Tombusviridae

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Tombusviridae
Virus classification
Group: Group IV ((+)ssRNA)
Family: Tombusviridae
Genera

Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are currently 71 species in this family, divided among 13 genera.[1][2] The name is derived from the type species of the Tombusvirus genus, Tomato bushy stunt virus (TBSV).[3]

Genome[edit]

All Tombusviridae have a non-segmented 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.

Structure[edit]

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][5]

Genus Structure Symmetry Capsid Genomic arrangement Genomic segmentation
Tombusvirus Icosahedral T=3 Non-enveloped Linear Monopartite
Gallantivirus Icosahedral T=3 Non-enveloped Linear Monopartite
Macanavirus Icosahedral T=3 Non-enveloped Linear Monopartite
Dianthovirus Icosahedral T=3 Non-enveloped Linear Bipartite
Carmovirus Icosahedral T=3 Non-enveloped Linear Monopartite
Alphanecrovirus Icosahedral T=3 Non-enveloped Linear Monopartite
Avenavirus Icosahedral T=3 Non-enveloped Linear Monopartite
Panicovirus Icosahedral T=3 Non-enveloped Linear Monopartite
Betanecrovirus Icosahedral T=3 Non-enveloped Linear Monopartite
Aureusvirus Icosahedral T=3 Non-enveloped Linear Monopartite
Umbravirus Icosahedral T=3 Non-enveloped Linear Monopartite
Machlomovirus Icosahedral T=3 Non-enveloped Linear Monopartite
Zeavirus Icosahedral T=3 Non-enveloped Linear Monopartite

Life cycle[edit]

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]

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 ineffective.[5]

Genus Host details Tissue tropism Entry details Release details Replication site Assembly site Transmission
Tombusvirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Gallantivirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Macanavirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Dianthovirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Carmovirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Alphanecrovirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Avenavirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Panicovirus Plants: panicae None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Betanecrovirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Aureusvirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Umbravirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Machlomovirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed
Zeavirus Plants None Viral movement; mechanical inoculation Viral movement Cytoplasm Cytoplasm Mechanical: contact; seed

Replication[edit]

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.[citation needed]

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[6][7]), 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.[citation needed]

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.[8]

Notes[edit]

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.[citation needed]

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.[5]

Taxonomy[edit]

Group: ssRNA(+)

[2]

Pelarspovirus is an additional genus that has been proposed.[9]

References[edit]

  1. ^ a b c "Viral Zone". ExPASy. Retrieved 15 June 2015. 
  2. ^ a b ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. 
  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 ICTVdB—The Universal Virus Database, version 3 00.074. Tombusviridae
  6. ^ 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 338578Freely accessible. PMID 3047682. 
  7. ^ 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 254280Freely accessible. PMID 14581548. 
  8. ^ 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
  9. ^ Castaño A, Ruiz L, Hernández C (2009) Insights into the translational regulation of biologically active open reading frames of Pelargonium line pattern virus. Virology 386(2):417–426

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