FBXO9

FBXO9 is the substrate-recognition subunit of an SCF (SKP1–CUL1–RBX1) E3 ubiquitin ligase that targets a diverse set of substrates for proteasomal degradation, thereby governing cell fate, proteostasis, and oncogenic signaling. Through its F-box motif, FBXO9 ubiquitinates Neurog2 downstream of Sox10 to direct neural crest progenitors toward gliogenesis (PMID:32029586), ubiquitinates ATP6V1A to impair V-ATPase assembly and suppress pro-metastatic Wnt signaling (PMID:38486234), and targets the tumor suppressor FBXW7 for degradation in hepatocellular carcinoma (PMID:35847937). FBXO9 also recognizes a GSK-3β-phosphorylated degron on YAP, catalyzing K48-linked polyubiquitination at K76 to promote YAP turnover in an Akt-modulated manner (PMID:40902979), and degrades PD-L1 to enhance antitumor immunity (PMID:41646985), DPPA5 to restrain pluripotency (PMID:38227647), and p53 to regulate ferroptosis susceptibility in osteoclasts (PMID:35003915).

1. 2016 Low

   Initial evidence that the FBXO9 ortholog CG5961 is required for neuronal tissue integrity in Drosophila established that the gene has a conserved role in nervous system development, motivating functional studies of the mammalian protein.

   Evidence UAS-GAL4 directed expression and RNAi in Drosophila eye and dopaminergic neurons

   PMID:27173356

   Open questions at the time

   • Drosophila system only, no mammalian validation
   • no substrate identified
   • lifespan phenotype lacks mechanistic explanation
2. 2019 Medium

   Demonstration that FBXO9 functions as an SCF E3 ligase subunit whose loss increases proteasome activity in AML established its role in proteostasis regulation in hematopoietic malignancy.

   Evidence Conditional CRISPR/Cas9 knockout mouse model with quantitative mass spectrometry and in vitro proteasome activity assay

   PMID:31684170

   Open questions at the time

   • specific proteasomal substrates targeted by FBXO9 in AML not identified
   • mechanism linking FBXO9 loss to increased proteasome activity unknown
3. 2020 High

   Identification of Neurog2 as a direct FBXO9 substrate linked FBXO9-mediated ubiquitination to a developmental cell-fate switch, showing that Sox10 induces FBXO9 to degrade Neurog2 and promote gliogenesis over neurogenesis in neural crest progenitors.

   Evidence Gain/loss-of-function in avian neural crest progenitors, co-immunoprecipitation, ubiquitination assay, epistasis analysis

   PMID:32029586

   Open questions at the time

   • degron on Neurog2 not mapped
   • whether phosphorylation primes Neurog2 for FBXO9 recognition not tested
4. 2021 Medium

   Discovery that FBXO9 ubiquitinates p53 and promotes its degradation expanded the substrate repertoire to a major tumor suppressor, linking FBXO9 to ferroptosis regulation in osteoclasts.

   Evidence Co-immunoprecipitation, knockdown/overexpression with functional readouts of ferroptosis markers

   PMID:35003915

   Open questions at the time

   • single lab study without in vitro reconstitution
   • ubiquitination site on p53 not mapped
   • relationship to MDM2-mediated p53 degradation not addressed
5. 2022 Medium

   Identification of FBXW7 as an FBXO9 substrate revealed an unusual E3-degrades-E3 regulatory circuit in hepatocellular carcinoma, with ZNF143 transcriptionally driving FBXO9 expression.

   Evidence Reciprocal co-immunoprecipitation, ubiquitination assay, gain/loss-of-function in vitro and in vivo, transcription factor binding assay

   PMID:35847937

   Open questions at the time

   • degron on FBXW7 not mapped
   • functional consequences on FBXW7 substrate pool not fully characterized
6. 2024 High

   Two studies expanded FBXO9 substrate repertoire to ATP6V1A and DPPA5: ubiquitination of ATP6V1A sequesters it with HSPA8 in the cytoplasm to impair V-ATPase assembly and Wnt signaling, while degradation of DPPA5 restricts pluripotency induction.

   Evidence Mass spectrometry, CRISPR-KO, in vivo mouse tumor model, ubiquitination assay (ATP6V1A); RNAi screen with reprogramming functional readouts (DPPA5)

   PMID:38227647 PMID:38486234

   Open questions at the time

   • ubiquitination sites on ATP6V1A not mapped
   • DPPA5 interaction domain on FBXO9 not defined
   • whether HSPA8 sequestration is a general feature of FBXO9 substrate handling is unknown
7. 2025 High

   Mechanistic dissection of YAP as an FBXO9 substrate revealed the first phosphodegron-dependent recognition mode for FBXO9: GSK-3β phosphorylates YAP at Ser338/Thr342 to create a degron recognized by FBXO9, which then catalyzes K48-linked polyubiquitination at K76.

   Evidence In vitro ubiquitination assay, site-directed mutagenesis of K76 and phosphorylation sites, pharmacological Akt inhibition, co-immunoprecipitation

   PMID:40902979

   Open questions at the time

   • structural basis of FBXO9-phosphodegron interaction not determined
   • whether other FBXO9 substrates use analogous phosphodegrons is untested
8. 2026 Medium

   Demonstration that FBXO9 ubiquitinates PD-L1 to block its maturation and promote antitumor T cell responses extended FBXO9 function to immune checkpoint regulation.

   Evidence Co-immunoprecipitation, ubiquitination assay, in vivo pancreatic tumor model with cytotoxic T cell functional readouts

   PMID:41646985

   Open questions at the time

   • PD-L1 ubiquitination sites not mapped
   • whether FBXO9-mediated PD-L1 degradation is phosphorylation-dependent is unknown
   • single cancer type tested

• A unifying structural and biochemical framework for how FBXO9 discriminates among its many substrates — including whether phosphodegron recognition (established for YAP) is a general mechanism — remains to be defined.
• no crystal or cryo-EM structure of FBXO9 or an FBXO9–substrate complex
• substrate degron motifs mapped only for YAP
• in vivo physiological relevance established mainly for Neurog2 and ATP6V1A; other substrates lack genetic models