Abstract
Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH3). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. Azotobacter vinelandii is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in A. vinelandii remain unknown to date.Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium A. vinelandii DJ (iDT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. iDT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism.
Highlights
Azotobacter vinelandii is a gram-negative soil bacterium capable of converting atmospheric nitrogen gas (N2) into soluble ammonia (NH3) as well as into other important nitrogenous compounds (Gyurjan et al, 1995; Howard and Rees, 1996)
A draft model of A. vinelandii DJ was reconstructed using the genome annotation from PATRIC (Genome ID: 322710.5)
Five manually curated and validated M-Models were used as protein homology templates: Escherichia coli str
Summary
Azotobacter vinelandii is a gram-negative soil bacterium capable of converting atmospheric nitrogen gas (N2) into soluble ammonia (NH3) as well as into other important nitrogenous compounds (Gyurjan et al, 1995; Howard and Rees, 1996). A. vinelandii has been shown to grow under a broad range of heterotrophic conditions and is able to metabolize, different sugars, alcohols, and organic acids as well as nitrogen-containing compounds (Nagai et al, 1972; Quiroz-Rocha et al, 2017; Sahoo et al, 2014; Shawky et al, 1987). Only two core M-models of Azotobacter vinelandii are available that contain a reduced number of metabolic reactions These core reactions are in general related to nitrogen fixation or PHB and alginate production, disregarding most of the central metabolism of the microorganism (e.g. TCA cycle, lipid metabolism and some amino acids synthesis) (García et al, 2018; Inomura et al, 2018). Our model was successfully validated using high-throughput phenotypic data and physiological data
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