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Adnaviria

December 18, 2023

Adnaviria is a realm of viruses that includes archaeal viruses that 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 of alpha-helix bundle containing four helices. The virion consists of the genome encased in capsid proteins to form a helical nucleoprotein complex. For some viruses, this helix is surrounded by a lipid membrane called an envelope. 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.

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

See text

Adnaviria was established in 2020 after cryogenic electron microscopy showed that the viruses in the realm were related due to a shared MCP, A-DNA, and general virion structure. Viruses in Adnaviria infect hyperthermophilic archaea, 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 in Adnaviria have 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 edit

Adnaviria takes 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, -viria is the suffix used for virus realms. The sole kingdom in the realm, Zilligvirae, is named after Wolfram Zillig (1925–2005) for his research on hyperthermophilic archaea, with the virus kingdom suffix -virae. The name of the sole phylum, Taleaviricota, is derived from Latin talea, 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 from Georgian toki (თოკი), meaning "thread", and the suffix used for virus classes, -viricetes.[2]

Characteristics edit

Viruses in Adnaviria infect 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 are hyperthermophiles and acidophiles microorganisms from the archaea domain.[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. For rudiviruses, this is a homodimer, whereas for lipothrixviruses and tristromaviruses,[8] it is a heterodimer of paralogous MCPs. The MCPs of viruses in Adnaviria contain 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 edit

Viruses in Adnaviria have 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 are glycosyltransferases, ribbon-helix-helix transcription factors, and anti-CRISPR proteins. Adnaviruses are morphologically similar to non-archaeal filamentous viruses but their virions are built from different capsid proteins. Viruses of Clavaviridae, a family of filamentous archaeal viruses morphologically similar to adnaviruses, likewise possess MCPs that show no relation to the MCPs of viruses in Adnaviria and for that reason are excluded from the realm.[2]

Classification edit

Adnaviria is 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 order Sulfolobales, containing the families Lipothrixviridae and Rudiviridae
          • Order: Maximonvirales, which contains viruses that infect archaea of the Candidatus order Menathophagales, currently containing the single species Yumkaaxvirus pescaderoense
          • Order: Primavirales, which contains viruses that infect archaea of the order Thermoproteales, containing the family Tristromaviridae

History edit

Viruses of Adnaviria began 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 families Lipothrixviridae and Rudiviridae were then united under the order Ligamenvirales in 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 establishing Adnaviria in the same year.[8][20]

See also edit

References edit

  1. ^ a b Krupovic, 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. PMC 8274609. PMID 34011550.
  2. ^ a b c d e Krupovic 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). Retrieved 20 July 2021.
  3. ^ a b c "Lipothrixviridae". International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.[dead link]
  4. ^ a b c "Rudiviridae". International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.[dead link]
  5. ^ a b c Prangishvili 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. PMID 30540248. S2CID 54475961.
  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. ISSN 0022-538X. PMC 8274609. PMID 34011550.
  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. ISSN 2047-217X. PMC 9366995. PMID 35950839.
  8. ^ a b Wang 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. PMC 7189273. PMID 32368353.
  9. ^ Prangshvili D, Krupovic M (July 2016). "Create genus Alphatristromavirus within the new family Tristromaviridae and remove genus Alphalipothrixvirus from the family Lipothrixviridae" (PDF). International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.
  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. PMC 2675988. PMID 19158076.
  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. PMID 32665595. S2CID 220516514.
  12. ^ "Virus Taxonomy: 2022 Release". International Committee on Taxonomy of Viruses (ICTV). March 2021. Retrieved 20 July 2021.
  13. ^ a b Snyder 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. PMID 25866378.
  14. ^ Stedman K. "Wolfram ASM Letter" (PDF). Portland State University. Retrieved 20 July 2021.
  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 archaebacterium Thermoproteus tenax". Mol Gen Genet. 192 (1–2): 39–45. doi:10.1007/BF00327644. S2CID 46094905.
  16. ^ "ICTV Taxonomy history: Betatristromavirus TTV1". International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.
  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. PMC 1460677. PMID 10430569.
  18. ^ "ICTV Taxonomy history: Ligamenvirales". International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.
  19. ^ Prangishvili D, Krupovic M (21 June 2012). "Create the order Ligamenvirales containing the families Rudiviridae and Lipothrixviridae" (PDF). International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.
  20. ^ "ICTV Taxonomy history: Adnaviria". International Committee on Taxonomy of Viruses (ICTV). Retrieved 20 July 2021.

External links edit

  •   Media related to Adnaviria at Wikimedia Commons

December 18, 2023
adnaviria, realm, viruses, that, includes, archaeal, viruses, that, have, filamentous, virion, body, linear, double, stranded, genome, genome, exists, form, encodes, dimeric, major, capsid, protein, that, contains, sirv2, fold, type, alpha, helix, bundle, cont. Adnaviria is a realm of viruses that includes archaeal viruses that 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 of alpha helix bundle containing four helices The virion consists of the genome encased in capsid proteins to form a helical nucleoprotein complex For some viruses this helix is surrounded by a lipid membrane called an envelope 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 AdnaviriaAcidianus filamentous virus 3 AFV3 virionVirus classification unranked VirusRealm AdnaviriaKingdom ZilligviraePhylum TaleaviricotaClass TokiviricetesSubtaxaSee textAdnaviria was established in 2020 after cryogenic electron microscopy showed that the viruses in the realm were related due to a shared MCP A DNA and general virion structure Viruses in Adnaviria infect hyperthermophilic archaea 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 in Adnaviria have 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 Contents 1 Etymology 2 Characteristics 3 Phylogenetics 4 Classification 5 History 6 See also 7 References 8 External linksEtymology editAdnaviria takes 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 viria is the suffix used for virus realms The sole kingdom in the realm Zilligvirae is named after Wolfram Zillig 1925 2005 for his research on hyperthermophilic archaea with the virus kingdom suffix virae The name of the sole phylum Taleaviricota is derived from Latin talea 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 from Georgian toki თოკი meaning thread and the suffix used for virus classes viricetes 2 Characteristics editViruses in Adnaviria infect 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 are hyperthermophiles and acidophiles microorganisms from the archaea domain 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 For rudiviruses this is a homodimer whereas for lipothrixviruses and tristromaviruses 8 it is a heterodimer of paralogous MCPs The MCPs of viruses in Adnaviria contain 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 editViruses in Adnaviria have 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 are glycosyltransferases ribbon helix helix transcription factors and anti CRISPR proteins Adnaviruses are morphologically similar to non archaeal filamentous viruses but their virions are built from different capsid proteins Viruses of Clavaviridae a family of filamentous archaeal viruses morphologically similar to adnaviruses likewise possess MCPs that show no relation to the MCPs of viruses in Adnaviria and for that reason are excluded from the realm 2 Classification editAdnaviria is 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 order Sulfolobales containing the families Lipothrixviridae and Rudiviridae Order Maximonvirales which contains viruses that infect archaea of the Candidatus order Menathophagales currently containing the single species Yumkaaxvirus pescaderoense Order Primavirales which contains viruses that infect archaea of the order Thermoproteales containing the family TristromaviridaeHistory editViruses of Adnaviria began 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 families Lipothrixviridae and Rudiviridae were then united under the order Ligamenvirales in 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 establishing Adnaviria in the same year 8 20 See also edit nbsp Viruses portalList of higher virus taxaReferences edit a b Krupovic 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 PMC 8274609 PMID 34011550 a b c d e Krupovic 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 Retrieved 20 July 2021 a b c Lipothrixviridae International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 dead link a b c Rudiviridae International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 dead link a b c Prangishvili 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 PMID 30540248 S2CID 54475961 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 ISSN 0022 538X PMC 8274609 PMID 34011550 Silva Jorge Miguel Pratas Diogo Caetano Tania Matos Sergio 2022 08 11 The complexity landscape of viral genomes GigaScience 11 giac079 doi 10 1093 gigascience giac079 ISSN 2047 217X PMC 9366995 PMID 35950839 a b Wang 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 PMC 7189273 PMID 32368353 Prangshvili D Krupovic M July 2016 Create genus Alphatristromavirus within the new family Tristromaviridae and remove genus Alphalipothrixvirus from the family Lipothrixviridae PDF International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 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 PMC 2675988 PMID 19158076 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 PMID 32665595 S2CID 220516514 Virus Taxonomy 2022 Release International Committee on Taxonomy of Viruses ICTV March 2021 Retrieved 20 July 2021 a b Snyder 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 PMID 25866378 Stedman K Wolfram ASM Letter PDF Portland State University Retrieved 20 July 2021 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 archaebacterium Thermoproteus tenax Mol Gen Genet 192 1 2 39 45 doi 10 1007 BF00327644 S2CID 46094905 ICTV Taxonomy history Betatristromavirus TTV1 International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 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 PMC 1460677 PMID 10430569 ICTV Taxonomy history Ligamenvirales International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 Prangishvili D Krupovic M 21 June 2012 Create the order Ligamenvirales containing the families Rudiviridae and Lipothrixviridae PDF International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 ICTV Taxonomy history Adnaviria International Committee on Taxonomy of Viruses ICTV Retrieved 20 July 2021 External links edit nbsp Media related to Adnaviria at Wikimedia Commons Retrieved from https en wikipedia org w index php title Adnaviria amp oldid 1165159780, wikipedia, wiki, book, books, library,

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