title: Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501.
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.
authors: Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran. marashi@ut.ac.ir asad@ut.ac.ir.
authors: Parizad
authors: P
authors: Babaei
authors: Sayed-Amir
authors: SA
authors: Marashi
authors: Sedigheh
authors: S
authors: Asad
mesh_terms: D000693:Anaerobiosis / Q000187:drug effects; D018533:Biomass; D002244:Carbon / Q000494:pharmacology; D003198:Computer Simulation; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D007210:Indoleacetic Acids / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000187:drug effects / Q000235:genetics*; D008954:Models, Biological; D009154:Mutation / Q000235:genetics; D009584:Nitrogen / Q000378:metabolism; D009586:Nitrogen Fixation / Q000187:drug effects; D010100:Oxygen / Q000378:metabolism; D010641:Phenotype; D044223:Pseudomonas stutzeri / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*
chemical_list: D007210:Indoleacetic Acids; C030737:indoleacetic acid; D002244:Carbon; D009584:Nitrogen; D010100:Oxygen