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

positive sense In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, ...

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

plant

virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

es. There are three subfamilies, 17 genera, and 95 species in this family. The name is derived from ''

Tomato bushy stunt virus Tomato bushy stunt virus (TBSV) is a virus of the tombusvirus family. It was first reported in tomatoes in 1935 and primarily affects vegetable crops, though it is not generally considered an economically significant plant pathogen. Depending up ...

'' (TBSV).

Genome

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

genome In the fields of molecular biology and genetics, 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 ge ...

, 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 In molecular biology, the five-prime cap (5′ cap) is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation o ...

and a poly(A) tail, and it encodes 4–6

ORF ORF or Orf may refer to: * Norfolk International Airport, IATA airport code ORF * Observer Research Foundation, an Indian research institute * One Race Films, a film production company founded by Vin Diesel * Open reading frame, a portion of the ...

s. 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 thought to be 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 acid phosphodiester backbone, separatin ...

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 In geometry, an icosahedron ( or ) is a polyhedron with 20 faces. The name comes and . The plural can be either "icosahedra" () or "icosahedrons". There are infinitely many non- similar shapes of icosahedra, some of them being more symmetrica ...

(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 may ...

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

virion A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

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 Fungi of the order Chytridiales, like other members of its division, may either have a monocentric thallus or a polycentric rhizomycelium. When the ribosomal genes of members classified in this order were first examined using molecular techniqu ...

, 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 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 rootstock. The succ ...

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 world through the detection of Stimulus (physiology), stimuli. (For example, in the human body, the brain which is part of the cen ...

(+)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. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called ...

. 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 synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the ...

, 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 Glyceraldehyde 3-phosphate dehydrogenase (abbreviated GAPDH) () is an enzyme of about 37kDa that catalyzes the sixth step of glycolysis and thus serves to break down glucose for energy and carbon molecules. In addition to this long establishe ...

, 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 ''Alphanecrovirus'' is a genus of viruses, in the 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. The name is d ...

'' ** ''

Aureusvirus ''Aureusvirus'' is a genus of viruses, in the family ''Tombusviridae''. Plants serve as natural hosts. There are six species in this genus. Taxonomy The genus contains the following species: * '' Cucumber leaf spot virus'' * '' Elderberry aureu ...

'' ** '' Avenavirus'' ** '' Betacarmovirus'' ** ''

Betanecrovirus ''Betanecrovirus'' is a genus of viruses, in the 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. The name is de ...

'' ** '' Gallantivirus'' ** '' Gammacarmovirus'' ** '' Macanavirus'' ** '' Machlomovirus'' ** '' Panicovirus'' ** '' Pelarspovirus'' ** ''

Tombusvirus ''Tombusvirus'' is a genus of viruses, in the family '' Tombusviridae''. Plants serve as natural hosts. There are 17 species in this genus. Symptoms associated with this genus include mosaic. The name of the genus comes from ''Tomato bushy stunt ...

'' ** '' Zeavirus'' ** Species unassigned to a genus in ''Procedovirinae'': *** ''

Ahlum waterborne virus Ahlum is a village and a former municipality in the district Altmarkkreis Salzwedel, in Saxony-Anhalt, Germany Germany,, officially the Federal Republic of Germany, is a country in Central Europe. It is the second most populous co ...

'' *** '' Bena mild mosaic virus'' *** '' Chenopodium necrosis virus'' *** ''

Cucumber soil-borne virus Cucumber (''Cucumis sativus'') is a widely-cultivated creeping vine plant in the Cucurbitaceae family that bears usually cylindrical fruits, which are used as culinary vegetables.Trailing lespedeza virus 1'' *** '' Weddel waterborne virus'' * '' Regressovirinae'' ** '' Dianthovirus'' Lastly, one genus is unassigned to a subfamily: ''

Luteovirus ''Luteovirus'' is a genus of viruses, in the family ''Tombusviridae''. There are 13 species in this genus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via ...

''.

References

External links

Viralzone: Tombusviridae

ICTV
{{Taxonbar, from=Q3117439 Viral plant pathogens and diseases Virus families Riboviria