Author ORCID Identifier

Date of Award

Winter 2-1-2024

Document Type

Thesis (Ph.D.)

Department or Program

Biochemistry and Cell Biology

First Advisor

Christopher J Shoemaker


Autophagy is a lysosome-mediated pathway responsible for the degradation of unwanted cytosolic content. During autophagy, cytoplasmic components are enveloped by a newly generated vesicle (the autophagosome), trafficked to the lysosome, and degraded. The power of autophagy lies in its ability to selectively target specific substrates for degradation—a phenomenon known as selective autophagy.

Specialized proteins known as selective autophagy receptors play a crucial role in identifying and targeting autophagy cargo. Although historically overlooked as potential regulators, our understanding of autophagy receptors is evolving beyond the assumption that receptors merely bridge targets to pre-formed autophagosomal membranes. Previous insights were often based on a few model receptors, leaving broader mechanisms unexplored. Through my research, we uncovered an unexpected plasticity of autophagy mechanisms. This novel perspective, emphasizing the identity of the cargo in autophagy mechanisms, has reshaped our understanding of autophagosome formation, providing fresh insights into longstanding questions about autophagy target selection, induction mechanisms, and membrane mobilization.

We uncovered an autophagy-independent lysosomal degradation of well-known mitophagy receptors, BNIP3 and BNIP3L/NIX, which are constitutively delivered to lysosomes. This atypical route of lysosomal delivery of BNIP3 is the predominant pathway for its degradation, even during mitophagy induction. In tandem, we found BNIP3 oligomerization is required for this alternative lysosome route and not mitophagy induction per se. Through a genome-wide CRISPR screen, we unraveled the intricate network of factors that govern BNIP3 flux. We identified the endoplasmic reticulum insertion and the endolysosomal system as key regulators of BNIP3, operating alongside the ubiquitin-proteasome system. Disruption of these quality control mechanisms significantly impacts BNIP3-associated mitophagy and has broader implications for cellular physiology. Next, we uncovered a novel regulatory node that connects lipid peroxidation to mitophagy. In this case, loss of antioxidant enzyme GPX4 stabilizes BNIP3 to trigger mitophagy as part of a response to oxidative stress. Overall, our work demonstrates distinct BNIP3 fates, challenging the features of the receptor paradigm and novel regulatory mechanisms of membrane-embedded autophagy receptors.

Original Citation

Delgado, J. M., Shepard, L. W., Lamson, S. W., Liu, S. L., & Shoemaker, C. J. (2024). The ER membrane protein complex restricts mitophagy by controlling BNIP3 turnover. The EMBO journal, 43(1), 32–60.

Available for download on Friday, January 31, 2025