Regulation of LC3 lipidation by the autophagy-specific class III phosphatidylinositol-3 kinase complex

Mol Biol Cell. 2019 Apr 15;30(9):1098-1107. doi: 10.1091/mbc.E18-11-0743. Epub 2019 Feb 27.

Abstract

Autophagy is a conserved eukaryotic pathway critical for cellular adaptation to changes in nutrition levels and stress. The class III phosphatidylinositol (PI)3-kinase complexes I and II (PI3KC3-C1 and -C2) are essential for autophagosome initiation and maturation, respectively, from highly curved vesicles. We used a cell-free reaction that reproduces a key autophagy initiation step, LC3 lipidation, as a biochemical readout to probe the role of autophagy-related gene (ATG)14, a PI3KC3-C1-specific subunit implicated in targeting the complex to autophagy initiation sites. We reconstituted LC3 lipidation with recombinant PI3KC3-C1, -C2, or various mutant derivatives added to extracts derived from a CRISPR/Cas9-generated ATG14-knockout cell line. Both complexes C1 and C2 require the C-terminal helix of VPS34 for activity on highly curved membranes. However, only complex C1 supports LC3 lipidation through the curvature-targeting amphipathic lipid packing sensor (ALPS) motif of ATG14. Furthermore, the ALPS motif and VPS34 catalytic activity are required for downstream recruitment of WD-repeat domain phosphoinositide-interacting protein (WIPI)2, a protein that binds phosphatidylinositol 3-phosphate and its product phosphatidylinositol 3, 5-bisphosphate, and a WIPI-binding protein, ATG2A, but do not affect membrane association of ATG3 and ATG16L1, enzymes contributing directly to LC3 lipidation. These data reveal the nuanced role of the ATG14 ALPS in membrane curvature sensing, suggesting that the ALPS has additional roles in supporting LC3 lipidation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagy / physiology
  • Autophagy-Related Proteins
  • Carrier Proteins
  • Class III Phosphatidylinositol 3-Kinases / metabolism*
  • HEK293 Cells
  • Humans
  • Lipid Metabolism
  • Membrane Proteins / metabolism
  • Microtubule-Associated Proteins / metabolism*
  • Phosphatidylinositol Phosphates / metabolism

Substances

  • Autophagy-Related Proteins
  • Carrier Proteins
  • MAP1LC3A protein, human
  • Membrane Proteins
  • Microtubule-Associated Proteins
  • Phosphatidylinositol Phosphates
  • phosphatidylinositol 3-phosphate
  • Class III Phosphatidylinositol 3-Kinases