A system for inducible mitochondria-specific protein degradation in vivo

Targeted protein degradation systems developed for eukaryotes employ cytoplasmic machineries to perform proteolysis. This has prevented mitochondria-specific analysis of genome maintaining proteins that localize to both mitochondria and nucleus. Here, we present an inducible mitochondria-specific protein degradation system in Saccharomyces cerevisiae based on the Mesoplasma florum Lon (mf-Lon) protease and its corresponding ssrA tag (called PDT). We show that mitochondrially targeted mf-Lon protease efficiently and selectively degrades a PDT-tagged reporter protein localized to the mitochondrial matrix. The degradation can be induced by depleting adenine from the medium and tuned by altering the promoter strength of the MF-LON gene. Finally, we demonstrate that mf-Lon degrades endogenous, dually localized proteins inside mitochondria. In summary, our system is an efficient tool for analysis of intricate mitochondria-nuclear crosstalk essential for proper mitochondrial function. One-Sentence Summary Mitochondria-specific protein degradation of dually localized proteins