ChIP-exo and CRISPRi/a illuminate the role of Pdr1 and Yap1 in acetic acid tolerance in Saccharomyces cerevisiae.

Budding yeast Saccharomyces cerevisiae has great potential as a host organism for various biorefinery applications. Nevertheless, the utilization of renewable plant biomass as feedstock for yeast in industrial applications remains a bottleneck, largely due to the presence of inhibitory substances such as acetic acid that are released in the biomass pretreatment processes. Exposure to acetic acid leads to different cellular stress mechanisms, several of which are directed by transcription factors. In this work, the role of the transcription factors Pdr1 and Yap1 in acetic acid tolerance was investigated using ChIP-exo and CRISPR interference/activation (CRISPRi/a). Pdr1 is the main regulator of the pleiotropic drug response, whereas Yap1 governs the oxidative stress response. CRISPRa targeting YAP1 for overexpression conferred a higher specific growth rate of S. cerevisiae, whereas CRISPRi-based downregulation of PDR1 proved to be beneficial for growth in medium containing acetic acid. ChIP-exo experiments showed increased binding of Pdr1 or Yap1 to their target promoters in the presence of acetic acid, and a large number of promoters were bound by either transcription factor. Promoters of genes involved in amino acid synthesis or encoding ABC transporters had the highest level of binding enrichment in the presence of acetic acid. The results highlight the potential for developing more acetic acid-tolerant yeast by altering the expression of transcription factor-encoding genes and demonstrate how expression can be fine-tuned by CRISPRi/a.IMPORTANCEBiotechnological conversion of plant biomass into a variety of commodity chemicals and specialty molecules is an important step towards a bioeconomy. This study highlights the importance of two transcription factors, Pdr1 and Yap1, in the tolerance of Saccharomyces cerevisiae to acetic acid, a common inhibitor in bioprocesses using lignocellulosic biomass. CRISPR interference/activation and ChIP-exo were used to manipulate the expression and binding of these transcription factors in response to acetic acid stress. The study provides new insights into adaptation to acetic acid and suggests ways to improve yeast performance in industrial applications.