Intrinsic lipid binding activity of ATG16L1 supports efficient membrane anchoring and autophagy.

Leo J Dudley,Tim Michelberger,Ainara G Cabodevilla,Agata N Makar,Douglas R Houston,Xuejun Jiang,Joseph A Marsh,Sascha Martens,Noor Gammoh,Martin Sztacho

doi:10.15252/embj.2018100554

Abstract

Membrane targeting of autophagy‐related complexes is an important step that regulates their activities and prevents their aberrant engagement on non‐autophagic membranes. ATG16L1 is a core autophagy protein implicated at distinct phases of autophagosome biogenesis. In this study, we dissected the recruitment of ATG16L1 to the pre‐autophagosomal structure (PAS) and showed that it requires sequences within its coiled‐coil domain (CCD) dispensable for homodimerisation. Structural and mutational analyses identified conserved residues within the CCD of ATG16L1 that mediate direct binding to phosphoinositides, including phosphatidylinositol 3‐phosphate (PI3P). Mutating putative lipid binding residues abrogated the localisation of ATG16L1 to the PAS and inhibited LC3 lipidation. On the other hand, enhancing lipid binding of ATG16L1 by mutating negatively charged residues adjacent to the lipid binding motif also resulted in autophagy inhibition, suggesting that regulated recruitment of ATG16L1 to the PAS is required for its autophagic activity. Overall, our findings indicate that ATG16L1 harbours an intrinsic ability to bind lipids that plays an essential role during LC3 lipidation and autophagosome maturation.

Highlights

While some organelles, such as the endoplasmic reticulum (ER) or mitochondria, are generated by growing and budding from preexisting organelles, autophagosome formation is initiated through the de novo nucleation of membranous structures (Joshi et al, 2017)
We have identified highly conserved sequences within the coiled-coil domain (CCD) of ATG16L1 that mediate its direct interaction with lipids, thereby enhancing its pre-autophagosomal structures (PAS) localisation and autophagic activity
Biochemical fractionation further confirmed the finding that ATG16L1 accumulates in membrane fractions in the absence of ATG5 (Fig 1C), as well as in the absence of ATG3 (Gammoh et al, 2013). These results suggest a role for ATG16L1 in the membrane targeting of the ATG5 complex

Summary

Introduction

While some organelles, such as the endoplasmic reticulum (ER) or mitochondria, are generated by growing and budding from preexisting organelles, autophagosome formation is initiated through the de novo nucleation of membranous structures (Joshi et al, 2017). This process requires the activity of distinct protein complexes that act to relay upstream signals in order to facilitate the growth of precursor membranes known as pre-autophagosomal structures (PAS; Lamb et al, 2013). FIP200, a component of the ULK1 complex, and WIPI2b can both directly interact with ATG16L1, providing a mechanism for the localisation of the ATG5 complex to the PAS during mTORC1 inactivation (Gammoh et al, 2013; Nishimura et al, 2013; Dooley et al, 2014)

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