Affinage

WDR44

WD repeat-containing protein 44 · UniProt Q5JSH3

Length
913 aa
Mass
101.4 kDa
Annotated
2026-04-28
26 papers in source corpus 11 papers cited in narrative 12 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

WDR44 is a Rab11 effector that functions at the intersection of endosomal recycling, exocytic trafficking, and ciliogenesis. It binds GTP-Rab11 through an N-terminal Rab11-binding domain that engages the switch I, switch II, and interswitch regions of Rab11, while its C-terminal WD40 repeats mediate intramolecular autoinhibition and interdomain regulation; phosphorylation by Akt and SGK3 stabilizes the Rab11–WDR44 complex and reorganizes the Rab11-binding surface (PMID:10077598, PMID:36463963, PMID:31665227, PMID:31204173). WDR44 localizes to tubular recycling endosomes at ER membrane contact sites (via VAPA/B and GRAF2) where it suppresses ciliogenesis by competing with pro-ciliogenic Rab11 effectors such as FIP3/Rabin8, and it is required for GRAF2-dependent tubular endosome formation and Rab8/10/11-dependent export of cargoes including E-cadherin and MMP14 (PMID:32344433, PMID:31204173, PMID:38536441). Missense variants in the WDR44 WD40 domain cause X-linked ciliopathy through protein misfolding, proteasomal degradation, and disrupted interdomain regulation of Rab11 binding (PMID:38191484).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 1999 High

    Establishing WDR44 as a GTP-specific Rab11 effector resolved the identity of downstream partners mediating Rab11-dependent recycling and defined the N-terminal region as the Rab11-binding domain with autoinhibition by the C-terminal WD40 repeats.

    Evidence In vitro binding assays with GTP/GDP-loaded Rab11, domain truncation constructs blocking transferrin recycling, and rescue by co-expression of non-prenylatable Rab11 in MDCK/HeLa cells

    PMID:10077598 PMID:10464283

    Open questions at the time
    • Structural basis of the Rab11–WDR44 interface was unknown
    • Mechanism of WD40-mediated autoinhibition was not defined at atomic resolution
    • Physiological cargo specificity of WDR44 was uncharacterized
  2. 2019 High

    Connecting WDR44 to ciliogenesis revealed it as a phosphorylation-regulated negative regulator that sequesters Rab11 away from pro-ciliogenic effectors, establishing how growth factor signaling (LPA/PI3K/Akt) suppresses cilium formation at the molecular level.

    Evidence WDR44 siRNA promoting ciliogenesis and Rabin8 preciliary trafficking, phosphomimetic mutant blocking ciliogenesis, Co-IP showing Akt-dependent stabilization of Rab11a–WDR44 in RPE-1 cells; independent phosphoproteomics identifying Ser346 as an SGK3-specific site

    PMID:31204173 PMID:31665227

    Open questions at the time
    • How phosphorylation structurally reorganizes the Rab11-binding interface was unclear
    • Whether Akt and SGK3 phosphorylation have additive or distinct functional effects on ciliogenesis was not tested
    • In vivo validation in animal models of ciliogenesis was lacking
  3. 2020 High

    Identifying WDR44 as a GRAF2 binding partner at ER–endosome membrane contact sites explained how tubular recycling endosomes form and revealed WDR44's role in exocytic trafficking of E-cadherin, MMP14, and CFTR via Rab8/10/11-dependent pathways.

    Evidence Reciprocal Co-IP for direct GRAF2–WDR44 binding, colocalization with VAPA/B at ER–endosome contacts, siRNA knockdown disrupting tubular endosomes and cargo export in multiple cell lines

    PMID:32344433

    Open questions at the time
    • Whether WDR44 directly bridges GRAF2 and VAPA/B or acts through separate interactions was not resolved
    • The lipid requirements at membrane contact sites were not defined
    • Relative contribution of WDR44 to different cargo routes was not quantified
  4. 2022 High

    Structural and biochemical dissection of the Rab11–WDR44 interface revealed a more extensive switch II engagement compared to FIP3, providing a molecular explanation for effector competition and showing that SGK3 phosphorylation reorganizes the binding surface.

    Evidence AlphaFold2 modeling validated by HDX-MS, extensive site-directed mutagenesis of conserved residues, in vitro binding and kinase assays

    PMID:36463963

    Open questions at the time
    • No high-resolution experimental crystal or cryo-EM structure of the Rab11–WDR44 complex exists
    • Mechanism by which WD40-domain autoinhibition is relieved remains structurally unresolved
  5. 2024 High

    Discovery that WDR44 WD40 domain missense variants cause X-linked ciliopathy established pathogenic relevance and demonstrated that WD40 misfolding leads to proteasomal degradation, loss of interdomain regulation, and aberrant Rab11 binding correlating with disease severity.

    Evidence Patient variant characterization, zebrafish ciliopathy modeling, ciliogenesis assays, Co-IP of Rab11 binding, proteasome inhibitor rescue

    PMID:38191484

    Open questions at the time
    • How increased Rab11 binding from misfolded WD40 variants mechanistically disrupts ciliogenesis initiation is not fully elucidated
    • Genotype–phenotype correlations across a larger patient cohort are needed
  6. 2024 Medium

    Identification of BLTP2 as a genetic interactor and co-resident at ER–tubular endosome contact sites placed WDR44 within a lipid-transfer-associated membrane contact site complex that co-suppresses ciliogenesis.

    Evidence siRNA knockdown of BLTP2 enhancing ciliogenesis and eliminating WDR44-positive tubules, colocalization microscopy in HeLa and RPE-1 cells

    PMID:38536441

    Open questions at the time
    • Whether BLTP2 directly binds WDR44 or acts through shared membrane domains is unknown
    • The lipid species transferred at these contact sites and their effect on ciliogenesis are uncharacterized
    • Independent replication in additional cell types or in vivo models is lacking
  7. 2025 Medium

    Reconstitution of AP-4-mediated TGN vesicle formation revealed WDR44 as an essential cytosolic regulator, extending its trafficking roles beyond recycling endosomes to TGN export.

    Evidence In vitro vesicle formation assay with AP4ε-deficient HeLa cells coupled with label-free quantitative mass spectrometry

    PMID:41032520

    Open questions at the time
    • The specific molecular function of WDR44 in AP-4 vesicle budding is not defined
    • Whether WDR44 acts through Rab11 or independently in AP-4 export is unknown
    • Validation in intact cells with AP-4 cargo trafficking readouts is needed

Open questions

Synthesis pass · forward-looking unresolved questions
  • Major unresolved questions include the high-resolution structure of the Rab11–WDR44 complex, the mechanism by which WD40 autoinhibition is relieved, the identity of lipid species at WDR44-positive ER–endosome contact sites, and whether WDR44's lysosomal role in α-synuclein aggregation represents a disease-relevant function in Parkinson's disease.
  • No experimental high-resolution structure of the full-length WDR44 or Rab11–WDR44 complex
  • Mechanistic basis of WDR44 function in AP-4-mediated export is undefined
  • WDR44's role in α-synuclein aggregation at lysosomes awaits peer-reviewed validation

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 4 GO:0098772 molecular function regulator activity 2
Localization
GO:0005768 endosome 3 GO:0005783 endoplasmic reticulum 2 GO:0005829 cytosol 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 5 R-HSA-1852241 Organelle biogenesis and maintenance 3 R-HSA-162582 Signal Transduction 2
Partners
AKT1BLTP2FIP3GRAF2RAB11ASGK3VAPAVAPB
Complex memberships
GRAF2–WDR44 complexRab11–WDR44 complex

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 WDR44 (Rab11BP/Rabphilin-11) was identified as a downstream effector of Rab11 small GTPase, binding preferentially to GTP-Rab11 over GDP-Rab11 via its N-terminal region, with specificity for Rab11 over other Rab and Rho small G proteins. Protein isolation from bovine brain, in vitro binding assays with GTP- and GDP-loaded Rab11, colocalization by immunofluorescence in MDCK and HeLa cells The Journal of biological chemistry High 10077598 10464283
1999 The Rab11-binding site of WDR44 (Rab11BP) is located between residues 334–504 and is autoinhibited/masked by the C-terminal WD40 domain region; a truncated form lacking WD40 domains (aa 1–504) acts as a dominant negative to block transferrin recycling, phenocopying dominant-negative Rab11. Overexpression of truncated WDR44 constructs in transfected cells, transferrin recycling assay, rescue by co-expression of non-prenylatable Rab11 Proceedings of the National Academy of Sciences of the United States of America High 10077598
1999 WDR44 (Rabphilin-11) localizes to perinuclear regions (Golgi/recycling endosomes) and along microtubules oriented toward membrane lamellipodia; overexpression of its C-terminal fragment (aa 607–730) lacking the Rab11-binding domain reduced transferrin accumulation at perinuclear regions and inhibited cell migration. Immunofluorescence colocalization, nocodazole treatment, overexpression of dominant-negative C-terminal fragment, transferrin recycling assay, cell migration assay The Journal of biological chemistry Medium 10464283
2019 Akt phosphorylates WDR44 and stabilizes the Rab11a–WDR44 interaction; a WDR44 phosphomimetic mutant (at the Akt site) blocks ciliogenesis, and WDR44 depletion promotes Rabin8 preciliary trafficking and ciliogenesis-initiating events at the mother centriole. This identifies WDR44 as a negative regulator of ciliogenesis downstream of LPA/LPAR1/PI3K/Akt signaling. WDR44 siRNA knockdown, phosphomimetic mutant overexpression, Co-IP of Rab11a–WDR44 complex, live imaging of Rabin8 preciliary trafficking, ciliogenesis assays in RPE-1 cells Developmental cell High 31204173
2019 SGK3 kinase phosphorylates WDR44 at Ser346 in vivo and in vitro; this phosphorylation site is poorly phosphorylated by Akt due to an unfavorable n+1 residue, defining WDR44 as an SGK3-specific endosomal substrate. Phosphoproteomic screens (genetic and pharmacological), in vitro kinase assay with SGK3 and Akt, phospho-site mapping by mass spectrometry The Biochemical journal High 31665227
2020 WDR44 was identified as a direct binding partner of GRAF2 and localizes to a subset of tubular endosomes that are closely aligned with the ER via binding to VAPA/B (membrane contact sites); in the absence of GRAF2, WDR44-positive tubules are not observed. WDR44 and GRAF2 are essential for export of neosynthesized E-cadherin, MMP14, and CFTR ΔF508 via Rab8/10/11-dependent pathways. Co-immunoprecipitation (direct binding), colocalization by fluorescence microscopy, siRNA knockdown of GRAF2/WDR44 with cargo trafficking assay, dominant-negative mutant overexpression The Journal of cell biology High 32344433
2022 WDR44's Rab11-binding domain interacts with switch I, switch II, and the interswitch region of Rab11; HDX-MS revealed WDR44 forms a more extensive interface with the switch II helix of Rab11 compared to effector FIP3. Extensive mutagenesis of conserved WDR44 residues identified complex-disrupting mutations and defined the molecular basis of Rab11 specificity. SGK3 phosphorylation of WDR44 reorganizes the Rab11-binding surface. AlphaFold2 structural modeling, hydrogen/deuterium exchange mass spectrometry (HDX-MS), extensive mutagenesis, in vitro binding assays, SGK3 kinase assay The Journal of biological chemistry High 36463963
2024 Missense variants in WDR44's WD40 repeat domain cause X-linked ciliopathy by impairing ciliogenesis initiation; pathogenic missense variants lead to protein misfolding of WDR autonomous repeats and proteasomal degradation. Disease severity correlates with increased RAB11 binding. Interdomain interactions between the WDR domain and the NH2-terminal RAB11-binding domain (RBD) are disrupted by patient variants. Patient variant characterization, zebrafish modeling, ciliogenesis assays, Co-IP of Rab11 binding, proteasome inhibitor rescue, domain interaction studies Nature communications High 38191484
2024 BLTP2, a putative lipid transfer protein, genetically interacts with WDR44 in suppressing ciliogenesis; both proteins localize to membrane contact sites between the ER and tubular endosome network. BLTP2 depletion enhanced ciliogenesis and in the absence of BLTP2, WDR44-positive tubules were not observed. siRNA knockdown of BLTP2 with ciliogenesis assay, genetic interaction with WDR44 KD, fluorescence microscopy colocalization in HeLa and RPE-1 cells Molecular biology of the cell Medium 38536441
2025 WDR44 was identified as a cytosolic regulator essential for AP-4-mediated TGN export, discovered through an in vitro vesicle formation assay coupled with quantitative mass spectrometry. In vitro vesicle formation assay with AP4ε-deficient HeLa cells, label-free quantitative mass spectrometry Proceedings of the National Academy of Sciences of the United States of America Medium 41032520
2023 In C. elegans, the WDR44 ortholog SYM-4/WDR44 colocalizes with SYM-3/FAM102A to intracellular and membrane-associated puncta and likely functions in a complex involved in intracellular trafficking during embryonic morphogenesis; however, no evidence was found for a critical role in apical deposition of extracellular matrix components FBN-1 or NOAH-1. Fluorescence microscopy colocalization, proteomics, loss-of-function genetic analysis in C. elegans embryos Biology open Medium 37345480
2026 WDR44 localizes to the lysosomal membrane and drives de novo α-synuclein aggregation at that site; WDR44 knockdown markedly reduced α-synuclein aggregation in neuronal cultures and in vivo, while WDR44 overexpression enhanced aggregation in PD patient-derived iPSC neurons. WDR44 aberrantly accumulates in PD patient brains and colocalizes with Lewy body inclusions. Optogenetic-induced protein aggregation system, WDR44 siRNA knockdown, WDR44 overexpression in iPSC-derived neurons, in vivo models, immunofluorescence colocalization with lysosomal markers and Lewy bodies bioRxivpreprint Medium 41993512

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1999 Rab11BP/Rabphilin-11, a downstream target of rab11 small G protein implicated in vesicle recycling. The Journal of biological chemistry 81 10464283
1999 Identification of a putative effector protein for rab11 that participates in transferrin recycling. Proceedings of the National Academy of Sciences of the United States of America 74 10077598
2019 Akt Regulates a Rab11-Effector Switch Required for Ciliogenesis. Developmental cell 61 31204173
2015 FBN-1, a fibrillin-related protein, is required for resistance of the epidermis to mechanical deformation during C. elegans embryogenesis. eLife 56 25798732
1999 Functional overlap between the mec-8 gene and five sym genes in Caenorhabditis elegans. Genetics 42 10471705
2020 GRAF2, WDR44, and MICAL1 mediate Rab8/10/11-dependent export of E-cadherin, MMP14, and CFTR ΔF508. The Journal of cell biology 31 32344433
2008 Comprehensive spatiotemporal transcriptomic analyses of the ganglionic eminences demonstrate the uniqueness of its caudal subdivision. Molecular and cellular neurosciences 31 18316204
2003 Pathogenic Specialization and Pathotype Distribution of Puccinia hordei in Australia, 1992 to 2001. Plant disease 24 30812545
2004 The identities of sym-2, sym-3 and sym-4, three genes that are synthetically lethal with mec-8 in Caenorhabditis elegans. Genetics 19 15579686
2020 Discovery of Molecular DNA Methylation-Based Biomarkers through Genome-Wide Analysis of Response Patterns to BCG for Bladder Cancer. Cells 15 32764425
2019 Phosphoproteomics reveals that the hVPS34 regulated SGK3 kinase specifically phosphorylates endosomal proteins including Syntaxin-7, Syntaxin-12, RFIP4 and WDR44. The Biochemical journal 15 31665227
2024 Bridge-like lipid transfer protein family member 2 suppresses ciliogenesis. Molecular biology of the cell 13 38536441
1993 Five Nodulation Mutants of White Sweetclover (Melilotus alba Desr.) Exhibit Distinct Phenotypes Blocked at Root Hair Curling, Infection Thread Development, and Nodule Organogenesis. Plant physiology 13 12231990
2014 Genetic mapping of a new race specific resistance allele effective to Puccinia hordei at the Rph9/Rph12 locus on chromosome 5HL in barley. BMC plant biology 9 25526867
2024 Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation. Nature communications 8 38191484
2023 Effectors of anterior morphogenesis in C. elegans embryos. Biology open 8 37345480
2022 A new deep learning technique reveals the exclusive functional contributions of individual cancer mutations. The Journal of biological chemistry 6 35753349
2022 Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11. The Journal of biological chemistry 6 36463963
2019 Membrane Trafficking Decisions Regulate Primary Cilium Formation. Trends in cell biology 5 31221497
2025 The IAA-Producing Rhizobacterium Bacillus sp. SYM-4 Promotes Maize Growth and Yield. Plants (Basel, Switzerland) 4 40508264
2025 Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution. The New phytologist 4 40682296
2026 The Application of Saline-Alkali-Tolerant Growth-Promoting Endophytic Bacteria for Enhancing the Saline-Alkali Tolerance of Alfalfa. Biology 0 41892234
2026 WDR44 drives de novo α-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease. bioRxiv : the preprint server for biology 0 41993512
2025 Uncovering cargo clients and accessory factors of AP-1 and AP-4 through vesicle proteomics. Proceedings of the National Academy of Sciences of the United States of America 0 41032520
2024 WDR44 Loss-of-Function Promoter Deletion in a Male Newborn With a Ciliopathy Phenotype. American journal of medical genetics. Part A 0 39235309
2023 Pathways that affect anterior morphogenesis in C. elegans embryos. bioRxiv : the preprint server for biology 0 37163004