FBXL6

FBXL6 is an F-box/leucine-rich-repeat protein that functions as the substrate-recognition subunit of an SCF (Skp1–Cul1–F-box) E3 ubiquitin ligase, coupling K63-linked polyubiquitination to the stabilization and activation of oncogenic substrates and K48-linked polyubiquitination to the degradation of tumor suppressors. FBXL6 stabilizes HSP90AA1 via K63-linked ubiquitination, thereby preventing c-MYC degradation and establishing a c-MYC–FBXL6 transcriptional feed-forward loop, and similarly activates KRAS (at K128) and TKT (downstream of VRK2-mediated phosphorylation) through K63-linked ubiquitination to promote MEK/ERK/mTOR and ROS-mTOR signaling, respectively (PMID:32576198, PMID:38124228, PMID:37653031). Conversely, FBXL6 targets phospho-p53 (Ser315) and the CDK inhibitor CDKN1C/p57 for K48-linked polyubiquitination and proteasomal degradation, suppressing tumor-suppressive checkpoints and driving cell cycle progression (PMID:33568778, PMID:41443404). Independent of its oncogenic substrates, FBXL6 participates in cytosolic ribosome-associated quality control by ubiquitinating mistranslated mitochondrial ribosomal proteins; its loss causes MRP aggregation, altered mitochondrial metabolism, and impaired cell-cycle progression under oxidative stress (PMID:37267103).

1. 2020 High

   The first mechanistic characterization established that FBXL6 functions as an SCF E3 ligase subunit that K63-ubiquitinates HSP90AA1, stabilizing it to sustain c-MYC signaling, with c-MYC reciprocally transactivating FBXL6—revealing a feed-forward oncogenic loop.

   Evidence IP/MS substrate identification, Co-IP, in vivo ubiquitination assay, ChIP, luciferase reporter, shRNA KD, and xenograft models in gastric cancer cells

   PMID:32576198

   Open questions at the time

   • Whether the FBXL6–HSP90AA1–c-MYC loop operates in tissues beyond gastric cancer
   • Structural basis for FBXL6 recognition of HSP90AA1
   • Whether other SCF adaptors can substitute for FBXL6 in HSP90AA1 stabilization
2. 2021 High

   Discovery that FBXL6 can also deploy K48-linked ubiquitination—targeting phospho-p53 (Ser315) for proteasomal degradation—demonstrated that FBXL6 is not limited to K63 stabilization but can switch ubiquitin linkage type to degrade tumor suppressors, with p53 reciprocally repressing FBXL6 transcription.

   Evidence Co-IP, in vivo ubiquitination assay, MG132 rescue, ChIP on FBXL6 promoter, cell-cycle and apoptosis flow cytometry in hepatocellular carcinoma cells

   PMID:33568778

   Open questions at the time

   • Whether FBXL6 recognizes only Ser315-phosphorylated p53 or additional phospho-forms
   • How FBXL6 determines K48 versus K63 linkage on different substrates
   • Kinase(s) responsible for the Ser315 phosphorylation event that enables FBXL6 recruitment
3. 2022 Medium

   Functional epistasis experiments in keloid fibroblasts confirmed that the pro-proliferative activity of FBXL6 is c-MYC-dependent in a non-cancer context, generalizing the FBXL6–c-MYC axis beyond carcinomas.

   Evidence shRNA KD with c-MYC overexpression rescue, CCK-8 viability, Western blot in keloid fibroblasts

   PMID:35606330

   Open questions at the time

   • No direct ubiquitination or Co-IP data in this system—mechanism inferred from prior work
   • Whether fibroblast-specific cofactors modulate FBXL6 substrate selection
4. 2023 High

   Three independent studies broadened FBXL6's substrate repertoire to KRAS, TKT, and mitochondrial ribosomal proteins, revealing that FBXL6 activates RAS–RAF–MEK/ERK signaling through K63 ubiquitination of KRAS-K128, links VRK2-mediated TKT phosphorylation to metabolic reprogramming and immune evasion, and participates in cytosolic ribosome-associated quality control of mistranslated MRPs.

   Evidence Co-IP, site-directed mutagenesis (K128), RAS-GTP pulldown, transgenic mouse models for KRAS; Co-IP, phospho-mapping, Alb-Cre mouse models for TKT; FBXL6 KO, chaperone/RQC-factor interaction mapping, MRP aggregation and metabolic assays for quality control

   PMID:37267103 PMID:37653031 PMID:38124228

   Open questions at the time

   • Whether FBXL6-mediated K63 ubiquitination of KRAS and TKT uses the same E2 conjugating enzyme
   • Structural basis for how phospho-Thr287 on TKT promotes FBXL6 recruitment
   • Identity of the specific RQC factors required for FBXL6-dependent MRP ubiquitination
   • Whether the MRP quality-control function operates independently of the SCF complex
5. 2025 Medium

   The substrate catalog was further extended to ATAD3A (K63 stabilization driving aerobic glycolysis in TNBC) and CDKN1C/p57 (degradative ubiquitination promoting lung adenocarcinoma), consolidating FBXL6 as a dual-linkage E3 ligase targeting both oncogenic effectors and tumor suppressors.

   Evidence Co-IP and ubiquitination assays with xenograft models for ATAD3A; Co-IP, ubiquitination assay, shRNA/overexpression rescue, xenograft and metastasis models for CDKN1C

   PMID:40975350 PMID:41443404

   Open questions at the time

   • Ubiquitin-linkage specificity for CDKN1C not explicitly mapped (K48 inferred from degradation)
   • No structural or mutagenesis data identifying the FBXL6-binding degron on CDKN1C or ATAD3A
   • Whether ATAD3A stabilization and glycolysis induction are direct or partly mediated by downstream effectors

• The determinants of FBXL6 ubiquitin-linkage switching (K63 stabilization vs. K48 degradation), the identity of the E2 conjugating enzymes used for each substrate class, and the physiological role of FBXL6 in normal non-transformed tissues remain unresolved.
• No E2 enzyme identified for either K63 or K48 FBXL6-dependent reactions
• No structural model of FBXL6 LRR domain with any substrate
• Phenotype of whole-organism FBXL6 knockout in mammals not reported
• Regulatory post-translational modifications on FBXL6 itself are uncharacterized