Autophagy mediates the degradation of damaged proteins, organelles and pathogens, and plays a key role in health and disease. Thus, the identification of new mechanisms involved in the regulation of autophagy is of major interest. In particular, little is known about the role of lipids and lipid-binding proteins in the early steps of autophagosome biogenesis. Using target-agnostic, high-content, image-based identification of indicative phenotypic changes induced by small molecules, we have identified autogramins as a new class of autophagy inhibitor. Autogramins selectively target the recently discovered cholesterol transfer protein GRAM domain-containing protein 1A (GRAMD1A, which had not previously been implicated in autophagy), and directly compete with cholesterol binding to the GRAMD1A StART domain. GRAMD1A accumulates at sites of autophagosome initiation, affects cholesterol distribution in response to starvation and is required for autophagosome biogenesis. These findings identify a new biological function of GRAMD1A and a new role for cholesterol in autophagy.
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The authors declare that the data supporting the findings of this study are available within the paper and its supplementary information files. Additional raw data associated with all figures are available from the corresponding authors upon reasonable request. The atomic structure of the StART domain of GRAMD1C was deposited in the Protein Data Bank under the accession number 6GN5.
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This work was supported by the Max Planck Society (H.W.), DFG grant SPP 1623, ERC (ChemBioAP), Vetenskapsrådet (2018-04585) and the Knut and Alice Wallenberg Foundation (Y.-W.W). L.Laraia was supported by a fellowship from the Alexander von Humboldt Stiftung. D.P.C. is supported by a fellowship from the Canadian Institute of Health Research (MFE-152550). We thank S. Sievers and the Compound Management and Screening Center (COMAS), Dortmund, Germany, for compound screening. We thank R. Gasper-Schönenbrücher, K. Estel and the beamline staff for help with data collection at the SLS, Villigen, Switzerland. We thank S. Tooze for the kind gift of EGFP–WIPI2b cells. We acknowledge the Biochemical Imaging Center (BICU) at Umeå University and the National Microscopy Infrastructure, NMI (VR-RFI 2016-00968) for providing assistance in microscopy.
The authors declare no competing interests.
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Supplementary Tables 1–3 and Supplementary Figures 1–13
Mass spectrometry-based proteomics, raw data.
Kinase panel, complete data.
Live-cell imaging of HeLa cells simultaneously transfected with EGFP–WIPI1 and GRAMD1A–mCherry under starvation conditions.
Live-cell imaging of HeLa cells simultaneously transfected with EGFP–LC3 and GRAMD1A–mCherry under starvation conditions.
Additional live-cell imaging of HeLa cells simultaneously transfected with EGFP–LC3 and GRAMD1A–mCherry under starvation conditions.
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Laraia, L., Friese, A., Corkery, D.P. et al. The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis. Nat Chem Biol 15, 710–720 (2019). https://doi.org/10.1038/s41589-019-0307-5
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Protein & Cell (2021)
Nature Chemical Biology (2019)