CRISPRi reveals genes modulating yeast growth in lignocellulose hydrolysate

CRISPR interference screening of 129 protein kinases and 161 transcription factors in S. cerevisiae. Repression effects on yeast growth in oxygen-limited conditions were quantified in synthetic complete media (SCM), SCM supplemented with 10% lignocellulose hydrolysate and SCM supplemented with 45% of a mixture of growth-inhibiting lignocellulosic compounds. The aim of this project was to determine the reproducibility of CRISPRi effects across studies and to characterize CRISPRi for screening of phenotypes relevant for industrial biotechnology. We identify gene functions in general growth in oxygen-limited conditions, and specific for cellular fitness in lignocellulose hydrolysate. A further screen with a cocktail of lignocellulosic compounds enables us to explain hydrolysate-specific gene functions with roles in toxicity. Overall design: CRISPRi screens in bulk yeast populations on three selection conditions: competitive growth profiling over 25 generations days in SCM, 10% spruce hydrolysate and 45% lignocellulosic inhibitor cocktail.