Two-domain system

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The tree of life. Two domains of life are Bacteria (top branches) and Archaea (bottom branches, including eukaryotes). A Novel Representation Of The Tree Of Life.png
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 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 classifies 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 [4] It was preceded by the eocyte hypothesis of James A. Lake in the 1980s, [5] which was largely superseded by the three-domain system, due to evidence at the time.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, thereby making eukaryotes members of the domain Archaea. [10]

Contents

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:

  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:

Eukarya

Eukaryotes have a nucleus in their cells, and include:

Related Research Articles

<span class="mw-page-title-main">Kingdom (biology)</span> Taxonomic rank

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

<span class="mw-page-title-main">Domain (biology)</span> Taxonomic rank

In biological taxonomy, a domain, also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.

<span class="mw-page-title-main">Three-domain system</span> Hypothesis for classification of life

The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of Archaea from Bacteria as completely different organisms. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as Eukaryotes are considered as a clade of Archaea.

<span class="mw-page-title-main">Thermoproteota</span> Phylum of archaea

The Thermoproteota are prokaryotes that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones. Until recently all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells.

<span class="mw-page-title-main">Korarchaeota</span> Proposed phylum within the Archaea

The Korarchaeota is a proposed phylum within the Archaea. The name is derived from the Greek noun koros or kore, meaning young man or young woman, and the Greek adjective archaios which means ancient. They are also known as Xenarchaeota. The name is equivalent to Candidatus Korarchaeota, and they go by the name Xenarchaeota or Xenarchaea as well.

<span class="mw-page-title-main">Tubulin</span> Superfamily of proteins that make up microtubules

Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton. Microtubules function in many essential cellular processes, including mitosis. Tubulin-binding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division.

Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within a methanogenic archaeon or a bacterium. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome and eventually usurping its role. The hypothesis was first proposed by Philip Bell in 2001 and was further popularized with the discovery of large, complex DNA viruses that are capable of protein biosynthesis.

<span class="mw-page-title-main">Prokaryotic cytoskeleton</span> Structural filaments in prokaryotes

The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but advances in visualization technology and structure determination led to the discovery of filaments in these cells in the early 1990s. Not only have analogues for all major cytoskeletal proteins in eukaryotes been found in prokaryotes, cytoskeletal proteins with no known eukaryotic homologues have also been discovered. Cytoskeletal elements play essential roles in cell division, protection, shape determination, and polarity determination in various prokaryotes.

<span class="mw-page-title-main">Prokaryote</span> Unicellular organism lacking a membrane-bound nucleus

A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό 'before' and κάρυον 'nut, kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota.

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotic. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

<span class="mw-page-title-main">Eukaryote</span> Domain of life whose cells have nuclei

The eukaryotes constitute the domain of Eukarya or Eukaryota, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, and many unicellular organisms are eukaryotes. They constitute a major group of life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes.

<span class="mw-page-title-main">Eocyte hypothesis</span> Hypothesis in evolutionary biology

The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes. After his team at the University of California, Los Angeles discovered eocytes in 1984, James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: prokaryotes, which include Bacteria and Archaea, and karyotes, that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria.

<span class="mw-page-title-main">Lokiarchaeota</span> Phylum of archaea

Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group, also known as Marine Benthic Group B. Lokiarchaeota is part of the superphylum Asgard containing the phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota, and Helarchaeota. A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

<span class="mw-page-title-main">Proteoarchaeota</span> Proposed kingdom of archaea

"Proteoarchaeota" are a proposed archaeal kingdom thought to be closely related and possibly ancestral to the Eukaryotes.

<span class="mw-page-title-main">Eukaryogenesis</span> Process of forming the first eukaryotic cell

Eukaryogenesis, the process which created the eukaryotic cell and lineage, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The process is widely agreed to have involved symbiogenesis, in which archaea and bacteria came together to create the first eukaryotic common ancestor (FECA). This cell had a new level of complexity and capability, with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex, a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. It evolved into a population of single-celled organisms that included the last eukaryotic common ancestor (LECA), gaining capabilities along the way, though the sequence of the steps involved has been disputed, and may not have started with symbiogenesis. In turn, the LECA gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms.

<span class="mw-page-title-main">TACK</span> Clade of Archaea

TACK is a group of archaea, its name an acronym for Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota, the first groups discovered. They are found in different environments ranging from acidophilic thermophiles to mesophiles and psychrophiles and with different types of metabolism, predominantly anaerobic and chemosynthetic. TACK is a clade that is sister to the Asgard branch that gave rise to the eukaryotes. It has been proposed that the TACK clade be classified as Crenarchaeota and that the traditional "Crenarchaeota" (Thermoproteota) be classified as a class called "Sulfolobia", along with the other phyla with class rank or order.

<span class="mw-page-title-main">Ubiquitin-like protein</span> Family of small proteins

Ubiquitin-like proteins (UBLs) are a family of small proteins involved in post-translational modification of other proteins in a cell, usually with a regulatory function. The UBL protein family derives its name from the first member of the class to be discovered, ubiquitin (Ub), best known for its role in regulating protein degradation through covalent modification of other proteins. Following the discovery of ubiquitin, many additional evolutionarily related members of the group were described, involving parallel regulatory processes and similar chemistry. UBLs are involved in a widely varying array of cellular functions including autophagy, protein trafficking, inflammation and immune responses, transcription, DNA repair, RNA splicing, and cellular differentiation.

<span class="mw-page-title-main">Asgard (archaea)</span> Proposed superphylum of archaea

Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that contain eukaryotic signature proteins. It appears that the eukaryotes, the domain that contains the animals, plants, and fungi, emerged within the Asgard, in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over the three-domain system.

Archaeal translation is the process by which messenger RNA is translated into proteins in archaea. Not much is known on this subject, but on the protein level it seems to resemble eukaryotic translation.

<span class="mw-page-title-main">Marine prokaryotes</span> Marine bacteria and marine archaea

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

References

  1. ↑ Bolshoy, Alexander; Volkovich, Zeev (Vladimir); Kirzhner, Valery; Barzily, Zeev (2010), "Biological Classification", Genome Clustering, Studies in Computational Intelligence, 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. Bibcode:2015PNAS..112.6670R. doi: 10.1073/pnas.1420858112 . PMC   4450401 . PMID   25964353.
  3. 1 2 3 4 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. PMID   34863611. S2CID   244823103.
  4. 1 2 3 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. 1 2 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. 1 2 Archibald, John M. (2008). "The eocyte hypothesis and the origin of eukaryotic cells". Proceedings of the National Academy of Sciences. 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. ↑ 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.
  9. 1 2 Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W.; Anantharaman, Karthik; Starnawski, Piotr (2017). "Asgard archaea illuminate the origin of eukaryotic cellular complexity" (PDF). Nature. 541 (7637): 353–358. Bibcode:2017Natur.541..353Z. doi:10.1038/nature21031. OSTI   1580084. PMID   28077874. S2CID   4458094.
  10. ↑ 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.
  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". PLOS Genetics. 14 (3): e1007215. doi: 10.1371/journal.pgen.1007215 . PMC   5875737 . PMID   29596428.
  12. 1 2 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. S2CID   3541409.
  13. 1 2 3 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. PMC   6942926 . PMID   31819234.
  14. 1 2 Katscher, Friedrich (2004). "The History of the Terms Prokaryotes and Eukaryotes". Protist. 155 (2): 257–263. doi:10.1078/143446104774199637. PMID   15305800.
  15. ↑ Mayr, Ernst (1998). "Two empires or three?". Proceedings of the National Academy of Sciences. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi: 10.1073/pnas.95.17.9720 . PMC   33883 . PMID   9707542.
  16. ↑ Stanier, R. Y.; Van Niel, C. B. (1962). "The concept of a bacterium" (PDF). Archiv für Mikrobiologie. 42: 17–35. doi:10.1007/BF00425185. PMID   13916221. S2CID   29859498.
  17. ↑ Corliss, John O. (1986). "The Kingdoms of Organisms: From a Microscopist's Point of View". Transactions of the American Microscopical Society. 105 (1): 1–10. doi:10.2307/3226544. JSTOR   3226544.
  18. ↑ Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi: 10.1073/pnas.74.11.5088 . PMC   432104 . PMID   270744.
  19. ↑ Lake, James A.; Henderson, Eric; Oakes, Melanie; Clark, Michael W. (June 1984). "Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes". PNAS. 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. doi: 10.1073/pnas.81.12.3786 . PMC   345305 . PMID   6587394.
  20. ↑ Lake, J.A. (1987). "Prokaryotes and Archaebacteria Are Not Monophyletic: Rate Invariant Analysis of rRNA Genes Indicates That Eukaryotes and Eocytes Form a Monophyletic Taxon". Cold Spring Harbor Symposia on Quantitative Biology. 52: 839–846. doi:10.1101/SQB.1987.052.01.091. ISSN   0091-7451. PMID   3454292.
  21. ↑ Lake, James A. (1991). "Tracing origins with molecular sequences: metazoan and eukaryotic beginnings". Trends in Biochemical Sciences. 16 (2): 46–50. doi:10.1016/0968-0004(91)90020-V. PMID   1858129.
  22. 1 2 3 4 Koonin, Eugene V. (2015). "Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370 (1678): 20140333. doi:10.1098/rstb.2014.0333. PMC   4571572 . PMID   26323764.
  23. ↑ Oren, Aharon; Garrity, George M. (2021). "Valid publication of the names of forty-two phyla of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 71 (10): Online. doi: 10.1099/ijsem.0.005056 . ISSN   1466-5034. PMID   34694987. S2CID   239887308.
  24. ↑ Woese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi: 10.1073/pnas.87.12.4576 . PMC   54159 . PMID   2112744.
  25. ↑ Case, Emily (2008). "Teaching Taxonomy: How Many Kingdoms?". The American Biology Teacher. 70 (8): 472–477. doi:10.1662/0002-7685(2008)70[472:TTHMK]2.0.CO;2. S2CID   198969439.
  26. 1 2 Cox, Cymon J.; Foster, Peter G.; Hirt, Robert P.; Harris, Simon R.; Embley, T. Martin (2008). "The archaebacterial origin of eukaryotes". Proceedings of the National Academy of Sciences of the United States of America. 105 (51): 20356–20361. Bibcode:2008PNAS..10520356C. doi: 10.1073/pnas.0810647105 . PMC   2629343 . PMID   19073919.
  27. ↑ MacLeod, Fraser; Kindler, Gareth S.; Wong, Hon Lun; Chen, Ray; Burns, Brendan P. (2019). "Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes". AIMS Microbiology. 5 (1): 48–61. doi:10.3934/microbiol.2019.1.48. PMC   6646929 . PMID   31384702.
  28. ↑ Jüttner, Michael; Ferreira-Cerca, Sébastien (2022). "Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis". Molecular Biology and Evolution. 39 (4): msac054. doi:10.1093/molbev/msac054. PMC   8997704 . PMID   35275997.
  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. S2CID   8666687.
  30. ↑ Vishwanath, Prashanth; Favaretto, Paola; Hartman, Hyman; Mohr, Scott C.; Smith, Temple F. (2004). "Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes". Molecular Phylogenetics and Evolution. 33 (3): 615–625. doi:10.1016/j.ympev.2004.07.003. PMID   15522791.
  31. ↑ Rivera, Maria C.; Lake, James A. (2004). "The ring of life provides evidence for a genome fusion origin of eukaryotes". Nature. 431 (7005): 152–155. Bibcode:2004Natur.431..152R. doi:10.1038/nature02848. PMID   15356622. S2CID   4349149.
  32. ↑ Pisani, Davide; Cotton, James A.; McInerney, James O. (2007). "Supertrees disentangle the chimerical origin of eukaryotic genomes". Molecular Biology and Evolution. 24 (8): 1752–1760. doi: 10.1093/molbev/msm095 . PMID   17504772.
  33. ↑ Yutin, Natalya; Makarova, Kira S.; Mekhedov, Sergey L.; Wolf, Yuri I.; Koonin, Eugene V. (2008). "The deep archaeal roots of eukaryotes". Molecular Biology and Evolution. 25 (8): 1619–1630. doi:10.1093/molbev/msn108. PMC   2464739 . PMID   18463089.
  34. ↑ Yutin, Natalya; Wolf, Maxim Y.; Wolf, Yuri I.; Koonin, Eugene V. (2009). "The origins of phagocytosis and eukaryogenesis". Biology Direct. 4: 9. doi: 10.1186/1745-6150-4-9 . PMC   2651865 . PMID   19245710.
  35. ↑ Yutin, Natalya; Koonin, Eugene V. (2012). "Archaeal origin of tubulin". Biology Direct. 7: 10. doi: 10.1186/1745-6150-7-10 . PMC   3349469 . PMID   22458654.
  36. ↑ Samson, Rachel Y.; Dobro, Megan J.; Jensen, Grant J.; Bell, Stephen D. (2017). "The Structure, Function and Roles of the Archaeal ESCRT Apparatus". Prokaryotic Cytoskeletons. Subcellular Biochemistry. Vol. 84. pp. 357–377. doi:10.1007/978-3-319-53047-5_12. ISBN   978-3-319-53045-1. PMID   28500532.
  37. ↑ Pelve, Erik A.; Lindås, Ann-Christin; Martens-Habbena, Willm; de la Torre, José R.; Stahl, David A.; Bernander, Rolf (2011). "Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus". Molecular Microbiology. 82 (3): 555–566. doi: 10.1111/j.1365-2958.2011.07834.x . PMID   21923770. S2CID   1202516.
  38. ↑ Dobro, Megan J.; Samson, Rachel Y.; Yu, Zhiheng; McCullough, John; Ding, H. Jane; Chong, Parkson Lee-Gau; Bell, Stephen D.; Jensen, Grant J. (2013). "Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggests that spiraling filaments are involved in membrane scission". Molecular Biology of the Cell. 24 (15): 2319–2327. doi:10.1091/mbc.E12-11-0785. PMC   3727925 . PMID   23761076.
  39. ↑ Grau-Bové, Xavier; Sebé-Pedrós, Arnau; Ruiz-Trillo, Iñaki (2015). "The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin". Molecular Biology and Evolution. 32 (3): 726–739. doi:10.1093/molbev/msu334. PMC   4327156 . PMID   25525215.
  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 . PMC   2948915 . PMID   20936112.
  41. ↑ Makarova, Kira S.; Koonin, Eugene V.; Kelman, Zvi (2012). "The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes". Biology Direct. 7: 7. doi: 10.1186/1745-6150-7-7 . PMC   3307487 . PMID   22329974.
  42. ↑ Stairs, Courtney W.; Ettema, Thijs J.G. (2020). "The Archaeal Roots of the Eukaryotic Dynamic Actin Cytoskeleton". Current Biology. 30 (10): R521–R526. doi: 10.1016/j.cub.2020.02.074 . PMID   32428493. S2CID   218710903.
  43. 1 2 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 . PMC   6104171 . PMID   30158917.
  44. ↑ Jørgensen, Steffen Leth; Hannisdal, Bjarte; Lanzen, Anders; Baumberger, Tamara; Flesland, Kristin; Fonseca, Rita; Øvreås, Lise; Steen, Ida H; Thorseth, Ingunn H; Pedersen, Rolf B; Schleper, Christa (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 . PMC   3479504 . PMID   23027979.
  45. ↑ Jørgensen, Steffen Leth; Thorseth, Ingunn H; Pedersen, Rolf B; Baumberger, Tamara; Schleper, Christa (October 4, 2013). "Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge". Frontiers in Microbiology. 4: 299. doi: 10.3389/fmicb.2013.00299 . PMC   3790079 . PMID   24109477.
  46. 1 2 Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.; Zaremba-Niedzwiedzka, Katarzyna; Martijn, Joran; Lind, Anders E.; Eijk, Roel van; Schleper, Christa; Guy, Lionel (2015). "Complex archaea that bridge the gap between prokaryotes and eukaryotes". Nature. 521 (7551): 173–179. Bibcode:2015Natur.521..173S. doi:10.1038/nature14447. PMC   4444528 . PMID   25945739.
  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 . PMC   5484517 . PMID   28604769.
  48. ↑ Da Cunha, Violette; Gaïa, Morgan; Forterre, Patrick (2022). "The expanding Asgard archaea and their elusive relationships with Eukarya". mLife. 1 (1): 3–12. doi: 10.1002/mlf2.12012 . S2CID   247689333.
  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. PMC   5875737 . 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 . PMC   5875740 . PMID   29596421.
  51. ↑ Liu, Yang; Makarova, Kira S.; Huang, Wen-Cong; Wolf, Yuri I.; Nikolskaya, Anastasia N.; Zhang, Xinxu; Cai, Mingwei; Zhang, Cui-Jing; Xu, Wei; Luo, Zhuhua; Cheng, Lei (2021). "Expanded diversity of Asgard archaea and their relationships with eukaryotes". Nature. 593 (7860): 553–557. Bibcode:2021Natur.593..553L. doi:10.1038/s41586-021-03494-3. ISSN   0028-0836. PMID   33911286. S2CID   233447651.
  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". Science China Life Sciences. 65 (4): 818–829. doi:10.1007/s11427-021-1969-6. PMID   34378142. S2CID   236977853.
  53. ↑ López-García, Purificación; Moreira, David (2020). "Cultured Asgard Archaea Shed Light on Eukaryogenesis". Cell. 181 (2): 232–235. doi: 10.1016/j.cell.2020.03.058 . PMID   32302567. S2CID   215798394.
  54. ↑ Akıl, Caner; Robinson, Robert C. (2018). "Genomes of Asgard archaea encode profilins that regulate actin". Nature. 562 (7727): 439–443. Bibcode:2018Natur.562..439A. doi:10.1038/s41586-018-0548-6. PMID   30283132. S2CID   52917038.
  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. Bibcode:2017NatCo...8.1120H. doi:10.1038/s41467-017-01162-7. ISSN   2041-1723. PMC   5654768 . PMID   29066714.
  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". Proceedings of the National Academy of Sciences. 117 (33): 19904–19913. Bibcode:2020PNAS..11719904A. doi: 10.1073/pnas.2009167117 . PMC   7444086 . PMID   32747565.
  58. ↑ Liu, Yang; Makarova, Kira S.; Huang, Wen-Cong; Wolf, Yuri I.; Nikolskaya, Anastasia N.; Zhang, Xinxu; Cai, Mingwei; Zhang, Cui-Jing; Xu, Wei; Luo, Zhuhua; Cheng, Lei (2021). "Expanded diversity of Asgard archaea and their relationships with eukaryotes". Nature. 593 (7860): 553–557. Bibcode:2021Natur.593..553L. doi:10.1038/s41586-021-03494-3. PMID   33911286. S2CID   233447651.
  59. ↑ Hugenholtz, Philip (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): reviews0003.1. doi: 10.1186/gb-2002-3-2-reviews0003 . PMC   139013 . PMID   11864374.
  60. ↑ Oren, Aharon (2004). Godfray, H. C. J.; Knapp, S. (eds.). "Prokaryote diversity and taxonomy: current status and future challenges". Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences. 359 (1444): 623–638. doi:10.1098/rstb.2003.1458. PMC   1693353 . 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. PMC   6640209 . PMID   31354692.
  62. ↑ Seitz, Patrick; Blokesch, Melanie (2013). "Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria". FEMS Microbiology Reviews. 37 (3): 336–363. doi: 10.1111/j.1574-6976.2012.00353.x . PMID   22928673. S2CID   30861416.
  63. ↑ Bibb, Mervyn J. (2013). "Understanding and manipulating antibiotic production in actinomycetes". Biochemical Society Transactions. 41 (6): 1355–1364. doi:10.1042/BST20130214. PMID   24256223.
  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. Bibcode:2014ApEnM..80....2W. doi:10.1128/AEM.01143-13. PMC   3911012 . PMID   24162573.
  65. ↑ Schleifer, Karl Heinz (2009). "Classification of Bacteria and Archaea: Past, present and future". Systematic and Applied Microbiology. 32 (8): 533–542. doi:10.1016/j.syapm.2009.09.002. PMID   19819658.
  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; Fensome, Robert A.; Fredericq, Suzanne; James, Timothy Y. (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. S2CID   8060916.
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