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Autophagy is a fundamental degradation process conserved in eukaryotic cells, wherein autophagosomes are generated by cooperative actions of multiple Atg proteins in response to nutrient starvation.At the initial step of autophagosome formation, Atg13 plays a key role as a regulatory component responsible for organization of the PAS scaffold (the Atg1 complex composed of Atg 1, Atg 13, and the Atg1 7-Atg29-Atg31 ternary complex).Atg13 largely consists of two structural regions, the N-terminal stable domain having a HORMA fold (residues 1-268)and the C-terminal disordered region (residues 269-738), in which more than 40 Ser/Thr residues are phosphorylated by Tor1 kinase under nutrient-rich conditions.Upon nutrient starvation, Atg13 is immediately dephosphorylated, consequently leading to proper interaction with Atg1.Recently, we elucidated the molecular detail of the Atg13-Atg1 interaction;a short disordered segment of Atg13 (residues 460-521, named the MIM) directly interacts with the C-terminal domain of Atg1 (residues 587-897, named the tandem MIT), and this interaction is regulated by phosphorylation state of the Atg13MIM region.We also found that Atg13 binds to the Atg1 7-Atg29-Atg31 complex via its disordered region (residues 424-436, named the 17BR),and this interaction is also regulated by the starvation-dependent dephosphorylation of Atg13 (Ser428/Ser429 in the Atg1317BR region).We next investigated the molecular function of Atg13HORMA domain;the N-terminal HORMA domain is essential for autophagy, but its molecular function has not been established.Therefore, we searched for interaction partners of the Atg13HORMA domain and found that it binds Atg9, a multispanning membrane protein that exists on specific cytoplasmic vesicles (Atg9 vesicles).After the Atg1 complex is formed,Atg9 vesicles are recruited to the PAS and become part of the autophagosomal membrane.HORMA domain mutants, which are unable to interact with Atg9, impaired the PAS localization of Atg9 vesicles and exhibited severe defects in starvation-induced autophagy, suggesting that Atg9 vesicles are recruited to the PAS via the interaction with the Atg1 3HORMA domain.Based on these findings, we propose that the two distinct regions of Atg1 3 play crucial roles in distinct steps of autophagosome formation;at the first step, Atg13 forms a scaffold for the PAS via its C-terminal disordered region, and subsequently it recruits Atg9 vesicles via its N-terminal HORMA domain.