During autophagy, LC3 and GABARAP proteins become covalently attached to phosphatidylethanolamine (PE) on the growing autophagosome. This attachment is also reversible. Deconjugation (or delipidation) involves the proteolytic cleavage of an isopeptide bond between LC3 or GABARAP and the PE headgroup. This cleavage is carried about by the ATG4 family of proteases (ATG4A, B, C and D). Many studies have established that ATG4B is the most active of these proteases and is sufficient for autophagy progression in simple cells. Here we examine the second most active protease, ATG4A, to map out key regulatory motifs on the protein and to establish its activity in cells. We utilize fully in vitroreconstitution systems where we control the attachment of LC3/GABARAP members and discover a role for a carboxy-terminal (COOH-terminal) LC3-interacting region (LIR) on ATG4A in regulating its access to LC3/GABARAP. We then use a gene-edited cell line in which all four ATG4 proteases have been knocked out to establish that ATG4A is insufficient to support autophagy and is unable to support GABARAP proteins removal from the membrane. As a result, GABARAP proteins accumulate on membranes other than mature autophagosomes. These results suggest that to support efficient production and consumption of autophagosomes, additional factors are essential including possibly ATG4B itself, or one of its proteolytic products in the LC3 family.
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