Time-Resolved Proteomics Analysis of the Cell Wall-Enriched Fraction in Saccharomyces cerevisiae S288c during Batch Fermentation.

The yeast cell wall (YCW) is a dynamic and multifunctional structure that is essential for cellular integrity, stress resistance, and interactions with the surrounding environment. Its structural composition is strongly influenced by external factors, such as temperature, pH, and nutrients. In batch cultures, yeast grows in a closed system with limited nutrients, resulting in distinct growth phases that are associated with major metabolic transitions. Although the global proteomic changes during growth kinetics have been described, the temporal changes of cell wall protein (CWP) expression remain poorly understood. In this study, we investigated the kinetics of protein expression in the cell wall-enriched fraction of Saccharomyces cerevisiae S288c during a bioreactor-based batch cultivation in rich medium. A classical proteomics workflow was applied to capture the dynamic variation of protein expression at multiple time points in these fractions, with a focus on covalently linked CWPs (cCWPs). The results revealed qualitative and quantitative changes in cCWP expression correlated with metabolic shifts between growth phases. Proteins involved in cell wall remodeling and glycoprotein biosynthesis were particularly enriched at the initial sampling point, corresponding to the transition from flask cultivation to bioreactor conditions, when the overall cCWP abundance was the highest. Time-resolved quantitative proteomics, transcription factor analysis, and functional enrichment indicated the coordinated regulation of cell wall adaptation. Stationary phase-specific protein markers associated with glucose depletion were identified, providing insight into nutrient-limited cell wall remodeling.