Two-domain system

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. Prokaryotes (including bacteria)
2. Eukaryotes (including protozoans){{Cite journal |last=Katscher |first=Friedrich |date=2004 |title=The History of the Terms Prokaryotes and Eukaryotes |url=https://linkinghub.elsevier.com/retrieve/pii/S1434461004701820 |journal=Protist |language=en |volume=155 |issue=2 |pages=257–263 |doi=10.1078/143446104774199637|pmid=15305800 }}

These were later named empires, and Chatton's classification as the two-empire system.{{Cite journal |last=Mayr |first=Ernst |date=1998 |title=Two empires or three? |journal=Proceedings of the National Academy of Sciences |language=en |volume=95 |issue=17 |pages=9720–9723 |doi=10.1073/pnas.95.17.9720 |pmc=33883 |pmid=9707542|bibcode=1998PNAS...95.9720M |doi-access=free }} 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. 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.{{Cite journal |last1=Stanier |first1=R. Y. |last2=Van Niel |first2=C. B. |date=1962 |title=The concept of a bacterium |url=https://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol497_F13/papers/Stanier_archmicro62.pdf |journal=Archiv für Mikrobiologie |volume=42 |issue=1 |pages=17–35 |doi=10.1007/BF00425185 |pmid=13916221|bibcode=1962ArMic..42...17S |s2cid=29859498 }} 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."{{Cite journal |last=Corliss |first=John O. |date=1986 |title=The Kingdoms of Organisms: From a Microscopist's Point of View |url=https://www.jstor.org/stable/3226544 |journal=Transactions of the American Microscopical Society |volume=105 |issue=1 |pages=1–10 |doi=10.2307/3226544 |jstor=3226544}}

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.{{cite journal |vauthors=Woese CR, Fox GE |date=November 1977 |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=74 |issue=11 |pages=5088–90 |bibcode=1977PNAS...74.5088W |doi=10.1073/pnas.74.11.5088 |pmc=432104 |pmid=270744 |doi-access=free}} 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 {{cite journal |last1=Lake |first1=James A. |last2=Henderson |first2=Eric |last3=Oakes |first3=Melanie |last4=Clark |first4=Michael W. |date=June 1984 |title=Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes |journal=PNAS |volume=81 |issue=12 |pages=3786–3790 |bibcode=1984PNAS...81.3786L |doi=10.1073/pnas.81.12.3786 |pmc=345305 |pmid=6587394 |doi-access=free}} Lake further analysed the rRNA sequences of the four groups and suggested that eukaryotes originated from eocytes, and not archaebacteria, as was generally assumed.{{Cite journal |last=Lake |first=J.A. |date=1987 |title=Prokaryotes and Archaebacteria Are Not Monophyletic: Rate Invariant Analysis of rRNA Genes Indicates That Eukaryotes and Eocytes Form a Monophyletic Taxon |url=http://symposium.cshlp.org/cgi/doi/10.1101/SQB.1987.052.01.091 |journal=Cold Spring Harbor Symposia on Quantitative Biology |language=en |volume=52 |pages=839–846 |doi=10.1101/SQB.1987.052.01.091 |pmid=3454292 |issn=0091-7451}} This was the basis of the eocyte hypothesis. In 1988, he proposed the division of all life forms into two taxonomic groups:

1. Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes)
2. Parkaryotes{{NoteTag|not to be confused with parakaryote|name=Note}} (that consist of eubacteria and archaea such as halobacteria and methanogens){{Cite journal |last=Lake |first=James A. |date=1991 |title=Tracing origins with molecular sequences: metazoan and eukaryotic beginnings |url=https://linkinghub.elsevier.com/retrieve/pii/096800049190020V |journal=Trends in Biochemical Sciences |language=en |volume=16 |issue=2 |pages=46–50 |doi=10.1016/0968-0004(91)90020-V|pmid=1858129 }}

In 1990, Woese, Otto Kandler, and Mark Wheelis showed that archaea are a distinct group of organisms and that eocytes (renamed Crenarchaeota as a phylum of Archaea{{Cite journal |last=Koonin |first=Eugene V. |date=2015 |title=Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=370 |issue=1678 |pages=20140333 |doi=10.1098/rstb.2014.0333 |pmc=4571572 |pmid=26323764}} but corrected as Thermoproteota in 2021{{Cite journal |last1=Oren |first1=Aharon |last2=Garrity |first2=George M. |date=2021 |title=Valid publication of the names of forty-two phyla of prokaryotes |journal=International Journal of Systematic and Evolutionary Microbiology |volume=71 |issue=10 |pages=Online |doi=10.1099/ijsem.0.005056 |issn=1466-5034 |pmid=34694987|s2cid=239887308 |doi-access=free }}) are Archaea. They introduced the major division of life into the three-domain system comprising domain Eucarya, domain Bacteria, and domain Archaea.{{cite journal |vauthors=Woese CR, Kandler O, Wheelis ML |date=June 1990 |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=87 |issue=12 |pages=4576–9 |bibcode=1990PNAS...87.4576W |doi=10.1073/pnas.87.12.4576 |pmc=54159 |pmid=2112744 |doi-access=free}} 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."{{Cite journal |last=Case |first=Emily |date=2008 |title=Teaching Taxonomy: How Many Kingdoms? |url=https://bioone.org/journals/the-american-biology-teacher/volume-70/issue-8/0002-7685_2008_70_472_TTHMK_2.0.CO_2/Teaching-Taxonomy-How-Many-Kingdoms/10.1662/0002-7685(2008)70[472:TTHMK]2.0.CO;2.full |journal=The American Biology Teacher |volume=70 |issue=8 |pages=472–477 |doi=10.1662/0002-7685(2008)70[472:TTHMK]2.0.CO;2|s2cid=198969439 }}

The three-domain concept did not, however, resolve the issues with the relationship between Archaea and eukaryotes.{{Cite journal |last1=Cox |first1=Cymon J. |last2=Foster |first2=Peter G. |last3=Hirt |first3=Robert P. |last4=Harris |first4=Simon R. |last5=Embley |first5=T. Martin |date=2008 |title=The archaebacterial origin of eukaryotes |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=51 |pages=20356–20361 |doi=10.1073/pnas.0810647105 |pmc=2629343 |pmid=19073919|bibcode=2008PNAS..10520356C |doi-access=free }} 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."

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 promethearchaea represent the origin of eukaryotes.{{Cite journal |last1=MacLeod |first1=Fraser |last2=Kindler |first2=Gareth S. |last3=Wong |first3=Hon Lun |last4=Chen |first4=Ray |last5=Burns |first5=Brendan P. |date=2019 |title=Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes |journal=AIMS Microbiology |volume=5 |issue=1 |pages=48–61 |doi=10.3934/microbiol.2019.1.48 |pmc=6646929 |pmid=31384702}}{{Cite journal |last1=Jüttner |first1=Michael |last2=Ferreira-Cerca |first2=Sébastien |date=2022 |title=Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis |journal=Molecular Biology and Evolution |volume=39 |issue=4 |pages=msac054 |doi=10.1093/molbev/msac054 |pmc=8997704 |pmid=35275997}}

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.{{Cite journal |last1=Eme |first1=Laura |last2=Spang |first2=Anja |last3=Lombard |first3=Jonathan |last4=Stairs |first4=Courtney W. |last5=Ettema |first5=Thijs J. G. |date=2017 |title=Archaea and the origin of eukaryotes |url=https://pubmed.ncbi.nlm.nih.gov/29123225 |journal=Nature Reviews Microbiology |volume=15 |issue=12 |pages=711–723 |doi=10.1038/nrmicro.2017.133 |pmid=29123225|s2cid=8666687 }} 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 larger group, came to be supported by studies based on ribosome protein sequencing and phylogenetic analyses in 2004.{{Cite journal |last1=Vishwanath |first1=Prashanth |last2=Favaretto |first2=Paola |last3=Hartman |first3=Hyman |last4=Mohr |first4=Scott C. |last5=Smith |first5=Temple F. |date=2004 |title=Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes |url=https://pubmed.ncbi.nlm.nih.gov/15522791 |journal=Molecular Phylogenetics and Evolution |volume=33 |issue=3 |pages=615–625 |doi=10.1016/j.ympev.2004.07.003 |pmid=15522791|bibcode=2004MolPE..33..615V }}{{Cite journal |last1=Rivera |first1=Maria C. |last2=Lake |first2=James A. |date=2004 |title=The ring of life provides evidence for a genome fusion origin of eukaryotes |url=http://www.nature.com/articles/nature02848 |journal=Nature |language=en |volume=431 |issue=7005 |pages=152–155 |doi=10.1038/nature02848 |pmid=15356622|bibcode=2004Natur.431..152R |s2cid=4349149 }} Phylogenomic analysis of about 6000 gene sets from 185 bacterial, archaeal, and eukaryotic genomes in 2007 also suggested the origin of eukaryotes from Methanobacteriota (specifically the Thermoplasmatales).{{Cite journal |last1=Pisani |first1=Davide |last2=Cotton |first2=James A. |last3=McInerney |first3=James O. |date=2007 |title=Supertrees disentangle the chimerical origin of eukaryotic genomes |journal=Molecular Biology and Evolution |volume=24 |issue=8 |pages=1752–1760 |doi=10.1093/molbev/msm095 |pmid=17504772|doi-access=free }}

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." A study around the same time also found several genes common to eukaryotes and Crenarchaeota.{{Cite journal |last1=Yutin |first1=Natalya |last2=Makarova |first2=Kira S. |last3=Mekhedov |first3=Sergey L. |last4=Wolf |first4=Yuri I. |last5=Koonin |first5=Eugene V. |date=2008 |title=The deep archaeal roots of eukaryotes |journal=Molecular Biology and Evolution |volume=25 |issue=8 |pages=1619–1630 |doi=10.1093/molbev/msn108 |pmc=2464739 |pmid=18463089}} These accumulating evidences support the two-domain system.

In 2019, research led by Gergely J. Szöllősi assistant professor at ELTE has also concluded that two domains are the correct system. The studies conducted used simulations of more than 3,000 gene families. The study concluded that eukaryotes probably evolved from a bacterium entering an Promethearchaeati host (probably from the phylum Heimdallarchaeota).{{Cite journal |last1=Williams |first1=Tom A. |last2=Cox |first2=Cymon J. |last3=Foster |first3=Peter G. |last4=Szöllősi |first4=Gergely J. |last5=Embley |first5=T. Martin |date=January 2020 |title=Phylogenomics provides robust support for a two-domains tree of life |journal=Nature Ecology & Evolution |language=en |volume=4 |issue=1 |pages=138–147 |doi=10.1038/s41559-019-1040-x |pmid=31819234 |issn=2397-334X|pmc=6942926 }}{{Cite web |date=2019-12-10 |title=Birodalmak visszavágva: az ELTE és a Bristoli Egyetem közös sikere legkorábbi őseink kutatásában |url=https://mta.hu/tudomany_hirei/birodalmak-visszavagva-az-elte-es-a-bristoli-egyetem-kozos-sikere-legkorabbi-oseink-kutatasaban-110182 |access-date=2024-07-25 |website=MTA.hu |language=hu}}{{Cite web |last=Csaba |first=Molnár |date=2019-12-13 |title=Magyar kutató írja át az evolúció történetét |url=https://index.hu/techtud/2019/12/13/magyar_kutato_miatt_kell_alapvetoen_atrajzolni_az_elovilag_torzsfajat/ |access-date=2024-07-25 |website=index.hu |language=hu}}

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" are encoded in genomes of Thermoproteati (comprising the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) archaea, but not encoded in other archaea genomes. 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.{{Cite journal |last1=Yutin |first1=Natalya |last2=Wolf |first2=Maxim Y. |last3=Wolf |first3=Yuri I. |last4=Koonin |first4=Eugene V. |date=2009 |title=The origins of phagocytosis and eukaryogenesis |journal=Biology Direct |volume=4 |pages=9 |doi=10.1186/1745-6150-4-9 |pmc=2651865 |pmid=19245710 |doi-access=free }}

Tubulin-like proteins named artubulins are found in the genomes of several ammonium-oxidising Thaumarchaeota.{{Cite journal |last1=Yutin |first1=Natalya |last2=Koonin |first2=Eugene V. |date=2012 |title=Archaeal origin of tubulin |journal=Biology Direct |volume=7 |pages=10 |doi=10.1186/1745-6150-7-10 |pmc=3349469 |pmid=22458654 |doi-access=free }} Endosomal sorting complexes, required for transport (ESCRT III), involved in eukaryotic cell division, are found in all Thermoproteati groups.{{Cite book |last1=Samson |first1=Rachel Y. |last2=Dobro |first2=Megan J. |last3=Jensen |first3=Grant J. |last4=Bell |first4=Stephen D. |title=Prokaryotic Cytoskeletons |chapter=The Structure, Function and Roles of the Archaeal ESCRT Apparatus |series=Subcellular Biochemistry |date=2017 |chapter-url=https://pubmed.ncbi.nlm.nih.gov/28500532 |volume=84 |pages=357–377 |doi=10.1007/978-3-319-53047-5_12 |pmid=28500532|isbn=978-3-319-53045-1 }} The ESCRT-III-like proteins constitute the primary cell division system in these archaea.{{Cite journal |last1=Pelve |first1=Erik A. |last2=Lindås |first2=Ann-Christin |last3=Martens-Habbena |first3=Willm |last4=de la Torre |first4=José R. |last5=Stahl |first5=David A. |last6=Bernander |first6=Rolf |date=2011 |title=Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus |journal=Molecular Microbiology |volume=82 |issue=3 |pages=555–566 |doi=10.1111/j.1365-2958.2011.07834.x |pmid=21923770|s2cid=1202516 |doi-access=free }}{{Cite journal |last1=Dobro |first1=Megan J. |last2=Samson |first2=Rachel Y. |last3=Yu |first3=Zhiheng |last4=McCullough |first4=John |last5=Ding |first5=H. Jane |last6=Chong |first6=Parkson Lee-Gau |last7=Bell |first7=Stephen D. |last8=Jensen |first8=Grant J. |date=2013 |title=Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggests that spiraling filaments are involved in membrane scission |journal=Molecular Biology of the Cell |volume=24 |issue=15 |pages=2319–2327 |doi=10.1091/mbc.E12-11-0785 |pmc=3727925 |pmid=23761076}} Genes encoding the ubiquitin system are known from multiple genomes of Aigarchaeota.{{Cite journal |last1=Grau-Bové |first1=Xavier |last2=Sebé-Pedrós |first2=Arnau |last3=Ruiz-Trillo |first3=Iñaki |date=2015 |title=The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin |journal=Molecular Biology and Evolution |volume=32 |issue=3 |pages=726–739 |doi=10.1093/molbev/msu334 |pmc=4327156 |pmid=25525215}} Ubiquitin-related protein called Urm1 is also present in Crenarchaeota.{{Cite journal |last1=Makarova |first1=Kira S. |last2=Koonin |first2=Eugene V. |date=2010 |title=Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis |journal=Archaea |volume=2010 |pages=710303 |doi=10.1155/2010/710303 |pmc=2948915 |pmid=20936112|doi-access=free }} DNA replication system (GINS proteins) in Crenarchaeota and Halobacteria are similar to the CMG (CDC45, MCM, GINS) complex of eukaryotes.{{Cite journal |last1=Makarova |first1=Kira S. |last2=Koonin |first2=Eugene V. |last3=Kelman |first3=Zvi |date=2012 |title=The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes |journal=Biology Direct |volume=7 |pages=7 |doi=10.1186/1745-6150-7-7 |pmc=3307487 |pmid=22329974 |doi-access=free }} The presence of these eukaryotic proteins in Archaea indicates their direct relationship and that eukaryotes emerged from Archaea.{{Cite journal |last1=Stairs |first1=Courtney W. |last2=Ettema |first2=Thijs J.G. |date=2020 |title=The Archaeal Roots of the Eukaryotic Dynamic Actin Cytoskeleton |journal=Current Biology |language=en |volume=30 |issue=10 |pages=R521–R526 |doi=10.1016/j.cub.2020.02.074|pmid=32428493 |s2cid=218710903 |doi-access=free |bibcode=2020CBio...30.R521S }}

The discovery of Promethearchaeati, described as "eukaryote-like archaea",{{Cite journal |last1=Fournier |first1=Gregory P. |last2=Poole |first2=Anthony M. |date=2018 |title=A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree |journal=Frontiers in Microbiology |volume=9 |pages=1896 |doi=10.3389/fmicb.2018.01896 |pmc=6104171 |pmid=30158917|doi-access=free }} in 2012{{cite journal |last1=Jørgensen |first1=Steffen Leth |last2=Hannisdal |first2=Bjarte |last3=Lanzen |first3=Anders |last4=Baumberger |first4=Tamara |last5=Flesland |first5=Kristin |last6=Fonseca |first6=Rita |last7=Øvreås |first7=Lise |last8=Steen |first8=Ida H |last9=Thorseth |first9=Ingunn H |last10=Pedersen |first10=Rolf B |last11=Schleper |first11=Christa |date=September 5, 2012 |title=Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge |journal=PNAS |volume=109 |issue=42 |pages=E2846–55 |doi=10.1073/pnas.1207574109 |pmc=3479504 |pmid=23027979 |doi-access=free}}{{cite journal |last1=Jørgensen |first1=Steffen Leth |last2=Thorseth |first2=Ingunn H |last3=Pedersen |first3=Rolf B |last4=Baumberger |first4=Tamara |last5=Schleper |first5=Christa |date=October 4, 2013 |title=Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge |journal=Frontiers in Microbiology |volume=4 |pages=299 |doi=10.3389/fmicb.2013.00299 |pmc=3790079 |pmid=24109477 |doi-access=free}} and the following phylogenetic analyses have strengthened the two-domain view of life.{{Cite journal |last1=Spang |first1=Anja |last2=Saw |first2=Jimmy H. |last3=Jørgensen |first3=Steffen L. |last4=Zaremba-Niedzwiedzka |first4=Katarzyna |last5=Martijn |first5=Joran |last6=Lind |first6=Anders E. |last7=Eijk |first7=Roel van |last8=Schleper |first8=Christa |last9=Guy |first9=Lionel |date=2015 |title=Complex archaea that bridge the gap between prokaryotes and eukaryotes |journal=Nature |language=En |volume=521 |issue=7551 |pages=173–179 |bibcode=2015Natur.521..173S |doi=10.1038/nature14447 |pmc=4444528 |pmid=25945739}} Promethearchaea called Lokiarchaeota contain even more eukaryotic protein-genes than the Thermoproteati kingdom. 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;{{Cite journal |last1=Da Cunha |first1=Violette |last2=Gaia |first2=Morgan |last3=Gadelle |first3=Daniele |last4=Nasir |first4=Arshan |last5=Forterre |first5=Patrick |date=2017 |title=Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes |journal=PLOS Genetics |volume=13 |issue=6 |pages=e1006810 |doi=10.1371/journal.pgen.1006810 |pmc=5484517 |pmid=28604769 |doi-access=free }}{{Cite journal |last1=Da Cunha |first1=Violette |last2=Gaïa |first2=Morgan |last3=Forterre |first3=Patrick |date=2022 |title=The expanding Asgard archaea and their elusive relationships with Eukarya |journal=mLife |language=en |volume=1 |issue=1 |pages=3–12 |doi=10.1002/mlf2.12012|s2cid=247689333 |doi-access=free |pmid=38818326 |pmc=10989751 }} although the findings did not completely rule out the three-domain system.{{Cite journal |last1=Da Cunha |first1=Violette |last2=Gaia |first2=Morgan |last3=Nasir |first3=Arshan |last4=Forterre |first4=Patrick |date=2018 |title=Asgard archaea do not close the debate about the universal tree of life topology |journal=PLOS Genetics |volume=14 |issue=3 |pages=e1007215 |doi=10.1371/journal.pgen.1007215 |issn=1553-7404 |pmc=5875737 |pmid=29596428 |doi-access=free }}

As more Promethearchaeati 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 promethearchaea, and that Heimdallarchaeota are the closest relatives of eukaryotes.{{Cite journal |last1=Spang |first1=Anja |last2=Eme |first2=Laura |last3=Saw |first3=Jimmy H. |last4=Caceres |first4=Eva F. |last5=Zaremba-Niedzwiedzka |first5=Katarzyna |last6=Lombard |first6=Jonathan |last7=Guy |first7=Lionel |last8=Ettema |first8=Thijs J. G. |date=2018 |title=Asgard archaea are the closest prokaryotic relatives of eukaryotes |journal=PLOS Genetics |volume=14 |issue=3 |pages=e1007080 |doi=10.1371/journal.pgen.1007080 |pmc=5875740 |pmid=29596421 |doi-access=free }} Eukaryotic origin from Heimdallarchaeota is also supported by phylogenomic study in 2020. A new group of Promethearchaeati found in 2021 (provisionally named Wukongarchaeota) also indicated a deep root for eukaryotic origin.{{Cite journal |last1=Liu |first1=Yang |last2=Makarova |first2=Kira S. |last3=Huang |first3=Wen-Cong |last4=Wolf |first4=Yuri I. |last5=Nikolskaya |first5=Anastasia N. |last6=Zhang |first6=Xinxu |last7=Cai |first7=Mingwei |last8=Zhang |first8=Cui-Jing |last9=Xu |first9=Wei |last10=Luo |first10=Zhuhua |last11=Cheng |first11=Lei |date=2021 |title=Expanded diversity of Asgard archaea and their relationships with eukaryotes |journal=Nature |language=en |volume=593 |issue=7860 |pages=553–557 |doi=10.1038/s41586-021-03494-3 |pmid=33911286 |bibcode=2021Natur.593..553L |s2cid=233447651 |issn=0028-0836|pmc=11165668 }} A report in 2022 of another Promethearchaeati, named Njordarchaeota, indicates that Heimdallarchaeota-Wukongarchaeota branch is possibly the origin group for eukaryotes.{{Cite journal |last1=Xie |first1=Ruize |last2=Wang |first2=Yinzhao |last3=Huang |first3=Danyue |last4=Hou |first4=Jialin |last5=Li |first5=Liuyang |last6=Hu |first6=Haining |last7=Zhao |first7=Xiaoxiao |last8=Wang |first8=Fengping |date=2022 |title=Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes |url=https://link.springer.com/10.1007/s11427-021-1969-6 |journal=Science China Life Sciences |language=en |volume=65 |issue=4 |pages=818–829 |doi=10.1007/s11427-021-1969-6|pmid=34378142 |s2cid=236977853 }}

The promethearchaea contain at least 80 genes for eukaryotic signature proteins.{{Cite journal |last1=López-García |first1=Purificación |last2=Moreira |first2=David |date=2020 |title=Cultured Asgard Archaea Shed Light on Eukaryogenesis |journal=Cell |language=en |volume=181 |issue=2 |pages=232–235 |doi=10.1016/j.cell.2020.03.058|pmid=32302567 |s2cid=215798394 |doi-access=free }} In addition to actin, tubulin, ubiquitin, and ESCRT proteins found in Thermoproteati archaea, promethearchaea contain functional genes for several other eukaryotic proteins such as profilins,{{Cite journal |last1=Akıl |first1=Caner |last2=Robinson |first2=Robert C. |date=2018 |title=Genomes of Asgard archaea encode profilins that regulate actin |url=https://pubmed.ncbi.nlm.nih.gov/30283132 |journal=Nature |volume=562 |issue=7727 |pages=439–443 |doi=10.1038/s41586-018-0548-6 |pmid=30283132|bibcode=2018Natur.562..439A |s2cid=52917038 }} ubiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins),{{Cite journal |last1=Hennell James |first1=Rory |last2=Caceres |first2=Eva F. |last3=Escasinas |first3=Alex |last4=Alhasan |first4=Haya |last5=Howard |first5=Julie A. |last6=Deery |first6=Michael J. |last7=Ettema |first7=Thijs J. G. |last8=Robinson |first8=Nicholas P. |date=2017 |title=Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon |journal=Nature Communications |volume=8 |issue=1 |pages=1120 |doi=10.1038/s41467-017-01162-7 |issn=2041-1723 |pmc=5654768 |pmid=29066714|bibcode=2017NatCo...8.1120H }} membrane-trafficking systems (such as Sec23/24 and TRAPP domains), a variety of small GTPases (including Gtr/Rag family GTPase orthologues{{Cite journal |last1=Klinger |first1=Christen M. |last2=Spang |first2=Anja |last3=Dacks |first3=Joel B. |last4=Ettema |first4=Thijs J. G. |date=2016 |title=Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks |journal=Molecular Biology and Evolution |volume=33 |issue=6 |pages=1528–1541 |doi=10.1093/molbev/msw034 |pmid=26893300|doi-access=free }}), and gelsolins.{{Cite journal |last1=Akıl |first1=Caner |last2=Tran |first2=Linh T. |last3=Orhant-Prioux |first3=Magali |last4=Baskaran |first4=Yohendran |last5=Manser |first5=Edward |last6=Blanchoin |first6=Laurent |last7=Robinson |first7=Robert C. |date=2020 |title=Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea |journal=Proceedings of the National Academy of Sciences |language=en |volume=117 |issue=33 |pages=19904–19913 |doi=10.1073/pnas.2009167117 |pmc=7444086 |pmid=32747565|bibcode=2020PNAS..11719904A |doi-access=free }} Although this information do not completely resolve the three-domain and two-domain controversies, they are generally considered to favour the two-domain system.{{Cite journal |last1=Liu |first1=Yang |last2=Makarova |first2=Kira S. |last3=Huang |first3=Wen-Cong |last4=Wolf |first4=Yuri I. |last5=Nikolskaya |first5=Anastasia N. |last6=Zhang |first6=Xinxu |last7=Cai |first7=Mingwei |last8=Zhang |first8=Cui-Jing |last9=Xu |first9=Wei |last10=Luo |first10=Zhuhua |last11=Cheng |first11=Lei |date=2021 |title=Expanded diversity of Asgard archaea and their relationships with eukaryotes |journal=Nature |language=en |volume=593 |issue=7860 |pages=553–557 |doi=10.1038/s41586-021-03494-3|pmid=33911286 |bibcode=2021Natur.593..553L |s2cid=233447651 |pmc=11165668 }}

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.

It consists of all bacteria, which are prokaryotes (lacking nucleus), thus, Domain Bacteria is made up solely of prokaryotic organisms.{{Cite journal |last=Hugenholtz |first=Philip |date=2002 |title=Exploring prokaryotic diversity in the genomic era |journal=Genome Biology |language=en |volume=3 |issue=2 |pages=reviews0003.1 |doi=10.1186/gb-2002-3-2-reviews0003 |pmc=139013 |pmid=11864374 |doi-access=free }}{{Cite journal |last=Oren |first=Aharon |date=2004 |editor-last=Godfray |editor-first=H. C. J. |editor2-last=Knapp |editor2-first=S. |title=Prokaryote diversity and taxonomy: current status and future challenges |journal=Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences |language=en |volume=359 |issue=1444 |pages=623–638 |doi=10.1098/rstb.2003.1458 |pmc=1693353 |pmid=15253349}} Some examples are:

• Cyanobacteriota – photosynthesising bacteria related to the plastids of eukaryotes.{{Cite journal |last1=Moore |first1=Kelsey R. |last2=Magnabosco |first2=Cara |last3=Momper |first3=Lily |last4=Gold |first4=David A. |last5=Bosak |first5=Tanja |last6=Fournier |first6=Gregory P. |date=2019 |title=An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids |journal=Frontiers in Microbiology |volume=10 |pages=1612 |doi=10.3389/fmicb.2019.01612 |issn=1664-302X |pmc=6640209 |pmid=31354692|doi-access=free }}
• Spirochaetota – Gram-negative bacteria involved in human diseases like syphilis and lyme disease.{{Cite journal |last1=Seitz |first1=Patrick |last2=Blokesch |first2=Melanie |date=2013 |title=Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria |journal=FEMS Microbiology Reviews |language=en |volume=37 |issue=3 |pages=336–363 |doi=10.1111/j.1574-6976.2012.00353.x|pmid=22928673 |s2cid=30861416 |doi-access=free }}
• Actinomycetota – Gram-positive bacteria including Streptomyces species from which several antibiotics are derived including streptomycin, neomycin, bottromycins and chloramphenicol.{{Cite journal |last=Bibb |first=Mervyn J. |date=2013 |title=Understanding and manipulating antibiotic production in actinomycetes |url=https://pubmed.ncbi.nlm.nih.gov/24256223 |journal=Biochemical Society Transactions |volume=41 |issue=6 |pages=1355–1364 |doi=10.1042/BST20130214 |pmid=24256223}}{{Cite journal |last=Woodruff |first=H. Boyd |date=2014 |title=Selman A. Waksman, winner of the 1952 Nobel Prize for physiology or medicine |journal=Applied and Environmental Microbiology |volume=80 |issue=1 |pages=2–8 |bibcode=2014ApEnM..80....2W |doi=10.1128/AEM.01143-13 |pmc=3911012 |pmid=24162573}}

It comprises both prokaryotic and eukaryotic organisms.{{Cite journal |last=Schleifer |first=Karl Heinz |date=2009 |title=Classification of Bacteria and Archaea: Past, present and future |url=https://linkinghub.elsevier.com/retrieve/pii/S0723202009001258 |journal=Systematic and Applied Microbiology |language=en |volume=32 |issue=8 |pages=533–542 |doi=10.1016/j.syapm.2009.09.002|pmid=19819658 |bibcode=2009SyApM..32..533S }}

;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.{{Cite journal |last1=Adl |first1=Sina M. |last2=Simpson |first2=Alastair G. B. |last3=Farmer |first3=Mark A. |last4=Andersen |first4=Robert A. |last5=Anderson |first5=O. Roger |last6=Barta |first6=John R. |last7=Bowser |first7=Samuel S. |last8=Brugerolle |first8=Guy |last9=Fensome |first9=Robert A. |last10=Fredericq |first10=Suzanne |last11=James |first11=Timothy Y. |date=2005 |title=The new higher level classification of eukaryotes with emphasis on the taxonomy of protists |url=https://pubmed.ncbi.nlm.nih.gov/16248873 |journal=The Journal of Eukaryotic Microbiology |volume=52 |issue=5 |pages=399–451 |doi=10.1111/j.1550-7408.2005.00053.x |pmid=16248873 |s2cid=8060916}}
• Kingdom Fungi – eukaryotes such as mushroom, yeast, and mould; all fungi.
• Kingdom Plantae – all plants.
• Kingdom Animalia – all animals.

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Category:Biological classification

Category:High-level systems of taxonomy

Category:Domains (biology)