Two-domain system
The two-domain system is a
While the features of Asgard archaea do not completely rule out the three-domain system,[11][12] the notion that eukaryotes originated within 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, Asgard archaea contain genes that code for multiple such proteins.[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:
- Procaryotes (including bacteria)
- Eucaryotes (including protozoans)[14]
These were later named empires, and Chatton's classification as the
In 1977,
- Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes)
- Parkaryotes (that consist of eubacteria and archaea such as 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.
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
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
The Asgards contain at least 80 genes for eukaryotic signature proteins.
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:
- Cyanobacteria – photosynthesising bacteria related to the plastids of eukaryotes.[61]
- Gram-negative bacteria involved in human diseases like syphilis and lyme disease.[62]
- Gram-positive bacteria including Streptomyces species from which several antibiotics are derived including streptomycin, neomycin, bottromycins and chloramphenicol.[63][64]
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– eukaryotes such as mushroom, yeast, and mould.
- Kingdom Plantae– all plants.
- Kingdom Animalia– all animals.
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