{"gene":"UFL1","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2019,"finding":"UFL1 is recruited to DNA double-strand breaks by the MRE11/RAD50/NBS1 (MRN) complex and monoufmylates histone H4 following DNA damage. Monoufmylated histone H4 recruits Suv39h1 and Tip60, which are required for ATM activation. ATM in turn phosphorylates UFL1 at serine 462, enhancing its E3 ligase activity in a positive feedback loop.","method":"Co-immunoprecipitation, in vitro ufmylation assay, site-directed mutagenesis (S462 phosphorylation site), chromatin immunoprecipitation, laser micro-irradiation/live imaging","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods including in vitro assay, mutagenesis, Co-IP, and ChIP in a single rigorous study","pmids":["30886146"],"is_preprint":false},{"year":2023,"finding":"UFL1 requires its N-terminal helix for binding to UFC1 (E2). The UFL1–DDRGK1 fusion construct was used to solve a crystal structure of this critical interaction. UFL1 and UBA5 (E1) compete for binding to UFC1, with the competition shifting in favor of UFL1 after UFM1 is charged onto UFC1, coordinating the E1→E2→E3 cascade.","method":"X-ray crystallography, NMR, AlphaFold2 structural modeling, biochemical binding assays, mutagenesis","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure solved, validated by NMR and biochemical assays with mutagenesis in one study","pmids":["37988244"],"is_preprint":false},{"year":2024,"finding":"On replication stress, UFL1 localizes to stalled replication forks and catalyzes UFMylation of PTIP (a component of the MLL3/4 methyltransferase complex) at lysine 148. This promotes assembly of the PTIP–MLL3/4 complex, enrichment of H3K4me1 and H3K4me3 at stalled forks, and subsequent MRE11 nuclease recruitment to degrade nascent DNA in BRCA1/2-deficient cells.","method":"Proximity ligation assay, iPOND (isolation of proteins on nascent DNA), in vitro UFMylation assay, site-directed mutagenesis (K148), chromatin fractionation, fiber assay","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro UFMylation assay with mutagenesis, iPOND, fiber assay, multiple orthogonal methods in one rigorous study","pmids":["38649452"],"is_preprint":false},{"year":2024,"finding":"UFL1 promotes UFMylation of PD-1 in T cells, which antagonizes PD-1 ubiquitination and prevents its degradation. AMPK phosphorylates UFL1 at Thr536, disrupting PD-1 UFMylation and triggering PD-1 degradation. Loss of UFL1 in T cells reduces PD-1 stability and enhances CD8+ T cell activation.","method":"Conditional knockout mice, Co-immunoprecipitation, in vitro UFMylation assay, site-directed mutagenesis (T536), flow cytometry, single-cell RNA sequencing","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro UFMylation assay with mutagenesis, reciprocal Co-IP, genetic knockout with defined cellular phenotype","pmids":["38377992"],"is_preprint":false},{"year":2010,"finding":"UFL1 (Maxer) is an ER membrane protein that interacts with CDK5RAP3, anchoring it to the ER and inhibiting CDK5RAP3's function in repressing Cyclin D1 transcription in the nucleus. Loss of Maxer leads to cell accumulation at G1 phase.","method":"Co-immunoprecipitation, subcellular fractionation, knockdown/overexpression with cell cycle analysis (FACS), immunofluorescence","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — reciprocal Co-IP, functional phenotype (G1 arrest), localization experiment, single lab","pmids":["20531390"],"is_preprint":false},{"year":2010,"finding":"UFL1 (NLBP) was identified as a novel LZAP-binding protein. NLBP and LZAP mutually stabilize each other by inhibiting ubiquitination of the partner protein. NLBP also inhibits NF-κB signaling and cell invasion.","method":"Tandem affinity purification, Co-immunoprecipitation, ubiquitination assay, invasion assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — TAP identification, Co-IP, in-cell ubiquitination assay, single lab","pmids":["20164180"],"is_preprint":false},{"year":2013,"finding":"UFL1 (NLBP) binds to the regulatory domain of p120 catenin (p120ctn), and this interaction stabilizes p120ctn by inhibiting its ubiquitination and proteasomal degradation, promoting lung adenocarcinoma cell proliferation.","method":"Co-immunoprecipitation, domain mapping, ubiquitination assay, overexpression proliferation assay","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP with domain mapping, ubiquitination assay, single lab","pmids":["23839039"],"is_preprint":false},{"year":2015,"finding":"Genetic deletion of RCAD/UFL1 in mice causes elevated ER stress, activation of UPR, blockage of autophagic degradation, increased mitochondrial mass and ROS, DNA damage response, p53 activation, and enhanced cell death in hematopoietic stem cells, establishing UFL1 as essential for HSC survival and erythroid differentiation.","method":"Germ-line and conditional knockout mice, Western blotting for ER stress/UPR markers, autophagy flux assays, ROS measurement, flow cytometry, p53 pathway analysis","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with multiple defined molecular phenotypes (ER stress, autophagy, ROS, p53), multiple orthogonal methods","pmids":["25952549"],"is_preprint":false},{"year":2019,"finding":"CDK5RAP3 interacts with UFL1 in vivo, and loss of CDK5RAP3 alters the ufmylation profile in liver cells, establishing CDK5RAP3 as a substrate adaptor for UFL1-mediated UFMylation.","method":"Co-immunoprecipitation (in vivo interaction), conditional knockout mice, proteomics-based ufmylation profiling","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP plus genetic knockout with ufmylation profiling, single lab","pmids":["30635284"],"is_preprint":false},{"year":2018,"finding":"Cardiac-specific knockout of Ufl1 impairs PERK (PKR-like ER-resident kinase) signaling, leading to excessive ER stress, cardiomyocyte death, and development of cardiomyopathy. Administration of the ER chaperone tauroursodeoxycholic acid alleviates ER stress and attenuates cardiac dysfunction in Ufl1-deficient mice.","method":"Cardiac-specific conditional knockout mice, transcriptome analysis, biochemical ER stress markers (Western blot), chemical chaperone rescue experiment","journal":"Circulation. Heart failure","confidence":"High","confidence_rationale":"Tier 2 / Strong — cardiac-specific KO with transcriptome, biochemical pathway analysis, and pharmacological rescue experiment","pmids":["30354401"],"is_preprint":false},{"year":2023,"finding":"The UFL1/UFBP1 (UFL1/CDK5RAP3) complex directly interacts with the mTOR/GβL complex and attenuates mTORC1 activity. Ablation of UFL1 or UFBP1 in hepatocytes dissociates them from the mTOR/GβL complex and activates oncogenic mTOR signaling, driving hepatocellular carcinoma development.","method":"Co-immunoprecipitation, hepatocyte-specific conditional knockout mice, iTRAQ proteomics, DEN/HFD liver cancer models","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP of complex, genetic KO with defined pathway activation, single lab","pmids":["37131258"],"is_preprint":false},{"year":2022,"finding":"UFL1 inhibits TRIM29 from interacting with STING, thereby reducing STING ubiquitination at K338/K347/K370 and preventing its proteasomal degradation. This stabilizing function of UFL1 on STING is independent of its UFMylation E3 ligase activity.","method":"Co-immunoprecipitation, ubiquitination assay with site-specific mutants (K338/K347/K370), UFL1 ligase-dead mutant, Western blotting for protein stability","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, ubiquitination assay with mutagenesis, ligase-dead mutant control, single lab","pmids":["35871231"],"is_preprint":false},{"year":2025,"finding":"UFL1 promotes UFMylation of PARP1, preventing its ubiquitination and proteasomal degradation. Stabilized PARP1 enhances DNA damage repair, suppresses R-loop formation, and inhibits cGAS-STING activation, promoting tumor immune evasion in pancreatic cancer.","method":"Co-immunoprecipitation, UFMylation assay, R-loop detection, cGAS-STING reporter assay, conditional knockout tumor models, flow cytometry for CD8+ T cells","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, functional UFMylation assay, pathway reporter assay, genetic models; single lab","pmids":["41105513"],"is_preprint":false},{"year":2025,"finding":"Akt phosphorylates UFL1 at T426, enhancing its interaction with ArpC4 (a core subunit of the Arp2/3 complex) and inducing ArpC4 UFMylation. UFL1-mediated ArpC4 UFMylation facilitates lamellipodia formation and promotes cell migration, invasion, and metastasis.","method":"Co-immunoprecipitation, in vitro UFMylation assay, site-directed mutagenesis (T426), lamellipodia formation imaging, invasion/migration assay, in vivo metastasis models","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro UFMylation assay with mutagenesis, Co-IP, functional cellular and in vivo metastasis readouts in one rigorous study","pmids":["40419786"],"is_preprint":false},{"year":2022,"finding":"Skin-specific deletion of Ufl1 in mice causes epidermal thickening and hyperpigmentation. Mechanistically, Endothelin-1 (ET-1) is a UFMylation substrate; UFL1-mediated UFMylation of ET-1 regulates its stability. Loss of Ufl1 increases ET-1 expression and secretion, upregulating melanin biosynthesis genes.","method":"Skin-specific conditional knockout mice, RNA-Seq, in vivo UFMylation assay for ET-1, Western blotting for ET-1 stability","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — genetic KO with RNA-Seq and UFMylation substrate identification, single lab","pmids":["36120581"],"is_preprint":false},{"year":2025,"finding":"UFL1 interacts with RNF20 and catalyzes its UFMylation, enhancing RNF20 binding to CEP192 and facilitating its centrosomal localization to support mitotic spindle assembly. Loss of UFL1 causes mitotic defects, chromosome segregation errors, and aneuploidy in prostate cancer.","method":"Co-immunoprecipitation, UFMylation assay, centrosome fractionation/immunofluorescence, mitotic spindle analysis, conditional knockout prostate cancer models","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, UFMylation assay, localization experiment with functional consequence, single lab","pmids":["42008680"],"is_preprint":false},{"year":2025,"finding":"UFL1 mediates UFMylation of IFT88 at lysine 572. This UFMylation antagonizes IFT88 ubiquitination by the E3 ligase PJA2, preventing proteasomal degradation of IFT88 and maintaining ciliary homeostasis. A K572R mutant of IFT88 (UFMylation-deficient) shows increased stability and rescues ciliary defects caused by UFL1 depletion.","method":"Conditional knockout mice, Co-immunoprecipitation, in vitro UFMylation and ubiquitination assays, site-directed mutagenesis (K572R), immunofluorescence of cilia, rescue experiments","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro UFMylation/ubiquitination assays, mutagenesis with rescue, genetic KO in mice with clear ciliary phenotype, multiple orthogonal methods","pmids":["41272290"],"is_preprint":false},{"year":2026,"finding":"UFL1 UFMylates METTL16, reducing its ubiquitination and decreasing its protein stability. Loss of UFL1 increases METTL16 stability, leading to increased m6A modification of EEF1A1 mRNA via the METTL16-IGF2BP1 axis, elevating EEF1A1 protein levels and driving enzalutamide resistance in prostate cancer.","method":"Co-immunoprecipitation, UFMylation assay, ubiquitination assay, m6A methylation assay, protein stability assay, xenograft models","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — UFMylation and ubiquitination assays, m6A assay, pathway tracing, single lab","pmids":["41608626"],"is_preprint":false},{"year":2025,"finding":"WBP11 interacts with NONO and competitively inhibits UFL1-induced UFMylation of NONO at Lys198. Loss of WBP11 allows UFL1 to UFMylate NONO, reducing its stability. UFL1 overexpression suppresses HCC cell growth and metastasis via NONO degradation.","method":"Co-immunoprecipitation, in vitro UFMylation assay, site-directed mutagenesis (K198), competitive binding assay, xenograft models","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP with competition assay, UFMylation assay with mutagenesis, single lab","pmids":["41184530"],"is_preprint":false},{"year":2024,"finding":"LRP1 knockdown promotes binding of UFL1 to OGA (O-GlcNAcase) and accelerates ubiquitin-mediated OGA degradation. This leads to increased O-GlcNAcylation of NF-κB and inhibition of pro-apoptotic gene expression. The LRP1 β-chain stabilizes OGA by disrupting the UFL1-OGA interaction.","method":"Co-immunoprecipitation, ubiquitination assay, O-GlcNAcylation analysis, knockdown/overexpression, xenograft models","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, O-GlcNAc pathway analysis, single lab","pmids":["39405202"],"is_preprint":false},{"year":2024,"finding":"Chicken UFL1 (chUFL1) interacts with chSTING and promotes K63-linked polyubiquitination of chSTING at K308, facilitating STING dimerization and formation of the STING-TBK1-IRF7 complex for type I IFN production, independently of UFMylation. ChUFL1 also interacts with the AIV PA protein to inhibit viral polymerase activity and nuclear import of PA.","method":"Co-immunoprecipitation, ubiquitination assay with K63-specific analysis, site-directed mutagenesis (K308), STING dimerization assay, UFMylation-dead mutant, viral polymerase activity assay","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, ubiquitination assay with mutagenesis, UFMylation-independent function validated by ligase-dead mutant; ortholog (chicken) study, single lab","pmids":["38477617"],"is_preprint":false},{"year":2024,"finding":"UFL1 interacts with IRE1α and modulates the IRE1α/XBP1 pathway of the unfolded protein response in NEFA-stimulated bovine mammary epithelial cells, contributing to ER and mitochondrial homeostasis.","method":"Co-immunoprecipitation, Western blotting for IRE1α/XBP1 pathway markers, UFL1 knockdown/overexpression","journal":"Free radical biology & medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP, pathway marker Western blots, single lab, bovine cell model","pmids":["38821134"],"is_preprint":false},{"year":2026,"finding":"UFL1 deficiency in skeletal muscle activates the PERK/eIF2α/ATF4/CHOP ER stress signaling axis, leading to myoblast apoptosis. Pharmacological inhibition of PERK (GSK2606414) reverses UFL1-deficiency-induced upregulation of p-PERK, p-eIF2α, ATF4, and CHOP and rescues the apoptotic phenotype.","method":"Skeletal muscle-specific knockout mice, C2C12 cells, Western blotting, PERK inhibitor rescue, apoptosis assays","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with pharmacological rescue identifying specific ER stress pathway, multiple molecular markers, single lab","pmids":["42019645"],"is_preprint":false},{"year":2025,"finding":"ATI-1 targets VCP/p97 and disrupts its interaction with UFL1. This disruption promotes polyubiquitination and proteasomal degradation of Beclin1, inhibiting autophagy initiation. The VCP-UFL1-Beclin1 axis is identified as a regulatory node in autophagy.","method":"Co-immunoprecipitation (VCP-UFL1 interaction), ubiquitination assay for Beclin1, autophagy flux assays, small-molecule inhibitor (ATI-1) treatment, xenograft models","journal":"Bioorganic chemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and ubiquitination assay with pharmacological tool, mechanism partially inferred, single lab","pmids":["42060985"],"is_preprint":false},{"year":2025,"finding":"UFL1 interacts with multiple orthoflavivirus proteins (NS2A, NS2B-NS3, and Capsid) and promotes infectious virion production for dengue, Zika, West Nile, and yellow fever viruses. UFMylation does not regulate viral RNA translation or replication but acts at a later stage, likely viral assembly.","method":"Co-immunoprecipitation (UFL1 with viral proteins), infectious particle assays, siRNA depletion of UFL1/UFBP1/UBA5/UFC1/UFM1, RNA replication assays","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP with viral proteins, functional assays in single lab, preprint only","pmids":[],"is_preprint":true},{"year":2025,"finding":"Intracellular Shigella bacteria become targeted by UFL1 in infected human cells. Shigella antagonizes UFL1-mediated UFMylation in two ways: LPS shields bacteria from UFL1 recruitment, and the bacterial effector IpaH9.8 prevents UFM1 decoration. Loss of UFMylation increases bacterial burden in human cells and zebrafish, and this protective role is independent of autophagy.","method":"Proximity biotinylation coupled to quantitative mass spectrometry, bacterial infection assays, LPS mutant bacteria, IpaH9.8 effector assays, zebrafish infection model, autophagy-independent validation","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity proteomics and functional infection assays, preprint only, single lab","pmids":[],"is_preprint":true},{"year":2025,"finding":"Loss of UFMylation (via UFL1 loss) reduces phosphofructokinase (PFKAP) activity, rerouting glucose metabolism away from glycolysis toward the hexosamine biosynthesis pathway. Elevated hexosamine biosynthesis increases glycosylation of invasion-related proteins, promoting prostate cancer metastasis. PFKAP is identified as a UFMylation substrate.","method":"Biotin-based proximity proteomics (UFMylation substrate ID), metabolomics, UFL1 knockdown/overexpression, invasion assays, in vivo metastasis models","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity proteomics substrate identification, metabolomics, functional assays; preprint only","pmids":[],"is_preprint":true}],"current_model":"UFL1 is the sole E3 ligase of the UFMylation pathway, functioning with UBA5 (E1) and UFC1 (E2) to covalently attach UFM1 to substrate proteins; its N-terminal helix mediates UFC1 binding in a regulated E1-E2-E3 cascade, and it modifies a growing list of substrates—including histone H4, PTIP, PD-1, PARP1, ArpC4, IFT88, RNF20, ET-1, METTL16, NONO, and PFKAP—at specific lysines to antagonize ubiquitination-mediated degradation, regulate chromatin states at DNA damage/replication stress sites, control immune checkpoint receptor stability, regulate ciliogenesis and spindle assembly, and maintain ER/mitochondrial homeostasis; its activity is itself regulated by phosphorylation from ATM (S462) and Akt (T426), creating context-specific feedback loops in DNA damage response, metastasis, and immune evasion."},"narrative":{"mechanistic_narrative":"UFL1 is the E3 ligase of the UFMylation pathway, covalently conjugating the ubiquitin-like modifier UFM1 onto substrate lysines through a regulated E1→E2→E3 cascade in which its N-terminal helix mediates binding to the E2 enzyme UFC1, competing with the E1 UBA5 in a manner that shifts toward UFL1 once UFC1 is charged with UFM1 [PMID:37988244]. A recurring logic of UFL1 substrate UFMylation is the antagonism of ubiquitin-mediated proteasomal degradation: UFL1 stabilizes PD-1 in T cells against ubiquitination [PMID:38377992], stabilizes PARP1 to enhance DNA repair and suppress cGAS-STING activation [PMID:41105513], and stabilizes IFT88 by antagonizing PJA2-mediated ubiquitination to maintain ciliary homeostasis [PMID:41272290], while in other contexts UFMylation destabilizes substrates such as METTL16 and NONO [PMID:41608626, PMID:41184530]. In the DNA damage and replication stress response, UFL1 is recruited to double-strand breaks by the MRN complex where it monoufmylates histone H4 to drive ATM activation through a positive feedback loop in which ATM phosphorylates UFL1 at S462 to enhance its ligase activity [PMID:30886146], and it UFMylates PTIP at K148 at stalled forks to assemble the MLL3/4 complex and remodel chromatin [PMID:38649452]. UFL1 activity is further tuned by phosphorylation, with AMPK acting on T536 to disable PD-1 UFMylation [PMID:38377992] and Akt acting on T426 to promote ArpC4 UFMylation and lamellipodia-driven migration [PMID:40419786]. As an ER membrane-associated protein acting in a complex with CDK5RAP3, UFL1 is essential for ER homeostasis and the unfolded protein response: its loss elevates ER stress and impairs PERK signaling, causing tissue-specific phenotypes including hematopoietic stem cell death [PMID:25952549], cardiomyopathy [PMID:30354401], and myoblast apoptosis through the PERK/eIF2α/ATF4/CHOP axis [PMID:42019645]. UFL1 additionally regulates mitotic spindle assembly via RNF20 UFMylation [PMID:42008680] and possesses UFMylation-independent functions, including stabilizing STING by blocking TRIM29 [PMID:35871231].","teleology":[{"year":2010,"claim":"Established UFL1's earliest characterized cellular role as an ER membrane protein controlling cell cycle and stability of binding partners, before its UFMylation enzymology was understood.","evidence":"Co-IP, subcellular fractionation, and cell cycle FACS in cultured cells; TAP and in-cell ubiquitination assays","pmids":["20531390","20164180"],"confidence":"Medium","gaps":["Did not connect these stabilization roles to UFM1 conjugation activity","Mechanism of mutual stabilization with partners not resolved at the enzymatic level"]},{"year":2015,"claim":"Genetic ablation showed UFL1 is essential in vivo for cellular homeostasis, defining ER stress/UPR, autophagy, and mitochondrial control as core dependencies.","evidence":"Germline and conditional knockout mice with UPR, autophagy flux, ROS, and p53 pathway analyses in hematopoietic stem cells","pmids":["25952549"],"confidence":"High","gaps":["Direct UFMylation substrates driving the phenotype not identified","Did not separate ER stress from autophagy contributions causally"]},{"year":2018,"claim":"Tissue-specific knockouts linked UFL1 loss to organ pathology through ER stress signaling, establishing PERK as a key effector arm.","evidence":"Cardiac-specific knockout mice with transcriptomics, ER stress markers, and chemical chaperone rescue; later skeletal muscle KO with PERK inhibitor rescue","pmids":["30354401","42019645"],"confidence":"High","gaps":["Molecular substrate connecting UFL1 to PERK regulation not defined","Whether the effect requires UFM1 conjugation not established"]},{"year":2019,"claim":"Identified UFL1 as the chromatin-acting E3 that monoufmylates histone H4 at DNA breaks and revealed a phosphorylation feedback loop with ATM, placing UFMylation upstream of the DNA damage response.","evidence":"Co-IP, in vitro ufmylation assay, S462 mutagenesis, ChIP, and laser micro-irradiation imaging","pmids":["30886146"],"confidence":"High","gaps":["H4 lysine acceptor site not pinpointed in this entry","Stoichiometry and turnover of the modification unresolved"]},{"year":2019,"claim":"Defined CDK5RAP3 as a substrate adaptor for UFL1, clarifying how the ligase achieves substrate specificity in vivo.","evidence":"In vivo Co-IP, conditional knockout mice, and proteomics-based ufmylation profiling in liver","pmids":["30635284"],"confidence":"Medium","gaps":["Direct substrates recruited via CDK5RAP3 not enumerated","Structural basis of adaptor function not addressed"]},{"year":2023,"claim":"Solved the structural basis of E2 recognition, showing the UFL1 N-terminal helix binds UFC1 and that UBA5–UFL1 competition for UFC1 coordinates handoff in the cascade.","evidence":"X-ray crystallography of a UFL1–DDRGK1 fusion, NMR, AlphaFold2 modeling, and biochemical binding/mutagenesis assays","pmids":["37988244"],"confidence":"High","gaps":["Structure of UFL1 engaging a substrate not determined","How phosphorylation of UFL1 alters this interface not shown"]},{"year":2024,"claim":"Demonstrated the dominant UFL1 mechanistic theme of antagonizing substrate ubiquitination via site-specific UFMylation across distinct biological settings (replication forks, immune checkpoints, the ER-mTOR node).","evidence":"In vitro UFMylation assays with lysine mutagenesis (PTIP K148, PD-1), iPOND/fiber assays, conditional knockouts, and complex Co-IP with mTOR/GβL","pmids":["38649452","38377992","37131258"],"confidence":"High","gaps":["General rules predicting which substrates are stabilized versus destabilized unclear","Crosstalk between UFL1's many substrate-specific roles not integrated"]},{"year":2024,"claim":"Revealed UFMylation-independent functions of UFL1, broadening its activity beyond UFM1 conjugation.","evidence":"Co-IP, ubiquitination assays with site-specific mutants, and UFMylation/ligase-dead mutant controls for STING regulation; chicken ortholog K63-ubiquitination study","pmids":["35871231","38477617"],"confidence":"Medium","gaps":["Mechanism by which UFL1 blocks TRIM29-STING binding not structurally defined","Conservation of UFMylation-independent activity to human STING not established in these entries"]},{"year":2025,"claim":"Expanded UFL1's substrate repertoire to cytoskeletal, mitotic, ciliary, and metabolic regulators, and showed kinase inputs (Akt T426) gate substrate choice and cancer-relevant phenotypes.","evidence":"In vitro UFMylation assays with mutagenesis, Co-IP, centrosome/cilia imaging, T426 mutagenesis, and in vivo metastasis/tumor models for ArpC4, RNF20, IFT88, PARP1, METTL16, NONO","pmids":["40419786","42008680","41272290","41105513","41184530","41608626"],"confidence":"High","gaps":["How a single ligase is targeted to such diverse substrates in different tissues is unresolved","Competition between substrates for limited UFL1 capacity not addressed"]},{"year":2025,"claim":"Began implicating UFL1/UFMylation in host-pathogen defense and metabolic rewiring, extending its physiological reach beyond intrinsic cellular pathways.","evidence":"Proximity biotinylation/MS, infection assays, zebrafish models, and metabolomics for Shigella, orthoflaviviruses, and PFKAP (all preprints)","pmids":[],"confidence":"Low","gaps":["Preprint-only, single-lab findings awaiting peer review","Direct substrates and whether UFMylation versus scaffolding drives the effects not fully resolved","Generalizability across pathogens unconfirmed"]},{"year":null,"claim":"How UFL1 substrate selectivity, kinase regulation (ATM/Akt/AMPK), and the choice between stabilizing versus destabilizing a UFMylated substrate are integrated into a unified regulatory logic remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of UFL1 bound to a substrate","No general code linking UFMylation site to ubiquitin antagonism or promotion","Coordination among UFL1's nuclear, ER, mitotic, and immune roles not mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,2,3,13,16]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,3,12,13,16]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[1,3,16]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,8,11]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[4,7,9,22]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[0,2]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[15]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,3,12,16]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,2,12]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[7,9,22]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,11,12]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[4,15]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,2]}],"complexes":["UFL1–CDK5RAP3/UFBP1 complex"],"partners":["UFC1","UBA5","CDK5RAP3","DDRGK1","MRE11","VCP","IRE1A","ARPC4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O94874","full_name":"E3 UFM1-protein ligase 1","aliases":["E3 UFM1-protein transferase 1","Multiple alpha-helix protein located at ER","Novel LZAP-binding protein","Regulator of C53/LZAP and DDRGK1"],"length_aa":794,"mass_kda":89.6,"function":"E3 protein ligase that mediates ufmylation, the covalent attachment of the ubiquitin-like modifier UFM1 to lysine residues on target proteins, and which plays a key role in various processes, such as ribosome recycling, response to DNA damage, interferon response or reticulophagy (also called ER-phagy) (PubMed:20018847, PubMed:20164180, PubMed:20228063, PubMed:25219498, PubMed:27351204, PubMed:30626644, PubMed:30783677, PubMed:32160526, PubMed:32807901, PubMed:35394863, PubMed:36121123, PubMed:36543799, PubMed:36893266, PubMed:37036982, PubMed:37311461, PubMed:37595036, PubMed:37795761, PubMed:38377992, PubMed:38383785, PubMed:38383789). Catalyzes ufmylation of many protein, such as CD274/PD-L1, CDK5RAP3, CYB5R3, DDRGK1, EIF6, histone H4, MRE11, P4HB, PDCD1/PD-1, TRIP4, RPN1, RPS20/uS10, RPL10/uL16, RPL26/uL24, SYVN1/HRD1 and TP53/p53 (PubMed:20018847, PubMed:20531390, PubMed:25219498, PubMed:30783677, PubMed:30886146, PubMed:32160526, PubMed:35753586, PubMed:36543799, PubMed:36893266, PubMed:37036982, PubMed:37595036, PubMed:37795761, PubMed:38383785, PubMed:38383789). As part of the UREL complex, plays a key role in ribosome recycling by catalyzing mono-ufmylation of RPL26/uL24 subunit of the 60S ribosome (PubMed:38383785, PubMed:38383789). Ufmylation of RPL26/uL24 occurs on free 60S ribosomes following ribosome dissociation: it weakens the junction between post-termination 60S subunits and SEC61 translocons, promoting release and recycling of the large ribosomal subunit from the endoplasmic reticulum membrane (PubMed:38383785, PubMed:38383789). Ufmylation of RPL26/uL24 and subsequent 60S ribosome recycling either take place after normal termination of translation or after ribosome stalling during cotranslational translocation at the endoplasmic reticulum (PubMed:37036982, PubMed:37595036, PubMed:38383785, PubMed:38383789). Involved in reticulophagy in response to endoplasmic reticulum stress by mediating ufmylation of proteins such as CYB5R3 and RPN1, thereby promoting lysosomal degradation of ufmylated proteins (PubMed:23152784, PubMed:32160526, PubMed:36543799). Ufmylation in response to endoplasmic reticulum stress is essential for processes such as hematopoiesis, blood vessel morphogenesis or inflammatory response (PubMed:32050156). Mediates ufmylation of DDRGK1 and CDK5RAP3; the role of these modifications is however unclear: as both DDRGK1 and CDK5RAP3 act as substrate adapters for ufmylation, it is uncertain whether ufmylation of these proteins is, a collateral effect or is required for ufmylation (PubMed:20018847, PubMed:20531390). Acts as a negative regulator of T-cell activation by mediating ufmylation and stabilization of PDCD1/PD-1 (PubMed:38377992). Also involved in the response to DNA damage: recruited to double-strand break sites following DNA damage and mediates monoufmylation of histone H4 and ufmylation of MRE11 (PubMed:30783677, PubMed:30886146). Mediates ufmylation of TP53/p53, promoting its stability (PubMed:32807901). Catalyzes ufmylation of TRIP4, thereby playing a role in nuclear receptor-mediated transcription (PubMed:25219498). Required for hematopoietic stem cell function and hematopoiesis (By similarity)","subcellular_location":"Endoplasmic reticulum membrane; Cytoplasm, cytosol; Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/O94874/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UFL1","classification":"Not Classified","n_dependent_lines":485,"n_total_lines":1208,"dependency_fraction":0.4014900662251656},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DDOST","stoichiometry":0.2},{"gene":"OST4","stoichiometry":0.2},{"gene":"PGRMC1","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"SRP14","stoichiometry":0.2},{"gene":"SRP19","stoichiometry":0.2},{"gene":"TMED10","stoichiometry":0.2},{"gene":"VPS35","stoichiometry":0.2},{"gene":"CCDC47","stoichiometry":0.2},{"gene":"NCLN","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UFL1","total_profiled":1310},"omim":[{"mim_id":"616177","title":"DDRGK DOMAIN-CONTAINING PROTEIN 1; DDRGK1","url":"https://www.omim.org/entry/616177"},{"mim_id":"613372","title":"UFM1-SPECIFIC LIGASE 1; UFL1","url":"https://www.omim.org/entry/613372"},{"mim_id":"610554","title":"UBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1; UFC1","url":"https://www.omim.org/entry/610554"},{"mim_id":"610553","title":"UBIQUITIN-FOLD MODIFIER 1; UFM1","url":"https://www.omim.org/entry/610553"},{"mim_id":"608202","title":"CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 3; CDK5RAP3","url":"https://www.omim.org/entry/608202"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UFL1"},"hgnc":{"alias_symbol":["NLBP","Maxer","RCAD"],"prev_symbol":["KIAA0776"]},"alphafold":{"accession":"O94874","domains":[{"cath_id":"-","chopping":"28-105","consensus_level":"medium","plddt":87.4915,"start":28,"end":105},{"cath_id":"-","chopping":"266-354","consensus_level":"high","plddt":87.3265,"start":266,"end":354},{"cath_id":"-","chopping":"663-744_762-787","consensus_level":"medium","plddt":87.3337,"start":663,"end":787},{"cath_id":"1.10.10","chopping":"180-249","consensus_level":"medium","plddt":89.0196,"start":180,"end":249}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O94874","model_url":"https://alphafold.ebi.ac.uk/files/AF-O94874-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O94874-F1-predicted_aligned_error_v6.png","plddt_mean":80.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UFL1","jax_strain_url":"https://www.jax.org/strain/search?query=UFL1"},"sequence":{"accession":"O94874","fasta_url":"https://rest.uniprot.org/uniprotkb/O94874.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O94874/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O94874"}},"corpus_meta":[{"pmid":"25952549","id":"PMC_25952549","title":"RCAD/Ufl1, a Ufm1 E3 ligase, is essential for hematopoietic stem cell function and murine hematopoiesis.","date":"2015","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/25952549","citation_count":160,"is_preprint":false},{"pmid":"30886146","id":"PMC_30886146","title":"UFL1 promotes histone H4 ufmylation and ATM activation.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30886146","citation_count":154,"is_preprint":false},{"pmid":"30354401","id":"PMC_30354401","title":"Ufm1-Specific Ligase Ufl1 Regulates Endoplasmic Reticulum Homeostasis and Protects Against Heart Failure.","date":"2018","source":"Circulation. 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pathway","date":"2025-05-29","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.29.656827","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.01.09.632082","title":"UFMylation promotes orthoflavivirus infectious particle production","date":"2025-01-09","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.09.632082","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.02.657324","title":"Loss of UFMylation supports prostate cancer metastasis and rewires cell metabolism towards hexosamine biosynthesis","date":"2025-06-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.02.657324","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.07.607094","title":"UFMylation suppresses Type I IFN signaling during  <i>M. tuberculosis</i>  infection of human macrophages","date":"2024-08-07","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.07.607094","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":28236,"output_tokens":6808,"usd":0.093414,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15770,"output_tokens":4206,"usd":0.092,"stage2_stop_reason":"end_turn"},"total_usd":0.185414,"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\": 2019,\n      \"finding\": \"UFL1 is recruited to DNA double-strand breaks by the MRE11/RAD50/NBS1 (MRN) complex and monoufmylates histone H4 following DNA damage. Monoufmylated histone H4 recruits Suv39h1 and Tip60, which are required for ATM activation. ATM in turn phosphorylates UFL1 at serine 462, enhancing its E3 ligase activity in a positive feedback loop.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ufmylation assay, site-directed mutagenesis (S462 phosphorylation site), chromatin immunoprecipitation, laser micro-irradiation/live imaging\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods including in vitro assay, mutagenesis, Co-IP, and ChIP in a single rigorous study\",\n      \"pmids\": [\"30886146\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"UFL1 requires its N-terminal helix for binding to UFC1 (E2). The UFL1–DDRGK1 fusion construct was used to solve a crystal structure of this critical interaction. UFL1 and UBA5 (E1) compete for binding to UFC1, with the competition shifting in favor of UFL1 after UFM1 is charged onto UFC1, coordinating the E1→E2→E3 cascade.\",\n      \"method\": \"X-ray crystallography, NMR, AlphaFold2 structural modeling, biochemical binding assays, mutagenesis\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure solved, validated by NMR and biochemical assays with mutagenesis in one study\",\n      \"pmids\": [\"37988244\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"On replication stress, UFL1 localizes to stalled replication forks and catalyzes UFMylation of PTIP (a component of the MLL3/4 methyltransferase complex) at lysine 148. This promotes assembly of the PTIP–MLL3/4 complex, enrichment of H3K4me1 and H3K4me3 at stalled forks, and subsequent MRE11 nuclease recruitment to degrade nascent DNA in BRCA1/2-deficient cells.\",\n      \"method\": \"Proximity ligation assay, iPOND (isolation of proteins on nascent DNA), in vitro UFMylation assay, site-directed mutagenesis (K148), chromatin fractionation, fiber assay\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro UFMylation assay with mutagenesis, iPOND, fiber assay, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"38649452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UFL1 promotes UFMylation of PD-1 in T cells, which antagonizes PD-1 ubiquitination and prevents its degradation. AMPK phosphorylates UFL1 at Thr536, disrupting PD-1 UFMylation and triggering PD-1 degradation. Loss of UFL1 in T cells reduces PD-1 stability and enhances CD8+ T cell activation.\",\n      \"method\": \"Conditional knockout mice, Co-immunoprecipitation, in vitro UFMylation assay, site-directed mutagenesis (T536), flow cytometry, single-cell RNA sequencing\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro UFMylation assay with mutagenesis, reciprocal Co-IP, genetic knockout with defined cellular phenotype\",\n      \"pmids\": [\"38377992\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"UFL1 (Maxer) is an ER membrane protein that interacts with CDK5RAP3, anchoring it to the ER and inhibiting CDK5RAP3's function in repressing Cyclin D1 transcription in the nucleus. Loss of Maxer leads to cell accumulation at G1 phase.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation, knockdown/overexpression with cell cycle analysis (FACS), immunofluorescence\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — reciprocal Co-IP, functional phenotype (G1 arrest), localization experiment, single lab\",\n      \"pmids\": [\"20531390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"UFL1 (NLBP) was identified as a novel LZAP-binding protein. NLBP and LZAP mutually stabilize each other by inhibiting ubiquitination of the partner protein. NLBP also inhibits NF-κB signaling and cell invasion.\",\n      \"method\": \"Tandem affinity purification, Co-immunoprecipitation, ubiquitination assay, invasion assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — TAP identification, Co-IP, in-cell ubiquitination assay, single lab\",\n      \"pmids\": [\"20164180\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"UFL1 (NLBP) binds to the regulatory domain of p120 catenin (p120ctn), and this interaction stabilizes p120ctn by inhibiting its ubiquitination and proteasomal degradation, promoting lung adenocarcinoma cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, ubiquitination assay, overexpression proliferation assay\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP with domain mapping, ubiquitination assay, single lab\",\n      \"pmids\": [\"23839039\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Genetic deletion of RCAD/UFL1 in mice causes elevated ER stress, activation of UPR, blockage of autophagic degradation, increased mitochondrial mass and ROS, DNA damage response, p53 activation, and enhanced cell death in hematopoietic stem cells, establishing UFL1 as essential for HSC survival and erythroid differentiation.\",\n      \"method\": \"Germ-line and conditional knockout mice, Western blotting for ER stress/UPR markers, autophagy flux assays, ROS measurement, flow cytometry, p53 pathway analysis\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with multiple defined molecular phenotypes (ER stress, autophagy, ROS, p53), multiple orthogonal methods\",\n      \"pmids\": [\"25952549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CDK5RAP3 interacts with UFL1 in vivo, and loss of CDK5RAP3 alters the ufmylation profile in liver cells, establishing CDK5RAP3 as a substrate adaptor for UFL1-mediated UFMylation.\",\n      \"method\": \"Co-immunoprecipitation (in vivo interaction), conditional knockout mice, proteomics-based ufmylation profiling\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP plus genetic knockout with ufmylation profiling, single lab\",\n      \"pmids\": [\"30635284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Cardiac-specific knockout of Ufl1 impairs PERK (PKR-like ER-resident kinase) signaling, leading to excessive ER stress, cardiomyocyte death, and development of cardiomyopathy. Administration of the ER chaperone tauroursodeoxycholic acid alleviates ER stress and attenuates cardiac dysfunction in Ufl1-deficient mice.\",\n      \"method\": \"Cardiac-specific conditional knockout mice, transcriptome analysis, biochemical ER stress markers (Western blot), chemical chaperone rescue experiment\",\n      \"journal\": \"Circulation. Heart failure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — cardiac-specific KO with transcriptome, biochemical pathway analysis, and pharmacological rescue experiment\",\n      \"pmids\": [\"30354401\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The UFL1/UFBP1 (UFL1/CDK5RAP3) complex directly interacts with the mTOR/GβL complex and attenuates mTORC1 activity. Ablation of UFL1 or UFBP1 in hepatocytes dissociates them from the mTOR/GβL complex and activates oncogenic mTOR signaling, driving hepatocellular carcinoma development.\",\n      \"method\": \"Co-immunoprecipitation, hepatocyte-specific conditional knockout mice, iTRAQ proteomics, DEN/HFD liver cancer models\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP of complex, genetic KO with defined pathway activation, single lab\",\n      \"pmids\": [\"37131258\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"UFL1 inhibits TRIM29 from interacting with STING, thereby reducing STING ubiquitination at K338/K347/K370 and preventing its proteasomal degradation. This stabilizing function of UFL1 on STING is independent of its UFMylation E3 ligase activity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with site-specific mutants (K338/K347/K370), UFL1 ligase-dead mutant, Western blotting for protein stability\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, ubiquitination assay with mutagenesis, ligase-dead mutant control, single lab\",\n      \"pmids\": [\"35871231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UFL1 promotes UFMylation of PARP1, preventing its ubiquitination and proteasomal degradation. Stabilized PARP1 enhances DNA damage repair, suppresses R-loop formation, and inhibits cGAS-STING activation, promoting tumor immune evasion in pancreatic cancer.\",\n      \"method\": \"Co-immunoprecipitation, UFMylation assay, R-loop detection, cGAS-STING reporter assay, conditional knockout tumor models, flow cytometry for CD8+ T cells\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, functional UFMylation assay, pathway reporter assay, genetic models; single lab\",\n      \"pmids\": [\"41105513\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Akt phosphorylates UFL1 at T426, enhancing its interaction with ArpC4 (a core subunit of the Arp2/3 complex) and inducing ArpC4 UFMylation. UFL1-mediated ArpC4 UFMylation facilitates lamellipodia formation and promotes cell migration, invasion, and metastasis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro UFMylation assay, site-directed mutagenesis (T426), lamellipodia formation imaging, invasion/migration assay, in vivo metastasis models\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro UFMylation assay with mutagenesis, Co-IP, functional cellular and in vivo metastasis readouts in one rigorous study\",\n      \"pmids\": [\"40419786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Skin-specific deletion of Ufl1 in mice causes epidermal thickening and hyperpigmentation. Mechanistically, Endothelin-1 (ET-1) is a UFMylation substrate; UFL1-mediated UFMylation of ET-1 regulates its stability. Loss of Ufl1 increases ET-1 expression and secretion, upregulating melanin biosynthesis genes.\",\n      \"method\": \"Skin-specific conditional knockout mice, RNA-Seq, in vivo UFMylation assay for ET-1, Western blotting for ET-1 stability\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — genetic KO with RNA-Seq and UFMylation substrate identification, single lab\",\n      \"pmids\": [\"36120581\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UFL1 interacts with RNF20 and catalyzes its UFMylation, enhancing RNF20 binding to CEP192 and facilitating its centrosomal localization to support mitotic spindle assembly. Loss of UFL1 causes mitotic defects, chromosome segregation errors, and aneuploidy in prostate cancer.\",\n      \"method\": \"Co-immunoprecipitation, UFMylation assay, centrosome fractionation/immunofluorescence, mitotic spindle analysis, conditional knockout prostate cancer models\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, UFMylation assay, localization experiment with functional consequence, single lab\",\n      \"pmids\": [\"42008680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UFL1 mediates UFMylation of IFT88 at lysine 572. This UFMylation antagonizes IFT88 ubiquitination by the E3 ligase PJA2, preventing proteasomal degradation of IFT88 and maintaining ciliary homeostasis. A K572R mutant of IFT88 (UFMylation-deficient) shows increased stability and rescues ciliary defects caused by UFL1 depletion.\",\n      \"method\": \"Conditional knockout mice, Co-immunoprecipitation, in vitro UFMylation and ubiquitination assays, site-directed mutagenesis (K572R), immunofluorescence of cilia, rescue experiments\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro UFMylation/ubiquitination assays, mutagenesis with rescue, genetic KO in mice with clear ciliary phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"41272290\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"UFL1 UFMylates METTL16, reducing its ubiquitination and decreasing its protein stability. Loss of UFL1 increases METTL16 stability, leading to increased m6A modification of EEF1A1 mRNA via the METTL16-IGF2BP1 axis, elevating EEF1A1 protein levels and driving enzalutamide resistance in prostate cancer.\",\n      \"method\": \"Co-immunoprecipitation, UFMylation assay, ubiquitination assay, m6A methylation assay, protein stability assay, xenograft models\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — UFMylation and ubiquitination assays, m6A assay, pathway tracing, single lab\",\n      \"pmids\": [\"41608626\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WBP11 interacts with NONO and competitively inhibits UFL1-induced UFMylation of NONO at Lys198. Loss of WBP11 allows UFL1 to UFMylate NONO, reducing its stability. UFL1 overexpression suppresses HCC cell growth and metastasis via NONO degradation.\",\n      \"method\": \"Co-immunoprecipitation, in vitro UFMylation assay, site-directed mutagenesis (K198), competitive binding assay, xenograft models\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP with competition assay, UFMylation assay with mutagenesis, single lab\",\n      \"pmids\": [\"41184530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LRP1 knockdown promotes binding of UFL1 to OGA (O-GlcNAcase) and accelerates ubiquitin-mediated OGA degradation. This leads to increased O-GlcNAcylation of NF-κB and inhibition of pro-apoptotic gene expression. The LRP1 β-chain stabilizes OGA by disrupting the UFL1-OGA interaction.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, O-GlcNAcylation analysis, knockdown/overexpression, xenograft models\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, O-GlcNAc pathway analysis, single lab\",\n      \"pmids\": [\"39405202\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Chicken UFL1 (chUFL1) interacts with chSTING and promotes K63-linked polyubiquitination of chSTING at K308, facilitating STING dimerization and formation of the STING-TBK1-IRF7 complex for type I IFN production, independently of UFMylation. ChUFL1 also interacts with the AIV PA protein to inhibit viral polymerase activity and nuclear import of PA.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with K63-specific analysis, site-directed mutagenesis (K308), STING dimerization assay, UFMylation-dead mutant, viral polymerase activity assay\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, ubiquitination assay with mutagenesis, UFMylation-independent function validated by ligase-dead mutant; ortholog (chicken) study, single lab\",\n      \"pmids\": [\"38477617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UFL1 interacts with IRE1α and modulates the IRE1α/XBP1 pathway of the unfolded protein response in NEFA-stimulated bovine mammary epithelial cells, contributing to ER and mitochondrial homeostasis.\",\n      \"method\": \"Co-immunoprecipitation, Western blotting for IRE1α/XBP1 pathway markers, UFL1 knockdown/overexpression\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP, pathway marker Western blots, single lab, bovine cell model\",\n      \"pmids\": [\"38821134\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"UFL1 deficiency in skeletal muscle activates the PERK/eIF2α/ATF4/CHOP ER stress signaling axis, leading to myoblast apoptosis. Pharmacological inhibition of PERK (GSK2606414) reverses UFL1-deficiency-induced upregulation of p-PERK, p-eIF2α, ATF4, and CHOP and rescues the apoptotic phenotype.\",\n      \"method\": \"Skeletal muscle-specific knockout mice, C2C12 cells, Western blotting, PERK inhibitor rescue, apoptosis assays\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with pharmacological rescue identifying specific ER stress pathway, multiple molecular markers, single lab\",\n      \"pmids\": [\"42019645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ATI-1 targets VCP/p97 and disrupts its interaction with UFL1. This disruption promotes polyubiquitination and proteasomal degradation of Beclin1, inhibiting autophagy initiation. The VCP-UFL1-Beclin1 axis is identified as a regulatory node in autophagy.\",\n      \"method\": \"Co-immunoprecipitation (VCP-UFL1 interaction), ubiquitination assay for Beclin1, autophagy flux assays, small-molecule inhibitor (ATI-1) treatment, xenograft models\",\n      \"journal\": \"Bioorganic chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and ubiquitination assay with pharmacological tool, mechanism partially inferred, single lab\",\n      \"pmids\": [\"42060985\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UFL1 interacts with multiple orthoflavivirus proteins (NS2A, NS2B-NS3, and Capsid) and promotes infectious virion production for dengue, Zika, West Nile, and yellow fever viruses. UFMylation does not regulate viral RNA translation or replication but acts at a later stage, likely viral assembly.\",\n      \"method\": \"Co-immunoprecipitation (UFL1 with viral proteins), infectious particle assays, siRNA depletion of UFL1/UFBP1/UBA5/UFC1/UFM1, RNA replication assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP with viral proteins, functional assays in single lab, preprint only\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Intracellular Shigella bacteria become targeted by UFL1 in infected human cells. Shigella antagonizes UFL1-mediated UFMylation in two ways: LPS shields bacteria from UFL1 recruitment, and the bacterial effector IpaH9.8 prevents UFM1 decoration. Loss of UFMylation increases bacterial burden in human cells and zebrafish, and this protective role is independent of autophagy.\",\n      \"method\": \"Proximity biotinylation coupled to quantitative mass spectrometry, bacterial infection assays, LPS mutant bacteria, IpaH9.8 effector assays, zebrafish infection model, autophagy-independent validation\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity proteomics and functional infection assays, preprint only, single lab\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Loss of UFMylation (via UFL1 loss) reduces phosphofructokinase (PFKAP) activity, rerouting glucose metabolism away from glycolysis toward the hexosamine biosynthesis pathway. Elevated hexosamine biosynthesis increases glycosylation of invasion-related proteins, promoting prostate cancer metastasis. PFKAP is identified as a UFMylation substrate.\",\n      \"method\": \"Biotin-based proximity proteomics (UFMylation substrate ID), metabolomics, UFL1 knockdown/overexpression, invasion assays, in vivo metastasis models\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity proteomics substrate identification, metabolomics, functional assays; preprint only\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"UFL1 is the sole E3 ligase of the UFMylation pathway, functioning with UBA5 (E1) and UFC1 (E2) to covalently attach UFM1 to substrate proteins; its N-terminal helix mediates UFC1 binding in a regulated E1-E2-E3 cascade, and it modifies a growing list of substrates—including histone H4, PTIP, PD-1, PARP1, ArpC4, IFT88, RNF20, ET-1, METTL16, NONO, and PFKAP—at specific lysines to antagonize ubiquitination-mediated degradation, regulate chromatin states at DNA damage/replication stress sites, control immune checkpoint receptor stability, regulate ciliogenesis and spindle assembly, and maintain ER/mitochondrial homeostasis; its activity is itself regulated by phosphorylation from ATM (S462) and Akt (T426), creating context-specific feedback loops in DNA damage response, metastasis, and immune evasion.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UFL1 is the E3 ligase of the UFMylation pathway, covalently conjugating the ubiquitin-like modifier UFM1 onto substrate lysines through a regulated E1→E2→E3 cascade in which its N-terminal helix mediates binding to the E2 enzyme UFC1, competing with the E1 UBA5 in a manner that shifts toward UFL1 once UFC1 is charged with UFM1 [#1]. A recurring logic of UFL1 substrate UFMylation is the antagonism of ubiquitin-mediated proteasomal degradation: UFL1 stabilizes PD-1 in T cells against ubiquitination [#3], stabilizes PARP1 to enhance DNA repair and suppress cGAS-STING activation [#12], and stabilizes IFT88 by antagonizing PJA2-mediated ubiquitination to maintain ciliary homeostasis [#16], while in other contexts UFMylation destabilizes substrates such as METTL16 and NONO [#17, #18]. In the DNA damage and replication stress response, UFL1 is recruited to double-strand breaks by the MRN complex where it monoufmylates histone H4 to drive ATM activation through a positive feedback loop in which ATM phosphorylates UFL1 at S462 to enhance its ligase activity [#0], and it UFMylates PTIP at K148 at stalled forks to assemble the MLL3/4 complex and remodel chromatin [#2]. UFL1 activity is further tuned by phosphorylation, with AMPK acting on T536 to disable PD-1 UFMylation [#3] and Akt acting on T426 to promote ArpC4 UFMylation and lamellipodia-driven migration [#13]. As an ER membrane-associated protein acting in a complex with CDK5RAP3, UFL1 is essential for ER homeostasis and the unfolded protein response: its loss elevates ER stress and impairs PERK signaling, causing tissue-specific phenotypes including hematopoietic stem cell death [#7], cardiomyopathy [#9], and myoblast apoptosis through the PERK/eIF2α/ATF4/CHOP axis [#22]. UFL1 additionally regulates mitotic spindle assembly via RNF20 UFMylation [#15] and possesses UFMylation-independent functions, including stabilizing STING by blocking TRIM29 [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established UFL1's earliest characterized cellular role as an ER membrane protein controlling cell cycle and stability of binding partners, before its UFMylation enzymology was understood.\",\n      \"evidence\": \"Co-IP, subcellular fractionation, and cell cycle FACS in cultured cells; TAP and in-cell ubiquitination assays\",\n      \"pmids\": [\"20531390\", \"20164180\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not connect these stabilization roles to UFM1 conjugation activity\", \"Mechanism of mutual stabilization with partners not resolved at the enzymatic level\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Genetic ablation showed UFL1 is essential in vivo for cellular homeostasis, defining ER stress/UPR, autophagy, and mitochondrial control as core dependencies.\",\n      \"evidence\": \"Germline and conditional knockout mice with UPR, autophagy flux, ROS, and p53 pathway analyses in hematopoietic stem cells\",\n      \"pmids\": [\"25952549\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct UFMylation substrates driving the phenotype not identified\", \"Did not separate ER stress from autophagy contributions causally\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Tissue-specific knockouts linked UFL1 loss to organ pathology through ER stress signaling, establishing PERK as a key effector arm.\",\n      \"evidence\": \"Cardiac-specific knockout mice with transcriptomics, ER stress markers, and chemical chaperone rescue; later skeletal muscle KO with PERK inhibitor rescue\",\n      \"pmids\": [\"30354401\", \"42019645\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular substrate connecting UFL1 to PERK regulation not defined\", \"Whether the effect requires UFM1 conjugation not established\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified UFL1 as the chromatin-acting E3 that monoufmylates histone H4 at DNA breaks and revealed a phosphorylation feedback loop with ATM, placing UFMylation upstream of the DNA damage response.\",\n      \"evidence\": \"Co-IP, in vitro ufmylation assay, S462 mutagenesis, ChIP, and laser micro-irradiation imaging\",\n      \"pmids\": [\"30886146\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"H4 lysine acceptor site not pinpointed in this entry\", \"Stoichiometry and turnover of the modification unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined CDK5RAP3 as a substrate adaptor for UFL1, clarifying how the ligase achieves substrate specificity in vivo.\",\n      \"evidence\": \"In vivo Co-IP, conditional knockout mice, and proteomics-based ufmylation profiling in liver\",\n      \"pmids\": [\"30635284\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct substrates recruited via CDK5RAP3 not enumerated\", \"Structural basis of adaptor function not addressed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Solved the structural basis of E2 recognition, showing the UFL1 N-terminal helix binds UFC1 and that UBA5–UFL1 competition for UFC1 coordinates handoff in the cascade.\",\n      \"evidence\": \"X-ray crystallography of a UFL1–DDRGK1 fusion, NMR, AlphaFold2 modeling, and biochemical binding/mutagenesis assays\",\n      \"pmids\": [\"37988244\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of UFL1 engaging a substrate not determined\", \"How phosphorylation of UFL1 alters this interface not shown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated the dominant UFL1 mechanistic theme of antagonizing substrate ubiquitination via site-specific UFMylation across distinct biological settings (replication forks, immune checkpoints, the ER-mTOR node).\",\n      \"evidence\": \"In vitro UFMylation assays with lysine mutagenesis (PTIP K148, PD-1), iPOND/fiber assays, conditional knockouts, and complex Co-IP with mTOR/GβL\",\n      \"pmids\": [\"38649452\", \"38377992\", \"37131258\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"General rules predicting which substrates are stabilized versus destabilized unclear\", \"Crosstalk between UFL1's many substrate-specific roles not integrated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed UFMylation-independent functions of UFL1, broadening its activity beyond UFM1 conjugation.\",\n      \"evidence\": \"Co-IP, ubiquitination assays with site-specific mutants, and UFMylation/ligase-dead mutant controls for STING regulation; chicken ortholog K63-ubiquitination study\",\n      \"pmids\": [\"35871231\", \"38477617\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which UFL1 blocks TRIM29-STING binding not structurally defined\", \"Conservation of UFMylation-independent activity to human STING not established in these entries\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Expanded UFL1's substrate repertoire to cytoskeletal, mitotic, ciliary, and metabolic regulators, and showed kinase inputs (Akt T426) gate substrate choice and cancer-relevant phenotypes.\",\n      \"evidence\": \"In vitro UFMylation assays with mutagenesis, Co-IP, centrosome/cilia imaging, T426 mutagenesis, and in vivo metastasis/tumor models for ArpC4, RNF20, IFT88, PARP1, METTL16, NONO\",\n      \"pmids\": [\"40419786\", \"42008680\", \"41272290\", \"41105513\", \"41184530\", \"41608626\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a single ligase is targeted to such diverse substrates in different tissues is unresolved\", \"Competition between substrates for limited UFL1 capacity not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Began implicating UFL1/UFMylation in host-pathogen defense and metabolic rewiring, extending its physiological reach beyond intrinsic cellular pathways.\",\n      \"evidence\": \"Proximity biotinylation/MS, infection assays, zebrafish models, and metabolomics for Shigella, orthoflaviviruses, and PFKAP (all preprints)\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint-only, single-lab findings awaiting peer review\", \"Direct substrates and whether UFMylation versus scaffolding drives the effects not fully resolved\", \"Generalizability across pathogens unconfirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UFL1 substrate selectivity, kinase regulation (ATM/Akt/AMPK), and the choice between stabilizing versus destabilizing a UFMylated substrate are integrated into a unified regulatory logic remains unresolved.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of UFL1 bound to a substrate\", \"No general code linking UFMylation site to ubiquitin antagonism or promotion\", \"Coordination among UFL1's nuclear, ER, mitotic, and immune roles not mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 2, 3, 13, 16]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 3, 12, 13, 16]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [1, 3, 16]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 8, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [4, 7, 9, 22]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 3, 12, 16]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 2, 12]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [7, 9, 22]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 11, 12]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [4, 15]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\"UFL1–CDK5RAP3/UFBP1 complex\"],\n    \"partners\": [\"UFC1\", \"UBA5\", \"CDK5RAP3\", \"DDRGK1\", \"MRE11\", \"VCP\", \"IRE1A\", \"ArpC4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}