{"gene":"RAB41","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2005,"finding":"RN-Tre (previously described as a Rab5 GAP) acts as a GTPase-activating protein (GAP) for Rab41, not Rab5. The Rab5-specific GAP is RabGAP-5, while RN-Tre's substrate is Rab41.","method":"Functional GAP activity assays and substrate specificity analysis","journal":"Nature cell biology","confidence":"Medium","confidence_rationale":"Tier 1-2 / Weak — in vitro GAP activity assay reported in abstract, single lab, no mutagenesis details provided in abstract","pmids":["16086013"],"is_preprint":false},{"year":2013,"finding":"Rab41 is required for normal Golgi ribbon organization; siRNA-mediated depletion or overexpression of GDP-locked (inactive) Rab41 — but not wild-type or GTP-locked forms — fragments the Golgi ribbon into clustered punctate elements and causes accumulation of Golgi-associated vesicles. Rab41 depletion partially inhibits ER-to-Golgi transport of VSV-G protein but has little effect on endosome-to-Golgi transport. Rab41 knockdown also inhibits cell growth. Double knockdown with Rab6 causes Golgi fragmentation consistent with parallel pathways.","method":"siRNA knockdown, dominant-negative/constitutively active mutant overexpression, fluorescence and electron microscopy, VSV-G transport assay, genetic epistasis (double knockdown)","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (siRNA, dominant-negative/active mutants, EM, transport assay, epistasis) in single lab","pmids":["23936529"],"is_preprint":false},{"year":2016,"finding":"Rab41/6d interacts preferentially with GTP-locked form (vs. GDP-locked) with dynactin 6 (a dynactin complex subunit) and syntaxin 8, identified by yeast two-hybrid screen and verified by co-immunoprecipitation. Depletion of dynactin 6 or syntaxin 8 produces Golgi fragmentation phenotype matching Rab41 knockdown. Dynactin 6 interaction provides a molecular basis for Rab41's role in minus-end-directed motor recruitment and Golgi ribbon maintenance. None of the Rab41 effector hits overlapped with Rab6a/a' effectors.","method":"Yeast two-hybrid screen, co-immunoprecipitation with GTP- and GDP-locked mutants, siRNA knockdown with fluorescence microscopy","journal":"Frontiers in cell and developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with GTPase mutants, independent knockdown phenotype confirmation, two orthogonal methods in single lab","pmids":["26973836"],"is_preprint":false},{"year":2015,"finding":"Rab41 affects Golgi ribbon organization in a manner contrasting with Rab6; the balance between minus- and plus-end directed motor recruitment is proposed as the major Rab41-dependent factor in Golgi ribbon organization, based on effector studies linking Rab41 to motor proteins.","method":"Fluorescence microscopy-based Golgi organization analysis, effector interaction studies","journal":"International review of cell and molecular biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — review article summarizing findings, single lab, no new primary experimental data described in abstract","pmids":["25708460"],"is_preprint":false},{"year":2018,"finding":"Rab41 localizes to the Golgi apparatus under basal conditions but is relocated to S. pneumoniae-containing autophagic vesicles (PcAV) following induction of autophagy. Formation of PcAV requires intact Rab41-positive Golgi apparatus. E3 ligase Nedd4-1 is recruited to PcAV and generates K63-linked polyubiquitin chains that scaffold PcAV biogenesis for elimination of intracellular S. pneumoniae.","method":"Fluorescence microscopy tracking Rab41 relocalization, Golgi disruption experiments, ubiquitin linkage analysis, Nedd4-1 knockdown/overexpression","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live-cell imaging of relocalization plus functional perturbation with defined phenotypic readout, single lab, multiple orthogonal methods","pmids":["29582580"],"is_preprint":false},{"year":2023,"finding":"Rab41 is critical for maintaining acidification of xenophagolysosomes during bacterial infection. Rab41 translocates to damaged autophagic membranes via adaptor protein TOM1L2 and recruits AAA-ATPase VPS4 to complete ESCRT-mediated membrane repair in a GTPase activity-independent manner. Blocking bacterial cytolysin (via intrabody expression) inhibits ESCRT recruitment to xenophagolysosomes, demonstrating that ESCRT is recruited in response to bacterial toxin-induced membrane damage. The TOM1L2-Rab41 pathway is required for efficient bacterial clearance through xenophagy.","method":"Rab GTPase screen, confocal microscopy, intrabody expression, TOM1L2/VPS4 co-localization and functional analysis, GTPase-dead mutant experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (genetic screen, confocal imaging, intrabody inhibition, GTPase-independent mutant analysis, functional bacterial clearance assay) in single focused study","pmids":["37802980"],"is_preprint":false},{"year":2011,"finding":"RUSC2 RUN domain interacts with Rab41 (as well as Rab1 and Rab35), identified by genome-wide yeast two-hybrid analysis of RUN domain-containing proteins against 60 Rab isoforms.","method":"Yeast two-hybrid assay","journal":"Cell structure and function","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single yeast two-hybrid interaction, not validated by orthogonal method for Rab41 specifically, no functional follow-up on Rab41","pmids":["21737958"],"is_preprint":false}],"current_model":"RAB41 is a Golgi-resident Rab GTPase (whose GAP is RN-Tre) that maintains Golgi ribbon organization through GTP-dependent interactions with dynactin 6 (linking it to minus-end-directed dynein/dynactin motor recruitment) and syntaxin 8; it is required for ER-to-Golgi trafficking and cell growth, and during bacterial infection it relocates from the Golgi to autophagic membranes where it acts via the TOM1L2 adaptor to recruit VPS4 for ESCRT-mediated membrane repair of xenophagolysosomes damaged by bacterial toxins, facilitating efficient intracellular bacterial clearance."},"narrative":{"mechanistic_narrative":"RAB41 is a Golgi-resident Rab GTPase that maintains Golgi ribbon architecture and supports anterograde membrane trafficking, with a distinct stress-induced role in xenophagic clearance of intracellular bacteria [PMID:23936529, PMID:37802980]. Under basal conditions it organizes the Golgi ribbon: depletion or expression of a GDP-locked mutant fragments the ribbon into clustered punctate elements with accumulating vesicles, partially blocks ER-to-Golgi transport of VSV-G, and inhibits cell growth, while acting in parallel with Rab6 [PMID:23936529]. In its GTP-bound state RAB41 engages the dynactin subunit dynactin 6 and syntaxin 8, and loss of either partner reproduces the Golgi fragmentation phenotype, providing a molecular basis for RAB41-dependent recruitment of minus-end-directed motor machinery to the Golgi [PMID:26973836]. RN-Tre serves as its GTPase-activating protein [PMID:16086013]. Upon bacterial infection RAB41 relocalizes from the Golgi to pathogen-containing autophagic vesicles, whose formation depends on an intact RAB41-positive Golgi [PMID:29582580]; on damaged autophagic membranes it is recruited via the adaptor TOM1L2 and, independently of its GTPase activity, recruits the AAA-ATPase VPS4 to drive ESCRT-mediated membrane repair, sustaining xenophagolysosome acidification and efficient bacterial clearance [PMID:37802980].","teleology":[{"year":2005,"claim":"Established that RAB41 has a dedicated regulator by reassigning RN-Tre, previously thought to act on Rab5, as the GAP for RAB41, defining how its GTP cycle is switched off.","evidence":"in vitro GAP activity and substrate specificity assays","pmids":["16086013"],"confidence":"Medium","gaps":["No mutagenesis details or structural basis of GAP recognition provided","GEF and full regulatory cycle not defined","Cellular consequence of RN-Tre-mediated inactivation untested"]},{"year":2013,"claim":"Defined RAB41's core cellular function by showing it is required for Golgi ribbon integrity and anterograde ER-to-Golgi transport, distinguishing it functionally from Rab6.","evidence":"siRNA knockdown, dominant-negative/constitutively-active mutant overexpression, EM, VSV-G transport assay, and double-knockdown epistasis in cultured cells","pmids":["23936529"],"confidence":"High","gaps":["Effectors mediating the Golgi phenotype not identified in this study","Mechanism linking RAB41 to cell growth unresolved","Whether transport defect is direct or secondary to Golgi fragmentation unclear"]},{"year":2016,"claim":"Identified RAB41 effectors, showing GTP-dependent binding to dynactin 6 and syntaxin 8 and providing a molecular mechanism — minus-end motor recruitment — for its Golgi ribbon role.","evidence":"yeast two-hybrid screen with GTP/GDP-locked mutant Co-IP validation and effector knockdown phenotyping","pmids":["26973836"],"confidence":"High","gaps":["Direct demonstration of motor recruitment to Golgi membranes not shown","Stoichiometry and assembly of RAB41-dynactin complex undefined","Functional role of syntaxin 8 interaction not separately dissected"]},{"year":2018,"claim":"Revealed a stress-induced relocalization program in which RAB41 moves from Golgi to bacteria-containing autophagic vesicles, linking Golgi integrity to anti-bacterial autophagy.","evidence":"fluorescence imaging of relocalization, Golgi disruption, ubiquitin-linkage analysis, and Nedd4-1 perturbation during S. pneumoniae infection","pmids":["29582580"],"confidence":"Medium","gaps":["Mechanism driving RAB41 relocalization from Golgi not defined","Direct molecular role of RAB41 at PcAV not yet established here","Relationship between Nedd4-1 ubiquitination and RAB41 unclear"]},{"year":2023,"claim":"Mechanistically resolved RAB41's anti-bacterial role, showing it is recruited to damaged autophagic membranes via TOM1L2 and recruits VPS4 for ESCRT-mediated repair in a GTPase-independent manner.","evidence":"Rab GTPase screen, confocal microscopy, intrabody inhibition of bacterial cytolysin, TOM1L2/VPS4 colocalization, GTPase-dead mutant analysis, and bacterial clearance assays","pmids":["37802980"],"confidence":"High","gaps":["How TOM1L2 selects RAB41 in a GTPase-independent mode is unresolved","Structural basis of RAB41-VPS4 recruitment not defined","Whether basal Golgi role and repair role share regulators is untested"]},{"year":null,"claim":"How RAB41 switches between its GTP-dependent Golgi-organizing function and its GTPase-independent membrane-repair function, and what GEF activates it, remain unknown.","evidence":"","pmids":[],"confidence":"Low","gaps":["No GEF identified for RAB41","No structural model of RAB41 in either complex","Trigger and trafficking route for Golgi-to-autophagosome relocalization undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,1,2]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1,2,4]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[4,5]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4,5]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[5]}],"complexes":[],"partners":["DCTN6","STX8","TOM1L2","VPS4","RN-TRE"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86YS6","full_name":"Ras-related protein Rab-43","aliases":["Ras-related protein Rab-41"],"length_aa":212,"mass_kda":23.3,"function":"The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (PubMed:16086013, PubMed:17562788, PubMed:17684057, PubMed:18664496, PubMed:21255211, PubMed:29069590). Involved in retrograde transport from the endocytic pathway to the Golgi apparatus (PubMed:17684057). Required for the structural integrity of the Golgi complex (PubMed:17684057, PubMed:18664496). Also controls the anterograde ER-to-Golgi transport of nascent G-protein-coupled receptors (including ADRA2A, ADRA2B, ADRA2C, ADRA1B, ADRB2 and AGTR1) and regulates the ER sorting of GPCR members by virtue of its ability to interact directly (PubMed:18664496, PubMed:29069590). Involved in the transport of Shiga toxin from early and recycling endosomes to the trans-Golgi network (PubMed:17562788). Plays a role in the maturation of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis (PubMed:21255211)","subcellular_location":"Golgi apparatus; Golgi apparatus, cis-Golgi network membrane; Golgi apparatus, trans-Golgi network membrane; Endoplasmic reticulum membrane; Endoplasmic reticulum-Golgi intermediate compartment membrane; Cytoplasmic vesicle, phagosome membrane","url":"https://www.uniprot.org/uniprotkb/Q86YS6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RAB41","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RAB41","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"retina","ntpm":53.5}],"url":"https://www.proteinatlas.org/search/RAB41"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q86YS6","domains":[{"cath_id":"3.40.50.300","chopping":"13-185","consensus_level":"high","plddt":93.6755,"start":13,"end":185}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YS6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YS6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YS6-F1-predicted_aligned_error_v6.png","plddt_mean":84.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RAB41","jax_strain_url":"https://www.jax.org/strain/search?query=RAB41"},"sequence":{"accession":"Q86YS6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86YS6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86YS6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YS6"}},"corpus_meta":[{"pmid":"16086013","id":"PMC_16086013","title":"A GTPase-activating protein controls Rab5 function in endocytic trafficking.","date":"2005","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/16086013","citation_count":188,"is_preprint":false},{"pmid":"16684812","id":"PMC_16684812","title":"Rab3A and Rab27A cooperatively regulate the docking step of dense-core vesicle exocytosis in PC12 cells.","date":"2006","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/16684812","citation_count":160,"is_preprint":false},{"pmid":"21737958","id":"PMC_21737958","title":"Genome-wide investigation of the Rab binding activity of RUN domains: development of a novel tool that specifically traps GTP-Rab35.","date":"2011","source":"Cell structure and function","url":"https://pubmed.ncbi.nlm.nih.gov/21737958","citation_count":60,"is_preprint":false},{"pmid":"29582580","id":"PMC_29582580","title":"Molecular mechanisms of Streptococcus pneumoniae-targeted autophagy via pneumolysin, Golgi-resident Rab41, and Nedd4-1-mediated K63-linked ubiquitination.","date":"2018","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29582580","citation_count":45,"is_preprint":false},{"pmid":"25708460","id":"PMC_25708460","title":"How Rab proteins determine Golgi structure.","date":"2015","source":"International review of cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25708460","citation_count":38,"is_preprint":false},{"pmid":"23936529","id":"PMC_23936529","title":"Rab41 is a novel regulator of Golgi apparatus organization that is needed for ER-to-Golgi trafficking and cell growth.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23936529","citation_count":19,"is_preprint":false},{"pmid":"35237504","id":"PMC_35237504","title":"SP1-Mediated Upregulation of circFAM126A Promotes Proliferation and Epithelial-Mesenchymal Transition of Oral Squamous Cell Carcinoma via Regulation of RAB41.","date":"2022","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/35237504","citation_count":11,"is_preprint":false},{"pmid":"37802980","id":"PMC_37802980","title":"Rab41-mediated ESCRT machinery repairs membrane rupture by a bacterial toxin in xenophagy.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37802980","citation_count":10,"is_preprint":false},{"pmid":"26973836","id":"PMC_26973836","title":"Identification of Rab41/6d Effectors Provides an Explanation for the Differential Effects of Rab41/6d and Rab6a/a' on Golgi Organization.","date":"2016","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/26973836","citation_count":9,"is_preprint":false},{"pmid":"15018353","id":"PMC_15018353","title":"Isolation, expression pattern of a novel human RAB gene RAB41 and characterization of its intronless homolog RAB41P.","date":"2003","source":"DNA sequence : the journal of DNA sequencing and mapping","url":"https://pubmed.ncbi.nlm.nih.gov/15018353","citation_count":3,"is_preprint":false},{"pmid":"37240180","id":"PMC_37240180","title":"Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37240180","citation_count":3,"is_preprint":false},{"pmid":"41443816","id":"PMC_41443816","title":"[Rab GTPase network-driven remodeling of membrane trafficking and intracellular bacterial dynamics during infection].","date":"2025","source":"Nihon saikingaku zasshi. Japanese journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/41443816","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8057,"output_tokens":1996,"usd":0.027055,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8946,"output_tokens":2465,"usd":0.053178,"stage2_stop_reason":"end_turn"},"total_usd":0.080233,"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\": 2005,\n      \"finding\": \"RN-Tre (previously described as a Rab5 GAP) acts as a GTPase-activating protein (GAP) for Rab41, not Rab5. The Rab5-specific GAP is RabGAP-5, while RN-Tre's substrate is Rab41.\",\n      \"method\": \"Functional GAP activity assays and substrate specificity analysis\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Weak — in vitro GAP activity assay reported in abstract, single lab, no mutagenesis details provided in abstract\",\n      \"pmids\": [\"16086013\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Rab41 is required for normal Golgi ribbon organization; siRNA-mediated depletion or overexpression of GDP-locked (inactive) Rab41 — but not wild-type or GTP-locked forms — fragments the Golgi ribbon into clustered punctate elements and causes accumulation of Golgi-associated vesicles. Rab41 depletion partially inhibits ER-to-Golgi transport of VSV-G protein but has little effect on endosome-to-Golgi transport. Rab41 knockdown also inhibits cell growth. Double knockdown with Rab6 causes Golgi fragmentation consistent with parallel pathways.\",\n      \"method\": \"siRNA knockdown, dominant-negative/constitutively active mutant overexpression, fluorescence and electron microscopy, VSV-G transport assay, genetic epistasis (double knockdown)\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (siRNA, dominant-negative/active mutants, EM, transport assay, epistasis) in single lab\",\n      \"pmids\": [\"23936529\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Rab41/6d interacts preferentially with GTP-locked form (vs. GDP-locked) with dynactin 6 (a dynactin complex subunit) and syntaxin 8, identified by yeast two-hybrid screen and verified by co-immunoprecipitation. Depletion of dynactin 6 or syntaxin 8 produces Golgi fragmentation phenotype matching Rab41 knockdown. Dynactin 6 interaction provides a molecular basis for Rab41's role in minus-end-directed motor recruitment and Golgi ribbon maintenance. None of the Rab41 effector hits overlapped with Rab6a/a' effectors.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation with GTP- and GDP-locked mutants, siRNA knockdown with fluorescence microscopy\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with GTPase mutants, independent knockdown phenotype confirmation, two orthogonal methods in single lab\",\n      \"pmids\": [\"26973836\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rab41 affects Golgi ribbon organization in a manner contrasting with Rab6; the balance between minus- and plus-end directed motor recruitment is proposed as the major Rab41-dependent factor in Golgi ribbon organization, based on effector studies linking Rab41 to motor proteins.\",\n      \"method\": \"Fluorescence microscopy-based Golgi organization analysis, effector interaction studies\",\n      \"journal\": \"International review of cell and molecular biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — review article summarizing findings, single lab, no new primary experimental data described in abstract\",\n      \"pmids\": [\"25708460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Rab41 localizes to the Golgi apparatus under basal conditions but is relocated to S. pneumoniae-containing autophagic vesicles (PcAV) following induction of autophagy. Formation of PcAV requires intact Rab41-positive Golgi apparatus. E3 ligase Nedd4-1 is recruited to PcAV and generates K63-linked polyubiquitin chains that scaffold PcAV biogenesis for elimination of intracellular S. pneumoniae.\",\n      \"method\": \"Fluorescence microscopy tracking Rab41 relocalization, Golgi disruption experiments, ubiquitin linkage analysis, Nedd4-1 knockdown/overexpression\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live-cell imaging of relocalization plus functional perturbation with defined phenotypic readout, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"29582580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Rab41 is critical for maintaining acidification of xenophagolysosomes during bacterial infection. Rab41 translocates to damaged autophagic membranes via adaptor protein TOM1L2 and recruits AAA-ATPase VPS4 to complete ESCRT-mediated membrane repair in a GTPase activity-independent manner. Blocking bacterial cytolysin (via intrabody expression) inhibits ESCRT recruitment to xenophagolysosomes, demonstrating that ESCRT is recruited in response to bacterial toxin-induced membrane damage. The TOM1L2-Rab41 pathway is required for efficient bacterial clearance through xenophagy.\",\n      \"method\": \"Rab GTPase screen, confocal microscopy, intrabody expression, TOM1L2/VPS4 co-localization and functional analysis, GTPase-dead mutant experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (genetic screen, confocal imaging, intrabody inhibition, GTPase-independent mutant analysis, functional bacterial clearance assay) in single focused study\",\n      \"pmids\": [\"37802980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RUSC2 RUN domain interacts with Rab41 (as well as Rab1 and Rab35), identified by genome-wide yeast two-hybrid analysis of RUN domain-containing proteins against 60 Rab isoforms.\",\n      \"method\": \"Yeast two-hybrid assay\",\n      \"journal\": \"Cell structure and function\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single yeast two-hybrid interaction, not validated by orthogonal method for Rab41 specifically, no functional follow-up on Rab41\",\n      \"pmids\": [\"21737958\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RAB41 is a Golgi-resident Rab GTPase (whose GAP is RN-Tre) that maintains Golgi ribbon organization through GTP-dependent interactions with dynactin 6 (linking it to minus-end-directed dynein/dynactin motor recruitment) and syntaxin 8; it is required for ER-to-Golgi trafficking and cell growth, and during bacterial infection it relocates from the Golgi to autophagic membranes where it acts via the TOM1L2 adaptor to recruit VPS4 for ESCRT-mediated membrane repair of xenophagolysosomes damaged by bacterial toxins, facilitating efficient intracellular bacterial clearance.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RAB41 is a Golgi-resident Rab GTPase that maintains Golgi ribbon architecture and supports anterograde membrane trafficking, with a distinct stress-induced role in xenophagic clearance of intracellular bacteria [#1, #5]. Under basal conditions it organizes the Golgi ribbon: depletion or expression of a GDP-locked mutant fragments the ribbon into clustered punctate elements with accumulating vesicles, partially blocks ER-to-Golgi transport of VSV-G, and inhibits cell growth, while acting in parallel with Rab6 [#1]. In its GTP-bound state RAB41 engages the dynactin subunit dynactin 6 and syntaxin 8, and loss of either partner reproduces the Golgi fragmentation phenotype, providing a molecular basis for RAB41-dependent recruitment of minus-end-directed motor machinery to the Golgi [#2]. RN-Tre serves as its GTPase-activating protein [#0]. Upon bacterial infection RAB41 relocalizes from the Golgi to pathogen-containing autophagic vesicles, whose formation depends on an intact RAB41-positive Golgi [#4]; on damaged autophagic membranes it is recruited via the adaptor TOM1L2 and, independently of its GTPase activity, recruits the AAA-ATPase VPS4 to drive ESCRT-mediated membrane repair, sustaining xenophagolysosome acidification and efficient bacterial clearance [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established that RAB41 has a dedicated regulator by reassigning RN-Tre, previously thought to act on Rab5, as the GAP for RAB41, defining how its GTP cycle is switched off.\",\n      \"evidence\": \"in vitro GAP activity and substrate specificity assays\",\n      \"pmids\": [\"16086013\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No mutagenesis details or structural basis of GAP recognition provided\", \"GEF and full regulatory cycle not defined\", \"Cellular consequence of RN-Tre-mediated inactivation untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined RAB41's core cellular function by showing it is required for Golgi ribbon integrity and anterograde ER-to-Golgi transport, distinguishing it functionally from Rab6.\",\n      \"evidence\": \"siRNA knockdown, dominant-negative/constitutively-active mutant overexpression, EM, VSV-G transport assay, and double-knockdown epistasis in cultured cells\",\n      \"pmids\": [\"23936529\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Effectors mediating the Golgi phenotype not identified in this study\", \"Mechanism linking RAB41 to cell growth unresolved\", \"Whether transport defect is direct or secondary to Golgi fragmentation unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified RAB41 effectors, showing GTP-dependent binding to dynactin 6 and syntaxin 8 and providing a molecular mechanism — minus-end motor recruitment — for its Golgi ribbon role.\",\n      \"evidence\": \"yeast two-hybrid screen with GTP/GDP-locked mutant Co-IP validation and effector knockdown phenotyping\",\n      \"pmids\": [\"26973836\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Direct demonstration of motor recruitment to Golgi membranes not shown\", \"Stoichiometry and assembly of RAB41-dynactin complex undefined\", \"Functional role of syntaxin 8 interaction not separately dissected\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed a stress-induced relocalization program in which RAB41 moves from Golgi to bacteria-containing autophagic vesicles, linking Golgi integrity to anti-bacterial autophagy.\",\n      \"evidence\": \"fluorescence imaging of relocalization, Golgi disruption, ubiquitin-linkage analysis, and Nedd4-1 perturbation during S. pneumoniae infection\",\n      \"pmids\": [\"29582580\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Mechanism driving RAB41 relocalization from Golgi not defined\", \"Direct molecular role of RAB41 at PcAV not yet established here\", \"Relationship between Nedd4-1 ubiquitination and RAB41 unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mechanistically resolved RAB41's anti-bacterial role, showing it is recruited to damaged autophagic membranes via TOM1L2 and recruits VPS4 for ESCRT-mediated repair in a GTPase-independent manner.\",\n      \"evidence\": \"Rab GTPase screen, confocal microscopy, intrabody inhibition of bacterial cytolysin, TOM1L2/VPS4 colocalization, GTPase-dead mutant analysis, and bacterial clearance assays\",\n      \"pmids\": [\"37802980\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"How TOM1L2 selects RAB41 in a GTPase-independent mode is unresolved\", \"Structural basis of RAB41-VPS4 recruitment not defined\", \"Whether basal Golgi role and repair role share regulators is untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RAB41 switches between its GTP-dependent Golgi-organizing function and its GTPase-independent membrane-repair function, and what GEF activates it, remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No GEF identified for RAB41\", \"No structural model of RAB41 in either complex\", \"Trigger and trafficking route for Golgi-to-autophagosome relocalization undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DCTN6\", \"STX8\", \"TOM1L2\", \"VPS4\", \"RN-Tre\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}