WDR41

WDR41 is a β-propeller (WD-repeat) protein that functions as the lysosomal targeting module of the C9ORF72-SMCR8-WDR41 complex, a regulator of autophagy and lysosomal signaling (PMID:27103069, PMID:27193190, PMID:27617292, PMID:27494456, PMID:32848248). WDR41 constitutively assembles with C9ORF72 and SMCR8 into a heterotrimer—which can further dimerize into a dimer of heterotrimers—binding the DENN domain of SMCR8 through its C-terminal helix and N-terminal β-strand without directly contacting C9ORF72 (PMID:32848248, PMID:32303654). WDR41 is required to recruit the complex to lysosomes upon amino acid starvation, doing so by directly engaging the lysosomal cationic amino acid transporter PQLC2 via a short peptide motif in a flexible WDR41 loop that inserts into a cavity exposed by the inward-facing conformation of PQLC2, a transceptor mechanism whose binding site is masked when PQLC2 transports arginine, lysine, or histidine (PMID:31851326, PMID:33597295). This recruitment is starvation-dependent but independent of mTORC1 inhibition or autophagy induction, and constitutive lysosomal targeting of C9ORF72 bypasses the requirement for WDR41 in mTORC1 activation (PMID:29995611). At the lysosome the C9ORF72-SMCR8 subcomplex acts as a GTPase-activating protein principally for ARF-family GTPases—with SMCR8 Arg147 inserting as the catalytic arginine finger into the active site—and with ~10-fold lower efficiency for RAB8A and RAB11A (PMID:32848248, PMID:32303654, PMID:34145292). The complex associates with the FIP200/ULK1 autophagy-initiation machinery, and loss of WDR41 phenocopies SMCR8 loss, causing prolonged TLR signaling, accumulation of LysoTracker-positive vesicles, and delayed phagosome maturation (PMID:27193190, PMID:30442666). Separately, WDR41 restrains tumor characteristics in triple-negative breast cancer cells by suppressing AKT/GSK-3β/β-catenin signaling (PMID:32394588).

1. 2016 High

   Established that WDR41 is not an isolated protein but an obligate member of a C9ORF72-SMCR8 complex with GTPase-regulating activity controlling autophagy, defining its core functional context.

   Evidence Reciprocal Co-IP, in vitro GTPase/GEF assays, and autophagy flux assays across multiple cell systems including neuronal cultures and Smcr8 knockout mice

   PMID:27103069 PMID:27193190 PMID:27494456 PMID:27617292

   Open questions at the time

   • Early assays reported GEF activity toward RAB8a/RAB39b, leaving the directionality (GEF vs GAP) of the catalytic activity unresolved
   • Did not define which subunit carries catalytic activity
   • Did not localize the complex's site of action
2. 2016 Medium

   Placed the complex upstream of autophagy initiation by demonstrating physical and functional coupling to the FIP200/ULK1 machinery and ATG101.

   Evidence Co-IP with ULK1 complex components, subcellular fractionation/immunofluorescence, and Smcr8 knockout mouse autophagy assays

   PMID:27193190 PMID:27617292

   Open questions at the time

   • Golgi localization reported by immunofluorescence conflicts with later lysosomal recruitment models
   • Mechanism of ULK1 regulation not resolved at molecular level
3. 2018 High

   Defined WDR41's specific role as the subunit required for amino acid starvation-dependent lysosomal recruitment of the complex, separable from mTORC1 and autophagy induction.

   Evidence WDR41 knockout human and mouse cells, immunofluorescence localization, mTORC1 signaling assays, TLR/phagosome readouts, and constitutive lysosomal-targeting rescue

   PMID:29995611 PMID:30442666

   Open questions at the time

   • The lysosomal receptor engaged by WDR41 was not yet identified
   • How amino acid status is sensed was unknown
4. 2020 High

   Solved the architecture of the complex, showing WDR41 is a β-propeller binding the SMCR8 DENN domain and that this contact drives starvation-dependent lysosomal localization, while reclassifying the catalytic activity as GAP toward ARF-family and RAB8A/RAB11A GTPases.

   Evidence Cryo-EM structures (including 3.2 Å), Arg147 mutagenesis, and in vitro GAP assays with ARF, RAB8A, and RAB11A

   PMID:32303654 PMID:32848248

   Open questions at the time

   • Substrate-bound catalytic geometry not yet visualized
   • Relative substrate preference among GTPases not quantified
5. 2020 High

   Identified the lysosomal receptor PQLC2 as the direct WDR41 partner that links amino acid availability to complex recruitment.

   Evidence Reciprocal Co-IP of WDR41 with PQLC2, amino acid competition assays, and lysosomal localization assays

   PMID:31851326

   Open questions at the time

   • Structural basis of the WDR41-PQLC2 contact not yet defined
   • Downstream consequences of disrupting this interaction in vivo not established
6. 2021 High

   Resolved the molecular basis of substrate selectivity and the transceptor mechanism, showing a WDR41 loop motif reads out PQLC2 conformation and that SMCR8 Arg147 inserts into the ARF1 active site, with ARF as the primary substrate.

   Evidence Substrate-bound cryo-EM of ARF1-GDP-BeF3- complex, active-site and interface mutagenesis, comparative ARF1 vs RAB8A GAP assays, and PQLC2 conformational analysis with WDR41 loop mutagenesis

   PMID:33597295 PMID:34145292

   Open questions at the time

   • Physiological ARF effectors regulated by the complex not mapped
   • How GAP output integrates with ULK1/autophagy regulation unclear
7. 2020 Medium

   Linked WDR41 to tumor suppression in triple-negative breast cancer through the AKT/GSK-3β/β-catenin axis, extending its relevance beyond autophagy/lysosomal signaling.

   Evidence WDR41 knockdown/overexpression in MDA-MB-231 cells, AKT inhibitor rescue, xenografts, and Western blot for pathway components

   PMID:32394588

   Open questions at the time

   • No direct binding mechanism connecting WDR41 to AKT pathway components
   • Whether this depends on the C9ORF72-SMCR8 complex is unknown
   • Single cell-line context

• How the lysosomal GAP activity of the complex is mechanistically coupled to autophagy initiation, mTORC1 signaling, and the breast cancer AKT phenotype remains unresolved.
• The relevant ARF GTPase effectors at the lysosome are unidentified
• It is unclear whether WDR41's tumor-suppressive role operates through the canonical complex or independently