CFAP91 (cilia- and flagella-associated protein 91; also known as MAATS1 and AAT-1) is an axonemal protein of motile cilia and sperm flagella and the central subunit of the calmodulin- and spoke-associated complex (CSC) with CFAP61 and CFAP251. In the human respiratory axoneme it runs from the base of radial spoke 2 (RS2), contacts the nexin-dynein regulatory complex, and links the RS3 base subunits CFAP251 and CFAP61. The Chlamydomonas ortholog FAP91 binds the radial spoke base protein RSP3, and the CSC relays calcium/calmodulin-dependent regulatory signals from the radial spokes to the dynein arms. Loss of CFAP91 destabilizes the RS3 and RS2 bases and adjacent inner dynein arms in Tetrahymena, and in mouse sperm it is required for flagellar localization of the RS3 proteins CFAP251 and LRRC23, acting as a scaffold for RS3 assembly. Biallelic variants cause spermatogenic failure 51, with multiple morphological abnormalities of the sperm flagellum, radial spoke and central pair defects, and male infertility; Cfap91 knockout mice are infertile with defective sperm flagellum formation, whereas their airway and ependymal cilia elongate normally. Alternative promoters and splicing produce several isoforms; some short isoforms, first described as AMY-1 (MYCBP)-binding partners that associate with AKAP1 and PKA, localize to the cytoplasm or mitochondria when expressed in somatic cell lines.
Definition: A protein complex located at the bases of radial spokes 2 and 3 on the A tubule of axonemal outer doublet microtubules of motile cilia and flagella, composed of CFAP91 (FAP91/CaM-IP2), CFAP61 (FAP61/CaM-IP3) and CFAP251 (FAP251/CaM-IP4), that binds calmodulin and connects radial spokes 2 and 3 with the nexin-dynein regulatory complex.
Justification: The CSC is a defined three-subunit complex conserved from Chlamydomonas to human, but an OLS search of GO (2026-10-16; queries "calmodulin and spoke associated complex", "calmodulin- and spoke-associated complex", "CSC complex", "spoke-associated", "calmodulin complex") found no term for it; the nearest terms are the location terms GO:0120341 radial spoke base 2 and GO:0120342 radial spoke base 3. A complex term would let CFAP91, CFAP251 and CFAP61 carry in_complex. The same term is proposed in the CFAP61 and CFAP251 reviews. The parent given is protein-containing complex; the complex would also be part_of the axoneme.
Parent term: protein-containing complex
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001536 radial spoke stalk | ISS GO_REF:0000024 | MODIFY | Summary: Transferred from Chlamydomonas FAP91 (A8IH47) with a colocalizes_with qualifier. FAP91 binds the spoke-base protein RSP3, and CFAP91 is located at the bases of RS2 and RS3 rather than in a spoke stalk. Reason: The claim that CFAP91 sits with the radial spokes is sound, but the location is the spoke base. Chlamydomonas FAP91 binds RSP3 at the base of the spoke (PMID:17967944); Tetrahymena Cfap91 localizes at the base of RS2 and RS3 (PMID:36552811); in the human axoneme CFAP91 begins at the RS2 base and links the RS3 base subunits (PMID:37258679). GO:0120341 radial spoke base 2 and GO:0120342 radial spoke base 3 (both part_of a radial spoke, not of the stalk) state this directly; both are listed because CFAP91 spans the two bases. This is a lateral correction, not a refinement of the stalk term. Proposed replacements: radial spoke base 2 radial spoke base 3 Supporting Evidence: PMID:17967944 FAP91 directly interacts with radial spoke protein 3 (an AKAP), which is located at the base of the spoke PMID:36552811 Tetrahymena Cfap91 localizes at the base of radial spokes RS2 and RS3 and likely plays a role in the radial spoke(s) positioning and stability PMID:37258679 CFAP91, which begins at the base of RS2, interacts with the N-DRC |
| GO:0003341 cilium movement | ISS GO_REF:0000024 | ACCEPT | Summary: Transferred from Chlamydomonas FAP91. CSC loss impairs motility in Chlamydomonas, Tetrahymena CFAP91 knockouts beat in an uncoordinated manner at reduced frequency, and Trypanosoma TbCFAP91 knockdown impairs flagellar movement. Reason: Consistent evidence across three organisms that CFAP91 is part of the axonemal machinery that produces and regulates ciliary beating: the CSC mediates regulatory signals from the radial spokes to the dynein arms and anti-FAP91 antibodies alter dynein-driven sliding (PMID:17967944); Tetrahymena knockouts swim about a hundred times slower (PMID:36552811); TbCFAP91 knockdown impairs flagellar movement (PMID:32161152). This row covers motile cilia generally, beyond sperm. Supporting Evidence: PMID:17967944 In a microtubule sliding assay, the addition of antibodies generated against FAP91 to mutant axonemes with reduced dynein activity restores dynein activity to wild-type levels PMID:36552811 CFAP91-KO cells swam about a hundred times slower than wild-type cells PMID:32161152 Knockdown of TbCFAP91 using RNAi impaired flagellar movement led to CPC defects in Trypanosoma as observed in humans |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: Binary interaction with DPY30 (Q9C005) from the HuRI yeast two-hybrid reference map. Reason: Generic protein binding carries no functional information. The DPY30 interaction comes from a high-throughput screen and has no supporting functional context for CFAP91, so it does not support a more informative molecular function. Removal does not assert that the interaction is false. The functionally relevant partners of CFAP91 (CFAP251, CFAP61, LRRC23, RSP3) are captured instead by the radial-spoke-base location and radial spoke assembly terms. |
| GO:0005737 cytoplasm | EXP PMID:12223483 AAT-1, a novel testis-specific AMY-1-binding protein, forms ... | TOO GENERAL | Summary: AAT-1 (CFAP91) isoforms expressed in HeLa and mouse GC-1 cells were found in the cytoplasm, partly with mitochondria. Reason: True but uninformative: the endogenous protein is an axonemal component, and the accepted axoneme location (part_of cytoplasm in GO) already entails cytoplasm. The diffuse signal described here comes from isoforms expressed in transfected somatic cell lines (abstract only in cache), which does not establish a distinct physiological cytosolic pool. Supporting Evidence: PMID:12223483 AAT-1alpha was found to bind to and be colocalized in mitochondria with AMY-1 in human HeLa and mouse GC-1 cells |
| GO:0005737 cytoplasm | EXP PMID:15863901 Structure and characterization of AAT-1 isoforms. | TOO GENERAL | Summary: Long AAT-1 isoforms (AAT-1L, AAT-1M) were diffusely cytoplasmic when expressed in human cells. Reason: As for the other cytoplasm rows: correct but entailed by the accepted axoneme location, and the evidence is isoform expression in cultured cells (abstract only in cache). Supporting Evidence: PMID:15863901 While AAT-1L and AAT-1M were found to be localized diffusely in the cytoplasm, AAT-1S, like AAT-1alpha, was found to be localized in the mitochondria-like structure |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | TOO GENERAL | Summary: UniProt subcellular-location mapping to cytoplasm, derived from the AAT-1 papers. Reason: Entailed by the accepted axoneme location; adds no information beyond it. |
| GO:0005739 mitochondrion | EXP PMID:12223483 AAT-1, a novel testis-specific AMY-1-binding protein, forms ... | MARK AS OVER ANNOTATED | Summary: AAT-1alpha colocalized with AMY-1 in mitochondria in HeLa and GC-1 cells and formed a complex with AKAP1 (S-AKAP84/AKAP149) and PKA RII. Reason: The observation is real but narrow: one short isoform, expressed in somatic cell lines, colocalized with a mitochondrial partner (AKAP1 is an outer mitochondrial membrane AKAP). The annotation generalizes this to the gene product, whereas the endogenous protein in sperm and airway cilia is axonemal (PMID:37258679, PMID:40931011), and mitochondrial localization of endogenous CFAP91 in germ cells has not been shown. The claim therefore exceeds the evidence. Not removed, because the experiment itself (abstract only in cache) is not contradicted. ORGANELLES check (2026-10-25): the action holds. The isoform-specific pool is the deciding point, and the cached PMID:15863901 abstract states it explicitly. The displayed canonical sequence that GOA annotates is isoform 7 (AAT-1L in UniProt ALTERNATIVE PRODUCTS), and that abstract reports AAT-1L and AAT-1M as diffusely cytoplasmic; only the short AAT-1alpha and AAT-1S, which UniProt does not map to a named isoform, gave the mitochondrial pattern. With the endogenous protein axonemal, the organelle claim is not supported for the gene product (ASAH2 precedent of a non-representative construct). No sub-compartment row (rule 4); the only sub-mitochondrial hint is the AKAP1 partner, one indirect line. Supporting Evidence: PMID:12223483 AAT-1alpha was found to bind to and be colocalized in mitochondria with AMY-1 in human HeLa and mouse GC-1 cells PMID:15863901 While AAT-1L and AAT-1M were found to be localized diffusely in the cytoplasm, AAT-1S, like AAT-1alpha, was found to be localized in the mitochondria-like structure file:human/CFAP91/CFAP91-uniprot.txt Name=7; Synonyms=AAT-1L {ECO:0000303|PubMed:15863901}; |
| GO:0005739 mitochondrion | EXP PMID:15863901 Structure and characterization of AAT-1 isoforms. | MARK AS OVER ANNOTATED | Summary: The short isoform AAT-1S, like AAT-1alpha, localized to a mitochondria-like structure in transfected human cells. Reason: Same limitation as the PMID:12223483 row: isoform-specific overexpression in cultured cells, reported as a "mitochondria-like structure" (abstract only in cache), generalized to the gene product whose established location is the axoneme. ORGANELLES check (2026-10-25): the action holds. The same abstract reports the canonical isoform 7 (AAT-1L) and AAT-1M as diffusely cytoplasmic, so the mitochondrial pattern belongs to short isoforms only; see the PMID:12223483 row. Stays at the root (rule 4). Supporting Evidence: PMID:15863901 AAT-1S, like AAT-1alpha, was found to be localized in the mitochondria-like structure |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: UniProt subcellular-location mapping to mitochondrion, derived from the AAT-1 papers. Reason: Electronic restatement of the two EXP rows; same assessment. ORGANELLES check (2026-10-25): the SL-0173 keyword mapping is correct for the UniProt entry, but the entry's "Mitochondrion" statement rests only on the two AAT-1 papers, whose mitochondrial pattern is confined to short isoforms (canonical AAT-1L is cytoplasmic per PMID:15863901). Over-annotation, not a wrong mapping, so not REMOVE; actions on all three GO:0005739 rows agree. |
| GO:0005930 axoneme | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to axoneme. Reason: Correct. CFAP91 is resolved in the human respiratory axoneme (PMID:37258679), the Trypanosoma ortholog is axonemal (PMID:32161152), and Tetrahymena Cfap91 sits at the radial spoke bases (PMID:36552811). Supporting Evidence: PMID:37258679 CFAP91, which begins at the base of RS2, interacts with the N-DRC PMID:32161152 confirmed the axonemal localisation of the protein |
| GO:0005930 axoneme | ISS GO_REF:0000024 | ACCEPT | Summary: Transferred from Chlamydomonas FAP91; consistent with direct human and Tetrahymena data. Reason: Same claim as the IEA axoneme row, independently supported by the human axoneme structure (PMID:37258679). Supporting Evidence: PMID:37258679 a full-length RS3, which we show is built on a base of CFAP61, CFAP91 and CFAP251 |
| GO:0007283 spermatogenesis | IMP PMID:32161152 Biallelic variants in MAATS1 encoding CFAP91, a calmodulin-a... | MODIFY | Summary: Biallelic MAATS1 variants in six unrelated men cause MMAF with severe radial spoke and central pair defects (abstract only in cache). Reason: The phenotype reported is a defect of sperm flagellum formation, so spermatogenesis is correct but less specific than the evidence supports. GO:0120316 sperm flagellum assembly captures it and is a descendant of spermatogenesis, so this is a refinement, not a lateral move: an OLS hierarchicalAncestors query (2026-10-16) shows GO:0120316 part_of GO:0007286 spermatid development, which is part_of GO:0048515 spermatid differentiation, which is part_of GO:0007283 spermatogenesis (GO:0120316 is also is_a GO:0044458 motile cilium assembly and part_of GO:0030317 flagellated sperm motility). The replacement is independently supported by the Cfap91 knockout mouse, which has impaired sperm flagellum formation (PMID:40931011). CFAP91 contributes structure to the flagellum it is required to build (it scaffolds RS3 assembly), so it participates in this process. Proposed replacements: sperm flagellum assembly Supporting Evidence: PMID:32161152 TEM and immunostaining experiments in sperm cells showed severe central pair complex (CPC) and radial spokes defects PMID:40931011 Cfap91 knockout (KO) mice exhibit impaired sperm flagellum formation and male infertility |
| GO:0031514 motile cilium | ISS GO_REF:0000024 | ACCEPT | Summary: Transferred from Chlamydomonas FAP91. CFAP91 is present in human respiratory motile cilia and in sperm flagella. Reason: Correct and appropriately specific: CFAP91 is modelled in the human respiratory motile-cilium axoneme (PMID:37258679) and functions in mouse sperm flagella (PMID:40931011). Supporting Evidence: PMID:37258679 CFAP91, which begins at the base of RS2, interacts with the N-DRC |
| GO:1904158 axonemal central apparatus assembly | IMP PMID:32161152 Biallelic variants in MAATS1 encoding CFAP91, a calmodulin-a... | MARK AS OVER ANNOTATED | Summary: Patient sperm and Trypanosoma TbCFAP91 knockdown show central pair complex defects (abstract only in cache). Reason: The central pair defect is observed, but CFAP91 is not a central apparatus component: it is located on the outer doublets at the RS2/RS3 base (PMID:36552811, PMID:37258679), where it scaffolds radial spoke assembly (PMID:40931011). Loss of the central pair is a common downstream feature of disorganized MMAF axonemes, and the same paper reports radial spoke defects. The evidence establishes that CFAP91 is needed for a normal central apparatus, not that it does any of the work of assembling it, so the process claim exceeds the evidence. The direct process is captured by the proposed radial spoke assembly annotation. Supporting Evidence: PMID:32161152 Knockdown of TbCFAP91 using RNAi impaired flagellar movement led to CPC defects in Trypanosoma as observed in humans PMID:36552811 Tetrahymena Cfap91 localizes at the base of radial spokes RS2 and RS3 and likely plays a role in the radial spoke(s) positioning and stability |
| GO:0062177 radial spoke assembly | IMP PMID:40931011 Proximity labeling of axonemal protein CFAP91 identifies EFC... | NEW | Summary: Proposed process. CFAP91 scaffolds RS3 assembly in mouse sperm and is needed for stable docking of RS3 and the RS2 base in Tetrahymena. Reason: Participation: CFAP91 contributes structure that radial spoke assembly depends on. It physically links the RS3 base subunits CFAP251 and CFAP61 in the human axoneme (PMID:37258679); in Cfap91 knockout mouse sperm the RS3 proteins CFAP251 and LRRC23 fail to localize, and the authors conclude CFAP91 is an essential scaffolder of RS3 assembly (PMID:40931011); Tetrahymena knockouts lose stable RS3 and RS2-base docking (PMID:36552811); Chlamydomonas CSC knockdown impairs spoke assembly (PMID:21613541). Comparator check (QuickGO annotation search for GO:0062177, exact usage, taxa 9606 and 10090, 2026-10-16): LRRC23, an RS3 subunit in the same structural role and a CFAP91 co-immunoprecipitating partner, carries GO:0062177 by IMP and IBA in both human (Q53EV4) and mouse (O35125); the radial spoke proteins RSPH4A and RSPH9 also carry it, by IMP in mouse and by ISS/IEA transfer in human (no IBA). The term is not an ancestor or descendant of any other term carried or proposed for CFAP91. Supporting Evidence: PMID:40931011 Our findings establish CFAP91 as an essential scaffolder of RS3 assembly PMID:36552811 lack of Tetrahymena Cfap91 protein affects stable docking/positioning of the radial spoke RS3 and the base of RS2, and adjacent inner dynein arms PMID:21613541 the CSC is required for spoke assembly and wild-type motility |
| GO:0005200 structural constituent of cytoskeleton | IMP PMID:40931011 Proximity labeling of axonemal protein CFAP91 identifies EFC... | NEW | Summary: Proposed molecular function. CFAP91 is a non-catalytic, extended axonemal protein that links the RS2 base, N-DRC and RS3 base. Reason: CFAP91 has no informative molecular function annotation. Its established activity is structural, within the axoneme (a cytoskeletal structure): it runs from the RS2 base to the RS3 base subunits (PMID:37258679) and scaffolds RS3 (PMID:40931011). The term matches the CFAP61 review in this repository for the same complex. Comparable axonemal scaffolds currently carry no informative MF in GOA, so the choice is also raised as a question. Supporting Evidence: PMID:40931011 Our findings establish CFAP91 as an essential scaffolder of RS3 assembly PMID:37258679 CFAP91, which begins at the base of RS2, interacts with the N-DRC |
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Download this section (compressed HTML)Q: Do the short CFAP91 isoforms (AAT-1alpha, AAT-1S) that bind MYCBP/AMY-1 and AKAP1 have an endogenous, non-axonemal role (for example at mitochondria in spermatids or Leydig cells), or are these interactions overexpression artefacts?
Q: Is GO:0005200 structural constituent of cytoskeleton the right molecular function for non-catalytic axonemal scaffold subunits such as the CSC proteins, given that comparable proteins (LRRC23, CCDC39, CFAP61) currently carry no informative MF in GOA?
Q: Why is CFAP91 essential for sperm flagellum formation in mouse and human, while airway and ependymal cilia of Cfap91 knockout mice elongate normally? Is airway ciliary beating or RS3 occupancy affected?
Experiment: Use isoform-specific antibodies or endogenously tagged knock-in mice to localize the CFAP91 isoforms in spermatids, mature sperm and Leydig cells, combining immunofluorescence with mitochondrial markers and immuno-electron microscopy.
Hypothesis: Endogenous CFAP91 short isoforms are not mitochondrial in male germ cells.
Type: localization
Experiment: Cryo-electron tomography with subtomogram averaging of tracheal cilia from Cfap91 knockout mice, plus high-speed video analysis of ciliary beat frequency and waveform.
Hypothesis: CFAP91 loss removes RS3 and destabilizes the RS2 base in mammalian airway cilia, altering ciliary waveform despite normal ciliary length.
Type: structural biology / ciliary physiology
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