title: Programmed ribosomal frameshifting in decoding the SARS-CoV genome.
abstract: Programmed ribosomal frameshifting is an essential mechanism used for the expression of orf1b in coronaviruses. Comparative analysis of the frameshift region reveals a universal shift site U_UUA_AAC, followed by a predicted downstream RNA structure in the form of either a pseudoknot or kissing stem loops. Frameshifting in SARS-CoV has been characterized in cultured mammalian cells using a dual luciferase reporter system and mass spectrometry. Mutagenic analysis of the SARS-CoV shift site and mass spectrometry of an affinity tagged frameshift product confirmed tandem tRNA slippage on the sequence U_UUA_AAC. Analysis of the downstream pseudoknot stimulator of frameshifting in SARS-CoV shows that a proposed RNA secondary structure in loop II and two unpaired nucleotides at the stem I-stem II junction in SARS-CoV are important for frameshift stimulation. These results demonstrate key sequences required for efficient frameshifting, and the utility of mass spectrometry to study ribosomal frameshifting.
authors.affiliation: Department of Human Genetics, University of Utah, 15 N 2030 E, Room 7410, Salt Lake City, UT 84112-5330, USA.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
authors.forename: Clark M
authors.initials: CM
authors.lastname: Henderson
authors.forename: Christine B
authors.initials: CB
authors.lastname: Anderson
authors.forename: Raymond F
authors.initials: RF
authors.lastname: Gesteland
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
authors.forename: Michael T
authors.initials: MT
authors.lastname: Howard
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D017934:Coronavirus / Q000235:genetics*; D018965:Frameshifting, Ribosomal / Q000235:genetics*; D017930:Genes, Reporter; D016679:Genome, Viral; D006801:Humans; D008156:Luciferases / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*; D016415:Sequence Alignment; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D012367:RNA, Viral; D008156:Luciferases