Nucleotide sequence of raspberry bushy dwarf virus RNA-2: a bicistronic component of a bipartite genome.

Northern blot analysis with cDNA probes to RNA-3 (1 kb) of raspberry bushy dwarf virus (RBDV) revealed extensive sequence homology with RBDV RNA-2 (2.2 kb). Nucleotide sequencing showed that RNA-2 contains two large open reading frames (ORFs), of 1074 (5' ORF) and 822 (3' ORF) bases. The 3' ORF is virtually identical in sequence to RNA-3, which encodes the Mr 30509 (30K) coat protein. The 5' ORF encodes an Mr 38860 (39K) protein which slightly resembles the 32K protein encoded by RNA-3 of alfalfa mosaic virus (AlMV). RBDV RNA-2 resembles AlMV RNA-3 in being bicistronic and encoding a coat protein at the 3' end. Comparing RNA-1 and RNA-2 of RBDV, only the 18 3'-terminal nucleotides are identical in sequence but the 3'-terminal 71 nucleotides of each RNA species have the potential to form similar stem-loop structures.