Nucleotide sequence of the capsid protein gene of barley yellow mosaic virus

The sequence of the 3'-terminal 1370 nucleotides of barley yellow mosaic virus (BaYMV) RNA 1 was determined. The sequence contains a long open reading frame (ORF) of 1137 nucleotides and a non-coding region of 231 nucleotides upstream of the poly(A) tail. Mapping of the partial amino acid sequences of the capsid protein onto the putative translational product of the ORF indicates that the 3'-proximal region of RNA 1 encodes the capsid protein which consists of 297 amino acids with an Mr of 32334; the capsid protein is produced by proteolytic processing from a precursor polypeptide at a glutamine-alanine dipeptide. The removal of the N- and C-terminal regions of the capsid protein by mild proteolysis of intact virus particles indicates that both terminal regions are exposed on the external surfaces of virus particles. Alignment of the BaYMV capsid protein sequence with those of some potyviruses showed only small blocks of homology which contrast with the extensive matches among potyviruses. This fact together with the genome organization and the vector specificity clearly distinguishes BaYMV from potyviruses.