MKS-3 is the C. elegans ortholog of human TMEM67/meckelin, a transmembrane protein that localizes to the ciliary transition zone. It functions as a component of the MKS module (together with MKS-1, MKSR-1, MKSR-2, MKS-5, and MKS-6), which cooperates with the NPHP module to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis. MKS-3 is required for non-motile cilium assembly through genetic interactions with the NPHP module, and participates in restricting non-ciliary membrane proteins from entering the ciliary compartment, thereby establishing the transition zone as a selective barrier (ciliary gate).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0035869 ciliary transition zone | IBA GO_REF:0000033 | ACCEPT | Summary: MKS-3 localization to the ciliary transition zone is strongly supported by fluorescence microscopy studies in C. elegans. Williams et al. (2011) demonstrated that MKS-3/meckelin localizes specifically to the TZ region adjacent to where IFT proteins concentrate at the transition fibers/basal body. Reason: This is a core annotation for MKS-3. The IBA annotation is consistent with phylogenetic evidence from the MECKELIN family (PTHR21274) and is directly supported by experimental evidence in C. elegans (PMID:21422230). Supporting Evidence: PMID:21422230 Using fluorescently tagged proteins, we detect MKS/MKSR/NPHP proteins in a region corresponding to the TZ (adjacent to where IFT proteins concentrate at the TFs/BB). This is evident for MKS-1, MKS-1 related-1 (MKSR-1)/B9D1, MKS-1 related-2 (MKSR-2)/B9D2, MKS-3/meckelin, NPHP-1, and NPHP-4 file:worm/mks-3/mks-3-deep-research-falcon.md model: Edison Scientific Literature |
| GO:0060271 cilium assembly | IBA GO_REF:0000033 | ACCEPT | Summary: MKS-3 is involved in cilium assembly through functional interactions with the NPHP module. While mks-3 single mutants show relatively mild phenotypes, mks-3;nphp-4 double mutants exhibit severe ciliary defects including dye-filling defects, missing/shorter cilia, and TZ/BB membrane detachment. Reason: This annotation accurately captures MKS-3 involvement in ciliogenesis. The IBA annotation from phylogenetic inference is well-supported by experimental evidence in C. elegans showing MKS-3 participates in establishing BB/TZ membrane associations during early ciliogenesis (PMID:21422230). Supporting Evidence: PMID:21422230 MKS/MKSR/NPHP proteins establish basal body/TZ membrane attachments before or coinciding with intraflagellar transport-dependent axoneme extension PMID:21422230 Functional interactions between different MKS module components and the NPHP module are essential for an IFT-independent early stage of ciliogenesis, namely docking/anchoring of the BB/TZ to the membrane. |
| GO:0036038 MKS complex | IEA GO_REF:0000002 | ACCEPT | Summary: MKS-3 is a component of the MKS complex (MKS module), which consists of MKS-1, MKSR-1, MKSR-2, MKS-3, MKS-5, and MKS-6 in C. elegans. The complex localizes to the ciliary transition zone and functions in organizing Y-shaped links and establishing the ciliary gate. Reason: This IEA annotation from InterPro is well-supported. MKS-3 contains the Meckelin domain (IPR019170/Pfam:PF09773) which is a defining feature of this protein family. Experimental evidence confirms MKS-3 functions within the MKS module and genetically interacts with other module components. Supporting Evidence: PMID:21422230 We find that MKS-5/RPGRIP1L interacts with two distinct TZ functional modules, MKS/MKSR and NPHP, consisting of MKS-1/MKSR-1/MKSR-2/MKS-3/MKS-6 and NPHP-1/NPHP-4 proteins, respectively. PMID:21422230 These data suggest that mks-6 genetically interacts with the NPHP module and is associated with the MKS/MKSR module. |
| GO:0060271 cilium assembly | IEA GO_REF:0000002 | ACCEPT | Summary: Duplicate annotation to cilium assembly from InterPro mapping. This IEA annotation is consistent with the IBA annotation and experimental evidence. Reason: While this duplicates the IBA annotation for cilium assembly, it is appropriate to retain both as they derive from independent evidence sources (InterPro domain mapping vs. phylogenetic inference). Both correctly capture the role of MKS-3 in ciliogenesis. Supporting Evidence: PMID:21422230 MKS/MKSR/NPHP proteins establish basal body/TZ membrane attachments before or coinciding with intraflagellar transport-dependent axoneme extension |
| GO:1905515 non-motile cilium assembly | IGI PMID:21422230 MKS and NPHP modules cooperate to establish basal body/trans... | ACCEPT | Summary: This annotation captures that MKS-3 is required specifically for assembly of non-motile (primary/sensory) cilia. In C. elegans, the ciliated sensory neurons possess non-motile cilia. Williams et al. demonstrated that mks-3;nphp-4 double mutants have severe ciliogenesis defects in these sensory neurons. Reason: This is a more specific annotation than GO:0060271 (cilium assembly) and accurately reflects that C. elegans sensory neuron cilia are non-motile. The IGI evidence code is appropriate as the phenotype is observed in genetic interaction with nphp-4 (WB:WBGene00011261). This represents a core function of MKS-3. Supporting Evidence: PMID:21422230 Primary cilia protrude from most mammalian cells and modulate sensory processes, including chemo-, mechano-, and photo-reception PMID:21422230 We uncovered in double mutants multiple phenotypes, including missing or shorter cilia |
| GO:0035869 ciliary transition zone | IDA PMID:21422230 MKS and NPHP modules cooperate to establish basal body/trans... | ACCEPT | Summary: This IDA annotation documents the direct experimental demonstration of MKS-3 localization to the ciliary transition zone using fluorescence microscopy of tagged MKS-3 protein. Reason: This is a well-supported core annotation. The IDA evidence is appropriate as MKS-3 TZ localization was directly observed using MKS-3::GFP fusion protein imaging. This annotation complements the IBA annotation from phylogenetic inference. Supporting Evidence: PMID:21422230 Using fluorescently tagged proteins, we detect MKS/MKSR/NPHP proteins in a region corresponding to the TZ (adjacent to where IFT proteins concentrate at the TFs/BB). This is evident for MKS-1, MKS-1 related-1 (MKSR-1)/B9D1, MKS-1 related-2 (MKSR-2)/B9D2, MKS-3/meckelin, NPHP-1, and NPHP-4 |
| GO:1905349 ciliary transition zone assembly | IGI PMID:21422230 MKS and NPHP modules cooperate to establish basal body/trans... | NEW | Summary: MKS-3, as part of the MKS module, is required for proper assembly and organization of the ciliary transition zone. When MKS module components are disrupted together with NPHP-4, severe TZ defects are observed including missing Y-links and disrupted TZ structure. Reason: This annotation captures the role of MKS-3 in transition zone organization, which is distinct from but related to its localization there. The TEM studies show that mks-3;nphp-4 double mutants have disrupted TZ regions with missing Y-links. Supporting Evidence: PMID:21422230 mks-6;nphp-4 and mks-5;nphp-4 double mutants exhibit mispositioned and disrupted TZ regions, with clear disconnections between the BB/TZ region and membrane, accompanied by missing Y-links PMID:21422230 Phenotypes nearly identical to mks-6;nphp-4 mutants were observed in the mksr-1;nphp-4 strain |
| GO:1903565 negative regulation of protein localization to cilium | IMP PMID:21422230 MKS and NPHP modules cooperate to establish basal body/trans... | NEW | Summary: MKS-3, together with other TZ proteins, restricts inappropriate accumulation of non-ciliary membrane proteins within cilia. In mks/mksr mutants, proteins like RPI-2 and TRAM-1a that are normally excluded from cilia accumulate within the ciliary compartment, demonstrating the gating function. Reason: This is a critical annotation capturing the ciliary gate function of MKS-3. The paper directly demonstrates that TZ proteins including those in the MKS module establish a gate that modulates ciliary composition. When TZ proteins are disrupted, non-ciliary proteins inappropriately accumulate inside cilia. Supporting Evidence: PMID:21422230 the two modules restrict inappropriate accumulation of membrane-associated proteins inside cilia PMID:21422230 Together, our data showing abnormal accumulations of MKS-3, RPI-2, and TRAM-1a in TZ mutant cilia indicate that, in addition to their role in early ciliogenesis, most if not all TZ proteins normally function to maintain a boundary at the cilium base, establishing the TZ as a bona fide ciliary gate. |
| GO:0007635 chemosensory behavior | IMP PMID:21422230 MKS and NPHP modules cooperate to establish basal body/trans... | NEW | Summary: MKS-3 contributes to chemosensory behavior through its role in ciliary function. mks-3;nphp-4 double mutants show osmotic avoidance defects and impaired dye-filling, indicating compromised sensory cilium function. Reason: This annotation captures the physiological/behavioral consequence of MKS-3 function in sensory cilia. The osmotic avoidance assay tests chemosensory behavior that depends on functional sensory cilia. This should be marked as a secondary/non-core function. Supporting Evidence: PMID:21422230 both mks-5;nphp-4 and mks-6;nphp-4 double mutants exhibit strong dye-filling (Dyf) and osmotic avoidance (Osm) phenotypes |
| GO:0005198 structural molecule activity | IDA PMID:21422230 MKS and NPHP modules cooperate to establish basal body/trans... | NEW | Summary: MKS-3 contributes to the structural integrity of the MKS complex at the ciliary transition zone. The protein localizes to the TZ and functions together with other MKS module components to organize TZ architecture. Reason: This molecular function annotation captures MKS-3's role as a structural component of the MKS complex. Evidence shows MKS-3 is part of the TZ architecture and is required for proper organization of Y-links and membrane associations. This is more appropriate than generic protein binding as it describes the functional contribution. Supporting Evidence: PMID:21422230 We find that MKS-5/RPGRIP1L interacts with two distinct TZ functional modules, MKS/MKSR and NPHP, consisting of MKS-1/MKSR-1/MKSR-2/MKS-3/MKS-6 and NPHP-1/NPHP-4 proteins, respectively. |
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Download this section (compressed HTML)Q: What are the specific protein-protein interactions between MKS-3 and other MKS module components?
Q: Does MKS-3 directly interact with NPHP-1 or NPHP-4, or is the genetic interaction indirect?
Q: What is the molecular basis for MKS-3 localization to the transition zone?
Experiment: Co-immunoprecipitation of MKS-3 with other MKS module components to confirm physical interactions
Hypothesis: MKS-3 directly binds to other MKS module proteins at the transition zone
Experiment: Structure-function analysis of MKS-3 domains required for TZ localization
Hypothesis: Specific domains of MKS-3 are required for its localization and function at the TZ
Experiment: Super-resolution microscopy to define precise MKS-3 localization within the TZ
Hypothesis: MKS-3 localizes to a specific sub-compartment within the transition zone
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