ArticleNature communications2015
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 108 citations in OpenAlex.
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- From the Gut to the Brain: Transcriptomic Insights into Neonatal MeningitisPathogens (Basel, Switzerland) · 2025Article
- Analysis of stress response in multiple bacterial pathogens using a network biology approach.Scientific reports · 2025Article
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.Nucleic acids research · 2025Article
- iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets.Nucleic acids research · 2025Article
- Comparative Genomic and Phylogenetic Analysis ofTransboundary and emerging diseases · 2025Article
- An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets.Journal of microbiology (Seoul, Korea) · 2024Article
- Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches.PLoS genetics · 2024Article
- Engineering quorum sensing-based genetic circuits enhances growth and productivity robustness of industrial E. coli at low pH.Microbial cell factories · 2024Article
- Methods for studying microbial acid stress responses: from molecules to populations.FEMS microbiology reviews · 2024Review
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.mSystems · 2024Article
- Multitier regulation of theJournal of bacteriology · 2024Article
- Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress.World journal of microbiology & biotechnology · 2024Article
- CRISPR-dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria.Nucleic acids research · 2024Article
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
- A heritable iron memory enables decision-making inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- tRNA queuosine modification is involved in biofilm formation and virulence in bacteria.Nucleic acids research · 2023Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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