{"gene":"SH3GLB1","run_date":"2026-04-28T20:42:07","timeline":{"discoveries":[{"year":2001,"finding":"Bif-1 (SH3GLB1) was identified as a novel Bax-binding protein via yeast two-hybrid cloning. It contains a C-terminal SH3 domain, localizes to cytoplasm, and directly interacts with Bax as confirmed by co-immunoprecipitation and immunofluorescence. Overexpression of Bif-1 promotes Bax conformational change, caspase activation, and apoptotic cell death following IL-3 deprivation.","method":"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence, overexpression apoptosis assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Y2H, Co-IP, IF, functional assay) in a single foundational paper, highly cited","pmids":["11259440"],"is_preprint":false},{"year":2005,"finding":"Bif-1 plays a regulatory role in apoptotic activation of both Bax and Bak. RNAi-mediated knockdown of Bif-1 in HeLa cells abrogated Bax and Bak conformational change, cytochrome c release, and caspase-3 activation. Bif-1 heterodimerizes with Bax on mitochondria, and this interaction is enhanced by apoptosis induction prior to Bax conformational change. Bif-1 does not directly interact with Bak.","method":"RNA interference, Bif-1 knockout MEFs, co-immunoprecipitation, mitochondrial fractionation, caspase activity assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, clean KO/KD with defined apoptotic phenotype, replicated in multiple cell systems","pmids":["16227588"],"is_preprint":false},{"year":2007,"finding":"Bif-1 interacts with Beclin 1 through UVRAG and functions as a positive mediator of class III PI3-kinase (PI3KC3/Vps34). The SH3 domain of Bif-1 is sufficient for binding UVRAG, but both the BAR and SH3 domains are required to activate PI3KC3 and induce autophagosome formation. Upon nutrient deprivation, Bif-1 localizes to autophagosomes where it co-localizes with Atg5 and LC3. Loss of Bif-1 suppresses autophagosome formation.","method":"Co-immunoprecipitation, domain deletion mutants, siRNA knockdown, fluorescence microscopy, autophagosome formation assay","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, domain mapping, clean KO/KD, subcellular localization, highly cited foundational paper","pmids":["17891140"],"is_preprint":false},{"year":2008,"finding":"Bif-1 N-BAR domain stimulates BAX-driven mitochondrial outer membrane permeabilization (MOMP) in a reconstituted system using purified proteins and MOM-like liposomes. This stimulatory effect requires physical interaction between Bif-1 N-BAR and BAX and depends on the presence of cardiolipin. Large-scale morphological membrane rearrangements by Bif-1 N-BAR could be separated from functional BAX activation. DLP1/Drp1 did not stimulate BAX permeabilizing function.","method":"In vitro reconstitution with purified proteins and MOM-like liposomes, liposome permeabilization assay, domain mutant analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstitution with purified components, mutagenesis/domain dissection, multiple orthogonal readouts","pmids":["19074440"],"is_preprint":false},{"year":2008,"finding":"c-Src kinase directly binds to and phosphorylates Bif-1 on tyrosine 80. Src phosphorylation of Bif-1 suppresses the interaction between Bif-1 and Bax, thereby inhibiting Bax activation during anoikis. Apoptotic stimuli repress this phosphorylation event.","method":"In vitro kinase assay, co-immunoprecipitation, site-directed mutagenesis (Y80), anoikis apoptosis assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro kinase assay plus mutagenesis and functional consequence demonstrated","pmids":["18474606"],"is_preprint":false},{"year":2010,"finding":"A specific PI3K-III sub-complex containing VPS15, VPS34, Beclin 1, UVRAG, and BIF-1 (but not ATG14L) regulates both degradative endocytic receptor downregulation and cytokinesis. BIF-1 and UVRAG localize strongly to the midbody during cytokinesis.","method":"siRNA depletion of individual subunits, high-content microscopy, cytokinesis and receptor degradation assays, subcellular localization","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 — systematic siRNA screen with defined phenotypic readouts; single lab","pmids":["20643123"],"is_preprint":false},{"year":2010,"finding":"GSK-3β inhibition results in elevation of Bif-1 protein levels. Silencing Bif-1 expression abrogates GSK-3β-inhibition-induced autophagic response and necrotic cell death under serum starvation, placing Bif-1 downstream of GSK-3β in regulating autophagy-dependent cell death.","method":"siRNA knockdown, chemical inhibitors, cell death assays (apoptosis/necrosis markers), autophagy monitoring","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — genetic epistasis via siRNA with defined cellular phenotypes; single lab","pmids":["20159967"],"is_preprint":false},{"year":2011,"finding":"Bif-1's N-BAR domain is required for membrane binding and bending activity and mediates fission of Golgi membranes during autophagy induction. Loss of Bif-1 or inhibition of the PI3KC3 complex II suppresses starvation-induced Golgi fission and peripheral redistribution of Atg9. N-BAR domain mutants lacking membrane binding/bending activity fail to restore Golgi fission, Atg9 puncta formation, or autophagosome formation.","method":"N-BAR domain mutants, fluorescence microscopy (live-cell), Bif-1 knockout/knockdown cells, Atg9 trafficking assay","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 — structure-function analysis with domain mutants, clean KO cells, multiple readouts in single lab","pmids":["21068542"],"is_preprint":false},{"year":2013,"finding":"Bif-1 is indispensable for autophagy-dependent clearance of damaged mitochondria (mitophagy). Loss of Bif-1 results in accumulation of ER-associated immature autophagosomes and suppresses autophagosome maturation. Allelic loss of Bif-1 increases mitochondrial mass, accumulation of DNA damage, and upregulation of anti-apoptotic Mcl-1 in Myc-driven prelymphomatous cells.","method":"Bif-1 KO and haploinsufficient mice, Eμ-Myc transgenic lymphoma model, electron microscopy, mitophagy assay (CCCP treatment), flow cytometry","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic KO with multiple defined molecular phenotypes, electron microscopy, replicated in MEFs","pmids":["23287860"],"is_preprint":false},{"year":2013,"finding":"SH3GLB1 (Bif-1) is present on endolysosomal carriers containing nicotinic acetylcholine receptors (CHRN) in skeletal muscle neuromuscular junctions. SH3GLB1-positive CHRN vesicles are surrounded by autophagic marker LC3 in an ATG7-dependent fashion, placing SH3GLB1 in selective autophagy-mediated CHRN turnover regulated by TRIM63.","method":"Co-immunoprecipitation, immunofluorescence co-localization, ATG7 knockout mice, denervation model","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP and co-localization with genetic KO context; single lab","pmids":["24220501"],"is_preprint":false},{"year":2016,"finding":"Bif-1 interacts with Dynamin 2 (DNM2) and this interaction is enhanced upon nutrient starvation. Bif-1 and DNM2 cooperatively mediate fission of Atg9-containing membranes from a Rab11-positive reservoir during autophagy. Inhibition of DNM2 GTPase activity results in accumulation of Atg9-positive tubular structures. Atg9 trafficking to the Rab11 reservoir is Bif-1-independent, but membrane tubulation from this reservoir requires Bif-1.","method":"Co-immunoprecipitation (Bif-1–DNM2 interaction), DNM2 GTPase inhibitor, fluorescence microscopy, Bif-1 KD cells, live-cell imaging","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus functional dissection with inhibitor and KD; single lab","pmids":["26980706"],"is_preprint":false},{"year":2016,"finding":"Threonine-145 phosphorylation of SH3GLB1 regulates CHRN endocytic trafficking at the neuromuscular junction. Phosphomimetic T145E SH3GLB1 slows processing of endocytic CHRN vesicles, while phosphodeficient T145A augments it. Co-expression of RAB5 largely rescues the slowed processing induced by T145E. Phosphomutants alter expression of RAB5 activity regulators without changing RAB5 co-localization with CHRN vesicles.","method":"Overexpression of T145E and T145A phosphomutants, RAB5 co-expression rescue, in vivo neuromuscular junction imaging","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 — phosphomutant analysis with epistasis rescue experiment; single lab","pmids":["27715385"],"is_preprint":false},{"year":2016,"finding":"Bif-1 deficiency reduces basal adipose tissue lipolysis and impairs fasting/refeeding-induced lipid droplet clearance in the liver, promoting adipocyte hypertrophy and obesity. Bif-1 loss downregulates Atg9a and Lamp1 expression in adipose tissue, linking its membrane-curvature function to lipid catabolism.","method":"Bif-1 knockout mice, adipose tissue lipolysis assay, hepatic lipid droplet clearance assay, Western blotting","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — clean KO mouse model with defined metabolic and molecular phenotypes; single lab","pmids":["26857140"],"is_preprint":false},{"year":2017,"finding":"Calpain (CAPNS1-dependent) is required for dynamic flux of Atg9/Bif-1 vesicles from Golgi stacks toward autophagosomes upon thapsigargin-induced autophagy. CAPNS1 depletion causes Atg9 and Bif-1 to remain in GM130-positive Golgi stacks. A Bif-1 point mutant resistant to calpain processing leads to accumulation of endogenous p62 and LC3-II. Atg9 fails to interact with Vps34 in CAPNS1-depleted cells.","method":"CAPNS1 siRNA depletion, calpain-resistant Bif-1 point mutant, co-immunoprecipitation (Atg9-Vps34), fluorescence microscopy","journal":"Biology open","confidence":"Medium","confidence_rationale":"Tier 2 — point mutant analysis, Co-IP, and genetic depletion with defined phenotypes; single lab","pmids":["28302665"],"is_preprint":false},{"year":2018,"finding":"SRRM4 promotes alternative RNA splicing of the Bif-1 gene to produce neural-specific variants Bif-1b and Bif-1c in treatment-induced neuroendocrine prostate cancer. Bif-1a (predominant in adenocarcinoma) is pro-apoptotic, while Bif-1b and Bif-1c are anti-apoptotic under camptothecin and UV treatment.","method":"Whole transcriptome sequencing, SRRM4 overexpression/knockdown, isoform-specific apoptosis assays, patient tumor samples and xenografts","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 — isoform-specific functional assays with defined apoptotic phenotype and identification of splice regulator; single lab","pmids":["29759485"],"is_preprint":false},{"year":2019,"finding":"Upon cell stress, Bif-1 translocates to mitochondria and binds prohibitin-2 via its C-terminus (specifically via tryptophan-344), causing disruption of the prohibitin complex and proteolytic inactivation of the inner membrane fusion protein OPA1, leading to mitochondrial fragmentation and apoptosis. Bif-1 deficiency or W344 mutation prevents prohibitin-2 binding, OPA1 proteolysis, and mitochondrial fragmentation.","method":"Co-immunoprecipitation, domain deletion analysis, W344 point mutation, Bif-1 KO cells and mice, renal ischemia-reperfusion model, mitochondrial morphology analysis","journal":"Journal of the American Society of Nephrology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, site-directed mutagenesis, clean KO cells and in vivo model with multiple orthogonal readouts","pmids":["31126972"],"is_preprint":false},{"year":2020,"finding":"BIF-1 inhibits both mitochondrial respiration and glycolytic ATP production. CRISPR/Cas9 knockout of BIF-1 in melanoma cells results in increased mitochondrial respiration, metabolic acidification, and ATP production, promoting higher proliferation rates in vitro and in vivo, independent of effects on apoptosis and autophagy.","method":"CRISPR/Cas9 knockout, Seahorse metabolic assay, in vitro and in vivo proliferation assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — clean CRISPR KO with quantitative metabolic phenotype; single lab","pmids":["32493957"],"is_preprint":false},{"year":2022,"finding":"SUMO2 SUMOylates SH3GLB1 at position K82 (predicted and validated by co-IP and confocal co-localization). Ionizing radiation promotes the interaction between SUMO2 and SH3GLB1, and SH3GLB1 interacts with mitochondrial membrane proteins MFN1/2, TOM20, and Drp1 upon IR, mediating mitophagy activation. SH3GLB1 deficiency inhibits mitophagy and restores mitochondrial cristae.","method":"Co-immunoprecipitation, laser confocal microscopy, SH3GLB1 KO cells, mitophagy assay, bioinformatics prediction of SUMOylation site","journal":"European journal of pharmacology","confidence":"Low","confidence_rationale":"Tier 3 — Co-IP and co-localization for SUMOylation; K82 site based partly on prediction; single lab","pmids":["35487252"],"is_preprint":false},{"year":2012,"finding":"Bif-1 promotes EGFR endocytic degradation. Loss of Bif-1 sequesters internalized EGF in Rab5-positive endosomes, delays EGFR trafficking to lysosomes, impairs Rab7 recruitment and activation to EGF-positive vesicles, and prolongs ERK1/2 activation. Bif-1 suppression increases chemotactic cell migration in an EGFR-dependent manner.","method":"siRNA knockdown, fluorescence microscopy (Rab5, Rab7, EGF trafficking), EGFR degradation assay, ERK phosphorylation assay, migration assay with gefitinib rescue","journal":"Cancer biology & therapy","confidence":"Medium","confidence_rationale":"Tier 2 — KD with multiple mechanistic readouts (vesicle trafficking, Rab7 activation, EGFR degradation) and inhibitor rescue; single lab","pmids":["22785202"],"is_preprint":false},{"year":2025,"finding":"SH3GLB1 is required for nuclear localization of the NOTCH2 intracellular domain (N2ICD) and NOTCH2 pathway activation in glioblastoma cells under hypoxia. SH3GLB1 is transcriptionally induced by HIF-2A under hypoxic conditions, and its genetic depletion reduces tumorigenic potential and impairs tumor growth in vivo.","method":"Genetic depletion (siRNA/shRNA), nuclear fractionation, NOTCH2 signaling assay, in vivo xenograft, HIF-2A transcription factor binding analysis","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 — single lab, limited mechanistic detail on how SH3GLB1 enables N2ICD nuclear localization","pmids":["40639082"],"is_preprint":false}],"current_model":"SH3GLB1/Bif-1 is a multifunctional endophilin protein with N-BAR and SH3 domains that (1) binds Bax (interaction inhibited by c-Src phosphorylation at Y80) and cooperates with cardiolipin to stimulate BAX/BAK conformational change and mitochondrial outer membrane permeabilization during apoptosis; (2) uses its SH3 domain to bind UVRAG and thereby joins the Beclin1–UVRAG–PI3KC3 complex to promote autophagosome nucleation; (3) employs its N-BAR membrane-bending activity to drive Golgi fission and Atg9/Dynamin2-dependent vesicle generation for autophagosome biogenesis; (4) mediates mitophagy by facilitating ATG9-containing membrane delivery to damaged mitochondria; and (5) promotes apoptotic mitochondrial fragmentation by translocating to mitochondria and binding prohibitin-2 (via W344) to disrupt the prohibitin complex and induce OPA1 proteolysis."},"narrative":{"teleology":[{"year":2001,"claim":"The initial discovery that Bif-1 is a Bax-interacting protein established a direct molecular link between an endophilin-family BAR/SH3 protein and mitochondrial apoptosis.","evidence":"Yeast two-hybrid screen with Bax bait followed by co-immunoprecipitation, immunofluorescence, and overexpression apoptosis assays in IL-3-deprived cells","pmids":["11259440"],"confidence":"High","gaps":["Endogenous stoichiometry and kinetics of Bif-1–Bax interaction unknown","Whether Bif-1 directly activates Bax or acts as a scaffold unresolved","Bak interaction status not addressed"]},{"year":2005,"claim":"Extending beyond overexpression, loss-of-function studies showed Bif-1 is required for both Bax and Bak conformational activation, cytochrome c release, and caspase-3 activation, establishing it as a non-redundant upstream regulator of intrinsic apoptosis.","evidence":"siRNA knockdown in HeLa and Bif-1 knockout MEFs with co-immunoprecipitation, mitochondrial fractionation, and caspase assays","pmids":["16227588"],"confidence":"High","gaps":["Mechanism by which Bif-1 promotes Bak activation without direct binding unclear","Tissue-specific requirements not tested"]},{"year":2007,"claim":"Discovery that Bif-1 links to the Beclin 1–UVRAG–PI3KC3 autophagy complex via its SH3 domain revealed a second major function in autophagosome nucleation, distinct from its apoptotic role.","evidence":"Co-immunoprecipitation with domain deletion mapping, siRNA knockdown, fluorescence co-localization with Atg5 and LC3 upon nutrient deprivation","pmids":["17891140"],"confidence":"High","gaps":["Whether Bif-1 membrane-bending activity is required for PI3KC3 activation versus autophagosome membrane supply not separated","Regulation of Bif-1–UVRAG interaction unknown"]},{"year":2008,"claim":"Two studies resolved regulatory and biophysical mechanisms: reconstitution showed Bif-1 N-BAR stimulates Bax-mediated liposome permeabilization in a cardiolipin-dependent manner, while c-Src phosphorylation at Y80 was identified as a negative switch that disrupts the Bif-1–Bax interaction during anoikis.","evidence":"Purified protein reconstitution on MOM-like liposomes with domain mutants (PMID:19074440); in vitro kinase assay with Y80 mutagenesis and anoikis assay (PMID:18474606)","pmids":["19074440","18474606"],"confidence":"High","gaps":["Whether Y80 phosphorylation also regulates autophagy function not tested","Structural basis of cardiolipin requirement unresolved","Kinase(s) that dephosphorylate Y80 upon apoptosis not identified"]},{"year":2010,"claim":"Bif-1 was placed in a specific PI3KC3 sub-complex (with UVRAG, not ATG14L) that regulates endocytic receptor degradation and cytokinesis, revealing non-autophagic functions of this complex.","evidence":"Systematic siRNA depletion of PI3KC3 subunits with high-content microscopy for cytokinesis and receptor degradation phenotypes","pmids":["20643123"],"confidence":"Medium","gaps":["Direct contribution of Bif-1 membrane bending to cytokinesis not tested","Whether midbody localization is dependent on UVRAG not determined"]},{"year":2011,"claim":"Structure-function analysis showed that Bif-1 N-BAR membrane-bending activity drives Golgi fission and Atg9 redistribution during starvation, mechanistically separating its membrane-remodeling role from PI3KC3 activation in autophagosome biogenesis.","evidence":"N-BAR domain mutants lacking membrane binding/bending in Bif-1 KO cells with live-cell imaging of Golgi fission and Atg9 puncta","pmids":["21068542"],"confidence":"High","gaps":["Lipid specificity of N-BAR binding on Golgi membranes not characterized","Whether N-BAR acts alone or requires co-factors for fission unknown"]},{"year":2012,"claim":"Bif-1 was shown to promote EGFR endocytic degradation by facilitating Rab7 recruitment, establishing it as a regulator of endosome-to-lysosome trafficking beyond autophagy.","evidence":"siRNA knockdown with EGF trafficking imaging, Rab5/Rab7 co-localization, EGFR degradation kinetics, and gefitinib rescue of migration phenotype","pmids":["22785202"],"confidence":"Medium","gaps":["Whether Bif-1 acts directly on Rab7 activation or indirectly via PI3KC3-UVRAG not resolved","Applicability to other receptor tyrosine kinases untested"]},{"year":2013,"claim":"Bif-1 was shown to be indispensable for mitophagy; its loss caused accumulation of immature autophagosomes at the ER and increased mitochondrial mass, linking its membrane-remodeling activity to organelle quality control and tumor suppression in a Myc-driven lymphoma model.","evidence":"Bif-1 KO and haploinsufficient mice crossed to Eμ-Myc transgenic model, electron microscopy, CCCP-induced mitophagy assay","pmids":["23287860"],"confidence":"High","gaps":["Molecular mechanism of ER-to-autophagosome maturation arrest not identified","Whether Bif-1 directly senses mitochondrial damage unknown"]},{"year":2016,"claim":"Bif-1 was found to cooperate with Dynamin 2 in fission of Atg9-containing membranes from a Rab11-positive recycling endosome reservoir, defining the vesicle source and scission machinery for autophagosome membrane supply.","evidence":"Co-immunoprecipitation of Bif-1–DNM2, DNM2 GTPase inhibitor causing Atg9-positive tubule accumulation, live-cell imaging in Bif-1 KD cells","pmids":["26980706"],"confidence":"Medium","gaps":["Direct biochemical reconstitution of Bif-1/DNM2-mediated membrane fission not performed","Whether other BAR proteins compensate partially not addressed"]},{"year":2016,"claim":"Bif-1 deficiency in mice impaired adipose tissue lipolysis and hepatic lipid droplet clearance, extending its autophagy/membrane-remodeling role to whole-body lipid metabolism.","evidence":"Bif-1 KO mice with adipose and liver metabolic phenotyping, Western blot for Atg9a and Lamp1","pmids":["26857140"],"confidence":"Medium","gaps":["Cell-autonomous versus systemic contribution not separated","Lipid droplet autophagy mechanism not detailed"]},{"year":2017,"claim":"Calpain-dependent processing of Bif-1 was identified as a regulatory step for release of Atg9/Bif-1 vesicles from the Golgi during ER-stress-induced autophagy, adding a protease-based control layer.","evidence":"CAPNS1 siRNA, calpain-resistant Bif-1 mutant, Co-IP of Atg9–Vps34 interaction in depleted cells","pmids":["28302665"],"confidence":"Medium","gaps":["Exact cleavage site and cleavage product identity not mapped","Whether calpain processing affects apoptotic function not tested"]},{"year":2018,"claim":"SRRM4-mediated alternative splicing was shown to generate neural-specific Bif-1 isoforms (Bif-1b/c) with anti-apoptotic properties, in contrast to the pro-apoptotic canonical Bif-1a, revealing isoform-specific functional switching in neuroendocrine prostate cancer.","evidence":"Whole-transcriptome sequencing, SRRM4 overexpression/knockdown, isoform-specific apoptosis assays in patient tumors and xenografts","pmids":["29759485"],"confidence":"Medium","gaps":["Structural basis for isoform-specific apoptotic reversal not determined","Whether splice variants differ in autophagy function untested"]},{"year":2019,"claim":"A stress-induced mitochondrial translocation pathway was elucidated whereby Bif-1 binds prohibitin-2 via W344, disrupting the PHB1/PHB2 complex and triggering OPA1 proteolysis to drive mitochondrial fragmentation, providing a mechanistic link between Bif-1 and inner membrane dynamics.","evidence":"Reciprocal Co-IP, W344 point mutant, Bif-1 KO cells and mice, renal ischemia-reperfusion in vivo model with mitochondrial morphology analysis","pmids":["31126972"],"confidence":"High","gaps":["Signal triggering Bif-1 mitochondrial translocation not identified","Whether PHB2 disruption also affects cristae-dependent apoptosis independently of OPA1 not tested"]},{"year":2020,"claim":"CRISPR knockout revealed that Bif-1 suppresses both mitochondrial respiration and glycolysis, identifying a metabolic tumor-suppressor function independent of its canonical apoptosis and autophagy roles.","evidence":"CRISPR/Cas9 KO in melanoma cells, Seahorse metabolic flux assays, in vitro and in vivo proliferation assays","pmids":["32493957"],"confidence":"Medium","gaps":["Molecular mechanism by which Bif-1 suppresses respiration and glycolysis not identified","Whether this reflects a direct metabolic activity or indirect consequence of mitochondrial remodeling unclear"]},{"year":null,"claim":"Key unresolved questions include: the structural basis of Bif-1 N-BAR selectivity for different organelle membranes, the identity of signals directing Bif-1 mitochondrial translocation, how Bif-1 directly suppresses mitochondrial metabolism, and whether the multiple post-translational modifications (Y80 phosphorylation, T145 phosphorylation, SUMOylation, calpain cleavage) act in a coordinated regulatory network.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of full-length Bif-1 or its complexes exists","Integrated PTM regulatory logic not tested","Isoform-specific functions in autophagy remain unexplored"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[3,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,15]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,10]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[1,15,17]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[7,13]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[2,9,10]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[18]}],"pathway":[{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[0,1,3,4,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,7,8,10,13]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[18,5]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[8,15]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[12,16]}],"complexes":["Beclin 1–UVRAG–PI3KC3 complex"],"partners":["BAX","UVRAG","BECN1","PHB2","DNM2","ATG9A","SRC"],"other_free_text":[]},"mechanistic_narrative":"SH3GLB1 (Bif-1) is an N-BAR and SH3 domain-containing endophilin family protein that couples membrane remodeling to apoptosis, autophagy, and endosomal trafficking. In apoptosis, SH3GLB1 directly binds Bax on mitochondria to promote Bax/Bak conformational activation and mitochondrial outer membrane permeabilization in a cardiolipin-dependent manner, a function negatively regulated by c-Src phosphorylation at Y80; it also translocates to mitochondria under stress to bind prohibitin-2 via W344, disrupting the prohibitin complex and triggering OPA1 proteolysis and mitochondrial fragmentation [PMID:11259440, PMID:19074440, PMID:18474606, PMID:31126972]. In autophagy, SH3GLB1 uses its SH3 domain to engage UVRAG within the Beclin 1–PI3KC3 complex to promote autophagosome nucleation, while its N-BAR domain drives Golgi membrane fission and generation of Atg9/Dynamin 2-containing vesicles required for autophagosome biogenesis and mitophagy [PMID:17891140, PMID:21068542, PMID:26980706, PMID:23287860]. SH3GLB1 additionally facilitates endolysosomal EGFR degradation by promoting Rab7 recruitment to endosomes, and its loss leads to prolonged EGFR/ERK signaling, metabolic reprogramming with increased mitochondrial respiration and glycolysis, and impaired lipid catabolism [PMID:22785202, PMID:32493957, PMID:26857140]."},"prefetch_data":{"uniprot":{"accession":"Q9Y371","full_name":"Endophilin-B1","aliases":["Bax-interacting factor 1","Bif-1","SH3 domain-containing GRB2-like protein B1"],"length_aa":365,"mass_kda":40.8,"function":"May be required for normal outer mitochondrial membrane dynamics (PubMed:15452144). Required for coatomer-mediated retrograde transport in certain cells (By similarity). May recruit other proteins to membranes with high curvature. May promote membrane fusion (PubMed:11604418). Involved in activation of caspase-dependent apoptosis by promoting BAX/BAK1 activation (PubMed:16227588). Isoform 1 acts proapoptotic in fibroblasts (By similarity). Involved in caspase-independent apoptosis during nutrition starvation and involved in the regulation of autophagy. Activates lipid kinase activity of PIK3C3 during autophagy probably by associating with the PI3K complex II (PI3KC3-C2) (PubMed:17891140). Associated with PI3KC3-C2 during autophagy may regulate the trafficking of ATG9A from the Golgi complex to the peripheral cytoplasm for the formation of autophagosomes by inducing Golgi membrane tubulation and fragmentation (PubMed:21068542). Involved in regulation of degradative endocytic trafficking and cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123). Isoform 2 acts antiapoptotic in neuronal cells; involved in maintenance of mitochondrial morphology and promotes neuronal viability (By similarity)","subcellular_location":"Cytoplasm; Golgi apparatus membrane; Mitochondrion outer membrane; Cytoplasmic vesicle, autophagosome membrane; Midbody","url":"https://www.uniprot.org/uniprotkb/Q9Y371/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SH3GLB1","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000097033","cell_line_id":"CID000670","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":2},{"compartment":"golgi","grade":1}],"interactors":[{"gene":"SH3GLB2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000670","total_profiled":1310},"omim":[{"mim_id":"609288","title":"SH3 DOMAIN, GRB2-LIKE, ENDOPHILIN B2; SH3GLB2","url":"https://www.omim.org/entry/609288"},{"mim_id":"609287","title":"SH3 DOMAIN, GRB2-LIKE, ENDOPHILIN B1; SH3GLB1","url":"https://www.omim.org/entry/609287"},{"mim_id":"300127","title":"OLIGOPHRENIN 1; OPHN1","url":"https://www.omim.org/entry/300127"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SH3GLB1"},"hgnc":{"alias_symbol":["CGI-61","KIAA0491","Bif-1","PPP1R70"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y371","domains":[{"cath_id":"1.20.1270.60","chopping":"33-252","consensus_level":"high","plddt":94.9022,"start":33,"end":252},{"cath_id":"2.30.30.40","chopping":"306-362","consensus_level":"high","plddt":91.1561,"start":306,"end":362}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y371","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y371-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y371-F1-predicted_aligned_error_v6.png","plddt_mean":83.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SH3GLB1","jax_strain_url":"https://www.jax.org/strain/search?query=SH3GLB1"},"sequence":{"accession":"Q9Y371","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y371.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y371/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y371"}},"corpus_meta":[{"pmid":"17891140","id":"PMC_17891140","title":"Bif-1 interacts with Beclin 1 through UVRAG and regulates autophagy and tumorigenesis.","date":"2007","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17891140","citation_count":725,"is_preprint":false},{"pmid":"16227588","id":"PMC_16227588","title":"Loss of Bif-1 suppresses Bax/Bak conformational change and mitochondrial apoptosis.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16227588","citation_count":164,"is_preprint":false},{"pmid":"20643123","id":"PMC_20643123","title":"A phosphatidylinositol 3-kinase class III sub-complex containing VPS15, VPS34, Beclin 1, UVRAG and BIF-1 regulates cytokinesis and degradative endocytic traffic.","date":"2010","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/20643123","citation_count":154,"is_preprint":false},{"pmid":"11259440","id":"PMC_11259440","title":"Molecular cloning and characterization of Bif-1. 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It contains a C-terminal SH3 domain, localizes to cytoplasm, and directly interacts with Bax as confirmed by co-immunoprecipitation and immunofluorescence. Overexpression of Bif-1 promotes Bax conformational change, caspase activation, and apoptotic cell death following IL-3 deprivation.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence, overexpression apoptosis assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Y2H, Co-IP, IF, functional assay) in a single foundational paper, highly cited\",\n      \"pmids\": [\"11259440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Bif-1 plays a regulatory role in apoptotic activation of both Bax and Bak. RNAi-mediated knockdown of Bif-1 in HeLa cells abrogated Bax and Bak conformational change, cytochrome c release, and caspase-3 activation. Bif-1 heterodimerizes with Bax on mitochondria, and this interaction is enhanced by apoptosis induction prior to Bax conformational change. Bif-1 does not directly interact with Bak.\",\n      \"method\": \"RNA interference, Bif-1 knockout MEFs, co-immunoprecipitation, mitochondrial fractionation, caspase activity assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, clean KO/KD with defined apoptotic phenotype, replicated in multiple cell systems\",\n      \"pmids\": [\"16227588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Bif-1 interacts with Beclin 1 through UVRAG and functions as a positive mediator of class III PI3-kinase (PI3KC3/Vps34). The SH3 domain of Bif-1 is sufficient for binding UVRAG, but both the BAR and SH3 domains are required to activate PI3KC3 and induce autophagosome formation. Upon nutrient deprivation, Bif-1 localizes to autophagosomes where it co-localizes with Atg5 and LC3. Loss of Bif-1 suppresses autophagosome formation.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion mutants, siRNA knockdown, fluorescence microscopy, autophagosome formation assay\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, domain mapping, clean KO/KD, subcellular localization, highly cited foundational paper\",\n      \"pmids\": [\"17891140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Bif-1 N-BAR domain stimulates BAX-driven mitochondrial outer membrane permeabilization (MOMP) in a reconstituted system using purified proteins and MOM-like liposomes. This stimulatory effect requires physical interaction between Bif-1 N-BAR and BAX and depends on the presence of cardiolipin. Large-scale morphological membrane rearrangements by Bif-1 N-BAR could be separated from functional BAX activation. DLP1/Drp1 did not stimulate BAX permeabilizing function.\",\n      \"method\": \"In vitro reconstitution with purified proteins and MOM-like liposomes, liposome permeabilization assay, domain mutant analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution with purified components, mutagenesis/domain dissection, multiple orthogonal readouts\",\n      \"pmids\": [\"19074440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"c-Src kinase directly binds to and phosphorylates Bif-1 on tyrosine 80. Src phosphorylation of Bif-1 suppresses the interaction between Bif-1 and Bax, thereby inhibiting Bax activation during anoikis. Apoptotic stimuli repress this phosphorylation event.\",\n      \"method\": \"In vitro kinase assay, co-immunoprecipitation, site-directed mutagenesis (Y80), anoikis apoptosis assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro kinase assay plus mutagenesis and functional consequence demonstrated\",\n      \"pmids\": [\"18474606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"A specific PI3K-III sub-complex containing VPS15, VPS34, Beclin 1, UVRAG, and BIF-1 (but not ATG14L) regulates both degradative endocytic receptor downregulation and cytokinesis. BIF-1 and UVRAG localize strongly to the midbody during cytokinesis.\",\n      \"method\": \"siRNA depletion of individual subunits, high-content microscopy, cytokinesis and receptor degradation assays, subcellular localization\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — systematic siRNA screen with defined phenotypic readouts; single lab\",\n      \"pmids\": [\"20643123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"GSK-3β inhibition results in elevation of Bif-1 protein levels. Silencing Bif-1 expression abrogates GSK-3β-inhibition-induced autophagic response and necrotic cell death under serum starvation, placing Bif-1 downstream of GSK-3β in regulating autophagy-dependent cell death.\",\n      \"method\": \"siRNA knockdown, chemical inhibitors, cell death assays (apoptosis/necrosis markers), autophagy monitoring\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis via siRNA with defined cellular phenotypes; single lab\",\n      \"pmids\": [\"20159967\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Bif-1's N-BAR domain is required for membrane binding and bending activity and mediates fission of Golgi membranes during autophagy induction. Loss of Bif-1 or inhibition of the PI3KC3 complex II suppresses starvation-induced Golgi fission and peripheral redistribution of Atg9. N-BAR domain mutants lacking membrane binding/bending activity fail to restore Golgi fission, Atg9 puncta formation, or autophagosome formation.\",\n      \"method\": \"N-BAR domain mutants, fluorescence microscopy (live-cell), Bif-1 knockout/knockdown cells, Atg9 trafficking assay\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — structure-function analysis with domain mutants, clean KO cells, multiple readouts in single lab\",\n      \"pmids\": [\"21068542\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Bif-1 is indispensable for autophagy-dependent clearance of damaged mitochondria (mitophagy). Loss of Bif-1 results in accumulation of ER-associated immature autophagosomes and suppresses autophagosome maturation. Allelic loss of Bif-1 increases mitochondrial mass, accumulation of DNA damage, and upregulation of anti-apoptotic Mcl-1 in Myc-driven prelymphomatous cells.\",\n      \"method\": \"Bif-1 KO and haploinsufficient mice, Eμ-Myc transgenic lymphoma model, electron microscopy, mitophagy assay (CCCP treatment), flow cytometry\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic KO with multiple defined molecular phenotypes, electron microscopy, replicated in MEFs\",\n      \"pmids\": [\"23287860\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SH3GLB1 (Bif-1) is present on endolysosomal carriers containing nicotinic acetylcholine receptors (CHRN) in skeletal muscle neuromuscular junctions. SH3GLB1-positive CHRN vesicles are surrounded by autophagic marker LC3 in an ATG7-dependent fashion, placing SH3GLB1 in selective autophagy-mediated CHRN turnover regulated by TRIM63.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence co-localization, ATG7 knockout mice, denervation model\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP and co-localization with genetic KO context; single lab\",\n      \"pmids\": [\"24220501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Bif-1 interacts with Dynamin 2 (DNM2) and this interaction is enhanced upon nutrient starvation. Bif-1 and DNM2 cooperatively mediate fission of Atg9-containing membranes from a Rab11-positive reservoir during autophagy. Inhibition of DNM2 GTPase activity results in accumulation of Atg9-positive tubular structures. Atg9 trafficking to the Rab11 reservoir is Bif-1-independent, but membrane tubulation from this reservoir requires Bif-1.\",\n      \"method\": \"Co-immunoprecipitation (Bif-1–DNM2 interaction), DNM2 GTPase inhibitor, fluorescence microscopy, Bif-1 KD cells, live-cell imaging\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus functional dissection with inhibitor and KD; single lab\",\n      \"pmids\": [\"26980706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Threonine-145 phosphorylation of SH3GLB1 regulates CHRN endocytic trafficking at the neuromuscular junction. Phosphomimetic T145E SH3GLB1 slows processing of endocytic CHRN vesicles, while phosphodeficient T145A augments it. Co-expression of RAB5 largely rescues the slowed processing induced by T145E. Phosphomutants alter expression of RAB5 activity regulators without changing RAB5 co-localization with CHRN vesicles.\",\n      \"method\": \"Overexpression of T145E and T145A phosphomutants, RAB5 co-expression rescue, in vivo neuromuscular junction imaging\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — phosphomutant analysis with epistasis rescue experiment; single lab\",\n      \"pmids\": [\"27715385\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Bif-1 deficiency reduces basal adipose tissue lipolysis and impairs fasting/refeeding-induced lipid droplet clearance in the liver, promoting adipocyte hypertrophy and obesity. Bif-1 loss downregulates Atg9a and Lamp1 expression in adipose tissue, linking its membrane-curvature function to lipid catabolism.\",\n      \"method\": \"Bif-1 knockout mice, adipose tissue lipolysis assay, hepatic lipid droplet clearance assay, Western blotting\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO mouse model with defined metabolic and molecular phenotypes; single lab\",\n      \"pmids\": [\"26857140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Calpain (CAPNS1-dependent) is required for dynamic flux of Atg9/Bif-1 vesicles from Golgi stacks toward autophagosomes upon thapsigargin-induced autophagy. CAPNS1 depletion causes Atg9 and Bif-1 to remain in GM130-positive Golgi stacks. A Bif-1 point mutant resistant to calpain processing leads to accumulation of endogenous p62 and LC3-II. Atg9 fails to interact with Vps34 in CAPNS1-depleted cells.\",\n      \"method\": \"CAPNS1 siRNA depletion, calpain-resistant Bif-1 point mutant, co-immunoprecipitation (Atg9-Vps34), fluorescence microscopy\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — point mutant analysis, Co-IP, and genetic depletion with defined phenotypes; single lab\",\n      \"pmids\": [\"28302665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SRRM4 promotes alternative RNA splicing of the Bif-1 gene to produce neural-specific variants Bif-1b and Bif-1c in treatment-induced neuroendocrine prostate cancer. Bif-1a (predominant in adenocarcinoma) is pro-apoptotic, while Bif-1b and Bif-1c are anti-apoptotic under camptothecin and UV treatment.\",\n      \"method\": \"Whole transcriptome sequencing, SRRM4 overexpression/knockdown, isoform-specific apoptosis assays, patient tumor samples and xenografts\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — isoform-specific functional assays with defined apoptotic phenotype and identification of splice regulator; single lab\",\n      \"pmids\": [\"29759485\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Upon cell stress, Bif-1 translocates to mitochondria and binds prohibitin-2 via its C-terminus (specifically via tryptophan-344), causing disruption of the prohibitin complex and proteolytic inactivation of the inner membrane fusion protein OPA1, leading to mitochondrial fragmentation and apoptosis. Bif-1 deficiency or W344 mutation prevents prohibitin-2 binding, OPA1 proteolysis, and mitochondrial fragmentation.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion analysis, W344 point mutation, Bif-1 KO cells and mice, renal ischemia-reperfusion model, mitochondrial morphology analysis\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, site-directed mutagenesis, clean KO cells and in vivo model with multiple orthogonal readouts\",\n      \"pmids\": [\"31126972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BIF-1 inhibits both mitochondrial respiration and glycolytic ATP production. CRISPR/Cas9 knockout of BIF-1 in melanoma cells results in increased mitochondrial respiration, metabolic acidification, and ATP production, promoting higher proliferation rates in vitro and in vivo, independent of effects on apoptosis and autophagy.\",\n      \"method\": \"CRISPR/Cas9 knockout, Seahorse metabolic assay, in vitro and in vivo proliferation assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean CRISPR KO with quantitative metabolic phenotype; single lab\",\n      \"pmids\": [\"32493957\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SUMO2 SUMOylates SH3GLB1 at position K82 (predicted and validated by co-IP and confocal co-localization). Ionizing radiation promotes the interaction between SUMO2 and SH3GLB1, and SH3GLB1 interacts with mitochondrial membrane proteins MFN1/2, TOM20, and Drp1 upon IR, mediating mitophagy activation. SH3GLB1 deficiency inhibits mitophagy and restores mitochondrial cristae.\",\n      \"method\": \"Co-immunoprecipitation, laser confocal microscopy, SH3GLB1 KO cells, mitophagy assay, bioinformatics prediction of SUMOylation site\",\n      \"journal\": \"European journal of pharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP and co-localization for SUMOylation; K82 site based partly on prediction; single lab\",\n      \"pmids\": [\"35487252\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Bif-1 promotes EGFR endocytic degradation. Loss of Bif-1 sequesters internalized EGF in Rab5-positive endosomes, delays EGFR trafficking to lysosomes, impairs Rab7 recruitment and activation to EGF-positive vesicles, and prolongs ERK1/2 activation. Bif-1 suppression increases chemotactic cell migration in an EGFR-dependent manner.\",\n      \"method\": \"siRNA knockdown, fluorescence microscopy (Rab5, Rab7, EGF trafficking), EGFR degradation assay, ERK phosphorylation assay, migration assay with gefitinib rescue\",\n      \"journal\": \"Cancer biology & therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with multiple mechanistic readouts (vesicle trafficking, Rab7 activation, EGFR degradation) and inhibitor rescue; single lab\",\n      \"pmids\": [\"22785202\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SH3GLB1 is required for nuclear localization of the NOTCH2 intracellular domain (N2ICD) and NOTCH2 pathway activation in glioblastoma cells under hypoxia. SH3GLB1 is transcriptionally induced by HIF-2A under hypoxic conditions, and its genetic depletion reduces tumorigenic potential and impairs tumor growth in vivo.\",\n      \"method\": \"Genetic depletion (siRNA/shRNA), nuclear fractionation, NOTCH2 signaling assay, in vivo xenograft, HIF-2A transcription factor binding analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, limited mechanistic detail on how SH3GLB1 enables N2ICD nuclear localization\",\n      \"pmids\": [\"40639082\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SH3GLB1/Bif-1 is a multifunctional endophilin protein with N-BAR and SH3 domains that (1) binds Bax (interaction inhibited by c-Src phosphorylation at Y80) and cooperates with cardiolipin to stimulate BAX/BAK conformational change and mitochondrial outer membrane permeabilization during apoptosis; (2) uses its SH3 domain to bind UVRAG and thereby joins the Beclin1–UVRAG–PI3KC3 complex to promote autophagosome nucleation; (3) employs its N-BAR membrane-bending activity to drive Golgi fission and Atg9/Dynamin2-dependent vesicle generation for autophagosome biogenesis; (4) mediates mitophagy by facilitating ATG9-containing membrane delivery to damaged mitochondria; and (5) promotes apoptotic mitochondrial fragmentation by translocating to mitochondria and binding prohibitin-2 (via W344) to disrupt the prohibitin complex and induce OPA1 proteolysis.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SH3GLB1 (Bif-1) is an N-BAR and SH3 domain-containing endophilin family protein that couples membrane remodeling to apoptosis, autophagy, and endosomal trafficking. In apoptosis, SH3GLB1 directly binds Bax on mitochondria to promote Bax/Bak conformational activation and mitochondrial outer membrane permeabilization in a cardiolipin-dependent manner, a function negatively regulated by c-Src phosphorylation at Y80; it also translocates to mitochondria under stress to bind prohibitin-2 via W344, disrupting the prohibitin complex and triggering OPA1 proteolysis and mitochondrial fragmentation [PMID:11259440, PMID:19074440, PMID:18474606, PMID:31126972]. In autophagy, SH3GLB1 uses its SH3 domain to engage UVRAG within the Beclin 1–PI3KC3 complex to promote autophagosome nucleation, while its N-BAR domain drives Golgi membrane fission and generation of Atg9/Dynamin 2-containing vesicles required for autophagosome biogenesis and mitophagy [PMID:17891140, PMID:21068542, PMID:26980706, PMID:23287860]. SH3GLB1 additionally facilitates endolysosomal EGFR degradation by promoting Rab7 recruitment to endosomes, and its loss leads to prolonged EGFR/ERK signaling, metabolic reprogramming with increased mitochondrial respiration and glycolysis, and impaired lipid catabolism [PMID:22785202, PMID:32493957, PMID:26857140].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"The initial discovery that Bif-1 is a Bax-interacting protein established a direct molecular link between an endophilin-family BAR/SH3 protein and mitochondrial apoptosis.\",\n      \"evidence\": \"Yeast two-hybrid screen with Bax bait followed by co-immunoprecipitation, immunofluorescence, and overexpression apoptosis assays in IL-3-deprived cells\",\n      \"pmids\": [\"11259440\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous stoichiometry and kinetics of Bif-1–Bax interaction unknown\", \"Whether Bif-1 directly activates Bax or acts as a scaffold unresolved\", \"Bak interaction status not addressed\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Extending beyond overexpression, loss-of-function studies showed Bif-1 is required for both Bax and Bak conformational activation, cytochrome c release, and caspase-3 activation, establishing it as a non-redundant upstream regulator of intrinsic apoptosis.\",\n      \"evidence\": \"siRNA knockdown in HeLa and Bif-1 knockout MEFs with co-immunoprecipitation, mitochondrial fractionation, and caspase assays\",\n      \"pmids\": [\"16227588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which Bif-1 promotes Bak activation without direct binding unclear\", \"Tissue-specific requirements not tested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Discovery that Bif-1 links to the Beclin 1–UVRAG–PI3KC3 autophagy complex via its SH3 domain revealed a second major function in autophagosome nucleation, distinct from its apoptotic role.\",\n      \"evidence\": \"Co-immunoprecipitation with domain deletion mapping, siRNA knockdown, fluorescence co-localization with Atg5 and LC3 upon nutrient deprivation\",\n      \"pmids\": [\"17891140\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Bif-1 membrane-bending activity is required for PI3KC3 activation versus autophagosome membrane supply not separated\", \"Regulation of Bif-1–UVRAG interaction unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Two studies resolved regulatory and biophysical mechanisms: reconstitution showed Bif-1 N-BAR stimulates Bax-mediated liposome permeabilization in a cardiolipin-dependent manner, while c-Src phosphorylation at Y80 was identified as a negative switch that disrupts the Bif-1–Bax interaction during anoikis.\",\n      \"evidence\": \"Purified protein reconstitution on MOM-like liposomes with domain mutants (PMID:19074440); in vitro kinase assay with Y80 mutagenesis and anoikis assay (PMID:18474606)\",\n      \"pmids\": [\"19074440\", \"18474606\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Y80 phosphorylation also regulates autophagy function not tested\", \"Structural basis of cardiolipin requirement unresolved\", \"Kinase(s) that dephosphorylate Y80 upon apoptosis not identified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Bif-1 was placed in a specific PI3KC3 sub-complex (with UVRAG, not ATG14L) that regulates endocytic receptor degradation and cytokinesis, revealing non-autophagic functions of this complex.\",\n      \"evidence\": \"Systematic siRNA depletion of PI3KC3 subunits with high-content microscopy for cytokinesis and receptor degradation phenotypes\",\n      \"pmids\": [\"20643123\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct contribution of Bif-1 membrane bending to cytokinesis not tested\", \"Whether midbody localization is dependent on UVRAG not determined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Structure-function analysis showed that Bif-1 N-BAR membrane-bending activity drives Golgi fission and Atg9 redistribution during starvation, mechanistically separating its membrane-remodeling role from PI3KC3 activation in autophagosome biogenesis.\",\n      \"evidence\": \"N-BAR domain mutants lacking membrane binding/bending in Bif-1 KO cells with live-cell imaging of Golgi fission and Atg9 puncta\",\n      \"pmids\": [\"21068542\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Lipid specificity of N-BAR binding on Golgi membranes not characterized\", \"Whether N-BAR acts alone or requires co-factors for fission unknown\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Bif-1 was shown to promote EGFR endocytic degradation by facilitating Rab7 recruitment, establishing it as a regulator of endosome-to-lysosome trafficking beyond autophagy.\",\n      \"evidence\": \"siRNA knockdown with EGF trafficking imaging, Rab5/Rab7 co-localization, EGFR degradation kinetics, and gefitinib rescue of migration phenotype\",\n      \"pmids\": [\"22785202\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Bif-1 acts directly on Rab7 activation or indirectly via PI3KC3-UVRAG not resolved\", \"Applicability to other receptor tyrosine kinases untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Bif-1 was shown to be indispensable for mitophagy; its loss caused accumulation of immature autophagosomes at the ER and increased mitochondrial mass, linking its membrane-remodeling activity to organelle quality control and tumor suppression in a Myc-driven lymphoma model.\",\n      \"evidence\": \"Bif-1 KO and haploinsufficient mice crossed to Eμ-Myc transgenic model, electron microscopy, CCCP-induced mitophagy assay\",\n      \"pmids\": [\"23287860\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of ER-to-autophagosome maturation arrest not identified\", \"Whether Bif-1 directly senses mitochondrial damage unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Bif-1 was found to cooperate with Dynamin 2 in fission of Atg9-containing membranes from a Rab11-positive recycling endosome reservoir, defining the vesicle source and scission machinery for autophagosome membrane supply.\",\n      \"evidence\": \"Co-immunoprecipitation of Bif-1–DNM2, DNM2 GTPase inhibitor causing Atg9-positive tubule accumulation, live-cell imaging in Bif-1 KD cells\",\n      \"pmids\": [\"26980706\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical reconstitution of Bif-1/DNM2-mediated membrane fission not performed\", \"Whether other BAR proteins compensate partially not addressed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Bif-1 deficiency in mice impaired adipose tissue lipolysis and hepatic lipid droplet clearance, extending its autophagy/membrane-remodeling role to whole-body lipid metabolism.\",\n      \"evidence\": \"Bif-1 KO mice with adipose and liver metabolic phenotyping, Western blot for Atg9a and Lamp1\",\n      \"pmids\": [\"26857140\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell-autonomous versus systemic contribution not separated\", \"Lipid droplet autophagy mechanism not detailed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Calpain-dependent processing of Bif-1 was identified as a regulatory step for release of Atg9/Bif-1 vesicles from the Golgi during ER-stress-induced autophagy, adding a protease-based control layer.\",\n      \"evidence\": \"CAPNS1 siRNA, calpain-resistant Bif-1 mutant, Co-IP of Atg9–Vps34 interaction in depleted cells\",\n      \"pmids\": [\"28302665\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Exact cleavage site and cleavage product identity not mapped\", \"Whether calpain processing affects apoptotic function not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"SRRM4-mediated alternative splicing was shown to generate neural-specific Bif-1 isoforms (Bif-1b/c) with anti-apoptotic properties, in contrast to the pro-apoptotic canonical Bif-1a, revealing isoform-specific functional switching in neuroendocrine prostate cancer.\",\n      \"evidence\": \"Whole-transcriptome sequencing, SRRM4 overexpression/knockdown, isoform-specific apoptosis assays in patient tumors and xenografts\",\n      \"pmids\": [\"29759485\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis for isoform-specific apoptotic reversal not determined\", \"Whether splice variants differ in autophagy function untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"A stress-induced mitochondrial translocation pathway was elucidated whereby Bif-1 binds prohibitin-2 via W344, disrupting the PHB1/PHB2 complex and triggering OPA1 proteolysis to drive mitochondrial fragmentation, providing a mechanistic link between Bif-1 and inner membrane dynamics.\",\n      \"evidence\": \"Reciprocal Co-IP, W344 point mutant, Bif-1 KO cells and mice, renal ischemia-reperfusion in vivo model with mitochondrial morphology analysis\",\n      \"pmids\": [\"31126972\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal triggering Bif-1 mitochondrial translocation not identified\", \"Whether PHB2 disruption also affects cristae-dependent apoptosis independently of OPA1 not tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"CRISPR knockout revealed that Bif-1 suppresses both mitochondrial respiration and glycolysis, identifying a metabolic tumor-suppressor function independent of its canonical apoptosis and autophagy roles.\",\n      \"evidence\": \"CRISPR/Cas9 KO in melanoma cells, Seahorse metabolic flux assays, in vitro and in vivo proliferation assays\",\n      \"pmids\": [\"32493957\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism by which Bif-1 suppresses respiration and glycolysis not identified\", \"Whether this reflects a direct metabolic activity or indirect consequence of mitochondrial remodeling unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the structural basis of Bif-1 N-BAR selectivity for different organelle membranes, the identity of signals directing Bif-1 mitochondrial translocation, how Bif-1 directly suppresses mitochondrial metabolism, and whether the multiple post-translational modifications (Y80 phosphorylation, T145 phosphorylation, SUMOylation, calpain cleavage) act in a coordinated regulatory network.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of full-length Bif-1 or its complexes exists\", \"Integrated PTM regulatory logic not tested\", \"Isoform-specific functions in autophagy remain unexplored\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [3, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 15]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [1, 15, 17]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [7, 13]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [2, 9, 10]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [18]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [0, 1, 3, 4, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 7, 8, 10, 13]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [18, 5]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [8, 15]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [12, 16]}\n    ],\n    \"complexes\": [\n      \"Beclin 1–UVRAG–PI3KC3 complex\"\n    ],\n    \"partners\": [\n      \"BAX\",\n      \"UVRAG\",\n      \"BECN1\",\n      \"PHB2\",\n      \"DNM2\",\n      \"ATG9A\",\n      \"SRC\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}