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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| Two-domain system | 2/2 | https://en.wikipedia.org/wiki/Two-domain_system | reference | science, encyclopedia | 2026-05-05T09:07:51.348037+00:00 | kb-cron |
=== 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. 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. 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). 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. 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). 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. Tubulin-like proteins named artubulins are found in the genomes of several ammonium-oxidising Thaumarchaeota. Homologs for a unique class of endosomal sorting complexes required for transport (ESCRT) involved in eukaryotic cell division, known as ESCRT-III, are found in all Thermoproteati groups. The ESCRT-III-like proteins constitute the primary cell division system in these archaea. Genes encoding the ubiquitin system are known from multiple genomes of Aigarchaeota. Ubiquitin-related protein called Urm1 is also present in Crenarchaeota. DNA replication system (GINS proteins) in Crenarchaeota and Halobacteria are similar to the CMG (CDC45, MCM, GINS) complex of eukaryotes. The presence of these eukaryotic proteins in Archaea indicates their direct relationship and that eukaryotes emerged from Archaea.
=== Promethearchaea are the last eukaryotic common ancestor === The discovery of Promethearchaeati, described as "eukaryote-like archaea", in 2012 and the following phylogenetic analyses have strengthened the two-domain view of life. 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; although the findings did not completely rule out the three-domain system. 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. 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. A report in 2022 of another Promethearchaeati, named Njordarchaeota, indicates that Heimdallarchaeota-Wukongarchaeota branch is possibly the origin group for eukaryotes. The promethearchaea contain at least 80 genes for eukaryotic signature proteins. 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, ubiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins), membrane-trafficking systems (such as Sec23/24 and TRAPP domains), a variety of small GTPases (including Gtr/Rag family GTPase orthologues), and gelsolins. Although this information do not completely resolve the three-domain and two-domain controversies, they are generally considered to favour the two-domain system.
== 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.
=== Domain Bacteria === It consists of all bacteria, which are prokaryotes (lacking nucleus), thus, Domain Bacteria is made up solely of prokaryotic organisms. Some examples are:
Cyanobacteriota – photosynthesising bacteria related to the plastids of eukaryotes. Spirochaetota – Gram-negative bacteria involved in human diseases like syphilis and lyme disease. Actinomycetota – Gram-positive bacteria including Streptomyces species from which several antibiotics are derived including streptomycin, neomycin, bottromycins and chloramphenicol.
=== Domain Archaea === It comprises both prokaryotic and eukaryotic organisms.
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. Kingdom Fungi – eukaryotes such as mushroom, yeast, and mould; all fungi. Kingdom Plantae – all plants. Kingdom Animalia – all animals.
== See also == Two-empire system Three-domain system Domain (biology)
== Notes ==
== References ==