Structure of the nucleocapsid protein gene of rice yellow stunt rhabdovirus

The complete nucleotide sequence of the N protein gene of rice yellow stunt rhabdovirus (RYSV) was determined by sequencing of cDNA clones derived from the viral genomic RNA. The 3' end of the N gene (messenger sense) was defined by sequence analysis of cDNA clones generated from the N protein mRNA by 3'RACE. The 5' end sequence of the gene was putatively assigned as 5'-AACAC-3'; this sequence is found in the presumed 3' leader/N gene junction region. The mRNA encoding the RYSV N protein is 1714 nt comprising a 15-nt untranslated 5' leader sequence followed by an open reading frame (ORF) of 1563 nt and a 136-nt untranslated 3' region. The calculated molecular mass of the N protein encoded by the ORF is 58,400 Da, which is larger in size than N proteins of other rhabdoviruses. Amino acid composition analysis shows that the RYSV N protein is rather basic with a predicted isoelectric point of 10.04; indeed, a large highly basic region could be found at the carboxy terminal portion of the protein. Amino acid sequence comparison between N proteins of RYSV and sonchus yellow net virus, both of which belong to the same genus Nucleorhabdovirus, revealed an overall 30% identity, with three relatively conserved blocks of 14-20 amino acid residues. Moreover, the hydropathy profiles of the two proteins are generally similar. The structural similarities between the N protein of RYSV and that of lettuce necrotic yellows virus, the type member of the genus Cytorhabdovirus, and those of animal rhabdoviruses, are less significant. Nucleotide sequence determination of 5' and 3' regions flanking the RYSV N gene identified a 14-nt common sequence that is very similar to the consensus gene junction sequences of other plant and animal rhabdoviruses.