Molecular mechanism of bacterial persistence by HipA

Mol Cell. 2013 Oct 24;52(2):248-54. doi: 10.1016/j.molcel.2013.08.045. Epub 2013 Oct 3.


HipA of Escherichia coli is a eukaryote-like serine-threonine kinase that inhibits cell growth and induces persistence (multidrug tolerance). Previously, it was proposed that HipA inhibits cell growth by the phosphorylation of the essential translation factor EF-Tu. Here, we provide evidence that EF-Tu is not a target of HipA. Instead, a genetic screen reveals that the overexpression of glutamyl-tRNA synthetase (GltX) suppresses the toxicity of HipA. We show that HipA phosphorylates conserved Ser(239) near the active center of GltX and inhibits aminoacylation, a unique example of an aminoacyl-tRNA synthetase being inhibited by a toxin encoded by a toxin-antitoxin locus. HipA only phosphorylates tRNA(Glu)-bound GltX, which is consistent with the earlier finding that the regulatory motif containing Ser(239) changes configuration upon tRNA binding. These results indicate that HipA mediates persistence by the generation of "hungry" codons at the ribosomal A site that trigger the synthesis of (p)ppGpp, a hypothesis that we verify experimentally.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Aminoacylation
  • Anti-Bacterial Agents / pharmacology
  • Binding Sites / genetics
  • Drug Tolerance*
  • Escherichia coli / drug effects
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Glutamate-tRNA Ligase / chemistry
  • Glutamate-tRNA Ligase / genetics
  • Glutamate-tRNA Ligase / metabolism
  • Guanosine Pentaphosphate / metabolism
  • Models, Genetic
  • Models, Molecular
  • Mutation
  • Peptide Elongation Factor Tu / genetics
  • Peptide Elongation Factor Tu / metabolism
  • Phosphorylation
  • Protein Biosynthesis
  • Protein Structure, Tertiary
  • Protein-Serine-Threonine Kinases / genetics
  • Protein-Serine-Threonine Kinases / metabolism*
  • RNA, Transfer, Glu / genetics
  • RNA, Transfer, Glu / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Serine / chemistry
  • Serine / genetics
  • Serine / metabolism


  • Anti-Bacterial Agents
  • Escherichia coli Proteins
  • RNA, Transfer, Glu
  • hipA protein, E coli
  • Guanosine Pentaphosphate
  • Serine
  • Adenosine Triphosphate
  • Protein-Serine-Threonine Kinases
  • Peptide Elongation Factor Tu
  • Glutamate-tRNA Ligase