ArticleMolecular systems biology2013
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell.
Article in Molecular systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
75 citing papers in PubMed, 1 synthesis or guideline pooled it, 140 citations in OpenAlex.
- Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.PLoS computational biology · 2022Pooled it
- RfaH licenses RNA polymerase for long-range transcription.bioRxiv : the preprint server for biology · 2026Article
- Carvacrol Modulates Tetracycline Susceptibility and Resistance Gene Expression in Multidrug-ResistantAnimals : an open access journal from MDPI · 2026Article
- Differentiation between regulated and disrupted growth arrests allows tailoring of effective treatments for antibiotic persistence.Science advances · 2026Article
- How DoesACS synthetic biology · 2024Article
- Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity.Biophysical journal · 2022Article
- The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.Nucleic acids research · 2022Article
- Global pleiotropic effects in adaptively evolvedOpen biology · 2022Article
- Accurate characterization of dynamic microbial gene expression and growth rate profiles.Synthetic biology (Oxford, England) · 2022Article
- Quantifying the regulatory role of individual transcription factors in Escherichia coli.Cell reports · 2021Article
- Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.Biomolecules · 2021Review
- Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli.mSystems · 2021Article
- Systematic alteration of in vitro metabolic environments reveals empirical growth relationships in cancer cell phenotypes.Cell reports · 2021Article
- cAMP Receptor Protein Positively Regulates the Expression of Genes Involved in the Biosynthesis ofFrontiers in microbiology · 2021Article
- FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.ACS synthetic biology · 2020Article
- Predictive biology: modelling, understanding and harnessing microbial complexity.Nature reviews. Microbiology · 2020Review
- Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium.Molecular biology reports · 2020Article
- Article
- Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation.Microorganisms · 2019Review
- Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program.PLoS computational biology · 2019Article
15 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
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA-binding transcription factors and other specific regulators. We present a model-based approach to distinguish between these two effects using time-resolved measurements of promoter activities. We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E. coli. Our results show that the transcriptional response of the network is controlled by the physiological state of the cell and the signaling metabolite cyclic AMP (cAMP). The absence of a strong regulatory effect of transcription factors suggests that they are not the main coordinators of gene expression changes during growth transitions, but rather that they complement the effect of global physiological control mechanisms. This change of perspective has important consequences for the interpretation of transcriptome data and the design of biological networks in biotechnology and synthetic biology.
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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.