Autophagy-related protein 1 orchestrates autophagy initiation and feedback degradation in Alternaria alternata

Background Autophagy plays an essential role in fungal development and stress adaptation, yet its regulatory mechanisms in filamentous fungi remain incompletely understood. We functionally characterized Alternaria alternata Atg1 (AaAtg1), a serine/threonine kinase, and demonstrated its dual roles in autophagy initiation and flux modulation. Results Deletion of AaAtg1 abolishes autophagosome formation and autophagic flux, impairs peroxisome degradation, and leads to hypersensitivity to oxidative stress, as well as reduced virulence. AaAtg1 physically interacts with core autophagy proteins AaAtg13 and AaAtg8, and its vacuolar degradation is AaAtg8-dependent. Structure-guided mutagenesis of the Atg8-family interacting motif (AIM) disrupts AaAtg1–AaAtg8 binding in yeast two-hybrid assays but not in bimolecular fluorescence complementation, suggesting partial functional retention in vivo . Intriguingly, AIM mutations do not impair autophagy; instead, some transformants exhibit elevated autophagic activity, suggesting a potential negative regulatory role of AIM in autophagy tuning. Conclusions These findings reveal a noncanonical feedback mechanism in which AaAtg8 facilitates AaAtg1 degradation to modulate autophagic output. Our study elucidates the structure–function relationship of AaAtg1 and uncovers a dual regulatory mechanism that coordinates autophagy progression and stress adaptation in the plant-pathogenic fungus.