Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

Cell Rep. 2015 Aug 25;12(8):1289-99. doi: 10.1016/j.celrep.2015.07.043. Epub 2015 Aug 13.


Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 68 genes in 51 transcription units (TUs) belong to these regulons. Among them, 48 genes showed more than 2-fold changes in expression level under single-TF-knockout conditions. This reconstruction expands the genome-wide roles of these factors to include direct activation of genes related to amino acid biosynthesis (methionine and aromatic amino acids), cell wall synthesis (lipid A biosynthesis and peptidoglycan growth), and divalent metal ion transport (Mn(2+), Zn(2+), and Mg(2+)). Investigating the co-regulation of these genes with other stress-response TFs reveals that they are independently regulated by stress-specific TFs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / biosynthesis
  • Cations, Divalent / metabolism
  • Escherichia coli / genetics
  • Escherichia coli Proteins / genetics*
  • Gene Expression Regulation, Bacterial
  • Gene Regulatory Networks*
  • Genome, Bacterial*
  • Ion Transport
  • Oxidative Stress*
  • Repressor Proteins / genetics*


  • Amino Acids
  • Cations, Divalent
  • Escherichia coli Proteins
  • Repressor Proteins
  • oxyR protein, E coli
  • oxyS small RNA, E coli