Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1988 Sep;85(18):6627–6631. doi: 10.1073/pnas.85.18.6627

Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA.

M J Rogers 1, D Söll 1
PMCID: PMC282030  PMID: 3045821

Abstract

Analysis of the in vivo amber suppressor activity of mutants derived from two Escherichia coli serine tRNAs shows that substitution of 2 base pairs in the acceptor helix changes a serine suppressor tRNA to an efficient glutamine acceptor. Determination of the amino acid inserted in vivo into protein by this tRNA shows that these changes reduce the tRNA recognition by seryl-tRNA synthetase while increasing that of glutaminyl-tRNA synthetase. This implies that misaminoacylation in vivo is dependent on the competition by different synthetases for the tRNA. In addition, the "translational efficiency" of tRNA is an integral part in observing misaminoacylation in vivo.

Full text

PDF
6627

Selected References

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

  1. Celis J. E., Piper P. W. Compilation of mutant suppressor tRNA sequences. Nucleic Acids Res. 1982 Jan 22;10(2):r83–r91. doi: 10.1093/nar/10.2.762-b. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Crothers D. M., Seno T., Söll G. Is there a discriminator site in transfer RNA? Proc Natl Acad Sci U S A. 1972 Oct;69(10):3063–3067. doi: 10.1073/pnas.69.10.3063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Grosjean H., Nicoghosian K., Haumont E., Söll D., Cedergren R. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Res. 1985 Aug 12;13(15):5697–5706. doi: 10.1093/nar/13.15.5697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hooper M. L., Russell R. L., Smith J. D. Mischarging in mutant tyrosine transfer RNAs. FEBS Lett. 1972 Apr 15;22(1):149–155. doi: 10.1016/0014-5793(72)80241-2. [DOI] [PubMed] [Google Scholar]
  5. Inokuchi H., Hoben P., Yamao F., Ozeki H., Söll D. Transfer RNA mischarging mediated by a mutant Escherichia coli glutaminyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1984 Aug;81(16):5076–5080. doi: 10.1073/pnas.81.16.5076. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Inokuchi H., Yamao F., Sakano H., Ozeki H. Identification of transfer RNA suppressors in Escherichia coli. I. Amber suppressor su+2, an anticodon mutant of tRNA2Gln. J Mol Biol. 1979 Aug 25;132(4):649–662. doi: 10.1016/0022-2836(79)90380-2. [DOI] [PubMed] [Google Scholar]
  7. Kim S. H., Suddath F. L., Quigley G. J., McPherson A., Sussman J. L., Wang A. H., Seeman N. C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. doi: 10.1126/science.185.4149.435. [DOI] [PubMed] [Google Scholar]
  8. Knowlton R. G., Yarus M. Discrimination between aminoacyl groups on su+ 7 tRNA by elongation factor Tu. J Mol Biol. 1980 Jun 5;139(4):721–732. doi: 10.1016/0022-2836(80)90057-1. [DOI] [PubMed] [Google Scholar]
  9. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lapointe J., Söll D. Glutamyl transfer ribonucleic acid synthetase of Escherichia coli. II. Interaction with intact glutamyl transfer ribonucleic acid. J Biol Chem. 1972 Aug 25;247(16):4975–4981. [PubMed] [Google Scholar]
  11. McClain W. H., Nicholas H. B., Jr Differences between transfer RNA molecules. J Mol Biol. 1987 Apr 20;194(4):635–642. doi: 10.1016/0022-2836(87)90240-3. [DOI] [PubMed] [Google Scholar]
  12. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Murgola E. J. tRNA, suppression, and the code. Annu Rev Genet. 1985;19:57–80. doi: 10.1146/annurev.ge.19.120185.000421. [DOI] [PubMed] [Google Scholar]
  15. Normanly J., Masson J. M., Kleina L. G., Abelson J., Miller J. H. Construction of two Escherichia coli amber suppressor genes: tRNAPheCUA and tRNACysCUA. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6548–6552. doi: 10.1073/pnas.83.17.6548. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Normanly J., Ogden R. C., Horvath S. J., Abelson J. Changing the identity of a transfer RNA. Nature. 1986 May 15;321(6067):213–219. doi: 10.1038/321213a0. [DOI] [PubMed] [Google Scholar]
  17. Raftery L. A., Yarus M. Systematic alterations in the anticodon arm make tRNA(Glu)-Suoc a more efficient suppressor. EMBO J. 1987 May;6(5):1499–1506. doi: 10.1002/j.1460-2075.1987.tb02392.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Roberts T. M., Swanberg S. L., Poteete A., Riedel G., Backman K. A plasmid cloning vehicle allowing a positive selection for inserted fragments. Gene. 1980 Dec;12(1-2):123–127. doi: 10.1016/0378-1119(80)90022-0. [DOI] [PubMed] [Google Scholar]
  19. Robertus J. D., Ladner J. E., Finch J. T., Rhodes D., Brown R. S., Clark B. F., Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974 Aug 16;250(467):546–551. doi: 10.1038/250546a0. [DOI] [PubMed] [Google Scholar]
  20. Sampson J. R., Uhlenbeck O. C. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci U S A. 1988 Feb;85(4):1033–1037. doi: 10.1073/pnas.85.4.1033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Schimmel P. R., Söll D. Aminoacyl-tRNA synthetases: general features and recognition of transfer RNAs. Annu Rev Biochem. 1979;48:601–648. doi: 10.1146/annurev.bi.48.070179.003125. [DOI] [PubMed] [Google Scholar]
  23. Schimmel P. Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu Rev Biochem. 1987;56:125–158. doi: 10.1146/annurev.bi.56.070187.001013. [DOI] [PubMed] [Google Scholar]
  24. Schulman L. H., Pelka H. In vitro conversion of a methionine to a glutamine-acceptor tRNA. Biochemistry. 1985 Dec 3;24(25):7309–7314. doi: 10.1021/bi00346a043. [DOI] [PubMed] [Google Scholar]
  25. Seong B. L., RajBhandary U. L. Escherichia coli formylmethionine tRNA: mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. Proc Natl Acad Sci U S A. 1987 Jan;84(2):334–338. doi: 10.1073/pnas.84.2.334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Shimura Y., Aono H., Ozeki H., Sarabhai A., Lamfrom H., Abelson J. Mutant tyrosine tRNA of altered amino acid specificity. FEBS Lett. 1972 Apr 15;22(1):144–148. doi: 10.1016/0014-5793(72)80240-0. [DOI] [PubMed] [Google Scholar]
  27. Sprinzl M., Hartmann T., Meissner F., Moll J., Vorderwülbecke T. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1987;15 (Suppl):r53–188. doi: 10.1093/nar/15.suppl.r53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tamura F., Nishimura S., Ohki M. The E. coli divE mutation, which differentially inhibits synthesis of certain proteins, is in tRNASer1. EMBO J. 1984 May;3(5):1103–1107. doi: 10.1002/j.1460-2075.1984.tb01936.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Thorbjarnardóttir S., Uemura H., Dingermann T., Rafnar T., Thorsteinsdóttir S., Söll D., Eggertsson G. Escherichia coli supH suppressor: temperature-sensitive missense suppression caused by an anticodon change in tRNASer2. J Bacteriol. 1985 Jan;161(1):207–211. doi: 10.1128/jb.161.1.207-211.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Westhof E., Dumas P., Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J Mol Biol. 1985 Jul 5;184(1):119–145. doi: 10.1016/0022-2836(85)90048-8. [DOI] [PubMed] [Google Scholar]
  31. Yaniv M., Folk W. R., Berg P., Soll L. A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J Mol Biol. 1974 Jun 25;86(2):245–260. doi: 10.1016/0022-2836(74)90016-3. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. 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]
  34. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any fragment of DNA. Nucleic Acids Res. 1982 Oct 25;10(20):6487–6500. doi: 10.1093/nar/10.20.6487. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES