ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system_Nguyen et al

Published: 26-03-2021| Version 1 | DOI: 10.17632/rmz22dfn8j.1
Thanh Ngọc Nguyen,
Benjamin Scott Padman,
Susanne Zellner,
Grace Khuu,
Louise Uoselis,
Wai Kit Lam,
Marvin Skulsuppaisarn,
Runa S. J. Lindblom,
Emily M. Watts,
Christian Behrends,
Michael Lazarou


The sequestration of damaged mitochondria within double-membrane structures termed autophagosomes is a key step of PINK1/Parkin mitophagy. The ATG4 family of proteases are thought to regulate autophagosome formation exclusively by processing the ubiquitin-like ATG8 family (LC3/GABARAPs). We discover that human ATG4s promote autophagosome formation independently of their protease activity and of ATG8 family processing. ATG4 proximity networks reveal a role for ATG4s and their proximity partners, including the immune-disease protein LRBA, in ATG9A vesicle trafficking to mitochondria. Artificial intelligence-directed 3D electron microscopy of phagophores shows that ATG4s promote phagophore-ER contacts during the lipid-transfer phase of autophagosome formation. We also show that ATG8 removal during autophagosome maturation does not depend on ATG4 activity. Instead, we find that ATG4s can disassemble ATG8-protein conjugates, revealing a role for ATG4s as deubiquitinating-like enzymes. These findings establish non-canonical roles of the ATG4 family beyond the ATG8 lipidation axis and provide an AI-driven framework for rapid 3D electron microscopy.