Rational design and directed evolution of a bacterial-type glutaminyl-tRNA synthetase precursor

Nucleic Acids Res. 2012 Sep;40(16):7967-74. doi: 10.1093/nar/gks507. Epub 2012 May 31.

Abstract

Protein biosynthesis requires aminoacyl-transfer RNA (tRNA) synthetases to provide aminoacyl-tRNA substrates for the ribosome. Most bacteria and all archaea lack a glutaminyl-tRNA synthetase (GlnRS); instead, Gln-tRNA(Gln) is produced via an indirect pathway: a glutamyl-tRNA synthetase (GluRS) first attaches glutamate (Glu) to tRNA(Gln), and an amidotransferase converts Glu-tRNA(Gln) to Gln-tRNA(Gln). The human pathogen Helicobacter pylori encodes two GluRS enzymes, with GluRS2 specifically aminoacylating Glu onto tRNA(Gln). It was proposed that GluRS2 is evolving into a bacterial-type GlnRS. Herein, we have combined rational design and directed evolution approaches to test this hypothesis. We show that, in contrast to wild-type (WT) GlnRS2, an engineered enzyme variant (M110) with seven amino acid changes is able to rescue growth of the temperature-sensitive Escherichia coli glnS strain UT172 at its non-permissive temperature. In vitro kinetic analyses reveal that WT GluRS2 selectively acylates Glu over Gln, whereas M110 acylates Gln 4-fold more efficiently than Glu. In addition, M110 hydrolyzes adenosine triphosphate 2.5-fold faster in the presence of Glu than Gln, suggesting that an editing activity has evolved in this variant to discriminate against Glu. These data imply that GluRS2 is a few steps away from evolving into a GlnRS and provides a paradigm for studying aminoacyl-tRNA synthetase evolution using directed engineering approaches.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Amino Acyl-tRNA Synthetases / chemistry*
  • Amino Acyl-tRNA Synthetases / genetics
  • Amino Acyl-tRNA Synthetases / metabolism
  • Catalytic Domain
  • Directed Molecular Evolution
  • Escherichia coli / enzymology
  • Glutamate-tRNA Ligase / chemistry*
  • Glutamate-tRNA Ligase / genetics
  • Glutamate-tRNA Ligase / metabolism
  • Glutamic Acid / metabolism
  • Helicobacter pylori / enzymology
  • Molecular Sequence Data
  • Protein Engineering
  • RNA, Transfer, Gln / metabolism
  • Sequence Alignment
  • Temperature
  • Transfer RNA Aminoacylation

Substances

  • RNA, Transfer, Gln
  • Glutamic Acid
  • Amino Acyl-tRNA Synthetases
  • Glutamate-tRNA Ligase
  • glutaminyl-tRNA synthetase