A hybrid strategy for growth-associated production of sophorolipid using a reconstructed genome-scale metabolic model for the fructophilic yeast Starmerella bombicola

Metabolic modeling of Starmerella bombicola as a model yeast of the Wickerhamiella/Starmerella (W/S) clade is advantageous for studying the characteristics of this clade and to apply for the metabolic engineering of this industrial yeast. A genome-scale metabolic network named iEM759 was reconstructed for S. bombicola using the information from databases, literature, and experimental data generated in this research. iEM759 was evaluated using the growth phenotypic data and experimental data for respiration. It appropriately predicted batch growth of S. bombicola on glucose with the final biomass concentration of 1.16 g/l which is close to the experimental value of 1.1 g/l and the predicted biomass growth yield for ATP and P/O ratio was also comparable with the reported experimental data. The model was then applied to investigate the fructophily of this yeast as well as the effect of by-products on growth and sophorolipid production under oxygen-limited conditions. In agreement with experimental reports, iEM759 correctly predicts the production of mannitol on fructose under oxygen shortage and the preference of glycerol over ethanol by S. bombicola. Finally, the model was used to couple sophorolipid and biomass production, which, using nine knockouts, resulted in a strong envelope with non-zero sophorolipid production and maximum sophorolipid and biomass production rates of 0.97 mmol/gDCW/h and 0.0062 1/h, respectively. The knockout strategy found is a hybrid strategy that combines multiple approaches including increasing the need for redox balance, controlling growth, and providing more precursors for sophorolipid.