HipBA-promoter structures reveal the basis of heritable multidrug tolerance

Nature. 2015 Aug 6;524(7563):59-64. doi: 10.1038/nature14662. Epub 2015 Jul 29.


Multidrug tolerance is largely responsible for chronic infections and caused by a small population of dormant cells called persisters. Selection for survival in the presence of antibiotics produced the first genetic link to multidrug tolerance: a mutant in the Escherichia coli hipA locus. HipA encodes a serine-protein kinase, the multidrug tolerance activity of which is neutralized by binding to the transcriptional regulator HipB and hipBA promoter. The physiological role of HipA in multidrug tolerance, however, has been unclear. Here we show that wild-type HipA contributes to persister formation and that high-persister hipA mutants cause multidrug tolerance in urinary tract infections. Perplexingly, high-persister mutations map to the N-subdomain-1 of HipA far from its active site. Structures of higher-order HipA-HipB-promoter complexes reveal HipA forms dimers in these assemblies via N-subdomain-1 interactions that occlude their active sites. High-persistence mutations, therefore, diminish HipA-HipA dimerization, thereby unleashing HipA to effect multidrug tolerance. Thus, our studies reveal the mechanistic basis of heritable, clinically relevant antibiotic tolerance.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Down-Regulation / genetics
  • Drug Resistance, Multiple, Bacterial / drug effects
  • Drug Resistance, Multiple, Bacterial / genetics*
  • Drug Tolerance / genetics
  • Escherichia coli / drug effects*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli / pathogenicity
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial / genetics
  • Humans
  • Models, Molecular
  • Mutation / genetics
  • Operon / genetics
  • Phenotype
  • Promoter Regions, Genetic / genetics*
  • Protein Multimerization
  • Protein Structure, Tertiary / genetics
  • Transcription, Genetic / genetics
  • Urinary Bladder / microbiology
  • Urinary Bladder / pathology
  • Urinary Tract Infections / drug therapy
  • Urinary Tract Infections / microbiology


  • Anti-Bacterial Agents
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • hipB protein, E coli
  • hipA protein, E coli

Associated data

  • PDB/4YG1
  • PDB/4YG4
  • PDB/4YG7