Synthetic Quantitative Array Technology Identifies the Ubp3-Bre5 Deubiquitinase Complex as a Negative Regulator of Mitophagy

• Published in: Cell reports (Cambridge) 2015-02, Vol.10 (7), p.1215-1225
• Main Authors: Müller, Matthias, Kötter, Peter, Behrendt, Christina, Walter, Elena, Scheckhuber, Christian Q., Entian, Karl-Dieter, Reichert, Andreas S.
• Format: Article
• Language: English
• Subjects: Autophagy - drug effects; Endopeptidases - genetics; Endopeptidases - metabolism; Genome, Fungal; Mitochondria - metabolism; Mitochondrial Degradation - drug effects; Mutagenesis; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sirolimus - pharmacology; Ubiquitination
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2015.01.044

Mitophagy is crucial to ensuring mitochondrial quality control. However, the molecular mechanism and regulation of mitophagy are still not fully understood. Here, we developed a quantitative methodology termed synthetic quantitative array (SQA) technology, which allowed us to perform a genome-wide screen for modulators of rapamycin-induced mitophagy in S. cerevisiae. SQA technology can be easily employed for other enzyme-based reporter systems and widely applied in yeast research. We identified 86 positive and 10 negative regulators of mitophagy. Moreover, SQA-based analysis of non-selective autophagy revealed that 63 of these regulators are specific for mitophagy and 33 regulate autophagy in general. The Ubp3-Bre5 deubiquitination complex was found to inhibit mitophagy but, conversely, to promote other types of autophagy, including ribophagy. This complex translocates dynamically to mitochondria upon induction of mitophagy. These findings point to a role of ubiquitination in mitophagy in yeast and suggest a reciprocal regulation of distinct autophagy pathways. [Display omitted] •Development of an enzyme-based high-throughput screening technique in S. cerevisiae•Genome-wide quantitative screen for modulators of rapamycin-induced mitophagy•Identification of 86 positive and 10 negative regulators of mitophagy•Reciprocal regulation of mitophagy and other autophagy pathways by deubiquitination Müller et al. developed a method, termed synthetic quantitative array technology, to screen for mitophagy modulators in yeast. Using this method, they identified the Ubp3-Bre5 deubiquitination complex, which inhibits mitophagy but promotes other types of autophagy. Deubiquitination thus appears to regulate a switch between distinct autophagy pathways.