We used iYali4 the GEM of Y. lipolytica by Kerkhoven et al., and an updated version for Y. lipolytica W29 to study citrate optimization. Growth rate on glucose and nitrogen-limited mineral medium was predicted by the model based on glucose specific consumption rate adequately fitted to the experimental results (Table (Table11 and Fig. 1). It was noted that iYali4 and the other GEMs did not integrate the alternative oxidase (AOX) reaction. So we added the AOX reaction as part of the electron transfer chain (ETC), based on the hypothesis that this enzyme has a protective effect against ROS generation in Y. lipolytica and probably on citrate production30,31,35. The stoichiometry of AOX reaction were determined from literature and in coherence with iYali4 ETC reaction: ubiquinol + 0.25 02 =  > ubiquinone + 0.5 H2O32. AOX reaction is doesn’t contribute to proton pumping across the mitochondrial membrane48.

Kinetic physiological parameters.

Experimental data obtained from batch (n = 1) of Y. lipolytica culture. Citrate and isocitrate are produced upon cultures reach stationary phase.

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