title: Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase.
abstract: RNA templates of 33 nucleotides containing the brome mosaic virus (BMV) core subgenomic promoter were used to determine the promoter elements recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiate RNA synthesis. Nucleotides at positions -17, -14, -13, and -11 relative to the subgenomic initiation site must be maintained for interaction with the RdRp. Changes to every other nucleotide at these four positions allow predictions for the base-specific functional groups required for RdRp recognition. RdRp contact of the nucleotide at position -17 was suggested with a template competition assay. Comparison of the BMV subgenomic promoter to those from other plant and animal alphaviruses shows a remarkable degree of conservation of the nucleotides required for BMV subgenomic RNA synthesis. We show that the RdRp of the plant-infecting BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animal-infecting Semliki Forest virus. The sequence-specific recognition of RNA by the BMV RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405, USA.
authors.forename: R W
authors.initials: RW
authors.lastname: Siegel
authors.forename: S
authors.initials: S
authors.lastname: Adkins
authors.forename: C C
authors.initials: CC
authors.lastname: Kao
mesh_terms: D000818:Animals; D001483:Base Sequence; D017795:Bromovirus / Q000201:enzymology* / Q000235:genetics*; D017124:Conserved Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D010942:Plant Viruses / Q000235:genetics; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism; D012672:Semliki forest virus / Q000201:enzymology* / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D014780:Viruses / Q000235:genetics
chemical_list: D012367:RNA, Viral; D012321:DNA-Directed RNA Polymerases