ArticleNature communications2019
Systematic identification of metabolites controlling gene expression in E. coli.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 119 citations in OpenAlex.
- Profiling large-scale protein occupancy on bacterial genomes using IPOD-HR.Nature protocols · 2026Review
- E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients.Molecular systems biology · 2026Article
- A Robust Isotope Ratio LC-MS/MS Workflow for High-Throughput Metabolic Profiling of Bacteria.Analytical chemistry · 2026Article
- Disentangling factors affecting bacterial transcriptional regulatory network inference.iScience · 2026Article
- A systems-level atlas of carbon-response transcriptional states inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics.bioRxiv : the preprint server for biology · 2026Article
- Metab8D: a metabolic regulome network from multiomics and machine learning.Communications biology · 2026Article
- A Clue for the Hen and Egg Question: The Simultaneous Formation of Uracil and Amino Acids Under Simulated Hadean Conditions.Life (Basel, Switzerland) · 2026Article
- The transcription factor Vca0578 (DsvR) mediated expression of ZapC is required to promote cell division during lytic transglycosylase insufficiency inbioRxiv : the preprint server for biology · 2026Article
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- Predicting input signals of transcription factors in Escherichia coli.Molecular systems biology · 2025Article
- Bacteriophage T4 propagation in E.coli exposed to severe substrate limitation.Virology journal · 2025Article
- Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.NPJ biofilms and microbiomes · 2025Article
- Congruence between noise and plasticity in protein expression.Scientific reports · 2025Article
- Mapping protein-metabolite interactions iniScience · 2025Article
- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- Counterintuitive method improves yields of isotopically labelled proteins expressed in flask-cultured Escherichia coli.Journal of biomolecular NMR · 2025Article
- Controlled burn: interconnections between energy-spilling pathways and metabolic signaling in bacteria.Journal of bacteriology · 2025Review
- Leveraging the microbiome to combat antibiotic resistant gynecological infections.npj antimicrobials and resistance · 2025Review
- Regulation of gene expression through protein-metabolite interactions.npj metabolic health and disease · 2025Review
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. These interactions are usually measured with in vitro assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that control transcription factors in E. coli. By switching an E. coli culture between starvation and growth, we induce strong metabolite concentration changes and gene expression changes. Using Network Component Analysis we calculate the activities of 209 transcriptional regulators and correlate them with metabolites. This approach captures, for instance, the in vivo kinetics of CRP regulation by cyclic-AMP. By testing correlations between all pairs of transcription factors and metabolites, we predict putative effectors of 71 transcription factors, and validate five interactions in vitro. These results show that combining transcriptomics and metabolomics generates hypotheses about metabolism-transcription interactions that drive transitions between physiological states.
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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.