Affinage

FBXL12

F-box/LRR-repeat protein 12 · UniProt Q9NXK8

Length
326 aa
Mass
37.0 kDa
Annotated
2026-06-09
21 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

FBXL12 is the substrate-recognition F-box subunit of an SCF (Skp1-Cul1-F-box) E3 ubiquitin ligase that controls cell-cycle progression, genome stability, and cell differentiation by directing the polyubiquitylation and proteasomal turnover of distinct substrates (PMID:23324393, PMID:18660753, PMID:26124079). Unusually, its F-box domain mediates binding both to Skp1 and to substrate, as shown when SCF(FBXL12) recognizes Ku80 upon its loading at DNA double-strand breaks and removes it from DNA to regulate the balance between NHEJ and resection-dependent repair (PMID:23324393, PMID:35575473); this neddylation-dependent clearance restricts Ku occupancy at DNA ends and preserves transcription near breaks (PMID:39058590). In the replication-stress response, CHK1-dependent phosphorylation of FANCD2 generates a phosphodegron recognized by FBXL12, clearing FANCD2 from chromatin to permit replication fork restart, and FBXL12 loss causes FANCD2 accumulation, excessive DNA damage, and sensitization to WEE1 inhibition (PMID:37591242). FBXL12 also enforces cell-cycle and differentiation transitions by degrading CDK inhibitors and metabolic enzymes: it targets p57KIP2 in a phosphorylation-dependent, TGF-β-induced manner in osteoblasts (PMID:18660753), degrades CaMKI to impose G1 arrest (PMID:23707388), degrades p27/Cdkn1b downstream of pre-TCR signaling to drive proliferation of β-selected thymocytes (PMID:31451788), and ubiquitylates ALDH3-family enzymes to enable trophoblast stem cell and DP-to-SP thymocyte differentiation in vivo (PMID:26124079, PMID:26999371). Additional substrates and regulatory inputs include K63-linked ubiquitylation of MYH14 driving microglial cytoskeletal reorganization (PMID:40830106), ALDH1A1 ubiquitylation controlled by the sorcin-PAX5 axis in pancreatic cancer (PMID:40055736), and an alternative F-box-lacking isoform (Fbl12ΔF) that relocalizes full-length FBXL12 from nucleus to cytoplasm to modulate SCF(FBXL12) activity (PMID:29124172).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2008 High

    Established FBXL12 as a functional SCF substrate-recognition subunit by identifying its first substrate and linking its activity to a signaling-driven differentiation outcome.

    Evidence Co-IP, in vitro ubiquitination, RNAi and dominant-negative FBL12ΔF in primary osteoblasts

    PMID:18660753

    Open questions at the time
    • Phosphorylation site/kinase generating the p57KIP2 degron not defined
    • Single cell-type context
  2. 2013 High

    Showed FBXL12 acts in DNA repair by recognizing DNA-bound Ku80, defining a role beyond cell-cycle inhibitor turnover and revealing the unusual dual role of its F-box domain in Skp1 and substrate binding.

    Evidence Cell-free Xenopus egg extract, immunodepletion, F-box screen for DSB-binding proteins, ubiquitylation and degradation assays, domain mutagenesis

    PMID:23324393

    Open questions at the time
    • Recruitment mechanism to DSBs in intact cells not resolved
    • Structural basis for F-box-mediated substrate binding unknown
  3. 2013 Medium

    Connected FBXL12 to G1 arrest by identifying CaMKI as a degradation substrate whose loss disrupts cyclin D1/Cdk4 assembly and p27 phosphorylation.

    Evidence Overexpression/knockdown, proteasome inhibition, p27 phosphosite mutagenesis, cell-cycle analysis in lung epithelia

    PMID:23707388

    Open questions at the time
    • Direct ubiquitination of CaMKI by SCF(FBXL12) not reconstituted in this study
    • Methods detail limited
  4. 2015 High

    Demonstrated an in vivo developmental role by showing SCF(FBXL12) degrades ALDH3 to permit trophoblast stem cell differentiation, with knockout, phenocopy and chemical rescue.

    Evidence Reciprocal Co-IP, in vivo ubiquitination, FBXL12 knockout mice, TSC rescue, ALDH3 inhibitor gossypol

    PMID:26124079

    Open questions at the time
    • Signal triggering ALDH3 degradation during differentiation not defined
  5. 2015 Medium

    Identified an alternative F-box-lacking isoform (Fbl12ΔF) as an endogenous regulatory mechanism that controls SCF(FBXL12) activity through subcellular relocalization.

    Evidence Alternative promoter reporter assays, RT-PCR, UV induction, Co-IP, subcellular fractionation

    PMID:29124172

    Open questions at the time
    • Functional consequence of relocalization on specific substrates not measured
    • Physiological role of UV induction unclear
  6. 2016 High

    Generalized the FBXL12-ALDH3 axis to T-cell development, showing a cell-autonomous DP-to-SP differentiation block in knockouts.

    Evidence FBXL12 knockout mice, bone marrow transplantation, fetal thymic organ culture, flow cytometry

    PMID:26999371

    Open questions at the time
    • How ALDH3 accumulation mechanistically blocks differentiation not resolved
  7. 2019 High

    Placed FBXL12 in pre-TCR signaling by showing its induction drives p27/Cdkn1b degradation to license β-selected thymocyte proliferation, acting additively with Notch-induced Fbxl1.

    Evidence In vivo genetic epistasis, conditional knockouts, polyubiquitination assays, cell-cycle analysis

    PMID:31451788

    Open questions at the time
    • Mechanism of pre-TCR-driven transcriptional induction not detailed
  8. 2022 Medium

    Refined the DNA-repair role by showing FBXL12 depletion in quiescent G0 cells promotes DNA end resection, implicating it in NHEJ-versus-resection pathway choice.

    Evidence CRISPR/Cas9 whole-genome screen, FBXL12 depletion, resection assays in G0 versus cycling cells

    PMID:35575473

    Open questions at the time
    • Why the effect is G0-specific not mechanistically explained
    • Single resection readout
  9. 2023 High

    Defined a phosphodegron-driven mechanism in which CHK1-phosphorylated FANCD2 is cleared from chromatin by FBXL12 to enable replication fork restart, with therapeutic implications.

    Evidence In vitro reconstitution with phosphodegron mutants, chromatin fractionation, DNA fiber assays, FANCD2-deficient cell complementation, WEE1-inhibitor sensitivity

    PMID:37591242

    Open questions at the time
    • Structural recognition of the phosphodegron not solved
  10. 2024 Medium

    Quantified the FBXL12/neddylation pathway as restricting Ku occupancy to ~1–2 molecules per DNA end and linked its misregulation to impaired transcription near breaks.

    Evidence FBXL12 depletion, neddylation inhibition, live-cell imaging, ChIP, transcription assays near DSBs

    PMID:39058590

    Open questions at the time
    • Coordination with DNA-PKcs and CtIP/ATM mechanisms not fully resolved
    • Single lab
  11. 2025 Medium

    Expanded the substrate range to K63-linked ubiquitylation of MYH14 in microglia and showed m6A modification of Fbxl12 mRNA tunes its expression during spinal cord injury healing.

    Evidence Multiomics, m6A analysis, overexpression in microglia, K63-ubiquitylation assay, migration/cytoskeletal assays, in vivo SCI model

    PMID:40830106

    Open questions at the time
    • Non-degradative K63 function of MYH14 ubiquitylation mechanistically incomplete
    • Abstract-level detail
  12. 2025 Medium

    Linked FBXL12 to ferroptosis via ALDH1A1 ubiquitylation under control of the sorcin-PAX5 transcriptional axis in pancreatic cancer.

    Evidence Co-IP, ChIP, luciferase assays, proteomics, FBXL12 expression manipulation, ubiquitination assays, PAX5 imaging

    PMID:40055736

    Open questions at the time
    • Direct vs indirect ALDH1A1 ubiquitylation not isolated from upstream transcriptional effects
  13. 2025 Low

    Raised a non-canonical possibility that FBXL12 binds CRY1 at K151 to influence circadian period independent of ubiquitin-driven degradation.

    Evidence Site-directed mutagenesis, luciferase complementation interaction assay, circadian rescue in Cry1/2-deficient cells

    PMID:40869282

    Open questions at the time
    • No direct ubiquitination assay for the CRY1 interaction performed
    • Mechanistic interpretation speculative; not independently confirmed

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unknown how FBXL12 selects among its many divergent substrates and how its localization, isoform expression, and post-transcriptional regulation are integrated to specify outcomes in different cell types.
  • No structural model of FBXL12 substrate recognition
  • Determinants of substrate choice across tissues undefined
  • Relationship between degradative and non-degradative interactions unclear

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0016874 ligase activity 3 GO:0060090 molecular adaptor activity 1
Localization
GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 1 GO:0005829 cytosol 1
Pathway
R-HSA-73894 DNA Repair 4 R-HSA-1266738 Developmental Biology 3 R-HSA-1640170 Cell Cycle 3 R-HSA-392499 Metabolism of proteins 3 R-HSA-168256 Immune System 2
Complex memberships
SCF(FBXL12) (Skp1-Cul1-F-box) E3 ubiquitin ligase

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2013 FBXL12 is the F-box protein subunit of an SCF (Skp1-Cul1-F-box) E3 ubiquitin ligase complex that recognizes and polyubiquitylates Ku80 upon its binding to DNA double-strand breaks (DSBs), leading to Ku80 removal from DNA and proteasomal degradation. Fbxl12 was found to be recruited to DSBs in a DSB- and Ku-dependent manner in Xenopus laevis egg extract; immunodepletion of Fbxl12 prevented Cul1 and Skp1 binding to DSBs and blocked Ku80 ubiquitylation. Uniquely, the F-box domain of Fbxl12 was required for binding to both Skp1 and its substrate Ku80. Cell-free Xenopus laevis egg extract system, immunodepletion, F-box protein screen for DSB-binding proteins, ubiquitylation assays Cell cycle (Georgetown, Tex.) High 23324393
2008 FBXL12 (FBL12) forms an SCF(FBL12) E3 ubiquitin ligase complex and directly ubiquitinates the CDK inhibitor p57KIP2 in a phosphorylation-dependent manner. TGF-β1 stimulation induces p57KIP2 degradation via this pathway in osteoblasts. Inhibition of FBL12 by RNAi suppressed p57KIP2 degradation; a dominant-negative FBL12ΔF mutant increased steady-state p57KIP2 levels and promoted osteoblast differentiation, while wild-type FBL12 inhibited differentiation. Co-immunoprecipitation, in vitro ubiquitination assay, RNAi knockdown, dominant-negative overexpression, primary osteoblast differentiation assay EMBO reports High 18660753
2013 Fbxl12 mediates the proteasomal degradation of CaMKI (Ca2+/calmodulin-dependent kinase I) via the ubiquitin-proteasome pathway, causing G1 arrest in lung epithelia. Fbxl12-induced CaMKI degradation disrupts cyclin D1/Cdk4 complex assembly and attenuates CaMKI-mediated phosphorylation of p27 at Thr157/Thr198 (human) or Thr170/Thr197 (mouse), altering p27 subcellular localization. Known inducers of G1 arrest increase Fbxl12 levels in cells. Overexpression and knockdown of Fbxl12, proteasome inhibitor experiments, p27 phosphorylation site mutagenesis, cell cycle analysis Cellular signalling Medium 23707388
2015 FBXL12 interacts specifically with members of the ALDH3 family and mediates their polyubiquitylation, targeting ALDH3 for proteasomal degradation. This activity is essential for trophoblast stem cell (TSC) differentiation during placental development. FBXL12-deficient mice show ALDH3 accumulation in the placenta, impaired junctional zone formation, and a TSC differentiation defect that is phenocopied by forced ALDH3 expression in wild-type TSCs and rescued by ALDH3 inhibitor gossypol. Co-immunoprecipitation, in vivo ubiquitination assay, FBXL12 knockout mice, overexpression/rescue experiments in TSCs, ALDH3 inhibitor treatment Stem cells (Dayton, Ohio) High 26124079
2016 The SCF(FBXL12) complex targets ALDH3 for degradation in thymocytes. FBXL12 is most abundant in CD4+CD8+ (DP) thymocytes and declines upon differentiation to SP cells. FBXL12-null mice show a differentiation block at the DP-to-SP transition associated with ALDH3 accumulation. This block is cell-autonomous, demonstrated by bone marrow transplants from FBXL12-null donors into wild-type recipients and by fetal thymic organ culture. FBXL12 knockout mice, bone marrow transplantation, fetal thymic organ culture, flow cytometry for T-cell subsets, protein level analysis Genes to cells : devoted to molecular & cellular mechanisms High 26999371
2019 Fbxl12 is an SCF subunit whose expression is induced by pre-TCR signaling at the β-selection stage of T cell development. The SCF(Fbxl12) complex targets Cdkn1b (p27) for polyubiquitination and proteasomal degradation, promoting cell cycle progression and proliferation of β-selected thymocytes. Fbxl12 and Fbxl1 (induced by Notch) function additively to degrade Cdkn1b. Genetic epistasis in mouse T cell development, conditional knockouts, polyubiquitination assays, cell cycle analysis, transcriptional induction assays Nature immunology High 31451788
2023 CHK1-mediated phosphorylation of FANCD2 creates a phosphodegron that is recognized by FBXL12, triggering FANCD2 proteasomal degradation at stalled replication forks. This clears FANCD2 from chromatin and promotes replication fork restart under conditions of CYCLIN E- and drug-induced replication stress. Phosphodegron-mutant FANCD2 cannot rescue fork progression in FANCD2-deficient fibroblasts. In the absence of FBXL12, FANCD2 accumulates on chromatin, causing replication stress and excessive DNA damage. FBXL12 depletion sensitizes cancer cells to WEE1 inhibition. In vitro reconstitution with phosphodegron mutants, FBXL12 depletion, chromatin fractionation, DNA fiber assay, FANCD2-deficient cell complementation, drug sensitivity assays Molecular cell High 37591242
2024 A neddylation/FBXL12-dependent process actively removes loaded Ku molecules from DNA ends throughout the cell cycle, restricting Ku accumulation to ~1–2 molecules per DNA end in cells. This mechanism operates in concert with DNA-PKcs (structural, not kinase activity) and a CtIP/ATM-dependent S-phase mechanism. Misregulation of Ku loading by disrupting FBXL12 leads to impaired transcription near DNA ends. FBXL12 depletion, neddylation inhibition, live-cell imaging, ChIP, transcription assays near DSBs Cell reports Medium 39058590
2022 Depletion of FBXL12 in G0 (quiescent) cells promotes extensive DNA end resection at DSBs, consistent with FBXL12's role in removing KU70/KU80 from DSBs to regulate the balance between NHEJ and resection-dependent repair pathways. This effect was specifically observed in G0 cells and not in proliferating G1 or G2 cells. CRISPR/Cas9 whole-genome screen, FBXL12 depletion, DNA end resection assays in G0 vs cycling cells eLife Medium 35575473
2015 An intronic region of Fbxl12 acts as an alternative promoter, producing a short isoform of Fbl12 that lacks the F-box domain (Fbl12ΔF). UV irradiation increases Fbl12ΔF mRNA in cells. Fbl12ΔF can bind full-length Fbl12 and promote its relocalization from nucleus to cytoplasm, potentially modulating SCF(Fbl12) activity. Reporter assays for alternative promoter activity, RT-PCR, UV irradiation, co-immunoprecipitation, subcellular fractionation/localization Biochemistry and biophysics reports Medium 29124172
2025 FBXL12 catalyzes K63-linked ubiquitylation of Myosin heavy chain 14 (MYH14) in activated microglia, promoting cytoskeletal reorganization and migration. In the context of spinal cord injury, m6A modification of Fbxl12 mRNA specifically promotes FBXL12 synthesis in activated microglia, and FBXL12 overexpression maintains a scar-less healing microglial phenotype, reducing extracellular matrix deposition. Multiomics, m6A modification analysis, overexpression in microglia, K63-ubiquitylation assay, migration/cytoskeletal assays, in vivo spinal cord injury model Signal transduction and targeted therapy Medium 40830106
2025 FBXL12 mediates ubiquitination of ALDH1A1, and this process is regulated by the sorcin-PAX5 signaling axis. Sorcin sequesters PAX5 in the cytoplasm, reducing FBXL12 expression and ALDH1A1 ubiquitination. Disruption of the sorcin-PAX5 interaction (e.g., by celastrol binding to Cys194 of sorcin) promotes PAX5 nuclear translocation, induces FBXL12 expression, increases ALDH1A1 ubiquitylation, and triggers ferroptosis in pancreatic cancer cells. Co-IP, ChIP, luciferase assays, proteomics, FBXL12 expression manipulation, ubiquitination assays, PAX5 translocation imaging Journal of hematology & oncology Medium 40055736
2025 CRY1 K151Q/R mutants show enhanced binding to FBXL12 (but not FBXL3) while exhibiting more stability than wild-type CRY1, without increased ubiquitination-linked degradation. This suggests FBXL12 interacts with CRY1 at K151 through a ubiquitination-independent mechanism that influences circadian period by modulating core clock protein interactions. Site-directed mutagenesis, luciferase complementation assay (protein-protein interaction), circadian rescue assay in Cry1/2-deficient cells International journal of molecular sciences Low 40869282

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2019 Leucine Rich Repeat Proteins: Sequences, Mutations, Structures and Diseases. Protein and peptide letters 57 30526451
2013 An SCF complex containing Fbxl12 mediates DNA damage-induced Ku80 ubiquitylation. Cell cycle (Georgetown, Tex.) 55 23324393
2008 A new ubiquitin ligase involved in p57KIP2 proteolysis regulates osteoblast cell differentiation. EMBO reports 39 18660753
2020 Expression of CAMK1 and its association with clinicopathologic characteristics in pancreatic cancer. Journal of cellular and molecular medicine 36 33342045
2019 Notch and the pre-TCR coordinate thymocyte proliferation by induction of the SCF subunits Fbxl1 and Fbxl12. Nature immunology 30 31451788
2022 DNA-PK promotes DNA end resection at DNA double strand breaks in G0 cells. eLife 21 35575473
2013 Fbxl12 triggers G1 arrest by mediating degradation of calmodulin kinase I. Cellular signalling 19 23707388
2015 FBXL12-Mediated Degradation of ALDH3 is Essential for Trophoblast Differentiation During Placental Development. Stem cells (Dayton, Ohio) 16 26124079
2025 Disruption of the sorcin‒PAX5 protein‒protein interaction induces ferroptosis by promoting the FBXL12-mediated ubiquitination of ALDH1A1 in pancreatic cancer. Journal of hematology & oncology 14 40055736
2023 FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress. Molecular cell 13 37591242
2024 Identification of the main barriers to Ku accumulation in chromatin. Cell reports 11 39058590
2012 Identification of differentially expressed genes induced by energy restriction using annealing control primer system from the liver and adipose tissues of broilers. Poultry science 9 22399737
2016 FBXL12 regulates T-cell differentiation in a cell-autonomous manner. Genes to cells : devoted to molecular & cellular mechanisms 7 26999371
2025 RNA-seq reveals transcriptomic differences in circadian-related genes of the choroid plexus in a preclinical chronic migraine model. bioRxiv : the preprint server for biology 5 40501738
2025 F-box/LRR-repeat protein 12 reorchestrated microglia to inhibit scarring and achieve adult spinal cord injury repair. Signal transduction and targeted therapy 2 40830106
2024 Identification of the main barriers to Ku accumulation in chromatin. bioRxiv : the preprint server for biology 2 38260538
2025 Multiplex design and discovery of proximity handles for programmable proteome editing. bioRxiv : the preprint server for biology 1 41279570
2015 The intronic region of Fbxl12 functions as an alternative promoter regulated by UV irradiation. Biochemistry and biophysics reports 1 29124172
2025 Analysis of Potential Genes, Oxidative, Metabolic, and Hormonal Markers Associated with Postpartum Disorder Susceptibility in Barki Sheep (Ovis aries). Veterinary sciences 0 40266925
2025 CRY1 Lysine 151 Regulates Circadian Rhythms Through Ubiquitination-Independent Protein Interactions. International journal of molecular sciences 0 40869282
2023 Fork restart: unloading FANCD2 to travel ahead. Molecular cell 0 37863027

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