Taxonomic Structure of the Family
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Tombusviridae |
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Virions exhibit a T = 3 icosahedral symmetry and are composed of 180 protein subunits (Fig. 1). Virions are formed with capsid proteins having one of two distinct phylogenetic origins. The virions from the genera Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, and Tombusvirus, have a rounded outline, a granular surface, and a diameter of about 32-35 nm. Each subunit folds into three distinct structural domains: R, the N-terminal internal domain interacting with RNA; S, the shell domain constituting the capsid backbone; and P, the protruding C-terminal domain, which gives the virus its granular appearance. P domains are clustered in pairs to form 90 projections. These dimeric contacts are important in the assembly and stabilization of the virion structure. The R domain, which contains many positively charged residues, binds RNA. The S domain forms a barrel structure made up of -strands. Two Ca2+ binding sites stabilize contacts between adjacent S domains. The virions of viruses in the genera Machlomovirus, Necrovirus, and Panicovirus are composed of capsid proteins that lack the protruding domain. Consequently, the surfaces of the virions have a smooth appearance. They range in diameter between 30-32 nm. The shell domain is related to the capsid proteins in the genus Sobemovirus.
Physicochemical and Physical Properties
Virions sediment as one component with an S20w of 118-140S, have a buoyant density ranging from 1.34-1.36 g/cm3 in CsCl, and a virion Mr of 8.2-8.9 106. Virions are stable at acidic pH, but expand above pH 7 and in the presence of EDTA. Lowering pH or adding Ca++ recompacts the particles. Virions are resistant to elevated temperatures (thermal inactivation usually occurs above 80°C) and are insensitive to organic solvents and non-ionic detergents.
With the exception of those of the genus Dianthovirus, virions contain a single molecule of positive sense, linear ssRNA, that constitutes about 17% of the particle weight, and has a size ranging from 3.7 to 4.7 kb, depending on the genus. Dianthovirus virions contain two genomic RNAs. The large RNA1 is approximately 3.9 kb and the smaller RNA2 is 1.5 kb. The 3-ends are not polyadenylated. The 5-terminus is protected but the presence of a cap was demonstrated only for Carnation mottle virus, Red clover necrotic mosaic virus and Maize chlorotic mottle virus (MCMV). Addition of a cap analogue to in vitro RNA transcripts enhances infectivity little or not at all. Defective interfering (DI) RNAs occur in some genera. In addition some members have satellite RNAs or satellite viruses associated with them.
All virions are composed of 180 copies of a single capsid protein (CP) type. Virions are composed of one of two phylogenetically distinct groups of CP. Those CPs form one phylogenetically conserved group, containing a protruding domain, possess a single major CP having a Mr of 37-48 103. In those genera that have a CP from the second phylogenetically distinct group, lacking a protruding domain, the CPs range in size from Mr 25-29 103.
None reported.
None reported.
Genome Organization and Replication
Even though variability exists in the number and location of genes within members of the family, a number of organizational features are highly conserved (Fig. 2). The unifying feature of the family is that each member species possesses a highly conserved polymerase that is interrupted by an in-frame termination codon that is periodically suppressed to express catalytic quantities of the core polymerase containing the canonical “GDD” motif. Dianthoviruses utilize a -1 ribosomal frameshifting mechanism to accomplish the same result. The polymerase is further characterized by possessing no obvious helicase motif. In this description, as well as those for each genus, the polymerase is labeled as a single ORF with the readthrough portion labeled ORF 1RT or ORF 1FS. With the exception of MCMV, the polymerase is the first 5-proximal ORF encountered when translated from the genomic RNA. Genomes of members of the genera Dianthovirus and Avenavirus encode 3 ORFs while all others encode 4 ORFs. The genera Machlomovirus and Panicovirus have additional terminator readthrough and ribosomal frameshifting events to extend putative movement protein and accessory ORFs. Products of the 5-proximal ORFs1 and 1RT or 1FS are expressed by translation of the genomic RNA, whereas translation products of the internal and 3-proximal ORFs 2, 3 and 4, are expressed through sgRNAs. dsRNAs corresponding in size to virus-related RNAs (genomic and subgenomic) are present in infected tissues. For all genera, the CP ORF is either internal or 3-proximal and requires the synthesis of a sgRNA for expression in vivo.
Nonstructural proteins include the phylogenetically conserved polymerase proteins of Mr 22-50 103 and its readthrough product of Mr 82-112 103. The family utilizes at least three phylogenetically distinct movement proteins. The avenaviruses, carmoviruses, machlomoviruses, necroviruses, and panicoviruses encode a Mr of 7-9 and 9 103 movement protein that in all these genera, excluding Avenavirus, is associated with another small ORF encoding a polypeptide of Mr 8-9 103. Genomes of the genera Tombusvirus and Aureusvirus encode a Mr 22-27 103 movement protein and that of the genus Dianthovirus utilizes the third type of movement protein whose size is around Mr 35 103. The genera Tombusvirus and Aureusvirus encode an accessory protein of Mr 14-19 103 whose function is involved in increasing symptom severity. The genera Panicovirus and Machlomovirus also have several additional accessory ORFs whose functions have not been determined.
Replication occurs in the cytoplasm, possibly in membranous vesicles that may be associated with endoplasmic reticulum, or modified organelles such as peroxisomes, mitochondria and, more rarely, chloroplasts. Virions are assembled in the cytoplasm and occasionally in mitochondria and nuclei. Virions accumulate, sometimes in crystalline form, in the cytoplasm and in vacuoles.
Virions are efficient immunogens. Antisera yield single precipitin lines in immunodiffusion tests. Depending on the genus, serological cross-reactivity among species ranges from nil to near-homologous titers. Many serologically related strains have been identified in several species.
The natural host range of individual virus species is relatively narrow. Members can either infect monocotyledonous or dicotyledonous plants, but no species can infect both. The experimental host range is wide. Infection is often limited to the root system, but when hosts are invaded systemically, viruses enter all tissues. Many members induce a necrosis symptom on the foliar parts of the plant. Diseases are characterized by mottling, crinkling, necrosis, and deformation of foliage. Some virus species infections are symptomless in their natural hosts.
All species are readily transmitted by mechanical inoculation and through plant material used for propagation. Some may be transmitted by contact and through seeds. Viruses are often found in natural environments, i.e., surface waters and soils from which they can be acquired without assistance of vectors. Transmission by the chytrid fungi in the genus Olpidium and beetles has also been reported for members of several genera. Most, if not all, members can be transmitted through the soil either dependent on, or independent of, a biological vector.
Geographical distribution of particular species varies from wide to restricted. The majority of the species occur in temperate regions. Legume-infecting carmoviruses and one tentative member of the genus Dianthovirus have been recorded from tropical areas.
Distinctive cytopathological features occur in association with exceedingly high accumulations of virus particles in cells and “multivesicular bodies”, i.e., cytoplasmic membranous inclusions originated from profoundly modified mitochondria and/or peroxisomes.
List of Genus Demarcation Criteria in the Family
The list of criteria demarcating genera in the family are:
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Structural criteria: T = 3 icosahedral virions 28-35 nm in diameter that are insensitive to organic solvents, composed of 180 copies of a single subunit. | |
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Genomic criteria: genome composed of positive polarity ssRNA on one or two segments with the total genome size being less that 5.5 kb. | |
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Polymerase criteria: gene interrupted by either a termination codon or a-1 ribosomal frameshifting element that is periodically readthrough. Polymerase with at least 25% amino acid sequence identity. Polymerase located at or near the 5-end of the genomic RNA. | |
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Capsid protein criteria: one of two phylogenetic origins; a CP with a protruding domain having 25% amino acid sequence identity with other CPs in the family having a protruding domain, a CP lacking a protruding domain with 20% or higher sequence identity with the sobemovirus CP. CP expressed from a sgRNA in vivo. | |
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Transmission criteria: virions that are mechanically transmissible. Soil transmission either with or without the aid of a biological vector. |
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