ArticleBMC systems biology2017
Coordinated regulation of acid resistance in Escherichia coli.
Article in BMC systems biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
What it found
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Who cites it
53 citing papers in PubMed, 147 citations in OpenAlex.
- Metabolic responses to benzoic acid stress and glutamine transport-dependent vulnerabilities in Escherichia coli revealed by NMR metabolomics.World journal of microbiology & biotechnology · 2026Article
- Integrated Transcriptomics and Metabolomic Profiling Suggests That Thymol Adaptation Induces Multi-Layered Envelope and Metabolic Perturbations That SensitizeInternational journal of molecular sciences · 2026Article
- Genomic island-encoded LmiA regulates acid resistance and biofilm formation in enterohemorrhagicGut microbes · 2025Article
- Condensation of the RNA chaperone Hfq is coupled to inhibition of glucose uptake and contributes to the stabilization of regulatory RNAs in nitrogen-starved Escherichia coli.Nucleic acids research · 2025Article
- Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.Nature communications · 2025Article
- Fur-regulated urease contributes to the environmental adaptation ofMicrobiology spectrum · 2025Article
- Antimicrobial Activity of Glycyrrhizinic Acid Is pH-Dependent.ACS applied bio materials · 2024Article
- Integrated multi-omics unveil the impact of H-phosphinic analogs of glutamate and α-ketoglutarate on Escherichia coli metabolism.The Journal of biological chemistry · 2024Article
- A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation.bioRxiv : the preprint server for biology · 2024Article
- Methods for studying microbial acid stress responses: from molecules to populations.FEMS microbiology reviews · 2024Review
- Achieving robust synthetic tolerance in industrialSynthetic and systems biotechnology · 2024Article
- Multitier regulation of theJournal of bacteriology · 2024Article
- Enhancing Escherichia coli abiotic stress resistance through ornithine lipid formation.Applied microbiology and biotechnology · 2024Article
- RpoS and the bacterial general stress response.Microbiology and molecular biology reviews : MMBR · 2024Review
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
- TheJournal of bacteriology · 2023Article
- ThebioRxiv : the preprint server for biology · 2023Article
- Expanded roles of lactate-sensing LldR in transcription regulation of theMicrobial genomics · 2023Article
- Transcription-replication interactions reveal principles of bacterial genome regulation.Research square · 2023Article
- Model-driven experimental design workflow expands understanding of regulatory role of Nac inNAR genomics and bioinformatics · 2023Article
Corrections and comments
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Authors and funding
69 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundEnteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored.
resultsWe utilized a combination of ChIP-Seq and gene expression analysis to experimentally map the regulatory interactions of four TFs: nac, ntrC, ompR, and csiR. Our data identified all previously in vivo confirmed direct interactions and revealed several others previously inferred from gene expression data. Our data demonstrate that nac and csiR directly modulate AR, and leads to a regulatory network model in which all four TFs participate in coordinating acid resistance, glutamate metabolism, and nitrogen metabolism. This model predicts a novel mechanism for AR1 by which the decarboxylation enzymes of AR2 are used with internally derived glutamate. This hypothesis makes several testable predictions that we confirmed experimentally.
conclusionsOur data suggest that the regulatory network underlying AR is complex and deeply interconnected with the regulation of GABA and glutamate metabolism, nitrogen metabolism. These connections underlie and experimentally validated model of AR1 in which the decarboxylation enzymes of AR2 are used with internally derived glutamate.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.