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Tombusviridae

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Tombusviridae
Virus classification Edit this classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Kitrinoviricota
Class: Tolucaviricetes
Order: Tolivirales
Family: Tombusviridae

Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are three subfamilies, 17 genera, and 95 species in this family.[1][2] The name is derived from Tomato bushy stunt virus (TBSV).[3]

Genome

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Tombusviridae genome map

All viruses in the family have a non-segmented (monopartite) linear genome, with the exception of Dianthoviruses, whose genome is bipartite.[4] The genome is approximately 4.6–4.8kb in length, lacks a 5' cap and a poly(A) tail, and it encodes 4–6 ORFs. The polymerase encodes an amber stop codon which is the site of a readthrough event within ORF1, producing two products necessary for replication. There is no helicase encoded by the virus.[5]

Structure

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The RNA is encapsulated in an icosahedral (T=3) capsid, composed of 180 units of a single coat protein 27–42K in size; the virion measures 28–35 nm in diameter, and it is not enveloped.[1][6]

Life cycle

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Viral replication is cytoplasmic, and is lysogenic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. Translation takes place by leaky scanning, −1 ribosomal frameshifting, viral initiation, and suppression of termination. The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host. Transmission routes are mechanical, seed borne, and contact.[1][7]

Viruses in this family are primarily soil-borne, some transmitted by fungal species of the order Chytridiales, others by no known vector. Virions may spread by water, root growth into infected soil, contact between plants, pollen, or seed, depending on the virus species. These viruses may be successfully transmitted by grafting or mechanical inoculation, and both the virion and the genetic material alone are infective.[6]

Replication

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Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive sense ( )RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis.[5]

The level of RNA synthesis has been shown to be affected by the cis-acting properties of certain elements on the RNA (such as RNA1 and 2[8][9]), which include core promoter sequences which regulate the site of initiation for the complementary RNA strand synthesis. This mechanism is thought to be recognised by RNA-dependent RNA polymerase, found encoded within the genome.[5][7][10]

Viruses in Tombusviridae have been found to co-opt GAPDH, a host metabolic enzyme, for use in the replication center. GAPDH may bind to the (−)RNA strand and keep it in the replicase complex, allowing ( )RNA strands synthesized from it to be exported and accumulate in the host cell. Downregulation of GAPDH reduced viral RNA accumulation, and eliminated the surplus of ( )RNA copies.[11]

Notes

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Research has shown that infection of plants from tombusviruses contain defective interfering RNAs that are born directly from the viruses RNA genome, and no host genome. Viral DI RNAs with their small size and cis-acting elements are good templates both in vivo and in vitro on which to study RNA replication.[12][13][14]

Sub-genomic RNA is used in the synthesis of some proteins; they are generated by premature termination of (−)strand synthesis. sgRNAs and sgRNA negative-sense templates are found in infected cells.[6]

Taxonomy

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The family contains the following subfamilies and genera (-virinae denotes subfamily and -virus denotes genus):[2]

Lastly, one genus is unassigned to a subfamily: Luteovirus.[2]

References

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  1. ^ a b c "Viral Zone". ExPASy. Retrieved 15 June 2015.
  2. ^ a b c "Virus Taxonomy: 2020 Release". International Committee on Taxonomy of Viruses (ICTV). March 2021. Retrieved 16 May 2021.
  3. ^ Habili, N. and Symons, R. H. (1989). Evolutionary relationship between luteoviruses and other RNA plant viruses based on sequence motifs in their putative RNA polymerases and nucleic acid helicases. Nucleic Acids Research 17:23, 9543–55
  4. ^ Wiley InterScience Encyclopedia of Life Sciences: Tombusviridae
  5. ^ a b c ICTV: Family - Tombusviridae, in: Virus Taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses 2012, pp 1111-1138, 23 November 2011, doi:10.1016/B978-0-12-384684-6.00096-3
  6. ^ a b c ICTVdB—The Universal Virus Database, version 3 00.074. Tombusviridae
  7. ^ a b Beth L. Nicholson, Pui Kei K. Lee, K. A. White: Internal RNA replication elements are prevalent in Tombusviridae, in: Front. Microbiol., 06 August 2012, doi:10.3389/fmicb.2012.00279
  8. ^ Lommel SA, Weston-Fina M, Xiong Z, Lomonossoff GP (September 1988). "The nucleotide sequence and gene organization of red clover necrotic mosaic virus RNA-2". Nucleic Acids Res. 16 (17): 8587–602. doi:10.1093/nar/16.17.8587. PMC 338578. PMID 3047682.
  9. ^ Mizumoto H, Tatsuta M, Kaido M, Mise K, Okuno T (November 2003). "Cap-independent translational enhancement by the 3' untranslated region of red clover necrotic mosaic virus RNA1". J. Virol. 77 (22): 12113–21. doi:10.1128/JVI.77.22.12113-12121.2003. PMC 254280. PMID 14581548.
  10. ^ K. Andrew White, Peter D. Nagy: Advances in the Molecular Biology of Tombusviruses: Gene Expression, Genome Replication, and Recombination, in: Progress in Nucleic Acid Research and Molecular Biology, Vol. 78, 2004, pp. 187-226, doi:10.1016/S0079-6603(04)78005-8
  11. ^ Wang, R. and Nagy, P. (2008) Tomato bushy stunt virus Co-Opts the RNA-Binding Function of a Host Metabolic Enzyme for Viral Genomic RNA Synthesis. Cell Host & Microbe 3:3 178–187
  12. ^ NCBI: Defective interfering RNA-4 of tomato bushy stunt virus (TBSV-P DI-4) and Defective interfering RNA-5 of tomato bushy stunt virus (TBSV-P DI-5)
  13. ^ Yamamura, Yoshimi; Scholthof, Herman B. (1 September 2005). "Tomato bushy stunt virus: a resilient model system to study virus-plant interactions". Molecular Plant Pathology. 6 (5): 491–502. doi:10.1111/j.1364-3703.2005.00301.x. PMID 20565674.
  14. ^ Scholthof, Karen-Beth G.; Scholthof, Herman B.; Jackson, Andrew O. (1 August 1995). "The Effect of Defective Interfering RNAs on the Accumulation of Tomato Bushy Stunt Virus Proteins and Implications for Disease Attenuation". Virology. 211 (1): 324–328. doi:10.1006/viro.1995.1410. PMID 7645230.
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