Eocyte hypothesis

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Karyota
Urzwerg.jpg
Ignicoccus hospitalis (and its symbiote Nanoarchaeum equitans)
Scientific classification
Domain:
Archaea
(unranked):
Karyota

Lake et al. 1988[1]
Domain & Regnum
Synonyms
  • proto-eukaryotic group
  • Karyotes

The eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota (formerly known as eocytes), a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major phylum of archaea, the Euryarchaeota.[2][3]

Schematic representation

Introduction[]

The eocyte hypothesis gained considerable attention after its introduction due to the interest in determining the origin of the eukaryotic cell. This hypothesis has primarily been in contrast with the three-domain system introduced by Carl Woese in 1977. Additional evidence supporting the eocyte hypothesis was published in the 1980s, but despite fairly unequivocal evidence, support waned in favor of the three-domain system.[1][2]

Genomic advancements[]

With advancements in genomics, the eocyte hypothesis experienced a revival beginning in the mid-2000s. As more archaeal genomes were sequenced, numerous genes coding for eukaryotic traits have been discovered in various archaean phyla, seemingly providing support for the eocyte hypothesis. Proteomics based research has also found supporting data with the use of elongation factor 1-α (eEF-1), a common housekeeping protein, to compare structural homology between eukaryotic and archaean lineages.[4] Furthermore, other proteins have been sequenced through proteomics with homologous structures in heat shock proteins found in both eukaryotes and archaea. The structure of these heat shock proteins were identified through X-ray crystallography to find the three dimensional structure of the proteins.[5] These proteins however have differing purposes as the eukaryote heat shock protein is a part of the T-complex while the archaeal heat shock protein is a molecular chaperone.[5] This creates an issue with the sequence homology that has been seen between 70 kilodalton heat shock proteins in eukaryotes and gram negative bacteria.[6]

Studies[]

In addition to a Crenarchaeal origin of eukaryotes, some studies have suggested that eukaryotes may also have originated in the Thaumarchaeota.[2][7][8][9][10]

A superphylum — TACK — has been proposed that includes the Thaumarchaeota, Crenarchaeota, and other groups of archaea,[11] so that this superphylum may be related to the origin of eukaryotes. It is seen that eukaryotes share a large number of proteins with members of the TACK superphylum and that these complex archaea may have had rudimentary phagocytosis abilities to engulf bacteria.[12]

As a result of metagenomic analysis of material found nearby hydrothermal vents, another superphylum — Asgard — has been named and proposed to be more closely related to the original eukaryote and a sister group to TACK more recently. Asgard consists of phyla Lokiarchaeota (found first), Heimdallarchaeota (possibly related closest to eukaryotes) and others.[13][14]

Root of the eocyte tree[]

The eocyte tree root may be located in the RNA world; that is, the root organism may have been a ribocyte (also known as a ribocell). For cellular DNA and DNA handling, an "out of virus" scenario has been proposed: storing genetic information in DNA may have been an innovation performed by viruses and later handed over to ribocytes twice, once transforming them into bacteria and once transforming them into archaea.[15][16]

Although archaeal viruses are not as well-studied as bacterial phages, it is thought that dsDNA viruses led to the incorporation of the viral genome into archaeal genomes.[17] The transduction of genetic material through a viral vector led to an increase in complexity in the pre-eukaryotic cells.[18] All these findings do not change the eocyte tree as given here in principle, but examine a higher resolution of it.

Arguments against[]

Due to the similarities found between eukaryotes and both archaea and bacteria, it is thought that a major source of the genetic variation is through horizontal gene transfer.[19] Horizontal gene transfer explains why archaeal sequences are found in bacteria and bacterial sequences are found in archaea.[19] This could explain why elongation factors found in archaea and eukaryotes are so similar, the data currently out is obscured as horizontal gene transfer, vertical gene transfer, or endosymbiosis and could be behind the gene sequence similarity.[6] The eocyte hypothesis also has troubles due to the endosymbiotic theory, with the archaea being able to phagocytize bacteria for the formation of membrane-bound organelles.[20] It is thought that these ancestral prokaryotes began to have ectosymbiotic relationships with other prokaryotes and gradually engulfed these symbiotes through cell membrane protrusions.[21]

Although more recent data provides evidence in favour of the relationship between eukaryotes and Crenarchaeota through the analysis of elongation factors, earlier experimentation with elongation factors provided evidence against such a relationship.[22] Hasegawa et al. uses these elongation factors to show that eukaryotes and archaebacteria are more closely related than archaebacteria and eubacteria than is explained in this 2 tree system.[22]

Competing hypothesis[]

A competing hypothesis is that prokaryotes evolved towards thriving in higher temperatures to evade viruses through the thermoreductive hypothesis, however this does not account for the arising of eukaryotes and only takes into consideration the prokaryotic origins.[23] However decrease in complexity from a more complex origin is the basis of reductive evolution where a commensal relationship occurs, while this reduction explained in the thermoreduction hypothesis uses a parasitic relationship with viruses to explain the movement of complex pre-eukaryotes to a more harsh environment; that being ocean floor hydrothermal vents.[24]

References[]

  1. ^ a b Lake, James A. (1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature. 331 (6152): 184–186. Bibcode:1988Natur.331..184L. doi:10.1038/331184a0. PMID 3340165. S2CID 4368082.
  2. ^ a b c Archibald, John M. (23 December 2008). "The eocyte hypothesis and the origin of eukaryotic cells". PNAS. 105 (51): 20049–20050. Bibcode:2008PNAS..10520049A. doi:10.1073/pnas.0811118106. PMC 2629348. PMID 19091952.
  3. ^ Lake, James A.; Henderson, Eric; Oakes, Melanie; Clark, Michael W. (June 1984). "Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes". PNAS. 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. doi:10.1073/pnas.81.12.3786. PMC 345305. PMID 6587394.
  4. ^ Roger, A; Sandblom, O; Doolittle, W.F.; Philippe, H (1999). "An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes". Molecular Biology and Evolution. 16 (2): 218–233. doi:10.1093/oxfordjournals.molbev.a026104. PMID 10028289.
  5. ^ a b Rivera, Maria; Lake, James (July 3, 1992). "Evidence That Eukaryotes and Eocyte Prokaryotes are Immediate Relatives". Science. 257 (5066): 74–76. Bibcode:1992Sci...257...74R. doi:10.1126/science.1621096. PMID 1621096.
  6. ^ a b Gupta, R.S.; Singh, B. (1994). "Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic nucleus". Current Biology. 4 (12): 1104–1114. doi:10.1016/s0960-9822(00)00249-9. PMID 7704574. S2CID 2568264.
  7. ^ 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" (PDF). Proceedings of the Royal Society B. 278 (1708): 1009–1018. doi:10.1098/rspb.2010.1427. PMC 3049024. PMID 20880885. Archived from the original (PDF) on 3 March 2016. Retrieved 5 October 2012.
  8. ^ Poole, Anthony M.; Neumann, Nadja (2011). "Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis" (PDF). Research in Microbiology. 162 (1): 71–76. doi:10.1016/j.resmic.2010.10.002. PMID 21034814. Retrieved 5 October 2012.
  9. ^ Guy, Lionel; Ettema, Thijs J. G. (December 2011). "The archaeal 'TACK' superphylum and the origin of eukaryotes". Trends in Microbiology. 19 (12): 580–587. doi:10.1016/j.tim.2011.09.002. PMID 22018741.
  10. ^ Cox, Cymon J.; Foster, Peter G.; Hirt, Robert P.; Harris, Simon R.; Embley, T. Martin (23 December 2008). "The archaebacterial origin of eukaryotes". PNAS. 105 (51): 20356–20361. Bibcode:2008PNAS..10520356C. doi:10.1073/pnas.0810647105. PMC 2629343. PMID 19073919.
  11. ^ Guy, L.; Ettema, T.J. (19 December 2011). "The archaeal 'TACK' superphylum and the origin of eukaryotes". Trends Microbiol. 19 (12): 580–587. doi:10.1016/j.tim.2011.09.002. PMID 22018741.
  12. ^ Koonin, Eugene (26 September 2015). "Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?". Philosophical Transactions of the Royal Society B: Biological Sciences. 370 (1678): 20140333. doi:10.1098/rstb.2014.0333. PMC 4571572. PMID 26323764.
  13. ^ Eme, Laura; Spang, Anja; Lombard, Jonathan; Stairs, Courtney W.; Ettema, Thijs J. G. (10 November 2017). "Archaea and the origin of eukaryotes". Nature Reviews Microbiology. 15 (12): 711–723. doi:10.1038/nrmicro.2017.133. ISSN 1740-1534. PMID 29123225. S2CID 8666687.
  14. ^ Zaremba-Niedzwiedzka, K; et al. (2017). "Asgard archaea illuminate the origin of eukaryotic cellular complexity". Nature. 541 (7637): 353–358. Bibcode:2017Natur.541..353Z. doi:10.1038/nature21031. OSTI 1580084. PMID 28077874. S2CID 4458094.
  15. ^ Forterre, Patrick; Krupovic, Mart (2012). "The Origin of Virions and Virocells: The Escape Hypothesis Revisited". Viruses: Essential Agents of Life. pp. 43–60. doi:10.1007/978-94-007-4899-6_3. ISBN 978-94-007-4898-9.
  16. ^ Patrick Forterre: Evolution - Die wahre Natur der Viren, in: Spektrum August 2017, S. 37 (Online-Artikel vom 19. Juli 2017) (German)
  17. ^ Zilig, W (1996). "Viruses, plasmids, and other genetic elements of thermophilic and hyperthermophilic Archaea". FEMS Microbiology Reviews. 18 (2–3): 225–236. doi:10.1016/0168-6445(96)00014-9. PMID 8639330.
  18. ^ P, Forterre (2013). "The Common Ancestor of Archaea and Eukarya Was Not as Archaeon". Archaea. 2013: 372396. doi:10.1155/2013/372396. PMC 3855935. PMID 24348094.
  19. ^ a b Leonard, C.J.; Aravind, L; Koonin, E.V. (1998). "Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the "Eukaryotic" Protein Kinase Superfamily". Genome Research. 8 (10): 1038–1047. doi:10.1101/gr.8.10.1038. PMID 9799791.
  20. ^ Davidov, Y; Jurkevitch, E (2009). "Predation between prokaryotes and the origin of eukaryotes". BioEssays. 31 (7): 748–757. doi:10.1002/bies.200900018. PMID 19492355. S2CID 8796311.
  21. ^ Baum, David (28 October 2014). "An inside-out origin for the eukaryotic cell". BMC Biology. 12: 776. doi:10.1186/s12915-014-0076-2. PMC 4210606. PMID 25350791.
  22. ^ a b Hasegawa, Masami; Iwabe, Naoyuko; Mukohata, Yasuo; Miyata, Takashi (11 April 1990). "Close evolutionary relatedness of archaebacteria, Methanococcus and Halobacterium, to eukaryotes demonstrated by composite phylogenetic trees of elongation factors EF-Tu and EF-G: Eocyte tree is unlikely". The Japanese Journal of Genetics. 65 (3): 109–114. doi:10.1266/jjg.65.109.
  23. ^ Forterre, P (April 1995). "Thermoreduction, a hypothesis for the origin of prokaryotes". Comptes Rendus de l'Académie des Sciences, Série III. 318 (4): 415–22. PMID 7648354.
  24. ^ Martin, William F.; Garg, Sriram; Zimorski, Verena (2015). "Endosymbiotic theories for eukaryote origin". Philosophical Transactions of the Royal Society B: Biological Sciences. 370 (1678): 20140330. doi:10.1098/rstb.2014.0330. PMC 4571569. PMID 26323761.
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