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Assembly and dynamics of the autophagy-initiating Atg1 complex

Stjepanovic, Goran, Davies, Christopher W., Stanley, Robin E., Ragusa, Michael J., Kim, Do Jin, Hurley, James H.
Proceedings of the National Academy of Sciences of the United States of America 2014 v.111 no.35 pp. 12793-12798
Saccharomyces cerevisiae, autophagy, mass spectrometry, models
The autophagy-related 1 (Atg1) complex of Saccharomyces cerevisiae has a central role in the initiation of autophagy following starvation and TORC1 inactivation. The complex consists of the protein kinase Atg1, the TORC1 substrate Atg13, and the trimeric Atg17–Atg31–Atg29 scaffolding subcomplex. Autophagy is triggered when Atg1 and Atg13 assemble with the trimeric scaffold. Here we show by hydrogen–deuterium exchange coupled to mass spectrometry that the mutually interacting Atg1 early autophagy targeting/tethering domain and the Atg13 central domain are highly dynamic in isolation but together form a stable complex with ∼100-nM affinity. The Atg1–Atg13 complex in turn binds as a unit to the Atg17–Atg31–Atg29 scaffold with ∼10-μM affinity via Atg13. The resulting complex consists primarily of a dimer of pentamers in solution. These results lead to a model for autophagy initiation in which Atg1 and Atg13 are tightly associated with one another and assemble transiently into the pentameric Atg1 complex during starvation.