Mapping and expression of southern bean mosaic virus genomic and subgenomic RNAs

The coat protein of the cowpea strain of southern bean mosaic sobemovirus (SBMV-C) is translated from a subgenomic RNA (sgRNA) that is synthesized in the virus-infected cell. Like the SBMV-C genomic RNA, the sgRNA has a viral protein (VPg) covalently bound to its 5' end. The mechanism(s) by which ribosomes initiate translation on the SBMV-C RNAs is not known. To begin to characterize the translation of the sgRNA it was first necessary to precisely map its 5' end. Primer extension was used to identify SBMV-C nucleotide (nt) 3241 as the transcription start site. As a control, the 5' end of the genomic RNA was also mapped. Surprisingly, the 5' terminal nt of this RNA was identified as SBMV-C nt 2. The primary structure of the 5' ends of these two RNAs is therefore expected to be VPg-ACAAAA. Precise mapping of the 5' end of the sgRNA of the bean strain of SBMV (SBMV-B) demonstrated that it has these same elements. Translation of coat protein from the SBMV-C sgRNA and p21 from the SBMV-C genomic RNA was compared using a cell-free system. The results of these experiments were consistent with translation of these proteins by a 5' end-dependent scanning mechanism rather than by internal ribosome binding.