Structure of the Nucleocapsid Protein Gene of Rice Yellow Stunt Rhabdovirus

Abstract

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.