{"gene":"DNAJC13","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2001,"finding":"RME-8 (DNAJC13 ortholog in C. elegans) is required for receptor-mediated and fluid-phase endocytosis; it localizes to the limiting membrane of large endosomes and functions in endosomal trafficking prior to the lysosome, as demonstrated by loss-of-function mutants that fail to accumulate endocytosis markers in coelomocytes.","method":"Genetic analysis of C. elegans mutants, fluorescence localization, endocytosis marker uptake assays","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean loss-of-function genetic analysis with defined cellular phenotype, localization by live imaging, replicated across cell types","pmids":["11451999"],"is_preprint":false},{"year":2004,"finding":"Drosophila Rme-8 interacts specifically with Hsc70-4 via its J-domain (biochemical and genetic interaction), and is required for clathrin-dependent endocytosis; rme-8 mutants phenocopy Hsc70-4 mutants, placing them in a common pathway.","method":"Drosophila genetic screen (dominant-negative dynamin interaction), biochemical pulldown, genetic epistasis, endocytosis tracer uptake assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal biochemical and genetic evidence, multiple orthogonal methods in one study","pmids":["15051737"],"is_preprint":false},{"year":2005,"finding":"Mammalian RME-8 (DNAJC13) was identified in clathrin-coated vesicle proteomics from rat liver; affinity selection assays identify Hsc70 as its major binding partner via the DnaJ domain; RME-8 is tightly associated with microsomal membranes and co-localizes with endosomal markers. siRNA knockdown does not affect transferrin endocytosis but reduces EGF internalization and disrupts trafficking of cation-independent mannose 6-phosphate receptor and cathepsin D sorting.","method":"Proteomic analysis of clathrin-coated vesicles, affinity selection (pulldown), subcellular fractionation, co-localization, siRNA knockdown with cargo trafficking readouts","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (proteomics, pulldown, KD with multiple cargo readouts) in single study on mammalian protein","pmids":["16179350"],"is_preprint":false},{"year":2008,"finding":"Human RME-8 (DNAJC13) is a peripheral membrane protein associated via its N-terminal region, localizing primarily to early endosomes (co-localizes with early endosomal markers, confirmed by immunoelectron microscopy). Expression of C-terminally truncated mutants perturbs transferrin recycling and EGF degradation through early endosomes. It does not co-localize with late endosomal markers.","method":"Cloning and biochemical characterization, immunoelectron microscopy, dominant-active Rab co-localization, truncation mutant overexpression, endocytic pathway assays","journal":"Cell structure and function","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (immuno-EM, localization, functional mutants, trafficking assays) in single study","pmids":["18256511"],"is_preprint":false},{"year":2008,"finding":"RME-8 depletion leads to increased EGFR degradation (decreased steady-state EGFR levels at both surface and intracellular pools), implicating DNAJC13 in sorting decisions at endosomes that protect EGFR from degradation; transferrin receptor levels are unaffected.","method":"siRNA knockdown, receptor level quantification, degradation rate assays","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, clean KD with specific cargo phenotype but single method approach","pmids":["18307993"],"is_preprint":false},{"year":2009,"finding":"C. elegans RME-8 associates with retromer component SNX-1; loss of SNX-1, RME-8, or the clathrin chaperone Hsc70/HSP-1 leads to over-accumulation of endosomal clathrin, reduced clathrin dynamics, and missorting of MIG-14/Wntless to the lysosome instead of the Golgi. This defines a mechanism whereby retromer regulates endosomal clathrin dynamics through RME-8 and Hsc70.","method":"Co-immunoprecipitation, genetic epistasis in C. elegans, live fluorescence imaging of clathrin dynamics, cargo missorting assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, genetic epistasis, multiple cargo readouts, replicated across several mutants","pmids":["19763082"],"is_preprint":false},{"year":2013,"finding":"The DNAJC13 p.Asn855Ser mutation segregates with autosomal dominant Parkinson's disease; cellular analysis shows this mutation confers a toxic gain-of-function and impairs endosomal transport. DNAJC13 immunoreactivity was detected within Lewy body inclusions.","method":"Exome sequencing, Sanger sequencing, case-control genotyping, cellular functional analysis, immunohistochemistry","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic segregation plus cellular gain-of-function analysis, but mechanistic detail of cellular assay is limited in abstract","pmids":["24218364"],"is_preprint":false},{"year":2014,"finding":"RME-8 (DNAJC13) interacts with FAM21 (a subunit of the WASH complex) and with SNX1; loss of RME-8 causes altered kinetics of SNX1 membrane association and a pronounced increase in highly branched endosomal tubules containing WASH-complex-dependent cargo, indicating that RME-8 coordinates WASH complex activity with the membrane-tubulating function of sorting nexins.","method":"Co-immunoprecipitation, siRNA knockdown, live fluorescence imaging of endosomal tubules, cargo localization assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP, KD with multiple orthogonal phenotypic readouts (tubulation, cargo sorting), single lab","pmids":["24643499"],"is_preprint":false},{"year":2015,"finding":"In Drosophila, Rme-8 depletion causes Notch receptor accumulation in enlarged tubulated Rab4-positive endosomes and impairs Notch signaling. Simultaneous depletion of retromer component Vps26 or ESCRT-0 components Hrs/Stam with Rme-8 causes ectopic Notch activation, placing Rme-8 upstream and in opposition to these complexes in regulating Notch recycling versus degradation.","method":"Drosophila genetic epistasis (double knockdown/mutants), live and fixed fluorescence imaging, Notch signaling readouts","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic epistasis with multiple double-mutant combinations, specific endosomal localization phenotype, defined signaling readout","pmids":["26169355"],"is_preprint":false},{"year":2017,"finding":"SNX-1 and RME-8 together oppose the assembly of ESCRT-0/HGRS-1 degradative microdomains on endosomes; loss of snx-1 or rme-8 (but not other retromer components snx-3 or vps-35) increases endosomal coverage and intensity of HGRS-1-labeled microdomains and increases membrane-bound HGRS-1. Loss of hgrs-1 has little to no effect on SNX-1/RME-8 microdomains, indicating directionality of the interaction. The antagonism between recycling (RME-8/SNX-1) and degradative (ESCRT-0) microdomains is conserved in human HeLa cells.","method":"C. elegans genetics with in vivo fluorescence imaging of endosomal microdomains, siRNA knockdown in HeLa cells, membrane fractionation","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic specificity demonstrated by multiple retromer component comparisons, directionality tested, conserved in mammalian cells","pmids":["28053230"],"is_preprint":false},{"year":2018,"finding":"The PD-linked N855S mutant DNAJC13 causes α-synuclein accumulation in the endosomal compartment due to defective cargo trafficking from early to late/recycling endosomes. In human αSYN transgenic Drosophila, mutant DNAJC13 increases insoluble αSYN, induces dopaminergic neurodegeneration, rough eye phenotype, and age-dependent locomotor impairment.","method":"Cell-based trafficking assays, Drosophila in vivo model with behavioral and pathological readouts, biochemical fractionation","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple readouts (cell biology and in vivo), but mechanism of αSYN accumulation inferred from trafficking defects rather than direct biochemical reconstitution","pmids":["29309590"],"is_preprint":false},{"year":2019,"finding":"The DNAJC13 p.Asn855Ser knock-in mutation in primary cortical neurons (from a mouse knock-in model) significantly increases SNX1-enriched endosomal tubule formation without affecting SNX1 puncta density or WASH-retromer assembly, indicating a dominant-negative gain-of-function that disrupts SNX1 membrane-tubulation dynamics.","method":"Knock-in mouse model, primary cortical neuron cultures, fluorescence imaging of SNX1 tubules, quantitative morphometry","journal":"Neuroscience letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — novel knock-in model, specific cellular phenotype, but single lab and limited mechanistic detail in abstract","pmids":["31082451"],"is_preprint":false},{"year":2020,"finding":"DNAJC13 acts as a positive modulator of autophagy; knockdown reduces autophagic flux in C. elegans and human cell lines and impairs ATG9A trafficking from the recycling endosome, reducing ATG9A co-localization at LC3B-positive autophagic puncta. The PD-associated N855S mutant fails to enhance autophagy upon overexpression.","method":"siRNA knockdown and overexpression in human cells, C. elegans RNAi, ATG9A localization by fluorescence microscopy, autophagic flux assays (LC3B puncta, autophagy markers)","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (KD, OE, localization), two model systems, single lab","pmids":["32322926"],"is_preprint":false},{"year":2022,"finding":"Structure-function analysis of C. elegans RME-8 identified that: (1) the C-terminus is important for microdomain localization and substrate binding; (2) N-terminal sequences beyond the PH-like domain are important for endosome recruitment; (3) IWN4 and IWN3 domains are important for autoinhibitory DNAJ domain binding, with IWN3 playing a critical role in HRS/HGRS-1 uncoating activity. AlphaFold structural modeling combined with in vivo mutation analysis supports a model whereby SNX-1 and IWN domains control RME-8 conformation and productive exposure of its DNAJ domain, with SNX-1 acting as an activator and target of RME-8 uncoating activity.","method":"Random and site-directed mutagenesis, AlphaFold structural modeling, in vivo C. elegans fluorescence imaging of endosomal microdomains, phylogenetic analysis","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — mutagenesis with in vivo functional readouts and structural modeling, but structure is computational (AlphaFold) not experimental crystal/cryo-EM","pmids":["36279308"],"is_preprint":false},{"year":2023,"finding":"Loss of RME-8/DNAJC13 in C. elegans mechanosensory neurons and primary mouse cortical neurons causes accumulation of grossly elongated autolysosomal tubules, indicating a role in autophagic lysosome reformation (ALR). In C. elegans, this phenotype is shared with bec-1/beclin, vps-15/PIK3R4, and dyn-1/dynamin mutants (known ALR regulators). Loss of RME-8 causes severe depletion of clathrin from neuronal autolysosomes, phenocopying bec-1 and vps-15 mutants. Loss of RME-8/DNAJC13 also reduces autophagic flux in both systems.","method":"C. elegans genetics and live fluorescence imaging, primary mouse cortical neuron culture, autophagic flux assays, clathrin localization","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis across multiple mutants, conserved phenotype in two independent biological systems (C. elegans and mouse neurons), multiple readouts","pmids":["37942902"],"is_preprint":false},{"year":2024,"finding":"Genome-wide CRISPR interference screen identified DNAJC13 as a regulator of δ-opioid receptor (DOR) trafficking through the endosomal-lysosomal pathway; DNAJC13 controls trafficking of multiple GPCRs and regulates the composition of the endosomal proteome and endosomal homeostasis.","method":"Genome-wide CRISPRi screen using GPCR-APEX2/AUR trafficking biosensor, validation by loss-of-function with multiple GPCR trafficking readouts, quantitative proteomics of endosomal compartment","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genome-wide screen validated with orthogonal methods (multiple GPCRs, proteomics), rigorous biosensor approach, single lab","pmids":["39223388"],"is_preprint":false},{"year":2025,"finding":"DNAJC13 localizes to endosomes through its N-terminal PH-like domain binding to PI(3)P; the J domain (HPD catalytic triad) and a conserved YLT motif in the disordered C-terminus act as negative regulators of this localization. Mutation of either motif enhances endosomal localization and PI(3)P binding in vitro. The PH-like domain binds PI(3)P weakly in isolation and requires oligomerization for efficient PI(3)P binding and endosomal localization. Overexpression of derepressed mutants causes endosomal clustering and loss of membrane protein cargo recycling.","method":"Structure-function mutagenesis, PI(3)P binding assays in vitro, quantitative cell imaging, overexpression phenotypic analysis, quantitative proteomics","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro binding assay with mutagenesis, cell imaging, functional readout (cargo recycling), multiple orthogonal methods in one study","pmids":["40737286"],"is_preprint":false},{"year":2025,"finding":"The DNAJC13 N855S variant is less stable than wild-type protein and shows accelerated degradation. It fails to rescue impaired autophagy in DNAJC13 knockdown cells (loss-of-function), exerts a dominant-negative effect on cation-independent mannose-6-phosphate receptor distribution (without affecting overall cathepsin D levels or activity), and chronic DNAJC13 knockdown reduces expression of autophagy induction and biogenesis genes.","method":"Stable knockdown cell lines, transient N855S mutant expression, biochemical stability assays, co-localization by fluorescence microscopy, cathepsin D activity assays, gene expression analysis","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple cell biological methods, but single lab and the dominant-negative mechanism is inferred from co-localization rather than direct biochemical reconstitution","pmids":["40717240"],"is_preprint":false}],"current_model":"DNAJC13/RME-8 is an endosome-associated Hsc70 co-chaperone that localizes to early endosomes via its N-terminal PH-like domain binding to PI(3)P (regulated by autoinhibitory interactions involving its J domain HPD triad and C-terminal YLT motif requiring oligomerization for efficient membrane binding), where it associates with the retromer component SNX1 and the WASH complex subunit FAM21 to regulate endosomal clathrin dynamics through Hsc70 recruitment, promotes retrograde cargo recycling to the Golgi while opposing ESCRT-0-mediated degradative microdomain assembly, controls SNX1 membrane tubulation, regulates ATG9A trafficking and autophagic lysosome reformation by maintaining clathrin at autolysosome membranes, and controls GPCR and growth factor receptor sorting through the endosomal-lysosomal pathway; the Parkinson's disease-linked p.N855S mutation acts as both a dominant-negative and loss-of-function variant causing increased SNX1 tubulation, impaired endosomal cargo trafficking, α-synuclein accumulation, and reduced autophagy."},"narrative":{"mechanistic_narrative":"DNAJC13 (RME-8) is an endosome-associated DnaJ/Hsc70 co-chaperone that governs the balance between cargo recycling and degradation at the endosomal membrane [PMID:11451999, PMID:19763082]. It is recruited as a peripheral membrane protein to early endosomes through its N-terminal PH-like domain, which binds PI(3)P; this localization is held in check by autoinhibitory contacts involving the J-domain HPD triad and a conserved C-terminal YLT motif, and efficient membrane binding requires oligomerization, with derepressing mutations enhancing PI(3)P binding and endosomal clustering at the cost of cargo recycling [PMID:40737286]. At the membrane it engages Hsc70 through its DnaJ domain to drive clathrin uncoating dynamics [PMID:15051737, PMID:16179350], working together with the retromer-associated sorting nexin SNX1 and the WASH-complex subunit FAM21 to control SNX1 membrane tubulation and the sorting of cargo away from degradation [PMID:19763082, PMID:24643499]. DNAJC13 and SNX1 oppose the assembly of ESCRT-0 (HRS/HGRS-1) degradative microdomains, thereby favoring retrograde and recycling itineraries over lysosomal delivery, a conserved antagonism that determines the fate of cargoes including Wntless, EGFR, Notch, and multiple GPCRs [PMID:19763082, PMID:28053230, PMID:26169355, PMID:39223388]. Beyond classical endosomal sorting, DNAJC13 is a positive modulator of autophagy: it supports ATG9A trafficking from the recycling endosome and maintains clathrin at autolysosomal membranes to enable autophagic lysosome reformation [PMID:32322926, PMID:37942902]. The p.Asn855Ser substitution segregates with autosomal-dominant Parkinson's disease, acting as a combined loss-of-function and dominant-negative variant that destabilizes the protein, increases SNX1 tubulation, impairs cargo trafficking, promotes α-synuclein accumulation, and reduces autophagy [PMID:24218364, PMID:29309590, PMID:31082451, PMID:40717240].","teleology":[{"year":2001,"claim":"Established that the gene product is required for endocytosis and acts at endosomes before the lysosome, defining its compartment and stage of action.","evidence":"Loss-of-function genetics and endocytic marker uptake in C. elegans coelomocytes with live localization","pmids":["11451999"],"confidence":"High","gaps":["No molecular partners or biochemical mechanism identified","Mammalian relevance not yet tested"]},{"year":2004,"claim":"Identified Hsc70 as a functional partner acting through the J-domain, placing the protein in a chaperone-dependent endocytic pathway.","evidence":"Drosophila genetic screen, biochemical pulldown, and genetic epistasis with Hsc70-4","pmids":["15051737"],"confidence":"High","gaps":["Substrate of the Hsc70 co-chaperone activity not defined","Endosomal clathrin role not yet shown"]},{"year":2005,"claim":"Showed the mammalian protein is a clathrin-coated-vesicle/endosome component binding Hsc70 and selectively required for EGF and lysosomal-enzyme receptor trafficking but not transferrin endocytosis.","evidence":"CCV proteomics, affinity selection, fractionation, and siRNA knockdown with multiple cargo readouts in mammalian cells","pmids":["16179350"],"confidence":"High","gaps":["Mechanism distinguishing affected vs unaffected cargo unknown","Membrane recruitment determinants undefined"]},{"year":2008,"claim":"Localized the human protein specifically to early (not late) endosomes via its N-terminal region and linked it to recycling and degradative cargo flux.","evidence":"Immuno-EM, Rab co-localization, and truncation-mutant trafficking assays in human cells","pmids":["18256511","18307993"],"confidence":"High","gaps":["Lipid/protein basis of N-terminal membrane binding not resolved","EGFR sorting mechanism inferred from steady-state levels"]},{"year":2009,"claim":"Defined a retromer-linked mechanism in which the protein, SNX1, and Hsc70 control endosomal clathrin dynamics to route cargo to the Golgi rather than the lysosome.","evidence":"Reciprocal co-IP, genetic epistasis, live clathrin imaging, and Wntless missorting assays in C. elegans","pmids":["19763082"],"confidence":"High","gaps":["Direct biochemistry of clathrin uncoating not reconstituted","Whether SNX1 binding is direct unresolved"]},{"year":2015,"claim":"Placed the protein upstream of and in opposition to retromer and ESCRT-0 in deciding receptor recycling versus degradation, using Notch as a readout.","evidence":"Drosophila double-knockdown genetic epistasis with Vps26 and Hrs/Stam plus Notch signaling assays","pmids":["26169355"],"confidence":"High","gaps":["Molecular basis of the antagonism not defined","Mammalian Notch relevance not tested here"]},{"year":2014,"claim":"Linked the protein physically to the WASH complex (FAM21) and SNX1, showing it restrains branched endosomal tubulation and coordinates WASH activity with sorting-nexin tubulation.","evidence":"Reciprocal co-IP, siRNA knockdown, live tubule imaging, and cargo localization","pmids":["24643499"],"confidence":"High","gaps":["Direct vs indirect FAM21 interaction not dissected","How it limits tubulation mechanistically unclear"]},{"year":2017,"claim":"Demonstrated that the protein with SNX1 directly opposes ESCRT-0 degradative microdomain assembly with defined directionality, conserved from worm to human.","evidence":"C. elegans microdomain imaging with retromer-component specificity, membrane fractionation, and HeLa knockdown","pmids":["28053230"],"confidence":"High","gaps":["Biochemical mechanism limiting HGRS-1 membrane binding unknown","How specificity for ESCRT-0 vs retromer is achieved unresolved"]},{"year":2022,"claim":"Resolved the domain logic of conformational autoinhibition, showing IWN domains and SNX-1 gate productive exposure of the DnaJ domain for uncoating activity.","evidence":"Mutagenesis with in vivo microdomain imaging and AlphaFold modeling in C. elegans","pmids":["36279308"],"confidence":"Medium","gaps":["Structure is computational, not experimental","Conformational model not validated biochemically in mammals"]},{"year":2025,"claim":"Defined PI(3)P binding by the PH-like domain as the membrane-recruitment mechanism, regulated by autoinhibitory J-domain and YLT motifs and dependent on oligomerization.","evidence":"In vitro PI(3)P binding with mutagenesis, quantitative imaging, and overexpression cargo-recycling assays","pmids":["40737286"],"confidence":"High","gaps":["Oligomerization stoichiometry and trigger not defined","How autoinhibition is relieved on the membrane unclear"]},{"year":2020,"claim":"Extended function to autophagy, showing the protein promotes autophagic flux by enabling ATG9A trafficking from the recycling endosome.","evidence":"Knockdown/overexpression in human cells and C. elegans RNAi with ATG9A localization and LC3B flux assays","pmids":["32322926"],"confidence":"Medium","gaps":["Direct role in ATG9A vesicle formation vs sorting unclear","Connection to clathrin/Hsc70 activity not tested"]},{"year":2023,"claim":"Showed the protein maintains clathrin at autolysosomes to drive autophagic lysosome reformation, integrating its clathrin-uncoating role with late autophagy.","evidence":"C. elegans and mouse cortical neuron imaging, autophagic flux assays, and epistasis with ALR regulators","pmids":["37942902"],"confidence":"High","gaps":["Whether Hsc70 co-chaperone activity drives ALR clathrin dynamics untested","Substrate at autolysosome undefined"]},{"year":2024,"claim":"Generalized the cargo-sorting role to GPCR trafficking and endosomal proteome homeostasis via an unbiased genome-wide screen.","evidence":"Genome-wide CRISPRi screen with GPCR trafficking biosensors and endosomal proteomics in human cells","pmids":["39223388"],"confidence":"High","gaps":["Whether GPCR effects are direct or via global endosomal disruption unresolved","Specific sorting step for each GPCR undefined"]},{"year":2013,"claim":"Connected the gene to autosomal-dominant Parkinson's disease through the p.N855S variant, with disease-relevant trafficking impairment and Lewy-body immunoreactivity.","evidence":"Exome/Sanger sequencing, case-control genotyping, cellular functional analysis, and immunohistochemistry","pmids":["24218364"],"confidence":"Medium","gaps":["Whether variant is gain- or loss-of-function not resolved here","Mechanistic basis of trafficking defect unclear"]},{"year":2018,"claim":"Linked the N855S variant mechanistically to α-synuclein endosomal accumulation and dopaminergic neurodegeneration in vivo.","evidence":"Cell trafficking assays and α-synuclein transgenic Drosophila with behavioral and pathological readouts","pmids":["29309590"],"confidence":"Medium","gaps":["α-synuclein accumulation inferred from trafficking defect, not direct biochemistry","Relationship to neuronal autophagy not tested here"]},{"year":2019,"claim":"Showed in a physiological knock-in neuron model that N855S acts as a dominant-negative on SNX1 tubulation without disrupting WASH-retromer assembly.","evidence":"Knock-in mouse primary cortical neurons with quantitative SNX1 tubule morphometry","pmids":["31082451"],"confidence":"Medium","gaps":["Single lab, limited mechanistic detail","Link from tubulation defect to neurodegeneration not established"]},{"year":2025,"claim":"Clarified the dual nature of N855S as both destabilizing/loss-of-function and dominant-negative across autophagy and cargo-distribution phenotypes.","evidence":"Stable knockdown rescue, mutant stability assays, M6PR co-localization, cathepsin D activity, and autophagy gene expression in human cells","pmids":["40717240"],"confidence":"Medium","gaps":["Dominant-negative mechanism inferred from co-localization, not reconstituted","Cause of accelerated degradation undefined"]},{"year":null,"claim":"How autoinhibition is relieved on the membrane to productively expose the DnaJ domain and direct Hsc70-driven clathrin uncoating toward specific substrates remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No experimental high-resolution structure of the full-length protein or its membrane-bound conformation","Direct uncoating substrates at endosomes vs autolysosomes not biochemically defined","Quantitative link between specific trafficking defects and Parkinson's pathogenesis incomplete"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2,5,13]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[16]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,7,9]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,3,5,16]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3,16]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[14]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,2,5,7,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[12,14]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[5,9,16]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[6,10,17]}],"complexes":[],"partners":["HSPA8","SNX1","FAM21"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75165","full_name":"DnaJ homolog subfamily C member 13","aliases":["Required for receptor-mediated endocytosis 8","RME-8"],"length_aa":2243,"mass_kda":254.4,"function":"Involved in membrane trafficking through early endosomes, such as the early endosome to recycling endosome transport implicated in the recycling of transferrin and the early endosome to late endosome transport implicated in degradation of EGF and EGFR (PubMed:18256511, PubMed:18307993). Involved in the regulation of endosomal membrane tubulation and regulates the dynamics of SNX1 on the endosomal membrane; via association with WASHC2 may link the WASH complex to the retromer SNX-BAR subcomplex (PubMed:24643499)","subcellular_location":"Early endosome; Early endosome membrane; Endosome membrane","url":"https://www.uniprot.org/uniprotkb/O75165/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAJC13","classification":"Not Classified","n_dependent_lines":172,"n_total_lines":1208,"dependency_fraction":0.1423841059602649},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000138246","cell_line_id":"CID000024","localizations":[{"compartment":"vesicles","grade":3},{"compartment":"cytoplasmic","grade":1}],"interactors":[{"gene":"FKBP15","stoichiometry":10.0},{"gene":"CCT5","stoichiometry":0.2},{"gene":"CCT4","stoichiometry":0.2},{"gene":"MAP3K4","stoichiometry":0.2},{"gene":"KIAA1033","stoichiometry":0.2},{"gene":"FAM21A","stoichiometry":0.2},{"gene":"CCDC53","stoichiometry":0.2},{"gene":"BAIAP2L1","stoichiometry":0.2},{"gene":"ARFGEF1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000024","total_profiled":1310},"omim":[{"mim_id":"617019","title":"TRANSMEMBRANE PROTEIN 230; TMEM230","url":"https://www.omim.org/entry/617019"},{"mim_id":"616361","title":"PARKINSON DISEASE 21; PARK21","url":"https://www.omim.org/entry/616361"},{"mim_id":"614334","title":"DNAJ/HSP40 HOMOLOG, 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all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DNAJC13"},"hgnc":{"alias_symbol":["RME8","KIAA0678"],"prev_symbol":[]},"alphafold":{"accession":"O75165","domains":[{"cath_id":"2.30.29.30","chopping":"10-99","consensus_level":"high","plddt":89.1814,"start":10,"end":99},{"cath_id":"2.30.29.30","chopping":"111-225","consensus_level":"medium","plddt":91.9198,"start":111,"end":225},{"cath_id":"2.30.29.30","chopping":"229-328","consensus_level":"medium","plddt":90.2212,"start":229,"end":328},{"cath_id":"1.25.10","chopping":"340-502","consensus_level":"medium","plddt":87.3718,"start":340,"end":502},{"cath_id":"-","chopping":"504-589","consensus_level":"medium","plddt":90.3759,"start":504,"end":589},{"cath_id":"-","chopping":"616-685_750-822","consensus_level":"medium","plddt":81.4593,"start":616,"end":822},{"cath_id":"-","chopping":"850-934","consensus_level":"high","plddt":82.5364,"start":850,"end":934},{"cath_id":"-","chopping":"1544-1685","consensus_level":"medium","plddt":87.7683,"start":1544,"end":1685},{"cath_id":"-","chopping":"1686-1734_1745-1814","consensus_level":"medium","plddt":84.0463,"start":1686,"end":1814},{"cath_id":"-","chopping":"2046-2065_2081-2199","consensus_level":"medium","plddt":81.6219,"start":2046,"end":2199},{"cath_id":"1.25.40","chopping":"1392-1409_1417-1542","consensus_level":"medium","plddt":90.4563,"start":1392,"end":1542}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75165","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75165-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75165-F1-predicted_aligned_error_v6.png","plddt_mean":82.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAJC13","jax_strain_url":"https://www.jax.org/strain/search?query=DNAJC13"},"sequence":{"accession":"O75165","fasta_url":"https://rest.uniprot.org/uniprotkb/O75165.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75165/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75165"}},"corpus_meta":[{"pmid":"24218364","id":"PMC_24218364","title":"DNAJC13 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fluid-phase endocytosis; it localizes to the limiting membrane of large endosomes and functions in endosomal trafficking prior to the lysosome, as demonstrated by loss-of-function mutants that fail to accumulate endocytosis markers in coelomocytes.\",\n      \"method\": \"Genetic analysis of C. elegans mutants, fluorescence localization, endocytosis marker uptake assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean loss-of-function genetic analysis with defined cellular phenotype, localization by live imaging, replicated across cell types\",\n      \"pmids\": [\"11451999\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Drosophila Rme-8 interacts specifically with Hsc70-4 via its J-domain (biochemical and genetic interaction), and is required for clathrin-dependent endocytosis; rme-8 mutants phenocopy Hsc70-4 mutants, placing them in a common pathway.\",\n      \"method\": \"Drosophila genetic screen (dominant-negative dynamin interaction), biochemical pulldown, genetic epistasis, endocytosis tracer uptake assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal biochemical and genetic evidence, multiple orthogonal methods in one study\",\n      \"pmids\": [\"15051737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Mammalian RME-8 (DNAJC13) was identified in clathrin-coated vesicle proteomics from rat liver; affinity selection assays identify Hsc70 as its major binding partner via the DnaJ domain; RME-8 is tightly associated with microsomal membranes and co-localizes with endosomal markers. siRNA knockdown does not affect transferrin endocytosis but reduces EGF internalization and disrupts trafficking of cation-independent mannose 6-phosphate receptor and cathepsin D sorting.\",\n      \"method\": \"Proteomic analysis of clathrin-coated vesicles, affinity selection (pulldown), subcellular fractionation, co-localization, siRNA knockdown with cargo trafficking readouts\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (proteomics, pulldown, KD with multiple cargo readouts) in single study on mammalian protein\",\n      \"pmids\": [\"16179350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human RME-8 (DNAJC13) is a peripheral membrane protein associated via its N-terminal region, localizing primarily to early endosomes (co-localizes with early endosomal markers, confirmed by immunoelectron microscopy). Expression of C-terminally truncated mutants perturbs transferrin recycling and EGF degradation through early endosomes. It does not co-localize with late endosomal markers.\",\n      \"method\": \"Cloning and biochemical characterization, immunoelectron microscopy, dominant-active Rab co-localization, truncation mutant overexpression, endocytic pathway assays\",\n      \"journal\": \"Cell structure and function\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (immuno-EM, localization, functional mutants, trafficking assays) in single study\",\n      \"pmids\": [\"18256511\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"RME-8 depletion leads to increased EGFR degradation (decreased steady-state EGFR levels at both surface and intracellular pools), implicating DNAJC13 in sorting decisions at endosomes that protect EGFR from degradation; transferrin receptor levels are unaffected.\",\n      \"method\": \"siRNA knockdown, receptor level quantification, degradation rate assays\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, clean KD with specific cargo phenotype but single method approach\",\n      \"pmids\": [\"18307993\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"C. elegans RME-8 associates with retromer component SNX-1; loss of SNX-1, RME-8, or the clathrin chaperone Hsc70/HSP-1 leads to over-accumulation of endosomal clathrin, reduced clathrin dynamics, and missorting of MIG-14/Wntless to the lysosome instead of the Golgi. This defines a mechanism whereby retromer regulates endosomal clathrin dynamics through RME-8 and Hsc70.\",\n      \"method\": \"Co-immunoprecipitation, genetic epistasis in C. elegans, live fluorescence imaging of clathrin dynamics, cargo missorting assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, genetic epistasis, multiple cargo readouts, replicated across several mutants\",\n      \"pmids\": [\"19763082\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The DNAJC13 p.Asn855Ser mutation segregates with autosomal dominant Parkinson's disease; cellular analysis shows this mutation confers a toxic gain-of-function and impairs endosomal transport. DNAJC13 immunoreactivity was detected within Lewy body inclusions.\",\n      \"method\": \"Exome sequencing, Sanger sequencing, case-control genotyping, cellular functional analysis, immunohistochemistry\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic segregation plus cellular gain-of-function analysis, but mechanistic detail of cellular assay is limited in abstract\",\n      \"pmids\": [\"24218364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RME-8 (DNAJC13) interacts with FAM21 (a subunit of the WASH complex) and with SNX1; loss of RME-8 causes altered kinetics of SNX1 membrane association and a pronounced increase in highly branched endosomal tubules containing WASH-complex-dependent cargo, indicating that RME-8 coordinates WASH complex activity with the membrane-tubulating function of sorting nexins.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, live fluorescence imaging of endosomal tubules, cargo localization assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP, KD with multiple orthogonal phenotypic readouts (tubulation, cargo sorting), single lab\",\n      \"pmids\": [\"24643499\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"In Drosophila, Rme-8 depletion causes Notch receptor accumulation in enlarged tubulated Rab4-positive endosomes and impairs Notch signaling. Simultaneous depletion of retromer component Vps26 or ESCRT-0 components Hrs/Stam with Rme-8 causes ectopic Notch activation, placing Rme-8 upstream and in opposition to these complexes in regulating Notch recycling versus degradation.\",\n      \"method\": \"Drosophila genetic epistasis (double knockdown/mutants), live and fixed fluorescence imaging, Notch signaling readouts\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic epistasis with multiple double-mutant combinations, specific endosomal localization phenotype, defined signaling readout\",\n      \"pmids\": [\"26169355\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SNX-1 and RME-8 together oppose the assembly of ESCRT-0/HGRS-1 degradative microdomains on endosomes; loss of snx-1 or rme-8 (but not other retromer components snx-3 or vps-35) increases endosomal coverage and intensity of HGRS-1-labeled microdomains and increases membrane-bound HGRS-1. Loss of hgrs-1 has little to no effect on SNX-1/RME-8 microdomains, indicating directionality of the interaction. The antagonism between recycling (RME-8/SNX-1) and degradative (ESCRT-0) microdomains is conserved in human HeLa cells.\",\n      \"method\": \"C. elegans genetics with in vivo fluorescence imaging of endosomal microdomains, siRNA knockdown in HeLa cells, membrane fractionation\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic specificity demonstrated by multiple retromer component comparisons, directionality tested, conserved in mammalian cells\",\n      \"pmids\": [\"28053230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The PD-linked N855S mutant DNAJC13 causes α-synuclein accumulation in the endosomal compartment due to defective cargo trafficking from early to late/recycling endosomes. In human αSYN transgenic Drosophila, mutant DNAJC13 increases insoluble αSYN, induces dopaminergic neurodegeneration, rough eye phenotype, and age-dependent locomotor impairment.\",\n      \"method\": \"Cell-based trafficking assays, Drosophila in vivo model with behavioral and pathological readouts, biochemical fractionation\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple readouts (cell biology and in vivo), but mechanism of αSYN accumulation inferred from trafficking defects rather than direct biochemical reconstitution\",\n      \"pmids\": [\"29309590\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The DNAJC13 p.Asn855Ser knock-in mutation in primary cortical neurons (from a mouse knock-in model) significantly increases SNX1-enriched endosomal tubule formation without affecting SNX1 puncta density or WASH-retromer assembly, indicating a dominant-negative gain-of-function that disrupts SNX1 membrane-tubulation dynamics.\",\n      \"method\": \"Knock-in mouse model, primary cortical neuron cultures, fluorescence imaging of SNX1 tubules, quantitative morphometry\",\n      \"journal\": \"Neuroscience letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel knock-in model, specific cellular phenotype, but single lab and limited mechanistic detail in abstract\",\n      \"pmids\": [\"31082451\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"DNAJC13 acts as a positive modulator of autophagy; knockdown reduces autophagic flux in C. elegans and human cell lines and impairs ATG9A trafficking from the recycling endosome, reducing ATG9A co-localization at LC3B-positive autophagic puncta. The PD-associated N855S mutant fails to enhance autophagy upon overexpression.\",\n      \"method\": \"siRNA knockdown and overexpression in human cells, C. elegans RNAi, ATG9A localization by fluorescence microscopy, autophagic flux assays (LC3B puncta, autophagy markers)\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (KD, OE, localization), two model systems, single lab\",\n      \"pmids\": [\"32322926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Structure-function analysis of C. elegans RME-8 identified that: (1) the C-terminus is important for microdomain localization and substrate binding; (2) N-terminal sequences beyond the PH-like domain are important for endosome recruitment; (3) IWN4 and IWN3 domains are important for autoinhibitory DNAJ domain binding, with IWN3 playing a critical role in HRS/HGRS-1 uncoating activity. AlphaFold structural modeling combined with in vivo mutation analysis supports a model whereby SNX-1 and IWN domains control RME-8 conformation and productive exposure of its DNAJ domain, with SNX-1 acting as an activator and target of RME-8 uncoating activity.\",\n      \"method\": \"Random and site-directed mutagenesis, AlphaFold structural modeling, in vivo C. elegans fluorescence imaging of endosomal microdomains, phylogenetic analysis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — mutagenesis with in vivo functional readouts and structural modeling, but structure is computational (AlphaFold) not experimental crystal/cryo-EM\",\n      \"pmids\": [\"36279308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Loss of RME-8/DNAJC13 in C. elegans mechanosensory neurons and primary mouse cortical neurons causes accumulation of grossly elongated autolysosomal tubules, indicating a role in autophagic lysosome reformation (ALR). In C. elegans, this phenotype is shared with bec-1/beclin, vps-15/PIK3R4, and dyn-1/dynamin mutants (known ALR regulators). Loss of RME-8 causes severe depletion of clathrin from neuronal autolysosomes, phenocopying bec-1 and vps-15 mutants. Loss of RME-8/DNAJC13 also reduces autophagic flux in both systems.\",\n      \"method\": \"C. elegans genetics and live fluorescence imaging, primary mouse cortical neuron culture, autophagic flux assays, clathrin localization\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis across multiple mutants, conserved phenotype in two independent biological systems (C. elegans and mouse neurons), multiple readouts\",\n      \"pmids\": [\"37942902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Genome-wide CRISPR interference screen identified DNAJC13 as a regulator of δ-opioid receptor (DOR) trafficking through the endosomal-lysosomal pathway; DNAJC13 controls trafficking of multiple GPCRs and regulates the composition of the endosomal proteome and endosomal homeostasis.\",\n      \"method\": \"Genome-wide CRISPRi screen using GPCR-APEX2/AUR trafficking biosensor, validation by loss-of-function with multiple GPCR trafficking readouts, quantitative proteomics of endosomal compartment\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide screen validated with orthogonal methods (multiple GPCRs, proteomics), rigorous biosensor approach, single lab\",\n      \"pmids\": [\"39223388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DNAJC13 localizes to endosomes through its N-terminal PH-like domain binding to PI(3)P; the J domain (HPD catalytic triad) and a conserved YLT motif in the disordered C-terminus act as negative regulators of this localization. Mutation of either motif enhances endosomal localization and PI(3)P binding in vitro. The PH-like domain binds PI(3)P weakly in isolation and requires oligomerization for efficient PI(3)P binding and endosomal localization. Overexpression of derepressed mutants causes endosomal clustering and loss of membrane protein cargo recycling.\",\n      \"method\": \"Structure-function mutagenesis, PI(3)P binding assays in vitro, quantitative cell imaging, overexpression phenotypic analysis, quantitative proteomics\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro binding assay with mutagenesis, cell imaging, functional readout (cargo recycling), multiple orthogonal methods in one study\",\n      \"pmids\": [\"40737286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The DNAJC13 N855S variant is less stable than wild-type protein and shows accelerated degradation. It fails to rescue impaired autophagy in DNAJC13 knockdown cells (loss-of-function), exerts a dominant-negative effect on cation-independent mannose-6-phosphate receptor distribution (without affecting overall cathepsin D levels or activity), and chronic DNAJC13 knockdown reduces expression of autophagy induction and biogenesis genes.\",\n      \"method\": \"Stable knockdown cell lines, transient N855S mutant expression, biochemical stability assays, co-localization by fluorescence microscopy, cathepsin D activity assays, gene expression analysis\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple cell biological methods, but single lab and the dominant-negative mechanism is inferred from co-localization rather than direct biochemical reconstitution\",\n      \"pmids\": [\"40717240\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DNAJC13/RME-8 is an endosome-associated Hsc70 co-chaperone that localizes to early endosomes via its N-terminal PH-like domain binding to PI(3)P (regulated by autoinhibitory interactions involving its J domain HPD triad and C-terminal YLT motif requiring oligomerization for efficient membrane binding), where it associates with the retromer component SNX1 and the WASH complex subunit FAM21 to regulate endosomal clathrin dynamics through Hsc70 recruitment, promotes retrograde cargo recycling to the Golgi while opposing ESCRT-0-mediated degradative microdomain assembly, controls SNX1 membrane tubulation, regulates ATG9A trafficking and autophagic lysosome reformation by maintaining clathrin at autolysosome membranes, and controls GPCR and growth factor receptor sorting through the endosomal-lysosomal pathway; the Parkinson's disease-linked p.N855S mutation acts as both a dominant-negative and loss-of-function variant causing increased SNX1 tubulation, impaired endosomal cargo trafficking, α-synuclein accumulation, and reduced autophagy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAJC13 (RME-8) is an endosome-associated DnaJ/Hsc70 co-chaperone that governs the balance between cargo recycling and degradation at the endosomal membrane [#0, #5]. It is recruited as a peripheral membrane protein to early endosomes through its N-terminal PH-like domain, which binds PI(3)P; this localization is held in check by autoinhibitory contacts involving the J-domain HPD triad and a conserved C-terminal YLT motif, and efficient membrane binding requires oligomerization, with derepressing mutations enhancing PI(3)P binding and endosomal clustering at the cost of cargo recycling [#16]. At the membrane it engages Hsc70 through its DnaJ domain to drive clathrin uncoating dynamics [#1, #2], working together with the retromer-associated sorting nexin SNX1 and the WASH-complex subunit FAM21 to control SNX1 membrane tubulation and the sorting of cargo away from degradation [#5, #7]. DNAJC13 and SNX1 oppose the assembly of ESCRT-0 (HRS/HGRS-1) degradative microdomains, thereby favoring retrograde and recycling itineraries over lysosomal delivery, a conserved antagonism that determines the fate of cargoes including Wntless, EGFR, Notch, and multiple GPCRs [#5, #9, #8, #15]. Beyond classical endosomal sorting, DNAJC13 is a positive modulator of autophagy: it supports ATG9A trafficking from the recycling endosome and maintains clathrin at autolysosomal membranes to enable autophagic lysosome reformation [#12, #14]. The p.Asn855Ser substitution segregates with autosomal-dominant Parkinson's disease, acting as a combined loss-of-function and dominant-negative variant that destabilizes the protein, increases SNX1 tubulation, impairs cargo trafficking, promotes \\u03b1-synuclein accumulation, and reduces autophagy [#6, #10, #11, #17].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established that the gene product is required for endocytosis and acts at endosomes before the lysosome, defining its compartment and stage of action.\",\n      \"evidence\": \"Loss-of-function genetics and endocytic marker uptake in C. elegans coelomocytes with live localization\",\n      \"pmids\": [\"11451999\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No molecular partners or biochemical mechanism identified\", \"Mammalian relevance not yet tested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identified Hsc70 as a functional partner acting through the J-domain, placing the protein in a chaperone-dependent endocytic pathway.\",\n      \"evidence\": \"Drosophila genetic screen, biochemical pulldown, and genetic epistasis with Hsc70-4\",\n      \"pmids\": [\"15051737\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate of the Hsc70 co-chaperone activity not defined\", \"Endosomal clathrin role not yet shown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Showed the mammalian protein is a clathrin-coated-vesicle/endosome component binding Hsc70 and selectively required for EGF and lysosomal-enzyme receptor trafficking but not transferrin endocytosis.\",\n      \"evidence\": \"CCV proteomics, affinity selection, fractionation, and siRNA knockdown with multiple cargo readouts in mammalian cells\",\n      \"pmids\": [\"16179350\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism distinguishing affected vs unaffected cargo unknown\", \"Membrane recruitment determinants undefined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Localized the human protein specifically to early (not late) endosomes via its N-terminal region and linked it to recycling and degradative cargo flux.\",\n      \"evidence\": \"Immuno-EM, Rab co-localization, and truncation-mutant trafficking assays in human cells\",\n      \"pmids\": [\"18256511\", \"18307993\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Lipid/protein basis of N-terminal membrane binding not resolved\", \"EGFR sorting mechanism inferred from steady-state levels\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined a retromer-linked mechanism in which the protein, SNX1, and Hsc70 control endosomal clathrin dynamics to route cargo to the Golgi rather than the lysosome.\",\n      \"evidence\": \"Reciprocal co-IP, genetic epistasis, live clathrin imaging, and Wntless missorting assays in C. elegans\",\n      \"pmids\": [\"19763082\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemistry of clathrin uncoating not reconstituted\", \"Whether SNX1 binding is direct unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Placed the protein upstream of and in opposition to retromer and ESCRT-0 in deciding receptor recycling versus degradation, using Notch as a readout.\",\n      \"evidence\": \"Drosophila double-knockdown genetic epistasis with Vps26 and Hrs/Stam plus Notch signaling assays\",\n      \"pmids\": [\"26169355\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the antagonism not defined\", \"Mammalian Notch relevance not tested here\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked the protein physically to the WASH complex (FAM21) and SNX1, showing it restrains branched endosomal tubulation and coordinates WASH activity with sorting-nexin tubulation.\",\n      \"evidence\": \"Reciprocal co-IP, siRNA knockdown, live tubule imaging, and cargo localization\",\n      \"pmids\": [\"24643499\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs indirect FAM21 interaction not dissected\", \"How it limits tubulation mechanistically unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated that the protein with SNX1 directly opposes ESCRT-0 degradative microdomain assembly with defined directionality, conserved from worm to human.\",\n      \"evidence\": \"C. elegans microdomain imaging with retromer-component specificity, membrane fractionation, and HeLa knockdown\",\n      \"pmids\": [\"28053230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical mechanism limiting HGRS-1 membrane binding unknown\", \"How specificity for ESCRT-0 vs retromer is achieved unresolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved the domain logic of conformational autoinhibition, showing IWN domains and SNX-1 gate productive exposure of the DnaJ domain for uncoating activity.\",\n      \"evidence\": \"Mutagenesis with in vivo microdomain imaging and AlphaFold modeling in C. elegans\",\n      \"pmids\": [\"36279308\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structure is computational, not experimental\", \"Conformational model not validated biochemically in mammals\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined PI(3)P binding by the PH-like domain as the membrane-recruitment mechanism, regulated by autoinhibitory J-domain and YLT motifs and dependent on oligomerization.\",\n      \"evidence\": \"In vitro PI(3)P binding with mutagenesis, quantitative imaging, and overexpression cargo-recycling assays\",\n      \"pmids\": [\"40737286\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Oligomerization stoichiometry and trigger not defined\", \"How autoinhibition is relieved on the membrane unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended function to autophagy, showing the protein promotes autophagic flux by enabling ATG9A trafficking from the recycling endosome.\",\n      \"evidence\": \"Knockdown/overexpression in human cells and C. elegans RNAi with ATG9A localization and LC3B flux assays\",\n      \"pmids\": [\"32322926\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct role in ATG9A vesicle formation vs sorting unclear\", \"Connection to clathrin/Hsc70 activity not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed the protein maintains clathrin at autolysosomes to drive autophagic lysosome reformation, integrating its clathrin-uncoating role with late autophagy.\",\n      \"evidence\": \"C. elegans and mouse cortical neuron imaging, autophagic flux assays, and epistasis with ALR regulators\",\n      \"pmids\": [\"37942902\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Hsc70 co-chaperone activity drives ALR clathrin dynamics untested\", \"Substrate at autolysosome undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Generalized the cargo-sorting role to GPCR trafficking and endosomal proteome homeostasis via an unbiased genome-wide screen.\",\n      \"evidence\": \"Genome-wide CRISPRi screen with GPCR trafficking biosensors and endosomal proteomics in human cells\",\n      \"pmids\": [\"39223388\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether GPCR effects are direct or via global endosomal disruption unresolved\", \"Specific sorting step for each GPCR undefined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Connected the gene to autosomal-dominant Parkinson's disease through the p.N855S variant, with disease-relevant trafficking impairment and Lewy-body immunoreactivity.\",\n      \"evidence\": \"Exome/Sanger sequencing, case-control genotyping, cellular functional analysis, and immunohistochemistry\",\n      \"pmids\": [\"24218364\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether variant is gain- or loss-of-function not resolved here\", \"Mechanistic basis of trafficking defect unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Linked the N855S variant mechanistically to \\u03b1-synuclein endosomal accumulation and dopaminergic neurodegeneration in vivo.\",\n      \"evidence\": \"Cell trafficking assays and \\u03b1-synuclein transgenic Drosophila with behavioral and pathological readouts\",\n      \"pmids\": [\"29309590\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"\\u03b1-synuclein accumulation inferred from trafficking defect, not direct biochemistry\", \"Relationship to neuronal autophagy not tested here\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed in a physiological knock-in neuron model that N855S acts as a dominant-negative on SNX1 tubulation without disrupting WASH-retromer assembly.\",\n      \"evidence\": \"Knock-in mouse primary cortical neurons with quantitative SNX1 tubule morphometry\",\n      \"pmids\": [\"31082451\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, limited mechanistic detail\", \"Link from tubulation defect to neurodegeneration not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Clarified the dual nature of N855S as both destabilizing/loss-of-function and dominant-negative across autophagy and cargo-distribution phenotypes.\",\n      \"evidence\": \"Stable knockdown rescue, mutant stability assays, M6PR co-localization, cathepsin D activity, and autophagy gene expression in human cells\",\n      \"pmids\": [\"40717240\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Dominant-negative mechanism inferred from co-localization, not reconstituted\", \"Cause of accelerated degradation undefined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How autoinhibition is relieved on the membrane to productively expose the DnaJ domain and direct Hsc70-driven clathrin uncoating toward specific substrates remains unresolved.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No experimental high-resolution structure of the full-length protein or its membrane-bound conformation\", \"Direct uncoating substrates at endosomes vs autolysosomes not biochemically defined\", \"Quantitative link between specific trafficking defects and Parkinson's pathogenesis incomplete\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2, 5, 13]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [16]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 7, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 3, 5, 16]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3, 16]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 2, 5, 7, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [12, 14]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [5, 9, 16]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [6, 10, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"HSPA8\", \"SNX1\", \"FAM21\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}