Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.
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.
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Sang Woo
SW
Seo
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Donghyuk
D
Kim
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Richard
R
Szubin
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark. Electronic address: palsson@ucsd.edu.
Bernhard O
BO
Palsson
D000596:Amino Acids / Q000096:biosynthesis; D002413:Cations, Divalent / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D017136:Ion Transport; D018384:Oxidative Stress; D012097:Repressor Proteins / Q000235:genetics*; D058727:RNA, Small Untranslated
D000596:Amino Acids; D002413:Cations, Divalent; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; C499299:oxyR protein, E coli; C499686:oxyS small RNA, E coli; D058727:RNA, Small Untranslated