The complete nucleotide sequence of turnip mosaic potyvirus RNA

Abstract

The complete RNA genome of turnip mosaic potyvirus (TuMV) was amplified by seven consecutive reverse transcriptase-polymerase chain reactions and cloned into pUC9. The viral RNA is 9830 nucleotides long and contains a single open reading frame (ORF) of 9489 bases encoding a large polyprotein of 3863 amino acids with a calculated Mr of 358 000. The non-coding region (NCR) preceding the ORF is 129 nucleotides long and has a high AU content (70%). Its predicted secondary structure is characterized by a hairpin loop with a free energy loss of-69.9 kJ/mol. The termination codon is followed by an AU-rich NCR of 209 bases, excluding the poly(A) tail. Seven potential nuclear inclusion a proteinase (NIa-Pro) recognition heptapeptides are found in the polyprotein. Their sequences agree with consensus potyviral NIa-Pro cleavage sequences except for that at the 6K-VPg site, which is characterized by a glutamic acid residue preceding the hydrolysed peptide bond. The TuMV proteins are similar to their corresponding potyviral proteins.

The Polymerase Chain Reaction and Plant Disease Diagnosis

“…For example, related plant viroids or viruses have sequences in common that are exploited to amplify group-specific sequences subsequently differentiated by RFLP analyses (58,80,103,115,120,165). For PCR products greater than 500 bp, restriction endonucleases with four-base recognition sites are usually adequate, since any particular four-base sequence occurs an average of once per 256 bases.…”

“…Because of extensive genetic heterogeneity with many RNA viruses, the use of highly conserved sequences for primer design is recommended for detecting all individuals of a particular vires (20,117). Alternatively, all members of group of viruses may be detected using degenerate primers derived from conserved, reverse-translated viral amino acid sequences (80,103,115).…”

Nucleotide Sequence of the 3'-Terminal Region of Bean Yellow Mosaic Virus RNA and Resistance to Viral Infection in Transgenic Nicotiana benthamiana Expressing Its Coat Protein Gene.

“…The genome of potyvirus is composed of a single positive-sense RNA of approximate 10kb with a genomelinked protein (VPg) at the 5'-terminus and a poly(A) tract at the 3'-terminus7). The complete nucleotide sequences of several potyviruses, tobacco etch virus (TEV)1), tobacco vein mottling virus (TVMV)6), plum pox virus (PPV) 22), potato virus Y (PVY)32), pea seed-borne mosaic virus (PSbMV)16), pepper mottle virus (PepMoV)43), papaya ringspot virus (PRSV)46) and turnip mosaic virus (TuMV) 29), have been determined.…”

The nucleotide sequence and genome organization of the whitefly transmitted sweetpotato mild mottle virus: a close relationship with members of the family Potyviridae

“…Group- Table 1 Five of thé putative cleavage sites of thé Nia protease in thé génome of SPMMV and thé amino acid séquence adjacent to thé proposed sites ings were considérée significantly supportée when they were found in at least 95% of 1000 bootstrap replicates. The following members of thé family Potyviridae were used for séquence comparisons: Bymovirus: BaYMV (Kashiwazaki et al, 1990) and barley mild mosaic virus (BaMMV; Meyer and Dessens, 1996), Rymovirus: BrSMV (Gôtz and Maiss, 1995), Potyvirus: bean common mosaic virus (BCMV; Fang et al, 1995), johnsongrass mosaic virus (JGMV; Gough and Shukla, 1993), pepper mottle virus (PepMoV; Vance et al, 1992), plum pox virus (PPV; Lain et al, 1989), pea seedborne mosaic virus (PSbMV; Johansen et al, 1991), PVY (Robaglia et al, 1989), tobacco etch virus (TEV; Allison et al, 1986), turnip mosaic virus (TuMV; Nicolas and Laliberté, 1992) and tobacco vein mottling virus (TVMV; Domier et al, 1986). …”