title: An 'elaborated' pseudoknot is required for high frequency frameshifting during translation of HCV 229E polymerase mRNA.
abstract: The RNA polymerase gene (gene 1) of the human coronavirus 229E is approximately 20 kb in length and is located at the 5' end of the positive-strand genomic RNA. The coding sequence of gene 1 is divided into two large open reading frames, ORF1a and ORF1b, that overlap by 43 nucleotides. In the region of the ORF1a/ORF1b overlap, the genomic RNA displays two elements that are known to mediate (-1) ribosomal frameshifting. These are the slippery sequence, UUUAAAC, and a 3' pseudoknot structure. By introducing site-specific mutations into synthetic mRNAs, we have analysed the predicted structure of the HCV 229E pseudoknot and shown that besides the well-known stem structures, S1 and S2, a third stem structure, S3, is required for a high frequency of frameshifting. The requirement for an S3 stem is independent of the length of loop 2.
authors.affiliation: Institute of Virology, University of Würzburg, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Herold
authors.forename: S G
authors.initials: SG
authors.lastname: Siddell
mesh_terms: D000595:Amino Acid Sequence; D001482:Base Composition; D001483:Base Sequence; D017934:Coronavirus / Q000235:genetics*; D028941:Coronavirus 229E, Human; D004247:DNA; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D016368:Frameshift Mutation; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D004247:DNA; D012321:DNA-Directed RNA Polymerases