Proteomic Insights into Salt-Stress Tolerance in Zygosaccharomyces rouxii Revealed by Data-Independent Acquisition Mass Spectrometry

Abstract

Zygosaccharomyces rouxii is a halotolerant yeast commonly associated with high-salt fermentations, although its proteome-level adaptation mechanisms are little understood. DIA-based quantitative proteomics was used to characterize the salt-stress responses of Z. rouxii CGMCC 3791 grown at 0, 60, and 120 g/L NaCl. Principal component analysis demonstrated high repeatability and a unique proteome state at 120 g/L of NaCl. Differential analysis revealed 251 differentially expressed proteins (DEPs) (148 up, 103 down) at 60 g/L and 798 DEPs (549 up, 249 down) at 120 g/L, demonstrating significant concentration-dependent remodeling. Under severe stress, GO and KEGG enrichment consistently revealed the reinforcement of central carbon and energy metabolism, peroxisome-associated fatty acid turnover, oxidoreductase/redox activities, and translation and nucleotide metabolic pathways. Heatmap clustering and PPI networks revealed additional tightly coordinated modules that connect bioenergetics, redox regulation, and the translational capacity. These findings provide a proteome-scale framework for understanding halotolerance in Z. rouxii and guidance for future high-salt fermentation engineering.