The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons.

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.

[1]  Franck A. P. Vendeix,et al.  Mechanism of expanding the decoding capacity of tRNAs by modification of uridines , 2007, Nature Structural &Molecular Biology.

[2]  M. Rodnina,et al.  Codon reading by tRNAAla with modified uridine in the wobble position. , 2007, Molecular cell.

[3]  J. Elf,et al.  Over expression of a tRNA(Leu) isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading. , 2005, Journal of molecular biology.

[4]  K. Nishiyama,et al.  Genes coding for SecG and Leu2-tRNA form an operon to give an unusual RNA comprising mRNA and a tRNA precursor. , 2005, Biochimica et biophysica acta.

[5]  Yuko Yamada,et al.  Bacillus subtilis tRNA(Pro) with the anticodon mo5UGG can recognize the codon CCC. , 2005, Biochimica et biophysica acta.

[6]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[7]  Paul F Agris,et al.  The role of modifications in codon discrimination by tRNALysUUU , 2004, Nature Structural &Molecular Biology.

[8]  S. J. Nasvall,et al.  The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. , 2004, RNA.

[9]  Paul F. Agris,et al.  Modified Nucleotides in tRNALys and tRNAVal are Important for Translocation , 2004 .

[10]  M. O’Connor.  Insertions in the anticodon loop of tRNA1Gln(sufG) and tRNA(Lys) promote quadruplet decoding of CAAA. , 2002, Nucleic acids research.

[11]  V. Ramakrishnan,et al.  Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit , 2001, Science.

[12]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  C. Squires,et al.  Isolation of kasugamycin resistant mutants in the 16 S ribosomal RNA of Escherichia coli. , 1999, Journal of molecular biology.

[14]  S. Yokoyama,et al.  A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell‐free translation system , 1999, FEBS letters.

[15]  P. Farabaugh,et al.  A new model for phenotypic suppression of frameshift mutations by mutant tRNAs. , 1998, Molecular cell.

[16]  G. Church,et al.  Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization , 1997, Journal of bacteriology.

[17]  G. Björk,et al.  Three modified nucleosides present in the anticodon stem and loop influence the in vivo aa-tRNA selection in a tRNA-dependent manner. , 1997, Journal of molecular biology.

[18]  C. Kurland,et al.  Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. , 1996, Journal of molecular biology.

[19]  D. Milton,et al.  Flagellin A is essential for the virulence of Vibrio anguillarum , 1996, Journal of bacteriology.

[20]  W. McClain,et al.  Functional Evidence for Indirect Recognition of G·U in tRNAAla by Alanyl-tRNA Synthetase , 1996, Science.

[21]  M Yarus,et al.  Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. , 1989, Journal of molecular biology.

[22]  B. Washburn,et al.  New method for generating deletions and gene replacements in Escherichia coli , 1989, Journal of bacteriology.

[23]  S. Yokoyama,et al.  Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[25]  N. Fairweather,et al.  Versatile low-copy-number plasmid vectors for cloning in Escherichia coli. , 1982, Gene.

[26]  T. Samuelsson,et al.  Aberrations of the classic codon reading scheme during protein synthesis in vitro. , 1980, The Journal of biological chemistry.

[27]  P. Elias,et al.  Relative efficiency of anticodons in reading the valine codons during protein synthesis in vitro. , 1979, The Journal of biological chemistry.

[28]  U Lagerkvist,et al.  "Two out of three": an alternative method for codon reading. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[29]  E. Lund,et al.  Spacer transfer RNAs in ribosomal RNA transcripts of E. coli: Processing of 30S ribosomal RNA in vitro , 1977, Cell.

[30]  F. Neidhardt,et al.  Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli , 1977, Journal of bacteriology.

[31]  J. Roth,et al.  Regulation of histidine operon does not require hisG enzyme. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[32]  D. Botstein,et al.  Specialized transduction of tetracycline resistance by phage P22 in Salmonella typhimurium. I. Transduction of R factor 222 by phage P22. , 1972, Virology.

[33]  S. Nishimura,et al.  Primary sequence of tRNA-Val-1 from Escherichia coli B. II. Isolation of large fragments by limited digestion with RNases, and overlapping of fragments to reduce the total primary sequence. , 1971, Biochemistry.

[34]  S. Nishimura,et al.  Structure of serine tRNA from Escherichia coli. I. Purification of serine tRNA's with different codon responses. , 1971, Biochimica et biophysica acta.

[35]  S. Nishimura,et al.  Restoration of valine acceptor activity by combining oligonucleotide fragments derived from a Bacillus subtilis ribonuclease digest of Escherichia coli valine transfer RNA. , 1969, Biochimica et biophysica acta.

[36]  F. Crick.  Codon--anticodon pairing: the wobble hypothesis. , 1966, Journal of molecular biology.

[37]  V. de Crécy-Lagard,et al.  Comparative RNomics and Modomics in Mollicutes: Prediction of Gene Function and Evolutionary Implications , 2007, IUBMB life.

[38]  H. Schmieger.  Phage P22-mutants with increased or decreased transduction abilities , 2004, Molecular and General Genetics MGG.

[39]  Toshimichi Ikemura,et al.  Codon usage tabulated from international DNA sequence databases: status for the year 2000 , 2000, Nucleic Acids Res..

[40]  Christopher Honeyma,et al.  Two out of Three , 1995 .

[41]  A. Pühler,et al.  A Broad Host Range Mobilization System for In Vivo Genetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria , 1983, Bio/Technology.

[42]  H. Malke.  R. W. Davis, D. Botstein and J. R. Roth, A Manual for Genetic Engineering, Advanced Bacterial Genetics. 251 S., 15 Abb. Cold Spring Harbor 1980. Cold Spring Harbor Laboratory. $ 28.20 , 1981 .

[43]  Jeffrey H. Miller.  Experiments in molecular genetics , 1972 .

[44]  Francis Crick,et al.  Codon-Anticodon Pairing : , 1966 .

[45]  H. Vogel,et al.  Acetylornithinase of Escherichia coli: partial purification and some properties. , 1956, The Journal of biological chemistry.