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Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli

ABSTRACT: Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli

PROVIDER: PRJNA277044 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1822660.fastq.gz	Fastqsanger.gz
	SRR1824560_1.fastq.gz	Fastqsanger.gz
	SRR1824560_2.fastq.gz	Fastqsanger.gz
	SRR1822661.fastq.gz	Fastqsanger.gz
	SRR1824561_1.fastq.gz	Fastqsanger.gz

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Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]

Project description:The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons are comprised of 45 genes in 31 transcription units (TUs), significantly expanding the current knowledge of the GadEWX regulatory network. We demonstrate that GadEWX directly and coherently regulate several proton efflux/influx and generating/consuming enzymes with pairs of negative-feedback loops to maintain pH homeostasis by controlling proton flow. In addition, GadEWX regulate genes with assorted functions including molecular chaperones, acid resistance, stress response, and other regulatory activities. These results present a comprehensive understating on how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress. A total of eight samples were analyzed. WT and gadEWX mutant cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.

2015-08-11 | E-GEOD-66481 | biostudies-arrayexpress

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq]

Project description:The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons are comprised of 45 genes in 31 transcription units (TUs), significantly expanding the current knowledge of the GadEWX regulatory network. We demonstrate that GadEWX directly and coherently regulate several proton efflux/influx and generating/consuming enzymes with pairs of negative-feedback loops to maintain pH homeostasis by controlling proton flow. In addition, GadEWX regulate genes with assorted functions including molecular chaperones, acid resistance, stress response, and other regulatory activities. These results present a comprehensive understating on how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress. A total of six samples were analyzed. GadE-8-myc, GadW-8 -myc, and GadX-8-myc tagged cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.

2015-08-11 | E-GEOD-66441 | biostudies-arrayexpress

Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.

Project description:The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the genome-wide regulatory role of GadEWX is still unknown. Here we comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons consist of 45 genes in 31 transcription units and 28 of these genes were associated with RpoS-binding sites. We demonstrate that GadEWX directly and coherently regulate several proton-generating/consuming enzymes with pairs of negative-feedback loops for pH homeostasis. In addition, GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. These results show how GadEWX simultaneously coordinate many cellular processes to produce the overall response of E. coli to acid stress.

| S-EPMC4918353 | biostudies-literature

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-08-11 | E-GEOD-66482 | biostudies-arrayexpress

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq]

2015-08-11 | GSE66441 | GEO

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]

2015-08-11 | GSE66481 | GEO

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-08-11 | GSE66482 | GEO

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