Genome Scale Constraint-Based Metabolic Reconstruction of Propionibacterium Freudenreichii DSM 20271

Abstract Propionibacterium is an anaerobic bacterium with a history of use in the production of Swiss cheese and, more recently, several industrial bioproducts. While the use of this strain for the production of organic acids and secondary metabolites has gained growing interest, the industrial application of the strain requires further improvement in the yield and productivity of the target products. Systems modeling and analysis of metabolic networks are widely leveraged to gain holistic insights into the metabolic features of biotechnologically important strains and to devise metabolic engineering and culture optimization strategies for economically viable bioprocess development. In the present study, a high-quality genome-scale metabolic model of P. freudenreichii ssp. freudenreichii strain DSM 20271 was developed based on the strain’s genome annotation and biochemical and physiological data. The model covers the functions of 23% of the strain’s ORFs and accounts for 711 metabolic reactions and 647 unique metabolites. Literature-based reconstruction of the central metabolism and rigorous refinement of annotation data for establishing gene-protein-reaction associations renders the model a curated omic-scale knowledge base of the organism. Validation of the model against experimental data indicates that the reconstruction can capture the key structural and functional features of P. freudenreichii metabolism, including the growth rate, the pattern of flux distribution, the strain’s aerotolerance behavior, and the change in the mode of metabolic activity during the transition from an anaerobic to an aerobic growth regime. The model also includes an accurately curated pathway of cobalamin biosynthesis, which was used to examine the capacity of the strain to produce vitamin B12 precursors. Constraint-based reconstruction and analysis of the P. freudenreichii metabolic network also provided novel insights into the complexity and robustness of P. freudenreichii energy metabolism. The developed reconstruction, hence, may be used as a platform for the development of P. freudenreichii-based microbial cell factories and bioprocesses.