Structural alterations far from the anticodon of the tRNA(GGG)(Pro) of Salmonella typhimurium induce +1 frameshifting at the peptidyl-site

Journal of Molecular Biology

Volumn 273, Issue 5, 1997, Pages 978-992

  Qian, Qiang ^a   Björk, Glenn R ^a  

^a UMEÅ UNIVERSITY   (Sweden)

Author keywords

+1 frameshifting; 1 methylguanosine; Anticodon loop; Ribosomal P site; tRNA(GGG)(Pro)

Indexed keywords

GUANINE DERIVATIVE; PROLINE TRANSFER RNA; TRANSLATION TERMINATION FACTOR;

ANTICODON; ARTICLE; BACTERIUM MUTANT; CONTROLLED STUDY; FRAMESHIFT MUTATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; RNA STRUCTURE; SALMONELLA TYPHIMURIUM; STOP CODON; SUPPRESSOR GENE;

EID: 0031567788     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1363     Document Type: Article

References (59)

1. Atkins, J. F., Elseviers, D. & Gorinni, L. (1972). Low activity of β-galactosidase in frameshift mutants of Escherichia coli. Proc Natl Acad. Sci. USA, 69, 1192-1195.
2. Atkins, J. F., Weiss, R. B., Thompson, S. & Gesteland, R. F. (1991). Towards a genetic dissection of the basis of triplet decoding, and its natural subversion: programmed reading frame shifts and hops. Annu. Rev. Genet. 25, 201-228.
3. Belcourt, M. F. & Farabaugh, P. J. (1990). Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell, 62, 339-352.
4. Björk, G. R. (1995a). Genetic dissection of synthesis and function of modified nucleosides in bacterial transfer RNA. Prog. Nucl. Acid Res. Mol. Biol. 50, 263-338.
5. Björk, G. R. (1995b). Biosynthesis and function of modified nucleosides in tRNA. In tRNA: Structure, Biosynthesis, and Function (Söll, D. & Rajbhandary, U. L., eds), pp. 165-205, American society for Microbiology, Washington, DC.
6. Björk, G. R. (1996). Stable RNA modification. In Escherichia coli and Salmonella: Cellular and Molecular Biology (Neidhardt, F. C., Curtiss, R., III, Ingraham, J. L., Lin, E. C. C., Low, K. B., Jr, Magasanik, B., Rezinoff, W. S., Riley, M., Schaetchter, M. & Umbarger, H. E., eds), 2nd edit., pp. 861-886, American Society for Microbiology, Washington, D.C..
7. Björk, G. R., Wikström, P. M. & Byström, A. S. (1989). Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science, 244, 986-989.
8. Bossi, L. & Roth, J. R. (1981). Four-base codons ACCA, ACCU and ACCC are recognized by frameshift suppressor sufj. Cell, 25, 489-496.
9. Bouadloun, F., Srichaiyo, T., Isaksson, L. A. & Björk, G. R. (1986). Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy. J. Bacterial, 166, 1022-1027.
10. Clark, B. F. C., Kjeldgaard, M., Barciszewski, J. & Sprinzl, M. (1995). Recognition of aminoacyl-tRNAs by protein elongation factors. In tRNA: Structure, Biosynthesis, and Function (Söll, D. & RajBhandary, U., eds), pp. 423-442, American Society for Microbiology, Washington, DC.
11. Curran, J. F. (1993). Analysis of effects of tRNA: message stability on frameshift frequency at the Escherichia coli RF2 programmed frameshift site. Nucl. Acids Res. 21, 1937-1843.
12. Curran, J. F. & Yarus, M. (1988). Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. J. Mol. Biol. 203, 75-83.
13. Curran, J. F. & Yarus, M. (1989). Rates of aminoacyltRNA selection at 29 sense codons in vivo. J. Mol. Biol. 209, 65-77.
14. Davis, W., Botstein, D. & Roth, J. R. (1980). A Manual for Genetic Engineering: Advanced Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
15. Ericson, J. U. & Björk, G. R. (1986). Pleiotropic effects induced by modification deficiency next to the anticodon of tRNA from Salmonella typhimurium LT2. J. Bacteriol. 166, 1013-1021.
16. Farabaugh, P. J. (1996). Programmed translational frameshifting. Microbiol. Rev. 60, 103-134.
17. Farabaugh, P. J., Zhao, H. & Vimaladithan, A. (1993). A novel programmed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell, 74, 93-103.
18. Freese, E., Bautz, E. & Freese, E. B. (1961). the chemical and mutagenic specificity of hydroxylamine. Proc. Natl Acad. Sci. USA, 47, 845-855.
19. Gaber, R. F. & Culbertson, M. R. (1984). Codon recognition during frameshift suppression in Saccharomyces cerevisiae. Mol. Cell. Biol. 4, 2052-2061.
20. Grosjean, H., Edqvist, J., Stråby, K. B. & Gieǵ, R. (1996). Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture. J. Mol. Biol. 255, 67-85.
21. Hagervall, T. G., Tuohy, T. M., Atkins, J. F. & Björk, G. R. (1993). Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation. J. Mol. Biol. 232, 756-765.
22. Hatfield, D., Feng, Y. X., Lee, B. J., Rein, A., Levin, J. G. & Oroszlan, S. (1989). Chromatographic analysis of the aminoacyl-tRNAs which are required for translation of codons at and around the ribosomal frameshift sites of HIV, HTLV-1, and BLV. Virology, 173, 736-742.
23. Hughes, D., Atkins, J. F. & Thompson, S. (1987). Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense read through. EMBO J. 6, 4235-4239.
24. Hüttenhofer, A., Weiss-Brummer, B., Dirheimer, G. & Martin, R. P. (1990). A novel type of +1 frameshift suppressor: a base substitution in the anticodon stem of a yeast mitochondrial serine-tRNA causes frameshift suppression. EMBO J. 9, 551-558.
25. Jörgensen, F., Adamski, F. M., Tate, W. P. & Kurland, C. G. (1993). Release factor-dependent false stops are infrequent in Escherichia coli. J. Mol. Biol. 230, 41-50.
26. Kurland, C. G. (1992). Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26, 29-50.
27. Li, J.-N., Esberg, B., Curran, J. & Björk, G. R. (1997). Three modified nucleosides present in the anticodon stem and loop influence in the in vivo aa-tRNA selection in a tRNA dependent manner. J. Mol. Biol. 271, 209-221.
28. Lim, V. I. (1995). Analysis of action of the wobble adenine on codon reading within the ribosome. J. Mol. Biol 252, 277-282.
29. Limbach, P. A., Crain, P. F. & McCloskey, J. A. (1994). Summary: the modified nucleosides of RNA. Nucl. Acids Res. 22, 2183-2196.
30. Lindsley, D. & Gallant, J. (1993). On the directional specificity of ribosome frameshifting at a "hungry" codon. Proc. Natl Acad. Sci. USA, 90, 5469-5473.
31. Newmark, R. A. & Cantor, C. R. (1968). Nuclear magnetic resonance study of the interactions of guanosine and cytidine in dimethyl sulfoxide. J. Am. Chem. Soc. 90, 5010-5017.
32. O'Mahony, D. J., Minis, B. H., Thompson, S., Murgola, E. J. & Atkins, J. F. (1989). Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting. Proc. Natl Acad. Sci. USA, 86, 7979-7983.
33. Olafsson, O., Ericsson, J. E., VanBogelen, R. & Björk, G. R. (1996). Mutation in the structural gene for release factor 1 (RF1) of Salmonella typhimurium inhibits cell division. J. Bacteriol. 178, 3829-3839.
34. Pande, S., Vimaladithan, A., Zhao, H. & Farabaugh, P. J. (1995). Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate bonding of aminoacyl-tRNA. Mol. Cell. Biol. 15, 298-304.
35. Peter, K., Lindsley, D., Peng, L. & Gallant, J. A. (1992). Context rules of rightward overlapping reading. New Biol. 4, 520-526.
36. Pochon, F. & Michelson, A. M. (1967). Polynucleotide analogues. XI. Poly N-1-methylguanylic acid and other methylated polynucleotides. Biochim. Biophys. Acta, 145, 321-327.
37. GGG of Salmonella typhimurium. J. Mol. Biol. 266, 283-296.
38. Riddle, D. L. & Carbon, J. (1973). Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nature New Biol. 242, 230-234.
39. Riddle, D. L. & Roth, J. R. (1970). Suppressors of frameshift mutations in Salmonella typhimurium. J. Mol. Biol. 54, 131-144.
40. Robertus, J. D., Ladner, J. E., Finch, J. R., Rhodes, D., Brown, R. S., Clark, B. F. & Klug, A. (1974). Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature, 250, 546-551.
41. Roth, J. R. (1974). Frameshift mutations. Annu. Rev. Genet. 8, 319-346.
42. Roth, J. R. (1981). Frameshift suppression. Cell, 24, 601-602.
43. Sanderson, K. E., Hessel, A. & Rudd, K. E. (1995). Genetic map of Salmonella typhimurium, edition VIII (review). Microbiol. Rev. 59, 241-303.
44. Schmieger, H. (1972). Phage P22mutants with increased or decreased transduction abilities. Mol. Gen. Genet. 119, 75-88.
45. Smith, D. & Yarus, M. (1989). Transfer RNA structure and coding specificity. II. A D-arm tertiary interaction that restricts coding range. J. Mol. Biol. 206, 503-511.
46. 2 from Salmonella typhimurium induces suppression of the frameshift mutations. Nucl. Acids Res. 20, 3463-3469.
47. Suddath, F. L., Quigley, G. J., McPherson, A., Sneden, D., Kim, S. H. & Rich, A. (1974). Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0 Å resolution. Nature, 248, 20-24.
48. Tate, W. P., Poole, E. S. & Mannering, S. A. (1996). Hidden infidelities of the translational stop sign. Prog. Nucl. Acid Res. Mol. Biol. 52, 293-335.
49. Tucker, S. D., Murgola, E. J. & Pagel, F. T. (1989). Missense and nonsense suppressors can correct frameshift mutations. Biochimie, 71, 729-739.
50. 2 which cause +1 frameshifting . Tolerance of DHU arm and other secondary mutations. J. Mol. Biol. 228, 1042-1054.
51. Uhlin, B. E. & Nordström, K. (1977). R plasmid gene dosage effects in Escherichia coli K12: copy mutants of the R plasmic R1drd-19. Plasmid, 1, 1-17.
52. Vimaladithan, A. & Farabaugh, P. J. (1994). Special peptidyl-tRNA molecules can promote translational frameshifting without slippage. Mol. Cell. Biol. 14, 8107-8116.
53. Vogel, H. J. & Bonner, D. M. (1956). Acetylornithinase of Escherichia coli: partial purification and some properties. J. Biol. Chem. 218, 97-106.
54. Weiss, R. B., Dunn, D. M., Atkins, J. F. & Gesteland, R. F. (1987). Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting. Cold Spring Harbor Symp. Quant. Biol. 52, 687-693.
55. Weiss, R. B., Dunn, D. M., Dahlberg, A. E., Atkins, J. F. & Gesteland, R. F. (1988). Reading frame switch caused by base-pair formation between the 3′ end of 16 S rRNA and them RNA during elongation of protein synthesis in Escherichia coli. EMBO J. 7, 1503-1507.
56. Yarus, M. (1982). Translational efficiency of transfer RNA's: uses of an extended anticodon. Science, 218, 646-652.
57. Yarus, M. & Smith, D. (1995). Transfer RNA on the ribosome: a waggle theory. In tRNA: Structure, Biosynthesis, and Function (Söll, D. & Rajbhandary, U., eds), pp. 443-469, American Society for Microbiology, Washington, DC.
58. Yokoyama, S. & Nishimura, S. (1995). Modified nucleosides and codon recognition. In tRNA: Structure, Biosynthesis, and Function (Söll, D. & Rajbhandary, U., eds), pp. 207-223, American Society for Microbiology, Washington, DC.
59. Yourno, J. & Tanemura, S. (1970). Restoration of in-phase translation by an unlinked suppressor of a frameshift mutation in Salmonella typhimurium. Nature, 225, 422-426.