Affinage

CEP104

Centrosomal protein of 104 kDa · UniProt O60308

Length
925 aa
Mass
104.4 kDa
Annotated
2026-06-09
12 papers in source corpus 10 papers cited in narrative 10 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CEP104 is a conserved centriolar and ciliary-tip protein that drives ciliogenesis and axoneme elongation through direct, microtubule-polymerizing activity of its TOG domain (PMID:23970417, PMID:27402853, PMID:32820051). The TOG domain directly binds tubulin and is essential for cilium elongation, while CEP104 functions downstream of CP110 removal from the mother centriole during ciliary assembly (PMID:32820051, PMID:26477546). Structurally, CEP104 carries a C2HC zinc-finger array that mediates binding to the centriole-capping CP110/CEP97 module and is competed for by the kinase NEK1, and an SXIP motif that recruits EB proteins—though neither interaction is required for elongation activity (PMID:28017521, PMID:27402853, PMID:32820051). At the ciliary tip CEP104 forms part of a central-pair cap complex whose loss destabilizes tip microtubule organization (PMID:23970417, PMID:37756660), and it partners with the Joubert syndrome protein CSPP1 in an intra-ciliary complex that controls axoneme length and Hedgehog signaling competence, governing Smoothened ciliary entry and GPR161 export upon pathway activation (PMID:31412255, PMID:32820051). Its activity is regulated by MAK kinase, which directly phosphorylates CEP104 downstream of the LF1/LF2/LF3 length-control complex to permit axonemal assembly (PMID:41231942). Loss-of-function mutations in CEP104 cause Joubert syndrome, consistent with its requirement for converting the mother centriole into a ciliary basal body (PMID:26477546). Beyond cilia, CEP104 localizes to cytoplasmic microtubule ends and stabilizes them to support neural tube closure and apical constriction [PMID:bio_10.1101_2025.06.12.659327].

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2013 High

    Established CEP104 as a bona fide ciliary-tip protein required for normal ciliogenesis, answering where it acts and that its loss disrupts ciliary structure.

    Evidence Tip-enrichment proteomics, immunolocalization, and loss-of-function in Chlamydomonas and vertebrate cells

    PMID:23970417

    Open questions at the time
    • Molecular activity at the tip undefined
    • No structural basis for microtubule association
  2. 2015 Medium

    Linked CEP104 to human disease and placed it early in ciliogenesis, showing it regulates conversion of the mother centriole into the basal body.

    Evidence Exome sequencing of Joubert syndrome families plus RNAi in RPE1 cells with ciliogenesis readout

    PMID:26477546

    Open questions at the time
    • Mechanism of basal-body conversion not resolved
    • Pathway placement based on single-lab RPE1 experiments
  3. 2016 High

    Defined the molecular architecture of CEP104, identifying a tubulin-binding TOG domain, a C2HC zinc-finger array, and partner-binding interfaces for CP110/CEP97, EB proteins, and NEK1.

    Evidence X-ray crystallography of the TOG domain with biochemical and competitive binding assays (two independent structural studies)

    PMID:27402853 PMID:28017521

    Open questions at the time
    • Functional consequence of NEK1/CP110 competition not tested in cells
    • Whether TOG-tubulin binding confers polymerase activity not yet shown
  4. 2019 High

    Connected CEP104 to Hedgehog signaling by identifying an intra-ciliary CEP104-CSPP1 complex controlling axoneme length and Smoothened translocation.

    Evidence Co-immunoprecipitation, zebrafish silencing, and RPE1 knockdown with Smoothened localization readout

    PMID:31412255

    Open questions at the time
    • How the complex gates Smoothened entry mechanistically unclear
    • CSPP1 recruitment shown to be CEP104-independent, leaving recruitment hierarchy open
  5. 2020 High

    Assigned microtubule-polymerizing activity to the TOG domain as the essential determinant of cilium elongation and dissected which interactions are dispensable.

    Evidence In vitro microtubule polymerization assay with domain-deletion/point-mutant rescue and Smoothened/GPR161 ciliary localization assays

    PMID:32820051

    Open questions at the time
    • Role of zinc-finger/SXIP interactions in vivo beyond elongation unresolved
    • How phosphoregulation modulates polymerase activity not addressed here
  6. 2023 High

    Placed CEP104 structurally within the central-pair cap complex at ciliary tips and within the centriolar distal-tip complex, establishing a CEP97-anchored recruitment hierarchy.

    Evidence Cryo-electron tomography and proteomics in Tetrahymena nulls; proximity-labeling interactome and null-mutant analysis in Drosophila

    PMID:37729913 PMID:37756660

    Open questions at the time
    • Stoichiometry of CEP104 within the cap complex undefined
    • Conservation of DTC hierarchy in vertebrate cilia not directly tested
  7. 2025 High

    Identified MAK kinase as a direct upstream regulator phosphorylating CEP104 to control axonemal assembly, integrating it into a length-control signaling axis.

    Evidence In vitro kinase assay, genetic epistasis relative to the LF1/LF2/LF3 complex, and loss-of-function phenotyping in Chlamydomonas

    PMID:41231942

    Open questions at the time
    • Phosphosites on CEP104 and their functional consequence not mapped
    • Whether MAK regulation operates in vertebrates unknown
  8. 2025 Medium

    Extended CEP104 function beyond cilia, showing it stabilizes cytoplasmic microtubules to drive neural tube closure via apical constriction.

    Evidence Live imaging and knockdown phenotyping in Xenopus embryos (preprint)

    PMID:bio_10.1101_2025.06.12.659327

    Open questions at the time
    • Not yet peer reviewed
    • Molecular basis for cytoplasmic microtubule stabilization distinct from ciliary role unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How CEP104's TOG-driven polymerase activity, partner competition (NEK1/CP110), and phosphoregulation are coordinated to switch between ciliary and cytoplasmic microtubule functions remains unresolved.
  • No integrated model of spatial/temporal regulation across compartments
  • Mechanism linking phosphorylation to polymerase output not established

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008092 cytoskeletal protein binding 3 GO:0140096 catalytic activity, acting on a protein 1
Localization
GO:0005815 microtubule organizing center 2 GO:0005929 cilium 2 GO:0005856 cytoskeleton 1
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 3 R-HSA-162582 Signal Transduction 2 R-HSA-1266738 Developmental Biology 1
Partners
CEP97CP110CSPP1EB1MAKNEK1
Complex memberships
CEP104-CSPP1 intra-ciliary complexcentral pair cap complexcentriole distal tip complex (DTC)

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2013 CEP104 (Chlamydomonas FAP256) localizes to the tips of both central pair and outer doublet microtubules in cilia/flagella, and remains at the tip during flagellar assembly and disassembly. Loss-of-function (null mutant in Chlamydomonas, RNAi in vertebrate cells) causes ciliogenesis defects and structural deformities at ciliary tips. Quantitative comparative proteomics (tip-enrichment assay), immunolocalization, null mutant analysis in Chlamydomonas, RNAi knockdown in vertebrate cells Journal of cell science High 23970417
2016 CEP104 contains a tubulin-binding TOG (tumor overexpressed gene) domain and a novel C2HC zinc finger array. The kinase NEK1 binds the zinc finger array and competes with the distal centriole-capping protein CP110 for binding to CEP104. X-ray crystallography (structural determination of TOG domain), biochemical binding assays, competitive binding experiments Structure (London, England : 1993) High 28017521
2016 The TOG domain of CEP104 directly binds tubulin. CEP104 also interacts with CP110, CEP97, and EB (end-binding) proteins. Crystal structure of the TOG domain was solved. X-ray crystallography, biophysical characterization (sequence analysis, binding assays) The Journal of biological chemistry High 27402853
2019 CEP104 interacts with the Joubert syndrome-associated ciliary tip protein CSPP1 at microtubules to regulate axoneme length. An intra-ciliary CEP104-CSPP1 complex is required for Smoothened ciliary translocation in response to Hedgehog pathway stimulation. CEP104 is not required for ciliary recruitment of CSPP1. Co-immunoprecipitation, zebrafish cep104 silencing (in vivo phenotypic analysis of cilia length/laterality), hTERT-RPE1 cell knockdown with Hedgehog pathway readout (Smoothened localization) Cell reports High 31412255
2020 The TOG domain of CEP104 possesses microtubule-polymerizing activity that is essential for cilium elongation. The N-terminal jelly-roll (JR) fold partially contributes to cilium elongation. The zinc-finger region mediates CP110 binding and the SXIP motif mediates EB1 binding, but neither interaction is required for cilium elongation activity. CEP104 functions after CP110 removal from the mother centriole during ciliogenesis. CEP104 is required for ciliary entry of Smoothened and export of GPR161 upon Hedgehog activation, with the TOG domain playing a critical role. Knockdown/rescue experiments with domain deletion/point mutants, in vitro microtubule polymerization assay, immunofluorescence of CP110 removal, Smoothened and GPR161 ciliary localization assays The Journal of biological chemistry High 32820051
2023 By cryo-electron tomography and subtomogram averaging of Tetrahymena cilia lacking CEP104/FAP256, CEP104 was found to be part of a central pair cap complex at ciliary tips. Loss of CEP104/FAP256 destabilizes ciliary tip microtubule organization and affects the central pair cap complex composition. Cryo-electron tomography, subtomogram averaging, proteomics of CEP104/FAP256-null cells The Journal of cell biology High 37756660
2023 In Drosophila, Cep104 is a component of the distal tip complex (DTC) of centrioles. Cep104 promotes centriole elongation through its microtubule-binding TOG domain. Cep104 null flies show defects in spermatid alignment and individualization during spermiogenesis, and Cep104 cooperates with Cep97 in this process. Cep97 is the central scaffolding unit required to recruit DTC components (including Cep104) to the distal tip. Proximity-labeling screen in Drosophila cells, null mutant analysis, domain function analysis (TOG domain), DTC interactome mapping Current biology : CB High 37729913
2025 Chlamydomonas MAK kinase (CrMAK) directly phosphorylates FAP256/CEP104 to regulate axonemal microtubule assembly. CrMAK acts downstream of the LF1/LF2/LF3 ciliary length-regulatory complex. Loss of CrMAK or its kinase activity causes aciliation. Dephosphorylation of FAP256/CEP104 impairs ciliary assembly. In vitro kinase assay (phosphorylation of FAP256/CEP104 by CrMAK), genetic epistasis (CrMAK loss-of-function relative to LF complex), loss-of-function phenotypic analysis Proceedings of the National Academy of Sciences of the United States of America High 41231942
2025 In Xenopus, CEP104 localizes to the ends of cytoplasmic microtubules (not only ciliary tip) and influences their stability. Downregulation of CEP104 leads to cytoplasmic microtubule instability and defects in multiciliated cell intercalation. CEP104 is required for neural tube closure through regulation of apical constriction, a process that cannot be explained solely by its ciliary or Hedgehog signaling roles. Live imaging and localization studies in Xenopus embryos, CEP104 knockdown with phenotypic readouts (neural tube closure, apical constriction, microtubule stability, multiciliated cell intercalation) bioRxivpreprint Medium bio_10.1101_2025.06.12.659327
2015 CEP104 loss-of-function mutations (splice-site, nonsense, frameshift) cause Joubert syndrome. Knockdown of CEP104 in RPE1 cells results in severe ciliogenesis defects, and CEP104 acts early during cilia formation by regulating conversion of the mother centriole into the cilia basal body. Exome/targeted sequencing for variant identification, RNAi knockdown in RPE1 cells with ciliogenesis readout American journal of human genetics Medium 26477546

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2013 Centrosomal protein CEP104 (Chlamydomonas FAP256) moves to the ciliary tip during ciliary assembly. Journal of cell science 63 23970417
2015 Joubert Syndrome in French Canadians and Identification of Mutations in CEP104. American journal of human genetics 62 26477546
2019 A CEP104-CSPP1 Complex Is Required for Formation of Primary Cilia Competent in Hedgehog Signaling. Cell reports 41 31412255
2016 The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase. Structure (London, England : 1993) 32 28017521
2016 Biophysical and Structural Characterization of the Centriolar Protein Cep104 Interaction Network. The Journal of biological chemistry 31 27402853
2023 CEP104/FAP256 and associated cap complex maintain stability of the ciliary tip. The Journal of cell biology 18 37756660
2020 Roles of TOG and jelly-roll domains of centrosomal protein CEP104 in its functions in cilium elongation and Hedgehog signaling. The Journal of biological chemistry 13 32820051
2019 Whole exome sequencing reveals novel CEP104 mutations in a Chinese patient with Joubert syndrome. Molecular genetics & genomic medicine 10 31625690
2021 CEP104 and CEP290; Genes with Ciliary Functions Cause Intellectual Disability in Multiple Families. Archives of Iranian medicine 6 34196201
2023 Cep104 is a component of the centriole distal tip complex that regulates centriole growth and contributes to Drosophila spermiogenesis. Current biology : CB 5 37729913
2022 CEP104 gene may involve in the pathogenesis of a new developmental disorder other than joubert syndrome. Molecular biology reports 4 35359234
2025 Chlamydomonas protein kinase MAK phosphorylates FAP256/CEP104 and regulates axonemal microtubule assembly. Proceedings of the National Academy of Sciences of the United States of America 0 41231942

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