Nucleotide sequence of tomato ringspot virus RNA1

Abstract

The nucleotide sequence of tomato ringspot nepovirus (TomRSV) RNA1 has been determined. TomRSV RNA1 is 8214 nucleotides in length, excluding the 3' poly(A) tail, and contains a single long open reading frame (ORF) of 6591 nucleotides beginning at the first AUG codon at nucleotide position 78. This ORF accounts for 80 % of the RNA1 sequence and would give rise to a polyprotein with a predicted molecular mass of 244 kDa. Amino acid sequence comparisons between portions of the TomRSV RNAl-encoded polyprotein and proteins encoded by several members of the picornavirns superfamily have provided information concerning the genomic organization and putative functions of TomRSV-encoded proteins. The putative TomRSV protease retains a conserved histidine residue present in the proteases encoded by members of the como-, poty-and poliovirus groups which is thought to be involved in dipeptide cleavage site recognition. Interestingly, this histidine residue is replaced by a leucine in the proteases of other sequenced nepoviruses. This suggests that the TomRSV protease shares dipeptide cleavage site specificity with that of como-, potyand picornaviruses rather than the other nepoviruses.

Proteolytic processing of tomato ringspot nepovirus 3C-like protease precursors: definition of the domains for the VPg, protease and putative RNA-dependent RNA polymerase.

“…The VPg sequence was : STIPSGSYADVYNARNMARVFRPQSVq. This sequence closely matches a portion of amino acid sequence of the P1 polyprotein deduced from the nucleotide sequence of the RNA-1 cDNA clone (nt 3714-3794) (Rott et al, 1995). The only difference observed with the published TomRSV sequence was the replacement of threonine at position 18 by alanine.…”

“…These proteins were not detected upon incubation of the translation products of plasmid pT7-NTB-VPg-Pro H"#)$D . Deletion of the conserved glutamine at the k1 position of the predicted NTB-VPg cleavage site (Rott et al, 1995) also eliminated processing (Fig. 6 b, lane 6).…”

“…Plasmid pMR10 containing the cDNA clone for the entire RNA-1 has been described (Rott et al, 1995). To construct plasmid pT7-NTB-VPg-Pro (Fig.…”

“…The protein contains 27 amino acids of which 26 were identified from the N terminus. The last amino acid was deduced as a Q based on the nucleotide sequence of the TomRSV RNA-1 cDNA clone (Rott et al, 1995). The VPg sequence was : STIPSGSYADVYNARNMARVFRPQSVq.…”

“…Nepoviruses have been subdivided into three subgroups (Mayo & Robinson, 1996) and TomRSV is the only member of nepovirus subgroup c for which the entire nucleotide sequence is known. RNA-1 contains a single long open reading frame beginning at an AUG codon at nucleotide position 78 (Rott et al, 1995). Based on amino acid sequence comparisons between the C-terminal portion of the TomRSV RNA-1-encoded polyprotein (P1) and polyproteins encoded by several members of the picornavirus superfamily, it has been predicted that RNA-1 encodes an NTP-binding protein (NTB), a VPg, a 3C-like protease (Pro) and an RNA-dependent RNA polymerase (Pol) (Rott et al, 1995).…”