Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons

Nucleic Acids Research

Volumn 31, Issue 22, 2003, Pages 6383-6391

  Takai, Kazuyuki ^a   Yokoyama, Shigeyuki ^b,c,d  

^a EHIME UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

^d RIKEN HARIMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CARBENE; CARBON; HYDROGEN; PURINE; TRANSFER RNA; URIDINE;

BACTERIAL STRAIN; BASE PAIRING; CODON; CONTROLLED STUDY; DNA MODIFICATION; ESCHERICHIA COLI; EUKARYOTE; EXPERIMENTAL MODEL; GENETIC CODE; HYDROGEN BOND; HYPOTHESIS; MOLECULAR MECHANICS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FUNCTION; PROTON TRANSPORT; REVIEW; SPECIES DIFFERENCE;

ANTICODON; CODON; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; PURINE NUCLEOTIDES; RNA, TRANSFER; THERMODYNAMICS; URIDINE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; NEGIBACTERIA; PROKARYOTA;

EID: 0345531141     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg839     Document Type: Review

References (61)

1. Crick, F.H.C. (1966) Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol., 19, 548-555.
2. Mizuno, H. and Sundaralingam, M. (1978) Stacking of Crick wobble pair and Watson-Crick pair: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon-anticodon wobble interaction. Nucleic Acids Res., 5, 4451-4461.
3. Yokoyama, S., Watanabe, T., Murao, K., Ishikura, H., Yamaizumi, Z., Nishimura, S. and Miyazawa, T. (1985) Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc. Natl Acad. Sci. USA, 82, 4905-4909.
4. Agris, P.F. (1991) Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified wobble hypothesis. Biochimie, 73, 1345-1349.
5. Arg. Biochemistry, 35, 6533-6538.
6. Leu from Escherichia coli. Biochemistry, 38, 207-217.
7. Takai, K., Okumura, S., Hosono, K., Yokoyama, S. and Takaku, H. (1999) A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system. FEBS Lett., 447, 1-4.
8. Lagerkvist, U. (1978) 'Two out of three': an alternative method for codon reading. Proc. Natl Acad. Sci. USA, 75, 1759-1762.
9. Lagerkvist, U. (1981) Unorthodox codon reading and the evolution of the genetic code. Cell, 23, 305-306.
10. Lys stabilize a canonical U-turn structure. Biochemistry, 39, 12575-12584.
11. Lys with hypermodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position. J. Mol. Biol., 284, 33-42.
12. Glu modulates the translation rate of glutamic acid codons in vivo. J. Mol. Biol., 284, 621-631.
13. Rozenski, J., Crain, P.F. and McCloskey, J.A. (1999) The RNA Modification Database: 1999 update. Nucleic Acids Res., 27, 196-197.
14. Sakamoto, K., Kawai, G., Niimi, T., Satoh, T., Sekine, M., Yamaizumi, Z., Nishimura, S., Miyazawa, T. and Yokoyama, S. (1993) A modified uridine in the first position of the anticodon of a minor species of arginine tRNA, the argU gene product, from Escherichia coli. Eur. J. Biochem., 216, 369-375.
15. Komine, Y., Adachi, T., Inokuchi, H. and Ozeki, H. (1990) Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J. Mol. Biol., 212, 579-598.
16. +6 a double mutant of a new species. J. Mol. Biol., 177, 627-644.
17. Arg. Nucleic Acids Res., 18, 5031-5036.
18. Suzuki, T., Suzuki, T., Wada, T., Saigo, K. and Watanabe, K. (2002) Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO J., 21, 6581-6589.
19. Marck, C. and Grosjean, H. (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189-1232.
20. Percudani, R. (2001) Restricted wobble rules for eukaryotic genomes. Trends Genet., 17, 133-135.
21. Barrell, B.G., Anderson, S., Bankier, A.T., de Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J., Staden, R. and Young, I.G. (1980) Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc. Natl Acad. Sci. USA, 77, 3164-3166.
22. Bonitz, S.G., Berlani, R., Coruzzi, G., Li, M., Macino, G., Nobrega, F.G., Nobrega, M.P., Thalenfeld, B.E. and Tzagoloff, A. (1980) Codon recognition rules in yeast mitochondria. Proc. Natl Acad. Sci. USA, 77, 3167-3170.
23. Heckman, J.E., Sarnoff, J., Alzner-DeWeerd, B., Yin, S., RajBhandary, U.L. (1980) Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc. Natl Acad. Sci. USA, 77, 3159-3163.
24. Andachi, Y., Yamao, F., Muto, A. and Osawa, S. (1989) Codon recognition pattern as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. J. Mol. Biol., 209, 37-54.
25. Lustig, F., Elias, P., Axberg, T., Samuelsson, T., Tittawella, I. and Lagerkvist, U. (1981) Codon reading and translational error. Reading of the glutamine and lysine codons during protein synthesis in vitro. J. Biol. Chem., 256, 2635-2643.
26. Mitra, S.K., Lustig, F., Åkesson, B., Axberg, T., Elias, P. and Lagerkvist, U. (1979) Relative efficiency of anticodons in reading the valine codons during protein synthesis in vitro. J. Biol. Chem., 254, 6397-6401.
27. Takai, K., Horie, N., Yamaizumi, Z., Nishimura, S., Miyazawa, T. and Yokoyama, S. (1994) Recognition of UUN codons by two leucine tRNA species from Escherichia coli. FEBS Lett., 344, 31-34.
28. +/polyamine system for polyuridine-dependent polyphenylalanine synthesis with near in vivo characteristics. Methods Enzymol., 164, 650-658.
29. Samuelsson, T., Axberg, T., Borén, T. and Lagerkvist, U. (1983) Unconventional reading of the glycine codons. J. Biol. Chem., 258, 13178-13184.
30. Lustig, F., Borén, T., Guindy, Y.S., Elias, P., Samuelsson, T., Gehrke, C.W., Kuo, K.C. and Lagerkvist, U. (1989) Codon discrimination and anticodon structural context. Proc. Natl Acad. Sci. USA, 86, 6873-6877.
31. Claesson, C., Samuelsson, T., Lustig, F. and Borén, T. (1990) Codon reading properties of an unmodified transfer RNA. FEBS Lett., 273, 173-176.
32. Lustig, F., Borén, T., Claesson, C., Simonsson, C., Barciszewska, M. and Lagerkvist, U. (1993) The nucleotide in position 32 of the tRNA anticodon loop determines ability of anticodon UCC to discriminate among glycine codons. Proc. Natl Acad. Sci. USA, 90, 3343-3347.
33. Claesson, C., Lustig, F., Borén, T., Simonsson, C., Barciszewska, M. and Lagerkvist, U. (1995) Glycine codon discrimination and the nucleotide in position 32 of the anticodon loop. J. Mol. Biol., 247, 191-196.
34. Inagaki, Y., Kojima, A., Bessho, Y., Hori, H., Ohama, T. and Osawa, S. (1995) Translation of synonymous codons in family boxes by Mycoplasma capricolum tRNAs with unmodified uridine or adenosine at the first anticodon position. J. Mol. Biol., 251, 486-492.
35. Ser in cell-free protein synthesis. Nucleic Acids Res., 24, 2894-2899.
36. Ser. Biochem. Biophys. Res. Commun., 257, 662-667.
37. Yarian, C., Townsend, H., Czestkowski, W., Sochacka, E., Malkiewicz, A.J., Guenther, R., Miskiewicz, A. and Agris, P.F. (2002) Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem., 277, 16391-16395.
38. Sekiya, T., Takeishi, K. and Ukita, T. (1969) Specificity of yeast glutamic acid transfer RNA for codon recognition. Biochim. Biophys Acta, 182, 411-426.
39. Arg. Biochim. Biophys Acta, 518, 530-534.
40. Brierley, I., Meredith, M.R., Bloys, A.J., Hagervall, T.G. (1997) Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: influence of tRNA anticodon modification on frameshifting. J. Mol. Biol., 270, 360-373.
41. Yokoyama, S. and Nishimura, S. (1995) Modified nucleosides and codon recognition. In: Söll, D. and RajBhandary, U. (eds), tRNA: Structure, Biosynthesis and Function. ASM Press, Washington, DC, pp. 207-223.
42. Lim, V.I. and Venclovas, C. (1992) Codon-anticodon pairing. A model for interacting codon-anticodon duplexes located at the ribosomal A- and P-sites. FEBS Lett., 313, 133-137.
43. Ogle, J.M., Carter, A.P. and Ramakrishnan, V. (2003) Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci., 28, 259-266.
44. Curran, J.F. (1998) Modified nucleosides in translation. In: Grosjean, H. and Benne, R. (eds), Modification and Editing of RNA. ASM Press, Washington, DC, pp. 493-516.
45. Tinoco, I., Jr, Borer, P.N., Dengler, B., Levine, M.D., Uhlenbeck, O., Crothers, D.M. and Gralla, J. (1973) Improved estimation of secondary structure in ribonucleic acids. Nature New Biol., 246, 40-41.
46. Turner, D.H., Sugimoto, N. and Freier, S.M. (1988) RNA structure prediction. Ann. Rev. Biophys. Biophys. Chem., 17, 167-192.
47. Lim, V.I. and Curran, J.F. (2001) Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA, 7, 942-957.
48. Hammett, L.P. (1970) Physical Organic Chemistry, 2nd Ed. McGraw Hill, New York, NY.
49. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York, NY. Japanese translation by Nishimura, Y., Springer-Verlag Tokyo, Japan.
50. Shibaev, V.N., Eliseeva, G.I. and Kochetkov, N.K. (1975) Interaction of uridine diphosphate glucose analogs with calf liver uridine diphosphate glucose dehydrogenase. Influence of substituents at C-5 of pyrimidine nucleus. Biochim. Biophys Acta, 403, 9-16.
51. Ogle, J.M., Brodersen, D.E., Clemons, W.M., Jr, Tarry, M.J., Carter, A.P., Ramakrishnan, V. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292, 897-902.
52. Wittwer, A.J., Tsai, L., Ching, W.M. and Stadtman, T.C. (1984) Identification and synthesis of a naturally occurring selenonucleoside in bacterial tRNAs: 5-[(methylamino)methyl]-2-selenouridine. Biochemistry, 23, 4650-4655.
53. Glu from Clostridium sticklandii. Arch. Biochem. Biophys., 244, 137-146.
54. Björk, G. (1998) Appendix 6: Modified nucleosides at positions 34 and 37 of tRNAs and their predicted coding capacities. In: Grosjean, H. and Benne, R. (eds), Modification and Editing of RNA. ASM Press, Washington, DC, pp. 577-581.
55. Phelps, S.R., Jerinic, O. and Joseph, S. (2002) Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol. Cell, 10, 799-807.
56. Carbon, J.A., Hung, L. and Jones, D.S. (1965) A reversible oxidative inactivation of specific transfer RNA species. Proc. Natl Acad. Sci. USA, 53, 979-986.
57. Lys transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J., 15, 6321-6334.
58. Gln and ATP at 2.8 Å resolution. Science, 246, 1135-1142.
59. Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G. and Yokoyama, S. (2001) Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat. Struct. Biol., 8, 189-191.
60. Ramakrishnan, V. (2002) Ribosome structure and the mechanism of translation. Cell, 108, 557-572.
61. Ogle, J.M., Murphy, F.V., Tarry, M.J. and Ramakrishnan, V. (2002) Selection of tRNA by the ribosome requires a transition from an open to closed form. Cell, 111, 721-732.