CILK1 (ciliogenesis associated kinase 1; formerly ICK, intestinal cell kinase, or MRK) is a serine/threonine protein kinase of the CMGC group. It is closely related to MAK and to C. elegans DYF-5 and Chlamydomonas LF4, and has a MAPK-like TDY activation motif. Full activation needs autophosphorylation of Tyr-159 followed by phosphorylation of Thr-157 by the CDK-activating kinase CCRK/CDK20. CILK1 travels into the cilium and concentrates at the ciliary tip, where it phosphorylates the kinesin-2 motor subunit KIF3A and regulates IFT turnaround and the speed of intraflagellar transport. Loss of CILK1 causes IFT-A, IFT-B and BBSome components to accumulate at ciliary tips, mislocalizes Hedgehog pathway components and changes cilium length; in many cell types cilia become elongated, while some neuronal progenitors show defective ciliogenesis. Overexpressed GFP-tagged CILK1 has been seen in the nucleus. A recessive CILK1 R272Q mutation, which impairs kinase activity and nuclear localization, causes the neonatal lethal ciliopathy endocrine-cerebro-osteodysplasia (ECO). Other variants cause cranioectodermal dysplasia, and heterozygous variants are associated with juvenile myoclonic epilepsy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IDA PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | KEEP AS NON CORE | Summary: Magnesium ion binding (IDA), from the original ICK cloning paper (abstract-only). Kinase assays require Mg2+ as the ATP cofactor. Reason: Generic cofactor requirement of protein kinases; correct but not informative. |
| GO:0004672 protein kinase activity | IDA PMID:19185282 A multiplex human syndrome implicates a key role for intesti... | ACCEPT | Summary: Protein kinase activity (IDA). In vitro kinase assays of ICK, impaired by the ECO-syndrome R272Q mutation. Reason: Experimentally supported; the more specific serine/threonine kinase term is also annotated. Supporting Evidence: PMID:19185282 Overall, the assay for 32 P incorporation suggests that the R272Q mutation significantly impairs kinase activity. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Protein kinase activity (IEA). Reason: Correct. |
| GO:0004674 protein serine/threonine kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Protein serine/threonine kinase activity (IBA). Reason: Core molecular function; CILK1 phosphorylates KIF3A. Supporting Evidence: PMID:24797473 ICK directly phosphorylated Kif3a, while inhibition of this Kif3a phosphorylation affected ciliary formation |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | ACCEPT | Summary: Protein serine/threonine kinase activity (IDA), original characterization. Reason: Core molecular function. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Protein serine/threonine kinase activity (IEA). Reason: Core molecular function. |
| GO:0005515 protein binding | IPI PMID:22939624 Quantitative analysis of HSP90-client interactions reveals p... | REMOVE | Summary: Protein binding with HSP90AB1 (P08238), quantitative HSP90 client analysis. CILK1 is an HSP90 kinase client. Reason: Generic protein binding; uninformative about CILK1 function (chaperone client relationship). |
| GO:0005515 protein binding | IPI PMID:27173435 An organelle-specific protein landscape identifies novel dis... | REMOVE | Summary: Protein binding with SMYD2 (Q9NRG4), ciliary organelle interactome. Reason: Generic protein binding; uninformative. |
| GO:0005515 protein binding | IPI PMID:32707033 Kinase Interaction Network Expands Functional and Disease Ro... | REMOVE | Summary: Protein binding with HSP90AB1 (P08238), kinase interaction network. Reason: Generic protein binding; uninformative. |
| GO:0005515 protein binding | IPI PMID:32707033 Kinase Interaction Network Expands Functional and Disease Ro... | REMOVE | Summary: Protein binding with FKBP5 (Q13451), kinase interaction network. Reason: Generic protein binding; uninformative (HSP90 co-chaperone). |
| GO:0005515 protein binding | IPI PMID:32707033 Kinase Interaction Network Expands Functional and Disease Ro... | REMOVE | Summary: Protein binding with SMYD2 (Q9NRG4), kinase interaction network. Reason: Generic protein binding; uninformative. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | REMOVE | Summary: Protein binding with FKBP5 (Q13451), BioPlex. Reason: Generic protein binding; uninformative. |
| GO:0005524 ATP binding | IDA PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | ACCEPT | Summary: ATP binding (IDA). Reason: Protein kinases bind ATP; correct. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP binding (IEA). Reason: Correct. |
| GO:0005634 nucleus | EXP PMID:12103360 The identification and subcellular localization of human MRK... | KEEP AS NON CORE | Summary: Nucleus (EXP). GFP-hMRK fusion localized to the nucleus in HeLa cells. Reason: Reported for overexpressed tagged protein; endogenous CILK1 function is ciliary. Nuclear localization may matter for activation by CCRK, but it is not the site of CILK1's established function. Supporting Evidence: PMID:12103360 The fluorescence microscopy results identified its nuclear localization. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Nucleus (IBA), inherited from a broad CMGC/MAPK-like kinase node. Reason: Consistent with overexpression data, but non-core. |
| GO:0005634 nucleus | IDA PMID:19185282 A multiplex human syndrome implicates a key role for intesti... | KEEP AS NON CORE | Summary: Nucleus (IDA). The R272Q mutant fails to localize to the nucleus. Reason: Supported experimentally (overexpression), non-core. Supporting Evidence: PMID:19185282 We also demonstrate that the R272Q mutant fails to localize at the nucleus and has diminished kinase activity. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Nucleus (IEA). Reason: As above. |
| GO:0005634 nucleus | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Nucleus (ISS from mouse). Reason: As above. |
| GO:0005737 cytoplasm | EXP PMID:15988018 Activation of a nuclear Cdc2-related kinase within a mitogen... | KEEP AS NON CORE | Summary: Cytoplasm (EXP), isoform 2 / tagged constructs. Reason: Correct but general. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Cytoplasm (IBA). Reason: Correct but general. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Cytoplasm (IEA). Reason: Correct but general. |
| GO:0005829 cytosol | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Cytosol (IEA). Reason: Correct but general. |
| GO:0005929 cilium | IBA GO_REF:0000033 | ACCEPT | Summary: Cilium (IBA). Reason: Core location; CILK1/DYF-5/LF4 orthologs act within cilia. |
| GO:0005929 cilium | IDA GO_REF:0000052 | ACCEPT | Summary: Cilium (IDA, immunofluorescence curation). Reason: Core location. |
| GO:0005929 cilium | IEA GO_REF:0000120 | ACCEPT | Summary: Cilium (IEA). Reason: Core location. |
| GO:0005929 cilium | ISS GO_REF:0000024 | ACCEPT | Summary: Cilium (ISS from mouse). Reason: Core location. |
| GO:0006468 protein phosphorylation | IDA PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | ACCEPT | Summary: Protein phosphorylation (IDA). Reason: Correct; CILK1 phosphorylates substrates such as KIF3A. |
| GO:0007165 signal transduction | TAS PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | KEEP AS NON CORE | Summary: Signal transduction (TAS), original characterization as a MAPK-like kinase. Reason: Very general; CILK1 is regulated by upstream kinases (CCRK) and influences Hedgehog signalling through cilia, but a signal-transduction role per se is not well defined. |
| GO:0035556 intracellular signal transduction | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Intracellular signal transduction (IBA), from a broad kinase family node. Reason: Generic kinase-family inference; not CILK1's defining role. |
| GO:0035556 intracellular signal transduction | IDA PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | KEEP AS NON CORE | Summary: Intracellular signal transduction (IDA), original characterization. Reason: As above. |
| GO:0035720 intraciliary anterograde transport | IEA GO_REF:0000107 | ACCEPT | Summary: Intraciliary anterograde transport (IEA from mouse). CILK1 regulates IFT at the ciliary tip; loss accumulates IFT components at tips and overexpression accumulates IFT-B at tips. Reason: CILK1 acts within the IFT system by phosphorylating the anterograde motor subunit KIF3A; its role is regulatory rather than as transport machinery, but the annotation is consistent with the ortholog evidence. Supporting Evidence: PMID:24797473 In contrast, overexpression of ICK induced the strong accumulation of IFT-B, but not IFT-A or BBSome components at ciliary tips. |
| GO:0035720 intraciliary anterograde transport | ISS GO_REF:0000024 | ACCEPT | Summary: Intraciliary anterograde transport (ISS from mouse). Reason: As above. |
| GO:0035721 intraciliary retrograde transport | IEA GO_REF:0000107 | ACCEPT | Summary: Intraciliary retrograde transport (IEA from mouse). Loss of ICK causes accumulation of IFT-A, IFT-B and BBSome at ciliary tips, indicating defective turnaround/retrograde return. Reason: Supported by mouse data on IFT turnaround. Supporting Evidence: PMID:24797473 Loss of ICK caused the accumulation of IFT-A, IFT-B, and BBSome components at the ciliary tips. |
| GO:0035721 intraciliary retrograde transport | ISS GO_REF:0000024 | ACCEPT | Summary: Intraciliary retrograde transport (ISS from mouse). Reason: As above. |
| GO:0036064 ciliary basal body | IEA GO_REF:0000107 | ACCEPT | Summary: Ciliary basal body (IEA from mouse). Reason: Wild-type ICK is enriched in the proximal cilium near basal bodies. Supporting Evidence: PMID:24853502 Wild-type ICK proteins were generally localized in the proximal region of cilia near the basal bodies, whereas kinase-dead ICK mutant proteins accumulated in the distal part of bulged ciliary tips. |
| GO:0036064 ciliary basal body | ISS GO_REF:0000024 | ACCEPT | Summary: Ciliary basal body (ISS from mouse). Reason: As above. |
| GO:0042073 intraciliary transport | IBA GO_REF:0000033 | ACCEPT | Summary: Intraciliary transport (IBA). The DYF-5/LF4/ICK kinase subfamily regulates IFT in algae, worms and mammals. Reason: Phylogenetically sound; CILK1 acts within the IFT system. Supporting Evidence: PMID:24797473 Here, we identified ICK localization at the tip of cilia as a regulator of ciliary transport. |
| GO:0042073 intraciliary transport | IEA GO_REF:0000107 | ACCEPT | Summary: Intraciliary transport (IEA from mouse). Reason: As above. |
| GO:0042073 intraciliary transport | ISS GO_REF:0000024 | ACCEPT | Summary: Intraciliary transport (ISS from mouse). Reason: As above. |
| GO:0060271 cilium assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Cilium assembly (IBA). Reason: Conserved requirement for proper ciliogenesis and length control. |
| GO:0060271 cilium assembly | IEA GO_REF:0000107 | ACCEPT | Summary: Cilium assembly (IEA from mouse). Reason: As above. |
| GO:0060271 cilium assembly | IMP PMID:24797473 ICK is essential for cell type-specific ciliogenesis and the... | ACCEPT | Summary: Cilium assembly (IMP). ICK is essential for proper ciliogenesis in developing tissues. Reason: Experimentally supported. Supporting Evidence: PMID:24797473 Our results suggest that ICK is a Kif3a kinase and essential for proper ciliogenesis in development by regulating ciliary transport at the tip of cilia. |
| GO:0097542 ciliary tip | IDA GO_REF:0000052 | ACCEPT | Summary: Ciliary tip (IDA, immunofluorescence curation). Reason: Core location. |
| GO:0097542 ciliary tip | IEA GO_REF:0000107 | ACCEPT | Summary: Ciliary tip (IEA from mouse). Reason: Core location. |
| GO:0097542 ciliary tip | IMP PMID:24797473 ICK is essential for cell type-specific ciliogenesis and the... | ACCEPT | Summary: Ciliary tip (IMP). Reason: ICK localizes at the tip of cilia. Supporting Evidence: PMID:24797473 Here, we identified ICK localization at the tip of cilia as a regulator of ciliary transport. |
| GO:0097546 ciliary base | IEA GO_REF:0000107 | ACCEPT | Summary: Ciliary base (IEA from mouse). Reason: Wild-type ICK enriched in the proximal cilium near basal bodies. |
| GO:0097546 ciliary base | ISS GO_REF:0000024 | ACCEPT | Summary: Ciliary base (ISS from mouse). Reason: As above. |
| GO:0106310 protein serine kinase activity | EXP PMID:10699974 Intestinal cell kinase (ICK) localizes to the crypt region a... | ACCEPT | Summary: Protein serine kinase activity (EXP). Reason: Correct; complements the Ser/Thr kinase term. |
| GO:0106310 protein serine kinase activity | EXP PMID:19185282 A multiplex human syndrome implicates a key role for intesti... | ACCEPT | Summary: Protein serine kinase activity (EXP), ECO syndrome study. Reason: Correct. Supporting Evidence: PMID:19185282 Overall, the assay for 32 P incorporation suggests that the R272Q mutation significantly impairs kinase activity. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Protein serine kinase activity (IEA, Rhea). Reason: Correct. |
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Download this section (compressed HTML)Q: Should CILK1's IFT role be captured with regulation terms (e.g. regulation of intraciliary anterograde/retrograde transport, GO:1905796/GO:1905799) rather than direct participation in intraciliary transport, given that it is a kinase acting on the motor rather than part of the transport machinery?
Q: Why does CILK1 loss elongate cilia in fibroblasts but impair ciliogenesis in some neuronal progenitors, and is a negative regulation of cilium assembly annotation warranted?
Q: Is nuclear localization of endogenous CILK1 physiologically relevant (e.g. for activation by CCRK), or an artefact of overexpression?
Experiment: Phospho-proteomics of cilia from CILK1-knockout versus kinase-dead knock-in human cells to identify substrates beyond KIF3A (e.g. IFT-B subunits) and map the sites.
Experiment: Live imaging of IFT train turnaround at the ciliary tip in CILK1-null and KIF3A phospho-site mutant cells to test whether KIF3A phosphorylation alone accounts for CILK1's effect on IFT.
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