Zacharias Thiel, David Marcellin, Carole Manneville, Benedikt Goretzki, Luca Egger, Rob Maher, Noémie Siccardi, Laura Torres, Alexandra Probst, Catrin Swantje Müller, Nathalie George, Markus Vogel, Sabine Sinterhauf, Alexandra Lavoisier, Ji‐Young Choi, Laurianne Forcellino, Alexandro Landshammer, Patrick Hauck, C. Be, Frédéric Villard, Sascha Gutmann, Marc De Meyer, Felix Freuler, Alexandra Hinniger, César Fernández Fernández, Suzanne Chau, Maude Patoor, Gilles Sansig, Gabriel Mitchell, Beat Nyfeler
Autophagy-based targeted degradation offers a powerful complement to proteasomal degradation leveraging the capacity and versatility of lysosomes to degrade complex cargo. However, it remains unclear which components of the autophagy-lysosomal pathway are most effective for targeted degradation. Here, we describe two orthogonal induced-proximity strategies to identify autophagy effectors capable of degrading organelles and soluble targets. Recruitment of autophagy cargo receptors, ATG8-like proteins, or the kinases ULK1 and TBK1 is sufficient to trigger mitophagy, while only autophagy cargo receptors capable of self-oligomerization degrade soluble cytosolic proteins. We further report a single-domain antibody against p62 and its use as a heterobifunctional degrader to clear mitochondria. Fusing the p62 single-domain antibody to PINK1 enables selective targeting of damaged mitochondria. Our study highlights the importance of avidity for targeted autophagy and suggests that autophagy cargo receptors are attractive entry points for the development of heterobifunctional degraders for organelles or protein aggregates.