ATG16L2 creates a VAIL-dedicated heterodimer with ATG16L1

Abstract The ATG8 conjugation machinery supports both canonical autophagy, in which ATG8 proteins are lipidated on forming autophagosomes, and CASM, in which ATG8 proteins are conjugated to stressed single-membrane compartments. How cells allocate this shared machinery between these competing membrane programs remains unclear. Here, we identify ATG16L2 as a specialized regulator of V-ATPase-responsive ATG8 lipidation (atg8ylation). ATG16L2 does not form stable homodimers and is inactive in the absence of ATG16L1, but it becomes functional through heterodimerization with ATG16L1. The ATG16L1-ATG16L2 heterodimer constitutes a VAIL-competent E3-like complex that is excluded from WIPI2-positive autophagic membranes but readily recruited to stressed lysosomes. ATG16L2 also confers VAIL activity onto the otherwise VAIL-deficient ATG16L1α isoform. We propose that ATG16L1 homodimers and ATG16L1–ATG16L2 heterodimers represent alternative assemblies of the ATG8 conjugation machinery: ATG16L1α homodimers are dedicated to WIPI2-positive autophagic membranes, whereas ATG16L1–ATG16L2 heterodimers containing either ATG16L1 isoform form a VAIL-selective assembly.