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

Scientific Reports
Sang Woo SeoBernhard Ø Palsson

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...Continue Reading

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Citations

Feb 3, 2018·Nucleic Acids Research·Donghyuk KimBernhard O Palsson
Apr 15, 2020·Infection and Immunity·D E KunkleJ E Bina
Aug 24, 2018·Nucleic Acids Research·Ye GaoBernhard O Palsson
Feb 29, 2020·Scientific Reports·Yukari Miyake, Kaneyoshi Yamamoto
Feb 10, 2021·Genes·Philip Ruelens, J Arjan G M de Visser
Jul 16, 2021·Frontiers in Microbiology·Valentina LucchiniVincent Trebosc

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Methods Mentioned

BETA
environmental stresses
environmental stress
immunoprecipitation
ChIP-exo
RNA-seq
gene knock-out

Software Mentioned

diChIPMunk
Cufflinks
SAM
RAST
Mock
RAST ( Annotation
Cuffdiff
bowtie
IP
ChIPMunk

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