Dataset Information

Alam2010 - Genome-scale metabolic network of Streptomyces coelicolor

ABSTRACT: Alam2010 - Genome-scale metabolic network of Streptomyces coelicolor This model is described in the article: Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. Alam MT, Merlo ME, STREAM Consortium, Hodgson DA, Wellington EM, Takano E, Breitling R. BMC Genomics 2010; 11: 202 Abstract: BACKGROUND: The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations. RESULTS: We reconstructed the stoichiometric matrix of S. coelicolor, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism. CONCLUSION: Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data. This model is hosted on BioModels Database and identified by: MODEL1507180005. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Nicolas Le Novère

PROVIDER: MODEL1507180005 | BioModels | 2015-07-30

REPOSITORIES: BioModels

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			Action	DRS
	MODEL1507180005?filename=MODEL1507180005-biopax2.owl	Owl
	MODEL1507180005?filename=MODEL1507180005-biopax3.owl	Owl
	MODEL1507180005?filename=MODEL1507180005.m	Other
	MODEL1507180005?filename=MODEL1507180005.pdf	Pdf
	MODEL1507180005?filename=MODEL1507180005.png	Other

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Publications

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor.

Alam Mohammad T MT Merlo Maria E ME Hodgson David A DA Wellington Elizabeth M H EM Takano Eriko E Breitling Rainer R

BMC genomics 20100326

<h4>Background</h4>The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations.<h4>Results</h4>We reconstructed the stoichiometric matrix of S. coelicolor, including the major anti ...[more]

PMID: 20338070

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