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. Epub 2019 Feb 18.


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.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Autophagy*
  • Autophagy-Related Proteins / genetics
  • Autophagy-Related Proteins / metabolism*
  • Binding Sites / genetics
  • Cell Membrane / metabolism*
  • Endosomes / metabolism
  • HEK293 Cells
  • Humans
  • Membrane Lipids / metabolism
  • Mice
  • Microtubule-Associated Proteins / metabolism*
  • Protein Binding
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • RAW 264.7 Cells
  • Sequence Homology, Amino Acid


  • ATG16L1 protein, human
  • Autophagy-Related Proteins
  • MAP1LC3B protein, human
  • Membrane Lipids
  • Microtubule-Associated Proteins
  • Protein Isoforms