Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy

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 phosphatidylethano...

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Main Authors: Lisa M Strong, Chunmei Chang, Julia F Riley, C Alexander Boecker, Thomas G Flower, Cosmo Z Buffalo, Xuefeng Ren, Andrea KH Stavoe, Erika LF Holzbaur, James H Hurley
Format: Article
Language:English
Published: eLife Sciences Publications Ltd 2021-09-01
Series:eLife
Subjects:
Online Access:https://elifesciences.org/articles/70372
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author Lisa M Strong
Chunmei Chang
Julia F Riley
C Alexander Boecker
Thomas G Flower
Cosmo Z Buffalo
Xuefeng Ren
Andrea KH Stavoe
Erika LF Holzbaur
James H Hurley
author_facet Lisa M Strong
Chunmei Chang
Julia F Riley
C Alexander Boecker
Thomas G Flower
Cosmo Z Buffalo
Xuefeng Ren
Andrea KH Stavoe
Erika LF Holzbaur
James H Hurley
author_sort Lisa M Strong
collection DOAJ
description 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-bladedß -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 ß-propeller blades 2 and 3. Mutation of residues at the interface reduces or blocks the recruitment of ATG12–5–16 L1 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 ATG12–5–16 L1 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.
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spelling doaj.art-3680dcace3464a88937af5f1d613cc8d2022-12-22T04:28:58ZengeLife Sciences Publications LtdeLife2050-084X2021-09-011010.7554/eLife.70372Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagyLisa M Strong0https://orcid.org/0000-0002-4293-8131Chunmei Chang1https://orcid.org/0000-0002-5607-7985Julia F Riley2https://orcid.org/0000-0001-8518-9786C Alexander Boecker3https://orcid.org/0000-0001-9701-5273Thomas G Flower4https://orcid.org/0000-0002-7890-6473Cosmo Z Buffalo5Xuefeng Ren6Andrea KH Stavoe7https://orcid.org/0000-0002-4073-4565Erika LF Holzbaur8https://orcid.org/0000-0001-5389-4114James H Hurley9https://orcid.org/0000-0001-5054-5445Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States; Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, United StatesDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States; Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, United StatesAligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, United States; Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United StatesAligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, United States; Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United StatesDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United StatesDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United StatesDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United StatesDepartment of Neurobiology and Anatomy, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, United StatesAligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, United States; Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United StatesDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States; Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, United StatesAutophagy 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-bladedß -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 ß-propeller blades 2 and 3. Mutation of residues at the interface reduces or blocks the recruitment of ATG12–5–16 L1 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 ATG12–5–16 L1 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.https://elifesciences.org/articles/70372autophagymitophagyparkinson's diseasex-ray crystallographyvesicle reconstitutionLC3
spellingShingle Lisa M Strong
Chunmei Chang
Julia F Riley
C Alexander Boecker
Thomas G Flower
Cosmo Z Buffalo
Xuefeng Ren
Andrea KH Stavoe
Erika LF Holzbaur
James H Hurley
Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy
eLife
autophagy
mitophagy
parkinson's disease
x-ray crystallography
vesicle reconstitution
LC3
title Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy
title_full Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy
title_fullStr Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy
title_full_unstemmed Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy
title_short Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy
title_sort structural basis for membrane recruitment of atg16l1 by wipi2 in autophagy
topic autophagy
mitophagy
parkinson's disease
x-ray crystallography
vesicle reconstitution
LC3
url https://elifesciences.org/articles/70372
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