly S, Wickstead B, Gull K (2011) Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc Biol Sci 278:1009–1018

    PubMed  CAS  Google Scholar 

  • Kierlin-Duncan MN, Sullenger BA (2007) Using 5′-PTMs to repair mutant beta-globin transcripts. RNA 13:1317–1327

    PubMed  CAS  Google Scholar 

  • Kilian O, Kroth PG (2004) Presequence acquisition during secondary endosymbiosis and the possible role of introns. J Mol Evol 58:712–721

    PubMed  CAS  Google Scholar 

  • Kim KM, Caetano-Anollés G (2011) The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol 11:140

    PubMed  CAS  Google Scholar 

  • Koga Y (2011) Early evolution of membrane lipids: how did the lipid divide occur? J Mol Evol (in press). doi:10.1007/s00239-011-9428-5

  • Koga Y, Kyuragi T, Nishihara M, Sone N (1998) Did archaeal and bacterial cells arise independently from non-cellular precursors? A hypothesis stating that the advent of membrane phospholipids with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent. J Mol Evol 46:54–63

    PubMed  CAS  Google Scholar 

  • Koonin EV (2006) The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct 1:22

    Google Scholar 

  • Koonin EV (2009) Intron-dominated genomes of early ancestors of eukaryotes. J Hered 100:618–623

    PubMed  CAS  Google Scholar 

  • Koonin EV, Martin W (2005) On the origin of genomes within inorganic compartments. Trends Genet 21:647–654

    PubMed  CAS  Google Scholar 

  • Krause M, Hirsh D (1987) A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49:753–761

    PubMed  CAS  Google Scholar 

  • Krylov DM, Nasmyth K, Koonin EV (2003) Evolution of eukaryotic cell cycle regulation: stepwise addition of regulatory kinases and late advent of CDKs. Curr Biol 13:173–177

    PubMed  CAS  Google Scholar 

  • Kubo N, Harada K, Hirai A, Kadowaki K (1999) A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: Common use of the same mitochondrial targeting signal for different proteins. Proc Natl Acad Sci USA 96:9207–9211

    PubMed  CAS  Google Scholar 

  • Küper U, Meyer C, Müller V, Rachel R, Huber H (2010) Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. Proc Natl Acad Sci USA 107:3152–3156

    PubMed  Google Scholar 

  • Kurland CG, Andersson SGE (2000) Origins and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64:786–820

    PubMed  CAS  Google Scholar 

  • Kurland CG, Canbäck B, Berg OG (2003) Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 100:9658–9662

    PubMed  CAS  Google Scholar 

  • Kurland CG, Collins LJ, Penny D (2006) Genomics and the irreducible nature of eukaryote cells. Science 312:1011–1014

    PubMed  CAS  Google Scholar 

  • Kurland CG, Canbäck B, Berg OG (2007) The origins of modern proteomes. Biochimie 89:1454–1463

    PubMed  CAS  Google Scholar 

  • Kuwabara T, Minaba M, Iwayama Y, Inouye I, Nakashima M, Marumo K, Maruyama A, Sugai A, Itoh T, Ishibashi J, Urabe T, Kamekura M (2005) Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount. Int J Syst Evol Microbiol 55:2507–2514

    PubMed  CAS  Google Scholar 

  • Kuwabara T, Minaba M, Ogi N, Kamekura M (2007) Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 57:437–443

    PubMed  CAS  Google Scholar 

  • Lake JA (1988) Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331:184–186

    PubMed  CAS  Google Scholar 

  • Lake JA, Skophammer RG, Herbold CW, Servin JA (2009) Genome beginnings: rooting the tree of life. Phil Trans R Soc Lond B Biol Sci 364:2177–2185

    CAS  Google Scholar 

  • Lane N, Martin W (2010) The energetics of genome complexity. Nature 467:929–934

    PubMed  CAS  Google Scholar 

  • Lang KM, Spritz RA (1987) In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences. Mol Cell Biol 7:3428–3437

    PubMed  CAS  Google Scholar 

  • Lang DF, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Ann Rev Gen 33:351–397

    CAS  Google Scholar 

  • Lee KC, Webb R, Fuerst JA (2009a) The cell cycle of the planctomycete Gemmata obscuriglobus with respect to compartmentation. BMC Cell Biol 10:4

    PubMed  Google Scholar 

  • Lee KC, Webb RI, Janssen PH, Sangwan P, Romeo T, Staley JT, Fuerst JA (2009b) Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes. BMC Microbiol 9:5

    Google Scholar 

  • Leipe DD, Aravind L, Koonin EV (1999) Did DNA replication evolve twice independently? Nucleic Acids Res 27:3389–3401

    PubMed  CAS  Google Scholar 

  • Lidie KB, van Dolah FM (2007) Spliced leader RNA-mediated trans-splicing in a dinoflagellate, Karenia brevis. J Eukaryot Microbiol 54:427–435

    PubMed  CAS  Google Scholar 

  • Lidie KB, Ryan JC, Barbier M, Van Dolah FM (2005) Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarray. Mar Biotechnol (NY) 7:481–493

    CAS  Google Scholar 

  • Lindsay MR, Webb RI, Strous M, Jetten MS, Butler MK, Forde RJ, Fuerst JA (2001) Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch Microbiol 175:413–429

    PubMed  CAS  Google Scholar 

  • Lombard J, Moreira D (2011) Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life. Mol Biol Evol 28:87–99

    PubMed  CAS  Google Scholar 

  • Long M, de Souza SJ, Rosenberg C, Gilbert W (1996) Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor. Proc Natl Acad Sci USA 93:7727–7731

    PubMed  CAS  Google Scholar 

  • Lonhienne TG, Sagulenko E, Webb RI, Lee KC, Franke J, Devos DP, Nouwens A, Carroll BJ, Fuerst JA (2010) Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus. Proc Natl Acad Sci USA 107:12883–12888

    PubMed  CAS  Google Scholar 

  • López-García P, Moreira D (2001) The syntrophy hypothesis for the origin of eukaryotes. In: Seckbach J (ed) Symbiosis: mechanisms and models. Kluwer Academic Publishers, Dordrecht, pp 131–146

    Google Scholar 

  • López-García P, Moreira D (2006) Selective forces for the origin of the eukaryotic nucleus. Bioessays 28:525–533

    PubMed  Google Scholar 

  • Lukeš J, Leander BS, Keeling PJ (2009) Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci USA 106:9963–9970

    PubMed  Google Scholar 

  • Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63:528–537

    PubMed  Google Scholar 

  • Lynch M (2007) The origins of genome architecture. Sinauer, Sunderland

    Google Scholar 

  • Makarova KS, Yutin N, Bell SD, Koonin EV (2010) Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol 8:731–741

    PubMed  CAS  Google Scholar 

  • Mansfield SG, Clark RH, Puttaraju M, Kole J, Cohn JA, Mitchell LG, Garcia-Blanco MA (2003) 5′ exon replacement and repair by spliceosome-mediated RNA trans-splicing. RNA 9:1290–1297

    PubMed  CAS  Google Scholar 

  • Margulis L, Dolan MF, Guerrero R (2000) The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists. Proc Natl Acad Sci USA 97:6954–6959

    PubMed  CAS  Google Scholar 

  • Margulis L, Chapman M, Guerrero R, Hall J (2006) The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proc Natl Acad Sci USA 103:13080–13085

    PubMed  CAS  Google Scholar 

  • Marletaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco Y (2008) Chaetognath transcriptome reveals ancestral and unique features among bilaterians. Genome Biol 9:R94

    PubMed  Google Scholar 

  • Martin W, Koonin EV (2006) Introns and the origin of nucleus-cytosol compartmentalization. Nature 440:41–45

    PubMed  CAS  Google Scholar 

  • Martin W, Müller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37–41

    PubMed  CAS  Google Scholar 

  • Martin W, Russell MJ (2003) On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Phil Trans R Soc Lond B 358:59–85

    CAS  Google Scholar 

  • Mat WK, Xue H, Wong JT (2008) The genomics of LUCA. Front Biosci 13:5605–5613

    PubMed  CAS  Google Scholar 

  • Maynard Smith J, Szathmáry E (1995) The major evolutionary transitions. W. II. Freeman, Oxford

    Google Scholar 

  • McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM (2011) Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays (in press). doi:10.1002/bies.201100045

  • Moreira D, López-García P (1998) Symbiosis between methanogenic archaea and δ-proteobacteria as the origin of eukaryotes: the Syntrophic hypothesis. J Mol Evol 47:517–530

    PubMed  CAS  Google Scholar 

  • Morigaki K, Dallavalle S, Walde P, Colonna S, Luisi PL (1997) Autopoietic self-reproduction of a chiral fatty acid vesicles. J Am Chem Soc 119:292–301

    CAS  Google Scholar 

  • Murphy W, Watkins K, Agabian N (1986) Identification of a novel Y branch structure in trypanosome mRNA processing: evidence for trans-splicing. Cell 47:517–525

    PubMed  CAS  Google Scholar 

  • Nassoy P, Goldman M, Bouloussa O, Rondolez F (1995) Spontaneous chiral segregation in bidimensional films. Phys Rev Lett 75:457–460

    PubMed  CAS  Google Scholar 

  • Nather DJ, Rachel R (2004) The outer membrane of the hyperthermophilic archaeon Ignicoccus: dynamics, ultrastructure and composition. Biochem Soc Trans 32:199–203

    PubMed  CAS  Google Scholar 

  • Neumann N, Lundin D, Poole AM (2010) Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PloS One 5:e13241

    PubMed  Google Scholar 

  • Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K (2009) Phylogenetic positions of Glaucophyta, green plants (Archaeplatida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol 53:872–880

    PubMed  Google Scholar 

  • O’Connor T, Sundberg K, Carroll H, Clement M, Snell Q (2010) Analysis of long branch extraction and long branch shortening. BMC Genomics 11:S14

    PubMed  Google Scholar 

  • O’Reilly AJ, Dacks JB, Field MC (2011) Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PLoS One 6:e19308

    PubMed  Google Scholar 

  • Otto SP, Lenormand T (2002) Resolving the paradox of sex and recombination. Nat Rev Genet 3:252–261

    PubMed  CAS  Google Scholar 

  • Palmer JD (2003) The symbiotic birth and spread of plastids: How many times and whodunit? J Phycol 39:4–11

    CAS  Google Scholar 

  • Panigrahi AK, Ernst NL, Domingo GJ, Fleck M, Salavati R, Stuart KD (2006) Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA 2:1038–1049

    Google Scholar 

  • Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA (2006) Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2:e220

    PubMed  Google Scholar 

  • Patron NJ, Durnford DG, Kopriva S (2008) Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfers. BMC Evol Biol 8:39

    PubMed  Google Scholar 

  • Patthy L (1999) Genome evolution and the evolution of exon-shuffling–A review. Gene 238:103–114

    PubMed  CAS  Google Scholar 

  • Penny D, Poole AM (1999) The nature of the last universal common ancestor. Curr Opin Gen Dev 9:672–677

    CAS  Google Scholar 

  • Penny D, Hoeppner MP, Poole AM, Jeffares DC (2009) An overview of the introns-first theory. J Mol Evol 69:527–540

    PubMed  CAS  Google Scholar 

  • Peretó J, López-García P, Moreira D (2004) Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem Sci 29:469–477

    PubMed  Google Scholar 

  • Pertseva MN, Shpakov AO (2009) The prokaryotic origin and evolution of eukaryotic chemosignaling systems. Neurosci Behav Physiol 39:793–804

    PubMed  CAS  Google Scholar 

  • Pettitt J, Harrison N, Stansfield I, Connolly B, Müller B (2010) The evolution of spliced leader trans-splicing in nematodes. Biochem Soc Trans 38:1125–1130

    PubMed  CAS  Google Scholar 

  • Pilhofer M, Rappl K, Eckl C, Bauer AP, Ludwig W, Schleifer KH, Petroni G (2008) Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and phylogenetic comparison with rRNA genes. J Bacteriol 190:3192–3202

    PubMed  CAS  Google Scholar 

  • Pina M, Bize A, Forterre P, Prangishvili D (2011) The archeoviruses. FEMS Microbiol Rev (in press). doi:10.1111/j.1574-6976.2011.00280.x

  • Pisani D, Cotton JA, McInerney JO (2007) Supertrees disentangle the chimeric origin of eukaryotic genomes. Mol Biol Evol 24:1752–1760

    PubMed  CAS  Google Scholar 

  • Poole AM (2006) Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes? Biol Direct 1:36

    Google Scholar 

  • Poole AM (2009) Horizontal gene transfer at the earliest stages of the evolution of life. Res Microbiol 160:473–480

    PubMed  CAS  Google Scholar 

  • Poole AM, Logan DT (2005) Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 22:1444–1455

    PubMed  CAS  Google Scholar 

  • Poole AM, Neumann N (2011) Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis. Res Microbiol 162:71–76

    PubMed  Google Scholar 

  • Poole AM, Penny D (2007) Evaluating hypotheses for the origin of eukaryotes. Bioessays 29:74–84

    PubMed  Google Scholar 

  • Poole AM, Jeffares D, Penny D (1998) The path from RNA world. J Mol Evol 46:1–17

    PubMed  CAS  Google Scholar 

  • Poole AM, Jeffares D, Penny D (1999) Prokaryotes, the new kids on the block. Bioessays 21:880–889

    PubMed  CAS  Google Scholar 

  • Popper K (1959) The logic of scientific discovery. Basic Books, New York

    Google Scholar 

  • Pouchkina-Stantcheva N, Tunnacliffe A (2005) Splice leader RNA-mediated trans-splicing in Phylum Rotifera. Mol Biol Evol 22:1482–1489

    PubMed  CAS  Google Scholar 

  • Rachel R, Wyschkony I, Riehl S, Huber H (2002) The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon. Archaea 1:9–18

    PubMed  CAS  Google Scholar 

  • Rest JS, Mindell DP (2003) Retroids in archaea: phylogeny and lateral origins. Mol Biol Evol 20:1134–1142

    PubMed  CAS  Google Scholar 

  • Rice WR (2002) Experimental tests of the adaptive significance of sexual recombination. Nat Rev Genet 3:241–251

    PubMed  CAS  Google Scholar 

  • Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152–155

    PubMed  CAS  Google Scholar 

  • Rodríguez-Trelles F, Tarrío R, Ayala FJ (2006) Origins and evolution of spiceosomal introns. Annu Rev Genet 40:47–76

    PubMed  Google Scholar 

  • Rogerson ML, Robinson BH, Bucak S, Walde P (2006) Kinetic studies of the interaction of fatty acids with phosphatidylcholine vesicles (liposomes). Colloids Surf B Biointerfaces 48:24–34

    PubMed  CAS  Google Scholar 

  • Sackmann E (1982) Physikalische grundlagen der molekularen organisation und dynamik von membranen. In: Hoppe W, Lohmann W, Markl H, Ziegler H (eds) Biophysik. Springer, Berlin, pp 439–471

    Google Scholar 

  • Saier MH Jr (1994) Protein uptake into E. coli during Bdellovibrio infection. A process of reverse secretion? FEBS Lett 337:14–17

    PubMed  CAS  Google Scholar 

  • Sales-Pardo M, Chan AOB, Amaral LAN, Guimerà R (2007) Evolution of protein families: is it possible to distinguish between domains of life? Gene 402:81–93

    PubMed  CAS  Google Scholar 

  • Samson RY, Obita T, Freund SM, Williams RL, Bell SD (2008) A role for the ESCRT system in cell division in archaea. Science 322:1710–1713

    PubMed  CAS  Google Scholar 

  • Santarella-Mellwig R, Franke J, Jaedicke A, Gorjanacz M, Bauer U, Budd A, Mattaj IW, Devos DP (2010) The compartmentalized bacteria of the Planctomycetes–Verrucomicrobia–Chlamydiae superphylum have membrane coat-like proteins. PLoS Biol 8:e1000281

    PubMed  Google Scholar 

  • Saruhashi S, Hamada K, Miyata D, Horiike T, Shinozawa T (2008) Comprehensive analysis of the origin of eukaryotic genomes. Genes Genet Syst 83:285–291

    PubMed  Google Scholar 

  • Schaeffer P, Cami B, Hotchkiss RD (1976) Fusion of bacterial protoplasts. Proc Natl Acad Sci USA 73:2151–2155

    PubMed  CAS  Google Scholar 

  • Schmidt U, Podar M, Stahl U, Perlman PS (1996) Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations. RNA 2:1161–1172

    PubMed  CAS  Google Scholar 

  • Schneider A, Bursa D, Lithgow T (2008) The direct route: a simplified pathway for protein import into the mitochondrion of trypanosomes. Trends Cell Biol 18:12–18

    PubMed  CAS  Google Scholar 

  • Searcy DG (2003) Metabolic integration during the evolutionary origin of mitochondria. Cell Res 13:229–238

    PubMed  CAS  Google Scholar 

  • Shimada H, Yamagishi A (2011) Stability of heterochiral hybrid membrane made of bacterial sn-G3P lipids and archaeal sn-G1P lipids. Biochemistry 50:4114–4120

    PubMed  CAS  Google Scholar 

  • Shinozawa T, Horiike T, Hamada K (2001) Nucleus symbiosis hypothesis: formation of eukaryotic cell nuclei by the symbiosis of Archaea in Bacteria. In: Seckbach J (ed) Symbiosis: mechanisms and models. Kluwer Academic Publishers, Dordrecht, pp 229–235

    Google Scholar 

  • Skophammer RG, Servin JA, Herbold CW, Lake JA (2007) Evidence for a Gram positive, eubacterial root of the tree of life. Mol Biol Evol 24:1761–1768

    PubMed  CAS  Google Scholar 

  • Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449–1452

    PubMed  CAS  Google Scholar 

  • Speijer D (2011) Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity. Bioessays 33:344–349

    PubMed  Google Scholar 

  • Sterrer W (2002) On the origin of sex as vaccination. J Theor Biol 216:387–396

    PubMed  Google Scholar 

  • Stoltzfus A (1999) On the possibility of constructive neutral evolution. J Mol Evol 49:169–181

    PubMed  CAS  Google Scholar 

  • Stover N, Steele R (2001) Trans-spliced leader addition to mRNAs in a cnidarian. Proc Natl Acad Sci 98:5693–5698

    PubMed  CAS  Google Scholar 

  • Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, Le Paslier D (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790–794

    PubMed  Google Scholar 

  • Tamura A, Matsumoto A, Manire GP, Higashi N (1971) Electron microscopic observations on the structure of the envelopes of mature elementary bodies and developmental reticulate forms of Chlamydia psittaci. J Bacteriol 105:355–360

    PubMed  CAS  Google Scholar 

  • Tekle YI, Grant JR, Kovner AH, Townsend JP, Katz LA (2010) Identification of new molecular markers for assembling the eukaryotic tree of life. Mol Phylogenet Evol 55:1177–1182

    PubMed  CAS  Google Scholar 

  • Tessier LH, Keller M, Chan RL, Fournier R, Weil JH, Imbault P (1991) Short leader sequences may be transferred from small RNAs to pre-mature mRNAs by trans-splicing in Euglena. EMBO J 10:2621–2625

    PubMed  CAS  Google Scholar 

  • Tourasse NJ, Gouy M (1999) Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Mol Phylogenet Evol 13:159–168

    PubMed  CAS  Google Scholar 

  • Toxvaerd S (2009) Origin of homochirality in biosystems. Int J Mol Sci 10:1290–1299

    PubMed  CAS  Google Scholar 

  • Uragami M, Miyake Y, Regen SL (2000) Influence of headgroup chirality on the mixing behavior of phophatidylglycerol mimics in fluid bilayers. Langmuir 16:3491–3496

    CAS  Google Scholar 

  • Valadkhan S, Jaladat Y (2010) The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine. Proteomics 10:4128–4141

    PubMed  CAS  Google Scholar 

  • Valentine DL (2007) Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat Rev Microbiol 5:316–323

    PubMed  CAS  Google Scholar 

  • van Niftrik L, van Helden M, Kirchen S, van Donselaar EG, Harhangi HR, Webb RI, Fuerst JA, Op den Camp HJ, Jetten MS, Strous M (2010) Intracellular localization of membrane-bound ATPases in the compartmentalized anammox bacterium ‘Candidatus Kuenenia stuttgartiensis′. Mol Microbiol 77:701–715

    PubMed  Google Scholar 

  • Vendenberghe A, Meedel T, Hastings K (2001) mRNA 5′-leader trans-splicing in the chordates. Genes Dev 15:294–303

    Google Scholar 

  • Vesteg M, Krajčovič J (2007) On the origin of meiosis and sex. Riv Biol 100:147–161

    PubMed  Google Scholar 

  • Vesteg M, Krajčovič J (2008a) On the origin of eukaryotic cytoskeleton. Riv Biol 101:47–56

    Google Scholar 

  • Vesteg M, Krajčovič J (2008b) Origin of eukaryotic cells as a symbiosis of parasitic α-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes. Commun Integr Biol 1:104–113

    PubMed  CAS  Google Scholar 

  • Vesteg M, Krajčovič J (2010) The origin of Eukarya as a stress response of two-membrane-bounded sexual pre-karyote to an aggressive alphaproteobacterial periplasmic infection. In: Seckbach J, Grube M (eds) Symbioses and stress: joint ventures in biology, cellular origin, life in extreme habitats and astrobiology, vol 17. Springer Science+Business Media B.V., Hidelberg, pp 63–81

  • Vesteg M, Krajčovič J, Ebringer L (2006) On the origin of eukaryotes and their endomembranes. Riv Biol 99:445–466

    Google Scholar 

  • Vesteg M, Vacula R, Burey S, Löffelhardt W, Drahovská H, Martin W, Krajčovič J (2009a) Expression of nucleus-encoded genes for chloroplast proteins in the flagellate Euglena gracilis. J Eukaryot Microbiol 56:159–166

    PubMed  CAS  Google Scholar 

  • Vesteg M, Vacula R, Krajčovič J (2009b) On the origin of chloroplasts, import mechanisms of chloroplast-targeted proteins, and loss of photosynthetic ability. Folia Microbiol (Praha) 54:303–321

    CAS  Google Scholar 

  • Vesteg M, Vacula R, Steiner JM, Mateášiková B, Löffelhardt W, Brejová B, Krajčovič J (2010) A possible role for short introns in the acquisition of stroma-targeting peptides in the flagellate Euglena gracilis. DNA Res 17:223–231

    PubMed  CAS  Google Scholar 

  • Vollhardt D, Emrich G, Gutberlet T, Fuhrhop JH (1996) Chiral discrimination and pattern formation in N-dodecylmannonamide monolayers at the air-water interphase. Langmuir 12:5659–5663

    CAS  Google Scholar 

  • von Dohlen CD, Kohler S, Alsop ST, McManus WR (2001) Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts. Nature 412:433–436

    Google Scholar 

  • Wächtershäuser G (1988) Before enzymes and templates: theory of surface metabolism. Microbiol Rev 52:452–484

    PubMed  Google Scholar 

  • Wächtershäuser G (1992) Groundworks for an evolutionary biochemistry–the iron-sulfur world. Prog Biophys Mol Biol 58:85–201

    PubMed  Google Scholar 

  • Wächtershäuser G (2003) From pre-cells to Eukarya—a tale of two lipids. Mol Microbiol 47:13–22

    PubMed  Google Scholar 

  • Wächtershäuser G (2006) From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Phil Trans R Soc B 361:1787–1808

    PubMed  Google Scholar 

  • Wally V, Klausegger A, Koller U, Lochmüller H, Krause S, Wiche G, Mitchell LG, Hintner H, Bauer JW (2008) 5′ trans-splicing repair of the PLEC1 gene. J Invest Dermatol 128:568–574

    PubMed  CAS  Google Scholar 

  • Wernegreen JJ (2005) For better or worse: genomic consequences of intracellular mutualism and parasitism. Curr Opin Genet Dev 15:572–583

    PubMed  CAS  Google Scholar 

  • Wischmann C, Schuster W (1995) Transfer of rps10 from the mitochondrion to the nucleus in Arabidopsis thaliana: Evidence for RNA-mediated transfer and exon shuffling at the integration site. FEBS Lett 374:152–156

    PubMed  CAS  Google Scholar 

  • Woese CR (1983) The primary lines of descent and the universal ancestor. In: Bendall DS (ed) Evolution from molecules to men. Cambridge University Press, Cambridge, pp 209–233

    Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Res 51:221–271

    CAS  Google Scholar 

  • Woese CR (1998) The universal ancestor. Proc Natl Acad Sci USA 95:6854–6859

    PubMed  CAS  Google Scholar 

  • Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392–8396

    PubMed  CAS  Google Scholar 

  • Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99:8742–8747

    PubMed  CAS  Google Scholar 

  • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090

    PubMed  CAS  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Toward a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. Proc Natl Acad Sci USA 87:4576–4579

    PubMed  CAS  Google Scholar 

  • Wong JT-Z, Chen J, Mat W-K, Ng S-K, Xue H (2007) Polyphasic evidence delineating the root of life and roots of biological domains. Gene 403:39–52

    PubMed  CAS  Google Scholar 

  • Woolfit M, Bromham L (2003) Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. Mol Biol Evol 20:1545–1555

    PubMed  CAS  Google Scholar 

  • Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV (2008) The deep archaeal roots of eukaryotes. Mol Biol Evol 25:1619–1630

    PubMed  CAS  Google Scholar 

  • Yutin N, Wolf MY, Wolf YI, Koonin EV (2009) The origins of phagocytosis and eukaryogenesis. Biol Direct 4:9

    PubMed  Google Scholar 

  • Zenkin N, Yuzenkova Y, Severinov K (2006) Transcript-assisted transcriptional proofreading. Science 313:518–520

    PubMed  CAS  Google Scholar 

  • Zhang H, Lin S (2009) Retrieval of missing spliced leader in dinoflagellates. PLoS One 4:e4129

    PubMed  Google Scholar 

  • Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S (2007) Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci 104:4618–4623

    PubMed  CAS  Google Scholar 

  • Zhaxybayeva O, Lapierre P, Gogarten JP (2005) Ancient gene duplications and the root(s) of the tree of life. Protoplasma 227:53–64

    PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by grant VEGA Grant No. 1/0416/09 from the Ministry of Education of the Slovak Republic to J. K., and it is the result of the project implementation: “Centre of excellence for exploitation of informational biomacromolecules in disease prevention and improvement of quality of life”, ITMS 26240120003, supported by the Research and Development Operational Programme funded by the ERDF. We wish to thank anonymous reviewers for their useful comments and suggestions that contributed to the final version of this manuscript. We thank Ray Marshall (Department of Languages, Faculty of Natural Sciences, Comenius University, Bratislava) for the language revision of this manuscript.

Author information

Authors and Affiliations

  1. Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovakia

    Matej Vesteg & Juraj Krajčovič

  2. Faculty of Natural Sciences, Institute of Cell Biology and Biotechnology, Comenius University, Bratislava, Slovakia

    Matej Vesteg & Juraj Krajčovič

Authors
  1. Matej Vesteg
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Juraj Krajčovič
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Juraj Krajčovič.

Additional information

Communicated by S. Hohmann.

Currently the authors M. Vesteg and J. Krajčovič are at Comenius University.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vesteg, M., Krajčovič, J. The falsifiability of the models for the origin of eukaryotes. Curr Genet 57, 367–390 (2011). https://doi.org/10.1007/s00294-011-0357-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00294-011-0357-z

Keywords

Search

Navigation