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Background   Saccharomyces cerevisiae  is widely used in traditional brewing and modern fermentation industries to produce biofuels, chemicals and other bioproducts, but challenged by various harsh industrial conditions, such as hyperosmotic, thermal and ethanol stresses. Thus, its stress tolerance enhancement has been attracting broad interests. Recently, CRISPR/Cas-based genome editing technology offers unprecedented tools to explore genetic modifications and performance improvement of  S. cerevisiae .    Results  Here, we presented that the Target-AID (activation-induced cytidine deaminase) base editor of enabling C-to-T substitutions could be harnessed to generate in situ nucleotide changes on the  S. cerevisiae  genome, thereby introducing protein point mutations in cells. The general transcription factor gene  SPT15  was targeted, and total 36 mutants with diversified stress tolerances were obtained. Among them, the 18 tolerant mutants against hyperosmotic, thermal and ethanol stresses showed more than 1.5-fold increases of fermentation capacities. These mutations were mainly enriched at the N-terminal region and the convex surface of the saddle-shaped structure of Spt15. Comparative transcriptome analysis of three most stress-tolerant (A140G, P169A and R238K) and two most stress-sensitive (S118L and L214V) mutants revealed common and distinctive impacted global transcription reprogramming and transcriptional regulatory hubs in response to stresses, and these five amino acid changes had different effects on the interactions of Spt15 with DNA and other proteins in the RNA Polymerase II transcription machinery according to protein structure alignment analysis.    Conclusions  Taken together, our results demonstrated that the Target-AID base editor provided a powerful tool for targeted in situ mutagenesis in  S. cerevisiae  and more potential targets of Spt15 residues for enhancing yeast stress tolerance.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13068-021-02005-w.

Stress tolerance enhancement via SPT15 base editing in Saccharomyces cerevisiae