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J. Biol. Chem., Vol. 280, Issue 27, 25887-25891, July 8, 2005

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The Bacterial YbaK Protein Is a Cys-tRNA^Pro and Cys-tRNA^Cys Deacylase^*

Benfang Ruan and Dieter Söll¶

From the Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, Connecticut 06520-8114

Bacterial prolyl-tRNA synthetases and some smaller paralogs, YbaK and ProX, can hydrolyze misacylated Cys-tRNA^Pro or Ala-tRNA^Pro. To assess the significance of this quality control editing reaction in vivo, we tested Escherichia coli ybaK for its ability to suppress the E. coli thymidylate synthase thyA:146CCA missense mutant strain, which requires Cys-tRNA^Pro for growth in the absence of thymine. Missense suppression was observed in a ybaK deletion background, suggesting that YbaK functions as a Cys-tRNA^Pro deacylase in vivo. In vitro studies with the full set of 20 E. coli aminoacyl-tRNAs revealed that the Haemophilus influenzae and E. coli YbaK proteins are moderately general aminoacyl-tRNA deacylases that preferentially hydrolyze Cys-tRNA^Pro and Cys-tRNA^Cys and are also weak deacylases that cleave Gly-tRNA, Ala-tRNA, Ser-tRNA, Pro-tRNA, and Met-tRNA. The ProX protein acted as an aminoacyl-tRNA deacylase that cleaves preferentially Ala-tRNA and Gly-tRNA. The potential of H. influenzae YbaK to hydrolyze in vivo correctly charged Cys-tRNA^Cys was tested in E. coli strain X2913 (ybaK⁺). Overexpression of H. influenzae ybaK decreased the in vivo ratio of Cys-tRNA^Cys to tRNA^Cys from 65 to 35% and reduced the growth rate of strain X2913 by 30% in LB medium. These data suggest that YbaK-mediated hydrolysis of aminoacyl-tRNA can influence cell growth.

Received for publication, February 25, 2005 , and in revised form, April 25, 2005.

^* This work was supported by grants from the National Institute of General Medical Sciences and the Department of Energy. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^¶ To whom correspondence should be addressed: Dept. of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, 266 Whitney Ave., New Haven, CT 06520-8114. Tel.: 203-432-6200; Fax: 203-432-6202; E-mail: soll{at}trna.chem.yale.edu.

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