Affinage

CCNF

Cyclin-F · UniProt P41002

Length
786 aa
Mass
87.6 kDa
Annotated
2026-04-28
21 papers in source corpus 11 papers cited in narrative 11 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

Cyclin F (CCNF/FBXO1) is the substrate-recognition subunit of the SCF^CyclinF E3 ubiquitin ligase complex, which mediates Lys48-linked ubiquitination and proteasomal degradation of key cell-cycle and homeostatic substrates including E2F1/E2F2/E2F3a transcription factors, RRM2, and HIV-1 Vif (PMID:36607545, PMID:34201347, PMID:28184007). Through recognition of specific degron motifs in substrates — regulated by MEK/ERK-dependent phosphorylation in the case of E2Fs — SCF^CyclinF controls G1/S cell-cycle progression, ubiquitin-proteasome system homeostasis, and autophagosome–lysosome fusion, and it modulates VCP ATPase activity via direct physical interaction (PMID:36607545, PMID:37220877, PMID:28852778, PMID:31577344). Missense mutations in CCNF cause familial ALS/FTD by elevating aberrant Lys48-ubiquitylation, disrupting free ubiquitin pools in motor neurons, hyperactivating cytoplasmic VCP to promote TDP-43 aggregation, and impairing autophagic clearance (PMID:27080313, PMID:37220877, PMID:31577344, PMID:28852778). Loss of CCNF in zebrafish produces motor neuron axonal outgrowth defects and selective vulnerability to endoplasmic reticulum stress, confirming a direct requirement for CCNF in motor neuron maintenance (PMID:38474336).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1994 Medium

    Identification of CCNF as a novel cyclin-family member related to A- and B-type cyclins established the gene as a cell-cycle-associated factor, but its specific biochemical function was unknown.

    Evidence cDNA sequencing and Northern blot analysis of human transcript

    PMID:7896286

    Open questions at the time
    • No enzymatic or functional activity defined
    • No interacting partners identified
    • Cyclin-box homology alone did not establish CDK dependency
  2. 2016 High

    Discovery that cyclin F is the substrate-recognition (F-box) subunit of an SCF E3 ubiquitin ligase, and that ALS/FTD-associated mutations cause accumulation of ubiquitinated proteins including TDP-43 in neuronal cells, established CCNF as a disease-linked ubiquitin ligase component.

    Evidence Whole-exome sequencing of ALS/FTD families; mutant CCNF expression in neuronal cells with ubiquitination assays and immunoblot

    PMID:27080313

    Open questions at the time
    • Endogenous substrates beyond TDP-43 not identified
    • Mechanism by which mutations alter ligase activity undefined
    • No in vivo validation of motor neuron phenotype
  3. 2017 High

    Characterization of the S621G mutant revealed that disease-linked cyclin F elevates Lys48-ubiquitylation of autophagy-related proteins, physically interacts with p62/SQSTM1, and impairs autophagosome–lysosome fusion, connecting SCF^CyclinF dysfunction to proteostasis failure via autophagy.

    Evidence K48-linkage-specific ubiquitin IP with mass spectrometry; autophagy flux markers (LC3, Lamp2) in Neuro-2A and SH-SY5Y cells; Co-IP of cyclin F and p62

    PMID:28852778

    Open questions at the time
    • Whether p62 is a direct ubiquitination substrate or an adaptor not resolved
    • Autophagy defect not confirmed in patient-derived neurons at this stage
  4. 2017 High

    Demonstration that SCF^CyclinF targets HIV-1 Vif for K48-linked ubiquitination and proteasomal degradation — via a cyclin F-specific degron motif in Vif — expanded the substrate repertoire to viral proteins and revealed host antiviral restriction function.

    Evidence Reciprocal Co-IP, degron mutagenesis, ubiquitination assays, proteasome inhibitor rescue, APOBEC3G restoration upon Vif degradation

    PMID:28184007

    Open questions at the time
    • Physiological relevance in HIV-infected patients not tested
    • Degron specificity for other viral substrates unknown
  5. 2017 Medium

    Expression of ALS-linked CCNF mutants in zebrafish embryos caused motor neuron axonopathy, spinal cord apoptosis, and impaired motor responses, providing the first in vivo evidence that mutant CCNF is neurotoxic.

    Evidence Transient overexpression of mutant human CCNF in zebrafish; caspase-3 immunostaining; photomotor response assay

    PMID:28444311

    Open questions at the time
    • Overexpression model does not distinguish gain-of-function from dominant-negative effects
    • Endogenous loss-of-function phenotype not assessed
    • No mammalian in vivo model
  6. 2019 High

    Discovery that cyclin F directly binds and stimulates VCP ATPase activity, and that ALS mutations enhance this interaction causing cytoplasmic mislocalization and VCP hyperactivation that drives TDP-43 aggregation, provided a concrete pathogenic mechanism linking two ALS genes.

    Evidence Co-IP and colocalization; domain-mapping pulldowns; in vitro VCP ATPase activity assay; TDP-43 aggregation assay in transfected cells

    PMID:31577344

    Open questions at the time
    • Structural basis of cyclin F–VCP interface unresolved
    • Whether VCP is itself a ubiquitination substrate of SCF^CyclinF unknown
    • TDP-43 aggregation not validated in patient-derived neurons
  7. 2021 Medium

    Identification of RRM2 as an SCF^CyclinF substrate and of FBXL8/FZR1 as E3 ligases that target CCNF itself for degradation established bidirectional regulation of cyclin F abundance and a new substrate relevant to DNA replication.

    Evidence Co-IP of FBXL8/FZR1 with CCNF; double knockdown causing CCNF accumulation; CCNF overexpression reducing RRM2 levels

    PMID:34201347

    Open questions at the time
    • Direct ubiquitination of RRM2 by SCF^CyclinF not demonstrated with purified components
    • Physiological contexts (cell cycle phase) not resolved
    • Single-lab finding awaiting independent replication
  8. 2023 High

    Identification of E2F1/E2F2/E2F3a as direct SCF^CyclinF substrates, degraded via specific Arg/Ile and Arg/Val degron motifs regulated by MEK/ERK phosphorylation, established cyclin F as a master regulator of G1/S progression through E2F turnover.

    Evidence Reciprocal Co-IP; degron motif mutagenesis (RI/AA, RV/AA); ubiquitination and cycloheximide chase assays; MEK/ERK inhibitor treatment; FBXO1 knockdown with cell-cycle analysis

    PMID:36607545

    Open questions at the time
    • In vivo cell-cycle phenotype of CCNF loss in mammals not examined
    • Whether all three E2Fs are targeted simultaneously or in different contexts is unclear
  9. 2023 High

    Patient iPSC-derived motor neurons carrying CCNF S621G showed increased ubiquitinated protein loads and altered UPS component ubiquitination; active-site double mutations restoring ligase function rescued free ubiquitin levels, proving that SCF^CyclinF E3 ligase activity directly controls ubiquitin homeostasis in motor neurons.

    Evidence iPSC-derived motor neurons from CCNF S621G patients; ubiquitin profiling; active-site double-mutant rescue in NSC-34 cells

    PMID:37220877

    Open questions at the time
    • Specific ubiquitin-modified substrates driving motor neuron vulnerability not identified
    • Rescue not performed in patient neurons
    • Relationship between UPS dysfunction and autophagy defects not integrated
  10. 2024 Medium

    CRISPR knockout of ccnf in zebrafish confirmed a direct requirement for CCNF in motor neuron axonal outgrowth and revealed selective vulnerability to ER stress but not oxidative stress, distinguishing the stress-response pathways downstream of CCNF loss.

    Evidence CRISPR/Cas9 ccnf knockout zebrafish; motor neuron morphology; pharmacological ER and oxidative stress challenges

    PMID:38474336

    Open questions at the time
    • Mechanism linking CCNF loss to ER stress sensitivity unknown
    • Mammalian knockout model still lacking
    • Transcriptomic/proteomic characterization of knockout neurons not performed

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of SCF^CyclinF substrate recognition and VCP interaction, the full catalogue of physiological substrates in motor neurons, the relative contributions of UPS dysfunction versus autophagy impairment versus VCP hyperactivation to ALS/FTD pathogenesis, and validation of these mechanisms in mammalian in vivo models.
  • No crystal or cryo-EM structure of SCF^CyclinF with any substrate
  • No mammalian in vivo conditional knockout model
  • Integration of UPS, autophagy, and VCP pathways into unified pathogenic cascade not achieved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0098772 molecular function regulator activity 2
Localization
GO:0005634 nucleus 1
Pathway
R-HSA-392499 Metabolism of proteins 5 R-HSA-1643685 Disease 3 R-HSA-5357801 Programmed Cell Death 2 R-HSA-1640170 Cell Cycle 1 R-HSA-9612973 Autophagy 1
Partners
CUL1E2F1E2F2E2F3RRM2SKP1SQSTM1VCP
Complex memberships
SCF^CyclinF (SKP1-CUL1-CyclinF)

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 CCNF encodes cyclin F, a novel member of the cyclin family related to A- and B-type cyclins by sequence, located on chromosome 16p13.3. cDNA sequencing, Northern blot analysis, exon-intron boundary determination Genomics Medium 7896286
2016 Cyclin F (CCNF) functions as the substrate-binding subunit of an SCF (SKP1-CUL1-F-box) E3 ubiquitin-protein ligase complex (SCF^CyclinF); ALS/FTD-associated missense mutations cause abnormal ubiquitination and accumulation of ubiquitinated proteins including TDP-43 and an SCF^CyclinF substrate in neuronal cells. Whole-exome sequencing for mutation identification; transfection of mutant CCNF in neuronal cells with ubiquitination assays and western blot for substrate accumulation Nature communications High 27080313
2017 The ALS/FTD-linked cyclin F p.S621G mutation causes elevated Lys48-linked ubiquitylation of proteins in neuronal cells, and proteomic analysis identified autophagy pathway proteins (p62/SQSTM1, heat shock proteins, chaperonin components) as targets; mutant cyclin F impairs autophagosomal-lysosome fusion, and cyclin F physically interacts with p62. Transfection of mutant CCNF (S621G) in Neuro-2A and SH-SY5Y cells; K48-linkage-specific ubiquitin immunoprecipitation followed by mass spectrometry proteomics; autophagy marker analysis (p62, LC3, Lamp2) by immunoblot and immunofluorescence Cellular and molecular life sciences : CMLS High 28852778
2017 Cyclin F (CCNF) interacts with HIV-1 Vif protein; Vif is a substrate of the SCF^CyclinF E3 ligase complex, which mediates K48-linked ubiquitination and proteasomal degradation of Vif, thereby restoring APOBEC3G levels and restricting viral infectivity. A cyclin F-specific amino acid motif in the C-terminal region of Vif is required for this interaction. Co-immunoprecipitation, overexpression and knockdown studies, mutational analysis of Vif degron motif, ubiquitination assays, proteasome inhibitor experiments, APOBEC3G expression analysis The Journal of biological chemistry High 28184007
2017 Expression of ALS-linked mutant CCNF in zebrafish embryos causes increased caspase-3 activation and cell death in the spinal cord, motor neuron axonopathy (shortened primary motor axons, aberrant branching), and reduced photomotor response; proteomic analysis of in vitro models identified disruption of caspase-3-mediated cell death pathways. Transient overexpression of human mutant CCNF in zebrafish embryos; immunostaining for cleaved caspase-3; motor response (photomotor response) assay; label-free quantitative proteomics of in vitro models Human molecular genetics Medium 28444311
2019 Cyclin F physically binds to VCP (valosin-containing protein, also an ALS gene) via the N-terminal region of Cyclin F, and the two proteins colocalize in the nucleus. Cyclin F enhances VCP ATPase activity in vitro. ALS-associated CCNF mutations increase Cyclin F binding to VCP and further elevate VCP ATPase activity while causing cytoplasmic mislocalization of Cyclin F. Elevated VCP ATPase activity promotes cytoplasmic TDP-43 aggregation. Co-immunoprecipitation and colocalization experiments; domain-mapping pulldowns; in vitro ATPase activity assay; overexpression of mutant CCNF in transfected cells; TDP-43 aggregation assay Human molecular genetics High 31577344
2021 Label-free quantitative proteomics of HEK293 cells expressing multiple ALS-associated CCNF mutations (K97R, S195R, S509P, R574Q, S621G) bioinformatically predicted and immunoblot-validated activation of neuronal apoptosis pathways; iPSC-derived cells from S621G patients showed the same pathway activation. Label-free quantitative proteomics of transfected HEK293 cells; pathway bioinformatics; immunoblot validation; iPSC-derived patient cell proteomics Frontiers in molecular neuroscience Medium 33986643
2021 CCNF protein is targeted for degradation by the E3 ligases FBXL8 and FZR1 (demonstrated by Co-IP pulldown); double knockdown of FBXL8 and FZR1 causes CCNF accumulation. CCNF itself pulls down RRM2 (ribonucleotide reductase subunit 2) and CCNF overexpression reduces RRM2 levels, indicating RRM2 is a substrate of SCF^CyclinF. Co-immunoprecipitation (FBXL8 and FZR1 pulldown of CCNF); double knockdown experiments; CCNF overexpression with RRM2 protein level measurement Cancers Medium 34201347
2023 FBXO1 (Cyclin F) directly binds E2F1, E2F2, and E2F3a transcription factors through Arg/Ile and Arg/Val degron motifs in their dimerization domains, mediating K48-linked ubiquitination and proteasomal degradation of E2Fs. MEK/ERK-dependent phosphorylation of threonine residues near these degron motifs regulates FBXO1-E2F interaction and E2F protein stability. Knockdown of FBXO1 elevated E2F levels and delayed G1/S cell cycle transition, inhibiting cancer cell proliferation. Co-immunoprecipitation; domain/motif mutation analysis (RI/AA, RV/AA); ubiquitination assays; cycloheximide chase for half-life; specific kinase inhibitors; FBXO1 knockdown with cell cycle analysis Archives of pharmacal research High 36607545
2023 The ALS-associated CCNF S621G variant causes ubiquitin-proteasome system (UPS) dysfunction in iPSC-derived motor neurons, with increased ubiquitinated protein abundance and altered ubiquitination of key UPS components. Overexpression of CCNF in NSC-34 cells alters free ubiquitin levels; double mutations that reduce CCNF's ability to form an active E3 ligase complex improved UPS function and increased free monomeric ubiquitin, establishing that the E3 ligase activity of CCNF is central to its role in ubiquitin homeostasis. iPSC-derived motor neurons from CCNF S621G patients; ubiquitin abundance and UPS component ubiquitination analysis; overexpression in NSC-34 cells with free ubiquitin measurement; active-site double-mutant analysis with UPS functional assay Human molecular genetics High 37220877
2024 CRISPR/Cas9-mediated loss of ccnf in zebrafish causes abnormal motor neuron development and axonal outgrowth defects, and ccnf-deficient zebrafish show selective sensitization to endoplasmic reticulum stress but not oxidative stress, establishing a direct role for CCNF in motor neuron axonal maintenance in vivo. CRISPR/Cas9 genome editing in zebrafish to generate ccnf knockout; motor neuron morphology and axonal outgrowth analysis; pharmacological stress (ER stress, oxidative stress) with motor response readout Cells Medium 38474336

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2016 CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia. Nature communications 178 27080313
2017 Pathogenic mutation in the ALS/FTD gene, CCNF, causes elevated Lys48-linked ubiquitylation and defective autophagy. Cellular and molecular life sciences : CMLS 43 28852778
2017 Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype. Human molecular genetics 40 28444311
2019 Pathogenic mutations in the ALS gene CCNF cause cytoplasmic mislocalization of Cyclin F and elevated VCP ATPase activity. Human molecular genetics 28 31577344
2017 Cyclin F/FBXO1 Interacts with HIV-1 Viral Infectivity Factor (Vif) and Restricts Progeny Virion Infectivity by Ubiquitination and Proteasomal Degradation of Vif Protein through SCFcyclin F E3 Ligase Machinery. The Journal of biological chemistry 25 28184007
2021 A Novel Signature of CCNF-Associated E3 Ligases Collaborate and Counter Each Other in Breast Cancer. Cancers 17 34201347
2017 Mutations of CCNF gene is rare in patients with amyotrophic lateral sclerosis and frontotemporal dementia from Mainland China. Amyotrophic lateral sclerosis & frontotemporal degeneration 17 28281833
2017 Investigating CCNF mutations in a Taiwanese cohort with amyotrophic lateral sclerosis. Neurobiology of aging 17 29102476
2023 The Skp1-Cullin1-FBXO1 complex is a pleiotropic regulator required for the formation of gametes and motile forms in Plasmodium berghei. Nature communications 15 36898988
2021 Unbiased Label-Free Quantitative Proteomics of Cells Expressing Amyotrophic Lateral Sclerosis (ALS) Mutations in CCNF Reveals Activation of the Apoptosis Pathway: A Workflow to Screen Pathogenic Gene Mutations. Frontiers in molecular neuroscience 14 33986643
1994 A novel cyclin gene (CCNF) in the region of the polycystic kidney disease gene (PKD1). Genomics 14 7896286
2023 MEKs/ERKs-mediated FBXO1/E2Fs interaction interference modulates G1/S cell cycle transition and cancer cell proliferation. Archives of pharmacal research 8 36607545
2019 Generation and characterization of a human induced pluripotent stem cell line UOWi005-A from dermal fibroblasts derived from a CCNFS621G familial amyotrophic lateral sclerosis patient using mRNA reprogramming. Stem cell research 8 31445393
2023 Genetic and Phenotypic Spectrum of Amyotrophic Lateral Sclerosis Patients with CCNF Variants from a Large Chinese Cohort. Molecular neurobiology 7 37171577
2018 Screening for CCNF Mutations in a Chinese Amyotrophic Lateral Sclerosis Cohort. Frontiers in aging neuroscience 6 30008669
2023 ALS-linked CCNF variant disrupts motor neuron ubiquitin homeostasis. Human molecular genetics 4 37220877
2023 CCNF is a potential pancancer biomarker and immunotherapy target. Frontiers in oncology 3 37168372
2024 Zebrafish CCNF and FUS Mediate Stress-Specific Motor Responses. Cells 2 38474336
2023 Behavioural Variant Frontotemporal Dementia due to CCNF Gene Mutation: A Case Report. Current Alzheimer research 1 37872794
2025 Expanding the genetic spectrum of corticobasal syndrome: novel CCNF p.M394L variant from a South Asian cohort. Neurocase 0 41069067
2024 Exploring the Role of CCNF Variants in Italian ALS Patients. Genes 0 39766833