Tombusviridae
Encyclopedia
Tombusviridae is a family of single-stranded positive sense
Sense (molecular biology)
In molecular biology and genetics, sense is a concept used to compare the polarity of nucleic acid molecules, such as DNA or RNA, to other nucleic acid molecules...

 RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 plant virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...

es. The name is derived from the type species of the Tombusvirus genus, Tomato bushy stunt virus
Tomato bushy stunt virus
Tomato bushy stunt virus is a tombusvirus first reported in tomatoes in 1935. Depending upon the host, TBSV causes stunting of growth, leaf mottling, and deformed or absent fruit. The virus is transmitted manually through the use of contaminated cutting tools...

 (TBSV). Viruses in this family are classified as Type IV viruses in the Baltimore classification
Baltimore classification
The Baltimore classification, developed by David Baltimore, is a virus classification system that groups viruses into families, depending on their type of genome and their method of replication....

, and are part of the luteovirus
Luteoviridae
The Luteoviridae are a family of viruses, including the following genera:*Genus Luteovirus; type species: Barley yellow dwarf virus-PAV*Genus Polerovirus; type species: Potato leafroll virus...

 supergroup.

The RNA is encapsulated in an icosahedral
Icosahedron
In geometry, an icosahedron is a regular polyhedron with 20 identical equilateral triangular faces, 30 edges and 12 vertices. It is one of the five Platonic solids....

 (T=3) capsid
Capsid
A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic...

, 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.

Viruses in this family are primarily soil-borne, some transmitted by fungal species of the order Chytridiales
Chytridiales
Fungi of the order Chytridiales, like other members of its phylum, 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 techniques, it was discovered that the order contained some...

, 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
Grafting is a horticultural technique whereby tissues from one plant are inserted into those of another so that the two sets of vascular tissues may join together. This vascular joining is called inosculation...

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

Genome organization and replication

All Tombusviridae have a single linear genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

, with the exception of Dianthoviruses, whose genome is in two parts. The genome is approximately 4.6-4.8kb in length, with a 5' cap
5' cap
The 5' cap is a specially altered nucleotide on the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes. The process of 5' capping is vital to creating mature messenger RNA, which is then able to undergo translation...

, and it encodes 4-6 ORF
Open reading frame
In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...

s. The polymerase encodes an amber stop codon
Stop codon
In the genetic code, a stop codon is a nucleotide triplet within messenger RNA that signals a termination of translation. Proteins are based on polypeptides, which are unique sequences of amino acids. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide...

 which is the site of a readthrough event within ORF1, producing two products necessary for replication. There is no helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...

 encoded by the virus.

Members of Tombusviridae replicate
Replicate
Replicate may refer to:* In biology, replication is a process by which genetic material, a cell, or an organism reproduces or makes an exact copy or copies...

 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.

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), 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
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...

, found encoded within the genome.

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.

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.

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 Tombusviridae includes the following genera:
  • Genus Aureusvirus; type species: Pothos latent virus
  • Genus Avenavirus; type species: Oat chlorotic stunt virus
  • Genus Carmovirus
    Carmovirus
    Carmovirus is a genus of the family Tombusviridae. It is classified under the Baltimore classification system as a group IV virus, having a single-stranded, positive-sense RNA genome. Replication occurs in the cytoplasm. The genome is 3800-4300 base pairs long, although the viron contains a longer...

    ; type species: Carnation mottle virus
    Carnation mottle virus
    Carnation mottle virus is a plant pathogenic virus of the family Tombusviridae.-External links:**...

  • Genus Dianthovirus
    Dianthovirus
    The viruses of the genus Dianthovirus belong to the family Tombusviridae. Dianthoviruses are plant viruses. Examples of species of this genus include the type species, Carnation ringspot virus, Red clover necrotic mosaic virus and Sweet clover necrotic mosaic virus. The virus probably has a...

    ; type species: Carnation ringspot virus
    Carnation ringspot virus
    Carnation ringspot virus is a plant pathogenic virus of the family Tombusviridae.-External links:**...

  • Genus Machlomovirus
    Machlomovirus
    The Machlomovirus is a plant virus at the genus level under the family Tombusviridae.. The virus consist of a non-enveloped, round, icosahedral capsid of 30 nm. The whole gene is 4700 nucleotides in length.-External links:*...

    ; type species: Maize chlorotic mottle virus
    Maize chlorotic mottle virus
    Maize chlorotic mottle virus is a plant pathogenic virus.Maize chlorotic mottle virus is the type species of the genus Machlomovirus...

  • Genus Necrovirus; type species: Tobacco necrosis virus A
  • Genus Panicovirus; type species: Panicum mosaic virus
    Panicum mosaic virus
    Panicum mosaic virus is a pathogenic plant virus noted for causing the grass disease St. Augustine Decline. It is a positive-sense ssRNA virus and the type species of the genus Panicovirus, readily spread by humans through tools such as lawn mower blades, but not known to be spread via biological...

  • Genus Tombusvirus
    Tombusvirus
    The genus Tombusvirus are part of the family Tombusviridae and are members of group IV of the Baltimore classification of viruses. The genomes consist of positive sense single-stranded RNA with a genome size of 4800 nucleotides. The virions are non-enveloped with a diameter of 30 nm and have...

    ; type species: Tomato bushy stunt virus
    Tomato bushy stunt virus
    Tomato bushy stunt virus is a tombusvirus first reported in tomatoes in 1935. Depending upon the host, TBSV causes stunting of growth, leaf mottling, and deformed or absent fruit. The virus is transmitted manually through the use of contaminated cutting tools...


External links

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