Autophagy is a conserved pathway for cell survival during starvation and for clearance of damaged, toxic, or excess organelles and inclusions from the cell. Bulk cytosol, organelles, and other autophagic cargo are taken up within a double membrane vesicle known as the autophagosome. Autophagy is central to cell function and human health, yet the physical basis of autophagosome biogenesis is almost completely unknown. The proposed research will yield, in near-atomistic detail, the mechanism for the earliest stage in autophagosome biogenesis. We hypothesize that the key event in the initiation of the double membrane of the autophagosome is the clustering of high curvature vesicles containing the membrane protein Atg9 at the preautophagosomal structure (PAS). This event is orchestrated by the Atg1 complex, which in yeast consists of Atg1, Atg13, Atg17, Atg29, and Atg31. The latter three comprise the Atg17-Atg31-Atg29 subcomplex, which is the first to arrive at the PAS. We determined the structure of the Atg17-Atg31-Atg29 complex, revealing a remarkable S-shaped double crescent and suggesting a model for vesicle scaffolding. We also discovered that the C-terminal early autophagy targeting/tethering (EAT) domain of Atg1 is a potent sensor for high membrane curvature and tethers high curvature vesicles. These insights led us to a detailed hypothesis for the scaffolding and tethering of the vesicles that initiate autophagosome biogenesis.
The specific aims of this project are as follows: 1. we will understand how the Atg1 EAT domain tethers highly curved vesicles. Tethering will be assayed in vitro and correlated with function in yeast cells. The structural basis for tethering will be determined using scanning mutagenesis and hydrogen-deuterium exchange coupled to mass spectrometry. 2. The three dimensional structure of the Atg1 complex will be determined by SAXS and EM, and structural interfaces mapped by scanning mutagenesis to develop a pseudo-atomic model for the complex. 3. In a stringent test of the central hypothesis, an Atg9 lipopeptide based model for precursor vesicles will be used to reconstitute the early PAS in vitro. The model system will be used to probe whether Atg13 dephosphorylation during starvation triggers the assembly of a tethering-competent form of the Atg1 complex. Together, these aims will flesh out the main early events of autophagy initiation in mechanistic and structural detail.

Public Health Relevance

Autophagy is an ancient and conserved mechanism for cell survival under starvation and stress, with profound connections to aging, cancer, neurodegenerative diseases, and other complex diseases. Using novel protein expression, structural, and biochemical approaches, we have circumvented these obstacles for the Atg1 protein complex, and made key discoveries concerning the early non-catalytic role of this complex in tethering high curvature vesicles. This project will unveil the mechanism of autophagy initiation and regulation by the Atg1 complex in sufficient near-atomistic detail to support structurally and biochemically-based therapeutic development.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Membrane Biology and Protein Processing (MBPP)
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Ainsztein, Alexandra M
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University of California Berkeley
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Lin, Mary G; Schöneberg, Johannes; Davies, Christopher W et al. (2018) The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion. Mol Biol Cell 29:1228-1237
Bahrami, Amir Houshang; Lin, Mary G; Ren, Xuefeng et al. (2017) Scaffolding the cup-shaped double membrane in autophagy. PLoS Comput Biol 13:e1005817
Stjepanovic, Goran; Baskaran, Sulochanadevi; Lin, Mary G et al. (2017) Unveiling the role of VPS34 kinase domain dynamics in regulation of the autophagic PI3K complex. Mol Cell Oncol 4:e1367873
Stjepanovic, Goran; Baskaran, Sulochanadevi; Lin, Mary G et al. (2017) Vps34 Kinase Domain Dynamics Regulate the Autophagic PI 3-Kinase Complex. Mol Cell 67:528-534.e3
Hurley, James H; Young, Lindsey N (2017) Mechanisms of Autophagy Initiation. Annu Rev Biochem 86:225-244
Young, Lindsey N; Cho, Kelvin; Lawrence, Rosalie et al. (2016) Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy. Proc Natl Acad Sci U S A 113:8224-9
Hurley, James H; Nogales, Eva (2016) Next-generation electron microscopy in autophagy research. Curr Opin Struct Biol 41:211-216
Lin, Mary G; Hurley, James H (2016) Structure and function of the ULK1 complex in autophagy. Curr Opin Cell Biol 39:61-8
Davies, Christopher W; Stjepanovic, Goran; Hurley, James H (2015) How the Atg1 complex assembles to initiate autophagy. Autophagy 11:185-6
Köfinger, Jürgen; Ragusa, Michael J; Lee, Il-Hyung et al. (2015) Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site. Structure 23:809-818

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