Jump to content

Adnaviria

From Wikipedia, the free encyclopedia
(Redirected from Zilligvirae)
Adnaviria
Right hand rotation of A-DNA in standard CPK (Corey-Pauling-Koltun) coloring.
Virus classification Edit this classification
(unranked): Virus
Realm: Adnaviria
Kingdom: Zilligvirae
Phylum: Taleaviricota
Class: Tokiviricetes
Subtaxa

See text

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 adnaviruses, 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 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 and acidophilic archaea, i.e. archaea that inhabit very high temperature environments and highly acidic environments. 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, which refers 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, which means "rod" and refers 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), which means "thread", and the suffix used for virus classes, -viricetes.[2]

Characteristics

[edit]

Viruses in Adnaviria infect hyperthermophilic and acidophilic archaea and have linear, double-stranded DNA (dsDNA) genomes that range from about 16 to 56 kilobase pairs in length. The ends of their genomes contain inverted terminal repeats.[3][4][5] Their genomes exist in A-form, also called A-DNA,[1] a type of DNA that has a compact right-handed helix with more base pairs per turn than B-form DNA.[6] 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 that contains genomic A-DNA.[2] The A-form genome may be an adaptation to allow DNA survival under extreme conditions.[1] Furthermore, viruses in Adnaviria have high genome redundancy, which also might be an adaptation to survive such extreme environments.[7]

Negative contrast electron micrographs of virions of Sulfolobus islandicus filamentous virus, a lipothrixvirus. The length of the bars is 100 nm.

The nucleoprotein helix is composed of asymmetric units of two MCPs. For rudiviruses, this is homodimer, a molecule formed by the bonding of two identical MCPs. For lipothrixviruses and tristromaviruses,[8] it is heterodimer, a molecule formed by the bonding of two different MCPs that are paralogous, i.e. the result of a gene duplication event. The MCPs of viruses in Adnaviria contain a folded structure that consists of a type of alpha-helix bundle that contains four helices,[4] called the SIRV2 fold and named after Sulfolobus islandicus rod-shaped virus 2 (SIRV2).[2] The four-helix bundle is found at the end (C-terminus) of the protein while the beginning (N-terminus) of the protein has an extended α-helical arm that wraps tightly around the dsDNA genome to change it to A-form.[8] 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 and ungulaviruses have flexible virions about 410–2,200 nanometers (nm) in length and 24–38 nm in width in which the nucleoprotein helix is surrounded by a lipid envelope.[3][9][10] 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][11] Rudviruses have stiff, non-enveloped, rod-like virions about 600–900 by 23 nm.[4][9] At both ends of the virion, lipothrixviruses and ungulaviruses 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][12]

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.[13] 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, likewise possess MCPs and virion organization that show no relation to the MCPs and virion organization of viruses in Adnaviria and for that reason are excluded from the realm.[2][9]

Classification

[edit]

Adnaviria is monotypic down to the rank of its sole class, Tokiviricetes, which has three orders. This taxonomy is shown hereafter:[2][14]

History

[edit]

Viruses of Adnaviria began to be discovered in the 1980s by Wolfram Zillig and his colleagues.[15] To discover these viruses, Zillig developed the methods used to culture their hosts.[16] The first of these to be described were TTV1, TTV2, and TTV3 in 1983.[17] TTV1 was classified as the first lipothrixvirus but is now classified as a tristromavirus.[18] SIRV2, a rudivirus, became a model for studying virus-host interactions[15] after its discovery in 1998.[19] The families Lipothrixviridae and Rudiviridae were then united under the order Ligamenvirales in 2012 based on evidence of their relation.[20][21] Cryogenic electron microscopy would later show in 2020 that the MCPs of tristromaviruses contained a SIRV2-like fold like ligamenviruses, which provided justification for establishing Adnaviria in the same year.[8][22]

See also

[edit]

References

[edit]
  1. ^ a b c 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". J Virol. 95 (15): e0067321. doi:10.1128/JVI.00673-21. PMC 8274609. PMID 34011550.
  2. ^ a b c d e f 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). ictv.global. International Committee on Taxonomy of Viruses. Retrieved 20 July 2021.
  3. ^ a b c "Lipothrixviridae". ictv.global. International Committee on Taxonomy of Viruses. Retrieved 14 January 2025.
  4. ^ a b c "Rudiviridae". ictv.global. International Committee on Taxonomy of Viruses. Retrieved 14 January 2025.
  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. ^ Louten J (28 May 2022). Essential Human Virology. Academic Press. p. 28. ISBN 9780323914925. Retrieved 14 January 2025.
  7. ^ Silva JM, Pratas D, Caetano T, Matos S (11 August 2022). "The complexity landscape of viral genomes". Gigascience. 11: giac079. doi:10.1093/gigascience/giac079. ISSN 2047-217X. PMC 9366995. PMID 35950839.
  8. ^ a b c 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. ^ a b c d Pumpens P, Pushko P (22 May 2022). Virus-Like Particles. CRC Press. p. 2011–2016. ISBN 9781000569872. Retrieved 14 January 2025.
  10. ^ a b Krupovic M (2021). "Rename genus Gammalipothrixvirus to Captovirus and move it to a new family Ungulaviridae (Ligamenvirales)" (docx). ictv.global. International Committee on Taxonomy of Viruses. Retrieved 14 January 2025.
  11. ^ Prangshvili D, Krupovic M (July 2016). "Create genus Alphatristromavirus within the new family Tristromaviridae and remove genus Alphalipothrixvirus from the family Lipothrixviridae" (PDF). ictv.global. International Committee on Taxonomy of Viruses. Retrieved 20 July 2021.
  12. ^ 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.
  13. ^ 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.
  14. ^ "Virus Taxonomy: 2023 Release". ictv.global. International Committee on Taxonomy of Viruses. 30 October 2024. Retrieved 14 January 2025.
  15. ^ 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.
  16. ^ Stedman K. "Wolfram ASM Letter" (PDF). Portland State University. Retrieved 20 July 2021.
  17. ^ 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.
  18. ^ "ICTV Taxonomy history: Betatristromavirus TTV1". ictv.global. International Committee on Taxonomy of Viruses. Retrieved 20 July 2021.
  19. ^ 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.
  20. ^ "ICTV Taxonomy history: Ligamenvirales". ictv.global. International Committee on Taxonomy of Viruses. Retrieved 20 July 2021.
  21. ^ Prangishvili D, Krupovic M (21 June 2012). "Create the order Ligamenvirales containing the families Rudiviridae and Lipothrixviridae" (PDF). ictv.global. International Committee on Taxonomy of Viruses. Retrieved 20 July 2021.
  22. ^ "ICTV Taxonomy history: Adnaviria". ictv.global. International Committee on Taxonomy of Viruses. Retrieved 20 July 2021.
[edit]
  • Media related to Adnaviria at Wikimedia Commons

Retrieved from "https://en.wikipedia.org/w/index.php?title=Adnaviria&oldid=1269720844"