Transfer RNA modulates the editing mechanism used by class II prolyl-tRNA synthetase

J Biol Chem. 2008 Mar 14;283(11):7128-34. doi: 10.1074/jbc.M709902200. Epub 2008 Jan 7.

Abstract

Aminoacyl-tRNA synthetases catalyze the attachment of amino acids to their cognate tRNAs. To prevent errors in protein synthesis, many synthetases have evolved editing pathways by which misactivated amino acids (pre-transfer editing) and misacylated tRNAs (post-transfer editing) are hydrolyzed. Previous studies have shown that class II prolyl-tRNA synthetase (ProRS) possesses both pre- and post-transfer editing functions against noncognate alanine. To assess the relative contributions of pre- and post-transfer editing, presented herein are kinetic studies of an Escherichia coli ProRS mutant in which post-transfer editing is selectively inactivated, effectively isolating the pre-transfer editing pathway. When post-transfer editing is abolished, substantial levels of alanine mischarging are observed under saturating amino acid conditions, indicating that pre-transfer editing alone cannot prevent the formation of Ala-tRNA Pro. Steady-state kinetic parameters for aminoacylation measured under these conditions reveal that the preference for proline over alanine is 2000-fold, which is well within the regime where editing is required. Simultaneous measurement of AMP and Ala-tRNA Pro formation in the presence of tRNA Pro suggested that misactivated alanine is efficiently transferred to tRNA to form the mischarged product. In the absence of tRNA, enzyme-catalyzed Ala-AMP hydrolysis is the dominant form of editing, with "selective release" of noncognate adenylate from the active site constituting a minor pathway. Studies with human and Methanococcus jannaschii ProRS, which lack a post-transfer editing domain, suggest that enzymatic pre-transfer editing occurs within the aminoacylation active site. Taken together, the results reported herein illustrate how both pre- and post-transfer editing pathways work in concert to ensure accurate aminoacylation by ProRS.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Alanine / chemistry
  • Amino Acyl-tRNA Synthetases / chemistry*
  • Binding Sites
  • Escherichia coli / enzymology
  • Humans
  • Hydrolysis
  • Kinetics
  • Methanococcus / enzymology
  • Models, Biological
  • Models, Chemical
  • Nucleic Acid Conformation
  • RNA Editing*
  • RNA, Transfer / metabolism*
  • Time Factors

Substances

  • Adenosine Triphosphate
  • RNA, Transfer
  • Amino Acyl-tRNA Synthetases
  • prolyl T RNA synthetase
  • Alanine