ATG12, an ubiquitin-like modifier required for macroautophagy, has a single 
known conjugation target, another autophagy regulator called ATG5. Here, we 
identify ATG3 as a substrate for ATG12 conjugation. ATG3 is the E2-like enzyme 
necessary for ATG8/LC3 lipidation during autophagy. ATG12-ATG3 complex formation 
requires ATG7 as the E1 enzyme and ATG3 autocatalytic activity as the E2, 
resulting in the covalent linkage of ATG12 onto a single lysine on ATG3. 
Surprisingly, disrupting ATG12 conjugation to ATG3 does not affect 
starvation-induced autophagy. Rather, the lack of ATG12-ATG3 complex formation 
produces an expansion in mitochondrial mass and inhibits cell death mediated by 
mitochondrial pathways. Overall, these results unveil a role for ATG12-ATG3 in 
mitochondrial homeostasis and implicate the ATG12 conjugation system in cellular 
functions distinct from the early steps of autophagosome formation.