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

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 S...

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Main Authors: Sang Woo Seo, Donghyuk Kim, Richard Szubin, Bernhard O. Palsson
Format: Article
Language:English
Published: Elsevier 2015-08-01
Series:Cell Reports
Online Access:http://www.sciencedirect.com/science/article/pii/S2211124715008190
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spelling doaj-03c8f5a3813a4c8a9e5577608fc8c48b2020-11-25T01:16:17ZengElsevierCell Reports2211-12472015-08-011281289129910.1016/j.celrep.2015.07.043Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655Sang Woo Seo0Donghyuk Kim1Richard Szubin2Bernhard O. Palsson3Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USAThree 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 (Mn2+, Zn2+, and Mg2+). Investigating the co-regulation of these genes with other stress-response TFs reveals that they are independently regulated by stress-specific TFs.http://www.sciencedirect.com/science/article/pii/S2211124715008190
collection DOAJ
language English
format Article
sources DOAJ
author Sang Woo Seo
Donghyuk Kim
Richard Szubin
Bernhard O. Palsson
spellingShingle Sang Woo Seo
Donghyuk Kim
Richard Szubin
Bernhard O. Palsson
Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
Cell Reports
author_facet Sang Woo Seo
Donghyuk Kim
Richard Szubin
Bernhard O. Palsson
author_sort Sang Woo Seo
title Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
title_short Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
title_full Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
title_fullStr Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
title_full_unstemmed Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655
title_sort genome-wide reconstruction of oxyr and soxrs transcriptional regulatory networks under oxidative stress in escherichia coli k-12 mg1655
publisher Elsevier
series Cell Reports
issn 2211-1247
publishDate 2015-08-01
description 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 (Mn2+, Zn2+, and Mg2+). Investigating the co-regulation of these genes with other stress-response TFs reveals that they are independently regulated by stress-specific TFs.
url http://www.sciencedirect.com/science/article/pii/S2211124715008190
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AT donghyukkim genomewidereconstructionofoxyrandsoxrstranscriptionalregulatorynetworksunderoxidativestressinescherichiacolik12mg1655
AT richardszubin genomewidereconstructionofoxyrandsoxrstranscriptionalregulatorynetworksunderoxidativestressinescherichiacolik12mg1655
AT bernhardopalsson genomewidereconstructionofoxyrandsoxrstranscriptionalregulatorynetworksunderoxidativestressinescherichiacolik12mg1655
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