title: A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis.
abstract: RNA can adopt different conformations in response to changes in the metabolic status of cells, which can regulate processes such as transcription, translation, and RNA cleavage. We previously proposed that an RNA conformational switch in an untranslated satellite RNA (satC) of Turnip crinkle virus (TCV) regulates initiation of minus-strand synthesis (G. Zhang, J. Zhang, A. T. George, T. Baumstark, and A. E. Simon, RNA 12:147-162, 2006). This model was based on the lack of phylogenetically inferred hairpins or a known pseudoknot in the "preactive" structure assumed by satC transcripts in vitro. We now provide evidence that a second pseudoknot (Psi(2)), whose disruption reduces satC accumulation in vivo and enhances transcription by the TCV RNA-dependent RNA polymerase in vitro, stabilizes the preactive satC structure. Alteration of either Psi(2) partner caused nearly identical structural changes, including single-stranded-specific cleavages in the pseudoknot sequences and strong cleavages in a distal element previously proposed to mediate the conformational switch. These results indicate that the preactive structure identified in vitro has biological relevance in vivo and support a requirement for this alternative structure and a conformational switch in high-level accumulation of satC in vivo.
authors.affiliation: Department of Cell Biology and Molecular Genetics, Microbiology Building, University of Maryland-College Park, College Park, MD 20742, USA.
authors.forename: Jiuchun
authors.initials: J
authors.lastname: Zhang
authors.forename: Guohua
authors.initials: G
authors.lastname: Zhang
authors.forename: Rong
authors.initials: R
authors.lastname: Guo
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
authors.forename: Anne E
authors.initials: AE
authors.lastname: Simon
mesh_terms: D001483:Base Sequence; D015967:Gene Expression Regulation, Viral; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D010942:Plant Viruses / Q000235:genetics*; D012313:RNA / Q000737:chemistry; D019244:RNA, Satellite / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D014779:Virus Replication; D014780:Viruses / Q000235:genetics
chemical_list: D019244:RNA, Satellite; D012367:RNA, Viral; D012313:RNA