ArticlePLoS computational biology2010
The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- An ensemble of mathematical models showing diauxic growth behaviour.BMC systems biology · 2018Article
- Principal process analysis of biological models.BMC systems biology · 2018Article
- Analysis Tools for Interconnected Boolean Networks With Biological Applications.Frontiers in physiology · 2018Article
- Mathematical modelling of microbes: metabolism, gene expression and growth.Journal of the Royal Society, Interface · 2017Review
- Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.PLoS computational biology · 2017Article
- A novel characterization of amalgamated networks in natural systems.Scientific reports · 2015Article
- Coordination of microbial metabolism.Nature reviews. Microbiology · 2014Review
- QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.Bioinformatics (Oxford, England) · 2013Article
- A genome-wide screen for identifying all regulators of a target gene.Nucleic acids research · 2013Article
- Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model.BMC systems biology · 2013Article
- Shared control of gene expression in bacteria by transcription factors and global physiology of the cell.Molecular systems biology · 2013Article
- Analysis and Design of Stimulus Response Curves of E. coli.Metabolites · 2012Article
- Recent advances in engineering the central carbon metabolism of industrially important bacteria.Microbial cell factories · 2012Review
- The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene.BMC systems biology · 2011Article
- Toward a quantitative modeling of the synthesis of the pectate lyases, essential virulence factors in Dickeya dadantii.The Journal of biological chemistry · 2010Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulatory networks consist of direct interactions but also include indirect interactions mediated by metabolites and signaling molecules. We describe how these indirect interactions can be derived from a model of the underlying biochemical reaction network, using weak time-scale assumptions in combination with sensitivity criteria from metabolic control analysis. We apply this approach to a model of the carbon assimilation network in Escherichia coli. Our results show that the derived gene regulatory network is densely connected, contrary to what is usually assumed. Moreover, the network is largely sign-determined, meaning that the signs of the indirect interactions are fixed by the flux directions of biochemical reactions, independently of specific parameter values and rate laws. An inversion of the fluxes following a change in growth conditions may affect the signs of the indirect interactions though. This leads to a feedback structure that is at the same time robust to changes in the kinetic properties of enzymes and that has the flexibility to accommodate radical changes in the environment.
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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.