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Issue 11, 2015
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Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

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Abstract

Pseudomonas stutzeri A1501 is an endophytic bacterium capable of nitrogen fixation. This strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen and phytohormones. These interesting features encouraged us to study the metabolism of this microorganism at the systems-level. In this work, we present the first genome-scale metabolic model (iPB890) for P. stutzeri, involving 890 genes, 1135 reactions, and 813 metabolites. A combination of automatic and manual approaches was used in the reconstruction process. Briefly, using the metabolic networks of Pseudomonas aeruginosa and Pseudomonas putida as templates, a draft metabolic network of P. stutzeri was reconstructed. Then, the draft network was driven through an iterative and curative process of gap filling. In the next step, the model was evaluated using different experimental data such as specific growth rate, Biolog substrate utilization data and other experimental observations. In most of the evaluation cases, the model was successful in correctly predicting the cellular phenotypes. Thus, we posit that the iPB890 model serves as a suitable platform to explore the metabolism of P. stutzeri.

Graphical abstract: Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

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Publication details

The article was received on 30 Jan 2015, accepted on 11 Aug 2015 and first published on 12 Aug 2015


Article type: Paper
DOI: 10.1039/C5MB00086F
Author version available: Download Author version (PDF)
Citation: Mol. BioSyst., 2015,11, 3022-3032
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    Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

    P. Babaei, S. Marashi and S. Asad, Mol. BioSyst., 2015, 11, 3022
    DOI: 10.1039/C5MB00086F

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