DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide

J Bacteriol. 2001 Aug;183(15):4562-70. doi: 10.1128/JB.183.15.4562-4570.2001.


The genome-wide transcription profile of Escherichia coli cells treated with hydrogen peroxide was examined with a DNA microarray composed of 4,169 E. coli open reading frames. By measuring gene expression in isogenic wild-type and oxyR deletion strains, we confirmed that the peroxide response regulator OxyR activates most of the highly hydrogen peroxide-inducible genes. The DNA microarray measurements allowed the identification of several new OxyR-activated genes, including the hemH heme biosynthetic gene; the six-gene suf operon, which may participate in Fe-S cluster assembly or repair; and four genes of unknown function. We also identified several genes, including uxuA, encoding mannonate hydrolase, whose expression might be repressed by OxyR, since their expression was elevated in the DeltaoxyR mutant strain. In addition, the induction of some genes was found to be OxyR independent, indicating the existence of other peroxide sensors and regulators in E. coli. For example, the isc operon, which specifies Fe-S cluster formation and repair activities, was induced by hydrogen peroxide in strains lacking either OxyR or the superoxide response regulators SoxRS. These results expand our understanding of the oxidative stress response and raise interesting questions regarding the nature of other regulators that modulate gene expression in response to hydrogen peroxide.

Publication types

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

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Bacterial Proteins / physiology
  • Base Sequence
  • DNA, Bacterial
  • DNA-Binding Proteins*
  • Escherichia coli / drug effects
  • Escherichia coli / genetics*
  • Escherichia coli Proteins*
  • Hydrogen Peroxide / pharmacology*
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Operon
  • Regulon
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Repressor Proteins / physiology
  • Trans-Activators*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription Factors / physiology
  • Transcription, Genetic*


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Repressor Proteins
  • Trans-Activators
  • Transcription Factors
  • oxyR protein, E coli
  • SoxR protein, Bacteria
  • SoxS protein, E coli
  • Hydrogen Peroxide