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| Status |
Public on Aug 11, 2015 |
| Title |
Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq] |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Seo SW, Kim D |
| Citation(s) |
26258987 |
| |
| Submission date |
Mar 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
[email protected]
|
| Organization name |
UNIST
|
| Department |
Department of Chemical Engineering
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| Lab |
Systems Biology Lab
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| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
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| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
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| Platforms (1) |
| GPL17439 |
Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE66482 |
Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli |
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| Relations |
| BioProject |
PRJNA276918 |
| SRA |
SRP055726 |
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