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Title: Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]      
dateReleased:
08-11-2015
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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-66481
refinement:
raw
alternateIdentifiers:
66481
keywords:
functional genomics
dateModified:
08-19-2015
availability:
available
types:
gene expression
name:
Escherichia coli
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-66481/E-GEOD-66481.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-66481/E-GEOD-66481.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66481
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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