Deficiency of the autophagy gene ATG16L1 induces insulin resistance through KLHL9/KLHL13/CUL3-mediated IRS1 degradation

J Biol Chem. 2019 Nov 1;294(44):16172-16185. doi: 10.1074/jbc.RA119.009110. Epub 2019 Sep 12.


Connections between deficient autophagy and insulin resistance have emerged, however, the mechanism through which reduced autophagy impairs insulin-signaling remains unknown. We examined mouse embryonic fibroblasts lacking Atg16l1 (ATG16L1 KO mouse embryonic fibroblasts (MEFs)), an essential autophagy gene, and observed deficient insulin and insulin-like growth factor-1 signaling. ATG16L1 KO MEFs displayed reduced protein content of insulin receptor substrate-1 (IRS1), pivotal to insulin signaling, whereas IRS1myc overexpression recovered downstream insulin signaling. Endogenous IRS1 protein content and insulin signaling were restored in ATG16L1 KO mouse embryonic fibroblasts (MEF) upon proteasome inhibition. Through proximity-dependent biotin identification (BioID) and co-immunoprecipitation, we found that Kelch-like proteins KLHL9 and KLHL13, which together form an E3 ubiquitin (Ub) ligase complex with cullin 3 (CUL3), are novel IRS1 interactors. Expression of Klhl9 and Klhl13 was elevated in ATG16L1 KO MEFs and siRNA-mediated knockdown of Klhl9, Klhl13, or Cul3 recovered IRS1 expression. Moreover, Klhl13 and Cul3 knockdown increased insulin signaling. Notably, adipose tissue of high-fat fed mice displayed lower Atg16l1 mRNA expression and IRS1 protein content, and adipose tissue KLHL13 and CUL3 expression positively correlated to body mass index in humans. We propose that ATG16L1 deficiency evokes insulin resistance through induction of Klhl9 and Klhl13, which, in complex with Cul3, promote proteasomal IRS1 degradation.

Keywords: Akt PKB; E3 ubiquitin ligase; Kelch-like gene family; autophagy; autophagy-related protein 16L1 (ATG16L1); cell signaling; insulin; insulin receptor substrate 1 (IRS-1); insulin signaling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Autophagy / physiology
  • Autophagy-Related Proteins / deficiency*
  • Autophagy-Related Proteins / genetics
  • Autophagy-Related Proteins / metabolism
  • Cullin Proteins / metabolism
  • Fibroblasts / metabolism
  • Genes, Regulator
  • HEK293 Cells
  • Humans
  • Insulin / metabolism
  • Insulin Receptor Substrate Proteins / metabolism*
  • Insulin Resistance*
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Proteins / metabolism
  • Signal Transduction
  • Ubiquitin-Protein Ligase Complexes / metabolism


  • ATG16L1 protein, human
  • Atg16l1 protein, mouse
  • Autophagy-Related Proteins
  • Cul3 protein, mouse
  • Cullin Proteins
  • IRS1 protein, human
  • Insulin
  • Insulin Receptor Substrate Proteins
  • Irs1 protein, mouse
  • KLHL9 protein, human
  • Proteins
  • Ubiquitin-Protein Ligase Complexes