Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Abstract A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription unit...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Jina Yang, Byung-Kwan Cho, Bernhard O. Palsson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f174ac842fa942399323c16cd137063b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f174ac842fa942399323c16cd137063b
record_format	dspace
spelling	oai:doaj.org-article:f174ac842fa942399323c16cd137063b2021-12-02T12:30:51ZRevealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG165510.1038/s41598-017-02110-72045-2322https://doaj.org/article/f174ac842fa942399323c16cd137063b2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02110-7https://doaj.org/toc/2045-2322Abstract A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level in an OmpR knock-out strain. Specifically, we find that: 1) OmpR regulates mostly membrane-located gene products involved in diverse fundamental biological processes, such as narU (encoding nitrate/nitrite transporter), ompX (encoding outer membrane protein X), and nuoN (encoding NADH:ubiquinone oxidoreductase); 2) by investigating co-regulation of entire sets of genes regulated by other stress-response TFs, stresses are surprisingly independently regulated among each other; and, 3) a detailed investigation of the physiological roles of the newly discovered OmpR regulon genes reveals that activation of narU represents a novel strategy to significantly improve osmotic stress tolerance of E. coli. Thus, the genome-scale approach to elucidating regulons comprehensively identifies regulated genes and leads to fundamental discoveries related to stress responses.Sang Woo SeoYe GaoDonghyuk KimRichard SzubinJina YangByung-Kwan ChoBernhard O. PalssonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sang Woo Seo Ye Gao Donghyuk Kim Richard Szubin Jina Yang Byung-Kwan Cho Bernhard O. Palsson Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
description	Abstract A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level in an OmpR knock-out strain. Specifically, we find that: 1) OmpR regulates mostly membrane-located gene products involved in diverse fundamental biological processes, such as narU (encoding nitrate/nitrite transporter), ompX (encoding outer membrane protein X), and nuoN (encoding NADH:ubiquinone oxidoreductase); 2) by investigating co-regulation of entire sets of genes regulated by other stress-response TFs, stresses are surprisingly independently regulated among each other; and, 3) a detailed investigation of the physiological roles of the newly discovered OmpR regulon genes reveals that activation of narU represents a novel strategy to significantly improve osmotic stress tolerance of E. coli. Thus, the genome-scale approach to elucidating regulons comprehensively identifies regulated genes and leads to fundamental discoveries related to stress responses.
format	article
author	Sang Woo Seo Ye Gao Donghyuk Kim Richard Szubin Jina Yang Byung-Kwan Cho Bernhard O. Palsson
author_facet	Sang Woo Seo Ye Gao Donghyuk Kim Richard Szubin Jina Yang Byung-Kwan Cho Bernhard O. Palsson
author_sort	Sang Woo Seo
title	Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
title_short	Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
title_full	Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
title_fullStr	Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
title_full_unstemmed	Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
title_sort	revealing genome-scale transcriptional regulatory landscape of ompr highlights its expanded regulatory roles under osmotic stress in escherichia coli k-12 mg1655
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f174ac842fa942399323c16cd137063b
work_keys_str_mv	AT sangwooseo revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655 AT yegao revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655 AT donghyukkim revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655 AT richardszubin revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655 AT jinayang revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655 AT byungkwancho revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655 AT bernhardopalsson revealinggenomescaletranscriptionalregulatorylandscapeofomprhighlightsitsexpandedregulatoryrolesunderosmoticstressinescherichiacolik12mg1655
_version_	1718394313242574848

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Ejemplares similares