''Tombusviridae'' is a family of single-stranded positive sense

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

plant

virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...

es. The family contains 18 genera in 3 subfamilies. The name is derived from Tomato bushy stunt virus (TBSV).

Genome

All viruses in the family have a non-segmented (monopartite) linear

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

, with the exception of Dianthoviruses, whose genome is bipartite.Wiley InterScience Encyclopedia of Life Sciences: Tombusviridae
/ref> 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 Helicases are a class of enzymes that are vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic double helix, separating the two hybridized ...

encoded by the virus. 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

Structure

The RNA is encapsulated in an icosahedral (T=3)

capsid A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or m ...

, composed of 180 units of a single coat protein 27–42K in size; the

virion A virion (plural, ''viria'' or ''virions'') is an inert virus particle capable of invading a Cell (biology), cell. Upon entering the cell, the virion disassembles and the genetic material from the virus takes control of the cell infrastructure, t ...

measures 28–35 nm in diameter, and it is not enveloped.ICTVdB—The Universal Virus Database, version 3
00.074. ''Tombusviridae''

Life cycle

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. 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 Grafting or graftage is a horticulture, horticultural technique whereby tissues of plants are joined so as to continue their growth together. The upper part of the combined plant is called the scion () while the lower part is called the roots ...

or mechanical inoculation, and both the virion and the genetic material alone are infective.

Replication

Members of ''Tombusviridae'' replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive

sense A sense is a biological system used by an organism for sensation, the process of gathering information about the surroundings through the detection of Stimulus (physiology), stimuli. Although, in some cultures, five human senses were traditio ...

(+)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 Transcription is the process of copying a segment of DNA into RNA for the purpose of gene expression. Some segments of DNA are transcribed into RNA molecules that can encode proteins, called messenger RNA (mRNA). Other segments of DNA are transc ...

. The level of RNA synthesis has been shown to be affected by the

cis-acting ''Cis''-regulatory elements (CREs) or ''cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morpho ...

properties of certain elements on the RNA (such as RNA1 and 2), 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 In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template. Using the e ...

, found encoded within the genome.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.2012.00279K. 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 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.

Notes

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.NCBI
Defective interfering RNA-4 of tomato bushy stunt virus
(TBSV-P DI-4) an
Defective interfering RNA-5 of tomato bushy stunt virus
(TBSV-P DI-5) 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.

Taxonomy

The family contains the following subfamilies and genera (-''virinae'' denotes subfamily and -''virus'' denotes genus): * '' Calvusvirinae'' ** '' Umbravirus'' * '' Procedovirinae'' ** '' Alphacarmovirus'' ** '' Alphanecrovirus'' ** '' Aureusvirus'' ** '' Avenavirus'' ** '' Betacarmovirus'' ** '' Betanecrovirus'' ** '' Gallantivirus'' ** '' Gammacarmovirus'' ::* '' Macanavirus'' ::* '' Machlomovirus'' ::* '' Panicovirus'' ::* '' Pelarspovirus'' ::* '' Tombusvirus'' ::* '' Tralespevirus'' ::* '' Zeavirus'' * '' Regressovirinae'' ** '' Dianthovirus'' ** '' Luteovirus''

References

External links

Viralzone: Tombusviridae

ICTV
{{Authority control Viral plant pathogens and diseases Virus families Riboviria