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Issue 4, 2013
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Robustness analysis of a constraint-based metabolic model links cell growth and proteomics of Thermoanaerobacter tengcongensis under temperature perturbation

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Abstract

The integration of omic data with metabolic networks has been demonstrated to be an effective approach to elucidate the underlying metabolic mechanisms in life. Because the metabolic pathways of Thermoanaerobacter tengcongensis (T. tengcongensis) are incomplete, we used a 1-13C-glucose culture to monitor intracellular isotope-labeled metabolites by GC/MS and identified the gap gene in glucose catabolism, Re-citrate synthase. Based on genome annotation and biochemical information, we reconstructed the metabolic network of glucose metabolism and amino acid synthesis in T. tengcongensis, including 253 reactions, 227 metabolites, and 236 genes. Furthermore, we performed constraint based modeling (CBM)-derived robustness analysis on the model to study the dynamic changes of the metabolic network. By perturbing the culture temperature from 75 to 55 °C, we collected the bacterial growth rates and differential proteomes. Assuming that protein abundance changes represent metabolic flux variations, we proposed that the robustness analysis of the CBM model could decipher the effect of proteome change on the bacterial growth under perturbation. For approximately 73% of the reactions, the predicted cell growth changes due to such reaction flux variations matched the observed cell growth data. Our study, therefore, indicates that differential proteome data can be integrated with metabolic network modeling and that robustness analysis is a strong method for representing the dynamic change in cell phenotypes under perturbation.

Graphical abstract: Robustness analysis of a constraint-based metabolic model links cell growth and proteomics of Thermoanaerobacter tengcongensis under temperature perturbation

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Publication details

The article was received on 11 Apr 2012, accepted on 16 Jan 2013 and first published on 18 Jan 2013


Article type: Paper
DOI: 10.1039/C3MB25278G
Citation: Mol. BioSyst., 2013,9, 713-722
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    Robustness analysis of a constraint-based metabolic model links cell growth and proteomics of Thermoanaerobacter tengcongensis under temperature perturbation

    W. Tong, Z. Chen, Z. Cao, Q. Wang, J. Zhang, X. Bai, R. Wang and S. Liu, Mol. BioSyst., 2013, 9, 713
    DOI: 10.1039/C3MB25278G

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