ArticleMolecular systems biology2017
Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli.
Article in Molecular systems biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it, 141 citations in OpenAlex.
- Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.PLoS computational biology · 2022Pooled it
- A tripartite RpoS-CRP-cAMP-Cra circuit orchestrates metabolic reprogramming during stress adaptation.Nucleic acids research · 2026Article
- Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models.Molecular systems biology · 2026Article
- A Robust Isotope Ratio LC-MS/MS Workflow for High-Throughput Metabolic Profiling of Bacteria.Analytical chemistry · 2026Article
- Article
- Beyond Correlation: Constraint Architecture Explains Proteome-Metabolome Decoupling.International journal of molecular sciences · 2026Review
- Expanding the toolkit of LacI/GalR chimeras.PloS one · 2026Article
- Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.Environmental microbiome · 2025Article
- Predicting input signals of transcription factors in Escherichia coli.Molecular systems biology · 2025Article
- Controlled burn: interconnections between energy-spilling pathways and metabolic signaling in bacteria.Journal of bacteriology · 2025Review
- Systematic identification of allosteric effectors inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.PLoS computational biology · 2025Article
- Making sense of gene expression control by flux sensing.Nature metabolism · 2025Article
- Insights into the regulatory mechanisms and application prospects of the transcription factor Cra.Applied and environmental microbiology · 2024Review
- Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis.Plant biotechnology journal · 2024Article
- Fructose-1-kinase has pleiotropic roles inbioRxiv : the preprint server for biology · 2023Article
- Local flux coordination and global gene expression regulation in metabolic modeling.Nature communications · 2023Article
- Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms.The Analyst · 2023Article
- Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms.bioRxiv : the preprint server for biology · 2023Article
- Regulation of phosphate starvation-specific responses inMicrobiology (Reading, England) · 2023Review
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription networks consist of hundreds of transcription factors with thousands of often overlapping target genes. While we can reliably measure gene expression changes, we still understand relatively little why expression changes the way it does. How does a coordinated response emerge in such complex networks and how many input signals are necessary to achieve it? Here, we unravel the regulatory program of gene expression in Escherichia coli central carbon metabolism with more than 30 known transcription factors. Using a library of fluorescent transcriptional reporters, we comprehensively quantify the activity of central metabolic promoters in 26 environmental conditions. The expression patterns were dominated by growth rate-dependent global regulation for most central metabolic promoters in concert with highly condition-specific activation for only few promoters. Using an approximate mathematical description of promoter activity, we dissect the contribution of global and specific transcriptional regulation. About 70% of the total variance in promoter activity across conditions was explained by global transcriptional regulation. Correlating the remaining specific transcriptional regulation of each promoter with the cell's metabolome response across the same conditions identified potential regulatory metabolites. Remarkably, cyclic AMP, fructose-1,6-bisphosphate, and fructose-1-phosphate alone explained most of the specific transcriptional regulation through their interaction with the two major transcription factors Crp and Cra. Thus, a surprisingly simple regulatory program that relies on global transcriptional regulation and input from few intracellular metabolites appears to be sufficient to coordinate E. coli central metabolism and explain about 90% of the experimentally observed transcription changes in 100 genes.
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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.