title: Biologically-supported structural model for a viral satellite RNA.
abstract: Satellite RNAs (satRNAs) are a class of small parasitic RNA replicon that associate with different viruses, including plus-strand RNA viruses. Because satRNAs do not encode a polymerase or capsid subunit, they rely on a companion virus to provide these proteins for their RNA replication and packaging. SatRNAs recruit these and other required factors via their RNA sequences and structures. Here, through a combination of chemical probing analysis of RNA structure, phylogenetic structural comparisons, and viability assays of satRNA mutants in infected cells, the biological importance of a deduced higher-order structure for a 619 nt long tombusvirus satRNA was assessed. Functionally-relevant secondary and tertiary RNA structures were identified throughout the length of the satRNA. Notably, a 3'-terminal segment was found to adopt two mutually-exclusive RNA secondary structures, both of which were required for efficient satRNA accumulation. Accordingly, these alternative conformations likely function as a type of RNA switch. The RNA switch was also found to engage in a required long-range kissing-loop interaction with an upstream sequence. Collectively, these results establish a high level of conformational complexity within this small parasitic RNA and provide a valuable structural framework for detailed mechanistic studies.
authors.affiliation: Department of Biology, York University, Toronto, Ontario, M3J 1P3 Canada.
authors.forename: Peter
authors.initials: P
authors.lastname: Ashton
authors.affiliation: Department of Biology, York University, Toronto, Ontario, M3J 1P3 Canada.
authors.forename: Baodong
authors.initials: B
authors.lastname: Wu
authors.affiliation: Department of Biology, York University, Toronto, Ontario, M3J 1P3 Canada.
authors.forename: Jessica
authors.initials: J
authors.lastname: D'Angelo
authors.affiliation: Department of Mathematics and Statistics, York University, Toronto, Ontario, M3J 1P3 Canada.
authors.forename: Jörg
authors.initials: J
authors.lastname: Grigull
authors.affiliation: Department of Biology, York University, Toronto, Ontario, M3J 1P3 Canada kawhite@yorku.ca.
authors.forename: K Andrew
authors.initials: KA
authors.lastname: White
mesh_terms: D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D019244:RNA, Satellite / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*; D017864:Tombusvirus / Q000235:genetics
chemical_list: D019244:RNA, Satellite; D012367:RNA, Viral