Proteome trade-off between primary and secondary metabolism shapes acid stress induced bacterial exopolysaccharide production

Abstract The exopolysaccharide (EPS) produced by Lactiplantibacillus plantarum is a high-value bioproduct in food and health industries, and its biosynthesis has been found as a secondary metabolic pathway to mediate acid stress. To quantitatively investigate acid stress response in L. plantarum and model EPS production, this study measured metabolomics, proteomics and growth data for L. plantarum HMX2 cultured at 4 different pH values. The growth and metabolomics data showed that under acid stress, the EPS production flux was evidently enhanced while the glycolysis and cellular growth were inhibited. The following proteomic analysis found that EPS biosynthetic proteins were significantly up-regulated under acid stress and pinpointed Fur as the most probable transcriptional factor controlling EPS biosynthesis in L. plantarum . Furthermore, we identified a proteome trade-off between primary metabolism and EPS biosynthesis, which were then mechanistically depicted by a regulatory proteome constrained flux balance analysis (RPCFBA) model. As the first metabolic model that can simulate secondary metabolism, the RPCFBA model demonstrated good accuracy in predicting growth rates and EPS production fluxes of L. plantarum HMX2, validated by experimental data. The in-silico perturbation on carbon sources further showed the potential of applying the presented modeling framework to the design and control of microbial secondary metabolism.