Exogenous functional protein reprograms mitochondria centered metabolism and protein homeostasis in Zygosaccharomyces...

High salinity causes severe osmotic and oxidative stress to Zygosaccharomyces rouxii, a crucial yeast in soy sauce manufacturing. We used DIA-based quantitative proteomics to investigate whether a functional protein (casein containing astaxanthin) alters the salt-stress proteome of Z. rouxii CGMCC 3791 at 120 g/L NaCl. Multivariate analysis revealed a clear distinction between the NaCl-only and supplemented groups, with excellent repeatability. A total of 267 differently expressed proteins were discovered (52 up-regulated and 215 down-regulated; |FC| ≥ 1.5, p < 0.05), showing significant proteome remodeling. GO and KEGG/InterPro enrichment identified oxidative stress response, membrane lipid handling, vesicle/vacuolar autophagic regulation, ribosome-associated processes, and oxidative phosphorylation. Protein-protein interaction research identified hub modules centered on the ribosome and mitochondria. Taken together, these results suggest that functional protein supplementation is associated with coordinated changes in redox-related, membrane-associated, proteostasis-related, and energy-metabolism pathways in Z. rouxii under high-salt conditions, which may contribute to the observed improvement in survival.