Biology:Two-domain system

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Short description: Biological classification system
The tree of life. Two domains of life are Bacteria (top branches) and Archaea (bottom branches, including eukaryotes).

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 from development of knowledge of archaea diversity and challenges to the widely accepted three-domain system that defines life into Bacteria, Archaea, and Eukarya.[4] It was preceded by the eocyte hypothesis of James A. Lake in the 1980s,[5] which was largely superseded by the three-domain system, due to evidence at the time.[6] Better understanding of archaea, especially of their roles in the origin of eukaryotes through symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s.[7][8] The two-domain system became more widely accepted after the discovery of a large group (superphylum) of archaea called Asgard in 2017,[9] which evidence suggests to be the evolutionary root of eukaryotes, implying that eukaryotes are members of the domain Archaea.[10]

While the features of Asgard archaea do not directly rule out the three-domain system,[11][12] the notion that eukaryotes originated from archaea and thus belong to Archaea has been strengthened by genetic and proteomic studies.[13] 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 contain genes that code for multiple such proteins, indicating that "eukaryotic signature proteins" originated in archaea.[3]

Background

Classification of life into two main divisions is not a new concept, with the first such proposal by French biologist Édouard Chatton in 1938. Chatton distinguished organisms into:

  1. Procaryotes (including bacteria)
  2. Eucaryotes (including protozoans)[14]

These were later named empires, and Chatton's classification as the two-empire system.[15] Chatton used the name Eucaryotes only for protozoans, excluded other eukaryotes, and published in limited circulation so that his work was not recognised. His classification was rediscovered by Canadian bacteriologist Roger Yates Stanier of the University of California in Berkeley in 1961 while at the Pasteur Institute in Paris.[14] The next year, Stanier and his colleague Cornelis Bernardus van Niel published in Archiv für Mikrobiologie (now Archives of Microbiology) Chatton's classification with Eucaryotes eloborated to include higher algae, protozoans, fungi, plants and animals.[16] It became a popular system of classification, as John O. Corliss wrote in 1986: "[The] Chatton-Stanier concept of a kingdom (better, superkingdom) Prokaryota for bacteria (in the broadest sense) and a second superkingdom Eukaryota for all other organisms has been widely accepted with enthusiasm."[17]

In 1977, Carl Woese and George E. Fox classified prokaryotes into two groups (kingdoms), Archaebacteria (for methanogens, the first known archaea) and Eubacteria, based on their 16S ribosomal RNA (16S rRNA) genes.[18] In 1984, James A. Lake, Michael W. Clark, Eric Henderson, and Melanie Oakes of the University of California, Los Angeles described what was known as "a group of sulfur-dependent bacteria" as a new group of organisms called eocytes (for "dawn cells") and created a new kingdom Eocyta. With it they proposed the existence of four kingdoms, based on the structure and composition of the ribosomal subunits, namely Archaebacteria, Eubacteria, Eukaryote and Eocyta [19] Lake further analysed the rRNA sequences of the four groups and suggested that eukaryotes originated from eocytes, and not archaebacteria, as was generally assumed.[20] This was the basis of the eocyte hypothesis.[6] In 1988, he proposed the division of all life forms into two taxonomic groups:[5]

  1. Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes)
  2. Parkaryotes (that consist of eubacteria and archaea such as halobacteria and methanogens[21]

In 1990, Woese, Otto Kandler and Mark Wheelis showed that archaea are distinct group of organisms and that eocytes (renamed Crenarchaeota as a phylum of Archaea[22] but corrected as Thermoproteota in 2021[23]) are Archaea. They introduced the major division of life into the three-domain system comprising domain Eucarya, domain Bacteria and domain Archaea.[24] With a number of revisions of details and discoveries of several new archaea lineages, Woese's classification gradually gained acceptance as "arguably the best-developed and most widely-accepted scientific hypotheses [with the five-kingdom classification] regarding the evolutionary history of life."[25]

The three-domain concept did not, however, resolve the issues with the relationship between archaea and eukaryotes.[12][26] As Ford Doolittle, then at the Dalhousie University, put it in 2020: "[The] three-domain tree wrongly represents evolutionary relationships, presenting a misleading view about how eukaryotes evolved from prokaryotes. The three-domain tree does recognize a specific archaeal–eukaryotic affinity, but it would have the latter arising independently, not from within, the former."[4]

Concept

The two-domain system relies mainly on two key concepts that define eukaryotes as members of the domain Archaea and not as a separate domain: eukaryotes originated within Archaea, and Asgards represent the origin of eukaryotes.[27][28]

Eukaryotes evolved from archaea

The three-domain system presumes that eukaryotes are more closely related to archaea than to bacteria and are sister group to archaea, thus, it treats them as separate domain.[29] As more new archaea were discovered in the early 2000s, this distinction became doubtful as eukaryotes became deeply nested within archaea. The origin of eukaryotes from archaea, meaning the two are of the same group, came to be supported by studies based on ribosome protein sequencing and phylogenetic analyses in 2004.[30][31] Phylogenomic analysis of about 6000 gene sets from 185 bacterial, archaeal and eukaryotic genomes in 2007 also suggested origin of eukaryotes from Euryarchaeota (specifically the Thermoplasmatales).[32]

In 2008, researchers from Natural History Museum, London and Newcastle University reported a comprehensive analysis of 53 genes from archaea, bacteria and eukaryotes that included essential components of the nucleic acid replication, transcription, and translation machineries. The conclusion was that eukaryotes evolved from archaea, specifically Crenarchaeota (eocytes) and the results "favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life."[26] A study around the same time also found several genes common to eukaryotes and Crenarchaeota.[33] These accumulating evidences support the two-domain system.[22]

One of the distinctions of the domain Eukarya in the three-domain system is that eukaryotes have unique proteins such as actin (cytoskeletal microfilament involved in cell motility), tubulin (component of the large cytoskeleton, microtubule) and the ubiquitin system (protein degradation and recycling) that are not found in prokaryotes. However, these so-called "eukaryotic signature proteins"[3] are encoded in genomes of TACK (comprising the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) archaea, but not encoded in other archaea genomes.[22] The first eukaryotic proteins identified in Crenarchaeota were actin and actin-related proteins (Arp) 2 and 3, perhaps explaining the origin of eukaryotes by symbiogenic phagocytosis, in which an ancient archaeal host had an actin based mechanism by which to envelop other cells, like protomitochondrial bacteria.[34]

Tubulin-like proteins named artubulins are found in the genomes of several ammonium-oxidising Thaumarchaeota.[35] Endosomal sorting complexes, required for transport (ESCRT III), involved in eukaryotic cell division, are found in all TACK groups.[36] The ESCRT-III-like proteins constitute the primary cell division system in these archaea.[37][38] Genes encoding the ubiquitin system are known from multiple genomes of Aigarchaeota.[39] Ubiquitin-related protein called Urm1 is also present in Crenarchaeota.[40] DNA replication system (GINS proteins) in Crenarchaeota and Halobacteria are similar to the CMG (CDC45, MCM, GINS) complex of eukaryotes.[41] The presence of these eukaryotic proteins in archaea indicates their direct relationship and that eukaryotes emerged from archaea.[22][42]

Asgards are the last eukaryotic common ancestor

The discovery of Asgard, described as "eukaryote-like archaea",[43] in 2012[44][45] and the following phylogenetic analyses have strengthened the two-domain view of life.[46] Asgard Archaea called Lokiarchaeota contain even more eukaryotic protein-genes than the TACK group. Initial genetic analysis and later reanalysis showed that out of over 31 selected eukaryotic genes in the archaea, 75% of them directly support eukaryote-archaea grouping, meaning a single domain of Archaea including eukaryotes;[47][48] although the findings did not completely rule out the three-domain system.[49]

As more Asgard groups were subsequently discovered including Thorarchaeota, Odinarchaeota and Heimdallarchaeota, their relationships with eukaryotes became better established. Phylogenetic analyses using ribosomal RNA genes indicated that eukaryotes stemmed from Asgards, and that Heimdallarchaeota are the closest relatives of eukaryotes.[9][50] Eukaryotic origin from Heimdallarchaeota is also supported by phylogenomic study in 2020.[13] A new group of Asgard found in 2021 (provisionally named Wukongarchaeota) also indicated a deep root for eukaryotic origin.[51] A report in 2022 of another Asgard, named Njordarchaeota, indicates that Heimdallarchaeota-Wukongarchaeota branch is possibly the origin group for eukaryotes.[52]

The Asgards contain at least 80 genes for eukaryotic signature proteins.[53] In addition to actin, tubulin, ubiquitin and ESCRT proteins found in TACK archaea, Asgards contain functional genes for several other eukaryotic proteins such as profilins,[54] ubiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins),[55] membrane-trafficking systems (such as Sec23/24 and TRAPP domains), a variety of small GTPases[46] (including Gtr/Rag family GTPase orthologues[56]), and gelsolins.[57] Although this information do not completely resolve the three-domain and two-domain controversies,[43] they are generally considered to favour the two-domain system.[3][13][58]

Classification

The two-domain system defines classification of all known cellular life forms into two domains: Bacteria and Archaea. It overrides the domain Eukaryota recognised in the three-domain classification as one of the main domains. In contrast to the eocyte hypothesis, which proposed two major groups of life (similar to domains) and posited that archaea could be divided to both bacterial and eukaryotic groups, it merged archaea and eukaryotes into a single domain, bacteria entirely in a separate domain.[4]

Domain Bacteria

It consists of all bacteria, which are prokaryotes (lacking nucleus), thus, Domain Bacteria is made up solely of prokaryotic organisms.[59][60] Some examples are:

Domain Archaea

It comprises both prokaryotic and eukaryotic organisms.[65]

Archaea

Archaea are prokaryotic organisms, some examples are:

  • All methanogens – which produce the gas methane.
  • Most halophiles – which live in very salty water.
  • Most thermoacidophiles – which live in acidic high-temperature water.

Eukarya

Eukaryotes have a nucleus in their cells, and include:

  • Protists – many unicellular eukaryotes including malarial parasites, amoeba, and diatoms.[66]
  • Kingdom Fungi – multicellular eukaryotes such as mushroom, yeast, and mould.
  • Kingdom Plantae – all plants.
  • Kingdom Animalia – all animals.

References

  1. ↑ Bolshoy, Alexander; Volkovich, Zeev (Vladimir); Kirzhner, Valery; Barzily, Zeev (2010), "Biological Classification", Genome Clustering, Studies in Computational Intelligence (Berlin, Heidelberg: Springer Berlin Heidelberg) 286: pp. 17–22, doi:10.1007/978-3-642-12952-0_2, ISBN 978-3-642-12951-3, http://link.springer.com/10.1007/978-3-642-12952-0_2, 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. PMID 25964353. Bibcode: 2015PNAS..112.6670R. 
  3. ↑ 3.0 3.1 3.2 3.3 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?" (in en). Trends in Microbiology 30 (5): 421–431. doi:10.1016/j.tim.2021.11.003. PMID 34863611. https://linkinghub.elsevier.com/retrieve/pii/S0966842X21002699. 
  4. ↑ 4.0 4.1 4.2 Doolittle, W. Ford (2020). "Evolution: Two Domains of Life or Three?" (in en). Current Biology 30 (4): R177–R179. doi:10.1016/j.cub.2020.01.010. PMID 32097647. 
  5. ↑ 5.0 5.1 Lake, James A. (1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature 331 (6152): 184–186. doi:10.1038/331184a0. PMID 3340165. Bibcode: 1988Natur.331..184L. 
  6. ↑ 6.0 6.1 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. PMID 19091952. Bibcode: 2008PNAS..10520049A. 
  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. https://pubmed.ncbi.nlm.nih.gov/17187354. 
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  9. ↑ 9.0 9.1 Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W.; Anantharaman, Karthik et al. (2017). "Asgard archaea illuminate the origin of eukaryotic cellular complexity" (in En). Nature 541 (7637): 353–358. doi:10.1038/nature21031. PMID 28077874. Bibcode: 2017Natur.541..353Z. https://escholarship.org/content/qt0qh5400s/qt0qh5400s.pdf?t=pgp8bj. 
  10. ↑ Eme, Laura; Spang, Anja; Lombard, Jonathan; Stairs, Courtney W.; Ettema, Thijs J. G. (10 November 2017). "Archaea and the origin of eukaryotes" (in En). Nature Reviews Microbiology 15 (12): 711–723. doi:10.1038/nrmicro.2017.133. ISSN 1740-1534. PMID 29123225. https://zenodo.org/record/3451113. 
  11. ↑ Da Cunha, Violette; Gaia, Morgan; Nasir, Arshan; Forterre, Patrick (2018). "Asgard archaea do not close the debate about the universal tree of life topology" (in en). PLOS Genetics 14 (3): e1007215. doi:10.1371/journal.pgen.1007215. PMID 29596428. 
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  29. ↑ Eme, Laura; Spang, Anja; Lombard, Jonathan; Stairs, Courtney W.; Ettema, Thijs J. G. (2017). "Archaea and the origin of eukaryotes". Nature Reviews Microbiology 15 (12): 711–723. doi:10.1038/nrmicro.2017.133. PMID 29123225. https://pubmed.ncbi.nlm.nih.gov/29123225. 
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  40. ↑ Makarova, Kira S.; Koonin, Eugene V. (2010). "Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis". Archaea 2010: 710303. doi:10.1155/2010/710303. PMID 20936112. 
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  43. ↑ 43.0 43.1 Fournier, Gregory P.; Poole, Anthony M. (2018). "A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree". Frontiers in Microbiology 9: 1896. doi:10.3389/fmicb.2018.01896. PMID 30158917. 
  44. ↑ Jørgensen, Steffen Leth; Hannisdal, Bjarte; Lanzen, Anders; Baumberger, Tamara; Flesland, Kristin; Fonseca, Rita; Øvreås, Lise; Steen, Ida H et al. (September 5, 2012). "Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge". PNAS 109 (42): E2846–55. doi:10.1073/pnas.1207574109. PMID 23027979. 
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  47. ↑ Da Cunha, Violette; Gaia, Morgan; Gadelle, Daniele; Nasir, Arshan; Forterre, Patrick (2017). "Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes". PLOS Genetics 13 (6): e1006810. doi:10.1371/journal.pgen.1006810. PMID 28604769. 
  48. ↑ Da Cunha, Violette; Gaïa, Morgan; Forterre, Patrick (2022). "The expanding Asgard archaea and their elusive relationships with Eukarya" (in en). mLife 1 (1): 3–12. doi:10.1002/mlf2.12012. 
  49. ↑ 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. ISSN 1553-7404. PMID 29596428. 
  50. ↑ Spang, Anja; Eme, Laura; Saw, Jimmy H.; Caceres, Eva F.; Zaremba-Niedzwiedzka, Katarzyna; Lombard, Jonathan; Guy, Lionel; Ettema, Thijs J. G. (2018). "Asgard archaea are the closest prokaryotic relatives of eukaryotes". PLOS Genetics 14 (3): e1007080. doi:10.1371/journal.pgen.1007080. PMID 29596421. 
  51. ↑ Liu, Yang; Makarova, Kira S.; Huang, Wen-Cong; Wolf, Yuri I.; Nikolskaya, Anastasia N.; Zhang, Xinxu; Cai, Mingwei; Zhang, Cui-Jing et al. (2021). "Expanded diversity of Asgard archaea and their relationships with eukaryotes" (in en). Nature 593 (7860): 553–557. doi:10.1038/s41586-021-03494-3. ISSN 0028-0836. PMID 33911286. Bibcode: 2021Natur.593..553L. http://www.nature.com/articles/s41586-021-03494-3. 
  52. ↑ Xie, Ruize; Wang, Yinzhao; Huang, Danyue; Hou, Jialin; Li, Liuyang; Hu, Haining; Zhao, Xiaoxiao; Wang, Fengping (2022). "Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes" (in en). Science China Life Sciences 65 (4): 818–829. doi:10.1007/s11427-021-1969-6. PMID 34378142. https://link.springer.com/10.1007/s11427-021-1969-6. 
  53. ↑ López-García, Purificación; Moreira, David (2020). "Cultured Asgard Archaea Shed Light on Eukaryogenesis" (in en). Cell 181 (2): 232–235. doi:10.1016/j.cell.2020.03.058. PMID 32302567. 
  54. ↑ Akıl, Caner; Robinson, Robert C. (2018). "Genomes of Asgard archaea encode profilins that regulate actin". Nature 562 (7727): 439–443. doi:10.1038/s41586-018-0548-6. PMID 30283132. Bibcode: 2018Natur.562..439A. https://pubmed.ncbi.nlm.nih.gov/30283132. 
  55. ↑ Hennell James, Rory; Caceres, Eva F.; Escasinas, Alex; Alhasan, Haya; Howard, Julie A.; Deery, Michael J.; Ettema, Thijs J. G.; Robinson, Nicholas P. (2017). "Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon". Nature Communications 8 (1): 1120. doi:10.1038/s41467-017-01162-7. ISSN 2041-1723. PMID 29066714. Bibcode: 2017NatCo...8.1120H. 
  56. ↑ Klinger, Christen M.; Spang, Anja; Dacks, Joel B.; Ettema, Thijs J. G. (2016). "Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks". Molecular Biology and Evolution 33 (6): 1528–1541. doi:10.1093/molbev/msw034. PMID 26893300. 
  57. ↑ Akıl, Caner; Tran, Linh T.; Orhant-Prioux, Magali; Baskaran, Yohendran; Manser, Edward; Blanchoin, Laurent; Robinson, Robert C. (2020). "Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea" (in en). Proceedings of the National Academy of Sciences 117 (33): 19904–19913. doi:10.1073/pnas.2009167117. PMID 32747565. Bibcode: 2020PNAS..11719904A. 
  58. ↑ Liu, Yang; Makarova, Kira S.; Huang, Wen-Cong; Wolf, Yuri I.; Nikolskaya, Anastasia N.; Zhang, Xinxu; Cai, Mingwei; Zhang, Cui-Jing et al. (2021). "Expanded diversity of Asgard archaea and their relationships with eukaryotes" (in en). Nature 593 (7860): 553–557. doi:10.1038/s41586-021-03494-3. PMID 33911286. Bibcode: 2021Natur.593..553L. https://www.nature.com/articles/s41586-021-03494-3. 
  59. ↑ Hugenholtz, Philip (2002). "Exploring prokaryotic diversity in the genomic era" (in en). Genome Biology 3 (2): reviews0003.1. doi:10.1186/gb-2002-3-2-reviews0003. PMID 11864374. 
  60. ↑ Oren, Aharon (2004). Godfray, H. C. J.; Knapp, S.. eds. "Prokaryote diversity and taxonomy: current status and future challenges" (in en). Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359 (1444): 623–638. doi:10.1098/rstb.2003.1458. PMID 15253349. 
  61. ↑ Moore, Kelsey R.; Magnabosco, Cara; Momper, Lily; Gold, David A.; Bosak, Tanja; Fournier, Gregory P. (2019). "An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids". Frontiers in Microbiology 10: 1612. doi:10.3389/fmicb.2019.01612. ISSN 1664-302X. PMID 31354692. 
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  64. ↑ Woodruff, H. Boyd (2014). "Selman A. Waksman, winner of the 1952 Nobel Prize for physiology or medicine". Applied and Environmental Microbiology 80 (1): 2–8. doi:10.1128/AEM.01143-13. PMID 24162573. Bibcode: 2014ApEnM..80....2W. 
  65. ↑ Schleifer, Karl Heinz (2009). "Classification of Bacteria and Archaea: Past, present and future" (in en). Systematic and Applied Microbiology 32 (8): 533–542. doi:10.1016/j.syapm.2009.09.002. PMID 19819658. https://linkinghub.elsevier.com/retrieve/pii/S0723202009001258. 
  66. ↑ Adl, Sina M.; Simpson, Alastair G. B.; Farmer, Mark A.; Andersen, Robert A.; Anderson, O. Roger; Barta, John R.; Bowser, Samuel S.; Brugerolle, Guy et al. (2005). "The new higher level classification of eukaryotes with emphasis on the taxonomy of protists". The Journal of Eukaryotic Microbiology 52 (5): 399–451. doi:10.1111/j.1550-7408.2005.00053.x. PMID 16248873. https://pubmed.ncbi.nlm.nih.gov/16248873. 



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