{"gene":"PLEKHM1","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2007,"finding":"PLEKHM1 colocalizes with Rab7 on late endosomal/lysosomal vesicles in HEK293 and osteoclast-like cells, and this colocalization is dependent on prenylation of Rab7. Loss-of-function mutations in PLEKHM1 cause osteoclasts to fail to form ruffled borders and show defective bone resorption, establishing PLEKHM1 as essential for osteoclast vesicular transport.","method":"Confocal microscopy, electron microscopy, mutational analysis in patient osteoclasts and HEK293 cells","journal":"The Journal of Clinical Investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal localization with functional validation in patient cells and HEK293 cells, replicated across multiple labs in subsequent work","pmids":["17404618"],"is_preprint":false},{"year":2008,"finding":"The R714C mutation in PLEKHM1 impairs endosomal vesicle acidification and increases TRACP secretion in osteoclasts. RAW 264.7 cells expressing Plekhm1-R714C show reduced ability to acidify endosomal compartments and lower intracellular TRACP activity due to increased protein secretion compared to wild-type.","method":"In vitro osteoclast assays, transfection of wild-type vs. R714C mutant in HEK293 and RAW 264.7 cells, endosomal pH measurement, TRACP activity assays","journal":"Journal of Bone and Mineral Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional assay with mutagenesis in multiple cell lines, single lab","pmids":["17997709"],"is_preprint":false},{"year":2010,"finding":"PLEKHM1 directly interacts with Rab7 via a C-terminal RH (Rubicon homology) domain, and this interaction is critical for PLEKHM1's function in suppressing endocytic transport. Unlike Rubicon, PLEKHM1 does not simultaneously bind PI3-kinase and does not regulate autophagosome maturation.","method":"Database homology searches, direct binding assays, functional knockdown experiments","journal":"Molecular Biology of the Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct interaction mapped to specific domain, functional validation by depletion, replicated in subsequent studies","pmids":["20943950"],"is_preprint":false},{"year":2011,"finding":"LIS1 interacts with and colocalizes with PLEKHM1 in osteoclasts. Depletion of LIS1 inhibits Cathepsin K secretion and osteoclast lysosomal secretion, placing LIS1 upstream of PLEKHM1/dynein-mediated lysosomal trafficking.","method":"Co-immunoprecipitation, shRNA knockdown in bone marrow macrophages, resorption pit assay, immunofluorescence","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and functional knockdown in primary cells, single lab, multiple readouts","pmids":["22073305"],"is_preprint":false},{"year":2014,"finding":"PLEKHM1 directly interacts with the HOPS tethering complex and contains a LC3-interacting region (LIR) that mediates binding to autophagosomal membranes. Depletion of PLEKHM1 blocks lysosomal degradation of endocytic cargo (EGFR), impedes autophagy flux upon mTOR inhibition, and impairs clearance of protein aggregates in an autophagy- and LIR-dependent manner. PLEKHM1 thus bridges endocytic and autophagy pathways to the lysosome via simultaneous engagement of Rab7, HOPS, and LC3/GABARAP.","method":"Mass spectrometry (GTP-Rab7 pulldown, PLEKHM1 immunoprecipitation), yeast two-hybrid LIR screen, knockout MEFs, EGFR degradation assay, LC3 colocalization, puromycin aggregate clearance assay","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (MS, Y2H, KO cells, functional assays), replicated across labs","pmids":["25498145"],"is_preprint":false},{"year":2014,"finding":"Salmonella effector SifA directly binds the PLEKHM1 PH2 domain to exploit the PLEKHM1–Rab7–HOPS complex for mobilizing phagolysosomal membranes to the Salmonella-containing vacuole (SCV). Depletion of PLEKHM1 causes profound defects in SCV morphology and significantly dampens Salmonella proliferation in cells and mice.","method":"Direct binding assays (SifA-PH2 interaction), siRNA knockdown, bacterial infection assays in multiple cell types and mouse model","journal":"Cell Host & Microbe","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct protein-protein interaction mapped to specific domain, in vitro and in vivo functional validation, single rigorous study with multiple orthogonal methods","pmids":["25500191"],"is_preprint":false},{"year":2015,"finding":"TRAFD1 (FLN29) directly interacts with PLEKHM1, with binding mapped to the TRAFD1 zinc finger (aa 37–60) and the PLEKHM1 region between PH2 and C1 domains (aa 784–986). Stable knockdown of TRAFD1 in RAW 264.7 cells inhibits osteoclast resorption and acidification despite normal expression of acidification factors, placing TRAFD1 in the PLEKHM1/Rab7 vesicle-trafficking pathway.","method":"Mass spectrometry identification, domain mapping, stable shRNA knockdown, acidification and resorption assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — binding domain mapped by deletion analysis, functional knockdown with specific readouts, single lab","pmids":["25992615"],"is_preprint":false},{"year":2016,"finding":"DEF8 interacts with PLEKHM1 and promotes its binding to RAB7, while FAM98A and NDEL1 interact with PLEKHM1 to connect lysosomes to microtubules. Loss of PLEKHM1, DEF8, FAM98A, or NDEL1 abrogates the peripheral distribution of lysosomes and bone resorption in osteoclasts. Germline and conditional Plekhm1-knockout mice show increased trabecular bone mass and defective lysosome trafficking.","method":"Germline and conditional KO mouse generation, co-immunoprecipitation, lysosome positioning assays, bone resorption assays, siRNA knockdown of interacting proteins","journal":"JCI Insight","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple binding partners identified and validated with functional epistasis in KO mice and cells, multiple orthogonal methods","pmids":["27777970"],"is_preprint":false},{"year":2016,"finding":"A PLEKHM1 deletion mutation in exon 11 (c.3051_3052delCA) that impairs the Rubicon homology domain dramatically decreases interaction between PLEKHM1 and Rab7 by co-immunoprecipitation, and disturbs normal endocytosis (EGFR degradation) and autophagy (LC3-I/II ratio) in transfected HEK293 and U937 cells.","method":"Co-immunoprecipitation, immunofluorescence, EGFR degradation assay, LC3-I/II ratio, transfection in HEK293 and U937 cells","journal":"Journal of Bone and Mineral Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain-specific mutation with functional readouts in two cell lines, single lab","pmids":["27291868"],"is_preprint":false},{"year":2019,"finding":"Acute conversion of endosomal PI4P to PI(4,5)P2 causes Rab7 dissociation from late endosomes and releases PLEKHM1 from the membrane. Deletion of PI4K2A reduces PIP5Kγ-mediated PI(4,5)P2 production in Rab7-positive endosomes, leading to impaired Rab7 inactivation and increased LC3-positive structures with defective autophagosome-lysosome fusion, demonstrating that PLEKHM1 membrane association is regulated by a PI4P-PI(4,5)P2 cycle on late endosomes.","method":"Acute lipid conversion system (chemogenetic), PI4K2A deletion, live imaging, LC3 quantification, Rab7 dissociation assay","journal":"The EMBO Journal","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — acute pharmacological manipulation with direct measurement of PLEKHM1 membrane release and Rab7 cycling, multiple orthogonal approaches, genetic validation","pmids":["31368593"],"is_preprint":false},{"year":2023,"finding":"TRIM22 promotes autophagosome-lysosome fusion by directly mediating the association between GABARAP family proteins and PLEKHM1, independent of TRIM22's E3 ubiquitin ligase activity. This scaffolding function of TRIM22 facilitates autophagic clearance of protein aggregates.","method":"Co-immunoprecipitation, proximity ligation assay, TRIM22 knockout, autophagy flux assays, ligase-dead mutant","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with rescue, direct interaction assays, ligase-dead control, single lab","pmids":["38009729"],"is_preprint":false},{"year":2024,"finding":"Compound alanine mutations at the Y949-R954 region of the PLEKHM1 RH domain decrease protein stability, while compound mutations at L1011-I1018 decrease Rab7 binding; both impair lysosome trafficking and bone resorption in osteoclasts. Compound mutations at R1060-Q1068 are dispensable for Rab7 binding and PLEKHM1 function. Single mutations at the predicted interface (based on RUBICON crystal structure) failed to disrupt binding.","method":"Structure-guided mutagenesis based on RUBICON RH-Rab7 crystal structure, co-immunoprecipitation of mutants, lysosome trafficking assay, bone resorption assay in osteoclasts","journal":"JBMR Plus","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — structure-guided mutagenesis with functional readouts, single lab, relies on homologous crystal structure not direct PLEKHM1 structure","pmids":["38586475"],"is_preprint":false},{"year":2025,"finding":"PLEKHM1 overexpression in mouse substantia nigra impairs autophagic flux by reducing lysosomal and autolysosomal area, increasing LAMP1-LC3 colocalization, decreasing the autolysosome-to-autophagosome ratio, and causing p62 accumulation with impaired cargo degradation, demonstrating that elevated PLEKHM1 levels disrupt late-stage autophagy in vivo.","method":"rAAV-mediated PLEKHM1 overexpression in mouse brain, RFP-EGFP-LC3 autophagy reporter mice, LAMP1 colocalization, p62 staining, dopaminergic neuron quantification","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vivo functional evidence with autophagy reporter and multiple markers, single lab, single study","pmids":["40940751"],"is_preprint":false}],"current_model":"PLEKHM1 is a multivalent endolysosomal adaptor that simultaneously engages active (GTP-bound) RAB7 via its C-terminal RH domain, the HOPS tethering complex, and autophagosomal membranes via a conserved LIR motif that binds LC3/GABARAP proteins, thereby coordinating autophagosome-lysosome and endosome-lysosome fusion; its membrane association is dynamically regulated by a late endosomal PI4P-to-PI(4,5)P2 lipid conversion cycle, and it forms a molecular complex with DEF8, FAM98A, and NDEL1 to position lysosomes peripherally in osteoclasts, enabling ruffled border formation and bone resorption, while its loss causes osteopetrosis and its dysregulation impairs autophagic flux in neurons."},"narrative":{"mechanistic_narrative":"PLEKHM1 is a multivalent endolysosomal adaptor that coordinates the convergence of endocytic and autophagic cargo on the lysosome by simultaneously engaging active RAB7, the HOPS tethering complex, and LC3/GABARAP-decorated autophagosomal membranes [PMID:25498145]. It binds GTP-bound RAB7 directly through a C-terminal Rubicon-homology (RH) domain, an interaction required for its control of endocytic transport [PMID:20943950], and a conserved LC3-interacting region (LIR) couples this RAB7/HOPS platform to autophagosomal membranes so that PLEKHM1 drives lysosomal degradation of endocytic cargo such as EGFR, autophagic flux, and clearance of protein aggregates [PMID:25498145]. Its recruitment to late endosomes is dynamically switched by a PI4P-to-PI(4,5)P2 lipid conversion cycle that drives RAB7 inactivation and releases PLEKHM1 from the membrane [PMID:31368593]. In osteoclasts, PLEKHM1 forms a positioning machinery with DEF8 (which promotes its RAB7 binding), FAM98A, and NDEL1 to distribute lysosomes peripherally and link them to microtubules, enabling ruffled-border formation and bone resorption [PMID:27777970]; loss-of-function mutations in PLEKHM1 cause osteopetrosis through failure of osteoclast ruffled-border formation and defective bone resorption [PMID:17404618]. The pathway is exploited by the Salmonella effector SifA, which binds the PLEKHM1 PH2 domain to redirect phagolysosomal membranes to the Salmonella-containing vacuole [PMID:25500191], and excess PLEKHM1 itself disrupts late-stage autophagy in vivo, impairing autolysosome maturation and cargo degradation in neurons [PMID:40940751].","teleology":[{"year":2007,"claim":"Established PLEKHM1 as an essential factor in osteoclast vesicular transport by showing its RAB7-dependent localization to late endosomal/lysosomal membranes and the failure of ruffled-border formation when it is mutated.","evidence":"Confocal and electron microscopy with mutational analysis in patient osteoclasts and HEK293 cells","pmids":["17404618"],"confidence":"High","gaps":["Did not define the molecular domain mediating RAB7 association","Mechanism linking RAB7 colocalization to ruffled-border formation unresolved"]},{"year":2008,"claim":"Connected a disease mutation to organelle function by showing the R714C variant impairs endosomal acidification and increases TRACP secretion in osteoclasts.","evidence":"Transfection of wild-type vs R714C mutant in HEK293 and RAW 264.7 cells with endosomal pH and TRACP activity assays","pmids":["17997709"],"confidence":"Medium","gaps":["Did not show how the mutation mechanistically disrupts acidification","Single lab; R714C effect on RAB7 binding not tested"]},{"year":2010,"claim":"Identified the molecular basis of RAB7 engagement by mapping the interaction to a C-terminal Rubicon-homology domain and distinguishing PLEKHM1 from Rubicon in not binding PI3-kinase.","evidence":"Homology searches, direct binding assays, and functional knockdown of endocytic transport","pmids":["20943950"],"confidence":"High","gaps":["Autophagy role explicitly excluded here but later revised","No structural model of the RH-RAB7 interface"]},{"year":2014,"claim":"Defined PLEKHM1 as a tripartite adaptor bridging endocytic and autophagy pathways by demonstrating simultaneous binding to RAB7, HOPS, and LC3/GABARAP via a LIR motif, with functional control of EGFR degradation, autophagy flux, and aggregate clearance.","evidence":"GTP-RAB7 pulldown mass spectrometry, yeast two-hybrid LIR screen, knockout MEFs, and degradation/clearance assays","pmids":["25498145"],"confidence":"High","gaps":["Did not address how membrane recruitment is temporally regulated","Stoichiometry of the RAB7-HOPS-LC3 complex unresolved"]},{"year":2014,"claim":"Revealed pathogen hijacking of the adaptor by showing the Salmonella effector SifA binds the PLEKHM1 PH2 domain to redirect phagolysosomal membranes to the bacterial vacuole.","evidence":"Direct SifA-PH2 binding assays, siRNA knockdown, and infection assays in cells and mice","pmids":["25500191"],"confidence":"High","gaps":["Did not resolve how SifA binding alters native PLEKHM1-RAB7-HOPS function","Endogenous ligand of the PH2 domain unknown"]},{"year":2015,"claim":"Added TRAFD1 as a pathway component by mapping its zinc-finger to a PLEKHM1 region between the PH2 and C1 domains and showing its loss blocks osteoclast resorption and acidification.","evidence":"Mass spectrometry, deletion-based domain mapping, and stable shRNA knockdown with acidification/resorption readouts","pmids":["25992615"],"confidence":"Medium","gaps":["Functional consequence of the TRAFD1-PLEKHM1 interaction at the molecular level unclear","Single lab; not validated in other systems"]},{"year":2016,"claim":"Built the osteoclast lysosome-positioning machine by showing DEF8 promotes PLEKHM1-RAB7 binding and FAM98A/NDEL1 link lysosomes to microtubules, with KO mice displaying increased bone mass and defective lysosome trafficking.","evidence":"Germline and conditional KO mice, co-immunoprecipitation, lysosome positioning and bone resorption assays, and siRNA of partners","pmids":["27777970"],"confidence":"High","gaps":["Architecture of the DEF8-FAM98A-NDEL1-PLEKHM1 assembly not structurally defined","How microtubule coupling is regulated unresolved"]},{"year":2016,"claim":"Linked a disease deletion to mechanism by showing an exon 11 frameshift impairing the RH domain reduces PLEKHM1-RAB7 binding and disrupts EGFR degradation and LC3 conversion.","evidence":"Co-immunoprecipitation, EGFR degradation and LC3-I/II ratio assays in HEK293 and U937 cells","pmids":["27291868"],"confidence":"Medium","gaps":["Single lab; physiological phenotype not assessed in patient tissue","Does not distinguish endocytic from autophagic contributions"]},{"year":2019,"claim":"Established dynamic regulation of PLEKHM1 membrane association by showing a PI4P-to-PI(4,5)P2 conversion drives RAB7 dissociation and PLEKHM1 release, with PI4K2A loss impairing RAB7 inactivation and autophagosome-lysosome fusion.","evidence":"Chemogenetic acute lipid conversion, PI4K2A deletion, live imaging, and RAB7 dissociation assays","pmids":["31368593"],"confidence":"High","gaps":["Did not define the kinases/phosphatases acting upstream in physiological signaling","Whether PLEKHM1 directly senses lipids vs follows RAB7 unresolved"]},{"year":2023,"claim":"Identified a scaffolding regulator of fusion by showing TRIM22 bridges GABARAP proteins to PLEKHM1 independent of its E3 ligase activity to promote autophagic aggregate clearance.","evidence":"Co-immunoprecipitation, proximity ligation, TRIM22 knockout/rescue, and a ligase-dead mutant","pmids":["38009729"],"confidence":"Medium","gaps":["Single lab; structural basis of the TRIM22-PLEKHM1-GABARAP assembly unknown","Physiological contexts requiring TRIM22 vs LIR-direct binding undefined"]},{"year":2024,"claim":"Dissected the RH domain functionally by structure-guided mutagenesis, separating residues required for protein stability from those required for RAB7 binding, both impairing lysosome trafficking and bone resorption.","evidence":"Mutagenesis guided by the RUBICON RH-RAB7 crystal structure, co-IP, lysosome trafficking and bone resorption assays in osteoclasts","pmids":["38586475"],"confidence":"Medium","gaps":["Relies on a homologous structure, not a direct PLEKHM1-RAB7 structure","Single point mutations failed to disrupt binding, complicating interface assignment"]},{"year":2025,"claim":"Demonstrated that PLEKHM1 dosage is pathologically relevant by showing overexpression in substantia nigra impairs late-stage autophagy with p62 accumulation and reduced autolysosome maturation.","evidence":"rAAV PLEKHM1 overexpression in autophagy reporter mice with LAMP1/LC3/p62 markers","pmids":["40940751"],"confidence":"Medium","gaps":["Mechanism by which excess PLEKHM1 stalls fusion not defined","Single lab; relevance to human neurodegeneration not established"]},{"year":null,"claim":"How the membrane-binding, RAB7-binding, HOPS-binding, and LIR activities of PLEKHM1 are integrated into a stepwise, regulated fusion cycle, and the structure of the native PLEKHM1-RAB7 complex, remain unresolved.","evidence":"No direct experimental resolution in the available corpus","pmids":[],"confidence":"Low","gaps":["No experimental PLEKHM1 structure","Temporal coordination of partner engagement during a single fusion event undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,2,7]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,9]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,7]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4,9,10]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,4,7]}],"complexes":["HOPS complex","PLEKHM1-DEF8-FAM98A-NDEL1 lysosome-positioning complex"],"partners":["RAB7","HOPS","LC3","GABARAP","DEF8","FAM98A","NDEL1","TRIM22"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y4G2","full_name":"Pleckstrin homology domain-containing family M member 1","aliases":["162 kDa adapter protein","AP162"],"length_aa":1056,"mass_kda":117.4,"function":"Acts as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Acts as a dual effector of RAB7A and ARL8B that simultaneously binds these GTPases, bringing about clustering and fusion of late endosomes and lysosomes (PubMed:25498145, PubMed:28325809). Required for late stages of endolysosomal maturation, facilitating both endocytosis-mediated degradation of growth factor receptors and autophagosome clearance. Interaction with Arl8b is a crucial factor in the terminal maturation of autophagosomes and to mediate autophagosome-lysosome fusion (PubMed:25498145). Positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts (By similarity). May be involved in negative regulation of endocytic transport from early endosome to late endosome/lysosome implicating its association with Rab7 (PubMed:20943950). May have a role in sialyl-lex-mediated transduction of apoptotic signals (PubMed:12820725). Involved in bone resorption (By similarity) (Microbial infection) In case of infection contributes to Salmonella typhimurium pathogenesis by supporting the integrity of the Salmonella-containing vacuole (SCV) probably in concert with the HOPS complex and Rab7","subcellular_location":"Autolysosome membrane; Endosome membrane; Late endosome membrane; Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y4G2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PLEKHM1","classification":"Common Essential","n_dependent_lines":375,"n_total_lines":1208,"dependency_fraction":0.31043046357615894},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PLEKHM1","total_profiled":1310},"omim":[{"mim_id":"621516","title":"DIFFERENTIALLY EXPRESSED IN FDCP 8, MOUSE, HOMOLOG OF; DEF8","url":"https://www.omim.org/entry/621516"},{"mim_id":"620994","title":"RUN AND FYVE DOMAINS-CONTAINING PROTEIN 4; RUFY4","url":"https://www.omim.org/entry/620994"},{"mim_id":"619186","title":"PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN, FAMILY M, MEMBER 3; PLEKHM3","url":"https://www.omim.org/entry/619186"},{"mim_id":"618107","title":"OSTEOPETROSIS, AUTOSOMAL DOMINANT 3; OPTA3","url":"https://www.omim.org/entry/618107"},{"mim_id":"611497","title":"OSTEOPETROSIS, AUTOSOMAL RECESSIVE 6; OPTB6","url":"https://www.omim.org/entry/611497"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"esophagus","ntpm":29.0}],"url":"https://www.proteinatlas.org/search/PLEKHM1"},"hgnc":{"alias_symbol":["KIAA0356"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y4G2","domains":[{"cath_id":"1.20.58.900","chopping":"12-69_86-201","consensus_level":"high","plddt":90.2024,"start":12,"end":201},{"cath_id":"2.30.29.30","chopping":"538-628","consensus_level":"high","plddt":86.3918,"start":538,"end":628},{"cath_id":"2.30.29.30","chopping":"687-763","consensus_level":"high","plddt":85.5166,"start":687,"end":763},{"cath_id":"3.30.40.10","chopping":"784-997","consensus_level":"medium","plddt":85.6293,"start":784,"end":997},{"cath_id":"-","chopping":"1001-1054","consensus_level":"high","plddt":88.4356,"start":1001,"end":1054}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y4G2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y4G2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y4G2-F1-predicted_aligned_error_v6.png","plddt_mean":65.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PLEKHM1","jax_strain_url":"https://www.jax.org/strain/search?query=PLEKHM1"},"sequence":{"accession":"Q9Y4G2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y4G2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y4G2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y4G2"}},"corpus_meta":[{"pmid":"25498145","id":"PMC_25498145","title":"PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins.","date":"2014","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/25498145","citation_count":466,"is_preprint":false},{"pmid":"17404618","id":"PMC_17404618","title":"Involvement of PLEKHM1 in osteoclastic vesicular transport and osteopetrosis in incisors absent rats and humans.","date":"2007","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/17404618","citation_count":173,"is_preprint":false},{"pmid":"20943950","id":"PMC_20943950","title":"Rubicon and PLEKHM1 negatively regulate the endocytic/autophagic pathway via a novel Rab7-binding domain.","date":"2010","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/20943950","citation_count":131,"is_preprint":false},{"pmid":"25500191","id":"PMC_25500191","title":"PLEKHM1 regulates Salmonella-containing vacuole biogenesis and infection.","date":"2014","source":"Cell host & 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official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/17997709","citation_count":61,"is_preprint":false},{"pmid":"22073305","id":"PMC_22073305","title":"LIS1 regulates osteoclast formation and function through its interactions with dynein/dynactin and Plekhm1.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22073305","citation_count":44,"is_preprint":false},{"pmid":"27291868","id":"PMC_27291868","title":"Characterization of a Relatively Malignant Form of Osteopetrosis Caused by a Novel Mutation in the PLEKHM1 Gene.","date":"2016","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/27291868","citation_count":28,"is_preprint":false},{"pmid":"38009729","id":"PMC_38009729","title":"TRIM22 facilitates autophagosome-lysosome fusion by mediating the association of GABARAPs and 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England)","url":"https://pubmed.ncbi.nlm.nih.gov/40694017","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.31.667977","title":"RNF13 Regulates the Endolysosomal Pathway Through Interaction with the Small GTPase Arl8B","date":"2025-07-31","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.31.667977","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.19.25329954","title":"Shared Genetic Architecture Between Parkinson’s Disease and Sleep-Related Traits Implicates the<i>MAPT</i>Locus on Chromosome 17","date":"2025-06-20","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.19.25329954","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12404,"output_tokens":3600,"usd":0.045606,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11163,"output_tokens":4154,"usd":0.079833,"stage2_stop_reason":"end_turn"},"total_usd":0.125439,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"PLEKHM1 colocalizes with Rab7 on late endosomal/lysosomal vesicles in HEK293 and osteoclast-like cells, and this colocalization is dependent on prenylation of Rab7. Loss-of-function mutations in PLEKHM1 cause osteoclasts to fail to form ruffled borders and show defective bone resorption, establishing PLEKHM1 as essential for osteoclast vesicular transport.\",\n      \"method\": \"Confocal microscopy, electron microscopy, mutational analysis in patient osteoclasts and HEK293 cells\",\n      \"journal\": \"The Journal of Clinical Investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal localization with functional validation in patient cells and HEK293 cells, replicated across multiple labs in subsequent work\",\n      \"pmids\": [\"17404618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The R714C mutation in PLEKHM1 impairs endosomal vesicle acidification and increases TRACP secretion in osteoclasts. RAW 264.7 cells expressing Plekhm1-R714C show reduced ability to acidify endosomal compartments and lower intracellular TRACP activity due to increased protein secretion compared to wild-type.\",\n      \"method\": \"In vitro osteoclast assays, transfection of wild-type vs. R714C mutant in HEK293 and RAW 264.7 cells, endosomal pH measurement, TRACP activity assays\",\n      \"journal\": \"Journal of Bone and Mineral Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional assay with mutagenesis in multiple cell lines, single lab\",\n      \"pmids\": [\"17997709\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PLEKHM1 directly interacts with Rab7 via a C-terminal RH (Rubicon homology) domain, and this interaction is critical for PLEKHM1's function in suppressing endocytic transport. Unlike Rubicon, PLEKHM1 does not simultaneously bind PI3-kinase and does not regulate autophagosome maturation.\",\n      \"method\": \"Database homology searches, direct binding assays, functional knockdown experiments\",\n      \"journal\": \"Molecular Biology of the Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct interaction mapped to specific domain, functional validation by depletion, replicated in subsequent studies\",\n      \"pmids\": [\"20943950\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"LIS1 interacts with and colocalizes with PLEKHM1 in osteoclasts. Depletion of LIS1 inhibits Cathepsin K secretion and osteoclast lysosomal secretion, placing LIS1 upstream of PLEKHM1/dynein-mediated lysosomal trafficking.\",\n      \"method\": \"Co-immunoprecipitation, shRNA knockdown in bone marrow macrophages, resorption pit assay, immunofluorescence\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and functional knockdown in primary cells, single lab, multiple readouts\",\n      \"pmids\": [\"22073305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PLEKHM1 directly interacts with the HOPS tethering complex and contains a LC3-interacting region (LIR) that mediates binding to autophagosomal membranes. Depletion of PLEKHM1 blocks lysosomal degradation of endocytic cargo (EGFR), impedes autophagy flux upon mTOR inhibition, and impairs clearance of protein aggregates in an autophagy- and LIR-dependent manner. PLEKHM1 thus bridges endocytic and autophagy pathways to the lysosome via simultaneous engagement of Rab7, HOPS, and LC3/GABARAP.\",\n      \"method\": \"Mass spectrometry (GTP-Rab7 pulldown, PLEKHM1 immunoprecipitation), yeast two-hybrid LIR screen, knockout MEFs, EGFR degradation assay, LC3 colocalization, puromycin aggregate clearance assay\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (MS, Y2H, KO cells, functional assays), replicated across labs\",\n      \"pmids\": [\"25498145\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Salmonella effector SifA directly binds the PLEKHM1 PH2 domain to exploit the PLEKHM1–Rab7–HOPS complex for mobilizing phagolysosomal membranes to the Salmonella-containing vacuole (SCV). Depletion of PLEKHM1 causes profound defects in SCV morphology and significantly dampens Salmonella proliferation in cells and mice.\",\n      \"method\": \"Direct binding assays (SifA-PH2 interaction), siRNA knockdown, bacterial infection assays in multiple cell types and mouse model\",\n      \"journal\": \"Cell Host & Microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct protein-protein interaction mapped to specific domain, in vitro and in vivo functional validation, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"25500191\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TRAFD1 (FLN29) directly interacts with PLEKHM1, with binding mapped to the TRAFD1 zinc finger (aa 37–60) and the PLEKHM1 region between PH2 and C1 domains (aa 784–986). Stable knockdown of TRAFD1 in RAW 264.7 cells inhibits osteoclast resorption and acidification despite normal expression of acidification factors, placing TRAFD1 in the PLEKHM1/Rab7 vesicle-trafficking pathway.\",\n      \"method\": \"Mass spectrometry identification, domain mapping, stable shRNA knockdown, acidification and resorption assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — binding domain mapped by deletion analysis, functional knockdown with specific readouts, single lab\",\n      \"pmids\": [\"25992615\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"DEF8 interacts with PLEKHM1 and promotes its binding to RAB7, while FAM98A and NDEL1 interact with PLEKHM1 to connect lysosomes to microtubules. Loss of PLEKHM1, DEF8, FAM98A, or NDEL1 abrogates the peripheral distribution of lysosomes and bone resorption in osteoclasts. Germline and conditional Plekhm1-knockout mice show increased trabecular bone mass and defective lysosome trafficking.\",\n      \"method\": \"Germline and conditional KO mouse generation, co-immunoprecipitation, lysosome positioning assays, bone resorption assays, siRNA knockdown of interacting proteins\",\n      \"journal\": \"JCI Insight\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple binding partners identified and validated with functional epistasis in KO mice and cells, multiple orthogonal methods\",\n      \"pmids\": [\"27777970\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"A PLEKHM1 deletion mutation in exon 11 (c.3051_3052delCA) that impairs the Rubicon homology domain dramatically decreases interaction between PLEKHM1 and Rab7 by co-immunoprecipitation, and disturbs normal endocytosis (EGFR degradation) and autophagy (LC3-I/II ratio) in transfected HEK293 and U937 cells.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, EGFR degradation assay, LC3-I/II ratio, transfection in HEK293 and U937 cells\",\n      \"journal\": \"Journal of Bone and Mineral Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain-specific mutation with functional readouts in two cell lines, single lab\",\n      \"pmids\": [\"27291868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Acute conversion of endosomal PI4P to PI(4,5)P2 causes Rab7 dissociation from late endosomes and releases PLEKHM1 from the membrane. Deletion of PI4K2A reduces PIP5Kγ-mediated PI(4,5)P2 production in Rab7-positive endosomes, leading to impaired Rab7 inactivation and increased LC3-positive structures with defective autophagosome-lysosome fusion, demonstrating that PLEKHM1 membrane association is regulated by a PI4P-PI(4,5)P2 cycle on late endosomes.\",\n      \"method\": \"Acute lipid conversion system (chemogenetic), PI4K2A deletion, live imaging, LC3 quantification, Rab7 dissociation assay\",\n      \"journal\": \"The EMBO Journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — acute pharmacological manipulation with direct measurement of PLEKHM1 membrane release and Rab7 cycling, multiple orthogonal approaches, genetic validation\",\n      \"pmids\": [\"31368593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM22 promotes autophagosome-lysosome fusion by directly mediating the association between GABARAP family proteins and PLEKHM1, independent of TRIM22's E3 ubiquitin ligase activity. This scaffolding function of TRIM22 facilitates autophagic clearance of protein aggregates.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay, TRIM22 knockout, autophagy flux assays, ligase-dead mutant\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with rescue, direct interaction assays, ligase-dead control, single lab\",\n      \"pmids\": [\"38009729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Compound alanine mutations at the Y949-R954 region of the PLEKHM1 RH domain decrease protein stability, while compound mutations at L1011-I1018 decrease Rab7 binding; both impair lysosome trafficking and bone resorption in osteoclasts. Compound mutations at R1060-Q1068 are dispensable for Rab7 binding and PLEKHM1 function. Single mutations at the predicted interface (based on RUBICON crystal structure) failed to disrupt binding.\",\n      \"method\": \"Structure-guided mutagenesis based on RUBICON RH-Rab7 crystal structure, co-immunoprecipitation of mutants, lysosome trafficking assay, bone resorption assay in osteoclasts\",\n      \"journal\": \"JBMR Plus\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — structure-guided mutagenesis with functional readouts, single lab, relies on homologous crystal structure not direct PLEKHM1 structure\",\n      \"pmids\": [\"38586475\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PLEKHM1 overexpression in mouse substantia nigra impairs autophagic flux by reducing lysosomal and autolysosomal area, increasing LAMP1-LC3 colocalization, decreasing the autolysosome-to-autophagosome ratio, and causing p62 accumulation with impaired cargo degradation, demonstrating that elevated PLEKHM1 levels disrupt late-stage autophagy in vivo.\",\n      \"method\": \"rAAV-mediated PLEKHM1 overexpression in mouse brain, RFP-EGFP-LC3 autophagy reporter mice, LAMP1 colocalization, p62 staining, dopaminergic neuron quantification\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vivo functional evidence with autophagy reporter and multiple markers, single lab, single study\",\n      \"pmids\": [\"40940751\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PLEKHM1 is a multivalent endolysosomal adaptor that simultaneously engages active (GTP-bound) RAB7 via its C-terminal RH domain, the HOPS tethering complex, and autophagosomal membranes via a conserved LIR motif that binds LC3/GABARAP proteins, thereby coordinating autophagosome-lysosome and endosome-lysosome fusion; its membrane association is dynamically regulated by a late endosomal PI4P-to-PI(4,5)P2 lipid conversion cycle, and it forms a molecular complex with DEF8, FAM98A, and NDEL1 to position lysosomes peripherally in osteoclasts, enabling ruffled border formation and bone resorption, while its loss causes osteopetrosis and its dysregulation impairs autophagic flux in neurons.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PLEKHM1 is a multivalent endolysosomal adaptor that coordinates the convergence of endocytic and autophagic cargo on the lysosome by simultaneously engaging active RAB7, the HOPS tethering complex, and LC3/GABARAP-decorated autophagosomal membranes [#4]. It binds GTP-bound RAB7 directly through a C-terminal Rubicon-homology (RH) domain, an interaction required for its control of endocytic transport [#2], and a conserved LC3-interacting region (LIR) couples this RAB7/HOPS platform to autophagosomal membranes so that PLEKHM1 drives lysosomal degradation of endocytic cargo such as EGFR, autophagic flux, and clearance of protein aggregates [#4]. Its recruitment to late endosomes is dynamically switched by a PI4P-to-PI(4,5)P2 lipid conversion cycle that drives RAB7 inactivation and releases PLEKHM1 from the membrane [#9]. In osteoclasts, PLEKHM1 forms a positioning machinery with DEF8 (which promotes its RAB7 binding), FAM98A, and NDEL1 to distribute lysosomes peripherally and link them to microtubules, enabling ruffled-border formation and bone resorption [#7]; loss-of-function mutations in PLEKHM1 cause osteopetrosis through failure of osteoclast ruffled-border formation and defective bone resorption [#0]. The pathway is exploited by the Salmonella effector SifA, which binds the PLEKHM1 PH2 domain to redirect phagolysosomal membranes to the Salmonella-containing vacuole [#5], and excess PLEKHM1 itself disrupts late-stage autophagy in vivo, impairing autolysosome maturation and cargo degradation in neurons [#12].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established PLEKHM1 as an essential factor in osteoclast vesicular transport by showing its RAB7-dependent localization to late endosomal/lysosomal membranes and the failure of ruffled-border formation when it is mutated.\",\n      \"evidence\": \"Confocal and electron microscopy with mutational analysis in patient osteoclasts and HEK293 cells\",\n      \"pmids\": [\"17404618\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the molecular domain mediating RAB7 association\", \"Mechanism linking RAB7 colocalization to ruffled-border formation unresolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Connected a disease mutation to organelle function by showing the R714C variant impairs endosomal acidification and increases TRACP secretion in osteoclasts.\",\n      \"evidence\": \"Transfection of wild-type vs R714C mutant in HEK293 and RAW 264.7 cells with endosomal pH and TRACP activity assays\",\n      \"pmids\": [\"17997709\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not show how the mutation mechanistically disrupts acidification\", \"Single lab; R714C effect on RAB7 binding not tested\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified the molecular basis of RAB7 engagement by mapping the interaction to a C-terminal Rubicon-homology domain and distinguishing PLEKHM1 from Rubicon in not binding PI3-kinase.\",\n      \"evidence\": \"Homology searches, direct binding assays, and functional knockdown of endocytic transport\",\n      \"pmids\": [\"20943950\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Autophagy role explicitly excluded here but later revised\", \"No structural model of the RH-RAB7 interface\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined PLEKHM1 as a tripartite adaptor bridging endocytic and autophagy pathways by demonstrating simultaneous binding to RAB7, HOPS, and LC3/GABARAP via a LIR motif, with functional control of EGFR degradation, autophagy flux, and aggregate clearance.\",\n      \"evidence\": \"GTP-RAB7 pulldown mass spectrometry, yeast two-hybrid LIR screen, knockout MEFs, and degradation/clearance assays\",\n      \"pmids\": [\"25498145\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address how membrane recruitment is temporally regulated\", \"Stoichiometry of the RAB7-HOPS-LC3 complex unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed pathogen hijacking of the adaptor by showing the Salmonella effector SifA binds the PLEKHM1 PH2 domain to redirect phagolysosomal membranes to the bacterial vacuole.\",\n      \"evidence\": \"Direct SifA-PH2 binding assays, siRNA knockdown, and infection assays in cells and mice\",\n      \"pmids\": [\"25500191\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how SifA binding alters native PLEKHM1-RAB7-HOPS function\", \"Endogenous ligand of the PH2 domain unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Added TRAFD1 as a pathway component by mapping its zinc-finger to a PLEKHM1 region between the PH2 and C1 domains and showing its loss blocks osteoclast resorption and acidification.\",\n      \"evidence\": \"Mass spectrometry, deletion-based domain mapping, and stable shRNA knockdown with acidification/resorption readouts\",\n      \"pmids\": [\"25992615\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the TRAFD1-PLEKHM1 interaction at the molecular level unclear\", \"Single lab; not validated in other systems\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Built the osteoclast lysosome-positioning machine by showing DEF8 promotes PLEKHM1-RAB7 binding and FAM98A/NDEL1 link lysosomes to microtubules, with KO mice displaying increased bone mass and defective lysosome trafficking.\",\n      \"evidence\": \"Germline and conditional KO mice, co-immunoprecipitation, lysosome positioning and bone resorption assays, and siRNA of partners\",\n      \"pmids\": [\"27777970\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Architecture of the DEF8-FAM98A-NDEL1-PLEKHM1 assembly not structurally defined\", \"How microtubule coupling is regulated unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked a disease deletion to mechanism by showing an exon 11 frameshift impairing the RH domain reduces PLEKHM1-RAB7 binding and disrupts EGFR degradation and LC3 conversion.\",\n      \"evidence\": \"Co-immunoprecipitation, EGFR degradation and LC3-I/II ratio assays in HEK293 and U937 cells\",\n      \"pmids\": [\"27291868\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; physiological phenotype not assessed in patient tissue\", \"Does not distinguish endocytic from autophagic contributions\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established dynamic regulation of PLEKHM1 membrane association by showing a PI4P-to-PI(4,5)P2 conversion drives RAB7 dissociation and PLEKHM1 release, with PI4K2A loss impairing RAB7 inactivation and autophagosome-lysosome fusion.\",\n      \"evidence\": \"Chemogenetic acute lipid conversion, PI4K2A deletion, live imaging, and RAB7 dissociation assays\",\n      \"pmids\": [\"31368593\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the kinases/phosphatases acting upstream in physiological signaling\", \"Whether PLEKHM1 directly senses lipids vs follows RAB7 unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified a scaffolding regulator of fusion by showing TRIM22 bridges GABARAP proteins to PLEKHM1 independent of its E3 ligase activity to promote autophagic aggregate clearance.\",\n      \"evidence\": \"Co-immunoprecipitation, proximity ligation, TRIM22 knockout/rescue, and a ligase-dead mutant\",\n      \"pmids\": [\"38009729\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; structural basis of the TRIM22-PLEKHM1-GABARAP assembly unknown\", \"Physiological contexts requiring TRIM22 vs LIR-direct binding undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Dissected the RH domain functionally by structure-guided mutagenesis, separating residues required for protein stability from those required for RAB7 binding, both impairing lysosome trafficking and bone resorption.\",\n      \"evidence\": \"Mutagenesis guided by the RUBICON RH-RAB7 crystal structure, co-IP, lysosome trafficking and bone resorption assays in osteoclasts\",\n      \"pmids\": [\"38586475\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relies on a homologous structure, not a direct PLEKHM1-RAB7 structure\", \"Single point mutations failed to disrupt binding, complicating interface assignment\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated that PLEKHM1 dosage is pathologically relevant by showing overexpression in substantia nigra impairs late-stage autophagy with p62 accumulation and reduced autolysosome maturation.\",\n      \"evidence\": \"rAAV PLEKHM1 overexpression in autophagy reporter mice with LAMP1/LC3/p62 markers\",\n      \"pmids\": [\"40940751\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which excess PLEKHM1 stalls fusion not defined\", \"Single lab; relevance to human neurodegeneration not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the membrane-binding, RAB7-binding, HOPS-binding, and LIR activities of PLEKHM1 are integrated into a stepwise, regulated fusion cycle, and the structure of the native PLEKHM1-RAB7 complex, remain unresolved.\",\n      \"evidence\": \"No direct experimental resolution in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No experimental PLEKHM1 structure\", \"Temporal coordination of partner engagement during a single fusion event undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 2, 7]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4, 9, 10]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 4, 7]}\n    ],\n    \"complexes\": [\"HOPS complex\", \"PLEKHM1-DEF8-FAM98A-NDEL1 lysosome-positioning complex\"],\n    \"partners\": [\"RAB7\", \"HOPS\", \"LC3\", \"GABARAP\", \"DEF8\", \"FAM98A\", \"NDEL1\", \"TRIM22\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}