Mapping of the Red Clover Necrotic Mosaic Virus Subgenomic RNA

Abstract

The red clover necrotic mosaic dianthovirus capsid protein is expressedin vivofrom a subgenomic RNA (sgRNA) identical to the 3′-terminal 1.5 kb of RNA-1. The 5′ leader sequence of the capsid protein sgRNA is 62 nucleotides, contains a 14-nucleotide putative promoter sequence homologous to the RNA-1 5′ terminus, and exhibits a high level of similarity with the tobacco mosaic virus 5′ leader translational enhancer element Ω. Analysis of the RNA-1 secondary structure, in the region adjacent to the position where the 5′ end of the sgRNA was mapped, predicts a stable stem–loop which includes the putative sgRNA promoter element. It is suggested that this structure is important for recognition of the sgRNA transcriptional initiation from the full-length negative-sense RNA-1.