A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen.
A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen.
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DOI：
10.3389/fmicb.2014.00124
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发表时间：
2014
影响因子：
5.2
通讯作者：
Sawodny O
中科院分区：
文献类型：
--
作者：
Ederer M;Steinsiek S;Stagge S;Rolfe MD;Ter Beek A;Knies D;Teixeira de Mattos MJ;Sauter T;Green J;Poole RK;Bettenbrock K;Sawodny O
为了生物技术的目的，如生物燃料生产，废物处理或特定的生物催化功能，细菌的有效重新设计需要对能量供应，碳和氧化还原代谢的定量系统水平的理解。转录水平、代谢物浓度和代谢通量本身的测量给出了一个不完整的画面。不同测量值之间的相互依赖性对于系统级理解至关重要。数学建模有可能提供一个连贯的和定量的基因表达，代谢物浓度和代谢通量之间的相互作用的描述。当氧的可用性改变时，大肠杆菌在中枢代谢中经历重大适应。因此，氧反应的综合描述为我们理解碳、能量和氧化还原代谢提供了基准。我们提出了第一个全面的中心代谢模型的E。大肠杆菌，描述了稳态代谢在不同水平的氧气供应。模型的变量是代谢物浓度、基因表达水平、转录因子活性、代谢通量和生物量浓度。我们分析了该模型关于生产能力的中心代谢的E。杆菌特别是，我们预测如何前体和生物质浓度受产品形成。
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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影响因子：
3.1
作者：
Brown, PN;Hindmarsh, AC;Petzold, LR
通讯作者：
Petzold, LR
影响因子：
3.2
作者：
Bekker, Martijn;Alexeeva, Svetlana;Hellingwerf, Klaas
通讯作者：
Hellingwerf, Klaas
影响因子：
2.8
作者：
Bekker, M.;Kramer, G.;de Mattos, M. J. Teixeira
通讯作者：
de Mattos, M. J. Teixeira
影响因子：
14.9
作者：
Keseler IM;Mackie A;Peralta-Gil M;Santos-Zavaleta A;Gama-Castro S;Bonavides-Martínez C;Fulcher C;Huerta AM;Kothari A;Krummenacker M;Latendresse M;Muñiz-Rascado L;Ong Q;Paley S;Schröder I;Shearer AG;Subhraveti P;Travers M;Weerasinghe D;Weiss V;Collado-Vides J;Gunsalus RP;Paulsen I;Karp PD
通讯作者：
Karp PD
影响因子：
3.2
作者：
Georgellis, D;Lynch, AS;Lin, ECC
通讯作者：
Lin, ECC