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.

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

“…(ii) Compartmentalization, the definition of biomass reaction and uptakes and secretions: In the absence of information or experimental evidence about the compartmentalization and the cell content in P. veronii 1YdBTEX2, the cell compartment information (i.e., cytosol and periplasm), the transport mechanism between the compartments and the extracellular environment, the uptakes and secretions, and the biomass composition were obtained from two available models of closely related Pseudomonads: Pseudomonas putida [27][28][29] and Pseudomonas stutzeri. 30 The biomass reaction in a GEM designates the metabolic precursors that build the BBBs, i.e., DNA, RNA, amino acids, lipids and carbohydrates and their corresponding stoichiometric coefficients. (iii) Thermodynamic curation: In a thermodynamically curated model, the standard Gibb's free energy of a reaction and consequently the directionality of the reactions, i.e., reversible or irreversible, are associated with the reaction as additional constraints, which allow the performance of TFA.…”

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

“…This type of knowledge can be gained through the use of genome-scale models (GSM) and system-level multi-objective analyses of cellular processes. Genome-scale mathematical modeling of metabolic networks is a key tool of systems biology that has been used to examine the biochemical underpinnings of cellular phenotypes in microbes ranging from model organisms like Escherichia coli [2, 3] and baker’s yeast [4], to those of ecological and industrial interest [5–8], and even deadly pathogens [9, 10]. A number of models have also been developed for photosynthetic organisms, such as purple non-sulfur bacterium Rhodobacter sphaeroides [11] and cyanobacterium Synechococcus sp.…”

TEX-FBA: A constraint-based method for integrating gene expression, thermodynamics, and metabolomics data into genome-scale metabolic models

“…In particular, GEMs have been successfully used for engineering strains for optimizing the production of chemicals [2][3][4] and identifying drug targets for metabolic diseases, such as diabetes [5], cancer [6][7][8] and non-alcoholic fatty liver disease [9,10]. Increased availability of organisms' gene sequencing has led to an accumulation of available GEM reconstructions for a variety of bacteria and eukaryotic organisms [11][12][13][14][15][16][17][18][19][20].…”