Influence of ULK1 activity on the memory of ATG101 auto-activation dynamics

Abstract

The initiation of autophagy is marked by the prompt convergence of initiation proteins to form super molecular complexes in spatially-defined autophagic hubs. The recruitment and activation of the ULK-kinase complex is a pivotal event in starting the initiation cascade. ULK complex-component ATG101 is required for initiating autophagy in mammalian cells, but its function is unknown. Its HORMA domain interacts with the HORMA domain of ATG13 and transmembrane protein ATG9A to collectively form the essential autophagy initiation complex ATG9A-ATG13-ATG101. ATG101 has structurally malleable elements, reminiscent of topological conversions used in related metamorphic HORMA domain proteins to control the rate of complex formation. To elucidate the function of ATG101, we monitored the interaction kinetics of ATG101 with ATG13 and ATG9A, and observed that the interaction of ATG101 with ATG9A and ATG13 is exceptionally slow. Dramatic acceleration of complex formation is observed upon a change in the fold of ATG101 induced by its transient homo-dimerization, which in turn is initiated by phosphorylation by the ULK1 kinase. In an auto-catalytic mechanism, ATG101 dimers create a positive feedback to propagate activation to further ATG101 molecules in the absence of ULK1 activity. Despite the competitive nature of the interaction interfaces, homo-dimerization of ATG101 surprisingly accelerates its association to ATG13. Memory of ATG101 activation persists for many hours after dephosphorylation and continues to accelerate the assembly of the ATG9A-ATG13-ATG101 complex. Overall, this work proposes an unusual regulatory mechanism where UKL1 initiates an ATG101 auto activation cascade, whose memory creates a responsive positive feedback that dictates the assembly rate of a key complex in autophagy initiation.