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Asgard (archaea)

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Asgard
Scientific classificationEdit this classification
Domain: Archaea
Kingdom: Proteoarchaeota
Superphylum: Asgard
Katarzyna Zaremba-Niedzwiedzka[Wikidata],et al.2017
Phyla

see text

Synonyms
  • "Asgardarchaeota"Violette Da Cunha et al. 2017
  • "Asgardaeota"Whitman 2018
  • "Eukaryomorpha"Fournier & Poole 2018[1]

AsgardorAsgardarchaeota[2]is a proposedsuperphylumconsisting of a group ofarchaeathat contain eukaryotic signature proteins.[3]It appears that theeukaryotes,thedomainthat contains theanimals,plants,andfungi,emerged within the Asgard,[4]in a branch containing the Heimdallarchaeota.[5]This supports thetwo-domain systemof classification over thethree-domain system.[6][7]

Discovery and nomenclature

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In the summer of 2010, sediments were analysed from a gravitycoretaken in the rift valley on the Knipovich ridge in the Arctic Ocean, near theLoki's Castlehydrothermal ventsite. Specific sediment horizons previously shown to contain high abundances of novel archaeal lineages were subjected tometagenomic analysis.[8][9]In 2015, anUppsala University-led team proposed theLokiarchaeotaphylum based onphylogeneticanalyses using a set ofhighly conservedprotein-coding genes.[10]The group was named for the shape-shifting Norse godLoki,in an allusion to the hydrothermal vent complex from which the first genome sample originated.[11]The Loki of mythology has been described as "a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies",[12]analogous to the role of Lokiarchaeota in the debates about the origin of eukaryotes.[10][13]

In 2016, aUniversity of Texas-led team discoveredThorarchaeotafrom samples taken from theWhite Oak Riverin North Carolina, named in reference toThor,another Norse god.[14]Samples from Loki's Castle,Yellowstone National Park,Aarhus Bay,an aquifer near theColorado River,New Zealand'sRadiata Pool,hydrothermal vents nearTaketomi Island,Japan, and theWhite Oak Riverestuary in the United States contained Odinarchaeota and Heimdallarchaeota;[3]following the Norse deity naming convention, these groups were named forOdinandHeimdallrespectively. Researchers therefore named the superphylum containing these microbes "Asgard",after the home of the gods in Norse mythology.[3]Two Lokiarchaeota specimens have been cultured, enabling a detailed insight into their morphology.[15]

Description

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Proteins

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Asgard members encode many eukaryotic signature proteins, including novelGTPases,membrane-remodelling proteins likeESCRTandSNF7,aubiquitinmodifier system, andN-glycosylationpathway homologs.[3]

Asgard archaeons have a regulatedactincytoskeleton,and theprofilinsandgelsolinsthey use can interact with eukaryotic actins.[16][17]In addition, Asgard archaeatubulinfrom hydrothermal-living Odinarchaeota (OdinTubulin) was identified as a genuine tubulin. OdinTubulin forms protomers and protofilaments most similar to eukaryotic microtubules, yet assembles into ring systems more similar toFtsZ,indicating that OdinTubulin may represent an evolution intermediate between FtsZ andmicrotubule-forming tubulins.[18]They also seem to form vesicles undercryogenic electron microscopy.Some may have aPKD domainS-layer.[19]They also share the three-way ES39 expansion inLSU rRNAwith eukaryotes.[20]Gene clusters or operons encoding ribosomal proteins are often less conserved in their organization in the Asgard group than in other Archaea, suggesting that the order of ribosomal protein coding genes may follow the phylogeny.[21]

Metabolism

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  • Metabolic pathways of Asgard archaea, varying by phyla[22]
    Metabolic pathways of Asgard archaea, varying by phyla[22]
  • Metabolic pathways of Asgard archaea, varying by environment[22]
    Metabolic pathways of Asgard archaea, varying by environment[22]

Asgard archaea are generallyobligate anaerobes,though Kariarchaeota, Gerdarchaeota and Hodarchaeota may befacultative aerobes.[23]They have aWood–Ljungdahl pathwayand performglycolysis.Members can beautotrophs,heterotrophs,orphototrophsusingheliorhodopsin.[22]One member,CandidatusPrometheoarchaeum syntrophicum,issyntrophicwith a sulfur-reducing proteobacteria and amethanogenicarchaea.[19]

TheRuBisCOthey have is not carbon-fixing, but likely used for nucleoside salvaging.[22]

Ecology

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Asgard are widely distributed around the world, both geographically and by habitat. Many of the known clades are restricted to sediments, whereas Lokiarchaeota, Thorarchaeota and another clade occupy many different habitats. Salinity and depth are important ecological drivers for most Asgard archaea. Other habitats include the bodies of animals, the rhizosphere of plants, non-saline sediments and soils, the sea surface, and freshwater. In addition, Asgard are associated with several other microorganisms.[24]

Eukaryote-like features in subdivisions

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The phylum Heimdallarchaeota was found in 2017 to have N-terminal corehistone tails,a feature previously thought to be exclusively eukaryotic. Two other archaeal phyla, both outside of Asgard, were found to also have tails in 2018.[25]

In January 2020, scientists foundCandidatusPrometheoarchaeum syntrophicum,a member of the Lokiarcheota, engaging incross-feedingwith two bacterial species. Drawing an analogy tosymbiogenesis,they consider this relationship a possible link between the simpleprokaryoticmicroorganisms and the complexeukaryoticmicroorganisms occurring approximately two billion years ago.[26][19]

Phylogeny

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The phylogenetic relationships of the Asgard archaea have been studied by several teams in the 21st century.[5][4][27][23]Varying results have been obtained, for instance using 53 marker proteins from theGenome Taxonomy Database.[28][29][30]In 2023, Eme, Tamarit, Caceres and colleagues reported that the Eukaryota are deep within Asgard, as sister of Hodarchaeales within the Heimdallarchaeia.[31]

Proteoarchaeota

Taxonomy

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Further information:Eukaryogenesis
In the theory ofsymbiogenesis,a merger of anarchaeanand an aerobic bacterium created the eukaryotes, with aerobicmitochondria;a second merger addedchloroplasts,creating the green plants.[32]

In the depicted scenario, the Eukaryota are deep in the tree of Asgard. A favored scenario is syntrophy, where one organism depends on the feeding of the other. Anα-proteobacteriumwas incorporated to become themitochondrion.[33]In culture, extant Asgard archaea form various syntrophic dependencies.[34]Gregory Fournier and Anthony Poole have proposed that Asgard is part of "the Eukaryote tree", forming a superphylum they call "Eukaryomorpha" defined by "shared derived characters" (eukaryote signature proteins).[35]

The taxonomy is uncertain and the phylum names are therefore somewhat speculative. The list of phyla is based on theList of Prokaryotic names with Standing in Nomenclature(LPSN)[36]andNational Center for Biotechnology Information(NCBI).[37]

Genomic elements

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Viruses

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Several family-level groups of viruses associated with Asgard archaea have been discovered using metagenomics.[38][39][40]The viruses were assigned to Lokiarchaeia, Thorarchaeia, Odinarchaeia and Helarchaeia hosts using CRISPR spacer matching to the corresponding protospacers within the viral genomes. Two groups of viruses (called 'verdandiviruses') are related to archaeal and bacterial viruses of the classCaudoviricetes,i.e., viruses with icosahedral capsids and helical tails;[38][40]two other distinct groups (called 'skuldviruses') are distantly related to tailless archaeal and bacterial viruses with icosahedral capsids of the realmVaridnaviria;[38][39]and the third group of viruses (calledwyrdviruses) is related to archaea-specific viruses with lemon-shaped virus particles (familyHalspiviridae).[38][39]The viruses have been identified in deep-sea sediments[38][40]and a terrestrial hot spring of the Yellowstone National Park.[39]All these viruses display very low sequence similarity to other known viruses but are generally related to the previously described prokaryotic viruses,[41]with no meaningful affinity to viruses of eukaryotes.[42][38]

Mobile genetic elements

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In addition to viruses, several groups of crypticmobile genetic elementshave been discovered throughCRISPRspacer matching to be associated with Asgard archaea of the Lokiarchaeia, Thorarchaeia and Heimdallarchaeia lineages.[38][43]These mobile elements do not encode recognizable viral hallmark proteins and could represent either novel types of viruses or plasmids.

See also

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References

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  2. ^Da Cunha, Violette; Gaia, Morgan; Gadelle, Daniele; et al. (June 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.PMC5484517.PMID28604769.
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