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

Sang Woo Seo; Donghyuk Kim; Richard Szubin; Bernhard O Palsson

doi:10.1016/j.celrep.2015.07.043

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.

Authors

Sang Woo Seo¹, Donghyuk Kim¹, Richard Szubin¹, Bernhard O Palsson²

Affiliations

¹ Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
² 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: [email protected].

PMID: 26279566
DOI: 10.1016/j.celrep.2015.07.043

Abstract

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*

Substances

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