Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Apr 25;21(8):1941–1947. doi: 10.1093/nar/21.8.1941

Mosaic tile model for tRNA-enzyme recognition.

S V Steinberg 1, L L Kisselev 1
PMCID: PMC309436  PMID: 7684130

Abstract

An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucleotide and its neighbours as they are defined by the tertiary structure of the molecule. Informational content of each tile is calculated as its probability to occur exclusively in a set of cognate tRNAs. Based on this algorithm the identity sites of E. coli tRNA(Ala) and tRNA(Gln) were determined. The results are in a good agreement with the biochemical data and provide new information about identity sites of these tRNAs.

Full text

PDF
1941

Selected References

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

  1. Atilgan T., Nicholas H. B., Jr, McClain W. H. A statistical method for correlating tRNA sequence with amino acid specificity. Nucleic Acids Res. 1986 Jan 10;14(1):375–380. doi: 10.1093/nar/14.1.375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beresten S., Jahn M., Söll D. Aminoacyl-tRNA synthetase-induced cleavage of tRNA. Nucleic Acids Res. 1992 Apr 11;20(7):1523–1530. doi: 10.1093/nar/20.7.1523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. 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]
  4. Hayase Y., Jahn M., Rogers M. J., Sylvers L. A., Koizumi M., Inoue H., Ohtsuka E., Söll D. Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl-tRNA synthetase: a complete identity set. EMBO J. 1992 Nov;11(11):4159–4165. doi: 10.1002/j.1460-2075.1992.tb05509.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Komine Y., Adachi T., Inokuchi H., Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol. 1990 Apr 20;212(4):579–598. doi: 10.1016/0022-2836(90)90224-A. [DOI] [PubMed] [Google Scholar]
  7. Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. doi: 10.1073/pnas.72.11.4414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. McClain W. H., Chen Y. M., Foss K., Schneider J. Association of transfer RNA acceptor identity with a helical irregularity. Science. 1988 Dec 23;242(4886):1681–1684. doi: 10.1126/science.2462282. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. McClain W. H., Foss K., Jenkins R. A., Schneider J. Four sites in the acceptor helix and one site in the variable pocket of tRNA(Ala) determine the molecule's acceptor identity. Proc Natl Acad Sci U S A. 1991 Oct 15;88(20):9272–9276. doi: 10.1073/pnas.88.20.9272. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Normanly J., Abelson J. tRNA identity. Annu Rev Biochem. 1989;58:1029–1049. doi: 10.1146/annurev.bi.58.070189.005121. [DOI] [PubMed] [Google Scholar]
  14. Perona J. J., Swanson R. N., Rould M. A., Steitz T. A., Söll D. Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science. 1989 Dec 1;246(4934):1152–1154. doi: 10.1126/science.2686030. [DOI] [PubMed] [Google Scholar]
  15. Prather N. E., Murgola E. J., Mims B. H. Nucleotide substitution in the amino acid acceptor stem of lysine transfer RNA causes missense suppression. J Mol Biol. 1984 Jan 15;172(2):177–184. doi: 10.1016/s0022-2836(84)80036-4. [DOI] [PubMed] [Google Scholar]
  16. Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rogers M. J., Adachi T., Inokuchi H., Söll D. Switching tRNA(Gln) identity from glutamine to tryptophan. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3463–3467. doi: 10.1073/pnas.89.8.3463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Schimmel P. Parameters for the molecular recognition of transfer RNAs. Biochemistry. 1989 Apr 4;28(7):2747–2759. doi: 10.1021/bi00433a001. [DOI] [PubMed] [Google Scholar]
  20. Schulman L. H. Recognition of tRNAs by aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 1991;41:23–87. [PubMed] [Google Scholar]
  21. Smith D., Yarus M. Transfer RNA structure and coding specificity. II. A D-arm tertiary interaction that restricts coding range. J Mol Biol. 1989 Apr 5;206(3):503–511. doi: 10.1016/0022-2836(89)90497-x. [DOI] [PubMed] [Google Scholar]
  22. Sprinzl M., Dank N., Nock S., Schön A. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2127–2171. doi: 10.1093/nar/19.suppl.2127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Steinberg S. V., Kisselev L. L. Comparison of dissimilarity patterns of E coli, yeast and mammalian tRNAs. Biochimie. 1992 Apr;74(4):337–351. doi: 10.1016/0300-9084(92)90111-q. [DOI] [PubMed] [Google Scholar]
  24. Tamura K., Asahara H., Himeno H., Hasegawa T., Shimizu M. Identity elements of Escherichia coli tRNA(Ala). J Mol Recognit. 1991 Jul-Dec;4(4):129–132. doi: 10.1002/jmr.300040404. [DOI] [PubMed] [Google Scholar]
  25. Tsang T. H., Buck M., Ames B. N. Sequence specificity of tRNA-modifying enzymes. An analysis of 258 tRNA sequences. Biochim Biophys Acta. 1983 Nov 17;741(2):180–196. doi: 10.1016/0167-4781(83)90058-1. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Williams R. J., Nagel W., Roe B., Dudock B. Primary structure of E. coli alanine transfer RNA: relation to the yeast phenylalanyl tRNA synthetase recognition site. Biochem Biophys Res Commun. 1974 Oct 23;60(4):1215–1221. doi: 10.1016/0006-291x(74)90328-3. [DOI] [PubMed] [Google Scholar]
  28. Woo N. H., Roe B. A., Rich A. Three-dimensional structure of Escherichia coli initiator tRNAfMet. Nature. 1980 Jul 24;286(5771):346–351. doi: 10.1038/286346a0. [DOI] [PubMed] [Google Scholar]
  29. Yarus M. Intrinsic precision of aminoacyl-tRNA synthesis enhanced through parallel systems of ligands. Nat New Biol. 1972 Sep 27;239(91):106–108. doi: 10.1038/newbio239106a0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES