Nucleotide sequence and genome characterization of rice yellow mottle virus RNA

Abstract

The genome of rice yeUow mottle virus (RYMV) is a single-stranded positive-sense RNA that is not polyadenylated, and has an M r of 1.4 x 106. We present here the 4550 nucleotide (nt) sequence of RYMV RNA, and its predicted genomic organization. The RYMV genomic

Sobemoviruses

“…The complete nucleotide sequences of several sobemoviruses have been determined (58,61,114,70,86,112; A. C. Jeffries, J. P. Rathjen, and R. H. Symons, GenBank accession no. U31286; Y. M. Pinto and D. C. Baulcombe, GenBank accession no.…”

“…The theoretical or experimental molecular masses of different sobemovirus P1 proteins range between 11.7 and 24.3 kDa. It was hypothesized that ORF1 of RYMV-CI, unlike the corresponding proteins of other Sobemovirus species, encodes two polypeptides, with molecular masses of 18 and 19 kDa, due to readthrough of the UGA stop codon at nt 553 (114). However, in vitro translation of constructs containing the ORF1 coding region with two stop codons (at nt 553 and 599) or with one stop codon only (at nt 553) both produced two products, of 18 and 19 kDa (8).…”

“…Even less is known about the replication signals needed to initiate minus-strand synthesis at the 3Ј ends of sobemovirus genomic RNAs. A potential tRNA-like structure has been attributed to the 3Ј end of some sobemovirus genomic RNAs (86,114). However, for SBMV and SCPMV, it has been impossible to find an RNA sequence at the 3Ј end that has the potential to fold into a tRNA-resembling secondary structure (70,112).…”

“…The amino acid sequence of the SCPMV coat protein reported by Hermodson et al (40) showed that translation initiation occurs at the second AUG (nt 3271 to 3273) of ORF4 and is followed by the hydrolysis of the N-terminal methionine and acetylation of the subsequent alanine. Direct sequencing of the N terminus of the RYMV-CI and CfMV-NO coat proteins showed that they commence at the first AUG codon of the last ORF, at nt 3447 and 3093, respectively (61,114).…”

“…Interestingly, the coat protein of SCPMV grouped together with the Tobacco necrosis virus (TNV; genus Necrovirus, family Tombusviridae) coat protein rather than with the coat proteins of poleroviruses. The coat protein of RYMV-CI is also more closely related to that of TNV (114), indicating that coat proteins of sobemoviruses and necroviruses are phylogenetically related (Fig. 2) (17).…”