Structural basis for membrane recruitment of ATG16L1 by WIPI2 in Autophagy
- University of California, Berkeley, United States
- University of Pennsylvania, United States
- The University of Texas Health Science Center at Houston McGovern Medical School, United States
Abstract
Autophagy is a cellular process that degrades cytoplasmic cargo by engulfing it in a double membrane vesicle, known as the autophagosome, and delivering it to the lysosome. The ATG12-5-16L1 complex is responsible for conjugating members of the ubiquitin-like ATG8 protein family to phosphatidylethanolamine in the growing autophagosomal membrane, known as the phagophore. ATG12-5-16L1 is recruited to the phagophore by a subset of the phosphatidylinositol 3-phosphate-binding seven bladed â-propeller WIPI proteins. We determined the crystal structure of WIPI2d in complex with the WIPI2 interacting region (W2IR) of ATG16L1 comprising residues 207-230 at 1.85 Å resolution. The structure shows that the ATG16L1 W2IR adopts an alpha helical conformation and binds in an electropositive and hydrophobic groove between WIPI2 â-propeller blades 2 and 3. Mutation of residues at the interface reduces or blocks the recruitment of ATG12-5-16L1 and the conjugation of the ATG8 protein LC3B to synthetic membranes. Interface mutants show a decrease in starvation-induced autophagy. Comparisons across the four human WIPIs suggest that WIPI1 and 2 belong to a W2IR-binding subclass responsible for localizing ATG12-5-16L1 and driving ATG8 lipidation, whilst WIPI3 and 4 belong to a second W34IR-binding subclass responsible for localizing ATG2, and so directing lipid supply to the nascent phagophore. The structure provides a framework for understanding the regulatory node connecting two central events in autophagy initiation, the action of the autophagic PI 3-kinase complex on the one hand, and ATG8 lipidation on the other.
Data availability
Coordinates and structure factors have been deposited in the Protein Data Bank under accession code PDB 7MU2. Protocols have been deposited in protocols.io. Plasmids developed for this study will be deposited at Addgene.org. GUV source data are being deposited in Zenodo.
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Structural Basis for Membrane Recruitment of ATG16L1 by WIPI2 in Autophagy Raw GUV DataZenodo, doi:10.5281/zenodo.5387892.
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Crystal Structure of WIPI2 in complex with W2IR of ATG16L1Protein Data Bank, 7MU2.
Article and author information
Author details
C Alexander Boecker
Funding
Aligning Science Across Parkinson's (ASAP-000350)
- Erika LF Holzbaur
- James H Hurley
NIGMS (R01 GM111730)
- James H Hurley
NINDS (R00 NS109286)
- Andrea KH Stavoe
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Wade Harper, Harvard Medical School, United States
Version history
- Preprint posted: May 14, 2021 (view preprint)
- Received: May 14, 2021
- Accepted: September 1, 2021
- Accepted Manuscript published: September 10, 2021 (version 1)
- Version of Record published: September 21, 2021 (version 2)
- Version of Record updated: November 17, 2021 (version 3)
Copyright
© 2021, Strong et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Structural basis for membrane recruitment of ATG16L1 by WIPI2 in Autophagy
eLife 10:e70372.
https://doi.org/10.7554/eLife.70372
Further reading
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