ChIP-exo and CRISPRi/a illuminate the role of Pdr1 and Yap1 in acetic acid tolerance in Saccharomyces cerevisiae
Journal article, 2025

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 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 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 transcription factor-encoding genes and demonstrate how expression can be fine-tuned by CRISPRi/a.

stress responses

yeast

transcription factor

inhibitor stress

expression

Author

Ibai Lenitz Etxaburu

Chalmers, Life Sciences, Industrial Biotechnology

Christoph Sebastian Börlin

Chalmers, Life Sciences, Systems and Synthetic Biology

Luca Torello Pianale

Chalmers, Life Sciences, Industrial Biotechnology

Darshan Balachandran

Student at Chalmers

Jens B Nielsen

Chalmers, Life Sciences, Systems and Synthetic Biology

Florian David

Chalmers, Life Sciences, Systems and Synthetic Biology

Verena Siewers

Chalmers, Life Sciences, Systems and Synthetic Biology

Yvonne Nygård

Chalmers, Life Sciences, Industrial Biotechnology

Applied and Environmental Microbiology

0099-2240 (ISSN) 1098-5336 (eISSN)

Vol. In Press

CRISPRi for elucidating stress regulation in yeast

Swedish Research Council (VR) (2018-04713), 2019-09-01 -- 2023-08-31.

Subject Categories (SSIF 2025)

Molecular Biology

DOI

10.1128/aem.01824-24

PubMed

40035556

More information

Latest update

3/17/2025