ArticleFrontiers in microbiology2014
A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Quantitative proteomics reveals oxygen-induced adaptations inFrontiers in microbiology · 2024Article
- Integrating glycolysis, citric acid cycle, pentose phosphate pathway, and fatty acid beta-oxidation into a single computational model.Scientific reports · 2023Article
- Impact of Hydrogen Sulfide on Mitochondrial and Bacterial Bioenergetics.International journal of molecular sciences · 2021Review
- Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D.Nature communications · 2021Article
- Bacterial Oxidases of the CytochromeAntioxidants & redox signaling · 2021Review
- Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter.BMC biology · 2021Article
- Predicting microbial growth dynamics in response to nutrient availability.PLoS computational biology · 2021Article
- Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches.International journal of molecular sciences · 2020Review
- Deciphering the Adaptation ofGenes · 2018Article
- Mathematical models of microbial growth and metabolism: a whole-organism perspective.Science progress · 2017Review
- Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics.Genes · 2017Article
- Modeling and simulation of the redox regulation of the metabolism inBiotechnology for biofuels · 2017Article
- Variable-Internal-Stores models of microbial growth and metabolism with dynamic allocation of cellular resources.Journal of mathematical biology · 2017Article
- Homeostasis of metabolites inRoyal Society open science · 2016Article
- The Terminal Oxidase Cytochrome bd Promotes Sulfide-resistant Bacterial Respiration and Growth.Scientific reports · 2016Article
- A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information.Frontiers in molecular biosciences · 2016Article
- Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions.PloS one · 2014Article
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Authors and funding
12 authors.
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Abstract
The efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of energy supply, carbon, and redox metabolism. The measurement of transcript levels, metabolite concentrations and metabolic fluxes per se gives an incomplete picture. An appreciation of the interdependencies between the different measurement values is essential for systems-level understanding. Mathematical modeling has the potential to provide a coherent and quantitative description of the interplay between gene expression, metabolite concentrations, and metabolic fluxes. Escherichia coli undergoes major adaptations in central metabolism when the availability of oxygen changes. Thus, an integrated description of the oxygen response provides a benchmark of our understanding of carbon, energy, and redox metabolism. We present the first comprehensive model of the central metabolism of E. coli that describes steady-state metabolism at different levels of oxygen availability. Variables of the model are metabolite concentrations, gene expression levels, transcription factor activities, metabolic fluxes, and biomass concentration. We analyze the model with respect to the production capabilities of central metabolism of E. coli. In particular, we predict how precursor and biomass concentration are affected by product formation.
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