High resolution mapping of carnation mottle virus-associated RNAs.

Abstract The genomic coordinates from which carnation mottle virus (CarMV) subgenomic RNA 5′-ends originate have been determined by high resolution S, nuclease protection and primer-extension mapping techniques. The two, 3′-proximal subgenomic RNAs initiate at nucleotides 2532 and 2315 (counting from the genome 5′ terminus). These RNAs contain 1472 and 1689 nucleotides, respectively. There is substantial nucleotide sequence homology surrounding the transcriptional start sites of the two subgenomic RNAs. The 1.5-kb RNA uses the first AUG to initiate translation of viral coat protein. The first AUG on the 1.7-kb RNA begins a short open reading frame of 183 nucleotides. This region encodes a M r = 6746 polypeptide found by in vitro translation of authentic subgenomic RNA as well as synthetic SP6 transcripts. By SP6 transcription and cell-free translation, we have also mapped coding sequences for a previously identified CarMV gene product, p27, to the 5′ terminus of the viral genome.