Applying the auxin-based degron system for the inducible, reversible and complete protein degradation in Komagataella phaffii

The auxin-inducible degron (AID) system is a useful technique to rapidly deplete any protein of interest “on-demand.” In this study, we successfully established the AID system for the “biotech” yeast Komagataella phaffii. First, we tested different expression levels of TIR1 for auxin-induced degradation of the glycerol kinase Gut1. Moderate expression of TIR1 resulted in complete degradation of the target protein within several minutes. Second, we show that the absence of all three Wsc type sensors is detrimental to cell growth, which indicates that these are the dominant cell wall sensors this yeast. Third, down-regulation of Erg1, an essential enzyme of the ergosterol biosynthetic pathway, resulted in quick and efficient accumulation of squalene, a pharmaceutically relevant reagent. We conclude that AID is an extremely powerful tool that, for the first time, enables the analysis of gene essentiality and function in K. phaffii.