Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

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.
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SEEK ID: https://fairdomhub.org/publications/7

DOI: 10.1186/1471-2164-11-202

Projects: STREAM

Journal: BMC Genomics

Citation:

Date Published: 2010

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Citation
Alam, M. T., Merlo, M. E., (stream), T. S. T. R. E. A. M. C., Hodgson, D. A., Wellington, E. M. H., Takano, E., & Breitling, R. (2010). Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11(1), 202. http://doi.org/10.1186/1471-2164-11-202
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Created: 26th May 2010 at 15:17

Last updated: 26th May 2010 at 15:18

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