Skip to main content
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
. 1993 Aug 1;90(15):6919–6923. doi: 10.1073/pnas.90.15.6919

Dominant lethality by expression of a catalytically inactive class I tRNA synthetase.

E Schmidt 1, P Schimmel 1
PMCID: PMC47046  PMID: 8346197

Abstract

Alignment-guided mutagenesis was used to create an inactive, but toxic, aminoacyl-tRNA synthetase. An Asp-96-->Ala (D96A) replacement in the nucleotide binding fold of the class I Escherichia coli isoleucyl-tRNA synthetase inactivates the enzyme without disrupting its competence for binding isoleucine tRNA. Expression of plasmid-encoded mutant enzyme in a cell with a wild-type ileS chromosomal allele resulted in cell death. Introduction of a second K732T substitution previously shown to weaken tRNA binding gives an inactive D96A/K732T double mutant. Expression of the double mutant is not lethal to E. coli. D96A but not the double mutant significantly inhibited in vitro charging of isoleucine tRNA by the wild-type enzyme. The results suggest a dominant tRNA binding-dependent arrest of cell growth caused by a reduction in the pool of a specific tRNA. Specific tRNA binding drugs may have therapeutic applications for treatment of microbial pathogens.

Full text

PDF
6919

Images in this article

Selected References

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

  1. Bedouelle H., Guez V., Vidal-Cros A., Hermann M. Overproduction of tyrosyl-tRNA synthetase is toxic to Escherichia coli: a genetic analysis. J Bacteriol. 1990 Jul;172(7):3940–3945. doi: 10.1128/jb.172.7.3940-3945.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brunie S., Zelwer C., Risler J. L. Crystallographic study at 2.5 A resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP. J Mol Biol. 1990 Nov 20;216(2):411–424. doi: 10.1016/S0022-2836(05)80331-6. [DOI] [PubMed] [Google Scholar]
  3. Burbaum J. J., Schimmel P. Assembly of a class I tRNA synthetase from products of an artificially split gene. Biochemistry. 1991 Jan 15;30(2):319–324. doi: 10.1021/bi00216a002. [DOI] [PubMed] [Google Scholar]
  4. Clarke N. D., Lien D. C., Schimmel P. Evidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure. Science. 1988 Apr 22;240(4851):521–523. doi: 10.1126/science.3282306. [DOI] [PubMed] [Google Scholar]
  5. Csank C., Martindale D. W. Isoleucyl-tRNA synthetase from the ciliated protozoan Tetrahymena thermophila. DNA sequence, gene regulation, and leucine zipper motifs. J Biol Chem. 1992 Mar 5;267(7):4592–4599. [PubMed] [Google Scholar]
  6. Cusack S., Berthet-Colominas C., Härtlein M., Nassar N., Leberman R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A. Nature. 1990 Sep 20;347(6290):249–255. doi: 10.1038/347249a0. [DOI] [PubMed] [Google Scholar]
  7. Dardel F., Fayat G., Blanquet S. Molecular cloning and primary structure of the Escherichia coli methionyl-tRNA synthetase gene. J Bacteriol. 1984 Dec;160(3):1115–1122. doi: 10.1128/jb.160.3.1115-1122.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Di Nocera P. P., Blasi F., Di Lauro R., Frunzio R., Bruni C. B. Nucleotide sequence of the attenuator region of the histidine operon of Escherichia coli K-12. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4276–4280. doi: 10.1073/pnas.75.9.4276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Englisch U., Englisch S., Markmeyer P., Schischkoff J., Sternbach H., Kratzin H., Cramer F. Structure of the yeast isoleucyl-tRNA synthetase gene (ILS1). DNA-sequence, amino-acid sequence of proteolytic peptides of the enzyme and comparison of the structure to those of other known aminoacyl-tRNA synthetases. Biol Chem Hoppe Seyler. 1987 Aug;368(8):971–979. doi: 10.1515/bchm3.1987.368.2.971. [DOI] [PubMed] [Google Scholar]
  10. Eriani G., Delarue M., Poch O., Gangloff J., Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203–206. doi: 10.1038/347203a0. [DOI] [PubMed] [Google Scholar]
  11. Gemmill R. M., Wessler S. R., Keller E. B., Calvo J. M. leu operon of Salmonella typhimurium is controlled by an attenuation mechanism. Proc Natl Acad Sci U S A. 1979 Oct;76(10):4941–4945. doi: 10.1073/pnas.76.10.4941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ghosh G., Pelka H., Schulman L. H., Brunie S. Activation of methionine by Escherichia coli methionyl-tRNA synthetase. Biochemistry. 1991 Oct 8;30(40):9569–9575. doi: 10.1021/bi00104a002. [DOI] [PubMed] [Google Scholar]
  13. Ghosh G., Pelka H., Schulman L. H. Identification of the tRNA anticodon recognition site of Escherichia coli methionyl-tRNA synthetase. Biochemistry. 1990 Mar 6;29(9):2220–2225. doi: 10.1021/bi00461a003. [DOI] [PubMed] [Google Scholar]
  14. Hou Y. M., Shiba K., Mottes C., Schimmel P. Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):976–980. doi: 10.1073/pnas.88.3.976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Keller E. B., Calvo J. M. Alternative secondary structures of leader RNAs and the regulation of the trp, phe, his, thr, and leu operons. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6186–6190. doi: 10.1073/pnas.76.12.6186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Landick R., Carey J., Yanofsky C. Translation activates the paused transcription complex and restores transcription of the trp operon leader region. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4663–4667. doi: 10.1073/pnas.82.14.4663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lee F., Bertrand K., Bennett G., Yanofsky C. Comparison of the nucleotide sequences of the initial transcribed regions of the tryptophan operons of Escherichia coli and Salmonella typhimurium. J Mol Biol. 1978 May 15;121(2):193–217. doi: 10.1016/s0022-2836(78)80005-9. [DOI] [PubMed] [Google Scholar]
  19. Mechulam Y., Schmitt E., Panvert M., Schmitter J. M., Lapadat-Tapolsky M., Meinnel T., Dessen P., Blanquet S., Fayat G. Methionyl-tRNA synthetase from Bacillus stearothermophilus: structural and functional identities with the Escherichia coli enzyme. Nucleic Acids Res. 1991 Jul 11;19(13):3673–3681. doi: 10.1093/nar/19.13.3673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Nureki O., Muramatsu T., Suzuki K., Kohda D., Matsuzawa H., Ohta T., Miyazawa T., Yokoyama S. Methionyl-tRNA synthetase gene from an extreme thermophile, Thermus thermophilus HB8. Molecular cloning, primary-structure analysis, expression in Escherichia coli, and site-directed mutagenesis. J Biol Chem. 1991 Feb 15;266(5):3268–3277. [PubMed] [Google Scholar]
  21. Rould M. A., Perona J. J., Söll D., Steitz T. A. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science. 1989 Dec 1;246(4934):1135–1142. doi: 10.1126/science.2479982. [DOI] [PubMed] [Google Scholar]
  22. Schreier A. A., Schimmel P. R. Transfer ribonucleic acid synthetase catalyzed deacylation of aminoacyl transfer ribonucleic acid in the absence of adenosine monophosphate and pyrophosphate. Biochemistry. 1972 Apr 25;11(9):1582–1589. doi: 10.1021/bi00759a006. [DOI] [PubMed] [Google Scholar]
  23. Shepard A., Shiba K., Schimmel P. RNA binding determinant in some class I tRNA synthetases identified by alignment-guided mutagenesis. Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9964–9968. doi: 10.1073/pnas.89.20.9964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shiba K., Schimmel P. Functional assembly of a randomly cleaved protein. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1880–1884. doi: 10.1073/pnas.89.5.1880. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Shiba K., Schimmel P. Tripartite functional assembly of a large class I aminoacyl tRNA synthetase. J Biol Chem. 1992 Nov 15;267(32):22703–22706. [PubMed] [Google Scholar]
  26. Springer M., Mayaux J. F., Fayat G., Plumbridge J. A., Graffe M., Blanquet S., Grunberg-Manago M. Attenuation control of the Escherichia coli phenylalanyl-tRNA synthetase operon. J Mol Biol. 1985 Feb 20;181(4):467–478. doi: 10.1016/0022-2836(85)90420-6. [DOI] [PubMed] [Google Scholar]
  27. Starzyk R. M., Webster T. A., Schimmel P. Evidence for dispensable sequences inserted into a nucleotide fold. Science. 1987 Sep 25;237(4822):1614–1618. doi: 10.1126/science.3306924. [DOI] [PubMed] [Google Scholar]
  28. Tzagoloff A., Vambutas A., Akai A. Characterization of MSM1, the structural gene for yeast mitochondrial methionyl-tRNA synthetase. Eur J Biochem. 1989 Feb 1;179(2):365–371. doi: 10.1111/j.1432-1033.1989.tb14562.x. [DOI] [PubMed] [Google Scholar]
  29. Vidal-Cros A., Bedouelle H. Role of residue Glu152 in the discrimination between transfer RNAs by tyrosyl-tRNA synthetase from Bacillus stearothermophilus. J Mol Biol. 1992 Feb 5;223(3):801–810. doi: 10.1016/0022-2836(92)90991-r. [DOI] [PubMed] [Google Scholar]
  30. Walter P., Gangloff J., Bonnet J., Boulanger Y., Ebel J. P., Fasiolo F. Primary structure of the Saccharomyces cerevisiae gene for methionyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1983 May;80(9):2437–2441. doi: 10.1073/pnas.80.9.2437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Webster T., Tsai H., Kula M., Mackie G. A., Schimmel P. Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase. Science. 1984 Dec 14;226(4680):1315–1317. doi: 10.1126/science.6390679. [DOI] [PubMed] [Google Scholar]
  32. Yarus M., Berg P. On the properties and utility of a membrane filter assay in the study of isoleucyl-tRNA synthetase. Anal Biochem. 1970 Jun;35(2):450–465. doi: 10.1016/0003-2697(70)90207-1. [DOI] [PubMed] [Google Scholar]
  33. Yegian C. D., Stent G. S., Martin E. M. Intracellular condition of Escherichia coli transfer RNA. Proc Natl Acad Sci U S A. 1966 Apr;55(4):839–846. doi: 10.1073/pnas.55.4.839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zurawski G., Brown K., Killingly D., Yanofsky C. Nucleotide sequence of the leader region of the phenylalanine operon of Escherichia coli. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4271–4275. doi: 10.1073/pnas.75.9.4271. [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