The TRNA Specificity of Thermus Thermophilus EF-Tu

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2002 Mar 14

PMID 11891293

Citations 53

Authors

Haruichi Asahara

Olke C Uhlenbeck

Affiliations

Soon will be listed here.

Abstract

By introducing a GAC anticodon, 21 different Escherichia coli tRNAs were misacylated with either phenylalanine or valine and assayed for their affinity to Thermus thermophilus elongation factor Tu (EF-Tu)*GTP by using a ribonuclease protection assay. The presence of a common esterified amino acid permits the thermodynamic contribution of each tRNA body to the overall affinity to be evaluated. The E. coli elongator tRNAs exhibit a wide range of binding affinities that varied from -11.7 kcal/mol for Val-tRNA(Glu) to -8.1 kcal/mol for Val-tRNA(Tyr), clearly establishing EF-Tu*GTP as a sequence-specific RNA-binding protein. Because the ionic strength dependence of k(off) varied among tRNAs, some of the affinity differences are the results of a different number of phosphate contacts formed between tRNA and protein. Because EF-Tu is known to contact only the phosphodiester backbone of tRNA, the observed specificity must be a consequence of an indirect readout mechanism.

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References

Louie A, Jurnak F . Kinetic studies of Escherichia coli elongation factor Tu-guanosine 5'-triphosphate-aminoacyl-tRNA complexes. Biochemistry. 1985; 24(23):6433-9. DOI: 10.1021/bi00344a019. View

Asahara H, Himeno H, Tamura K, Hasegawa T, Watanabe K, Shimizu M . Recognition nucleotides of Escherichia coli tRNA(Leu) and its elements facilitating discrimination from tRNASer and tRNA(Tyr). J Mol Biol. 1993; 231(2):219-29. DOI: 10.1006/jmbi.1993.1277. View

Schon A, Kannangara C, Gough S, Soll D . Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature. 1988; 331(6152):187-90. DOI: 10.1038/331187a0. View

Sampson J, Uhlenbeck O . Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci U S A. 1988; 85(4):1033-7. PMC: 279695. DOI: 10.1073/pnas.85.4.1033. View

Hou Y, Schimmel P . A simple structural feature is a major determinant of the identity of a transfer RNA. Nature. 1988; 333(6169):140-5. DOI: 10.1038/333140a0. View

Schulman L, Pelka H . Anticodon switching changes the identity of methionine and valine transfer RNAs. Science. 1988; 242(4879):765-8. DOI: 10.1126/science.3055296. View

Sampson J, DiRenzo A, Behlen L, Uhlenbeck O . Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase. Science. 1989; 243(4896):1363-6. DOI: 10.1126/science.2646717. View

Himeno H, Hasegawa T, Ueda T, Watanabe K, Miura K, Shimizu M . Role of the extra G-C pair at the end of the acceptor stem of tRNA(His) in aminoacylation. Nucleic Acids Res. 1989; 17(19):7855-63. PMC: 334892. DOI: 10.1093/nar/17.19.7855. View

Forster C, Ott G, Forchhammer K, Sprinzl M . Interaction of a selenocysteine-incorporating tRNA with elongation factor Tu from E.coli. Nucleic Acids Res. 1990; 18(3):487-91. PMC: 333452. DOI: 10.1093/nar/18.3.487. View

10.

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; 212(4):579-98. DOI: 10.1016/0022-2836(90)90224-A. View

11.

Janiak F, Dell V, Abrahamson J, Watson B, Miller D, Johnson A . Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP: evidence for a new functional role for elongation factor Tu in protein biosynthesis. Biochemistry. 1990; 29(18):4268-77. DOI: 10.1021/bi00470a002. View

12.

Ott G, Schiesswohl M, Kiesewetter S, Forster C, Arnold L, Erdmann V . Ternary complexes of Escherichia coli aminoacyl-tRNAs with the elongation factor Tu and GTP: thermodynamic and structural studies. Biochim Biophys Acta. 1990; 1050(1-3):222-5. DOI: 10.1016/0167-4781(90)90170-7. View

13.

Himeno H, Hasegawa T, Ueda T, Watanabe K, Shimizu M . Conversion of aminoacylation specificity from tRNA(Tyr) to tRNA(Ser) in vitro. Nucleic Acids Res. 1990; 18(23):6815-9. PMC: 332736. DOI: 10.1093/nar/18.23.6815. View

14.

Tamura K, Himeno H, Asahara H, Hasegawa T, Shimizu M . Identity determinants of E. coli tRNA(Val). Biochem Biophys Res Commun. 1991; 177(2):619-23. DOI: 10.1016/0006-291x(91)91833-x. View

15.

Jahn M, Rogers M, Soll D . Anticodon and acceptor stem nucleotides in tRNA(Gln) are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature. 1991; 352(6332):258-60. DOI: 10.1038/352258a0. View

16.

Himeno H, Hasegawa T, Asahara H, Tamura K, Shimizu M . Identity determinants of E. coli tryptophan tRNA. Nucleic Acids Res. 1991; 19(23):6379-82. PMC: 329181. DOI: 10.1093/nar/19.23.6379. View

17.

Hasegawa T, Miyano M, Himeno H, Sano Y, Kimura K, Shimizu M . Identity determinants of E. coli threonine tRNA. Biochem Biophys Res Commun. 1992; 184(1):478-84. DOI: 10.1016/0006-291x(92)91219-g. View

18.

Sampson J, Behlen L, DiRenzo A, Uhlenbeck O . Recognition of yeast tRNA(Phe) by its cognate yeast phenylalanyl-tRNA synthetase: an analysis of specificity. Biochemistry. 1992; 31(17):4161-7. DOI: 10.1021/bi00132a002. View

19.

Tamura K, Himeno H, Asahara H, Hasegawa T, Shimizu M . In vitro study of E.coli tRNA(Arg) and tRNA(Lys) identity elements. Nucleic Acids Res. 1992; 20(9):2335-9. PMC: 312350. DOI: 10.1093/nar/20.9.2335. View

20.

Lee C, Dyson M, Mandal N, Varshney U, Bahramian B, RajBhandary U . Striking effects of coupling mutations in the acceptor stem on recognition of tRNAs by Escherichia coli Met-tRNA synthetase and Met-tRNA transformylase. Proc Natl Acad Sci U S A. 1992; 89(19):9262-6. PMC: 50106. DOI: 10.1073/pnas.89.19.9262. View