4. Discussion
Our results address critical questions in metabolism, such as changes in metabolic fluxes due to pH constraint, what shifts the metabolic pathways, and what induces cells to adjust the way they perform their metabolism, as illustrated by the shift in metabolism from pH 7 to 5. Our strategy proposes optimizing growth under the constraint of pH as the central principle shaping metabolism. The pH changes contribute to a redirection of metabolic fluxes (for example, shift to TCA cycle under acidic conditions) as the exchange rates of proton increase and cells aim to optimize their growth. This finding suggests that the developed charge-balanced models are capable of revealing the physiological properties of the cells and that the models are a more suitable platform for addressing the challenges of using these cells in bio-based production.
Our work also shows that a limit of pH in modeling could constrain cellular metabolism. This constraint is undoubtedly a universal and physical metabolism restriction that can be applied not only in eukaryotes (yeast) but also in prokaryotes (E. coli , Z. mobilis ). Besides, our principle of metabolic flux prediction provides an advantage over conventional FBA-based techniques, since it systematically investigates metabolism in order to perform better and more effectively in metabolic engineering approaches. The findings draw on previous research in S. cerevisiae and other microorganisms, which is aligned with our results that substrate concentration changes are a significant contributor to overall flux distribution changes(Daran-Lapujade et al., 2004; Gerosa et al., 2015; Valgepea, Adamberg, Seiman, & Vilu, 2013). Meanwhile, despite the value ofS. cerevisiae as an industrial microorganism, our observations into its regulatory metabolic flux at various pH levels may be of substantial benefit in systems metabolic engineering. Therefore, using genome-scale metabolic models to evaluate pH effect can provide comprehensive solutions to improve biofuels, biomedicine, and bio-based production, especially reduced products such as ethanol.