Transcriptomics-guided identification of engineering targets for improving salt tolerance in Saccharomyces cerevisiae

BACKGROUND: High-salinity conditions frequently impair the fermentation performance of Saccharomyces cerevisiae in industrial processes involving high-osmolarity substrates. Identifying genetic determinants that enhance salt tolerance is therefore essential for the development of robust yeast cell factories. In this study, a comparative transcriptomic analysis was performed to investigate the transcriptional responses of a salt-tolerant strain, E-158, and its parental strain, KF-7, under 1.25 M NaCl stress, with the aim of identifying potential targets for strain engineering. RESULTS: Comparative transcriptomic analysis revealed extensive transcriptional differences between E-158 and KF-7 under high-salt conditions, involving central carbon and nitrogen metabolism, peroxisome-associated oxidative stress responses, ion transport, cell wall-related processes, and sporulation-related pathways. Based on these profiles, two transcription factors (CUP9 and ZNF1) and three functional genes (DAL1, IDP2, and CTA1) were selected for functional validation. Overexpression or deletion of the transcription factors, as well as overexpression of the functional genes, was carried out in KF-7. Fermentation experiments under 1.25 M NaCl demonstrated that all engineered strains outperformed the parental strain. Among them, overexpression of CTA1 resulted in the greatest improvement, with glucose consumption and ethanol production increased by 35.04% and 45.66%, respectively, after 96 h of fermentation. CONCLUSIONS: This study demonstrates that comparative transcriptomics can serve as an effective strategy for identifying engineering targets associated with salt tolerance in S. cerevisiae. The evaluated genes provide potential targets for strain improvement and offer insights for the rational design of yeast cell factories suited for high-salinity biofuel and bioproduct fermentation processes.