Role of D-aminoacyl-tRNA Deacylase Beyond Chiral Proofreading as a Cellular Defense Against Glycine Mischarging by AlaRS

Elife. 2017 Mar 31;6:e24001. doi: 10.7554/eLife.24001.

Abstract

Strict L-chiral rejection through Gly-cisPro motif during chiral proofreading underlies the inability of D-aminoacyl-tRNA deacylase (DTD) to discriminate between D-amino acids and achiral glycine. The consequent Gly-tRNAGly 'misediting paradox' is resolved by EF-Tu in the cell. Here, we show that DTD's active site architecture can efficiently edit mischarged Gly-tRNAAla species four orders of magnitude more efficiently than even AlaRS, the only ubiquitous cellular checkpoint known for clearing the error. Also, DTD knockout in AlaRS editing-defective background causes pronounced toxicity in Escherichia coli even at low-glycine levels which is alleviated by alanine supplementation. We further demonstrate that DTD positively selects the universally invariant tRNAAla-specific G3•U70. Moreover, DTD's activity on non-cognate Gly-tRNAAla is conserved across all bacteria and eukaryotes, suggesting DTD's key cellular role as a glycine deacylator. Our study thus reveals a hitherto unknown function of DTD in cracking the universal mechanistic dilemma encountered by AlaRS, and its physiological importance.

Keywords: E. coli; amino acids; biochemistry; biophysics; chirality; genetic code; structural biology; tRNA synthetase; translation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alanine-tRNA Ligase / antagonists & inhibitors*
  • Aminoacyltransferases / metabolism*
  • Escherichia coli / enzymology*
  • Escherichia coli / metabolism*
  • Glycine / metabolism*

Substances

  • Aminoacyltransferases
  • Alanine-tRNA Ligase
  • Glycine

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.