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Team:Valencia-CIPF/Modelling
From 2013.igem.org
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| + | <li>Fischer, M. J., Meyer, S., Claudel, P., Bergdoll, M., & Karst, F. (2011). Metabolic engineering of monoterpene synthesis in yeast. Biotechnology and bioengineering, 108(8), 1883-1892. | ||
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Revision as of 16:07, 4 October 2013
Introduction of Modelling
Our team has done a modeling based on the model iFF708 whose authors Forster, Famili, et al. are. This has been validated experimentally [1].
The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information.
The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included. A total of 708 structural open reading frames (from now on ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network containing 1175 metabolic reactions and 584 metabolites [1]. The number of gene functions included in the reconstructed network corresponds to aproximately 16% of all characterized ORFs in S. cerevisiae.
The resulting metabolic network, iFF708, has been used in this project, together with the Flux Balance Analysis tools for assessing the productive capacity of this yeast in the production of 1,8-cineole y S-linalool (products of interest in our project), and geranyl diphosphate (precursor of these products). We also compared the results obtained for the wild type, with those obtained for the mutant ERG20_2 [2], a mutant that increases production of geranyl diphosphate (from now on GPP.
The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information.
The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included. A total of 708 structural open reading frames (from now on ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network containing 1175 metabolic reactions and 584 metabolites [1]. The number of gene functions included in the reconstructed network corresponds to aproximately 16% of all characterized ORFs in S. cerevisiae.
The resulting metabolic network, iFF708, has been used in this project, together with the Flux Balance Analysis tools for assessing the productive capacity of this yeast in the production of 1,8-cineole y S-linalool (products of interest in our project), and geranyl diphosphate (precursor of these products). We also compared the results obtained for the wild type, with those obtained for the mutant ERG20_2 [2], a mutant that increases production of geranyl diphosphate (from now on GPP.
Simulation and Results
References
- Förster J., Famili I., Fu P., Palsson B. Ø., and Nielsen J., 2003, “Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.,” Genome Res., 13(2), pp. 244–53.
- Fischer, M. J., Meyer, S., Claudel, P., Bergdoll, M., & Karst, F. (2011). Metabolic engineering of monoterpene synthesis in yeast. Biotechnology and bioengineering, 108(8), 1883-1892.
