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Adnaviria

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Adnaviria
Acidianus filamentous virus 3(AFV3) virion
Virus classificationEdit this classification
(unranked): Virus
Realm: Adnaviria
Kingdom: Zilligvirae
Phylum: Taleaviricota
Class: Tokiviricetes
Subtaxa

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Adnaviriais arealmofvirusesthat includesarchaeal virusesthat have a filamentous virion (i.e. body) and a linear, double-stranded DNA genome.[1]The genome exists in A-form (A-DNA) and encodes a dimeric major capsid protein (MCP) that contains the SIRV2 fold, a type ofAlpha -helixbundle containing four helices. The virion consists of the genome encased incapsidproteins to form a helical nucleoprotein complex. For some viruses, this helix is surrounded by alipidmembrane called anenvelope.Some contain an additional protein layer between the nucleoprotein helix and the envelope. Complete virions are long and thin and may be flexible or a stiff like a rod.

Adnaviriawas established in 2020 aftercryogenic electron microscopyshowed that the viruses in the realm were related due to a shared MCP, A-DNA, and general virion structure. Viruses inAdnaviriainfect hyperthermophilicarchaea,i.e. archaea that inhabit very high temperature environments such as hot springs. Their A-DNA genome may be an adaptation to this extreme environment. Viruses inAdnaviriahave potentially existed for a long time, as it is thought that they may have infected the last archaeal common ancestor. In general, they show no genetic relation to any viruses outside the realm.

Etymology

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Adnaviriatakes the first part of its name,Adna-, from A-DNA, referring to the A-form genomic DNA of all viruses in the realm. The second part, -viriais the suffix used for virus realms. The sole kingdom in the realm,Zilligvirae,is named afterWolfram Zillig(1925–2005) for his research on hyperthermophilic archaea, with the virus kingdom suffix -virae.The name of the sole phylum,Taleaviricota,is derived fromLatintalea,meaning "rod", referring to the morphology of viruses in the realm, and the virus phylum suffix -viricota.Lastly, the sole class in the realm,Tokiviricetes,is constructed fromGeorgiantoki(თოკი), meaning "thread", and the suffix used for virus classes, -viricetes.[2]

Characteristics

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Viruses inAdnaviriainfect hyperthermophilic archaea and have linear, double-stranded DNA (dsDNA) genomes ranging from about 16 to 56 kilobase pairs in length. The ends of their genomes contain inverted terminal repeats.[3][4][5]Notably, their genomes exist in A-form, also called A-DNA.[1]A-form is proposed to be an adaptation allowing DNA survival under extreme conditions since their hosts arehyperthermophilicandacidophilicmicroorganisms from thearchaeadomain.[6]Furthermore, Adnaviria viruses have high genome redundancy, an adaptation mechanism to survive such extreme environments.[7]

The creation of genomic A-DNA is caused by an interaction with major capsid protein (MCP) dimers, which, during virion assembly, cover pre-genomic B-DNA to form a helical nucleoprotein complex containing genomic A-DNA.[2]

The nucleoprotein helix is composed of asymmetric units of two MCPs. Forrudiviruses,this is a homodimer, whereas forlipothrixvirusesandtristromaviruses,[8]it is a heterodimer of paralogous MCPs. The MCPs of viruses inAdnaviriacontain a folded structure consisting of a type of Alpha -helix bundle that contains four helices[4]called the SIRV2 fold, named after the virus of the same name,Sulfolobus islandicus rod-shaped virus 2(SIRV2). Variations in the protein structure exist, but the same base structure is retained in all adnaviruses.[2]

Adnaviruses have filamentous virions, i.e. they are long, thin, and cylindrical. Lipothrixviruses have flexible virions about 900 nanometers (nm) in length and 24 nm in width in which the nucleoprotein helix is surrounded by a lipid envelope.[3]Tristromaviruses, about 400 by 32 nm, likewise have flexible virions with an envelope, and they contain an additional protein sheath layer between the nucleoprotein complex and the envelope.[5][9]Rudviruses have stiff, rod-like virions about 600–900 by 23 nm.[4]At both ends of the virion, lipothrixviruses have mop- or claw-like structures connected to a collar, whereas rudiviruses and tristromaviruses have plugs at each end from which bundles of thin filaments emanate.[3][5][10]

Phylogenetics

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Viruses inAdnaviriahave potentially existed for a long time, as it is thought that they may have infected the last archaeal common ancestor.[11]In general, they show no genetic relation to viruses outside the realm. The only genes that are shared with other viruses areglycosyltransferases,ribbon-helix-helixtranscription factors,and anti-CRISPRproteins. Adnaviruses are morphologically similar to non-archaeal filamentous viruses but their virions are built from different capsid proteins. Viruses ofClavaviridae,a family of filamentous archaeal viruses morphologically similar to adnaviruses, likewise possess MCPs that show no relation to the MCPs of viruses inAdnaviriaand for that reason are excluded from the realm.[2]

Classification

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Adnaviriais monotypic down to the rank of its sole class,Tokiviricetes,which has three orders. This taxonomy is shown hereafter:[2][12]

  • Realm:Adnaviria
    • Kingdom:Zilligvirae
      • Phylum:Taleaviricota
        • Class:Tokiviricetes
          • Order:Ligamenvirales,which contains viruses that infect archaea of the orderSulfolobales,containing the familiesLipothrixviridaeandRudiviridae
          • Order:Maximonvirales,which contains viruses that infect archaea of theCandidatusorderMenathophagales,currently containing the single speciesYumkaaxvirus pescaderoense
          • Order:Primavirales,which contains viruses that infect archaea of the orderThermoproteales,containing the familyTristromaviridae

History

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Viruses ofAdnaviriabegan to be discovered in the 1980s by Wolfram Zillig and his colleagues.[13]To discover these viruses, Zillig developed the methods used to culture their hosts.[14]The first of these to be described were TTV1, TTV2, and TTV3 in 1983.[15]TTV1 was classified as the first lipothrixvirus but is now classified as a tristromavirus.[16]SIRV2, a rudivirus, became a model for studying virus-host interactions[13]after its discovery in 1998.[17]The familiesLipothrixviridaeandRudiviridaewere then united under the orderLigamenviralesin 2012 based on evidence of their relation.[18][19]Cryogenic electron microscopy would later show in 2020 that the MCPs of tristromaviruses contained a SIRV2-like fold like ligamenviruses, providing justification for establishingAdnaviriain the same year.[8][20]

See also

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References

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  1. ^abKrupovic, M; Kuhn, JH; Wang, F; Baquero, DP; Dolja, VV; Egelman, EH; Prangishvili, D; Koonin, EV (12 July 2021)."Adnaviria:a new realm for archaeal filamentous viruses with linear A-form double-stranded DNA genomes ".Journal of Virology.95(15): e0067321.doi:10.1128/JVI.00673-21.PMC8274609.PMID34011550.
  2. ^abcdeKrupovic M, Kuhn JH, Wang F, Baquero DP, Egelman EH, Koonin EV, Prangishvili D (31 July 2020)."Create one new realm (Adnaviria) for classification of filamentous archaeal viruses with linear dsDNA genomes "(docx).International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.
  3. ^abc"Lipothrixviridae".International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.[dead link]
  4. ^abc"Rudiviridae".International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.[dead link]
  5. ^abcPrangishvili D, Rensen E, Mochizuki T, Krupovic M (February 2019)."ICTV Taxonomy Profile: Tristromaviridae"(PDF).J Gen Virol.100(2): 135–136.doi:10.1099/jgv.0.001190.PMID30540248.S2CID54475961.
  6. ^Krupovic, Mart; Kuhn, Jens H.; Wang, Fengbin; Baquero, Diana P.; Dolja, Valerian V.; Egelman, Edward H.; Prangishvili, David; Koonin, Eugene V. (2021-07-12). Sandri-Goldin, Rozanne M. (ed.)."Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes".Journal of Virology.95(15): e00673–21.doi:10.1128/JVI.00673-21.ISSN0022-538X.PMC8274609.PMID34011550.
  7. ^Silva, Jorge Miguel; Pratas, Diogo; Caetano, Tânia; Matos, Sérgio (2022-08-11)."The complexity landscape of viral genomes".GigaScience.11:giac079.doi:10.1093/gigascience/giac079.ISSN2047-217X.PMC9366995.PMID35950839.
  8. ^abWang F, Baquero DP, Su Z, Osinski T, Prangishvili D, Egelman EH, Krupovic M (29 April 2020)."Structure of a filamentous virus uncovers familial ties within the archaeal virosphere".Virus Evol.6(1): veaa023.doi:10.1093/ve/veaa023.PMC7189273.PMID32368353.
  9. ^Prangshvili D, Krupovic M (July 2016)."Create genusAlphatristromaviruswithin the new familyTristromaviridaeand remove genusAlphalipothrixvirusfrom the familyLipothrixviridae"(PDF).International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.
  10. ^Lawrence CM, Menon S, Eilers BJ, Bothner B, Khayat R, Douglas T, Young MJ (8 May 2009)."Structural and functional studies of archaeal viruses".J Biol Chem.284(19): 12599–12603.doi:10.1074/jbc.R800078200.PMC2675988.PMID19158076.
  11. ^Krupovic M, Dolja VV, Koonin EV (November 2020)."The LUCA and its complex virome"(PDF).Nat Rev Microbiol.18(11): 661–670.doi:10.1038/s41579-020-0408-x.PMID32665595.S2CID220516514.
  12. ^"Virus Taxonomy: 2022 Release".International Committee on Taxonomy of Viruses (ICTV). March 2021.Retrieved20 July2021.
  13. ^abSnyder JC, Buldoc B, Young MJ (May 2015)."40 Years of archaeal virology: Expanding viral diversity".Virology.479–480: 369–378.doi:10.1016/j.virol.2015.03.031.PMID25866378.
  14. ^Stedman K."Wolfram ASM Letter"(PDF).Portland State University.Retrieved20 July2021.
  15. ^Janekovic D, Wunderl S, Holz I, Zillig W, Gierl A, Neumann H (1983). "TTV1, TTV2 and TTV3, a family of viruses of the extremely thermophilic, anaerobic, sulfur reducing archaebacteriumThermoproteus tenax".Mol Gen Genet.192(1–2): 39–45.doi:10.1007/BF00327644.S2CID46094905.
  16. ^"ICTV Taxonomy history:Betatristromavirus TTV1".International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.
  17. ^Prangishvili D, Arnold HP, Gotz D, Ziese U, Holz I, Kristjansson JK, Zillig W (August 1999)."A novel virus family, the Rudiviridae: Structure, virus-host interactions and genome variability of the sulfolobus viruses SIRV1 and SIRV2".Genetics.152(4): 1387–1396.doi:10.1093/genetics/152.4.1387.PMC1460677.PMID10430569.
  18. ^"ICTV Taxonomy history:Ligamenvirales".International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.
  19. ^Prangishvili D, Krupovic M (21 June 2012)."Create the orderLigamenviralescontaining the familiesRudiviridaeandLipothrixviridae"(PDF).International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.
  20. ^"ICTV Taxonomy history:Adnaviria".International Committee on Taxonomy of Viruses (ICTV).Retrieved20 July2021.
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