{"gene":"UBE2F","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2016,"finding":"UBE2F, together with SAG (RBX2) and CUL5, forms a tri-complex that neddylates CUL5 to activate CRL5 (Cullin-RING Ligase 5), which in turn ubiquitylates the pro-apoptotic protein NOXA via K11 (not K48) ubiquitin linkage to target it for proteasomal degradation.","method":"Pulldown assay (in vivo complex formation), in vivo and in vitro ubiquitylation assays, K11R ubiquitin mutant rescue experiments, NOXA knockdown epistasis","journal":"Clinical Cancer Research","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro and in vivo ubiquitylation assays combined with linkage-specific mutagenesis (K11R) and epistatic rescue, multiple orthogonal methods in one study","pmids":["27591266"],"is_preprint":false},{"year":2018,"finding":"UBE2M acts as a dual E2 that, under stressed conditions, functions as a ubiquitylation E2 for the Parkin-DJ-1 E3 ligase to ubiquitylate and degrade UBE2F; this UBE2M-driven degradation of UBE2F leads to CRL5 inactivation and subsequent NOXA accumulation, establishing a negative regulatory axis between the two neddylation E2s.","method":"Molecular and biochemical assays establishing UBE2M as both neddylation E2 (via CUL3-Keap1) and ubiquitylation E2 (via Parkin-DJ-1) for UBE2F degradation; genetic knockdown and overexpression with phenotypic readout (lung cancer cell growth suppression)","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — dual-activity E2 established by multiple biochemical approaches, in vivo and in vitro, with genetic epistasis and functional consequence","pmids":["29932898"],"is_preprint":false},{"year":2020,"finding":"Platinum treatment impairs the interaction between UBE2F and RBX1 (Ring-box protein 1), an essential component of CRLs, thereby reducing proteasome-mediated UBE2F degradation. The resulting UBE2F accumulation promotes CUL5 neddylation and activates CRL5, leading to NOXA degradation and resistance to platinum-induced apoptosis.","method":"Co-immunoprecipitation (UBE2F-RBX1 association), immunoblotting, UBE2F knockout sensitization assays, NOXA protein-level readout","journal":"Cell Death & Disease","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — reciprocal interaction (Co-IP) plus KO functional validation, single lab with two orthogonal methods","pmids":["33184273"],"is_preprint":false},{"year":2024,"finding":"UBE2F neddylates CUL5 to activate the CRL5-ASB11 E3 ligase, which ubiquitylates and degrades DIRAS2 (a small GTPase/RAS family member and tumor suppressor). UBE2F deletion blocks DIRAS2 ubiquitylation, causing DIRAS2 accumulation that inactivates MAPK-c-Myc signaling; Diras2 deletion rescues the growth-suppressive phenotype of Ube2f deletion, establishing epistatic hierarchy.","method":"Mouse KrasG12D PDAC model with Ube2f conditional deletion, ubiquitylation assays for DIRAS2, Diras2 deletion rescue (epistasis), cell growth/survival assays","journal":"Developmental Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo mouse model plus ubiquitylation assays plus genetic epistasis (double KO rescue), multiple orthogonal methods","pmids":["38574733"],"is_preprint":false},{"year":2025,"finding":"UBE2F cooperates with E3 ligase SAG (RBX2) to neddylate RHEB at lysine K169, enhancing RHEB's lysosomal localization and GTP-binding affinity, thereby activating mTORC1 signaling. Liver-specific Ube2f knockout attenuates mTORC1 activity, steatosis, and tumorigenesis induced by Pten loss.","method":"Site-specific neddylation assay (K169 mutagenesis), lysosomal fractionation/localization, GTP-binding affinity assay, mTORC1 activity readout, liver-specific Ube2f KO mouse model","journal":"The EMBO Journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — site-specific mutagenesis identifying K169 neddylation site, biochemical GTP-binding and localization assays, in vivo KO mouse model with mTORC1 functional readout","pmids":["39762645"],"is_preprint":false},{"year":2025,"finding":"UBE2F-RBX2-mediated neddylation of CUL5 is required for pseudorabies virus (PRV) replication; shRNA-mediated silencing of UBE2F or RBX2 significantly decreases PRV replication, and pharmacological inhibition of CUL5 neddylation attenuates PRV replication.","method":"shRNA knockdown of UBE2F and RBX2, pharmacological inhibition of CUL5 neddylation, PRV replication assay","journal":"International Journal of Biological Macromolecules","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — genetic silencing and pharmacological inhibition with functional viral replication readout, single lab","pmids":["41478481"],"is_preprint":false},{"year":2026,"finding":"In CD8 T cells, UBE2F deficiency inhibits CUL5 neddylation, leading to accumulation of JUNB and upregulation of IL-2Rβ; increased IL-2Rβ hypersensitizes CD8 T cells to IL-15, thereby promoting self-renewal and survival across memory and exhausted CD8 T cell compartments.","method":"UBE2F ablation in CD8 T cells (genetic), CUL5 neddylation assay, JUNB protein accumulation, IL-2Rβ expression and IL-15 signaling readout, viral and tumor control models","journal":"The Journal of Experimental Medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined molecular pathway (CUL5→JUNB→IL-2Rβ→IL-15 sensitivity), single lab with multiple downstream readouts","pmids":["42188874"],"is_preprint":false},{"year":2022,"finding":"Structure-based virtual screening identified small molecule HA-9104 that binds UBE2F and reduces its protein levels, consequently inhibiting CUL5 neddylation and inactivating CRL5, leading to NOXA accumulation and apoptosis in lung cancer cells.","method":"Structure-based virtual screen and chemical optimization, direct binding assay (HA-9104 to UBE2F), CUL5 neddylation assay, NOXA accumulation readout, in vitro and in vivo xenograft models","journal":"Signal Transduction and Targeted Therapy","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct binding compound to UBE2F validated biochemically, functional neddylation and NOXA assays, single lab","pmids":["36253371"],"is_preprint":false}],"current_model":"UBE2F is a neddylation E2 conjugating enzyme that partners with E3 SAG/RBX2 to catalyze NEDD8 conjugation onto CUL5 (activating CRL5 ubiquitin ligase complexes) and onto the non-cullin substrate RHEB at K169 (enhancing lysosomal localization and mTORC1 activity); active CRL5 degrades substrates including NOXA (via K11-linked ubiquitin chains) and DIRAS2, thereby promoting cell survival, MAPK-c-Myc signaling, and viral replication, while UBE2F itself is subject to degradation via UBE2M acting as a ubiquitylation E2 for the Parkin-DJ-1 ligase under stress conditions."},"narrative":{"mechanistic_narrative":"UBE2F is a neddylation E2 conjugating enzyme that, in partnership with the E3 SAG/RBX2, catalyzes NEDD8 conjugation onto CUL5 to activate CRL5 (Cullin-RING Ligase 5) ubiquitin ligase complexes, a node that governs cell survival, proliferative signaling, immune cell fate, and viral replication [PMID:27591266, PMID:39762645]. Active CRL5 directs degradation of multiple substrates: it ubiquitylates the pro-apoptotic protein NOXA via K11-linked (rather than K48-linked) chains to suppress apoptosis [PMID:27591266], and through a CRL5-ASB11 complex it ubiquitylates and degrades the RAS-family tumor suppressor DIRAS2, thereby sustaining MAPK-c-Myc signaling [PMID:38574733]. Beyond cullin substrates, UBE2F together with SAG/RBX2 neddylates the small GTPase RHEB at K169, enhancing its lysosomal localization and GTP-binding affinity to drive mTORC1 activation and Pten-loss-driven hepatic steatosis and tumorigenesis [PMID:39762645]. UBE2F activity is itself constrained by a counter-regulatory neddylation E2, UBE2M, which acts as a ubiquitylation E2 for the Parkin-DJ-1 E3 ligase to target UBE2F for degradation under stress, linking the two E2s in a negative feedback axis that controls NOXA levels [PMID:29932898]. Through the CUL5 axis UBE2F also restrains JUNB accumulation and IL-2Rβ expression to set IL-15 sensitivity and self-renewal of CD8 T cells [PMID:42188874], and is required for pseudorabies virus replication [PMID:41478481]. UBE2F is pharmacologically tractable: the small molecule HA-9104 binds UBE2F, lowers its protein level, and inactivates CRL5 to trigger NOXA-dependent apoptosis [PMID:36253371].","teleology":[{"year":2016,"claim":"Established UBE2F's core enzymatic role by showing it forms a tri-complex with SAG/RBX2 and CUL5 to neddylate CUL5 and activate CRL5, defining a survival pathway via NOXA degradation.","evidence":"Pulldown, in vivo/in vitro ubiquitylation assays, K11R linkage-specific mutagenesis, and NOXA knockdown epistasis","pmids":["27591266"],"confidence":"High","gaps":["Did not address non-CUL5 neddylation substrates","Physiological contexts beyond cancer cells unexplored"]},{"year":2018,"claim":"Revealed how UBE2F levels are controlled, identifying UBE2M as a dual-activity E2 that drives UBE2F ubiquitylation/degradation via Parkin-DJ-1, creating a negative regulatory axis between the two neddylation E2s.","evidence":"Biochemical assays defining UBE2M dual activity, genetic knockdown/overexpression with lung cancer growth readout","pmids":["29932898"],"confidence":"High","gaps":["Stress signals that trigger UBE2M switch to ubiquitylation E2 not fully defined","Direct E3-substrate contacts on UBE2F not mapped"]},{"year":2020,"claim":"Connected UBE2F stability to chemoresistance, showing platinum disrupts UBE2F-RBX1 association to reduce UBE2F degradation, driving CRL5 activation and apoptosis resistance.","evidence":"Co-IP of UBE2F-RBX1, immunoblotting, UBE2F knockout sensitization assays, NOXA protein readout","pmids":["33184273"],"confidence":"Medium","gaps":["Single-lab evidence","Mechanism by which platinum perturbs the UBE2F-RBX1 interface unresolved"]},{"year":2022,"claim":"Demonstrated UBE2F is druggable by identifying HA-9104, a direct-binding small molecule that depletes UBE2F and inactivates CRL5 to induce apoptosis.","evidence":"Structure-based virtual screen, direct binding assay, CUL5 neddylation and NOXA accumulation readouts, xenograft models","pmids":["36253371"],"confidence":"Medium","gaps":["Binding-site/structural basis of HA-9104 engagement not resolved","Selectivity over other E2s not established"]},{"year":2024,"claim":"Extended the CRL5 substrate repertoire in vivo, showing UBE2F-driven CRL5-ASB11 degrades DIRAS2 to sustain MAPK-c-Myc signaling and tumor growth.","evidence":"KrasG12D PDAC mouse model with Ube2f conditional deletion, DIRAS2 ubiquitylation assays, Diras2 deletion epistatic rescue","pmids":["38574733"],"confidence":"High","gaps":["Whether ASB11 is the sole substrate receptor for DIRAS2 unclear","Generality across other tumor types untested"]},{"year":2025,"claim":"Uncovered a non-cullin neddylation substrate, showing UBE2F/SAG neddylates RHEB at K169 to enhance lysosomal localization, GTP binding, and mTORC1 activation in liver tumorigenesis.","evidence":"K169 site-specific neddylation/mutagenesis, lysosomal fractionation, GTP-binding assay, mTORC1 readout, liver-specific Ube2f KO mouse","pmids":["39762645"],"confidence":"High","gaps":["Whether other GTPases are neddylated substrates unknown","Crosstalk between RHEB neddylation and CRL5 substrate flux not addressed"]},{"year":2025,"claim":"Showed UBE2F-RBX2-mediated CUL5 neddylation is required for pseudorabies virus replication, implicating the pathway in host-virus biology.","evidence":"shRNA knockdown of UBE2F/RBX2, pharmacological CUL5 neddylation inhibition, PRV replication assay","pmids":["41478481"],"confidence":"Medium","gaps":["Single-lab evidence","CRL5 substrate(s) mediating the proviral effect not identified"]},{"year":2026,"claim":"Defined an immune-cell function, showing UBE2F-dependent CUL5 neddylation restrains JUNB/IL-2Rβ to tune IL-15 sensitivity and CD8 T cell self-renewal and survival.","evidence":"Genetic UBE2F ablation in CD8 T cells, CUL5 neddylation assay, JUNB/IL-2Rβ readouts, viral and tumor control models","pmids":["42188874"],"confidence":"Medium","gaps":["Single-lab evidence","CRL5 substrate receptor controlling JUNB not pinpointed"]},{"year":null,"claim":"How UBE2F substrate specificity is partitioned between cullin (CUL5) and non-cullin (RHEB) targets, and the structural basis of its E2-E3 pairing and pharmacological inhibition, remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model defining UBE2F substrate-selection determinants","Full non-cullin substrate set unknown","Tissue-specific regulation of UBE2F abundance incompletely mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,3,4]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,4]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[0]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[6]}],"complexes":["UBE2F-SAG(RBX2)-CUL5 neddylation complex","CRL5 (Cullin-RING Ligase 5)"],"partners":["RBX2","CUL5","RBX1","UBE2M","RHEB"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q969M7","full_name":"NEDD8-conjugating enzyme UBE2F","aliases":["NEDD8 carrier protein UBE2F","NEDD8 protein ligase UBE2F","NEDD8-conjugating enzyme 2","RING-type E3 NEDD8 transferase UBE2F","Ubiquitin-conjugating enzyme E2 F"],"length_aa":185,"mass_kda":21.1,"function":"Accepts the ubiquitin-like protein NEDD8 from the UBA3-NAE1 E1 complex and catalyzes its covalent attachment to other proteins (PubMed:19250909, PubMed:23201271). Together with the E3 ubiquitin ligase RNF7/RBX2, specifically neddylates cullin-5 (CUL5) (PubMed:19250909, PubMed:23201271, PubMed:23300442). Does not neddylate CUL1, CUL2, CUL3, CUL4A or CUL4B (PubMed:19250909, PubMed:23201271). Mediates neddylation of the CUL9-RBX1 complex (PubMed:38605244) (Microbial infection) Following infection by HIV-1 virus, participates to HIV-1 Vif protein-mediated ubiquitination and degradation of APOBEC3G by mediating neddylation of cullin-5 (CUL5)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q969M7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE2F","classification":"Not Classified","n_dependent_lines":38,"n_total_lines":1208,"dependency_fraction":0.03145695364238411},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/UBE2F","total_profiled":1310},"omim":[{"mim_id":"617700","title":"UBIQUITIN-CONJUGATING ENZYME E2 F; UBE2F","url":"https://www.omim.org/entry/617700"},{"mim_id":"616522","title":"DCN1 DOMAIN-CONTAINING PROTEIN 5; DCUN1D5","url":"https://www.omim.org/entry/616522"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBE2F"},"hgnc":{"alias_symbol":["NCE2"],"prev_symbol":[]},"alphafold":{"accession":"Q969M7","domains":[{"cath_id":"3.10.110.10","chopping":"30-183","consensus_level":"high","plddt":96.8012,"start":30,"end":183}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q969M7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q969M7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q969M7-F1-predicted_aligned_error_v6.png","plddt_mean":89.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE2F","jax_strain_url":"https://www.jax.org/strain/search?query=UBE2F"},"sequence":{"accession":"Q969M7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q969M7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q969M7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q969M7"}},"corpus_meta":[{"pmid":"27591266","id":"PMC_27591266","title":"Neddylation E2 UBE2F Promotes the Survival of Lung Cancer Cells by Activating CRL5 to Degrade NOXA via the K11 Linkage.","date":"2016","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/27591266","citation_count":108,"is_preprint":false},{"pmid":"29932898","id":"PMC_29932898","title":"UBE2M Is a Stress-Inducible Dual E2 for Neddylation and Ubiquitylation that Promotes Targeted Degradation of UBE2F.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/29932898","citation_count":75,"is_preprint":false},{"pmid":"36253371","id":"PMC_36253371","title":"A small molecule inhibitor of the UBE2F-CRL5 axis induces apoptosis and radiosensitization in lung cancer.","date":"2022","source":"Signal transduction and targeted therapy","url":"https://pubmed.ncbi.nlm.nih.gov/36253371","citation_count":47,"is_preprint":false},{"pmid":"33184273","id":"PMC_33184273","title":"Induction of NEDD8-conjugating enzyme E2 UBE2F by platinum protects lung cancer cells from apoptosis and confers to platinum-insensitivity.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/33184273","citation_count":23,"is_preprint":false},{"pmid":"38574733","id":"PMC_38574733","title":"The UBE2F-CRL5ASB11-DIRAS2 axis is an oncogene and tumor suppressor cascade in pancreatic cancer cells.","date":"2024","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/38574733","citation_count":17,"is_preprint":false},{"pmid":"34783226","id":"PMC_34783226","title":"NEDD8-conjugating enzyme E2 UBE2F confers radiation resistance by protecting lung cancer cells from apoptosis.","date":"2021","source":"Journal of Zhejiang University. Science. B","url":"https://pubmed.ncbi.nlm.nih.gov/34783226","citation_count":15,"is_preprint":false},{"pmid":"39762645","id":"PMC_39762645","title":"RHEB neddylation by the UBE2F-SAG axis enhances mTORC1 activity and aggravates liver tumorigenesis.","date":"2025","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/39762645","citation_count":7,"is_preprint":false},{"pmid":"41478481","id":"PMC_41478481","title":"The ubiquitin conjugating enzyme E2 F (UBE2F)-RING-box protein 2 (RBX2)-mediated neddylation of Cullin5 facilitates pseudorabies virus replication.","date":"2025","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/41478481","citation_count":2,"is_preprint":false},{"pmid":"42188874","id":"PMC_42188874","title":"Targeting UBE2F induces a resilience program enhancing CD8 T cell immunity.","date":"2026","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/42188874","citation_count":0,"is_preprint":false},{"pmid":"42099630","id":"PMC_42099630","title":"Integrated single-cell and bulk transcriptomic analyses reveal cDC1-centered ubiquitination dysregulation and identify UBE2F as a critical regulator in sepsis.","date":"2026","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42099630","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.26.672429","title":"Unbiased CRISPR Synthetic Lethal Screening for Genetic Vulnerabilities in Succinate Dehydrogenase (SDH)-loss Model of Paraganglioma","date":"2025-08-28","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.26.672429","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7830,"output_tokens":2399,"usd":0.029738,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9398,"output_tokens":3197,"usd":0.063458,"stage2_stop_reason":"end_turn"},"total_usd":0.093196,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"UBE2F, together with SAG (RBX2) and CUL5, forms a tri-complex that neddylates CUL5 to activate CRL5 (Cullin-RING Ligase 5), which in turn ubiquitylates the pro-apoptotic protein NOXA via K11 (not K48) ubiquitin linkage to target it for proteasomal degradation.\",\n      \"method\": \"Pulldown assay (in vivo complex formation), in vivo and in vitro ubiquitylation assays, K11R ubiquitin mutant rescue experiments, NOXA knockdown epistasis\",\n      \"journal\": \"Clinical Cancer Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro and in vivo ubiquitylation assays combined with linkage-specific mutagenesis (K11R) and epistatic rescue, multiple orthogonal methods in one study\",\n      \"pmids\": [\"27591266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"UBE2M acts as a dual E2 that, under stressed conditions, functions as a ubiquitylation E2 for the Parkin-DJ-1 E3 ligase to ubiquitylate and degrade UBE2F; this UBE2M-driven degradation of UBE2F leads to CRL5 inactivation and subsequent NOXA accumulation, establishing a negative regulatory axis between the two neddylation E2s.\",\n      \"method\": \"Molecular and biochemical assays establishing UBE2M as both neddylation E2 (via CUL3-Keap1) and ubiquitylation E2 (via Parkin-DJ-1) for UBE2F degradation; genetic knockdown and overexpression with phenotypic readout (lung cancer cell growth suppression)\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — dual-activity E2 established by multiple biochemical approaches, in vivo and in vitro, with genetic epistasis and functional consequence\",\n      \"pmids\": [\"29932898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Platinum treatment impairs the interaction between UBE2F and RBX1 (Ring-box protein 1), an essential component of CRLs, thereby reducing proteasome-mediated UBE2F degradation. The resulting UBE2F accumulation promotes CUL5 neddylation and activates CRL5, leading to NOXA degradation and resistance to platinum-induced apoptosis.\",\n      \"method\": \"Co-immunoprecipitation (UBE2F-RBX1 association), immunoblotting, UBE2F knockout sensitization assays, NOXA protein-level readout\",\n      \"journal\": \"Cell Death & Disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — reciprocal interaction (Co-IP) plus KO functional validation, single lab with two orthogonal methods\",\n      \"pmids\": [\"33184273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UBE2F neddylates CUL5 to activate the CRL5-ASB11 E3 ligase, which ubiquitylates and degrades DIRAS2 (a small GTPase/RAS family member and tumor suppressor). UBE2F deletion blocks DIRAS2 ubiquitylation, causing DIRAS2 accumulation that inactivates MAPK-c-Myc signaling; Diras2 deletion rescues the growth-suppressive phenotype of Ube2f deletion, establishing epistatic hierarchy.\",\n      \"method\": \"Mouse KrasG12D PDAC model with Ube2f conditional deletion, ubiquitylation assays for DIRAS2, Diras2 deletion rescue (epistasis), cell growth/survival assays\",\n      \"journal\": \"Developmental Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo mouse model plus ubiquitylation assays plus genetic epistasis (double KO rescue), multiple orthogonal methods\",\n      \"pmids\": [\"38574733\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UBE2F cooperates with E3 ligase SAG (RBX2) to neddylate RHEB at lysine K169, enhancing RHEB's lysosomal localization and GTP-binding affinity, thereby activating mTORC1 signaling. Liver-specific Ube2f knockout attenuates mTORC1 activity, steatosis, and tumorigenesis induced by Pten loss.\",\n      \"method\": \"Site-specific neddylation assay (K169 mutagenesis), lysosomal fractionation/localization, GTP-binding affinity assay, mTORC1 activity readout, liver-specific Ube2f KO mouse model\",\n      \"journal\": \"The EMBO Journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — site-specific mutagenesis identifying K169 neddylation site, biochemical GTP-binding and localization assays, in vivo KO mouse model with mTORC1 functional readout\",\n      \"pmids\": [\"39762645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UBE2F-RBX2-mediated neddylation of CUL5 is required for pseudorabies virus (PRV) replication; shRNA-mediated silencing of UBE2F or RBX2 significantly decreases PRV replication, and pharmacological inhibition of CUL5 neddylation attenuates PRV replication.\",\n      \"method\": \"shRNA knockdown of UBE2F and RBX2, pharmacological inhibition of CUL5 neddylation, PRV replication assay\",\n      \"journal\": \"International Journal of Biological Macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — genetic silencing and pharmacological inhibition with functional viral replication readout, single lab\",\n      \"pmids\": [\"41478481\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In CD8 T cells, UBE2F deficiency inhibits CUL5 neddylation, leading to accumulation of JUNB and upregulation of IL-2Rβ; increased IL-2Rβ hypersensitizes CD8 T cells to IL-15, thereby promoting self-renewal and survival across memory and exhausted CD8 T cell compartments.\",\n      \"method\": \"UBE2F ablation in CD8 T cells (genetic), CUL5 neddylation assay, JUNB protein accumulation, IL-2Rβ expression and IL-15 signaling readout, viral and tumor control models\",\n      \"journal\": \"The Journal of Experimental Medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined molecular pathway (CUL5→JUNB→IL-2Rβ→IL-15 sensitivity), single lab with multiple downstream readouts\",\n      \"pmids\": [\"42188874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Structure-based virtual screening identified small molecule HA-9104 that binds UBE2F and reduces its protein levels, consequently inhibiting CUL5 neddylation and inactivating CRL5, leading to NOXA accumulation and apoptosis in lung cancer cells.\",\n      \"method\": \"Structure-based virtual screen and chemical optimization, direct binding assay (HA-9104 to UBE2F), CUL5 neddylation assay, NOXA accumulation readout, in vitro and in vivo xenograft models\",\n      \"journal\": \"Signal Transduction and Targeted Therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct binding compound to UBE2F validated biochemically, functional neddylation and NOXA assays, single lab\",\n      \"pmids\": [\"36253371\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE2F is a neddylation E2 conjugating enzyme that partners with E3 SAG/RBX2 to catalyze NEDD8 conjugation onto CUL5 (activating CRL5 ubiquitin ligase complexes) and onto the non-cullin substrate RHEB at K169 (enhancing lysosomal localization and mTORC1 activity); active CRL5 degrades substrates including NOXA (via K11-linked ubiquitin chains) and DIRAS2, thereby promoting cell survival, MAPK-c-Myc signaling, and viral replication, while UBE2F itself is subject to degradation via UBE2M acting as a ubiquitylation E2 for the Parkin-DJ-1 ligase under stress conditions.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBE2F is a neddylation E2 conjugating enzyme that, in partnership with the E3 SAG/RBX2, catalyzes NEDD8 conjugation onto CUL5 to activate CRL5 (Cullin-RING Ligase 5) ubiquitin ligase complexes, a node that governs cell survival, proliferative signaling, immune cell fate, and viral replication [#0, #4]. Active CRL5 directs degradation of multiple substrates: it ubiquitylates the pro-apoptotic protein NOXA via K11-linked (rather than K48-linked) chains to suppress apoptosis [#0], and through a CRL5-ASB11 complex it ubiquitylates and degrades the RAS-family tumor suppressor DIRAS2, thereby sustaining MAPK-c-Myc signaling [#3]. Beyond cullin substrates, UBE2F together with SAG/RBX2 neddylates the small GTPase RHEB at K169, enhancing its lysosomal localization and GTP-binding affinity to drive mTORC1 activation and Pten-loss-driven hepatic steatosis and tumorigenesis [#4]. UBE2F activity is itself constrained by a counter-regulatory neddylation E2, UBE2M, which acts as a ubiquitylation E2 for the Parkin-DJ-1 E3 ligase to target UBE2F for degradation under stress, linking the two E2s in a negative feedback axis that controls NOXA levels [#1]. Through the CUL5 axis UBE2F also restrains JUNB accumulation and IL-2R\\u03b2 expression to set IL-15 sensitivity and self-renewal of CD8 T cells [#6], and is required for pseudorabies virus replication [#5]. UBE2F is pharmacologically tractable: the small molecule HA-9104 binds UBE2F, lowers its protein level, and inactivates CRL5 to trigger NOXA-dependent apoptosis [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established UBE2F's core enzymatic role by showing it forms a tri-complex with SAG/RBX2 and CUL5 to neddylate CUL5 and activate CRL5, defining a survival pathway via NOXA degradation.\",\n      \"evidence\": \"Pulldown, in vivo/in vitro ubiquitylation assays, K11R linkage-specific mutagenesis, and NOXA knockdown epistasis\",\n      \"pmids\": [\"27591266\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address non-CUL5 neddylation substrates\", \"Physiological contexts beyond cancer cells unexplored\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed how UBE2F levels are controlled, identifying UBE2M as a dual-activity E2 that drives UBE2F ubiquitylation/degradation via Parkin-DJ-1, creating a negative regulatory axis between the two neddylation E2s.\",\n      \"evidence\": \"Biochemical assays defining UBE2M dual activity, genetic knockdown/overexpression with lung cancer growth readout\",\n      \"pmids\": [\"29932898\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stress signals that trigger UBE2M switch to ubiquitylation E2 not fully defined\", \"Direct E3-substrate contacts on UBE2F not mapped\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Connected UBE2F stability to chemoresistance, showing platinum disrupts UBE2F-RBX1 association to reduce UBE2F degradation, driving CRL5 activation and apoptosis resistance.\",\n      \"evidence\": \"Co-IP of UBE2F-RBX1, immunoblotting, UBE2F knockout sensitization assays, NOXA protein readout\",\n      \"pmids\": [\"33184273\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab evidence\", \"Mechanism by which platinum perturbs the UBE2F-RBX1 interface unresolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated UBE2F is druggable by identifying HA-9104, a direct-binding small molecule that depletes UBE2F and inactivates CRL5 to induce apoptosis.\",\n      \"evidence\": \"Structure-based virtual screen, direct binding assay, CUL5 neddylation and NOXA accumulation readouts, xenograft models\",\n      \"pmids\": [\"36253371\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding-site/structural basis of HA-9104 engagement not resolved\", \"Selectivity over other E2s not established\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the CRL5 substrate repertoire in vivo, showing UBE2F-driven CRL5-ASB11 degrades DIRAS2 to sustain MAPK-c-Myc signaling and tumor growth.\",\n      \"evidence\": \"KrasG12D PDAC mouse model with Ube2f conditional deletion, DIRAS2 ubiquitylation assays, Diras2 deletion epistatic rescue\",\n      \"pmids\": [\"38574733\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ASB11 is the sole substrate receptor for DIRAS2 unclear\", \"Generality across other tumor types untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Uncovered a non-cullin neddylation substrate, showing UBE2F/SAG neddylates RHEB at K169 to enhance lysosomal localization, GTP binding, and mTORC1 activation in liver tumorigenesis.\",\n      \"evidence\": \"K169 site-specific neddylation/mutagenesis, lysosomal fractionation, GTP-binding assay, mTORC1 readout, liver-specific Ube2f KO mouse\",\n      \"pmids\": [\"39762645\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other GTPases are neddylated substrates unknown\", \"Crosstalk between RHEB neddylation and CRL5 substrate flux not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed UBE2F-RBX2-mediated CUL5 neddylation is required for pseudorabies virus replication, implicating the pathway in host-virus biology.\",\n      \"evidence\": \"shRNA knockdown of UBE2F/RBX2, pharmacological CUL5 neddylation inhibition, PRV replication assay\",\n      \"pmids\": [\"41478481\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab evidence\", \"CRL5 substrate(s) mediating the proviral effect not identified\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined an immune-cell function, showing UBE2F-dependent CUL5 neddylation restrains JUNB/IL-2R\\u03b2 to tune IL-15 sensitivity and CD8 T cell self-renewal and survival.\",\n      \"evidence\": \"Genetic UBE2F ablation in CD8 T cells, CUL5 neddylation assay, JUNB/IL-2R\\u03b2 readouts, viral and tumor control models\",\n      \"pmids\": [\"42188874\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab evidence\", \"CRL5 substrate receptor controlling JUNB not pinpointed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UBE2F substrate specificity is partitioned between cullin (CUL5) and non-cullin (RHEB) targets, and the structural basis of its E2-E3 pairing and pharmacological inhibition, remain open.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model defining UBE2F substrate-selection determinants\", \"Full non-cullin substrate set unknown\", \"Tissue-specific regulation of UBE2F abundance incompletely mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 3, 4]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0061650\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"UBE2F-SAG(RBX2)-CUL5 neddylation complex\", \"CRL5 (Cullin-RING Ligase 5)\"],\n    \"partners\": [\"RBX2\", \"CUL5\", \"RBX1\", \"UBE2M\", \"RHEB\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}