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Two-domain system

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The two-domain system is a biological classification by which all organisms in the tree of life are classified into two big domains, Bacteria and Archaea.[1][2][3] It emerged out of development in the knowledge of archaea diversity and challenge over the widely-accepted three-domain system that defines life into Bacteria, Archaea and Eukarya.[4] It was predicted by the eocyte hypothesis of James A. Lake in the 1980s,[5] which was largely superseded by the three-domain system due to better compelling evidences at the time.[6] Better understanding of archaea especially in their roles in the origin of eukaryotes by symbiogenesis with bacteria led to the revival of the eocyte hypothesis in the 2000s.[7][8][9] The two-domain system became widely appreciated after the discovery of a large group (superphylum) of archaea called Asgard in 2017,[10] which is described to be the evolutionary root of eukaryotes – implying that eukaryotes are members of the domain Archaea.[11]

While the features of Asgard archaea do not directly rule out the three-domain system,[12][13] the notion that eukaryotes originated from archaea and thus belong to Archaea has been strengthened by genetic and proteomic studies.[14] Under the three-domain system, Eukarya is mainly distinguished by the presence of "eukaryotic signature proteins" that are not found in archaea and bacteria. However, Asgards are found to contain genes that codes for several of such unique proteins, indicating that the proteins originated in archaea.[3]

References

  1. ^ Bolshoy, Alexander; Volkovich, Zeev (Vladimir); Kirzhner, Valery; Barzily, Zeev (2010), "Biological Classification", Genome Clustering, vol. 286, Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 17–22, doi:10.1007/978-3-642-12952-0_2, ISBN 978-3-642-12951-3, retrieved 2022-05-14
  2. ^ Raymann, Kasie; Brochier-Armanet, Céline; Gribaldo, Simonetta (2015). "The two-domain tree of life is linked to a new root for the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 112 (21): 6670–6675. doi:10.1073/pnas.1420858112. PMC 4450401. PMID 25964353.
  3. ^ a b Nobs, Stephanie-Jane; MacLeod, Fraser I.; Wong, Hon Lun; Burns, Brendan P. (2022). "Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?". Trends in Microbiology. 30 (5): 421–431. doi:10.1016/j.tim.2021.11.003.
  4. ^ Doolittle, W. Ford (2020). "Evolution: Two Domains of Life or Three?". Current Biology. 30 (4): R177 – R179. doi:10.1016/j.cub.2020.01.010. PMID 32097647.
  5. ^ 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.
  6. ^ 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.
  7. ^ Poole, Anthony M.; Penny, David (2007). "Evaluating hypotheses for the origin of eukaryotes". BioEssays. 29 (1): 74–84. doi:10.1002/bies.20516. PMID 17187354.
  8. ^ Archibald, John M. (2008). "The eocyte hypothesis and the origin of eukaryotic cells". Proceedings of the National Academy of Sciences. 105 (51): 20049–20050. doi:10.1073/pnas.0811118106. PMC 2629348. PMID 19091952.
  9. ^ Foster, Peter G.; Cox, Cymon J.; Embley, T. Martin (2009). "The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364 (1527): 2197–2207. doi:10.1098/rstb.2009.0034. PMC 2873002. PMID 19571240.
  10. ^ Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W.; Anantharaman, Karthik; Starnawski, Piotr (11 January 2017). "Asgard archaea illuminate the origin of eukaryotic cellular complexity" (PDF). Nature. 541 (7637): 353–358. Bibcode:2017Natur.541..353Z. doi:10.1038/nature21031. ISSN 1476-4687. OSTI 1580084. PMID 28077874. S2CID 4458094.
  11. ^ 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.
  12. ^ Da Cunha, Violette; Gaia, Morgan; Nasir, Arshan; Forterre, Patrick (2018). "Asgard archaea do not close the debate about the universal tree of life topology". PLOS Genetics. 14 (3): e1007215. doi:10.1371/journal.pgen.1007215. PMC 5875737. PMID 29596428.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  13. ^ Zhou, Zhichao; Liu, Yang; Li, Meng; Gu, Ji-Dong (2018). "Two or three domains: a new view of tree of life in the genomics era". Applied Microbiology and Biotechnology. 102 (7): 3049–3058. doi:10.1007/s00253-018-8831-x. PMID 29484479.
  14. ^ Williams, Tom A.; Cox, Cymon J.; Foster, Peter G.; Szöllősi, Gergely J.; Embley, T. Martin (2020). "Phylogenomics provides robust support for a two-domains tree of life". Nature Ecology & Evolution. 4 (1): 138–147. doi:10.1038/s41559-019-1040-x.
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