Figure 1 Negative contrast electron micrograph of stained (ammonium molybdate pH 7.0) particles of soil-borne wheat mosaic virus (SBWMV). The bar represents 200 nm. Inset: Negative contrast electron micrograph of particles SBWMV stained with 1% uranyl acetate. The bar represents 100 nm.
Figure 2 Genome organization of soil-borne wheat mosaic virus (SBWMV). The tRNA structure motifs at the 3′-ends of the RNAs are represented by a dark square, the methyl transferase (Met), Helicase (Hel) and RNA-dependent RNA polymerase (RdRp) motifs by asterisks and the readthrough of the polymerase and coat protein ORFs by RT and an arrow.
Figure 3 Percentage sequence identities of total RNAs of furoviruses.
Figure 4 Electron micrograph of purified barley stripe mosaic virus (BSMV) particles stained with 2% uranyl acetate. The particles are approximately 20 nm wide and have a length that varies depending on the size of the encapsidated RNA. The field was selected to represent monomers, but often a range of heterodisperse end-to-end aggregates up to 1000 nm in length predominate in purified preparations. The particles in the top left, bottom center, and upper left side of the micrograph are end-to-end aggregates that occur during purification. The bar represents 150 nm.
Figure 5 Genome organization of barley stripe mosaic virus (BSMV). The color rectangles and smaller solid black rectangles represent the ORFs, and the 3′-terminal tRNA-like structure, respectively. The 3′-proximal ORFs on each RNA terminate with an UAA that initiates the short poly (A) tract that directly precedes the 238 nt tRNA-like terminus. RNAα encodes a single protein, αa, with an amino-terminal methyl transferase domain (Mtr) and a carboxy-terminal helicase domain (Hel). This protein is referred to as the helicase subunit of the replicase (RdRp). RNAβ encodes five proteins: βa, the CP is translated from the genomic RNA; βb, a 58 kDa protein that contains a helicase domain. βb is translated from sgRNAβ1, whose promoter resides between positions −29 to −2 relative to the transcription start site; βc, a 17 kDa protein that is separated from the βb ORF by 173 nt; βd, a 14 kDa protein which overlaps the βb and the βc ORFs; and βd′, a 23 kDa translational extension product of unknown function. The βd, βd′, and βc proteins are translated from sgRNAβ2. The sgRNAβ2 promoter is located between nt –32 to –17 relative to its transcription start site. RNAγ encodes two proteins. The γa protein contains the GDD domain and is the polymerase subunit of the replicase. The cysteine-rich, 17 kDa γb protein has RNA binding ability, and is translated from a sgRNAγ, whose promoter lies between positions −21 to +2 relative to the transcription start site.
Figure 6 Negative contrast electron micrograph of virions of Indian peanut clump virus (L serotype) negatively stained with 2% phosphotungstic acid, pH 6. The bar represents 150 nm.
(Courtesy, G.H. Duncan.)
Figure 7 Genomic organization of peanut clump virus (PCV) RNAs. ORFs are indicated by rectangles and suppressible termination codon by an arrow (RT=readthrough).
Figure 8 Negative contrast electron micrograph of particles of potato mop-top virus. The gold-labeling shows the binding of monoclonal antibody SCR 68 to one extremity of the particles. The bar represents 100 nm.
(Courtesy I.M. Roberts.)
Figure 9 Genome organization typical of potato mop-top virus. Arrows indicate respectively the UGA and UAG stop codons that are thought to be suppressible, and solid squares indicate a 3′-terminal tRNA-like structure. Hel, helicase; Mt, methyltransferase; RdRp, RNA dependent RNA polymerase; RT, readthrough.
Figure 10 (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.
Figure 11 Genome organization of tobacco mosaic virus (TMV). Conserved replicase domains are indicated as shaded boxes. Genomic RNA is capped and is template for expression of the 126 and 183 kDa proteins. The 3′ distal movement and CP ORFs are expressed from individual 3′ co-terminal sgRNAs. CP=coat protein; MP=movement protein.
Figure 12 (Left) Diagram of a virion of tobacco rattle virus (TRV), in section. (Right) Negative contrast electron micrograph of particles of TRV. The bar represents 100 nm.
Figure 13 Genome organization and strategy of expression of tobacco rattle virus (TRV). The means by which P2b and P2c are expressed is unknown.
Figure 14 Phylogenetic (distance) trees based on the amino acid sequences of the entire replication protein, the Triple Gene Block protein 1 (TGB1), the movement protein and the coat protein. A single representative isolate of each sequenced species in the family was included. Numbers on branches indicate percentage of bootstrap support out of 1,000 bootstrap replications (when >60%). The scale indicates JTT amino acid distances. Trees produced in MEGA4. The BSMV replication protein was combined from two different genome components.
Figure 15 Bayesian phylogenetic tree of the nucleotide sequences of the fused Met–Hel–RdRp domains of the members of the six genera included in the family Virgaviridae together with some other related viruses. A total of 500 amino acid positions corresponding to 1,500 nt positions were used for the alignment. The tree was generated from a back-translated amino-acid alignment using MrBayes v3.1.2, employing the general time reversible model with gamma-shaped rate variation with a proportion of invariable sites; 1,000,000 generations of MCMC analysis were performed, to the point at which the average standard generation of split frequency between two parallel runs had reached 0.009565. Posterior probability values are indicated on the corresponding branches. Nearly identical trees were obtained by neighbour-joining and maximum composite likelihood methods. Genera and families (which are all monophyletic) have been collapsed into a triangle, the length of which corresponds to the variation found within the clade.