A stem-loop structure in the 5′ untranslated region of bean pod mottle virus RNA2 is specifically required for RNA2 accumulation

Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus of the family Secoviridae. Its RNA1 encodes all proteins needed for genome replication and is capable of autonomous replication. By contrast, BPMV RNA2 must utilize RNA-I-encoded proteins for replication. Here, we sought to identify RNA elements in RNA2 required for its replication. The exchange of 5 ' untranslated regions (UTRs) between genome segments revealed an RNA2-specific element in its 5 ' UTR. Further mapping localized a 66 nucleotide region that was predicted to fold into an RNA stem loop structure, designated SLC. Additional functional analysis indicated the importance of the middle portion of the stem and an adjacent two-base mismatch. This is the first report of a cis-acting RNA element in RNA2 of a bipartite secovirus.