Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolorCitation formats

  • External authors:
  • Mohammad T. Alam
  • Maria E. Merlo
  • David A. Hodgson
  • Elizabeth M H Wellington

Standard

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. / Alam, Mohammad T.; Merlo, Maria E.; Hodgson, David A.; Wellington, Elizabeth M H; Takano, Eriko; Breitling, Rainer.

In: BMC Genomics, Vol. 11, No. 1, 202, 26.03.2010.

Research output: Contribution to journalArticlepeer-review

Harvard

APA

Alam, M. T., Merlo, M. E., 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]. https://doi.org/10.1186/1471-2164-11-202

Vancouver

Author

Alam, Mohammad T. ; Merlo, Maria E. ; Hodgson, David A. ; Wellington, Elizabeth M H ; Takano, Eriko ; Breitling, Rainer. / Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. In: BMC Genomics. 2010 ; Vol. 11, No. 1.

Bibtex

@article{0175851286104976ac2cc9c980e09842,
title = "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. {\textcopyright} 2010 Alam et al; licensee BioMed Central Ltd.",
author = "Alam, {Mohammad T.} and Merlo, {Maria E.} and Hodgson, {David A.} and Wellington, {Elizabeth M H} and Eriko Takano and Rainer Breitling",
year = "2010",
month = mar,
day = "26",
doi = "10.1186/1471-2164-11-202",
language = "English",
volume = "11",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "Springer Nature",
number = "1",

}

RIS

TY - JOUR

T1 - Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

AU - Alam, Mohammad T.

AU - Merlo, Maria E.

AU - Hodgson, David A.

AU - Wellington, Elizabeth M H

AU - Takano, Eriko

AU - Breitling, Rainer

PY - 2010/3/26

Y1 - 2010/3/26

N2 - 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. © 2010 Alam et al; licensee BioMed Central Ltd.

AB - 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. © 2010 Alam et al; licensee BioMed Central Ltd.

U2 - 10.1186/1471-2164-11-202

DO - 10.1186/1471-2164-11-202

M3 - Article

VL - 11

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 202

ER -