ArticleMicrobial cell factories2016
Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli.
Article in Microbial cell factories, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 57 citations in OpenAlex.
- Strategies and applications for alleviating carbon catabolite repression.Synthetic and systems biotechnology · 2027Review
- DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks.Briefings in bioinformatics · 2025Article
- Discretised Flux Balance Analysis for Reaction-Diffusion Simulation of Single-Cell Metabolism.Bulletin of mathematical biology · 2024Article
- Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy.iScience · 2022Article
- Systems-based approaches to study immunometabolism.Cellular & molecular immunology · 2022Review
- Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis.Frontiers in bioengineering and biotechnology · 2022Review
- A forecast for large-scale, predictive biology: Lessons from meteorology.Cell systems · 2021Review
- Control and regulation of acetate overflow ineLife · 2021Article
- Computer-Aided Rational Design of Efficient NADPH Production System byFrontiers in bioengineering and biotechnology · 2020Article
- Self-replenishment cycles generate a threshold response.Scientific reports · 2019Article
- DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.BMC systems biology · 2018Article
- Bioprocessing strategies for cost-effective large-scale biogenic synthesis of nano-MgO from endophytic Streptomyces coelicolor strain E72 as an anti-multidrug-resistant pathogens agent.Scientific reports · 2018Article
- Antimicrobial activity of apple cider vinegar against Escherichia coli, Staphylococcus aureus and Candida albicans; downregulating cytokine and microbial protein expression.Scientific reports · 2018Article
- A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering.Frontiers in microbiology · 2018Review
- Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.PLoS computational biology · 2017Article
- Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli.Molecular systems biology · 2017Article
- Modeling and simulation of the redox regulation of the metabolism inBiotechnology for biofuels · 2017Article
- Coping with inevitable accidents in metabolism.Microbial biotechnology · 2017Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters.
resultsIn this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture.
conclusionsThis model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes.
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