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. 1995 Aug 15;14(16):4050–4055. doi: 10.1002/j.1460-2075.1995.tb00076.x

Cell growth inhibition by sequence-specific RNA minihelices.

D Hipps 1, P Schimmel 1
PMCID: PMC394483  PMID: 7664744

Abstract

RNA minihelices which reconstruct the 12 base pair acceptor-T psi C domains of transfer RNAs interact with their cognate tRNA synthetases. These substrates lack the anticodons of the genetic code and, therefore, cannot participate in steps of protein synthesis subsequent to aminoacylation. We report here that expression in Escherichia coli of either of two minihelices, each specific for a different amino acid, inhibited cell growth. Inhibition appears to be due to direct competition between the minihelix and its related tRNA for binding to their common synthetase. This competition, in turn, sharply lowers the pool of the specific charged tRNA for protein synthesis. Inhibition is relieved by single nucleotide changes which disrupt the minihelix-synthetase interaction. The results suggest that sequence-specific RNA minihelix substrates bind to cognate synthetases in vivo and can, in principle, act as cell growth regulators. Naturally occurring non-tRNA substrates for aminoacylation may serve a similar purpose.

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Selected References

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  1. Buechter D. D., Schimmel P. Aminoacylation of RNA minihelices: implications for tRNA synthetase structural design and evolution. Crit Rev Biochem Mol Biol. 1993;28(4):309–322. doi: 10.3109/10409239309078438. [DOI] [PubMed] [Google Scholar]
  2. Felden B., Florentz C., Westhof E., Giegé R. Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA. Biochimie. 1993;75(12):1143–1157. doi: 10.1016/0300-9084(93)90014-j. [DOI] [PubMed] [Google Scholar]
  3. Folk W. R., Berg P. Characterization of altered forms of glycyl transfer ribonucleic acid synthetase and the effects of such alterations on aminoacyl transfer ribonucleic acid synthesis in vivo. J Bacteriol. 1970 Apr;102(1):204–212. doi: 10.1128/jb.102.1.204-212.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Francklyn C., Schimmel P. Aminoacylation of RNA minihelices with alanine. Nature. 1989 Feb 2;337(6206):478–481. doi: 10.1038/337478a0. [DOI] [PubMed] [Google Scholar]
  5. Francklyn C., Shi J. P., Schimmel P. Overlapping nucleotide determinants for specific aminoacylation of RNA microhelices. Science. 1992 Feb 28;255(5048):1121–1125. doi: 10.1126/science.1546312. [DOI] [PubMed] [Google Scholar]
  6. Frugier M., Florentz C., Giegé R. Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide. EMBO J. 1994 May 1;13(9):2218–2226. doi: 10.1002/j.1460-2075.1994.tb06499.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Giegé R., Puglisi J. D., Florentz C. tRNA structure and aminoacylation efficiency. Prog Nucleic Acid Res Mol Biol. 1993;45:129–206. doi: 10.1016/s0079-6603(08)60869-7. [DOI] [PubMed] [Google Scholar]
  8. Hipps D., Shiba K., Henderson B., Schimmel P. Operational RNA code for amino acids: species-specific aminoacylation of minihelices switched by a single nucleotide. Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5550–5552. doi: 10.1073/pnas.92.12.5550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hou Y. M., Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature. 1988 May 12;333(6169):140–145. doi: 10.1038/333140a0. [DOI] [PubMed] [Google Scholar]
  10. Hou Y. M., Schimmel P. Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo. Biochemistry. 1989 Jun 13;28(12):4942–4947. doi: 10.1021/bi00438a005. [DOI] [PubMed] [Google Scholar]
  11. Hou Y. M., Schimmel P. Novel transfer RNAs that are active in Escherichia coli. Biochemistry. 1992 May 5;31(17):4157–4160. doi: 10.1021/bi00132a001. [DOI] [PubMed] [Google Scholar]
  12. Keng T., Webster T. A., Sauer R. T., Schimmel P. Gene for Escherichia coli glycyl-tRNA synthetase has tandem subunit coding regions in the same reading frame. J Biol Chem. 1982 Nov 10;257(21):12503–12508. [PubMed] [Google Scholar]
  13. Lewis J. A., Ames B. N. Histidine regulation in Salmonella typhimurium. XI. The percentage of transfer RNA His charged in vivo and its relation to the repression of the histidine operon. J Mol Biol. 1972 Apr 28;66(1):131–142. doi: 10.1016/s0022-2836(72)80011-1. [DOI] [PubMed] [Google Scholar]
  14. Masson J. M., Miller J. H. Expression of synthetic suppressor tRNA genes under the control of a synthetic promoter. Gene. 1986;47(2-3):179–183. doi: 10.1016/0378-1119(86)90061-2. [DOI] [PubMed] [Google Scholar]
  15. McClain W. H., Foss K. Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket". Science. 1988 Sep 30;241(4874):1804–1807. doi: 10.1126/science.2459773. [DOI] [PubMed] [Google Scholar]
  16. McClain W. H., Foss K. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science. 1988 May 6;240(4853):793–796. doi: 10.1126/science.2452483. [DOI] [PubMed] [Google Scholar]
  17. McClain W. H., Guerrier-Takada C., Altman S. Model substrates for an RNA enzyme. Science. 1987 Oct 23;238(4826):527–530. doi: 10.1126/science.2443980. [DOI] [PubMed] [Google Scholar]
  18. Mosteller R. D., Yanofsky C. Evidence that tryptophanyl transfer ribonucleic acid is not the corepressor of the tryptophan operon of Escherichia coli. J Bacteriol. 1971 Jan;105(1):268–275. doi: 10.1128/jb.105.1.268-275.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Musier-Forsyth K., Schimmel P. Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove. Nature. 1992 Jun 11;357(6378):513–515. doi: 10.1038/357513a0. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Rich A., RajBhandary U. L. Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem. 1976;45:805–860. doi: 10.1146/annurev.bi.45.070176.004105. [DOI] [PubMed] [Google Scholar]
  22. Sampson J. R., Saks M. E. Contributions of discrete tRNA(Ser) domains to aminoacylation by E.coli seryl-tRNA synthetase: a kinetic analysis using model RNA substrates. Nucleic Acids Res. 1993 Sep 25;21(19):4467–4475. doi: 10.1093/nar/21.19.4467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Schimmel P., Giegé R., Moras D., Yokoyama S. An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8763–8768. doi: 10.1073/pnas.90.19.8763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shiba K., Schimmel P., Motegi H., Noda T. Human glycyl-tRNA synthetase. Wide divergence of primary structure from bacterial counterpart and species-specific aminoacylation. J Biol Chem. 1994 Nov 25;269(47):30049–30055. [PubMed] [Google Scholar]
  25. Silberklang M., Gillum A. M., RajBhandary U. L. Use of in vitro 32P labeling in the sequence analysis of nonradioactive tRNAs. Methods Enzymol. 1979;59:58–109. doi: 10.1016/0076-6879(79)59072-7. [DOI] [PubMed] [Google Scholar]
  26. Taylor J. W., Ott J., Eckstein F. The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA. Nucleic Acids Res. 1985 Dec 20;13(24):8765–8785. doi: 10.1093/nar/13.24.8765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Trézéguet V., Edwards H., Schimmel P. A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae. Mol Cell Biol. 1991 May;11(5):2744–2751. doi: 10.1128/mcb.11.5.2744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Varshney U., Lee C. P., RajBhandary U. L. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J Biol Chem. 1991 Dec 25;266(36):24712–24718. [PubMed] [Google Scholar]
  29. Yarus M., Cline S. W. The structure of the phi 80d3 ilv+ Su+7 transducing phage and the origin of its Su+7 tRNA-gene containing fragment. Mol Gen Genet. 1979 Mar 5;170(3):283–289. doi: 10.1007/BF00267061. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. 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]
  32. Young R. A. Transcription termination in the Escherichia coli ribosomal RNA operon rrnC. J Biol Chem. 1979 Dec 25;254(24):12725–12731. [PubMed] [Google Scholar]
  33. de Boer H. A., Comstock L. J., Vasser M. The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc Natl Acad Sci U S A. 1983 Jan;80(1):21–25. doi: 10.1073/pnas.80.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]

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