MOIETIES IN AN RNA PROMOTER SPECIFICALLY RECOGNIZED BY A VIRAL RNA-DEPENDENT RNA-POLYMERASE

RNAs 33 nucleotides in length can direct accurate initiation of subgen omic RNA synthesis by the brome mosaic virus RNA-dependent RNA polymer ase (RdRp), provided that the native sequences are maintained at five positions: -17, -14, -13, -11, and the +1 initiation site. The functio nal groups in the bases of these essential nucleotides required to int eract with RdRp were examined by using chemically synthesized RNAs con taining base analogs at each of the five positions. Analysis using a t emplate competition assay revealed that the mode of recognition for th e initiation nucleotide (+1) is distinct from that of the other essent ial nucleotides in the promoter. Competition experiments also determin ed that three template nucleotides are sufficient for stable interacti on with RdRp, These results identify base moieties in the brome mosaic virus subgenomic promoter required for efficient RNA synthesis and su pport the hypothesis that the recognition of a RNA promoter by a viral RdRp is analogous to the recognition of DNA promoters by DNA-dependen t RNA polymerases.