FBXO40 (F-box only protein 40; "muscle disease-related protein") is a 709-residue FBXO-class F-box protein that serves as the substrate-recognition subunit of a cullin-RING SCF (SKP1-CUL1-RBX1-F-box) E3 ubiquitin ligase complex. Like other F-box proteins, it docks onto the SCF scaffold through its C-terminal F-box domain (interacting with SKP1/CUL1) while presenting an N-terminal substrate-binding module; FBXO40 carries a TRAF-type zinc finger and is not itself the catalytic RING subunit (catalysis is provided by RBX1, which recruits the ubiquitin-charged E2). FBXO40 expression is restricted essentially to heart and skeletal muscle, appears postnatally during muscle development, and is upregulated in denervation-induced (but not starvation-induced) muscle atrophy and reduced in Limb-girdle muscular dystrophy muscle. Its best-supported direct substrate is insulin receptor substrate 1 (IRS1): the SCF(FBXO40) complex (with co-precipitating SKP1, CUL1 and RBX1) ubiquitinates recombinant IRS1 in vitro in a manner enhanced by IGF1R-dependent IRS1 tyrosine phosphorylation, targeting IRS1 for proteasomal degradation and thereby attenuating the IGF-1/insulin -> IRS1 -> PI3K/AKT anabolic signaling axis in skeletal muscle. Loss of Fbxo40 increases IRS1 protein abundance (without changing Irs1 mRNA), prolongs IRS1 half-life, and produces myotube and whole-muscle hypertrophy in mice (and increased muscle mass in knockout pigs), a phenotype that is IRS1-dependent. FBXO40 transcription is induced by inflammatory STAT3 signaling (e.g. downstream of IL-6), linking it to catabolic insulin-resistance states. The protein localizes to the cytoplasm/cytosol.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (PAN-GO/IBA) assignment of cytoplasmic localization, consistent with FBXO40 acting as the substrate-recognition subunit of a cytoplasmic SCF complex.
Reason: Cytoplasmic localization is corroborated by direct overexpression in C2C12 myoblasts and by the UniProt subcellular location; it is the compartment in which an SCF substrate receptor would act.
Supporting Evidence:
PMID:17928169
By overexpressing in C2C12 cells, FBXO40 localized in cytoplasm.
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Combined automated electronic assignment of cytoplasmic localization, redundant with the IBA and ISS cytoplasm annotations.
Reason: Correct compartment; redundant with experimentally corroborated cytoplasmic localization.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0008270
zinc ion binding
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: InterPro-based electronic assignment of zinc ion binding from the TRAF-type zinc finger (IPR001293) present in FBXO40. A structural feature supporting substrate/protein interaction rather than a core function.
Reason: FBXO40 contains a TRAF-type zinc finger (residues 53-112) that plausibly coordinates zinc, but this is a structural domain attribute subsidiary to its role as an SCF substrate adaptor, not a standalone core molecular function.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
ZN_FING 53..112
|
|
GO:0061630
ubiquitin protein ligase activity
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: InterPro-based electronic assignment of ubiquitin protein ligase activity. F-box proteins are substrate-recognition adaptors, not the catalytic core of the SCF ligase; the catalytic RING activity resides in RBX1.
Reason: As an F-box substrate receptor, FBXO40 does not itself catalyze ubiquitin transfer (that is the RBX1 RING subunit); its molecular function is better captured as a ubiquitin-like ligase-substrate adaptor. This IEA term is propagated from the InterPro Fbxo30/Fbxo40 signature and over-attributes catalytic ligase activity to the adaptor.
Proposed replacements:
ubiquitin-like ligase-substrate adaptor activity
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
Probable substrate-recognition component of the SCF (SKP1-
|
|
GO:0042692
muscle cell differentiation
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Ensembl-Compara ortholog-based electronic transfer of muscle cell differentiation, mirroring the ISS annotation derived from the mouse ortholog and the muscle-restricted expression of FBXO40.
Reason: Consistent with FBXO40's muscle-restricted, postnatal-myogenesis-associated expression, but the involvement rests on expression correlation and family/ortholog propagation rather than direct experimental demonstration in human; keep as a non-core process.
Supporting Evidence:
PMID:17928169
All our data suggest that FBXO40 may function as a regulator involved in the postnatal myogenesis.
|
|
GO:0019005
SCF ubiquitin ligase complex
|
NAS
PMID:34445249 The SCF Complex Is Essential to Maintain Genome and Chromoso... |
ACCEPT |
Summary: ComplexPortal NAS assignment (CPX-7981, SCF FBXO40 variant) that FBXO40 is part of an SCF E3 ubiquitin ligase complex, consistent with its F-box domain and reported direct interactions with SKP1 and CUL1.
Reason: Core localization/complex membership for an F-box protein; supported by the F-box domain, the UniProt SUBUNIT statement, and the general SCF biology described in the cited review.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBUNIT: Directly interacts with SKP1 and CUL1. {ECO:0000250}.
PMID:34445249
These SCF complexes are distinguishable by variable F-box proteins, which determine substrate specificity.
|
|
GO:0031146
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
|
NAS
PMID:34445249 The SCF Complex Is Essential to Maintain Genome and Chromoso... |
ACCEPT |
Summary: ComplexPortal NAS assignment that FBXO40, as an SCF F-box receptor, participates in SCF-dependent proteasomal protein degradation. This is the expected biological process for an SCF substrate adaptor.
Reason: Consistent with the canonical role of F-box proteins in directing substrates to SCF-dependent proteasomal degradation, and now corroborated by FBXO40-specific evidence that SCF-FBXO40 ubiquitinates IRS1 to drive its proteasomal degradation (Shi et al. 2011, via the Falcon report).
Supporting Evidence:
PMID:34445249
group of 69 SCF E3 ubiquitin ligase complexes that primarily modify protein substrates with poly-ubiquitin chains to target them for proteasomal degradation
file:human/FBXO40/FBXO40-uniprot.txt
Ubl conjugation pathway
file:human/FBXO40/FBXO40-deep-research-falcon.md
FBXO40 acts as the **substrate-recognition subunit** of an SCF E3 ligase complex (**SCF-FBXO40**) that **ubiquitinates IRS1**, promoting its **ubiquitin–proteasome-dependent degradation** in skeletal muscle, thereby **limiting IGF-1/insulin signaling** through the IRS1–PI3K–AKT axis
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-8952618 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization derived from generic CRL1/neddylation pathway reactions in which the SCF complex participates. Consistent with cytoplasmic localization but pathway-context, not FBXO40-specific evidence.
Reason: Cytosol is a correct, more specific child of the cytoplasm localization, but this and the other identical Reactome cytosol annotations are propagated from generic cullin-RING-ligase pathway reactions rather than direct FBXO40 evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-8952620 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic CRL1/NEDD8 pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-8955241 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic CAND1/CRL pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-8955289 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic COMMD/CAND1/CRL pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-8956040 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic COP9-signalosome deneddylation pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-8956200 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic DCUN1D3/CRL1 pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-983140 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic ubiquitin-transfer pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-983147 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic ubiquitin-transfer pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-983156 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic polyubiquitination pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-983157 |
KEEP AS NON CORE |
Summary: Reactome TAS cytosol localization from a generic E3-substrate-E2 interaction pathway reaction. Redundant with the other Reactome cytosol annotations.
Reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
Supporting Evidence:
file:human/FBXO40/FBXO40-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
|
|
GO:0005737
cytoplasm
|
ISS
GO_REF:0000024 |
ACCEPT |
Summary: ISS transfer of cytoplasmic localization from the mouse ortholog (SKP1, UniProtKB:P62932 used as WITH). Consistent with the experimentally observed cytoplasmic localization of FBXO40.
Reason: Correct core compartment; corroborated by direct overexpression in C2C12 myoblasts and the UniProt subcellular location.
Supporting Evidence:
PMID:17928169
By overexpressing in C2C12 cells, FBXO40 localized in cytoplasm.
|
|
GO:0042692
muscle cell differentiation
|
ISS
PMID:17928169 FBXO40, a gene encoding a novel muscle-specific F-box protei... |
KEEP AS NON CORE |
Summary: ISS assignment of involvement in muscle cell differentiation, based on FBXO40's muscle-restricted, postnatal expression and its proposed role in postnatal myogenesis.
Reason: The cited study establishes muscle-specific expression and a postnatal-myogenesis association by expression/correlation, but does not directly demonstrate that FBXO40 drives muscle cell differentiation. The mechanistically best-defined muscle role of FBXO40 (Shi et al. 2011) is negative control of muscle growth/hypertrophy via SCF-dependent IRS1 degradation and attenuation of IGF-1/insulin-AKT signaling, rather than differentiation per se; retain this term as a plausible non-core process.
Supporting Evidence:
PMID:17928169
All our data suggest that FBXO40 may function as a regulator involved in the postnatal myogenesis.
file:human/FBXO40/FBXO40-deep-research-falcon.md
Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy in animal models, including mice and pigs
|
|
GO:0046627
negative regulation of insulin receptor signaling pathway
|
ISO
PMID:22033112 The SCF-FBXO40 complex induces IRS1 ubiquitination in skelet... |
NEW |
Summary: Proposed FBXO40-specific process inferred by orthology from mouse Fbxo40 (Shi et al. 2011, PMID:22033112; surfaced via the Falcon report) that SCF-FBXO40 ubiquitinates IRS1 to drive its proteasomal degradation, attenuating IGF-1/insulin -> IRS1 -> PI3K/AKT signaling in skeletal muscle.
Reason: Not currently in GOA, but a well-supported FBXO40-specific biological process. SCF-FBXO40 degrades IRS1 (enhanced by IGF1R-dependent IRS1 tyrosine phosphorylation), and Fbxo40 loss stabilizes IRS1 and causes IRS1-dependent muscle hypertrophy, defining FBXO40 as a negative regulator of insulin/IGF-1 receptor signaling. Evidence is recorded as ISO (inferred from the mouse ortholog; Shi et al. 2011, Dev Cell, PMID:22033112, identified via the Falcon report). The PMID is confirmed to exist but its full text was not read here, so the falcon report is cited as the supporting lead rather than an asserted experimental human quote.
Supporting Evidence:
file:human/FBXO40/FBXO40-deep-research-falcon.md
FBXO40 acts as the **substrate-recognition subunit** of an SCF E3 ligase complex (**SCF-FBXO40**) that **ubiquitinates IRS1**, promoting its **ubiquitin–proteasome-dependent degradation** in skeletal muscle, thereby **limiting IGF-1/insulin signaling** through the IRS1–PI3K–AKT axis
|
Q: What is the direct, experimentally validated substrate repertoire of FBXO40 in human skeletal muscle, and is IRS1 ubiquitination by the SCF-FBXO40 complex direct (e.g. reconstituted with purified components) rather than inferred from co-depletion phenotypes?
Q: Does FBXO40 substrate recruitment depend on the TRAF-type zinc finger, and does substrate engagement require phosphodegron recognition downstream of IGF1R/insulin-Akt signaling?
Q: Are the muscle cell differentiation and denervation-atrophy phenotypes a consequence of FBXO40-dependent substrate turnover, or do they reflect expression-correlated but indirect roles?
Q: How is FBXO40 transcription controlled by inflammatory STAT3/IL-6 signaling in skeletal muscle, and does pharmacologic STAT3 inhibition preserve IRS1/p-AKT and improve insulin sensitivity primarily through FBXO40 downregulation?
Experiment: Reconstitute the SCF-FBXO40 complex (SKP1, CUL1, RBX1, FBXO40) with a ubiquitin-charged E2 in vitro and assay ubiquitination of candidate substrates (e.g. IRS1) to establish direct adaptor function and chain topology.
Experiment: Perform affinity purification-mass spectrometry of tagged FBXO40 from skeletal myotubes (with and without proteasome/neddylation inhibition) to define the endogenous substrate and complex interactome and confirm SKP1/CUL1/RBX1 association.
Experiment: Generate FBXO40-knockout myoblasts/mice and quantify candidate-substrate levels and ubiquitination, myogenic differentiation, and the denervation-atrophy response to test whether phenotypes are substrate-turnover dependent.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
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We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
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FBXO40 (UniProt Q9UH90) is the human gene encoding F-box only protein 40 (also historically referenced as KIAA1195 / FBX40). The core functional literature on “Fbxo40/FBXO40” in mammals describes a muscle-enriched F-box protein that functions as the substrate-recognition module of an SCF (SKP1–CUL1–RBX1) Cullin-RING E3 ubiquitin ligase and targets IRS1 for ubiquitin-mediated proteasomal degradation (shi2011thescffbxo40complex pages 4-5, shi2011thescffbxo40complex pages 1-2, zhang2020stat3activationinduces pages 1-4). This aligns with the UniProt-provided identity and domain expectation for an F-box protein (adapter in an SCF complex), and the biology is consistent across primary and review sources (shi2011thescffbxo40complex pages 9-10, blondelle2020theroleof pages 11-13, zhang2020stat3activationinduces pages 1-4).
F-box proteins are typically substrate-recognition adaptors in SCF E3 ubiquitin ligase complexes, which minimally comprise SKP1, CUL1, RBX1 plus an F-box substrate adaptor. The SCF complex promotes substrate ubiquitination, often leading to proteasomal degradation.
For FBXO40 specifically, co-immunoprecipitation experiments show that IRS1 and each SCF component (Skp1, Cullin1, Rbx1) can be co-precipitated with Fbxo40, consistent with SCF assembly and adaptor function (shi2011thescffbxo40complex pages 4-5). Cropped figure panels in Shi et al. visually document this SCF-FBXO40 complex formation and associated assays (shi2011thescffbxo40complex media 7fb258a5, shi2011thescffbxo40complex media a3adc8ae, shi2011thescffbxo40complex media 6e110724, shi2011thescffbxo40complex media 54b10505).
Primary function: FBXO40 acts as the substrate-recognition subunit of an SCF E3 ligase complex (SCF-FBXO40) that ubiquitinates IRS1, promoting its ubiquitin–proteasome-dependent degradation in skeletal muscle, thereby limiting IGF-1/insulin signaling through the IRS1–PI3K–AKT axis (shi2011thescffbxo40complex pages 9-10, shi2011thescffbxo40complex pages 4-5, shi2011thescffbxo40complex pages 1-2).
This makes FBXO40 a regulatory node controlling growth-factor signal transduction, not an enzyme that catalyzes a small-molecule reaction.
Shi et al. report that tyrosine phosphorylation of IRS1 (in the context of IGF1R activation) markedly enhances IRS1 polyubiquitination by SCF-Fbxo40 in vitro, supporting phosphorylation-dependent substrate recognition/processing (shi2011thescffbxo40complex pages 4-5).
Shi et al. (Developmental Cell; Nov 2011; DOI: https://doi.org/10.1016/j.devcel.2011.09.011) provide direct evidence that immunoprecipitated SCF-Fbxo40 ubiquitinates recombinant IRS1 in vitro (shi2011thescffbxo40complex pages 6-8, shi2011thescffbxo40complex pages 4-5). The same work shows SCF complex membership (Skp1/Cul1/Rbx1 association) and IGF1R dependence for IRS1 turnover (shi2011thescffbxo40complex pages 4-5).
Quantitative datapoints (from reported excerpts):
- In differentiated myotubes, Fbxo40 knockdown prolonged IRS1 half-life to >6 hours (shi2011thescffbxo40complex pages 4-5).
- In vivo, Fbxo40 knockout muscle shows increased IRS1 protein by densitometry (IRS1/eIF4E WT 1 ± 0.28 vs KO 2.97 ± 0.56) (shi2011thescffbxo40complex pages 9-10).
FBXO40 expression is described as almost exclusively in heart and skeletal muscle (at the mRNA level) and increases during myogenic differentiation, supporting a striated-muscle-enriched role (shi2011thescffbxo40complex pages 4-5). A cullin-RING ligase review similarly emphasizes muscle enrichment and links FBXO40 to denervation contexts (blondelle2020theroleof pages 11-13).
By driving IRS1 turnover, FBXO40 dampens IGF-1 signaling output. Shi et al. show that Fbxo40 depletion preserves downstream AKT phosphorylation under IGF-1 stimulation and that hypertrophy from Fbxo40 knockdown is IRS1-dependent (shi2011thescffbxo40complex pages 8-9).
In mice, Fbxo40 knockout leads to increased growth and muscle mass:
- Body weight differences in growth phase were highly significant (p < 0.0001 KO vs WT for both sexes) with sample sizes n=26 KO females vs 22 WT females; n=19 KO males vs 15 WT males (shi2011thescffbxo40complex pages 9-10).
- At ~6 weeks, muscle wet weights (e.g., TA, EDL, PLA) were increased (p < 0.05) with n=33 KO vs n=20 WT (shi2011thescffbxo40complex pages 6-8, shi2011thescffbxo40complex pages 9-10).
These phenotypes are consistent with FBXO40 acting as a negative regulator of anabolic IGF-1/IRS1 signaling (shi2011thescffbxo40complex pages 9-10, shi2011thescffbxo40complex pages 8-9).
Zhang et al. (AJP Endocrinology and Metabolism; May 2020; DOI: https://doi.org/10.1152/ajpendo.00480.2019) connect FBXO40 to inflammation-driven insulin resistance: STAT3 activation (e.g., via IL-6) increases Fbxo40 expression, reducing IRS1 and p-AKT; Fbxo40 knockdown preserves IRS1/p-AKT despite IL-6 (zhang2020stat3activationinduces pages 1-4).
They further report that pharmacologic STAT3 inhibition (TTI-101) improved glucose tolerance and muscle insulin signaling in mouse models (CKD or high-fat diet), and muscle-specific Stat3 knockout improved glucose tolerance on high-fat diet (zhang2020stat3activationinduces pages 1-4). These data support an upstream inflammatory transcriptional control layer over FBXO40 in skeletal muscle.
High-confidence subcellular localization data for endogenous human FBXO40 is limited in the gathered primary excerpts. A focused review notes that forced expression in muscle cells yields a diffuse cytoplasmic localization (blondelle2020theroleof pages 11-13). Given IRS1 and much of proximal IGF-1/insulin signaling occurs in the cytoplasm and at the membrane-proximal signaling complex, this is consistent with function, but additional high-resolution localization studies would strengthen the annotation.
Direct “new” mechanistic discoveries about FBXO40’s biochemical role remain dominated by the 2011–2020 literature in the retrieved corpus; however, 2023–2024 work extends translational and systems-level contexts.
Yuan et al. (Journal of Cachexia, Sarcopenia and Muscle; Nov 2023; DOI: https://doi.org/10.1002/jcsm.13116) report in animal cachexia models that S-oxprenolol improved anabolic/catabolic signaling and significantly reduced FBXO-40 expression compared with placebo and R-oxprenolol, interpreting this as consistent with improved IRS1/anabolic signaling (yuan2023theatypicalβ‐blocker pages 4-6). The paper provides quantitative organ weight outcomes (e.g., in an LLC mouse model: gastrocnemius 75±2 mg placebo vs 87±2 mg with 10 mg S-oxprenolol; tibialis 25±1 vs 27±1 mg) (yuan2023theatypicalβ‐blocker pages 4-6).
While this does not prove FBXO40 is the sole driver of benefit, it strengthens the real-world relevance of the IRS1-targeting E3-ligase axis in muscle wasting pharmacology.
A TCGA-based prognostic model study in endometrial cancer (World Journal of Surgical Oncology; Jan 2023; DOI: https://doi.org/10.1186/s12957-022-02875-w) reports that FBXO40 expression (among ubiquitination-related genes) was associated with pathological grade (wang2023genesignatureand pages 4-7). This is an association study rather than mechanistic validation.
A cullin-RING ligase review summarizes that CRISPR/Cas9 Fbxo40 knockout pigs show ~4% increased muscle mass with elevated IRS1 and stimulated IGF1–AKT signaling (blondelle2020theroleof pages 11-13). Together with mouse knockout data, this supports FBXO40 as a tractable target for modulating muscle growth in preclinical/livestock contexts (shi2011thescffbxo40complex pages 9-10).
The STAT3–FBXO40 axis suggests therapeutic leverage points upstream of FBXO40 transcription (e.g., STAT3 inhibitors in inflammatory catabolic states) to improve insulin/anabolic signaling in muscle (zhang2020stat3activationinduces pages 1-4). This is supported experimentally in mice but is not yet a validated clinical approach specific to FBXO40.
Expert synthesis indicates FBXO40 is induced by denervation (and not necessarily by starvation-induced atrophy) and decreased in limb–girdle muscular dystrophy patients, implying potential context-specific biomarker relevance (blondelle2020theroleof pages 11-13). However, robust clinical biomarker validation metrics (sensitivity/specificity; prospective cohorts) were not present in the retrieved excerpts.
The 2020 review on cullin-RING ligases in striated muscle positions FBXO40 as a muscle-specific SCF substrate adaptor that regulates IGF1–AKT signaling via IRS1 degradation, and highlights denervation induction and disease-associated expression changes as important contexts (blondelle2020theroleof pages 11-13). This aligns with the primary mechanistic findings (shi2011thescffbxo40complex pages 4-5).
Open Targets lists only weak, sparse disease-target associations for FBXO40 (ENSG00000163833), with low scores and limited evidence count (e.g., “central nervous system cancer”, “ovarian dysfunction”, etc.), indicating that direct human genetics/clinical evidence linking FBXO40 to specific diseases remains limited in this resource (OpenTargets Search: -FBXO40). This supports a cautious interpretation: FBXO40 is mechanistically well-defined in muscle signaling, but disease causality/clinical utility remains underdeveloped.
FBXO40 (UniProt Q9UH90) is a muscle-enriched F-box protein that serves as the substrate-recognition adaptor in an SCF (SKP1–CUL1–RBX1) E3 ubiquitin ligase complex. Its best-supported direct substrate is IRS1, which it ubiquitinates (enhanced by IGF1R-dependent IRS1 tyrosine phosphorylation) to promote proteasomal degradation, thereby attenuating IGF-1/insulin → IRS1 → PI3K/AKT signaling and limiting muscle hypertrophy. FBXO40 expression/function is responsive to anabolic IGF-1 stimulation and can be transcriptionally upregulated by inflammatory STAT3 signaling (e.g., IL-6), linking it to catabolic insulin resistance contexts. Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy in animal models, including mice and pigs (shi2011thescffbxo40complex pages 4-5, zhang2020stat3activationinduces pages 1-4, shi2011thescffbxo40complex pages 9-10).
| Topic | Key findings | Evidence type | Year | Citation |
|---|---|---|---|---|
| identity/domains | Human FBXO40 corresponds to UniProt Q9UH90 and is consistently described in the literature as a muscle-enriched F-box protein; this matches its expected role as an SCF substrate-recognition component rather than a catalytic enzyme. | Database + review + primary | 2011–2020 | UniProt Q9UH90 / FBXO40; Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011; Blondelle et al., Role of Cullin-RING Ligases in Striated Muscle — https://doi.org/10.3390/ijms21217936 (shi2011thescffbxo40complex pages 9-10, blondelle2020theroleof pages 11-13) |
| molecular function | FBXO40 functions as a substrate-recognition subunit of a Cullin-RING E3 ubiquitin ligase that promotes ubiquitin-proteasome-dependent degradation of IRS1, thereby limiting IGF1/insulin signaling in skeletal muscle. | Primary | 2011 | Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011 (shi2011thescffbxo40complex pages 9-10, shi2011thescffbxo40complex pages 4-5, shi2011thescffbxo40complex pages 1-2) |
| E3 complex | FBXO40 co-immunoprecipitates with IRS1 and canonical SCF components Skp1, Cullin1, and Rbx1; immunoprecipitated SCF-FBXO40 ubiquitinates recombinant IRS1 in vitro. | Primary | 2011 | Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011 (shi2011thescffbxo40complex pages 6-8, shi2011thescffbxo40complex pages 4-5, shi2011thescffbxo40complex media 7fb258a5) |
| confirmed substrate | IRS1 is the best-supported direct substrate. Its ubiquitination is enhanced by tyrosine phosphorylation and IGF1R activation; FBXO40 knockdown prolongs IRS1 half-life to >6 h and increases muscle IRS1 protein without changing Irs1 mRNA. | Primary | 2011 | Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011 (shi2011thescffbxo40complex pages 4-5, shi2011thescffbxo40complex pages 8-8) |
| regulation | IGF1 signaling promotes FBXO40-dependent IRS1 turnover in differentiated myotubes. In inflammatory/catabolic settings, STAT3 binds the Fbxo40 promoter; IL-6/STAT3 raises Fbxo40 expression and lowers IRS1 and p-Akt, while Fbxo40 knockdown preserves IRS1/p-Akt. | Primary | 2011, 2020 | Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011; Zhang et al., Stat3 activation induces insulin resistance via Fbxo40 — https://doi.org/10.1152/ajpendo.00480.2019 (shi2011thescffbxo40complex pages 4-5, zhang2020stat3activationinduces pages 1-4) |
| tissue/cell type | FBXO40 is expressed almost exclusively in skeletal muscle and heart, increases during myogenic differentiation, and is implicated mainly in differentiated myotubes/myofibers rather than broadly across tissues. | Primary + review | 2011, 2020 | Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011; Blondelle et al., Role of Cullin-RING Ligases in Striated Muscle — https://doi.org/10.3390/ijms21217936 (shi2011thescffbxo40complex pages 4-5, blondelle2020theroleof pages 11-13) |
| subcellular localization | Review evidence describes exogenous/forced FBXO40 as showing diffuse cytoplasmic localization in muscle cells; direct high-resolution localization evidence remains limited in the gathered sources. | Review | 2020 | Blondelle et al., Role of Cullin-RING Ligases in Striated Muscle — https://doi.org/10.3390/ijms21217936 (blondelle2020theroleof pages 11-13) |
| phenotypes | Fbxo40 knockdown causes myotube hypertrophy and this depends on IRS1. Fbxo40 knockout mice show increased IRS1 protein and larger body/muscle size during growth; one summary reports IRS1/eIF4E densitometry ~1.0 in WT vs ~2.97 in KO muscle. Review evidence also notes CRISPR Fbxo40 knockout pigs with ~4% higher muscle mass. | Primary + review | 2011, 2020 | Shi et al., SCF-Fbxo40 complex induces IRS1 ubiquitination — https://doi.org/10.1016/j.devcel.2011.09.011; Blondelle et al., Role of Cullin-RING Ligases in Striated Muscle — https://doi.org/10.3390/ijms21217936 (shi2011thescffbxo40complex pages 9-10, shi2011thescffbxo40complex pages 8-9, blondelle2020theroleof pages 11-13) |
| 2023-2024 developments/applications | Recent literature uses FBXO40 mainly as a mechanistic/therapeutic node in muscle wasting and insulin-resistance contexts rather than as a validated clinical target. Open Targets shows only weak, sparse disease associations outside muscle-focused literature, underscoring limited direct human disease validation so far. | Database | 2023–2024 platform context | Open Targets FBXO40 disease-association summary — https://platform.opentargets.org/target/ENSG00000163833 (OpenTargets Search: -FBXO40) |
Table: This table compacts the strongest gathered evidence for human FBXO40/Q9UH90, emphasizing its role as a muscle-enriched SCF E3-ligase substrate receptor for IRS1. It also distinguishes primary mechanistic evidence from review and database-level associations to support functional annotation.
Cropped figure panels from Shi et al. (2011) show the core biochemical and phenotypic evidence: SCF complex co-IP and in vitro IRS1 ubiquitination, IRS1 elevation in KO muscle, and muscle hypertrophy quantification (shi2011thescffbxo40complex media 7fb258a5, shi2011thescffbxo40complex media a3adc8ae, shi2011thescffbxo40complex media 6e110724, shi2011thescffbxo40complex media 54b10505).
References
(shi2011thescffbxo40complex pages 4-5): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(shi2011thescffbxo40complex pages 1-2): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(zhang2020stat3activationinduces pages 1-4): Liping Zhang, Zihong Chen, Ying Wang, David J. Tweardy, and William E. Mitch. Stat3 activation induces insulin resistance via a muscle-specific e3 ubiquitin ligase fbxo40. May 2020. URL: https://doi.org/10.1152/ajpendo.00480.2019, doi:10.1152/ajpendo.00480.2019. This article has 47 citations.
(shi2011thescffbxo40complex pages 9-10): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(blondelle2020theroleof pages 11-13): Jordan Blondelle, Andrea Biju, and Stephan Lange. The role of cullin-ring ligases in striated muscle development, function, and disease. International Journal of Molecular Sciences, 21:7936, Oct 2020. URL: https://doi.org/10.3390/ijms21217936, doi:10.3390/ijms21217936. This article has 27 citations.
(shi2011thescffbxo40complex media 7fb258a5): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(shi2011thescffbxo40complex media a3adc8ae): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(shi2011thescffbxo40complex media 6e110724): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(shi2011thescffbxo40complex media 54b10505): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(shi2011thescffbxo40complex pages 6-8): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(shi2011thescffbxo40complex pages 8-9): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
(yuan2023theatypicalβ‐blocker pages 4-6): Luping Yuan, Jochen Springer, Sandra Palus, Silvia Busquets, Queralt Jové, Edson Alves de Lima Junior, Markus S. Anker, Stephan von Haehling, Natalia Álvarez Ladrón, Oliver Millman, Annemijn Oosterlee, Agata Szymczyk, Francisco Javier López‐Soriano, Stefan D. Anker, Andrew J.S. Coats, and Josep M. Argiles. The atypical β‐blocker s‐oxprenolol reduces cachexia and improves survival in a rat cancer cachexia model. Journal of Cachexia, Sarcopenia and Muscle, 14:653-660, Nov 2023. URL: https://doi.org/10.1002/jcsm.13116, doi:10.1002/jcsm.13116. This article has 17 citations and is from a domain leading peer-reviewed journal.
(dombrecht2023molecularmechanismsof pages 4-5): Dorien Dombrecht, Ulrike Van Daele, Birgit Van Asbroeck, David Schieffelers, Pieter‐Jan Guns, Nick Gebruers, Jill Meirte, and Eric van Breda. Molecular mechanisms of post‐burn muscle wasting and the therapeutic potential of physical exercise. Journal of Cachexia, Sarcopenia and Muscle, 14:758-770, Feb 2023. URL: https://doi.org/10.1002/jcsm.13188, doi:10.1002/jcsm.13188. This article has 31 citations and is from a domain leading peer-reviewed journal.
(xuan2024theemergingand pages 2-5): Zhuang Xuan, Jun Ruan, Canquan Zhou, and Zhi-ming Li. The emerging and diverse roles of f-box proteins in spermatogenesis and male infertility. Cell Regeneration, Jun 2024. URL: https://doi.org/10.1186/s13619-024-00196-9, doi:10.1186/s13619-024-00196-9. This article has 5 citations.
(wang2023genesignatureand pages 4-7): Ziwei Wang, Shuangshuang Cheng, Y. Liu, Rong-wei Zhao, Jun Zhang, Xing Zhou, Wan Shu, Dilu Feng, and Hongbo Wang. Gene signature and prognostic value of ubiquitination-related genes in endometrial cancer. World Journal of Surgical Oncology, Jan 2023. URL: https://doi.org/10.1186/s12957-022-02875-w, doi:10.1186/s12957-022-02875-w. This article has 14 citations and is from a peer-reviewed journal.
(OpenTargets Search: -FBXO40): Open Targets Query (-FBXO40, 5 results). Buniello, A. et al. (2025). Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research.
(shi2011thescffbxo40complex pages 8-8): Jun Shi, Liqing Luo, John Eash, Chikwendu Ibebunjo, and David J. Glass. The scf-fbxo40 complex induces irs1 ubiquitination in skeletal muscle, limiting igf1 signaling. Developmental cell, 21 5:835-47, Nov 2011. URL: https://doi.org/10.1016/j.devcel.2011.09.011, doi:10.1016/j.devcel.2011.09.011. This article has 170 citations and is from a highest quality peer-reviewed journal.
UPS|E3 ubiquitin and UBL ligases|Cul1 substrate receptor|F-box|TRAF-type ZnF ; PN-node mapping: F-box subtype/type = no_mapping; group = mapped, ok_for_propagation_to_go, GO:1990756; class = context_only/too_broad (GO:0061630).This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.
id: Q9UH90
gene_symbol: FBXO40
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
FBXO40 (F-box only protein 40; "muscle disease-related protein") is a 709-residue
FBXO-class F-box protein that serves as the substrate-recognition subunit of a
cullin-RING SCF (SKP1-CUL1-RBX1-F-box) E3 ubiquitin ligase complex. Like other
F-box proteins, it docks onto the SCF scaffold through its C-terminal F-box domain
(interacting with SKP1/CUL1) while presenting an N-terminal substrate-binding
module; FBXO40 carries a TRAF-type zinc finger and is not itself the catalytic
RING subunit (catalysis is provided by RBX1, which recruits the ubiquitin-charged
E2). FBXO40 expression is restricted essentially to heart and skeletal muscle,
appears postnatally during muscle development, and is upregulated in
denervation-induced (but not starvation-induced) muscle atrophy and reduced in
Limb-girdle muscular dystrophy muscle. Its best-supported direct substrate is
insulin receptor substrate 1 (IRS1): the SCF(FBXO40) complex (with co-precipitating
SKP1, CUL1 and RBX1) ubiquitinates recombinant IRS1 in vitro in a manner enhanced by
IGF1R-dependent IRS1 tyrosine phosphorylation, targeting IRS1 for proteasomal
degradation and thereby attenuating the IGF-1/insulin -> IRS1 -> PI3K/AKT anabolic
signaling axis in skeletal muscle. Loss of Fbxo40 increases IRS1 protein abundance
(without changing Irs1 mRNA), prolongs IRS1 half-life, and produces myotube and
whole-muscle hypertrophy in mice (and increased muscle mass in knockout pigs), a
phenotype that is IRS1-dependent. FBXO40 transcription is induced by inflammatory
STAT3 signaling (e.g. downstream of IL-6), linking it to catabolic insulin-resistance
states. The protein localizes to the cytoplasm/cytosol.
existing_annotations:
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetic (PAN-GO/IBA) assignment of cytoplasmic localization, consistent with FBXO40 acting as the substrate-recognition subunit of a cytoplasmic SCF complex.
action: ACCEPT
reason: Cytoplasmic localization is corroborated by direct overexpression in C2C12 myoblasts and by the UniProt subcellular location; it is the compartment in which an SCF substrate receptor would act.
supported_by:
- reference_id: PMID:17928169
supporting_text: "By overexpressing in C2C12 cells, FBXO40 localized in cytoplasm."
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: Combined automated electronic assignment of cytoplasmic localization, redundant with the IBA and ISS cytoplasm annotations.
action: ACCEPT
reason: Correct compartment; redundant with experimentally corroborated cytoplasmic localization.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0008270
label: zinc ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro-based electronic assignment of zinc ion binding from the TRAF-type zinc finger (IPR001293) present in FBXO40. A structural feature supporting substrate/protein interaction rather than a core function.
action: KEEP_AS_NON_CORE
reason: FBXO40 contains a TRAF-type zinc finger (residues 53-112) that plausibly coordinates zinc, but this is a structural domain attribute subsidiary to its role as an SCF substrate adaptor, not a standalone core molecular function.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "ZN_FING 53..112"
- term:
id: GO:0061630
label: ubiquitin protein ligase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro-based electronic assignment of ubiquitin protein ligase activity. F-box proteins are substrate-recognition adaptors, not the catalytic core of the SCF ligase; the catalytic RING activity resides in RBX1.
action: MODIFY
reason: As an F-box substrate receptor, FBXO40 does not itself catalyze ubiquitin transfer (that is the RBX1 RING subunit); its molecular function is better captured as a ubiquitin-like ligase-substrate adaptor. This IEA term is propagated from the InterPro Fbxo30/Fbxo40 signature and over-attributes catalytic ligase activity to the adaptor.
proposed_replacement_terms:
- id: GO:1990756
label: ubiquitin-like ligase-substrate adaptor activity
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "Probable substrate-recognition component of the SCF (SKP1-"
- term:
id: GO:0042692
label: muscle cell differentiation
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: Ensembl-Compara ortholog-based electronic transfer of muscle cell differentiation, mirroring the ISS annotation derived from the mouse ortholog and the muscle-restricted expression of FBXO40.
action: KEEP_AS_NON_CORE
reason: Consistent with FBXO40's muscle-restricted, postnatal-myogenesis-associated expression, but the involvement rests on expression correlation and family/ortholog propagation rather than direct experimental demonstration in human; keep as a non-core process.
supported_by:
- reference_id: PMID:17928169
supporting_text: "All our data suggest that FBXO40 may function as a regulator involved in the postnatal myogenesis."
- term:
id: GO:0019005
label: SCF ubiquitin ligase complex
evidence_type: NAS
original_reference_id: PMID:34445249
qualifier: part_of
review:
summary: ComplexPortal NAS assignment (CPX-7981, SCF FBXO40 variant) that FBXO40 is part of an SCF E3 ubiquitin ligase complex, consistent with its F-box domain and reported direct interactions with SKP1 and CUL1.
action: ACCEPT
reason: Core localization/complex membership for an F-box protein; supported by the F-box domain, the UniProt SUBUNIT statement, and the general SCF biology described in the cited review.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBUNIT: Directly interacts with SKP1 and CUL1. {ECO:0000250}."
- reference_id: PMID:34445249
supporting_text: "These SCF complexes are distinguishable by variable F-box proteins, which determine substrate specificity."
- term:
id: GO:0031146
label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
evidence_type: NAS
original_reference_id: PMID:34445249
qualifier: involved_in
review:
summary: ComplexPortal NAS assignment that FBXO40, as an SCF F-box receptor, participates in SCF-dependent proteasomal protein degradation. This is the expected biological process for an SCF substrate adaptor.
action: ACCEPT
reason: Consistent with the canonical role of F-box proteins in directing substrates to SCF-dependent proteasomal degradation, and now corroborated by FBXO40-specific evidence that SCF-FBXO40 ubiquitinates IRS1 to drive its proteasomal degradation (Shi et al. 2011, via the Falcon report).
supported_by:
- reference_id: PMID:34445249
supporting_text: "group of 69 SCF E3 ubiquitin ligase complexes that primarily modify protein substrates with poly-ubiquitin chains to target them for proteasomal degradation"
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "Ubl conjugation pathway"
- reference_id: file:human/FBXO40/FBXO40-deep-research-falcon.md
supporting_text: 'FBXO40 acts as the **substrate-recognition subunit** of an SCF E3 ligase complex (**SCF-FBXO40**) that **ubiquitinates IRS1**, promoting its **ubiquitin–proteasome-dependent degradation** in skeletal muscle, thereby **limiting IGF-1/insulin signaling** through the IRS1–PI3K–AKT axis'
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-8952618
qualifier: located_in
review:
summary: Reactome TAS cytosol localization derived from generic CRL1/neddylation pathway reactions in which the SCF complex participates. Consistent with cytoplasmic localization but pathway-context, not FBXO40-specific evidence.
action: KEEP_AS_NON_CORE
reason: Cytosol is a correct, more specific child of the cytoplasm localization, but this and the other identical Reactome cytosol annotations are propagated from generic cullin-RING-ligase pathway reactions rather than direct FBXO40 evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-8952620
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic CRL1/NEDD8 pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-8955241
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic CAND1/CRL pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-8955289
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic COMMD/CAND1/CRL pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-8956040
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic COP9-signalosome deneddylation pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-8956200
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic DCUN1D3/CRL1 pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic CRL pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-983140
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic ubiquitin-transfer pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-983147
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic ubiquitin-transfer pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-983156
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic polyubiquitination pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-983157
qualifier: located_in
review:
summary: Reactome TAS cytosol localization from a generic E3-substrate-E2 interaction pathway reaction. Redundant with the other Reactome cytosol annotations.
action: KEEP_AS_NON_CORE
reason: Correct compartment but propagated from generic ubiquitin-conjugation pathway reactions rather than FBXO40-specific evidence.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}."
- term:
id: GO:0005737
label: cytoplasm
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: located_in
review:
summary: ISS transfer of cytoplasmic localization from the mouse ortholog (SKP1, UniProtKB:P62932 used as WITH). Consistent with the experimentally observed cytoplasmic localization of FBXO40.
action: ACCEPT
reason: Correct core compartment; corroborated by direct overexpression in C2C12 myoblasts and the UniProt subcellular location.
supported_by:
- reference_id: PMID:17928169
supporting_text: "By overexpressing in C2C12 cells, FBXO40 localized in cytoplasm."
- term:
id: GO:0042692
label: muscle cell differentiation
evidence_type: ISS
original_reference_id: PMID:17928169
qualifier: involved_in
review:
summary: ISS assignment of involvement in muscle cell differentiation, based on FBXO40's muscle-restricted, postnatal expression and its proposed role in postnatal myogenesis.
action: KEEP_AS_NON_CORE
reason: The cited study establishes muscle-specific expression and a postnatal-myogenesis association by expression/correlation, but does not directly demonstrate that FBXO40 drives muscle cell differentiation. The mechanistically best-defined muscle role of FBXO40 (Shi et al. 2011) is negative control of muscle growth/hypertrophy via SCF-dependent IRS1 degradation and attenuation of IGF-1/insulin-AKT signaling, rather than differentiation per se; retain this term as a plausible non-core process.
supported_by:
- reference_id: PMID:17928169
supporting_text: "All our data suggest that FBXO40 may function as a regulator involved in the postnatal myogenesis."
- reference_id: file:human/FBXO40/FBXO40-deep-research-falcon.md
supporting_text: Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy in animal models, including mice and pigs
- term:
id: GO:0046627
label: negative regulation of insulin receptor signaling pathway
evidence_type: ISO
original_reference_id: PMID:22033112
qualifier: involved_in
review:
summary: Proposed FBXO40-specific process inferred by orthology from mouse Fbxo40 (Shi et al. 2011, PMID:22033112; surfaced via the Falcon report) that SCF-FBXO40 ubiquitinates IRS1 to drive its proteasomal degradation, attenuating IGF-1/insulin -> IRS1 -> PI3K/AKT signaling in skeletal muscle.
action: NEW
reason: Not currently in GOA, but a well-supported FBXO40-specific biological process. SCF-FBXO40 degrades IRS1 (enhanced by IGF1R-dependent IRS1 tyrosine phosphorylation), and Fbxo40 loss stabilizes IRS1 and causes IRS1-dependent muscle hypertrophy, defining FBXO40 as a negative regulator of insulin/IGF-1 receptor signaling. Evidence is recorded as ISO (inferred from the mouse ortholog; Shi et al. 2011, Dev Cell, PMID:22033112, identified via the Falcon report). The PMID is confirmed to exist but its full text was not read here, so the falcon report is cited as the supporting lead rather than an asserted experimental human quote.
supported_by:
- reference_id: file:human/FBXO40/FBXO40-deep-research-falcon.md
supporting_text: 'FBXO40 acts as the **substrate-recognition subunit** of an SCF E3 ligase complex (**SCF-FBXO40**) that **ubiquitinates IRS1**, promoting its **ubiquitin–proteasome-dependent degradation** in skeletal muscle, thereby **limiting IGF-1/insulin signaling** through the IRS1–PI3K–AKT axis'
references:
- id: PMID:22033112
title: The SCF-FBXO40 complex induces IRS1 ubiquitination in skeletal muscle, limiting IGF1 signaling.
findings: []
reference_review:
relevance: HIGH
correctness: UNVERIFIED
review_notes: Primary mouse/C2C12 study (Shi et al., Dev Cell 2011) identified by the Falcon deep-research report as the basis for the IRS1/insulin-signaling biology. PMID confirmed to exist via PubMed, but the full text was not read here; the FBXO40-specific NEW annotation is therefore recorded as ISO (ortholog inference) and the falcon report is cited as the supporting lead.
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:17928169
title: FBXO40, a gene encoding a novel muscle-specific F-box protein, is upregulated
in denervation-related muscle atrophy.
findings:
- statement: FBXO40 is a novel muscle-specific F-box protein expressed only in heart and skeletal muscle, detectable postnatally (~2 weeks after birth), localizing to the cytoplasm in C2C12 cells, decreased in LGMD dystrophic muscle, and upregulated in denervation- but not starvation-related muscle atrophy; proposed to regulate postnatal myogenesis.
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified (Gene 2007;404:53-60, DOI 10.1016/j.gene.2007.08.020); abstract-only in cache (full_text_available false). Directly establishes muscle-specific expression, cytoplasmic localization, and the postnatal-myogenesis association underlying the muscle cell differentiation annotations.
- id: PMID:34445249
title: The SCF Complex Is Essential to Maintain Genome and Chromosome Stability.
findings:
- statement: Review describing the SCF (SKP1-CUL1-F-box) family of ~69 E3 ubiquitin ligase complexes in which variable F-box proteins determine substrate specificity and target substrates with poly-ubiquitin chains for proteasomal degradation.
reference_section_type: ABSTRACT
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified (Int J Mol Sci 2021;22:8544, DOI 10.3390/ijms22168544); abstract-only in cache. A family-level SCF review (not FBXO40-specific) used by ComplexPortal as the NAS basis for SCF-complex membership and SCF-dependent catabolic process; supports the generic SCF framing but not FBXO40-specific substrate claims.
- id: file:human/FBXO40/FBXO40-deep-research-falcon.md
title: Falcon deep research report for human FBXO40
findings:
- statement: FBXO40 is the muscle-enriched substrate-recognition subunit of an SCF (SKP1-CUL1-RBX1) E3 ubiquitin ligase that ubiquitinates IRS1 to promote its proteasomal degradation, limiting IGF-1/insulin signaling through the IRS1-PI3K-AKT axis.
supporting_text: 'FBXO40 acts as the **substrate-recognition subunit** of an SCF E3 ligase complex (**SCF-FBXO40**) that **ubiquitinates IRS1**, promoting its **ubiquitin–proteasome-dependent degradation** in skeletal muscle, thereby **limiting IGF-1/insulin signaling** through the IRS1–PI3K–AKT axis'
- statement: FBXO40 co-immunoprecipitates with IRS1 and the canonical SCF components SKP1, CUL1 and RBX1, and immunoprecipitated SCF-FBXO40 ubiquitinates recombinant IRS1 in vitro.
supporting_text: co-immunoprecipitation experiments show that **IRS1 and each SCF component (Skp1, Cullin1, Rbx1)** can be co-precipitated with Fbxo40, consistent with SCF assembly and adaptor function
- statement: IRS1 tyrosine phosphorylation downstream of IGF1R activation markedly enhances IRS1 polyubiquitination by SCF-FBXO40, indicating phosphorylation-dependent substrate recognition.
supporting_text: '**tyrosine phosphorylation** of IRS1 (in the context of **IGF1R activation**) markedly enhances IRS1 polyubiquitination by SCF-Fbxo40 in vitro, supporting phosphorylation-dependent substrate recognition/processing'
- statement: Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy that is IRS1-dependent, including increased muscle mass in CRISPR knockout pigs.
supporting_text: Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy in animal models, including mice and pigs
- statement: FBXO40 transcription is induced by inflammatory STAT3 signaling (e.g. IL-6), linking it to catabolic insulin-resistance contexts.
supporting_text: '**STAT3 activation** (e.g., via **IL-6**) increases Fbxo40 expression, reducing IRS1 and p-AKT; Fbxo40 knockdown preserves IRS1/p-AKT despite IL-6'
reference_review:
relevance: HIGH
correctness: UNVERIFIED
review_notes: 'Falcon (Edison Scientific) deep-research synthesis. Findings name primary literature (Shi et al., Dev Cell 2011, DOI 10.1016/j.devcel.2011.09.011, establishing IRS1 as the direct SCF-FBXO40 substrate and KO hypertrophy; Zhang et al., AJP Endocrinol Metab 2020, DOI 10.1152/ajpendo.00480.2019, STAT3/IL-6 induction). These are treated as leads supporting the IRS1/IGF-1 signaling core function; the primary full texts were not read here, so the synthesis is marked UNVERIFIED rather than VERIFIED.'
- id: Reactome:R-HSA-8952618
title: AcM-UBE2M transfers NEDD8 to CRL1 E3 ubiquitin ligase complex
findings: []
- id: Reactome:R-HSA-8952620
title: NEDD8:AcM-UBE2M binds CRL1 E3 ubiquitin ligase complex
findings: []
- id: Reactome:R-HSA-8955241
title: CAND1 binds cytosolic CRL E3 ubiquitin ligases
findings: []
- id: Reactome:R-HSA-8955289
title: COMMDs displace CAND1 from cytosolic CRL E3 ubiquitin ligase complexes
findings: []
- id: Reactome:R-HSA-8956040
title: COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
findings: []
- id: Reactome:R-HSA-8956200
title: MyrG-DCUN1D3 binds CRL1 E3 ubiquitin ligase complex
findings: []
- id: Reactome:R-HSA-983140
title: Transfer of Ub from E2 to substrate and release of E2
findings: []
- id: Reactome:R-HSA-983147
title: Release of E3 from polyubiquitinated substrate
findings: []
- id: Reactome:R-HSA-983156
title: Polyubiquitination of substrate
findings: []
- id: Reactome:R-HSA-983157
title: Interaction of E3 with substrate and E2-Ub complex
findings: []
core_functions:
- description: Substrate-recognition subunit (F-box adaptor) of a muscle-expressed
SCF (SKP1-CUL1-RBX1-FBXO40) E3 ubiquitin ligase complex that recruits specific
substrates and presents them for SCF-dependent poly-ubiquitination and
proteasomal degradation. Catalytic ubiquitin transfer is provided by the RBX1
RING subunit, not by FBXO40 itself.
molecular_function:
id: GO:1990756
label: ubiquitin-like ligase-substrate adaptor activity
locations:
- id: GO:0005737
label: cytoplasm
supported_by:
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "Probable substrate-recognition component of the SCF (SKP1-"
- reference_id: file:human/FBXO40/FBXO40-uniprot.txt
supporting_text: "SUBUNIT: Directly interacts with SKP1 and CUL1. {ECO:0000250}."
directly_involved_in:
- id: GO:0031146
label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
- description: Muscle-specific negative regulator of IGF-1/insulin signaling that, as
the SCF(FBXO40) substrate receptor, recognizes IRS1 (preferentially when tyrosine-phosphorylated
downstream of activated IGF1R) and targets it for proteasomal degradation, thereby
attenuating IRS1 -> PI3K/AKT anabolic signaling and limiting skeletal-muscle growth;
loss of FBXO40 stabilizes IRS1 and causes IRS1-dependent muscle hypertrophy.
molecular_function:
id: GO:1990756
label: ubiquitin-like ligase-substrate adaptor activity
locations:
- id: GO:0005737
label: cytoplasm
supported_by:
- reference_id: file:human/FBXO40/FBXO40-deep-research-falcon.md
supporting_text: 'FBXO40 acts as the **substrate-recognition subunit** of an SCF E3 ligase complex (**SCF-FBXO40**) that **ubiquitinates IRS1**, promoting its **ubiquitin–proteasome-dependent degradation** in skeletal muscle, thereby **limiting IGF-1/insulin signaling** through the IRS1–PI3K–AKT axis'
- reference_id: file:human/FBXO40/FBXO40-deep-research-falcon.md
supporting_text: '**tyrosine phosphorylation** of IRS1 (in the context of **IGF1R activation**) markedly enhances IRS1 polyubiquitination by SCF-Fbxo40 in vitro, supporting phosphorylation-dependent substrate recognition/processing'
directly_involved_in:
- id: GO:0046627
label: negative regulation of insulin receptor signaling pathway
proposed_new_terms: []
suggested_questions:
- question: What is the direct, experimentally validated substrate repertoire of FBXO40
in human skeletal muscle, and is IRS1 ubiquitination by the SCF-FBXO40 complex
direct (e.g. reconstituted with purified components) rather than inferred from
co-depletion phenotypes?
- question: Does FBXO40 substrate recruitment depend on the TRAF-type zinc finger,
and does substrate engagement require phosphodegron recognition downstream of
IGF1R/insulin-Akt signaling?
- question: Are the muscle cell differentiation and denervation-atrophy phenotypes
a consequence of FBXO40-dependent substrate turnover, or do they reflect
expression-correlated but indirect roles?
- question: How is FBXO40 transcription controlled by inflammatory STAT3/IL-6 signaling
in skeletal muscle, and does pharmacologic STAT3 inhibition preserve IRS1/p-AKT and
improve insulin sensitivity primarily through FBXO40 downregulation?
suggested_experiments:
- description: Reconstitute the SCF-FBXO40 complex (SKP1, CUL1, RBX1, FBXO40) with a
ubiquitin-charged E2 in vitro and assay ubiquitination of candidate substrates
(e.g. IRS1) to establish direct adaptor function and chain topology.
- description: Perform affinity purification-mass spectrometry of tagged FBXO40 from
skeletal myotubes (with and without proteasome/neddylation inhibition) to
define the endogenous substrate and complex interactome and confirm SKP1/CUL1/RBX1
association.
- description: Generate FBXO40-knockout myoblasts/mice and quantify candidate-substrate
levels and ubiquitination, myogenic differentiation, and the denervation-atrophy
response to test whether phenotypes are substrate-turnover dependent.