Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole

Abstract

Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.

p62-mediated phase separation at the intersection of the ubiquitin-proteasome system and autophagy

“…This activity is conferred by the cargo receptors upon recognition of their cargo. For example, in S. cerevisiae, the Atg19 cargo receptor recruits the scaffold protein Atg11 and the Atg12-Atg5-Atg16 complex to the precursor amminopeptidase I ( prApe1), cargo in the cytoplasm-to-vacuole targeting (Cvt) pathway (Fracchiolla et al, 2016;Kamber et al, 2015;Shintani et al, 2002;Torggler et al, 2016). Optineurin and NDP52 recruit the autophagy machinery to damaged mitochondria in mammalian cells (Lazarou et al, 2015).…”

Canonical and noncanonical functions of ULK/Atg1

“…Interaction with Atg13 mediates the self-association and activation of Atg1 via autophosphorylation of the evolutionarily conserved threonine 226 residue [8,9]. Meanwhile, the scaffolding complexes promote clustering and stimulation of Atg1’s catalytic activity [10••]: Atg11–cargo complexes recruit Atg1 to the vacuole to promote sequestration of cargo for selective autophagy, and the Atg17–Atg29–Atg31 complex recruits Atg1–Atg13 to the preautophagosomal structure (PAS) for bulk autophagy. Thus, spatiotemporal activation of Atg1 is regulated via association with Atg13 and the autophagy or Cvt-specific scaffolding complexes.…”

Liquid–liquid phase separation in autophagy

“…The kinase activity of Atg1 is low under nutrient-rich conditions but is activated upon autophagy induction (Kamada et al, 2000;Torggler et al, 2016). Activated Atg1 phosphorylates various Atg proteins, such as Atg2 and Atg9, that are important for autophagy initiation (Noda and Fujioka, 2015).…”