Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase

Proc Natl Acad Sci U S A. 1997 Oct 14;94(21):11238-43. doi: 10.1073/pnas.94.21.11238.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Bromovirus / enzymology*
  • Bromovirus / genetics*
  • Conserved Sequence
  • DNA-Directed RNA Polymerases / metabolism*
  • Nucleic Acid Conformation
  • Plant Viruses / genetics
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic*
  • RNA, Viral / genetics
  • RNA, Viral / metabolism
  • Semliki forest virus / enzymology*
  • Semliki forest virus / genetics*
  • Sequence Alignment
  • Sequence Analysis, RNA
  • Viruses / genetics

Substances

  • RNA, Viral
  • DNA-Directed RNA Polymerases