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Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification
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Kadir, Tuty Asmawaty Abdul, Mannan, Ahmad A., Kierzek, Andrzej M., McFadden, Johnjoe and Shimizu, Kazuyuki (2010) Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. Microbial Cell Factories, 9 . 88. doi:10.1186/1475-2859-9-88
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Official URL: https://doi.org/10.1186/1475-2859-9-88
Abstract
Background:
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.
Results:
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 CO 2 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 CO 2 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.
Conclusions:
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.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QA Mathematics Q Science > QR Microbiology |
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| Divisions: | Faculty of Science > Engineering | |||||||||
| Library of Congress Subject Headings (LCSH): | Escherichia coli -- Metabolism -- Mathematical modles, Escherichia coli -- Metabolism -- Simulation methods | |||||||||
| Journal or Publication Title: | Microbial Cell Factories | |||||||||
| Publisher: | BioMed Central Ltd. | |||||||||
| ISSN: | 1475-2859 | |||||||||
| Official Date: | 19 November 2010 | |||||||||
| Dates: |
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| Date of first compliant deposit: | 30 May 2018 | |||||||||
| Volume: | 9 | |||||||||
| Article Number: | 88 | |||||||||
| DOI: | 10.1186/1475-2859-9-88 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access | |||||||||
| RIOXX Funder/Project Grant: |
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