Figure 1 (Top row, left) Diagrammatic representation of a particle of Tomato bushy stunt virus (TBSV); (Top row, right) Negative contrast electron micrograph of TBSV particles. (Bottom row, left) Diagrammatic representation of a particle of Tobacco necrosis virus (TNV); (Bottom row, right) Negative contrast electron micrograph of TNV particles. The bars represent 50 nm.
Figure 2 Genome organization of the type species for each genus in the family Tombusviridae. Boxes represent known and predicted ORFs. Similarly shaded boxes represent proteins with extensive sequence conservation. The shaded boxes represent ORFs encoding the phylogenetically conserved polymerase. Hatched boxes represent capsid protein (CP) encoding ORFs. Right-hatched boxes identify CPs lacking a protruding domain that are related to those of the genus Sobemovirus while those which are left-hatched represent tombusvirus-like CPs that contain protruding domains. Black boxes represent viral movement proteins that have a high degree of sequence conservation at the carboxyl-terminus. Unshaded boxes identify movement proteins (Dianthovirus, tombusvirus ORF3, panicovirus ORF3, carmovirus ORF3) involved in movement with no sequence similarity, or other unrelated ORFs whose proteins encode an accessory function. RT: translational readthrough of termination codon. -1 FS: -1 ribosomal frameshifting event. CP: capsid protein. CRSV: Carnation ringspot virus; TBSV: Tomato bushy stunt virus; PoLV: Pothos latent virus; OCSV: Oat chlorotic stunt virus; CarMV: Carnation mottle virus; TNV-A: Tobacco necrosis virus A; PMV: Panicum mosaic virus; MCMV: Maize chlorotic mottle virus.
Figure 3 Genome organization and replication strategy of Pothos latent virus (PoLV). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the Tombusviridae. Left-hatched box identifies the capsid protein (CP) that is highly conserved among other genera within the Tombusviridae that share a protruding domain. The gray boxes identify ORFs whose proteins are unique to the genus. Lines underneath depict the genomic RNA and two sgRNAs that are synthesized in infected cells and allow for the expression of ORF2 and ORFs 3 and 4 from sgRNAs 1 and 2, respectively. RT = termination codon that is readthrough.
Figure 4 Genome organization of Oat chlorotic stunt virus (OCSV). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the family Tombusviridae. Left-hatched box identifies the capsid protein (CP) that is highly conserved among other genera within the family Tombusviridae that share a protruding domain. The black box identifies the putative cell-to-cell movement protein that exhibits sequence conservation with similar proteins in the genera Carmovirus, Machlomovirus, Necrovirus, and Panicovirus. RT = termination codon that is readthrough.
Figure 5 (Left) Diagrammatic representation of a particle of Turnip crinkle virus (TCV) (from Hopper et al., 1984, with permission). (Right) Negative contrast electron micrograph of TCV particles. The bar represents 50 nm.
Figure 6 Genome organization and replication strategy of Carnation mottle virus (CarMV). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within or to the right or beside. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the family Tombusviridae. Left-hatched box identifies the capsid protein (CP) that is conserved among other genera within the family Tombusviridae that have a protruding domain. The black box identifies one of the two proteins involved in cell-to-cell movement that exhibits carboxyl-terminal sequence conservation with like proteins in the genera Avenavirus, Machlomovirus, Necrovirus, and Panicovirus. An ORF whose protein (p9K), also involved in movement, shares no sequence similarity with other viruses in the Tombusviridae. Lines underneath the gene map depict the genomic RNA and the two sgRNAs that are synthesized in infected cells and allow for the expression of ORFs 2 and 3, and ORF4 from sgRNAs 1 and 2, respectively. RT = amber termination codon that is readthrough.
Figure 7 (Left) Diagrammatic representation of a particle of Red clover necrotic mosaic virus (RCNMV) (from Hopper et al., 1984, with permission). (Right) Negative contrast electron micrograph of RCNMV particles. The bar represents 50 nm.
Figure 8 Genome organization and replication strategy of Carnation ringspot virus (CRSV). Boxes represent known ORFs with the sizes of the respective proteins (or readthrough products) indicated within. Shaded ORFs on RNA1 indicate polymerase proteins that have a high degree of sequence conservation within the family Tombusviridae. Left-hatched box on RNA1 identifies the capsid protein (CP) that is highly conserved among other genera within the family Tombusviridae that have a protruding domain. The gray box on RNA2 identifies the ORF that encodes the movement protein. This protein exhibits a small region of sequence conservation with movement proteins in the family Bromoviridae. The line under RNA1 depicts the 1.5 kb capsid protein sgRNA. -1 FS = location of site of -1 ribosomal frameshifting.
Figure 9 (Left) Diagrammatic representation of a particle of Maize chlorotic mottle virus (MCMV). (Right) Negative contrast electron micrograph of MCMV virions. The bar represents 100 nm.
Figure 10 Genome organization and replication strategy of Maize chlorotic mottle virus (MCMV). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the family Tombusviridae. Right-hatched box identifies the capsid protein (CP) that is highly conserved among those genera within the family Tombusviridae that lack a protruding domain. The black box identifies the putative cell-to-cell movement protein that exhibits sequence conservation with like proteins in the genera Avenavirus, Carmovirus, Necrovirus, and Panicovirus. The gray boxes identify ORFs not having significant sequence similarity with a known viral protein. The 1.1 kb capsid protein sgRNA is illustrated as a line below the genomic RNA. RT = termination codon that is readthrough.
Figure 11 (Left) Diagram of (T = 3) Tobacco necrosis virus A (TNV-A) virion. (Right) Negative contrast electron micrograph of TNV-A virions. The bar represents 50 nm.
Figure 12 Genome organization and replication strategy of Tobacco necrosis virus A (TNV-A). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the Tombusviridae. Right-hatched box identifies the capsid protein (CP) that is highly conserved among other genera within the Tombusviridae that lack a protruding domain. The black box identifies one of the two proteins involved in cell-to-cell movement that exhibits sequence conservation with a like protein in the genera Avenavirus, Carmovirus, Machlomovirus, and Panicovirus. The gray boxes identify ORFs whose proteins share no sequence similarity with other viruses in the Tombusviridae. Lines underneath the gene map depict the two sgRNAs that are synthesized in infected cells; these allow for the expression of ORFs 2 and 3 and ORF4 from sgRNA-1 and 2, respectively. RT = amber termination codon that can be readthrough.
Figure 13 (Left) Diagrammatic representation of a particle of Panicum mosaic virus (PMV). (Right) Negative contrast electron micrograph of PMV particles. The bar represents 50 nm.
Figure 14 Genome organization and replication strategy of Panicum mosaic virus (PMV). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within, or beside. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the family Tombusviridae. Right-hatched box identifies the capsid protein (CP) that is highly conserved among other genera within the family Tombusviridae that lack a protruding domain. The black box identifies the putative cell-to-cell movement protein that exhibits sequence conservation with like proteins in the genera Avenavirus, Carmovirus, Machlomovirus, and Necrovirus. The gray boxes identify ORFs not having significant sequence similarity with a known viral protein. The 1.5 kb sgRNA is illustrated as a line below the genomic RNA. RT = amber termination codon that can be readthrough. -1 FS = Site of a -1 ribosomal frameshift event.
Figure 15 (Left) Diagrammatic representation of a particle of Tomato bushy stunt virus (TBSV) (from Hopper et al., 1984, with permission). (Right) Negative contrast electron micrograph of TBSV particles. The bar represents 50 nm.
Figure 16 Genome organization and replication strategy of Tomato bushy stunt virus (TBSV). Boxes represent known and predicted ORFs with the sizes of the respective proteins (or readthrough products) indicated within. Shaded ORFs indicate polymerase proteins that have a high degree of sequence conservation within the Tombusviridae. Left-hatched box identifies the capsid protein (CP) that is highly conserved among other genera within the family Tombusviridae that have a protruding domain. The gray boxes identify ORFs whose proteins are unique to the genus. Lines underneath depict the two sgRNAs that are synthesized in infected cells and allow for the expression of ORF2 and ORFs 3 and 4 from sgRNAs 1 and 2, respectively. RT = Amber termination codon that is readthrough.
Figure 17 Phylogenetic trees of representative members of the genera of the family Tombusviridae. The trees were made with capsid protein (top) and polymerase (bottom) amino acid sequences. The PILEUP program was used for the alignment of the sequences. A multiple data set was generated by SEQBOOT using aligned sequences as input, distance measures was computed utilizing PROTDIST, and parsimony trees were generated by DNAPARS and CONSENSE programs. A bootstrap analysis was performed (1000 replicates) to test the strength of the nodes and the values are indicated on the tree branches. CMV capsid protein and TMV polymerase sequences are unrelated protein sequences used as out-groups. (Provided by F. Grieco.)
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