Distinct functions of ATG16L1 isoforms in membrane binding and LC3B lipidation in autophagy-related processes

Nat Cell Biol. 2019 Mar;21(3):372-383. doi: 10.1038/s41556-019-0274-9.

Alf Håkon Lystad ¹ ², Sven R Carlsson ³, Laura R de la Ballina ⁴ ⁵, Karlina J Kauffman ⁶, Shanta Nag ⁶, Tamotsu Yoshimori ⁷, Thomas J Melia ⁶, Anne Simonsen ⁸ ⁹

Affiliations

1 Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. a.h.lystad@medisin.uio.no.
2 Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. a.h.lystad@medisin.uio.no.
3 Department of Medical Biochemistry and Biophysics, University of Umeå, Umeå, Sweden. sven.carlsson@umu.se.
4 Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
5 Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
6 Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
7 Department of Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
8 Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. anne.simonsen@medisin.uio.no.
9 Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. anne.simonsen@medisin.uio.no.

PMID: 30778222 DOI: 10.1038/s41556-019-0274-9

Abstract

Covalent modification of LC3 and GABARAP proteins to phosphatidylethanolamine in the double-membrane phagophore is a key event in the early phase of macroautophagy, but can also occur on single-membrane structures. In both cases this involves transfer of LC3/GABARAP from ATG3 to phosphatidylethanolamine at the target membrane. Here we have purified the full-length human ATG12-5-ATG16L1 complex and show its essential role in LC3B/GABARAP lipidation in vitro. We have identified two functionally distinct membrane-binding regions in ATG16L1. An N-terminal membrane-binding amphipathic helix is required for LC3B lipidation under all conditions tested. By contrast, the C-terminal membrane-binding region is dispensable for canonical Autophagy but essential for VPS34-independent LC3B lipidation at perturbed endosomes. We further show that the ATG16L1 C-terminus can compensate for WIPI2 depletion to sustain lipidation during starvation. This C-terminal membrane-binding region is present only in the β-isoform of ATG16L1, showing that ATG16L1 isoforms mechanistically distinguish between different LC3B lipidation mechanisms under different cellular conditions.

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