Atg1 kinase regulates autophagosome‐vacuole fusion by controlling SNARE bundling

Autophagy mediates the degradation of cytoplasmic material. Upon autophagy induction, autophagosomes form a sealed membrane around the cargo and fuse with the lytic compartment to release the cargo for degradation. In order to avoid premature fusion of immature autophagosomal membranes with the lytic compartment, this process needs to be tightly regulated. Several factors mediating autophagosome–vacuole fusion have recently been identified. In budding yeast, autophagosome–vacuole fusion requires the R‐SNARE Ykt6 on the autophagosome, together with the three Q‐SNAREs Vam3, Vam7, and Vti1 on the vacuole. However, how these SNAREs are regulated during the fusion process is poorly understood. In this study, we investigate the regulation of Ykt6. We found that Ykt6 is directly phosphorylated by Atg1 kinase, which keeps this SNARE in an inactive state. Ykt6 phosphorylation prevents SNARE bundling by disrupting its interaction with the vacuolar SNAREs Vam3 and Vti1, thereby preventing premature autophagosome–vacuole fusion. These findings shed new light on the regulation of autophagosome–vacuole fusion and reveal a further step in autophagy controlled by the Atg1 kinase.