Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Dec 15;25(24):4899–4906. doi: 10.1093/nar/25.24.4899

Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase.

M Sissler 1, G Eriani 1, F Martin 1, R Giegé 1, C Florentz 1
PMCID: PMC147145  PMID: 9396794

Abstract

Gene cloning, overproduction and an efficient purification protocol of yeast arginyl-tRNA synthetase (ArgRS) as well as the interaction patterns of this protein with cognate tRNAArgand non-cognate tRNAAspare described. This work was motivated by the fact that the in vitro transcript of tRNAAspis of dual aminoacylation specificity and is not only aspartylated but also efficiently arginylated. The crystal structure of the complex between class II aspartyl-tRNA synthetase (AspRS) and tRNAAsp, as well as early biochemical data, have shown that tRNAAspis recognized by its variable region side. Here we show by footprinting with enzymatic and chemical probes that transcribed tRNAAspis contacted by class I ArgRS along the opposite D arm side, as is homologous tRNAArg, but with idiosyncratic interaction patterns. Besides protection, footprints also show enhanced accessibility of the tRNAs to the structural probes, indicative of conformational changes in the complexed tRNAs. These different patterns are interpreted in relation to the alternative arginine identity sets found in the anticodon loops of tRNAArgand tRNAAsp. The mirror image alternative interaction patterns of unmodified tRNAAspwith either class I ArgRS or class II AspRS, accounting for the dual identity of this tRNA, are discussed in relation to the class defining features of the synthetases. This study indicates that complex formation between unmodified tRNAAspand either ArgRS and AspRS is solely governed by the proteins.

Full Text

The Full Text of this article is available as a PDF (331.6 KB).

Selected References

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

  1. Amann E., Ochs B., Abel K. J. Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene. 1988 Sep 30;69(2):301–315. doi: 10.1016/0378-1119(88)90440-4. [DOI] [PubMed] [Google Scholar]
  2. Arnez J. G., Steitz T. A. Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP. Biochemistry. 1996 Nov 26;35(47):14725–14733. doi: 10.1021/bi961532o. [DOI] [PubMed] [Google Scholar]
  3. Becker H. D., Giegé R., Kern D. Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus. Biochemistry. 1996 Jun 11;35(23):7447–7458. doi: 10.1021/bi9601058. [DOI] [PubMed] [Google Scholar]
  4. Biou V., Yaremchuk A., Tukalo M., Cusack S. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 1994 Mar 11;263(5152):1404–1410. doi: 10.1126/science.8128220. [DOI] [PubMed] [Google Scholar]
  5. Cavarelli J., Moras D. Recognition of tRNAs by aminoacyl-tRNA synthetases. FASEB J. 1993 Jan;7(1):79–86. doi: 10.1096/fasebj.7.1.8422978. [DOI] [PubMed] [Google Scholar]
  6. Cavarelli J., Rees B., Ruff M., Thierry J. C., Moras D. Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. Nature. 1993 Mar 11;362(6416):181–184. doi: 10.1038/362181a0. [DOI] [PubMed] [Google Scholar]
  7. Dietrich A., Romby P., Maréchal-Drouard L., Guillemaut P., Giegé R. Solution conformation of several free tRNALeu species from bean, yeast and Escherichia coli and interaction of these tRNAs with bean cytoplasmic Leucyl-tRNA synthetase. A phosphate alkylation study with ethylnitrosourea. Nucleic Acids Res. 1990 May 11;18(9):2589–2597. doi: 10.1093/nar/18.9.2589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dock-Bregeon A. C., Moras D. Conformational changes and dynamics of tRNAs: evidence from hydrolysis patterns. Cold Spring Harb Symp Quant Biol. 1987;52:113–121. doi: 10.1101/sqb.1987.052.01.016. [DOI] [PubMed] [Google Scholar]
  9. Ebel J. P., Giegé R., Bonnet J., Kern D., Befort N., Bollack C., Fasiolo F., Gangloff J., Dirheimer G. Factors determining the specificity of the tRNA aminoacylation reaction. Non-absolute specificity of tRNA-aminoacyl-tRNA synthetase recognition and particular importance of the maximal velocity. Biochimie. 1973 May;55(5):547–557. doi: 10.1016/s0300-9084(73)80415-8. [DOI] [PubMed] [Google Scholar]
  10. Ehresmann C., Baudin F., Mougel M., Romby P., Ebel J. P., Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109–9128. doi: 10.1093/nar/15.22.9109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Eriani G., Dirheimer G., Gangloff J. Isolation and characterization of the gene coding for Escherichia coli arginyl-tRNA synthetase. Nucleic Acids Res. 1989 Jul 25;17(14):5725–5736. doi: 10.1093/nar/17.14.5725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Favorova O. O., Fasiolo F., Keith G., Vassilenko S. K., Ebel J. P. Partial digestion of tRNA--aminoacyl-tRNA synthetase complexes with cobra venom ribonuclease. Biochemistry. 1981 Feb 17;20(4):1006–1011. doi: 10.1021/bi00507a055. [DOI] [PubMed] [Google Scholar]
  13. Florentz C., Briand J. P., Romby P., Hirth L., Ebel J. P., Glegé R. The tRNA-like structure of turnip yellow mosaic virus RNA: structural organization of the last 159 nucleotides from the 3' OH terminus. EMBO J. 1982;1(2):269–276. doi: 10.1002/j.1460-2075.1982.tb01158.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Frugier M., Florentz C., Schimmel P., Giegé R. Triple aminoacylation specificity of a chimerized transfer RNA. Biochemistry. 1993 Dec 21;32(50):14053–14061. doi: 10.1021/bi00213a039. [DOI] [PubMed] [Google Scholar]
  15. Frugier M., Söll D., Giegé R., Florentz C. Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases. Biochemistry. 1994 Aug 23;33(33):9912–9921. doi: 10.1021/bi00199a013. [DOI] [PubMed] [Google Scholar]
  16. Gangloff J., Jaozara R., Dirheimer G. Study of the interaction of yeast arginyl-tRNA synthetase with yeast tRNAArg2 and tRNAArg3 by partial digestions with cobra venom ribonuclease. Eur J Biochem. 1983 May 16;132(3):629–637. doi: 10.1111/j.1432-1033.1983.tb07410.x. [DOI] [PubMed] [Google Scholar]
  17. Gangloff J., Keith G., Ebel J. P., Dirheimer G. Structure of aspartate-tRNA from brewer's yeast. Nat New Biol. 1971 Mar 24;230(12):125–126. doi: 10.1038/newbio230125a0. [DOI] [PubMed] [Google Scholar]
  18. Gangloff J., Schutz A., Dirheimer G. Arginyl-tRNA synthetase from baker's yeast. Purification and some properties. Eur J Biochem. 1976 May 17;65(1):177–182. doi: 10.1111/j.1432-1033.1976.tb10403.x. [DOI] [PubMed] [Google Scholar]
  19. Giegé R., Florentz C., Kern D., Gangloff J., Eriani G., Moras D. Aspartate identity of transfer RNAs. Biochimie. 1996;78(7):605–623. doi: 10.1016/s0300-9084(96)80007-1. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Girjes A. A., Hobson K., Chen P., Lavin M. F. Cloning and characterization of cDNA encoding a human arginyl-tRNA synthetase. Gene. 1995 Oct 27;164(2):347–350. doi: 10.1016/0378-1119(95)00502-w. [DOI] [PubMed] [Google Scholar]
  22. Ibba M., Hong K. W., Sherman J. M., Sever S., Söll D. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6953–6958. doi: 10.1073/pnas.93.14.6953. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S. Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII. Science. 1994 Sep 30;265(5181):2077–2082. doi: 10.1126/science.8091229. [DOI] [PubMed] [Google Scholar]
  24. Keith G., Dirheimer G. Reinvestigation of the primary structure of brewer's yeast tRNA 3 Arg. Biochem Biophys Res Commun. 1980 Jan 15;92(1):116–119. doi: 10.1016/0006-291x(80)91527-2. [DOI] [PubMed] [Google Scholar]
  25. Kolchanov N. A., Titov I. I., Vlassova I. E., Vlassov V. V. Chemical and computer probing of RNA structure. Prog Nucleic Acid Res Mol Biol. 1996;53:131–196. doi: 10.1016/S0079-6603(08)60144-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Massire C., Gaspin C., Westhof E. DRAWNA: a program for drawing schematic views of nucleic acids. J Mol Graph. 1994 Sep;12(3):201-6, 196. doi: 10.1016/0263-7855(94)80088-x. [DOI] [PubMed] [Google Scholar]
  27. McClain W. H. Transfer RNA identity. FASEB J. 1993 Jan;7(1):72–78. doi: 10.1096/fasebj.7.1.8422977. [DOI] [PubMed] [Google Scholar]
  28. Mewes H. W., Albermann K., Heumann K., Liebl S., Pfeiffer F. MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res. 1997 Jan 1;25(1):28–30. doi: 10.1093/nar/25.1.28. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Moras D., Comarmond M. B., Fischer J., Weiss R., Thierry J. C., Ebel J. P., Giegé R. Crystal structure of yeast tRNAAsp. Nature. 1980 Dec 25;288(5792):669–674. doi: 10.1038/288669a0. [DOI] [PubMed] [Google Scholar]
  30. Nureki O., Niimi T., Muramatsu T., Kanno H., Kohno T., Florentz C., Giegé R., Yokoyama S. Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli. J Mol Biol. 1994 Feb 25;236(3):710–724. doi: 10.1006/jmbi.1994.1184. [DOI] [PubMed] [Google Scholar]
  31. Peattie D. A., Gilbert W. Chemical probes for higher-order structure in RNA. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679–4682. doi: 10.1073/pnas.77.8.4679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Perona J. J., Rould M. A., Steitz T. A. Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry. 1993 Aug 31;32(34):8758–8771. doi: 10.1021/bi00085a006. [DOI] [PubMed] [Google Scholar]
  33. Perret V., Garcia A., Grosjean H., Ebel J. P., Florentz C., Giegé R. Relaxation of a transfer RNA specificity by removal of modified nucleotides. Nature. 1990 Apr 19;344(6268):787–789. doi: 10.1038/344787a0. [DOI] [PubMed] [Google Scholar]
  34. Perret V., Garcia A., Puglisi J., Grosjean H., Ebel J. P., Florentz C., Giegé R. Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. Biochimie. 1990 Oct;72(10):735–743. doi: 10.1016/0300-9084(90)90158-d. [DOI] [PubMed] [Google Scholar]
  35. Pütz J., Florentz C., Benseler F., Giegé R. A single methyl group prevents the mischarging of a tRNA. Nat Struct Biol. 1994 Sep;1(9):580–582. doi: 10.1038/nsb0994-580. [DOI] [PubMed] [Google Scholar]
  36. Pütz J., Puglisi J. D., Florentz C., Giegé R. Identity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase. Science. 1991 Jun 21;252(5013):1696–1699. doi: 10.1126/science.2047878. [DOI] [PubMed] [Google Scholar]
  37. Rees B., Cavarelli J., Moras D. Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase. Biochimie. 1996;78(7):624–631. doi: 10.1016/s0300-9084(96)80008-3. [DOI] [PubMed] [Google Scholar]
  38. Romby P., Moras D., Bergdoll M., Dumas P., Vlassov V. V., Westhof E., Ebel J. P., Giegé R. Yeast tRNAAsp tertiary structure in solution and areas of interaction of the tRNA with aspartyl-tRNA synthetase. A comparative study of the yeast phenylalanine system by phosphate alkylation experiments with ethylnitrosourea. J Mol Biol. 1985 Aug 5;184(3):455–471. doi: 10.1016/0022-2836(85)90294-3. [DOI] [PubMed] [Google Scholar]
  39. Rould M. A., Perona J. J., Steitz T. A. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 1991 Jul 18;352(6332):213–218. doi: 10.1038/352213a0. [DOI] [PubMed] [Google Scholar]
  40. 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]
  41. Rudinger J., Puglisi J. D., Pütz J., Schatz D., Eckstein F., Florentz C., Giegé R. Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5882–5886. doi: 10.1073/pnas.89.13.5882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A., Podjarny A., Rees B., Thierry J. C., Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science. 1991 Jun 21;252(5013):1682–1689. doi: 10.1126/science.2047877. [DOI] [PubMed] [Google Scholar]
  43. Saks M. E., Sampson J. R., Abelson J. N. The transfer RNA identity problem: a search for rules. Science. 1994 Jan 14;263(5144):191–197. doi: 10.1126/science.7506844. [DOI] [PubMed] [Google Scholar]
  44. Sekine S., Nureki O., Sakamoto K., Niimi T., Tateno M., Go M., Kohno T., Brisson A., Lapointe J., Yokoyama S. Major identity determinants in the "augmented D helix" of tRNA(Glu) from Escherichia coli. J Mol Biol. 1996 Mar 8;256(4):685–700. doi: 10.1006/jmbi.1996.0118. [DOI] [PubMed] [Google Scholar]
  45. 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]
  46. Sissler M., Giegé R., Florentz C. Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts. EMBO J. 1996 Sep 16;15(18):5069–5076. [PMC free article] [PubMed] [Google Scholar]
  47. Vlassov V. V., Giegé R., Ebel J. P. Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea. Eur J Biochem. 1981 Sep;119(1):51–59. doi: 10.1111/j.1432-1033.1981.tb05575.x. [DOI] [PubMed] [Google Scholar]
  48. Vlassov V. V., Kern D., Romby P., Giegé R., Ebel J. P. Interaction of tRNAPhe and tRNAVal with aminoacyl-tRNA synthetases. A chemical modification study. Eur J Biochem. 1983 May 16;132(3):537–544. doi: 10.1111/j.1432-1033.1983.tb07395.x. [DOI] [PubMed] [Google Scholar]
  49. Vlassov V. V., Zuber G., Felden B., Behr J. P., Giegé R. Cleavage of tRNA with imidazole and spermine imidazole constructs: a new approach for probing RNA structure. Nucleic Acids Res. 1995 Aug 25;23(16):3161–3167. doi: 10.1093/nar/23.16.3161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. 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]

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

RESOURCES