Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.
Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.
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DOI：
10.1186/1475-2859-9-88
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发表时间：
2010-11-19
影响因子：
6.4
通讯作者：
Shimizu K
中科院分区：
文献类型：
--
作者：
Kadir TA;Mannan AA;Kierzek AM;McFadden J;Shimizu K
特别是为了工业应用的目的，模拟细胞响应于培养环境的变化和/或特定基因敲除的代谢变化是非常重要的。如果可以做到这一点，就可以在不进行详尽实验的情况下进行电池设计，并且可以筛选出有希望的候选者，然后通过对少数特别感兴趣的选择进行实验验证。虽然到目前为止已经提出了几种模型，但大多数都集中在特定的代谢途径上。优选的是对大肠杆菌中的整个主要代谢途径进行建模，允许基于细胞内通量估计能量产生和细胞合成，并且其可用于表征表型生长。本研究利用大肠杆菌的酶促反应模型，对大肠杆菌的糖酵解、TCA循环、磷酸戊糖（PP）途径和回补途径等主要代谢途径进行了模拟。杆菌一旦通过该模型计算细胞内通量，就可以估计比ATP产生速率、比CO2产生速率和比NADPH产生速率。由此计算的比ATP生产速率用于估计比生长速率。CO2产生速率可用于估计细胞产量，比NADPH产生速率可用于确定氧化PP途径的通量。模拟了分批培养和连续培养，并将细胞外和细胞内代谢物浓度的变化模式与实验数据进行了比较。此外，还模拟了敲除Ppc、Pck和Pyk等途径对代谢的影响。在Ppc突变体中，由于OAA浓度低，细胞难以生长，而Pck突变体不一定显示这种现象。通过考虑到较低的比ATP产生速率，适当地估计了Ppc突变体的较慢的生长速率。在Pyk突变体的情况下，酶水平调节变得清楚，使得Pyk敲除引起PEP浓度上调并激活Ppc，这引起MAL浓度增加并通过Mez支持减少的PYR，导致与野生型相似的表型生长特征。结果表明，该模型可用于模拟大肠杆菌的主要代谢过程。大肠杆菌中，了解细胞内的代谢变化，响应特定的途径基因敲除，考虑整个主要的代谢途径。模拟结果与实验数据的比较表明，该模型能够在一定程度上模拟特定基因敲除对代谢变化的影响。
It is quite important to simulate the metabolic changes of a cell in response to the change in culture environment and/or specific gene knockouts particularly for the purpose of application in industry. If this could be done, the cell design can be made without conducting exhaustive experiments, and one can screen out the promising candidates, proceeded by experimental verification of a select few of particular interest. Although several models have so far been proposed, most of them focus on the specific metabolic pathways. It is preferred to model the whole of the main metabolic pathways in Escherichia coli, allowing for the estimation of energy generation and cell synthesis, based on intracellular fluxes and that may be used to characterize phenotypic growth. In the present study, we considered the simulation of the main metabolic pathways such as glycolysis, TCA cycle, pentose phosphate (PP) pathway, and the anapleorotic pathways using enzymatic reaction models of E. coli. Once intracellular fluxes were computed by this model, the specific ATP production rate, the specific CO2 production rate, and the specific NADPH production rate could be estimated. The specific ATP production rate thus computed was used for the estimation of the specific growth rate. The CO2 production rate could be used to estimate cell yield, and the specific NADPH production rate could be used to determine the flux of the oxidative PP pathway. The batch and continuous cultivations were simulated where the changing patterns of extracellular and intra-cellular metabolite concentrations were compared with experimental data. Moreover, the effects of the knockout of such pathways as Ppc, Pck and Pyk on the metabolism were simulated. It was shown to be difficult for the cell to grow in Ppc mutant due to low concentration of OAA, while Pck mutant does not necessarily show this phenomenon. The slower growth rate of the Ppc mutant was properly estimated by taking into account the lower specific ATP production rate. In the case of Pyk mutant, the enzyme level regulation was made clear such that Pyk knockout caused PEP concentration to be up-regulated and activated Ppc, which caused the increase in MAL concentration and backed up reduced PYR through Mez, resulting in the phenotypic growth characteristics similar to the wild type. It was shown to be useful to simulate the main metabolism of E. coli for understanding metabolic changes inside the cell in response to specific pathway gene knockouts, considering the whole main metabolic pathways. The comparison of the simulation result with the experimental data indicates that the present model could simulate the effect of the specific gene knockouts to the changes in the metabolisms to some extent.
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影响因子：
56.9
作者：
Ishii, Nobuyoshi;Nakahigashi, Kenji;Tomita, Masaru
通讯作者：
Tomita, Masaru
影响因子：
3.8
作者：
Chassagnole, C;Noisommit-Rizzi, N;Reuss, M
通讯作者：
Reuss, M
影响因子：
9.9
作者：
Kotte, Oliver;Zaugg, Judith B.;Heinemann, Matthias
通讯作者：
Heinemann, Matthias
影响因子：
2.1
作者：
Peng, LF;Arauzo-Bravo, MJ;Shimizu, K
通讯作者：
Shimizu, K
影响因子：
2.9
作者：
HENKIN, J;ABELES, RH
通讯作者：
ABELES, RH