Missing WD40 Repeats in ATG16L1 Delays Canonical Autophagy and Inhibits Noncanonical Autophagy

Int J Mol Sci. 2024 Apr 19;25(8):4493. doi: 10.3390/ijms25084493.


Canonical autophagy is an evolutionarily conserved process that forms double-membrane structures and mediates the degradation of long-lived proteins (LLPs). Noncanonical autophagy (NCA) is an important alternative pathway involving the formation of microtubule-associated protein 1 light chain 3 (LC3)-positive structures that are independent of partial core autophagy proteins. NCA has been defined by the conjugation of ATG8s to single membranes (CASM). During canonical autophagy and NCA/CASM, LC3 undergoes a lipidation modification, and ATG16L1 is a crucial protein in this process. Previous studies have reported that the WDR domain of ATG16L1 is not necessary for canonical autophagy. However, our study found that WDR domain deficiency significantly impaired LLP degradation in basal conditions and slowed down LC3-II accumulation in canonical autophagy. We further demonstrated that the observed effect was due to a reduced interaction between ATG16L1 and FIP200/WIPI2, without affecting lysosome function or fusion. Furthermore, we also found that the WDR domain of ATG16L1 is crucial for chemical-induced NCA/CASM. The results showed that removing the WDR domain or introducing the K490A mutation in ATG16L1 significantly inhibited the NCA/CASM, which interrupted the V-ATPase-ATG16L1 axis. In conclusion, this study highlights the significance of the WDR domain of ATG16L1 for both canonical autophagy and NCA functions, improving our understanding of its role in autophagy.

Keywords: ATG16L1; WDR domain; canonical autophagy; noncanonical autophagy.

MeSH terms

  • Autophagy* / genetics
  • Autophagy-Related Proteins* / genetics
  • Autophagy-Related Proteins* / metabolism
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Lysosomes / metabolism
  • Membrane Proteins*
  • Microtubule-Associated Proteins* / genetics
  • Microtubule-Associated Proteins* / metabolism
  • Phosphate-Binding Proteins*
  • WD40 Repeats* / genetics


  • Autophagy-Related Proteins
  • ATG16L1 protein, human
  • Microtubule-Associated Proteins
  • Carrier Proteins
  • WIPI2 protein, human
  • Membrane Proteins
  • Phosphate-Binding Proteins

Grants and funding

This research was funded by the National Natural Science Foundation of China (31970699, 31671437), the Guangdong Basic and Applied Basic Research Foundation (2021A1515010766, 2019A1515011030), the Guangdong Provincial Key Laboratory of Construction Foundation (2019B030301005).