Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Jun 11;15(11):4669–4686. doi: 10.1093/nar/15.11.4669

The bases of the tRNA anticodon loop are independent by genetic criteria.

D Smith, L Breeden, E Farrell, M Yarus
PMCID: PMC340888  PMID: 3295781

Abstract

We employed two methods to study the translational role of interactions between anticodon loop nucleotides. Starting with a set of previously constructed weakly-suppressing anticodon loop mutants of Su7, we searched for second-site revertants that increase amber suppressor efficiency. Though hundreds of revertants were characterized, no second-site revertants were found in the anticodon loop. Second site reversion was detected in the D-stem, thereby demonstrating the efficacy of the search method. As a second method for detecting interactions, we used site-directed mutagenesis to construct multiple mutations in the anticodon loop. These multiple mutants are very weak suppressors and have translational activities that are equal to or lower than that predicted for the independent action of single mutations. We conclude that although the anticodon loop sequence of Su7 has an optimal structure for the translation of amber codons, we find no evidence that interactions between loop bases can enhance translational efficiency.

Full text

PDF
4669

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bare L. A., Uhlenbeck O. C. Specific substitution into the anticodon loop of yeast tyrosine transfer RNA. Biochemistry. 1986 Sep 23;25(19):5825–5830. doi: 10.1021/bi00367a072. [DOI] [PubMed] [Google Scholar]
  2. Bossi L. Context effects: translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J Mol Biol. 1983 Feb 15;164(1):73–87. doi: 10.1016/0022-2836(83)90088-8. [DOI] [PubMed] [Google Scholar]
  3. Bradley D., Park J. V., Soll L. TRNA2Gln Su+2 mutants that increase amber suppression. J Bacteriol. 1981 Feb;145(2):704–712. doi: 10.1128/jb.145.2.704-712.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cline S. W., Yarus M., Wier P. Construction of a systematic set of tRNA mutants by ligation of synthetic oligonucleotides into defined single-stranded gaps. DNA. 1986 Feb;5(1):37–51. doi: 10.1089/dna.1986.5.37. [DOI] [PubMed] [Google Scholar]
  5. Curran J. F., Yarus M. Base substitutions in the tRNA anticodon arm do not degrade the accuracy of reading frame maintenance. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6538–6542. doi: 10.1073/pnas.83.17.6538. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Degnen G. E., Cox E. C. Conditional mutator gene in Escherichia coli: isolation, mapping, and effector studies. J Bacteriol. 1974 Feb;117(2):477–487. doi: 10.1128/jb.117.2.477-487.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Denhardt D. T. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966 Jun 13;23(5):641–646. doi: 10.1016/0006-291x(66)90447-5. [DOI] [PubMed] [Google Scholar]
  8. Echols H., Lu C., Burgers P. M. Mutator strains of Escherichia coli, mutD and dnaQ, with defective exonucleolytic editing by DNA polymerase III holoenzyme. Proc Natl Acad Sci U S A. 1983 Apr;80(8):2189–2192. doi: 10.1073/pnas.80.8.2189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fowler R. G., Degnen G. E., Cox E. C. Mutational specificity of a conditional Escherichia coli mutator, mutD5. Mol Gen Genet. 1974;133(3):179–191. doi: 10.1007/BF00267667. [DOI] [PubMed] [Google Scholar]
  10. Fuller F. A family of cloning vectors containing the lacUV5 promoter. Gene. 1982 Jul-Aug;19(1):43–54. doi: 10.1016/0378-1119(82)90187-1. [DOI] [PubMed] [Google Scholar]
  11. Hirsh D. Tryptophan transfer RNA as the UGA suppressor. J Mol Biol. 1971 Jun 14;58(2):439–458. doi: 10.1016/0022-2836(71)90362-7. [DOI] [PubMed] [Google Scholar]
  12. Hohn B., Lechner H., Marvin D. A. Filamentous bacterial viruses. I. DNA synthesis during the early stages of infection with fd. J Mol Biol. 1971 Feb 28;56(1):143–154. doi: 10.1016/0022-2836(71)90090-8. [DOI] [PubMed] [Google Scholar]
  13. Marvin D. A., Hohn B. Filamentous bacterial viruses. Bacteriol Rev. 1969 Jun;33(2):172–209. doi: 10.1128/br.33.2.172-209.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Miller J. H., Albertini A. M. Effects of surrounding sequence on the suppression of nonsense codons. J Mol Biol. 1983 Feb 15;164(1):59–71. doi: 10.1016/0022-2836(83)90087-6. [DOI] [PubMed] [Google Scholar]
  15. Raftery L. A., Bermingham J. R., Jr, Yarus M. Mutation in the D arm enables a suppressor with a CUA anticodon to read both amber and ochre codons in Escherichia coli. J Mol Biol. 1986 Aug 5;190(3):513–517. doi: 10.1016/0022-2836(86)90020-3. [DOI] [PubMed] [Google Scholar]
  16. Raftery L. A., Yarus M. Site-specific mutagenesis of Escherichia coli gltT yields a weak, glutamic acid-inserting ochre suppressor. J Mol Biol. 1985 Jul 20;184(2):343–345. doi: 10.1016/0022-2836(85)90385-7. [DOI] [PubMed] [Google Scholar]
  17. Staudenbauer W. L. Involvement of DNA polymerases I and III in the replication of bacteriophage M-13. Eur J Biochem. 1974 Nov 1;49(1):249–256. doi: 10.1111/j.1432-1033.1974.tb03829.x. [DOI] [PubMed] [Google Scholar]
  18. Stefano J. E., Gralla J. D. Mutation-induced changes in RNA polymerase-lac ps promoter interactions. J Biol Chem. 1982 Dec 10;257(23):13924–13929. [PubMed] [Google Scholar]
  19. Sussman J. L., Holbrook S. R., Warrant R. W., Church G. M., Kim S. H. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol. 1978 Aug 25;123(4):607–630. doi: 10.1016/0022-2836(78)90209-7. [DOI] [PubMed] [Google Scholar]
  20. VOGEL H. J., BONNER D. M. Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem. 1956 Jan;218(1):97–106. [PubMed] [Google Scholar]
  21. Yarus M., Cline S. W., Wier P., Breeden L., Thompson R. C. Actions of the anticodon arm in translation on the phenotypes of RNA mutants. J Mol Biol. 1986 Nov 20;192(2):235–255. doi: 10.1016/0022-2836(86)90362-1. [DOI] [PubMed] [Google Scholar]
  22. Yarus M., Cline S., Raftery L., Wier P., Bradley D. The translational efficiency of tRNA is a property of the anticodon arm. J Biol Chem. 1986 Aug 15;261(23):10496–10505. [PubMed] [Google Scholar]
  23. Yarus M., McMillan C., 3rd, Cline S., Bradley D., Snyder M. Construction of a composite tRNA gene by anticodon loop transplant. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5092–5096. doi: 10.1073/pnas.77.9.5092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Yarus M. Translational efficiency of transfer RNA's: uses of an extended anticodon. Science. 1982 Nov 12;218(4573):646–652. doi: 10.1126/science.6753149. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES