VCP/p97 UFMylation stabilizes BECN1 and facilitates the initiation of autophagy.

ABSTRACT

Macroautophagy/autophagy is essential for the degradation and recycling of cytoplasmic materials. The initiation of this process is determined by phosphatidylinositol-3-kinase (PtdIns3K) complex, which is regulated by factor BECN1 (beclin 1). UFMylation is a novel ubiquitin-like modification that has been demonstrated to modulate several cellular activities. However, the role of UFMylation in regulating autophagy has not been fully elucidated. Here, we found that VCP/p97 is UFMylated on K109 by the E3 UFL1 (UFM1 specific ligase 1) and this modification promotes BECN1 stabilization and assembly of the PtdIns3K complex, suggesting a role for VCP/p97 UFMylation in autophagy initiation. Mechanistically, VCP/p97 UFMylation stabilizes BECN1 through ATXN3 (ataxin 3)-mediated deubiquitination. As a key component of the PtdIns3K complex, stabilized BECN1 facilitates assembly of this complex. Re-expression of VCP/p97, but not the UFMylation-defective mutant, rescued the VCP/p97 depletion-induced increase in MAP1LC3B/LC3B protein expression. We also showed that several pathogenic VCP/p97 mutations identified in a variety of neurological disorders and cancers were associated with reduced UFMylation, thus implicating VCP/p97 UFMylation as a potential therapeutic target for these diseases. Abbreviation ATG14autophagy related 14; Baf A1bafilomycin A1;CMT2Y Charcot-Marie-Toothdisease, axonal, 2Y; CYB5R3 cytochromeb5 reductase 3; DDRGK1 DDRGK domain containing 1; DMEMDulbecco'smodified Eagle's medium;ERendoplasmic reticulum; FBSfetalbovine serum;FTDALS6frontotemporaldementia and/or amyotrophic lateral sclerosis 6; IBMPFD1inclusion bodymyopathy with early-onset Paget disease with or withoutfrontotemporal dementia 1; LC-MS/MSliquid chromatography tandem mass spectrometry; MAP1LC3B/LC3Bmicrotubule associated protein 1 light chain 3 beta; MS massspectrometry; NPLOC4 NPL4 homolog, ubiquitin recognition factor;PIK3C3 phosphatidylinositol 3-kinase catalytic subunit type 3;PIK3R4 phosphoinositide-3-kinase regulatory subunit 4; PtdIns3Kphosphatidylinositol 3-kinase; RPL26 ribosomal protein L26; RPN1ribophorin I; SQSTM1/p62 sequestosome 1; UBA5 ubiquitin likemodifier activating enzyme 5; UFC1 ubiquitin-fold modifierconjugating enzyme 1; UFD1 ubiquitin recognition factor in ERassociated degradation 1; UFL1 UFM1 specific ligase 1; UFM1ubiquitin fold modifier 1; UFSP2 UFM1 specific peptidase 2; UVRAGUV radiation resistance associated; VCP/p97 valosin containingprotein; WT wild-type.