title: The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons.
abstract: According to Crick's wobble hypothesis, tRNAs with uridine at the wobble position (position 34) recognize A- and G-, but not U- or C-ending codons. However, U in the wobble position is almost always modified, and Salmonella enterica tRNAs containing the modified nucleoside uridine-5-oxyacetic acid (cmo(5)U34) at this position are predicted to recognize U- (but not C-) ending codons, in addition to A- and G-ending codons. We have constructed a set of S. enterica mutants with only the cmo(5)U-containing tRNA left to read all four codons in the proline, alanine, valine, and threonine family codon boxes. From the phenotypes of these mutants, we deduce that the proline, alanine, and valine tRNAs containing cmo(5)U read all four codons including the C-ending codons, while the corresponding threonine tRNA does not. A cmoB mutation, leading to cmo(5)U deficiency in tRNA, was introduced. Monitoring A-site selection rates in vivo revealed that the presence of cmo(5)U34 stimulated the reading of CCU and CCC (Pro), GCU (Ala), and GUC (Val) codons. Unexpectedly, cmo(5)U is critical for efficient decoding of G-ending Pro, Ala, and Val codons. Apparently, whereas G34 pairs with U in mRNA, the reverse pairing (U34-G) requires a modification of U34.
authors.affiliation: Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden.
authors.forename: S Joakim
authors.initials: SJ
authors.lastname: Näsvall
authors.forename: Peng
authors.initials: P
authors.lastname: Chen
authors.forename: Glenn R
authors.initials: GR
authors.lastname: Björk
mesh_terms: D000596:Amino Acids / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000187:drug effects / Q000235:genetics*; D005815:Genetic Code; D006147:Guanine; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics*; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000235:genetics; D019779:Salmonella enterica / Q000235:genetics; D012486:Salmonella typhimurium / Q000235:genetics; D014529:Uridine / Q000031:analogs & derivatives* / Q000494:pharmacology
chemical_list: D000596:Amino Acids; D003062:Codon; D012329:RNA, Bacterial; D012346:RNA, Transfer, Amino Acyl; C025230:uridine-5-oxyacetic acid; D006147:Guanine; D012343:RNA, Transfer; D014529:Uridine