title: Stable RNA structures can repress RNA synthesis in vitro by the brome mosaic virus replicase.
abstract: A 15-nucleotide (nt) unstructured RNA with an initiation site but lacking a promoter could direct the initiation of RNA synthesis by the brome mosaic virus (BMV) replicase in vitro. However, BMV RNA with a functional initiation site but a mutated promoter could not initiate RNA synthesis either in vitro or in vivo. To explain these two observations, we hypothesize that RNA structures that cannot function as promoters could prevent RNA synthesis by the BMV RNA replicase. We documented that four different nonpromoter stem-loops can inhibit RNA synthesis from an initiation-competent RNA sequence in vitro. Destabilizing these structures increased RNA synthesis. However, RNA synthesis was restored in full only when a BMV RNA promoter element was added in cis. Competition assays to examine replicase-RNA interactions showed that the structured RNAs have a lower affinity for the replicase than do RNAs lacking stable structures or containing a promoter element. The results characterize another potential mechanism whereby the BMV replicase can specifically recognize BMV RNAs.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhang
authors.forename: Chul-Hyun
authors.initials: CH
authors.lastname: Kim
authors.forename: K
authors.initials: K
authors.lastname: Sivakumaran
authors.forename: Cheng
authors.initials: C
authors.lastname: Kao
mesh_terms: D001483:Base Sequence; D001667:Binding, Competitive; D017795:Bromovirus / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D003587:Cytomegalovirus / Q000201:enzymology; D005416:Flavivirus / Q000201:enzymology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D020871:RNA Stability; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000378:metabolism*; D013045:Species Specificity; D014779:Virus Replication
chemical_list: D012367:RNA, Viral; D012324:RNA-Dependent RNA Polymerase