SEQUENCE-SPECIFIC RECOGNITION OF A SUBGENOMIC RNA PROMOTER BY A VIRAL-RNA POLYMERASE

RNA templates of 33 nucleotides containing the brome mosaic virus (BMV ) core subgenomic promoter were used to determine the promoter element s recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiat e RNA synthesis, Nucleotides at positions -17, -14, -13, and -11 relat ive to the subgenomic initiation site must be maintained for interacti on with the RdRp, Changes to every other nucleotide at these four posi tions allow predictions for the base-specific functional groups requir ed for RdRp recognition, RdRp contact of the nucleotide at position -1 7 was suggested with a template competition assay, Comparison of the B MV subgenomic promoter to those from other plant and animal alphavirus es shows a remarkable degree of conservation of the nucleotides requir ed for BMV subgenomic RNA synthesis. We show that the RdRp of the plan t-infecting BMV is capable of accurately, albeit inefficiently, initia ting RNA synthesis from the subgenomic promoter of the animal-infectin g Semliki Forest virus, The sequence-specific recognition of RNA by th e BMV RdRp is analogous to the recognition of DNA promoters by DNA-dep endent RNA polymerases.