Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Alam, M.T., Merlo, M.E., Hodgson, D.A., Wellington, E.M.H., Takano, E. and Breitling, R. (2010) Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11(202), pp. 1-9. (doi: 10.1186/1471-2164-11-202)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Breitling, Professor Rainer
• Authors: Alam, M.T., Merlo, M.E., Hodgson, D.A., Wellington, E.M.H., Takano, E., and Breitling, R.
• Subjects: Q Science > Q Science (General)
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: BMC Genomics
• Publisher: Biomed Central
• ISSN: 1471-2164
• ISSN (Online): 1471-2164
• Published Online: 26 March 2010
• Copyright Holders: Copyright © 2010 The Authors
• First Published: First published in BMC Genomics 11(202)
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher