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

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

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Donghyuk Kim

PROVIDER: E-GEOD-66482 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Seo Sang Woo SW Kim Donghyuk D O'Brien Edward J EJ Szubin Richard R Palsson Bernhard O BO

Nature communications 20150810

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 ...[more]

PMID: 26258987

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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 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.

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

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2015-08-13 | E-GEOD-65711 | biostudies-arrayexpress

Genome-scale reconstruction of the sigma factor network in E. coli

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2014-02-05 | E-GEOD-46737 | biostudies-arrayexpress

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling

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2012-07-29 | E-GEOD-35822 | biostudies-arrayexpress

Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]

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2014-09-09 | E-GEOD-54900 | biostudies-arrayexpress

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Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. With experimentally derived TSS datasets, we examined usage of multiple TSSs, length of 5' UTR (untranslated region), SD (Shine-Dalgarno) sequence motif, promoter sequence motif, and dinucleotide preference near TSS site. In addition, we used the TSS datasets to identify sRNAs (small RNAs) in E. coli and K. pneumoniae. Based on these analysis, we compared regulatory elements including promoter, 5' UTR and sRNAs between two species, and investigated similarities and differences of upstream regulatory regions. Moreover, sRNAs were also compared and analyzed in terms of their sequences and target sequences, presenting possible working mechanisms of K. pneumoniae sRNAs by transferring prior knowledge from E. coli sRNAs. Examination of transcription start sites by biological duplicates from E. coli and K. pneumoniae

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