Skip to main content
PMC 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
. 1977 Jun;74(6):2246–2250. doi: 10.1073/pnas.74.6.2246

Experimental evidence for kinetic proofreading in the aminoacylation of tRNA by synthetase.

T Yamane, J J Hopfield
PMCID: PMC432146  PMID: 329276

Abstract

The enzymatic aminoacylation of tRNA can be viewed as a means of proofreading either the amino acid or the tRNA or both. We have conducted further experimental tests of kinetic proofreading in discriminating between cognate and noncognate amino acids and tRNAs as follows: (formula: see text). In cases (i) and (ii) the amino acids are proofread, in cases (iii) and (iv) the tRNA is proofread, and in case (v), both the amino acid and the tRNA are proofread. ATP consumed per acylation was 400, 1.5, 40, 25, and 1000, respectively. High ATP/aminoacylation ratios are diagnostic for kinetic proofreading.

Full text

PDF
2246

Selected References

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

  1. Baldwin A. N., Berg P. Purification and properties of isoleucyl ribonucleic acid synthetase from Escherichia coli. J Biol Chem. 1966 Feb 25;241(4):831–838. [PubMed] [Google Scholar]
  2. Baldwin A. N., Berg P. Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase. J Biol Chem. 1966 Feb 25;241(4):839–845. [PubMed] [Google Scholar]
  3. Bonnet J., Ebel J. P. Correction of aminoacylation errors: evidence for a non significant role of the aminoacyl-tRNA synthetase catalysed deacylation of aminoacyl-tRNAs. FEBS Lett. 1974 Mar 1;39(3):259–262. doi: 10.1016/0014-5793(74)80125-0. [DOI] [PubMed] [Google Scholar]
  4. CONWAY T. W., LANSFORD E. M., Jr, SHIVE W. Purification and substrate specificity of a phenylalanine-activating enzyme from Escherichia coli 9723. J Biol Chem. 1962 Sep;237:2850–2854. [PubMed] [Google Scholar]
  5. Calendar R., Berg P. D-Tyrosyl RNA: formation, hydrolysis and utilization for protein synthesis. J Mol Biol. 1967 May 28;26(1):39–54. doi: 10.1016/0022-2836(67)90259-8. [DOI] [PubMed] [Google Scholar]
  6. Calendar R., Berg P. Purification and physical characterization of tyrosyl ribonucleic acid synthetases from Escherichia coli and Bacillus subtilis. Biochemistry. 1966 May;5(5):1681–1690. doi: 10.1021/bi00869a033. [DOI] [PubMed] [Google Scholar]
  7. Calendar R., Berg P. The catalytic properties of tyrosyl ribonucleic acid synthetases from Escherichia coli and Bacillus subtilis. Biochemistry. 1966 May;5(5):1690–1695. doi: 10.1021/bi00869a034. [DOI] [PubMed] [Google Scholar]
  8. Dietrich A., Kern D., Bonnet J., Giegé R., Ebel J. P. Interpretation of tRNA-mischarging kinetics. Eur J Biochem. 1976 Nov 1;70(1):147–158. doi: 10.1111/j.1432-1033.1976.tb10965.x. [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. Eldred E. W., Schimmel P. R. Investigation of the transfer of amino acid from a transfer ribonucleic acid synthetase-aminoacyl adenylate complex to transfer ribonucleic acid. Biochemistry. 1972 Jan 4;11(1):17–23. doi: 10.1021/bi00751a004. [DOI] [PubMed] [Google Scholar]
  11. Eldred E. W., Schimmel P. R. Rapid deacylation by isoleucyl transfer ribonucleic acid synthetase of isoleucine-specific transfer ribonucleic acid aminoacylated with valine. J Biol Chem. 1972 May 10;247(9):2961–2964. [PubMed] [Google Scholar]
  12. Etlinger J. D., Goldberg A. L. A soluble ATP-dependent proteolytic system responsible for the degradation of abnormal proteins in reticulocytes. Proc Natl Acad Sci U S A. 1977 Jan;74(1):54–58. doi: 10.1073/pnas.74.1.54. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fersht A. R., Jakes R. Demonstration of two reaction pathways for the aminoacylation of tRNA. Application of the pulsed quenched flow technique. Biochemistry. 1975 Jul 29;14(15):3350–3356. doi: 10.1021/bi00686a010. [DOI] [PubMed] [Google Scholar]
  14. Fersht A. R., Kaethner M. M. Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing. Biochemistry. 1976 Jul 27;15(15):3342–3346. doi: 10.1021/bi00660a026. [DOI] [PubMed] [Google Scholar]
  15. Fersht A. R., Kaethner M. M. Mechanism of aminoacylation of tRNA. Proof of the aminoacyl adenylate pathway for the isoleucyl- and tyrosyl-tRNA synthetases from Escherichia coli K12. Biochemistry. 1976 Feb 24;15(4):818–823. doi: 10.1021/bi00649a014. [DOI] [PubMed] [Google Scholar]
  16. Giegé R., Kern D., Ebel J. P., Grosjean H., de Henau S., Chantrenne H. Incorrect aminoacylations involving tRNAs or valyl-tRNA synthetase from Bacillus stearothermophilus. Eur J Biochem. 1974 Jun 15;45(2):351–362. doi: 10.1111/j.1432-1033.1974.tb03560.x. [DOI] [PubMed] [Google Scholar]
  17. Goldberg A. L., St John A. C. Intracellular protein degradation in mammalian and bacterial cells: Part 2. Annu Rev Biochem. 1976;45:747–803. doi: 10.1146/annurev.bi.45.070176.003531. [DOI] [PubMed] [Google Scholar]
  18. Grosjean H., Söll D. G., Crothers D. M. Studies of the complex between transfer RNAs with complementary anticodons. I. Origins of enhanced affinity between complementary triplets. J Mol Biol. 1976 May 25;103(3):499–519. doi: 10.1016/0022-2836(76)90214-x. [DOI] [PubMed] [Google Scholar]
  19. Haselkorn R., Rothman-Denes L. B. Protein synthesis. Annu Rev Biochem. 1973;42:397–438. doi: 10.1146/annurev.bi.42.070173.002145. [DOI] [PubMed] [Google Scholar]
  20. Hempfling W. P., Mainzer S. E. Effects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture. J Bacteriol. 1975 Sep;123(3):1076–1087. doi: 10.1128/jb.123.3.1076-1087.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hopfield J. J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci U S A. 1974 Oct;71(10):4135–4139. doi: 10.1073/pnas.71.10.4135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hopfield J. J., Yamane T., Yue V., Coutts S. M. Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. Proc Natl Acad Sci U S A. 1976 Apr;73(4):1164–1168. doi: 10.1073/pnas.73.4.1164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Hélène C., Brun F., Yaniv M. Fluorescence studies of interactions between Escherichia coli valyl-tRNA synthetase and its substrates. J Mol Biol. 1971 May 28;58(1):349–356. doi: 10.1016/0022-2836(71)90251-8. [DOI] [PubMed] [Google Scholar]
  24. Jakes R., Fersht A. R. Tyrosyl-tRNA synthetase from Escherichia coli. Stoichiometry of ligand binding and half-of-the-sites reactivity in aminoacylation. Biochemistry. 1975 Jul 29;14(15):3344–3350. doi: 10.1021/bi00686a009. [DOI] [PubMed] [Google Scholar]
  25. Lagunas R. Energy metabolism of Saccharomyces cerevisiae discrepancy between ATP balance and known metabolic functions. Biochim Biophys Acta. 1976 Sep 13;440(3):661–674. doi: 10.1016/0005-2728(76)90049-9. [DOI] [PubMed] [Google Scholar]
  26. Loftfield R. B., Eigner E. A. The specificity of enzymic reactions. Aminoacyl-soluble RNA ligases. Biochim Biophys Acta. 1966 Dec 28;130(2):426–448. doi: 10.1016/0304-4165(66)90239-x. [DOI] [PubMed] [Google Scholar]
  27. Loftfield R. B., Vanderjagt D. The frequency of errors in protein biosynthesis. Biochem J. 1972 Aug;128(5):1353–1356. doi: 10.1042/bj1281353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Mertes M., Peters M. A., Mahoney W., Yarus M. Isoleucylation of transfer RNA f Met (E. coli) by isoleucyl-transfer RNA synthetase from Escherichia coli. J Mol Biol. 1972 Nov 28;71(3):671–685. doi: 10.1016/s0022-2836(72)80031-7. [DOI] [PubMed] [Google Scholar]
  29. Miller D. L., Weissbach H. Studies on the purification and properties of factor Tu from E. coli. Arch Biochem Biophys. 1970 Nov;141(1):26–37. doi: 10.1016/0003-9861(70)90102-5. [DOI] [PubMed] [Google Scholar]
  30. Pearson R. L., Weiss J. F., Kelmers A. D. Improved separation of transfer RNA's on polychlorotrifuoroethylene-supported reversed-phase chromatography columns. Biochim Biophys Acta. 1971 Feb 11;228(3):770–774. doi: 10.1016/0005-2787(71)90748-9. [DOI] [PubMed] [Google Scholar]
  31. Remy P., Dirheimer G., Ebel J. P. Séparation des nucléosides mono-, di- et triphosphates par chromatographie sur couche mince de silice. J Chromatogr. 1967 Dec;31(2):609–612. doi: 10.1016/s0021-9673(01)86131-8. [DOI] [PubMed] [Google Scholar]
  32. Schlimme E., von der Haar F., Eckstein F., Cramer F. Chemically modified phenylalanine transfer ribonucleic acid from yeast. Synthesis and properties of tRNA Phe-C-Cs-A and the effect of adenosine 5'-O-(1-thiotriphosphate) on the activation of phenylalanine. Eur J Biochem. 1970 Jun;14(2):351–356. doi: 10.1111/j.1432-1033.1970.tb00296.x. [DOI] [PubMed] [Google Scholar]
  33. Schulman L. H., Pelka H., Sundari R. M. Structural requirements for recognition of Escherichia coli initiator and non-initiator transfer ribonucleic acids by bacterial T factor. J Biol Chem. 1974 Nov 25;249(22):7102–7110. [PubMed] [Google Scholar]
  34. Thompson R. C., Stone P. J. Proofreading of the codon-anticodon interaction on ribosomes. Proc Natl Acad Sci U S A. 1977 Jan;74(1):198–202. doi: 10.1073/pnas.74.1.198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Topal M. D., Fresco J. R. Base pairing and fidelity in codon-anticodon interaction. Nature. 1976 Sep 23;263(5575):289–293. doi: 10.1038/263289a0. [DOI] [PubMed] [Google Scholar]
  36. Topal M. D., Fresco J. R. Complementary base pairing and the origin of substitution mutations. Nature. 1976 Sep 23;263(5575):285–289. doi: 10.1038/263285a0. [DOI] [PubMed] [Google Scholar]
  37. VAUGHAN M., STEINBERG D. The specificity of protein biosynthesis. Adv Protein Chem. 1959;14:115–173. doi: 10.1016/s0065-3233(08)60610-5. [DOI] [PubMed] [Google Scholar]
  38. Yaniv M., Gros F. Studies on valyl-tRNA synthetase and tRNA from Escherichia coli. I. Purification and properties of the enzyme from normal Escherichia coli strains. J Mol Biol. 1969 Aug 28;44(1):1–15. doi: 10.1016/0022-2836(69)90401-x. [DOI] [PubMed] [Google Scholar]
  39. Yarus M., Berg P. Recognition of tRNA by isoleucyl-tRNA synthetase. Effect of substrates on the dynamics of tRNA-enzyme interaction. J Mol Biol. 1969 Jun 14;42(2):171–189. doi: 10.1016/0022-2836(69)90037-0. [DOI] [PubMed] [Google Scholar]
  40. 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]
  41. Yarus M. Phenylalanyl-tRNA synthetase and isoleucyl-tRNA Phe : a possible verification mechanism for aminoacyl-tRNA. Proc Natl Acad Sci U S A. 1972 Jul;69(7):1915–1919. doi: 10.1073/pnas.69.7.1915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Yarus M. Solvent and specificity. Binding and isoleucylation of phenylalanine transfer ribonucleic acid (Escherichia coli) by isoleucyl transfer ribonucleic acid synthetase from Escherichia coli. Biochemistry. 1972 Jun 6;11(12):2352–2361. doi: 10.1021/bi00762a022. [DOI] [PubMed] [Google Scholar]
  43. Yarus M. Why do organic solvents enhance mistakes in aminoacyl tRNA synthesis? Arch Biochem Biophys. 1976 May;174(1):350–354. doi: 10.1016/0003-9861(76)90355-6. [DOI] [PubMed] [Google Scholar]
  44. von der Haar F., Cramer F. Hydrolytic action of aminoacyl-tRNA synthetases from baker's yeast: "chemical proofreading" preventing acylation of tRNA(I1e) with misactivated valine. Biochemistry. 1976 Sep 7;15(18):4131–4138. doi: 10.1021/bi00663a034. [DOI] [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