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Expression analysis of Escherichia coli CC72 before and after osmotic stress

ABSTRACT: Expression analysis of Escherichia coli CC72 before and after osmotic stress

PROVIDER: PRJNA434430 | ENA |

REPOSITORIES: ENA

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Expression analysis of Escherichia coli CC72 before and after osmotic stress

Project description:Expression level of whole genome genes in Escherichia coli CC72 at early-exponential phase, and 10 min, 20 min and 45 min after osmotic stress. Venus was fused to the 3' end of rpoC in E. coli MG1655 to localize RNA polymerase as reported previously (C. Cagliero and D. J. Jin, 2013).

2018-04-11 | GSE110730 | GEO

ChIP-chip from Escherichia coli CC72 cells with RNAP β’ subunit before and after osmotic stress.

Project description:RNA polymerase (RNAP) is the key transcription machinery and its interaction with genomic DNA orchestrates gene expression in response to environmental cues. Dynamic interaction and localization between RNAP and nucleoid were observed before and after osmotic stress. Chromatin immunoprecipitation (ChIP) of RNAP β’ subunit together with chromatin profiling by ChIP-on-chip analysis demonstrated the dynamics of genome-wide RNAP-DNA interactions during osmotic stress.

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ChIP-chip from Escherichia coli CC72 cells with RNAP β’ subunit before and after osmotic stress.

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Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

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Project description:A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the 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 under OmpR knock-out condition. We find that OmpR tends to regulate mostly membrane-located gene products of diverse fundamental biological processes, such as narU, ompX, and nuoN. Investigating co-regulation of entire set of genes regulated by other stress-response TFs unveils that they are surprisingly independently regulated by TF(s) responding to each stress. Additionally, detailed investigation of physiological roles of newly discovered OmpR regulon reveals that activation of narU encoding nitrate/nitrite transporter is a relatively unique strategy of E. coli K-12 MG1655 to significantly improve cellular tolerance toward osmotic stress.

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