ArticlePLoS computational biology2012
Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- Dynamic metabolic modeling uncovers systems-level strategies to simultaneously maximize levan yield and substrate efficiency in Bacillus subtilis LY7.16.PLoS computational biology · 2026Article
- A common inducer molecule enhances sugar utilization by Shewanella oneidensis MR-1.Journal of industrial microbiology & biotechnology · 2023Article
- Integrative metabolic flux analysis reveals an indispensable dimension of phenotypes.Current opinion in biotechnology · 2022Review
- Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges.Microorganisms · 2021Review
- Aerobic radical polymerization mediated by microbial metabolism.Nature chemistry · 2020Article
- Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease.BMC bioinformatics · 2019Article
- System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris.BMC bioinformatics · 2019Article
- Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris.BMC systems biology · 2017Article
- Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions.Infection and immunity · 2016Article
- Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach.Frontiers in bioengineering and biotechnology · 2016Review
- Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.Frontiers in molecular biosciences · 2016Review
- OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism.PloS one · 2016Article
- Article
- Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function.Microbial cell factories · 2015Article
- Emergent biosynthetic capacity in simple microbial communities.PLoS computational biology · 2014Article
- Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics.Cell reports · 2014Article
- k-OptForce: integrating kinetics with flux balance analysis for strain design.PLoS computational biology · 2014Article
- Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model.Frontiers in bioengineering and biotechnology · 2014Article
- Predictive sulfur metabolism - a field in flux.Frontiers in plant science · 2014Review
- Metabolic flux analysis of Cyanothece sp. ATCC 51142 under mixotrophic conditions.Photosynthesis research · 2013Article
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4 authors.
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Abstract
Shewanella oneidensis MR-1 sequentially utilizes lactate and its waste products (pyruvate and acetate) during batch culture. To decipher MR-1 metabolism, we integrated genome-scale flux balance analysis (FBA) into a multiple-substrate Monod model to perform the dynamic flux balance analysis (dFBA). The dFBA employed a static optimization approach (SOA) by dividing the batch time into small intervals (i.e., ∼400 mini-FBAs), then the Monod model provided time-dependent inflow/outflow fluxes to constrain the mini-FBAs to profile the pseudo-steady-state fluxes in each time interval. The mini-FBAs used a dual-objective function (a weighted combination of "maximizing growth rate" and "minimizing overall flux") to capture trade-offs between optimal growth and minimal enzyme usage. By fitting the experimental data, a bi-level optimization of dFBA revealed that the optimal weight in the dual-objective function was time-dependent: the objective function was constant in the early growth stage, while the functional weight of minimal enzyme usage increased significantly when lactate became scarce. The dFBA profiled biologically meaningful dynamic MR-1 metabolisms: 1. the oxidative TCA cycle fluxes increased initially and then decreased in the late growth stage; 2. fluxes in the pentose phosphate pathway and gluconeogenesis were stable in the exponential growth period; and 3. the glyoxylate shunt was up-regulated when acetate became the main carbon source for MR-1 growth.
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