Model-driven analysis reveals oxidative stress adaptation enabling efficient energy utilization in a Crabtree-negative Saccharomyces cerevisiae.

ABSTRACT: The metabolic engineering of Saccharomyces cerevisiae to abolish the Crabtree effect via a pyruvate dehydrogenase bypass has enabled growth in minimal medium with glucose as the sole carbon source, although at a low growth rate. Adaptive laboratory evolution of the engineered strain (sZJD23), followed by reverse engineering, produced a variant (sZJD28) with significantly improved growth. This is mainly due to a mutation in MED2, which encodes a subunit of the mediator complex and, to a lesser extent, a mutation in GPD1, which encodes a glycerol-3-phosphate dehydrogenase. Here, using quantitative proteomics and enzyme-constrained genome-scale modelling, we show that these mutations jointly enable a more efficient strategy for oxidative stress adaptation and energy utilization. Specifically, the MED2 mutation reshapes the oxidative stress response, including peroxisomal detoxification, while the GPD1 mutation suppresses a suboptimal redox-balancing strategy in the primary strain. Collectively, these changes result in improved flux distribution, lower protein costs in energy metabolism, and potentially enhanced ATP availability. Our findings reveal how specific mutations coordinate stress tolerance and metabolic efficiency to restore growth in engineered Crabtree-negative yeast.

INSTRUMENT(S):

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Culture

SUBMITTER: Johannes Fuchs  

LAB HEAD: Eduard J Kerkhoven

PROVIDER: PXD074337 | Pride | 2026-02-13

REPOSITORIES: Pride