Virgaviridae

Genus: Tobamovirus


Genus: Tobamovirus

Distinguishing features

Tobamoviruses are the only members of the family to have a non-segmented genome. They have a “30K”-like cell-to-cell movement protein, are not vector-transmissible and when seed transmitted, the embryo is not affected. It is the largest genus in the family and the literature is extensive. For reviews of diversity and evolution within the genus see (Gibbs et al., 2015, Lartey et al., 1996, Stobbe et al., 2012).

Virion

Morphology

Virions are 18 nm in diameter and have a predominant length of 300–310 nm (Figure 1.Tobamovirus). Structure and assembly of the particles have been reviewed by (Klug 1999). Shorter virions produced by the encapsidation of subgenome-sized RNA are usually a minor component of the virion population, although virions of two species produce an abundant short virion of 32–34 nm. Virions often form large crystalline arrays visible by light microscopy.

Figure 1.Tobamovirus. (Left) Model of particle of tobacco mosaic virus (TMV). Also shown is the RNA as it is thought to participate in the assembly process. (Right) Negative contrast electron micrograph of TMV particle stained with uranyl acetate. The bar represents 100 nm.

Physicochemical and physical properties

Virion Mr is 40×106. Buoyant density in CsCl is 1.325 g cm−3. S20,w is 194S. Tobamoviruses have thermal inactivation points (10 min) of 90 °C and survive in plant sap for many years.

Nucleic acid

The genome is 6.3–6.6 kb in size. An approximately 70 nt long 5′-NTR contains many AAC repeats and few or no G nucleotides. The 0.2–0.4 kb 3′-NTR contains sequences that can be folded into pseudoknots followed by 3′-terminal sequences that can be folded into a tRNA-like, amino acid-accepting structure. The subgenomic mRNAs transcribed in infected cells also have a 5′-terminal cap and 3′-tRNA-like structure. The encapsidation signal is usually located within the ORF encoding the MP (Wilson and McNicol 1995) or within the ORF encoding the CP in the studied isolates of Cucumber green mottle mosaic virus and Sunn hemp mosaic virus.

Proteins

Virions contain a single structural protein (17–18 kDa). Two nonstructural proteins are expressed directly from the genomic RNA: a 124–132 kDa protein terminated by an amber (UAG) stop codon and a 181–189 kDa protein produced by readthrough of this stop codon, both of which are required for efficient replication. A third nonstructural protein (28–31 kDa) is required for cell-to-cell and long-distance movement and belongs to the “30K”-like cell-to-cell movement proteins. The MP is associated with plasmodesmata and has single-stranded nucleic acid binding activity in vitro. The CP is not required for cell-to-cell movement, but has a role in vascular tissue dependent virus accumulation. The replication proteins have also been implicated in virus movement. The MP and CP are expressed from individual 3′-co-terminal subgenomic mRNAs. The MP is expressed early during infection, whereas the CP is expressed later, and at higher levels. The MP and CP are not required for replication in single cells. The N-terminal one-third of the 124–132 kDa protein has similarity with methyltransferase/guanylyl transferases whereas the C-terminal one-third of the 124–132 kDa protein has similarity with RNA helicases (including an NTP-binding motif). The readthrough domain of the 181–189 kDa protein has motifs common to RdRPs.

Genome organization and replication

The single genomic RNA encodes at least four proteins. The 124–132 kDa and 181–189 kDa replication proteins are translated directly from the 5' proximal ORF of the genomic RNA. The 124–132 kDa replication protein contains the Mtr and Hel domains. The 181–189 kDa replication protein additionally contains the polymerase domain, synthesized by occasional readthrough of the leaky termination codon of the 124–132 kDa protein encoding ORF. The 181–189 kDa replication protein is the only protein required for replication in single cells, although the 124–132 kDa replication protein is also required for efficient replication. The  downstream ORFs encode the 28–31 kDa MP and 17–18 kDa CP, which are translated from their respective 3′ co-terminal sgRNAs, both of which contain a 5′ cap (Figure 2.Tobamovirus). In the members of some species, the MP ORF overlaps both the 181–189 kDa protein and the CP ORFs, whereas in other species it does not overlap either ORF or overlaps one of the ORFs. An ORF  that encodes a cysteine-rich protein is located between the 181-189 kDa and MP ORFs in passion fruit mosaic virus. a tobamovirus isolated from maypop, a plant classified in the order Malpighiales (Stobbe et al., 2012).

Figure 2.Tobamovirus. Genome organization of tobacco mosaic virus (TMV). Genomic RNA is capped and is template for expression of the 126 and 183 kDa proteins. The 3′ distal movement protein (MP) and capsid protein (CP) ORFs are expressed from separate 3′ co-terminal sgRNAs. The tRNA structure motif at the 3′-end of the RNA is represented by a dark square.

RNA replication occurs via several steps: (a) synthesis of viral replication proteins by translation of the genomic RNA; (b) translation-coupled binding of the replication proteins to a 5'-terminal region of the genomic RNA; (c) recruitment of the genomic RNA by replication proteins onto membranes and formation of a complex with host proteins TOM1 and ARL8; (d) synthesis of complementary (negative-strand) RNA in the complex; and (e) synthesis of progeny genomic RNA (Ishibashi and Ishikawa 2016).

Antigenicity

The virions act as strong immunogens and members of different species are serologically distinct.

Biology

Most species have moderate to wide host ranges under experimental conditions, although in nature host ranges are usually quite narrow. The viruses are found in all parts of host plants. Transmission occurs without the help of vectors by contact between plants and sometimes by seed, although this occurs in the absence of infection of the embryo. 

Species demarcation criteria

Many tobamoviruses that were historically designated as strains of tobacco mosaic virus are now defined as separate species based on nucleotide sequence data.

The criteria demarcating species in the genus are:

  • Sequence similarity: more than 90% whole genome nt sequence identity is considered to characterize strains of the same species. Most of the sequenced tobamoviruses of different species have considerably less than 90% sequence identity
  • Host range: however many of these viruses have wider and more overlapping host ranges in experimental rather than natural situations
  • Antigenic relationships between the CPs 

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)
Bell pepper mottle virusbell pepper mottle virusNetherlands DQ355023NC_009642Complete genomeBPMV-Netherlands
Brugmansia mild mottle virusBrugmansia mild mottle virus2373AM398436NC_010944Complete genomeBrMMV-2373
Cactus mild mottle viruscactus mild mottle virusKrEU043335NC_011803Complete genomeCMMoV-Kr
Clitoria yellow mottle virusClitoria yellow mottle virusLarrimah JN566124NC_016519Complete genomeCliYMV-Larrimah
Cucumber fruit mottle mosaic viruscucumber fruit mottle mosaic virusWangAF321057NC_002633Complete genomeCFMMV-Wang
Cucumber green mottle mosaic viruscucumber green mottle mosaic virusSHD12505NC_001801Complete genomeCGMMV-SH
Cucumber mottle viruscucumber mottle virusKubotaAB261167NC_008614Complete genomeCMoV-Kubota
Frangipani mosaic virusFrangipani mosaic virusP HM026454NC_014546Complete genomeFrMV-P
Hibiscus latent Fort Pierce virusHibiscus latent Fort Pierce virusJ AB917427NC_025381Complete genomeHLFPV-J
Hibiscus latent Singapore virusHibiscus latent Singapore virusSingapore AF395898NC_008310Complete genomeHLSV-Singapore
Kyuri green mottle mosaic virusKyuri green mottle mosaic virusC1AJ295948NC_003610Complete genomeKGMMV-C1
Maracuja mosaic virusmaracuja mosaic virusPeruDQ356949NC_008716Complete genomeMarMV-Peru
Obuda pepper virusObuda pepper virusTMV-ObD13438NC_003852Complete genomeObPV-TMV-Ob
Odontoglossum ringspot virusOdontoglossum ringspot virusX82130NC_001728Complete genomeORSV
Paprika mild mottle viruspaprika mild mottle virusJapanAB089381NC_004106Complete genomePaMMV-Japan
Passion fruit mosaic viruspassion fruit mosaic virusUSAHQ389540NC_015552Complete genomePFMV-USA
Pepper mild mottle viruspepper mild mottle virusSM81413NC_003630Complete genomePMMoV-S
Plumeria mosaic virusPlumeria mosaic virusPlu-Ind-1KJ395757NC_026816Complete genomePluMV-Plu-Ind-1
Rattail cactus necrosis-associated virusrattail cactus necrosis-associated virusSouth Korea JF729471NC_016442Complete genomeRCNaV-Soth Korea
Rehmannia mosaic virusRehmannia mosaic virusHenan EF375551NC_009041Complete genomeRheMV-Henan
Ribgrass mosaic virusribgrass mosaic virusKons.1105-R14HQ667979NC_002792Complete genomeRMV-Kons-1105-R14
Sammons's Opuntia virusSammons's Opuntia virusno entry in GenbankSOV
Streptocarpus flower break virusStreptocarpus flower break virusWillingmannAM040955NC_008365Complete genomeSFBV-Willingmann
Sunn-hemp mosaic virussunn-hemp mosaic virusU47034; J02413Partial genomeSHMV
Tobacco latent virustobacco latent virus; Nigerian tobacco latent virusAY137775Partial genomeTLV
Tobacco mild green mosaic virustobacco mild green mosaic virusSolisM34077NC_001556Complete genomeTMGMV-Solls
Tobacco mosaic virustobacco mosaic virusvariant 1V01408NC_001367Complete genomeTMV-variant 1
Tomato brown rugose fruit virustomato brown rugose fruit virusTom1-JoKT383474NC_028478Complete genomeTBRFV-Tom1-Jo
Tomato mosaic virustomato mosaic virusQueenslandAF332868NC_002692Complete genomeToMV-Queensland
Tomato mottle mosaic virustomato mottle mosaic virusMX5 KF477193NC_022230Complete genomeToMMV-MX5
Tropical soda apple mosaic virustropical soda apple mosaic virusOkeechobee KU659022NC_030229Complete genomeTSAMV-Okeechobee
Turnip vein-clearing virusturnip vein-clearing virusOSUU03387NC_001873Complete genomeTVCV-OSU
Ullucus mild mottle virusUllucus mild mottle virusno entry in GenbankUMMV
Wasabi mottle viruswasabi mottle virusShizuaAB017503NC_003355Complete genomeWMoV-Shizua
Yellow tailflower mild mottle virusyellow tailflower mild mottle virusCervantes KF495564NC_022801Complete genomeYTMMV-Cervantes
Youcai mosaic virusyoucai mosaic virus; oil-seed rape mosaic virusU30944NC_004422Complete genomeYoMV
Zucchini green mottle mosaic viruszucchini green mottle mosaic virusKAJ295949NC_003878Complete genomeZGMMV-K

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Derivation of names

Tobamo: from tobacco mosaic virus.

Related, Unclassified Viruses

Virus name

Accession number

Virus abbreviation

Abutilon yellow mosaic virus

EU559678*

AbYMV

Hoya chlorotic spot virus

KX434725

HCSV

* partial genome
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.
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