title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis.
abstract: Viral RNA replication provides a useful system to study the structure and function of RNAs and the mechanism of RNA synthesis from RNA templates. Previously we demonstrated that a 27 nt RNA from brome mosaic virus (BMV) can direct correct initiation of genomic plus-strand RNA synthesis by the BMV replicase. In this study, using biochemical, nuclear magnetic resonance, and thermodynamic analyses, we determined that the secondary structure of this 27 nt RNA can be significantly altered and retain the ability to direct RNA synthesis. In contrast, we find that position-specific changes in the RNA sequence will affect replicase recognition, modulate the polymerization process, and contribute to the differential accumulation of viral RNAs. These functional results are in agreement with the phylogenetic analysis of BMV and related viral sequences and suggest that a similar mechanism of RNA synthesis takes place for members of the alphavirus superfamily.
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405, USA.
authors.forename: K
authors.initials: K
authors.lastname: Sivakumaran
authors.forename: C H
authors.initials: CH
authors.lastname: Kim
authors.forename: R
authors.initials: R
authors.lastname: Tayon
authors.forename: C C
authors.initials: CC
authors.lastname: Kao
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D012367:RNA, Viral / Q000096:biosynthesis* / Q000737:chemistry; D017423:Sequence Analysis, RNA; D013698:Templates, Genetic
chemical_list: D012367:RNA, Viral; C023140:DNA replicase; D004259:DNA-Directed DNA Polymerase