Model for the cooperation of Atg13 and Atg8 on Atg1 regulation. Atg13 constitutively binds Atg1. Upon starvation, Atg1 is activated by autophosphorylation and in turn phosphorylates Atg13, which further increases its kinase activity. Atg1 binds to Atg8 via its LIR motif, which triggers its removal from the PAS and mediates its association with autophagosomes. Atg1 on autophagosomes may phosphorylate unknown substrates involved in autophagosome maturation. After autophagosomal fusion, the Atg1–Atg13 complex is degraded in the vacuole/lysosome, thereby limiting autophagic flux during starvation.