J. Biol. Chem. https://doi.org/10.1074/jbc.AC119.009977 (2019)

LC3 is a small ubiquitous soluble protein important in autophagy, a process of bulk degradation of cytoplasmic components. The cytosolic form of LC3 can be conjugated to membrane phospholipids and recruited to autophagosomal membranes. Given the similarities to the protein-modifying ubiquitin system, including structural homology between LC3 and ubiquitin and a role for deubiquitinase-like cysteine protease ATG4 in proteolytic processing and delipidation of LC3, Agrotis et al. searched for other non-phospholipid substrates for LC3 conjugation. The authors used a deconjugation-resistant form of LC3 and ATG4 knockouts to find that LC3 could stably modify cellular proteins, including ATG3, an E2-like conjugating enzyme involved in the LC3 lipidation reaction. The LC3B–ATG3 conjugates, of which at least one is mediated through ATG3 residue K243, are distinct from the thioester-linked covalent intermediate between LC3B and ATG3 that is known to form before LC3 lipidation. Finally, the authors showed that ATG4B can cleave the LC3B–ATG3 conjugates in a process that is analogous to the delipidation of LC3. These results broaden the scope of LC3 targets and potentially its range of functions.