FBXO40

UniProt ID: Q9UH90
Organism: Homo sapiens
Review Status: COMPLETE
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Gene 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 Review

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.
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

Core Functions

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.

Supporting Evidence:
  • file:human/FBXO40/FBXO40-uniprot.txt
    Probable substrate-recognition component of the SCF (SKP1-
  • file:human/FBXO40/FBXO40-uniprot.txt
    SUBUNIT: Directly interacts with SKP1 and CUL1. {ECO:0000250}.

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.

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
  • file:human/FBXO40/FBXO40-deep-research-falcon.md
    **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

References

The SCF-FBXO40 complex induces IRS1 ubiquitination in skeletal muscle, limiting IGF1 signaling.
Gene Ontology annotation through association of InterPro records with GO terms
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Combined Automated Annotation using Multiple IEA Methods
FBXO40, a gene encoding a novel muscle-specific F-box protein, is upregulated in denervation-related muscle atrophy.
  • 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.
The SCF Complex Is Essential to Maintain Genome and Chromosome Stability.
  • 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.
file:human/FBXO40/FBXO40-deep-research-falcon.md
Falcon deep research report for human FBXO40
  • 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.
    "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"
  • FBXO40 co-immunoprecipitates with IRS1 and the canonical SCF components SKP1, CUL1 and RBX1, and immunoprecipitated SCF-FBXO40 ubiquitinates recombinant IRS1 in vitro.
    "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"
  • IRS1 tyrosine phosphorylation downstream of IGF1R activation markedly enhances IRS1 polyubiquitination by SCF-FBXO40, indicating phosphorylation-dependent substrate recognition.
    "**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"
  • Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy that is IRS1-dependent, including increased muscle mass in CRISPR knockout pigs.
    "Loss of Fbxo40 increases IRS1 abundance and produces muscle hypertrophy in animal models, including mice and pigs"
  • FBXO40 transcription is induced by inflammatory STAT3 signaling (e.g. IL-6), linking it to catabolic insulin-resistance contexts.
    "**STAT3 activation** (e.g., via **IL-6**) increases Fbxo40 expression, reducing IRS1 and p-AKT; Fbxo40 knockdown preserves IRS1/p-AKT despite IL-6"
Reactome:R-HSA-8952618
AcM-UBE2M transfers NEDD8 to CRL1 E3 ubiquitin ligase complex
Reactome:R-HSA-8952620
NEDD8:AcM-UBE2M binds CRL1 E3 ubiquitin ligase complex
Reactome:R-HSA-8955241
CAND1 binds cytosolic CRL E3 ubiquitin ligases
Reactome:R-HSA-8955289
COMMDs displace CAND1 from cytosolic CRL E3 ubiquitin ligase complexes
Reactome:R-HSA-8956040
COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
Reactome:R-HSA-8956200
MyrG-DCUN1D3 binds CRL1 E3 ubiquitin ligase complex
Reactome:R-HSA-983140
Transfer of Ub from E2 to substrate and release of E2
Reactome:R-HSA-983147
Release of E3 from polyubiquitinated substrate
Reactome:R-HSA-983156
Polyubiquitination of substrate
Reactome:R-HSA-983157
Interaction of E3 with substrate and E2-Ub complex

Suggested Questions for Experts

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?

Suggested Experiments

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.

Deep Research

Falcon

(FBXO40-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 20 citations 2 artifacts 2026-06-13T06:56:25.407877

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
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

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.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: FBXO40 (human; UniProt Q9UH90) — functional annotation and translational context

0) Target verification (critical identity check)

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).

1) Key concepts and definitions (current understanding)

1.1 F-box proteins and SCF E3 ubiquitin ligases

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).

1.2 Primary molecular function (what FBXO40 “does”)

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.

1.3 Substrate specificity and regulation by phosphorylation

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).

2) Mechanistic evidence (primary studies) — pathways, substrates, phenotypes

2.1 Direct biochemical evidence: IRS1 ubiquitination by SCF-FBXO40

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).

2.2 Tissue specificity and cellular context

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).

2.3 IGF-1/insulin signaling pathway impact

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).

2.4 Organism-level phenotypes (loss of function)

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).

3) Regulation in catabolic/inflammatory states (STAT3/IL-6 axis)

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.

4) Subcellular localization

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.

5) Recent developments (2023–2024 prioritized)

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.

5.1 Cachexia intervention study implicating FBXO-40 (2023)

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.

5.2 Reviews and disease-context placement (2023–2024)

  • A burn-wasting review in JCSM (Feb 2023; DOI: https://doi.org/10.1002/jcsm.13188) lists Fbxo40 among “less elaborated” muscle E3 ligases involved in regulating the IGF-1/insulin pathway in atrophy contexts, illustrating its incorporation into current conceptual frameworks of atrogenes and muscle wasting (dombrecht2023molecularmechanismsof pages 4-5).
  • A 2024 review of F-box proteins in spermatogenesis notes FBXO40 is expressed at very low levels or not expressed in testis, consistent with muscle-enriched expression patterns rather than germline-essential roles (Jun 2024; DOI: https://doi.org/10.1186/s13619-024-00196-9) (xuan2024theemergingand pages 2-5).

5.3 Cancer-associated bioinformatics signal (human) (2023)

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.

6) Current applications and real-world implementations

6.1 Genetic manipulation to alter muscle mass (animal models)

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).

6.2 Therapeutic strategy logic: modulating upstream regulators

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.

6.3 Biomarker-style use in muscle wasting

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.

7) Expert opinion / authoritative synthesis

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).

8) Disease associations and database evidence (human)

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).


Evidence summary table

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.


Figures supporting core mechanistic claims (from primary paper)

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).

Limitations of the current evidence package

  • Subcellular localization: high-resolution localization of endogenous human FBXO40 was not directly retrieved; available statements are largely review-level and/or based on forced expression (blondelle2020theroleof pages 11-13).
  • 2023–2024 mechanistic novelty: most direct mechanistic substrate work remains anchored by Shi et al. (2011) and follow-on mechanistic studies; 2023–2024 literature in this retrieval mainly extends translational contexts (cachexia interventions; bioinformatic cancer signatures) rather than redefining FBXO40’s molecular function.

References

  1. (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.

  2. (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.

  3. (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.

  4. (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.

  5. (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.

  6. (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.

  7. (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.

  8. (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.

  9. (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.

  10. (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.

  11. (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.

  12. (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.

  13. (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.

  14. (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.

  15. (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.

  16. (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.

  17. (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.

Artifacts

Citations

  1. blondelle2020theroleof pages 11-13
  2. dombrecht2023molecularmechanismsof pages 4-5
  3. xuan2024theemergingand pages 2-5
  4. wang2023genesignatureand pages 4-7
  5. https://doi.org/10.1016/j.devcel.2011.09.011
  6. https://doi.org/10.1152/ajpendo.00480.2019
  7. https://doi.org/10.1002/jcsm.13116
  8. https://doi.org/10.1002/jcsm.13188
  9. https://doi.org/10.1186/s13619-024-00196-9
  10. https://doi.org/10.1186/s12957-022-02875-w
  11. https://doi.org/10.1016/j.devcel.2011.09.011;
  12. https://doi.org/10.3390/ijms21217936
  13. https://platform.opentargets.org/target/ENSG00000163833
  14. https://doi.org/10.1016/j.devcel.2011.09.011,
  15. https://doi.org/10.1152/ajpendo.00480.2019,
  16. https://doi.org/10.3390/ijms21217936,
  17. https://doi.org/10.1002/jcsm.13116,
  18. https://doi.org/10.1002/jcsm.13188,
  19. https://doi.org/10.1186/s13619-024-00196-9,
  20. https://doi.org/10.1186/s12957-022-02875-w,

📚 Additional Documentation

Pn Notes

(FBXO40-pn-notes.md)

FBXO40 PN Consistency Notes

  • Generated: 2026-06-18
  • Project: PROTEOSTASIS
  • Scope: PN consistency rereview against local AIGR review and available deep-research artifacts
  • UniProt: Q9UH90
  • AIGR review status: COMPLETE
  • Review batch: proteostasis-batch-2026-06-13
  • Batch change status: added

Source Files Checked

Deep Research Files

AIGR Review Snapshot

  • 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/core annotation action counts: ACCEPT: 5; KEEP_AS_NON_CORE: 13; MODIFY: 1; NEW: 1

PN Consistency Summary

  • Consistency: Consistent and the best-characterized of the set. Deep research (Falcon, anchored on Shi et al. 2011 PMID:22033112), review YAML, and PN mapping agree: muscle-restricted SCF substrate receptor whose validated substrate is IRS1, limiting IGF-1/insulin->IRS1->PI3K/AKT signaling. Review applies the KEY F-box PATTERN cleanly: MODIFY of the IEA catalytic GO:0061630 (ubiquitin protein ligase activity) -> GO:1990756 adaptor activity. No internal contradictions.
  • PN story / NEW pressure: PN asserts only the generic adaptor role, but FBXO40 has a real substrate-specific BP NOT in GOA. Review adds NEW GO:0046627 "negative regulation of insulin receptor signaling pathway" (OLS-verified real). Defensible: SCF-FBXO40 ubiquitinates IRS1, Fbxo40 loss stabilizes IRS1 and causes IRS1-dependent muscle hypertrophy. Honestly recorded as ISO (mouse ortholog; PMID:22033112 NOT in cache — confirmed). Conclusion: ADD GO:0046627 (already in the review). MF/CC otherwise captured.
  • Evidence alignment: PN cites only "15340381 / rev." Review uses PMID:17928169 (muscle-specific expression, VERIFIED), PMID:22033112 (IRS1, UNVERIFIED/ISO), PMID:34445249 (NAS), Falcon, Reactome. Substantial divergence: review carries the substrate-level primary literature PN lacks.
  • Verdict: Consistent; correct F-box MODIFY pattern; defensible verified NEW BP (GO:0046627). ACCEPT review. Recommended edits: none required; optionally [REF] upgrade PMID:22033112 to VERIFIED if full text read.

Full Consistency Review

  • UniProt: Q9UH90 · batch: proteostasis-batch-2026-06-13 · review status: COMPLETE
  • PN placement: 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).
  • Consistency: Consistent and the best-characterized of the set. Deep research (Falcon, anchored on Shi et al. 2011 PMID:22033112), review YAML, and PN mapping agree: muscle-restricted SCF substrate receptor whose validated substrate is IRS1, limiting IGF-1/insulin->IRS1->PI3K/AKT signaling. Review applies the KEY F-box PATTERN cleanly: MODIFY of the IEA catalytic GO:0061630 (ubiquitin protein ligase activity) -> GO:1990756 adaptor activity. No internal contradictions.
  • PN story / NEW pressure: PN asserts only the generic adaptor role, but FBXO40 has a real substrate-specific BP NOT in GOA. Review adds NEW GO:0046627 "negative regulation of insulin receptor signaling pathway" (OLS-verified real). Defensible: SCF-FBXO40 ubiquitinates IRS1, Fbxo40 loss stabilizes IRS1 and causes IRS1-dependent muscle hypertrophy. Honestly recorded as ISO (mouse ortholog; PMID:22033112 NOT in cache — confirmed). Conclusion: ADD GO:0046627 (already in the review). MF/CC otherwise captured.
  • Mapping strategy: Gene does not change the node. GO:1990756 matches; node-level scope correct. The FBXO40-specific GO:0046627 lives in the review as a NEW substrate-specific term, appropriately not propagated to the shared PN node (too specific for the group). Catalytic-ligase IEA correctly demoted per pattern.
  • Evidence alignment: PN cites only "15340381 / rev." Review uses PMID:17928169 (muscle-specific expression, VERIFIED), PMID:22033112 (IRS1, UNVERIFIED/ISO), PMID:34445249 (NAS), Falcon, Reactome. Substantial divergence: review carries the substrate-level primary literature PN lacks.
  • Verdict: Consistent; correct F-box MODIFY pattern; defensible verified NEW BP (GO:0046627). ACCEPT review. Recommended edits: none required; optionally [REF] upgrade PMID:22033112 to VERIFIED if full text read.

PN Dossier Context

  • review_batch: proteostasis-batch-2026-06-13
  • review_yaml: genes/human/FBXO40/FBXO40-ai-review.yaml
  • PN workbook rows: 1

PN row 1: Ubiquitin Proteasome System | E3 ubiquitin and UBL ligases | Cul1 substrate receptor | F-box | TRAF-type ZnF

  • UniProt: Q9UH90
  • In branches: UPS
  • Signature domains: IPR001810
  • Auxiliary domains: IPR001293
  • PN references (titles):
    • 15340381 / rev
  • PN-node mapping records (path + ancestors):
    • [subtype] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul1 substrate receptor|F-box|TRAF-type ZnF
      status=no_mapping scope= GO=[]
      rationale: Reviewed as a narrower substrate-receptor, adaptor, domain, or family subdivision already covered by the curated parent adaptor/receptor mapping. No additional direct GO mapping is needed at this node.
    • [type] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul1 substrate receptor|F-box
      status=no_mapping scope= GO=[]
      rationale: Reviewed as a narrower substrate-receptor, adaptor, domain, or family subdivision already covered by the curated parent adaptor/receptor mapping. No additional direct GO mapping is needed at this node.
    • [group] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul1 substrate receptor
      status=mapped scope=ok_for_propagation_to_go GO=[GO:1990756 ubiquitin-like ligase-substrate adaptor activity]
      rationale: This PN group captures substrate receptors/adaptors for cullin/UBL ligase systems. The shared GO molecular-function target is ubiquitin-like ligase-substrate adaptor activity.
    • [class] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases
      status=context_only scope=too_broad_to_propagate GO=[GO:0061630 ubiquitin protein ligase activity]
      rationale: This class is a genuine E3-ligase context, but its descendants include catalytic ligases, cullin scaffolds, substrate receptors, adaptors, cofactors, regulators, and UBL modifier systems. A class-level propagation would over-annotate.
    • [branch] Ubiquitin Proteasome System
      status=no_mapping scope= GO=[]
      rationale: Reviewed as the top-level UPS branch. It is a project taxonomy umbrella rather than a direct GO assertion; UPS propagation must come from manually curated child nodes.

Projected GO annotations (1)

  • GO:1990756 ubiquitin-like ligase-substrate adaptor activity | scope=ok_for_propagation_to_go | goa_status=new_to_goa | from=Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|Cul1 substrate receptor

Note

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.

📄 View Raw YAML

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.