NPHP-2 is the Caenorhabditis elegans ortholog of mammalian inversin (INVS/nephrocystin-2, NPHP2), an ankyrin-repeat protein that acts as a non-catalytic structural organizer within ciliated sensory neurons. Rather than localizing to the ciliary transition zone like the nephrocystins NPHP-1 and NPHP-4, NPHP-2 marks the ciliary inversin compartment (InvC), a proximal subregion of the doublet-based ciliary shaft immediately distal to the transition zone in amphid channel and phasmid cilia. There it is required for anchoring the proximal-cilium pool of signaling components, including the cyclic-nucleotide-gated channel subunit TAX-2, and for proper ciliary microtubule ultrastructural patterning, cilium placement and anchoring, and ciliogenesis. NPHP-2 functions redundantly within genetic modules (with nphp-1/nphp-4, and with the doublet-region genes arl-13, klp-11 and unc-119) and interacts genetically with Meckel-syndrome (MKS) transition-zone genes in a sensillum-dependent manner; these activities are modulated upstream of tubulin glutamylation and are antagonized by the HDAC-6 deacetylase. Its calcium-binding EF-hand domain is required for InvC targeting and function. NPHP-2 is not a component of the intraflagellar transport machinery and is dispensable for transition-zone protein localization and IFT.
Definition: The action of a protein that contributes to the structural organization and integrity of the ciliary inversin compartment (InvC), a proximal subdomain of the doublet-based ciliary shaft distal to the transition zone, for example by scaffolding the retention of proximal-ciliary signaling components without itself catalyzing a biochemical reaction.
Parent term: structural molecule activity
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
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GO:0003674
molecular_function
|
ND
GO_REF:0000015 |
ACCEPT |
Summary: Root molecular_function placeholder (ND = No biological Data). No specific molecular activity has been experimentally assigned to NPHP-2.
Reason: NPHP-2 is a non-catalytic ankyrin-repeat protein and no specific molecular function has been experimentally determined. Its role is that of a structural organizer/genetic modifier acting through protein-protein interactions and a calcium-binding EF-hand, but no discrete MF term is supported by direct evidence. The ND placeholder is appropriate; the MF darkness is captured in knowledge_gaps.
|
|
GO:0097543
ciliary inversin compartment
|
IDA
PMID:25335890 Ciliopathy proteins establish a bipartite signaling compartm... |
ACCEPT |
Summary: Direct experimental localization of NPHP-2 to the ciliary inversin compartment (InvC), the proximal/middle segment of the doublet-based ciliary shaft just distal to the transition zone. This is the core, defining localization of NPHP-2 and distinguishes it from the transition-zone nephrocystins NPHP-1/NPHP-4.
Reason: Core localization, supported by multiple independent C. elegans studies. The InvC is conserved and distinct from the doublet region, and NPHP-2 marks it specifically. This is the most informative cellular-component annotation for the gene.
Supporting Evidence:
PMID:25501555
We conclude that NPHP-2 marks a region of the cilium distinct from the doublet region, and propose that this region is analogous to the InvC of mammalian cilia.
PMID:22393243
the C. elegans inversin ortholog, NPHP-2, localizes to the middle segment of sensory cilia
|
|
GO:1904108
protein localization to ciliary inversin compartment
|
IMP
PMID:25335890 Ciliopathy proteins establish a bipartite signaling compartm... |
ACCEPT |
Summary: NPHP-2 is required to anchor/localize signaling components to the proximal ciliary (InvC) region; in AFD thermosensory neurons it anchors the cGMP-gated channel within the proximal cilium. This is a core biological process for NPHP-2 and is directly grounded in the source paper.
Reason: Well-supported experimental (IMP) annotation. The source reference explicitly shows NPHP-2 is required to anchor a cGMP-gated ion channel in the proximal ciliary region, which is exactly the InvC subdomain NPHP-2 defines. Represents the best-characterized functional role of the protein.
Supporting Evidence:
PMID:25335890
requires NPHP-2 (known as inversin in mammals) to anchor a cGMP-gated ion channel within the proximal ciliary region
|
Q: Does the NPHP-2 EF-hand bind calcium biochemically, and does calcium specify InvC localization, modulate NPHP-2 activity, or both?
Q: What are the direct binding partners of NPHP-2 in the ciliary inversin compartment, and do they include NEK8/ANKS6-type proteins?
Q: What upstream cue initially patterns the inversin compartment independently of the transition zone, doublet-region and IFT machinery?
Experiment: Proximity-labeling (TurboID) or immunoprecipitation of endogenously tagged NPHP-2 in ciliated sensory neurons to identify the InvC interactome.
Hypothesis: NPHP-2 scaffolds a defined set of proximal-ciliary proteins that retain signaling components (e.g. TAX-2/TAX-4) in the InvC.
Experiment: In vitro calcium-binding assays on the isolated EF-hand plus binding-dead point mutants assayed in vivo for InvC targeting and cGMP-gated channel anchoring.
Hypothesis: The EF-hand is a functional calcium sensor whose calcium binding is required for InvC targeting and/or NPHP-2 activity.
Experiment: Candidate and forward genetic screens for factors required to establish the InvC, using an InvC marker (NPHP-2 GFP territory) and channel-anchoring readouts.
Hypothesis: A dedicated patterning cue, distinct from TZ/doublet-region/IFT genes, defines the proximal InvC subdomain.
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: NPHP-2 has no assigned molecular function and no adequate GO molecular-function term to express one. It is a non-catalytic ankyrin-repeat protein whose role is to organize the ciliary inversin compartment and anchor proximal-ciliary signaling components, but GO has no structural-constituent-of-the-ciliary-inversin-compartment activity, so the gene reads as MF-dark despite a well-defined cellular and process-level role.
OPEN ONTOLOGYCURATION MF_DARK
What is known: It is firmly established that NPHP-2 = inversin localizes to and marks the InvC, is required for microtubule patterning, cilia anchoring/placement and ciliogenesis, and anchors the proximal-cilium cGMP-gated channel. What is missing is a molecular-function representation: the worm GOA record carries only a cellular-component and a biological-process term plus the ND molecular_function root.
Significance: This is the canonical structural/scaffold-subunit ontology gap shared across the ciliary inversin/nephrocystin gene set: a mechanistically well-understood organizer that cannot be annotated with an informative MF term, contributing to apparent molecular-function darkness.
What would resolve it: Develop/adopt a molecular-function term for a structural constituent of the ciliary inversin compartment (analogous to structural constituent of ribosome) and annotate NPHP-2 to it; see proposed_new_terms.
Provenance (the field's own admissions):
Proposed term (ontology gap):
Gap: How the ciliary inversin compartment is initially established and maintained, and which direct molecular partners recruit and retain NPHP-2 there, is unknown. NPHP-2 reaches and is restricted to the InvC independently of transition-zone, doublet-region and other InvC genes, so the factor(s) that pattern the compartment and the NPHP-2 interactome that executes its scaffolding function have not been identified.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Established: NPHP-2 marks the InvC and is required for microtubule patterning and cilia anchoring; its ciliary targeting/restriction does not require the tested TZ, doublet-region or InvC genes; the InvC is set up early in development. Not established: the upstream cue that patterns the InvC and the direct binding partners through which NPHP-2 organizes it.
Significance: Identifying the InvC-patterning cue and the NPHP-2 interactome would convert a marks-a-region, required-for-patterning description into a mechanism, and would explain how nephronophthisis (inversin) mutations disrupt proximal-ciliary signaling.
What would resolve it: Unbiased proximity-labeling/immunoprecipitation of tagged NPHP-2 in ciliated neurons, plus forward/candidate genetic screens for factors required for InvC establishment, with InvC-marker and channel-anchoring readouts.
Provenance (the field's own admissions):
Gap: Whether the NPHP-2 EF-hand actually binds calcium and, if so, whether the calcium signal specifies NPHP-2 localization, modulates its activity, or both, is undetermined. The EF-hand is only a predicted calcium-binding motif; it is required for InvC targeting and function, but the biochemical calcium binding and the origin of any calcium cue are unproven.
OPEN BIOLOGY MF_DARK
What is known: Established: deletion of the EF-hand abolishes NPHP-2 localization to amphid/phasmid cilia and impairs rescue, so the domain is functionally essential in those cells. Not established: direct Ca2+ binding by the domain, and the source/nature of the calcium signal it would sense.
Significance: If the EF-hand is a bona fide calcium sensor, NPHP-2 would gain a concrete molecular activity (calcium ion binding) linking ciliary calcium signaling to InvC organization; resolving this would also inform the conserved requirement for a calcium-binding domain in vertebrate inversin.
What would resolve it: In vitro calcium-binding assays on the isolated EF-hand, and separation-of-function EF-hand point mutants (binding-dead vs structural) tested for InvC targeting and channel anchoring in vivo.
Provenance (the field's own admissions):
Gap: The relationship between the ciliary NPHP-2/Y32G9A.6 and the canonical vertebrate-style Inversin complex is unresolved. In C. elegans the classical Inversin complex is built from MLT-4 (INVS), NEKL-2 (NEK8) and MLT-2 (ANKS6) and functions at epithelial junctions during molting rather than in cilia; whether ciliary NPHP-2 assembles an analogous NEK8/ANKS6-type module in the InvC, or acts independently, is not known.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Established: nphp-2/Y32G9A.6 is the ciliary inversin ortholog in the sensory-cilia literature, while the MLT-4/NEKL-2/MLT-2 complex acts at junctions in molting. Not established: whether the two systems share components or mechanism, and which worm protein is the true functional inversin ortholog in each context.
Significance: Clarifying the ortholog relationship determines how findings about the junctional Inversin complex (e.g. dimerization-dependent activation) transfer to ciliary NPHP-2 function and to human inversin/nephronophthisis biology.
What would resolve it: Systematic tagging/interaction mapping of NPHP-2, MLT-4, NEKL-2 and MLT-2 across ciliated and epithelial tissues, with cross-rescue and complex-composition assays.
Provenance (the field's own admissions):
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The gene nphp-2 (UniProt Q9BPN3; ORF Y32G9A.6/CELE_Y32G9A.6) encodes the Caenorhabditis elegans ortholog of mammalian Inversin (INVS/NPHP2), a protein causally linked to nephronophthisis type 2 (infantile nephronophthisis) in humans (OpenTargets Search: nephronophthisis-INVS, warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2). The assignment of Y32G9A.6 as the C. elegans inversin ortholog was confirmed through BLAST homology searches, the presence of an X-box promoter element (characteristic of ciliary genes regulated by the DAF-19 transcription factor), and conservation of key protein domains (warburtonpitt2015theciliopathygene pages 108-114, warburtonpitt2015theciliopathygene pages 104-108, warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4). Importantly, nphp-2 is distinct from mlt-4, another C. elegans ankyrin repeat-containing protein that was also identified in BLAST searches but lacks the X-box promoter and many inversin-specific domains (warburtonpitt2015theciliopathygene pages 108-114, warburtonpitt2015theciliopathygene pages 104-108).
NPHP-2 is an ankyrin repeat domain-containing protein with a multi-domain architecture that mirrors its mammalian counterpart. Its key domains include:
The protein is not an enzyme, transporter, or signaling receptor; rather, it functions as a structural/adapter protein and genetic modifier that coordinates ciliary compartment organization through proteinβprotein interactions mediated by its ankyrin repeats and calcium-sensing EF-hand domain.
The nphp-2 gene encodes two protein isoforms: NPHP-2L (full-length, longer isoform) and NPHP-2S (shorter isoform lacking a 22 amino acid region) (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2015theciliopathygene pages 108-114). Both are expressed in ciliated sensory neurons of C. elegans, including amphid and phasmid neurons (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4).
The subcellular localization of NPHP-2 is central to understanding its function:
This middle segment/InvC localization is distinct from most other ciliopathy-associated proteins (cystoproteins), which typically localize to the transition zone (warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4). The confinement of NPHP-2 to proximal ciliary subdomains is maintained by the transition zone barrier/ciliary zone of exclusion (CIZE), established by MKS-5/RPGRIP1L, which acts as a lipid gate restricting the diffusion of signaling proteins including NPHP-2 and GPCRs to distal ciliary domains (jensen2015formationofthe pages 1-2, jensen2015formationofthe pages 12-14).
NPHP-2 is not a component of the intraflagellar transport (IFT) machinery, and IFT velocities are not significantly affected by nphp-2 mutations (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2012ciliogenesisincaenorhabditis pages 7-8). Instead, NPHP-2 functions as a structural organizer of the ciliary middle segment and as a genetic nexus connecting multiple ciliopathy-related protein modules:
NPHP-2 is required for proper cilia formation, placement, and orientation. Loss of nphp-2 causes:
- Transition zone displacement and disorganization, with cilia dispersed over larger areas and anteriorly displaced phasmid cilia (warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4, warburtonpitt2015theciliopathygene pages 95-99).
- Dye-filling (Dyf) defects in phasmid neurons, indicating that cilia fail to properly contact the sensory pore (warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4, warburtonpitt2015theciliopathygene pages 95-99).
- Shortened phasmid dendrites (warburtonpitt2012ciliogenesisincaenorhabditis pages 8-9).
- In double mutants with nphp-4, severely compromised cilia with complete Dyf defects in both amphid and phasmid sensilla, demonstrating functional redundancy (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2015theciliopathygene pages 95-99).
NPHP-2 is required for proper microtubule ultrastructure within cilia. In nphp-2 mutants, amphid channel cilia exhibit lengthwise shifts with asynchronous microtubule doublet B-tubules and disorganized Y-links at the transition zone (warburtonpitt2014thenphp2and pages 2-3, warburtonpitt2014thenphp2and pages 4-5). In arl-13; nphp-2 double mutants, most amphid channel cilia are absent, and those present show only microtubule singlets with abnormal transition zone microtubules (warburtonpitt2014thenphp2and pages 4-5).
NPHP-2 regulates tubulin glutamylation, a critical post-translational modification. Notably, glutamylation is not required for ciliary targeting of InvC or doublet region components; rather, glutamylation is modulated by nphp-2, arl-13, and unc-119 (warburtonpitt2014thenphp2and pages 2-3, warburtonpitt2014thenphp2and pages 1-2).
NPHP-2 is required for the correct localization of ciliary signaling proteins, including the cyclic nucleotide-gated channel subunits TAX-2 and TAX-4 to the proximal cilium/InvC (warburtonpitt2015theciliopathygene pages 29-33). NPHP-2 also regulates the ciliary localization of sensory signaling molecules in a cell-type-dependent manner (blacque2014compartmentswithina pages 7-8).
NPHP-2 participates in multiple redundant genetic networks:
NPHP-2 is partially redundant with NPHP-1 and NPHP-4 for cilia formation and transition zone placement in both amphid and phasmid neurons (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2015theciliopathygene pages 104-108, warburtonpitt2015theciliopathygene pages 95-99). The nphp-2; nphp-4 double mutant displays dramatically exacerbated ciliary defects compared to either single mutant (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2015theciliopathygene pages 95-99). NPHP-2 physically interacts with NPHP-1 and NPHP-4, as well as with B9 domain proteins and MKS pathway components (warburtonpitt2015theciliopathygene pages 104-108, blacque2014compartmentswithina pages 7-8).
NPHP-2 genetically interacts with MKS pathway genes (mks-1, mks-3, mks-6, mksr-1, mksr-2) in a sensillum-specific manner to control cilia formation and placement (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2015theciliopathygene pages 104-108). The NPHP and MKS modules work redundantly to seal the ciliary compartment and establish transition zone barriers (cevik2013activetransportand pages 5-6).
NPHP-2 interacts with doublet region genes, forming two parallel redundant genetic modules: nphp-2 + klp-11 and arl-13 + unc-119, both of which are antagonized by HDAC-6 deacetylase and modulated by ARL-3 (warburtonpitt2014thenphp2and pages 2-3, warburtonpitt2014thenphp2and pages 1-2). These modules regulate cilia placement, ciliary microtubule ultrastructure, tubulin glutamylation, and the sizes of the NPHP-2/InvC and ARL-13/doublet region territories (warburtonpitt2014thenphp2and pages 2-3, warburtonpitt2014thenphp2and pages 1-2, warburtonpitt2014thenphp2and pages 4-5).
In mammals, inversin forms an Inversin complex (INV complex) with NEK8 and ANKS6 at the proximal ciliary shaft (beyrent2024dimerizationactivatesthe pages 1-2). In C. elegans, recent work by Beyrent et al. (2024) demonstrated that the C. elegans homologs MLT-4 (INVS), NEKL-2 (NEK8), and MLT-2 (ANKS6) form a tripartite Inversin complex that is activated by dimerization β dynamic switching between an inactive monomer and an active dimer gates complex output (beyrent2024dimerizationactivatesthe pages 1-2). However, NPHP-2/Y32G9A.6 is distinct from MLT-4; the initial BLAST analysis identified both as potential inversin homologs, but NPHP-2 was selected as the closer ortholog based on domain conservation and X-box promoter usage, while MLT-4 functions primarily in epidermal molting (warburtonpitt2015theciliopathygene pages 108-114, warburtonpitt2015theciliopathygene pages 104-108). The relationship between the NPHP-2 ciliary functions and the MLT-4/NEKL-2/MLT-2 Inversin complex remains an area of ongoing investigation.
Mammalian inversin has been proposed to act as a molecular switch between canonical Wnt/Ξ²-catenin and non-canonical Wnt/planar cell polarity (PCP) pathways by targeting cytoplasmic Dishevelled (Dvl) for degradation, thereby downregulating canonical Wnt signaling and promoting PCP signaling (veland2013inversinnephrocystin2isrequired pages 4-4, goggolidou2014wntandplanar pages 2-4, veland2013inversinnephrocystin2isrequired pages 1-2). Studies in invβ»/β» mouse embryonic fibroblasts showed elevated Ξ²-catenin signaling, upregulation of Wnt target genes, and defective ciliary localization of Dvl-3, leading to impaired cell polarity and migration (veland2013inversinnephrocystin2isrequired pages 4-4, veland2013inversinnephrocystin2isrequired pages 12-13). However, this model has been challenged by more recent in vivo studies showing no upregulation of canonical Wnt signaling and no nuclear Ξ²-catenin accumulation in invβ»/β» mice, leading to the conclusion that the role of inversin in Wnt signaling is now unclear (warburtonpitt2015theciliopathygene pages 40-44). Whether NPHP-2 plays a similar role in Wnt signaling in C. elegans has not been directly demonstrated; the C. elegans studies have focused primarily on ciliary structural and IFT-related functions rather than Wnt pathway regulation.
| Property | Summary |
|---|---|
| Gene name | nphp-2 (C. elegans); identified as the ciliary inversin/NPHP2 ortholog used in sensory-cilia studies, distinct from mlt-4 (warburtonpitt2015theciliopathygene pages 108-114, warburtonpitt2015theciliopathygene pages 104-108, warburtonpitt2012ciliogenesisincaenorhabditis pages 7-8) |
| ORF name | Y32G9A.6 / CELE_Y32G9A.6 (matches the UniProt target context and literature assignment) (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4) |
| Mammalian ortholog | Ortholog of mammalian INVS/NPHP2 (inversin) (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2012ciliogenesisincaenorhabditis pages 7-8) |
| Human disease association | Human INVS/NPHP2 is associated with nephronophthisis type 2 / infantile nephronophthisis (OpenTargets Search: nephronophthisis-INVS) |
| Protein isoforms | Two isoforms are described: NPHP-2L (full-length) and NPHP-2S (shorter isoform lacking a 22 aa region) (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2015theciliopathygene pages 108-114) |
| Domain structure | Conserved ankyrin repeat region, nuclear localization sequences (NLSs), destruction box (D-box), coil region, and predicted EF-hand Ca2+-binding domain; ankyrin repeats are a defining feature and EF-hand is functionally important in several cilia types (warburtonpitt2014thenphp2and pages 4-5, warburtonpitt2015theciliopathygene pages 108-114, warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2014thenphp2and pages 10-11) |
| Role of ankyrin repeats | Ankyrin-repeat region contributes to ciliary targeting, including evidence from AWB neurons (warburtonpitt2015theciliopathygene pages 29-33) |
| Role of EF-hand | EF-hand is required for robust ciliary localization and function in amphid channel and phasmid cilia; deletion causes faint/absent localization and poor rescue of mutant phenotypes, indicating Ca2+-dependent regulation (warburtonpitt2014thenphp2and pages 4-5, warburtonpitt2014thenphp2and pages 10-11) |
| Localization: NPHP-2L | Localizes mainly to the ciliary middle segment / Inversin compartment (InvC) of amphid and phasmid sensory cilia; this compartment is distinct from the transition zone (TZ) (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4, warburtonpitt2014thenphp2and pages 1-2) |
| Localization: NPHP-2S | Broader localization throughout the cell body, axon, dendrite, and cilium, while being excluded from the nucleus and transition zone (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2015theciliopathygene pages 108-114) |
| Expression pattern | Expressed in ciliated sensory neurons of C. elegans (including amphid and phasmid neurons) (warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4) |
| Primary biological function | Functions in ciliogenesis, cilia placement/orientation, transition zone placement, and organization of the proximal ciliary shaft/Inv compartment rather than as a core IFT factor (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4, warburtonpitt2012ciliogenesisincaenorhabditis pages 7-8, warburtonpitt2014thenphp2and pages 2-3) |
| Relationship to IFT | NPHP-2 is not required for gross IFT function; IFT velocities were not significantly altered in nphp-2 mutants, arguing its primary role is structural/organizational rather than IFT cargo transport (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2012ciliogenesisincaenorhabditis pages 7-8) |
| Key genetic interactions: NPHP module | Shows partially redundant interactions with nphp-1 and nphp-4 for cilia placement and ciliogenesis; nphp-2; nphp-4 double mutants are strongly synthetic (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3, warburtonpitt2015theciliopathygene pages 95-99) |
| Key genetic interactions: MKS/TZ module | Genetically interacts with mks-1, mks-3, mks-6, mksr-1, mksr-2 and other TZ-associated components in a sensillum-dependent manner (warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2, warburtonpitt2015theciliopathygene pages 104-108, warburtonpitt2015theciliopathygene pages 95-99) |
| Key genetic interactions: ARL-13/doublet-region module | Interacts with arl-13, klp-11, unc-119, with modules organized as nphp-2 + klp-11 and arl-13 + unc-119, antagonized by hdac-6; these modules regulate ciliary microtubule patterning and compartment size (warburtonpitt2014thenphp2and pages 2-3, warburtonpitt2014thenphp2and pages 1-2) |
| Ciliary signaling/protein localization roles | Required for localization of TAX-2 and partially for TAX-4 to the proximal cilium/InvC; also linked to compartmentalization of signaling proteins in cilia (warburtonpitt2015theciliopathygene pages 29-33, blacque2014compartmentswithina pages 7-8) |
| Mutant phenotypes | Dye-filling (Dyf) defects, transition zone/cilia displacement, mispositioned phasmid cilia, defective cilia orientation, and shorter phasmid dendrites; double mutants can show severe loss of cilia and major microtubule ultrastructural defects (warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4, warburtonpitt2012ciliogenesisincaenorhabditis pages 8-9, warburtonpitt2015theciliopathygene pages 95-99, warburtonpitt2014thenphp2and pages 4-5) |
| Microtubule/ultrastructure effects | Required for proper microtubule patterning, including alignment of doublet/singlet regions, Y-link organization, and regulation of tubulin glutamylation together with the ARL-13 module (warburtonpitt2014thenphp2and pages 2-3, warburtonpitt2014thenphp2and pages 1-2, warburtonpitt2014thenphp2and pages 4-5) |
| Subcompartment control | The MKS-5/RPGRIP1L-dependent transition zone/CIZE helps confine NPHP-2 and other signaling proteins to appropriate ciliary subdomains, supporting stable ciliary compartmentalization (jensen2015formationofthe pages 1-2, jensen2015formationofthe pages 12-14) |
Table: This table summarizes the verified identity, domains, localization, genetic interactions, and mutant phenotypes of the C. elegans ciliary protein NPHP-2/Y32G9A.6. It is useful as a compact reference for functional annotation and for distinguishing nphp-2 from other ankyrin-repeat proteins such as mlt-4.
NPHP-2 (Y32G9A.6) is the C. elegans ortholog of mammalian inversin/NPHP2, an ankyrin repeat and EF-hand domain-containing protein that functions as a ciliary structural organizer and genetic modifier rather than an enzyme or transporter. Its primary role is in the Inversin compartment (InvC) of sensory cilia, where it coordinates ciliogenesis, cilia placement and orientation, microtubule ultrastructural patterning, tubulin post-translational modifications, and ciliary protein compartmentalization. NPHP-2 acts as a physical and genetic nexus connecting the NPHP, MKS/transition zone, and doublet region protein modules. Its function requires calcium-sensing through its EF-hand domain and proteinβprotein interactions mediated by its ankyrin repeats. The protein serves as a valuable model for understanding ciliopathies, particularly nephronophthisis, and the molecular mechanisms underlying ciliary subcompartmentalization.
References
(OpenTargets Search: nephronophthisis-INVS): Open Targets Query (nephronophthisis-INVS, 14 results). Buniello, A. et al. (2025). Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research.
(warburtonpitt2012ciliogenesisincaenorhabditis pages 1-2): Simon R. F. Warburton-Pitt, Andrew R. Jauregui, Chunmei Li, Juan Wang, M. Leroux, and M. Barr. Ciliogenesis in caenorhabditis elegans requires genetic interactions between ciliary middle segment localized nphp-2 (inversin) and transition zone-associated proteins. Journal of Cell Science, 125:2592-2603, Jun 2012. URL: https://doi.org/10.1242/jcs.095539, doi:10.1242/jcs.095539. This article has 57 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2015theciliopathygene pages 108-114): Simon R. F. Warburton-Pitt. The ciliopathy gene nphp 2 functions in multiple gene networks and regulates ciliogenesis in c. elegans. ArXiv, Jan 2015. URL: https://doi.org/10.7282/t3v40wx3, doi:10.7282/t3v40wx3. This article has 0 citations.
(warburtonpitt2015theciliopathygene pages 104-108): Simon R. F. Warburton-Pitt. The ciliopathy gene nphp 2 functions in multiple gene networks and regulates ciliogenesis in c. elegans. ArXiv, Jan 2015. URL: https://doi.org/10.7282/t3v40wx3, doi:10.7282/t3v40wx3. This article has 0 citations.
(warburtonpitt2012ciliogenesisincaenorhabditis pages 3-4): Simon R. F. Warburton-Pitt, Andrew R. Jauregui, Chunmei Li, Juan Wang, M. Leroux, and M. Barr. Ciliogenesis in caenorhabditis elegans requires genetic interactions between ciliary middle segment localized nphp-2 (inversin) and transition zone-associated proteins. Journal of Cell Science, 125:2592-2603, Jun 2012. URL: https://doi.org/10.1242/jcs.095539, doi:10.1242/jcs.095539. This article has 57 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2015theciliopathygene pages 29-33): Simon R. F. Warburton-Pitt. The ciliopathy gene nphp 2 functions in multiple gene networks and regulates ciliogenesis in c. elegans. ArXiv, Jan 2015. URL: https://doi.org/10.7282/t3v40wx3, doi:10.7282/t3v40wx3. This article has 0 citations.
(warburtonpitt2014thenphp2and pages 4-5): Simon R. F. Warburton-Pitt, Malan Silva, Ken C. Q. Nguyen, David H. Hall, and Maureen M. Barr. The nphp-2 and arl-13 genetic modules interact to regulate ciliogenesis and ciliary microtubule patterning in c. elegans. PLoS Genetics, 10:e1004866, Dec 2014. URL: https://doi.org/10.1371/journal.pgen.1004866, doi:10.1371/journal.pgen.1004866. This article has 44 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2014thenphp2and pages 10-11): Simon R. F. Warburton-Pitt, Malan Silva, Ken C. Q. Nguyen, David H. Hall, and Maureen M. Barr. The nphp-2 and arl-13 genetic modules interact to regulate ciliogenesis and ciliary microtubule patterning in c. elegans. PLoS Genetics, 10:e1004866, Dec 2014. URL: https://doi.org/10.1371/journal.pgen.1004866, doi:10.1371/journal.pgen.1004866. This article has 44 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2012ciliogenesisincaenorhabditis pages 2-3): Simon R. F. Warburton-Pitt, Andrew R. Jauregui, Chunmei Li, Juan Wang, M. Leroux, and M. Barr. Ciliogenesis in caenorhabditis elegans requires genetic interactions between ciliary middle segment localized nphp-2 (inversin) and transition zone-associated proteins. Journal of Cell Science, 125:2592-2603, Jun 2012. URL: https://doi.org/10.1242/jcs.095539, doi:10.1242/jcs.095539. This article has 57 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2014thenphp2and pages 1-2): Simon R. F. Warburton-Pitt, Malan Silva, Ken C. Q. Nguyen, David H. Hall, and Maureen M. Barr. The nphp-2 and arl-13 genetic modules interact to regulate ciliogenesis and ciliary microtubule patterning in c. elegans. PLoS Genetics, 10:e1004866, Dec 2014. URL: https://doi.org/10.1371/journal.pgen.1004866, doi:10.1371/journal.pgen.1004866. This article has 44 citations and is from a domain leading peer-reviewed journal.
(jensen2015formationofthe pages 1-2): Victor L Jensen, Chunmei Li, Rachel V Bowie, Lara Clarke, Swetha Mohan, Oliver E Blacque, and Michel R Leroux. Formation of the transition zone by mks5/rpgrip1l establishes a ciliary zone of exclusion (cize) that compartmentalises ciliary signalling proteins and controls pip2 ciliary abundance. The EMBO Journal, 34:2537-2556, Oct 2015. URL: https://doi.org/10.15252/embj.201488044, doi:10.15252/embj.201488044. This article has 164 citations.
(jensen2015formationofthe pages 12-14): Victor L Jensen, Chunmei Li, Rachel V Bowie, Lara Clarke, Swetha Mohan, Oliver E Blacque, and Michel R Leroux. Formation of the transition zone by mks5/rpgrip1l establishes a ciliary zone of exclusion (cize) that compartmentalises ciliary signalling proteins and controls pip2 ciliary abundance. The EMBO Journal, 34:2537-2556, Oct 2015. URL: https://doi.org/10.15252/embj.201488044, doi:10.15252/embj.201488044. This article has 164 citations.
(warburtonpitt2012ciliogenesisincaenorhabditis pages 7-8): Simon R. F. Warburton-Pitt, Andrew R. Jauregui, Chunmei Li, Juan Wang, M. Leroux, and M. Barr. Ciliogenesis in caenorhabditis elegans requires genetic interactions between ciliary middle segment localized nphp-2 (inversin) and transition zone-associated proteins. Journal of Cell Science, 125:2592-2603, Jun 2012. URL: https://doi.org/10.1242/jcs.095539, doi:10.1242/jcs.095539. This article has 57 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2015theciliopathygene pages 95-99): Simon R. F. Warburton-Pitt. The ciliopathy gene nphp 2 functions in multiple gene networks and regulates ciliogenesis in c. elegans. ArXiv, Jan 2015. URL: https://doi.org/10.7282/t3v40wx3, doi:10.7282/t3v40wx3. This article has 0 citations.
(warburtonpitt2012ciliogenesisincaenorhabditis pages 8-9): Simon R. F. Warburton-Pitt, Andrew R. Jauregui, Chunmei Li, Juan Wang, M. Leroux, and M. Barr. Ciliogenesis in caenorhabditis elegans requires genetic interactions between ciliary middle segment localized nphp-2 (inversin) and transition zone-associated proteins. Journal of Cell Science, 125:2592-2603, Jun 2012. URL: https://doi.org/10.1242/jcs.095539, doi:10.1242/jcs.095539. This article has 57 citations and is from a domain leading peer-reviewed journal.
(warburtonpitt2014thenphp2and pages 2-3): Simon R. F. Warburton-Pitt, Malan Silva, Ken C. Q. Nguyen, David H. Hall, and Maureen M. Barr. The nphp-2 and arl-13 genetic modules interact to regulate ciliogenesis and ciliary microtubule patterning in c. elegans. PLoS Genetics, 10:e1004866, Dec 2014. URL: https://doi.org/10.1371/journal.pgen.1004866, doi:10.1371/journal.pgen.1004866. This article has 44 citations and is from a domain leading peer-reviewed journal.
(blacque2014compartmentswithina pages 7-8): Oliver E Blacque and Anna AWM Sanders. Compartments within a compartment. Organogenesis, 10:126-137, Jan 2014. URL: https://doi.org/10.4161/org.28830, doi:10.4161/org.28830. This article has 75 citations.
(cevik2013activetransportand pages 5-6): Sebiha Cevik, Anna A. W. M. Sanders, Erwin Van Wijk, Karsten Boldt, Lara Clarke, Jeroen van Reeuwijk, Yuji Hori, Nicola Horn, Lisette Hetterschijt, Anita Wdowicz, Andrea Mullins, Katarzyna Kida, Oktay I. Kaplan, Sylvia E. C. van Beersum, Ka Man Wu, Stef J. F. Letteboer, Dorus A. Mans, Toshiaki Katada, Kenji Kontani, Marius Ueffing, Ronald Roepman, Hannie Kremer, and Oliver E. Blacque. Active transport and diffusion barriers restrict joubert syndrome-associated arl13b/arl-13 to an inv-like ciliary membrane subdomain. PLoS Genetics, 9:e1003977, Dec 2013. URL: https://doi.org/10.1371/journal.pgen.1003977, doi:10.1371/journal.pgen.1003977. This article has 115 citations and is from a domain leading peer-reviewed journal.
(beyrent2024dimerizationactivatesthe pages 1-2): Erika Beyrent, Derek T. Wei, Gwendolyn M. Beacham, Sangwoo Park, Jian Zheng, Matthew J. Paszek, and Gunther Hollopeter. Dimerization activates the inversin complex in c. elegans. Molecular Biology of the Cell, Oct 2024. URL: https://doi.org/10.1091/mbc.e24-05-0218, doi:10.1091/mbc.e24-05-0218. This article has 5 citations and is from a domain leading peer-reviewed journal.
(veland2013inversinnephrocystin2isrequired pages 4-4): Iben R. Veland, Rodrick Montjean, Lorraine Eley, Lotte B. Pedersen, Albrecht Schwab, Judith Goodship, Karsten Kristiansen, Stine F. Pedersen, Sophie Saunier, and SΓΈren T. Christensen. Inversin/nephrocystin-2 is required for fibroblast polarity and directional cell migration. PLoS ONE, 8:e60193, Apr 2013. URL: https://doi.org/10.1371/journal.pone.0060193, doi:10.1371/journal.pone.0060193. This article has 86 citations and is from a peer-reviewed journal.
(goggolidou2014wntandplanar pages 2-4): Paraskevi Goggolidou. Wnt and planar cell polarity signaling in cystic renal disease. Organogenesis, 10:86-95, Oct 2014. URL: https://doi.org/10.4161/org.26766, doi:10.4161/org.26766. This article has 80 citations.
(veland2013inversinnephrocystin2isrequired pages 1-2): Iben R. Veland, Rodrick Montjean, Lorraine Eley, Lotte B. Pedersen, Albrecht Schwab, Judith Goodship, Karsten Kristiansen, Stine F. Pedersen, Sophie Saunier, and SΓΈren T. Christensen. Inversin/nephrocystin-2 is required for fibroblast polarity and directional cell migration. PLoS ONE, 8:e60193, Apr 2013. URL: https://doi.org/10.1371/journal.pone.0060193, doi:10.1371/journal.pone.0060193. This article has 86 citations and is from a peer-reviewed journal.
(veland2013inversinnephrocystin2isrequired pages 12-13): Iben R. Veland, Rodrick Montjean, Lorraine Eley, Lotte B. Pedersen, Albrecht Schwab, Judith Goodship, Karsten Kristiansen, Stine F. Pedersen, Sophie Saunier, and SΓΈren T. Christensen. Inversin/nephrocystin-2 is required for fibroblast polarity and directional cell migration. PLoS ONE, 8:e60193, Apr 2013. URL: https://doi.org/10.1371/journal.pone.0060193, doi:10.1371/journal.pone.0060193. This article has 86 citations and is from a peer-reviewed journal.
(warburtonpitt2015theciliopathygene pages 40-44): Simon R. F. Warburton-Pitt. The ciliopathy gene nphp 2 functions in multiple gene networks and regulates ciliogenesis in c. elegans. ArXiv, Jan 2015. URL: https://doi.org/10.7282/t3v40wx3, doi:10.7282/t3v40wx3. This article has 0 citations.
Gene: nphp-2 / Y32G9A.6 / WBGene00021304
UniProt: Q9BPN3 (TrEMBL, unreviewed, PE=4 Predicted), 812 aa, ANK-repeat protein.
Human ortholog: INVS (inversin / nephrocystin-2, NPHP2). Ciliary "inversin compartment" protein.
Project: CAEEL_CILIOPATHY (flagship). Reviewed as a transition-zone-adjacent / inversin-compartment protein.
From nphp-2-goa.tsv (all WB-assigned):
1. GO:0003674 molecular_function β ND, GO_REF:0000015 (root placeholder; no MF assigned).
2. GO:0097543 ciliary inversin compartment β IDA, PMID:25335890, located_in.
3. GO:1904108 protein localization to ciliary inversin compartment β IMP, PMID:25335890, involved_in.
Both experimental annotations trace to PMID:25335890 (Nguyen 2014, AFD thermosensory neuron paper).
AFD thermosensory neuron bipartite signaling compartment.
- PMID:25335890 β NPHP-2 anchors the cGMP-gated channel (TAX-2/TAX-4) in the
proximal cilium (the InvC region). This is the source of both GOA experimental annotations.
- PMID:25335890 β NPHP as base/TZ
ciliopathy proteins.
"Ciliogenesis in C. elegans requires genetic interactions between ciliary middle segment localized
NPHP-2 (inversin) and transition zone-associated proteins."
- PMID:22393243 β MIDDLE SEGMENT (InvC), NOT the transition zone. KEY distinction vs nphp-1/nphp-4.
- PMID:22393243.
- PMID:22393243.
- PMID:22393243 β NOT a TZ-assembly or IFT gene.
- PMID:22393243.
"The nphp-2 and arl-13 genetic modules interact to regulate ciliogenesis and ciliary microtubule
patterning in C. elegans." Most detailed nphp-2 paper.
- InvC conserved & distinct from doublet region:
PMID:25501555
PMID:25501555
- Two modules antagonized by hdac-6:
PMID:25501555
- Microtubule patterning + anchoring:
PMID:25501555
- Glutamylation is downstream:
PMID:25501555
- EF-hand required for InvC targeting & function:
PMID:25501555
PMID:25501555
- Ciliary targeting independent of TZ/DR/InvC genes:
PMID:25501555
- Marks a region distinct from the doublet region (= InvC):
PMID:25501555
- GAP statements (field's own admissions):
PMID:25501555
PMID:25501555
PMID:25501555
PMID:25501555
PMID:25501555
EF-hand mechanism unresolved:
PMID:25501555
Inversin complex activated by dimerization; but the worm complex is MLT-4/NEKL-2/MLT-2, functioning
at epithelial junctions in molting, NOT the ciliary NPHP-2/Y32G9A.6.
- PMID:39110529
- PMID:39110529
- PMID:39110529
Use only for the ortholog-assignment knowledge gap; do NOT attribute MLT-4 findings to nphp-2.
Genuine, corroborates all of the above. Adds: two isoforms (NPHP-2L middle-segment/InvC; NPHP-2S
broader, TZ/nucleus-excluded); ankyrin repeats support ciliary targeting (AWB); required for TAX-2
(and partly TAX-4) proximal-cilium localization; NPHP-2 not an enzyme/transporter β a structural
organizer/genetic modifier. Falcon file:-quotes are NOT validator-checked, so I anchor claims to
PMID quotes above wherever used.
KNOWN:
- NPHP-2 is the ciliary C. elegans inversin/INVS(NPHP2) ortholog; ANK-repeat protein, non-catalytic.
- Localizes to the ciliary inversin compartment (InvC) = middle/proximal doublet region of amphid &
phasmid sensory cilia, distal to the TZ (IDA, PMID:25335890; PMID:22393243; PMID:25501555).
- Required for microtubule ultrastructural patterning and cilia anchoring/placement; ciliogenesis
(redundant with nphp-1/nphp-4 and with arl-13/klp-11/unc-119 modules).
- Required to anchor/localize the cGMP-gated channel TAX-2(/TAX-4) in the proximal cilium
(PMID:25335890) β basis of GO:1904108 (protein localization to InvC, IMP).
- Regulates tubulin glutamylation (upstream), interacts genetically with MKS module and hdac-6.
- Its EF-hand (Ca-binding) domain is required for InvC targeting and function (PMID:25501555).
NOT KNOWN / uncertain:
- No direct molecular function assigned (ND at MF root is currently accurate); whether the EF-hand
actually binds Ca2+ biochemically (predicted, not shown) and whether Ca sensing specifies
localization vs modulates activity.
- How the InvC is initially established/patterned (field states this is unknown).
- Direct binding partners of NPHP-2 in the worm InvC; whether it scaffolds a NEK8/ANKS6-like
complex in cilia (the classical complex uses MLT-4 at junctions, PMID:39110529).
- Mechanism by which HDAC-6 antagonizes InvC/doublet-region gene function.
- Whether worm NPHP-2 has any Wnt/PCP role (mammalian inversin does; disputed; untested in worm).
id: Q9BPN3
gene_symbol: nphp-2
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:6239
label: Caenorhabditis elegans
description: NPHP-2 is the Caenorhabditis elegans ortholog of mammalian inversin (INVS/nephrocystin-2,
NPHP2), an ankyrin-repeat protein that acts as a non-catalytic structural organizer within ciliated
sensory neurons. Rather than localizing to the ciliary transition zone like the nephrocystins NPHP-1
and NPHP-4, NPHP-2 marks the ciliary inversin compartment (InvC), a proximal subregion of the doublet-based
ciliary shaft immediately distal to the transition zone in amphid channel and phasmid cilia. There it
is required for anchoring the proximal-cilium pool of signaling components, including the cyclic-nucleotide-gated
channel subunit TAX-2, and for proper ciliary microtubule ultrastructural patterning, cilium placement
and anchoring, and ciliogenesis. NPHP-2 functions redundantly within genetic modules (with nphp-1/nphp-4,
and with the doublet-region genes arl-13, klp-11 and unc-119) and interacts genetically with Meckel-syndrome
(MKS) transition-zone genes in a sensillum-dependent manner; these activities are modulated upstream
of tubulin glutamylation and are antagonized by the HDAC-6 deacetylase. Its calcium-binding EF-hand
domain is required for InvC targeting and function. NPHP-2 is not a component of the intraflagellar
transport machinery and is dispensable for transition-zone protein localization and IFT.
references:
- id: GO_REF:0000015
title: Use of the ND evidence code for Gene Ontology (GO) terms
findings: []
- id: PMID:25335890
title: Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans thermosensory
neuron.
findings:
- statement: NPHP-2 (mammalian inversin) anchors a cGMP-gated ion channel within the proximal ciliary
region of the AFD thermosensory neuron.
supporting_text: requires NPHP-2 (known as inversin in mammals) to anchor a cGMP-gated ion channel
within the proximal ciliary region
- statement: Nephronophthisis-associated proteins localize to the ciliary base of the AFD bipartite
compartment.
supporting_text: One compartment, a bona fide cilium, is delineated by proteins associated with Bardet-Biedl
syndrome (BBS), Meckel syndrome and nephronophthisis at its base
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified (Nguyen, Liou, Hall, Leroux 2014, J Cell Sci). Cached entry is abstract-only.
This is the WormBase source reference for both experimental GOA annotations (GO:0097543 IDA and
GO:1904108 IMP); the abstract explicitly states NPHP-2 anchors the cGMP-gated channel in the proximal
cilium, supporting the protein-localization-to-InvC annotation.
- id: PMID:22393243
title: Ciliogenesis in Caenorhabditis elegans requires genetic interactions between ciliary middle segment
localized NPHP-2 (inversin) and transition zone-associated proteins.
findings:
- statement: NPHP-2, the C. elegans inversin ortholog, localizes to the ciliary middle segment (inversin
compartment), not the transition zone.
supporting_text: the C. elegans inversin ortholog, NPHP-2, localizes to the middle segment of sensory
cilia
- statement: nphp-2 is partially redundant with nphp-1 and nphp-4 for cilia placement.
supporting_text: nphp-2 is partially redundant with nphp-1 and nphp-4
- statement: nphp-2 genetically interacts with MKS orthologs in a sensilla-dependent manner to control
cilia formation and placement.
supporting_text: nphp-2 also genetically interacts with MKS ciliopathy gene orthologs, including mks-1,
mks-3, mks-6, mksr-1 and mksr-2, in a sensilla-dependent manner to control cilia formation and placement
- statement: nphp-2 is not required for transition-zone protein localization or for IFT.
supporting_text: nphp-2 is not required for correct localization of the NPHP- and MKS-encoded ciliary
transition zone proteins or for intraflagellar transport (IFT)
- statement: NPHP-2 acts as a modifier of the NPHP and MKS pathways controlling cilia formation and
development.
supporting_text: nphp-2 plays an important role in C. elegans cilia by acting as a modifier of the
NPHP and MKS pathways to control cilia formation and development
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: 'PubMed-verified (Warburton-Pitt, Jauregui, Li, Wang, Leroux, Barr 2012, J Cell Sci).
Cached entry is abstract-only. Establishes the defining NPHP-2 features used in this review: middle-segment/InvC
(not TZ) localization, partial redundancy with nphp-1/nphp-4, sensillum-specific MKS genetic interactions,
and independence from TZ-protein localization and IFT.'
- id: PMID:25501555
title: The nphp-2 and arl-13 genetic modules interact to regulate ciliogenesis and ciliary microtubule
patterning in C. elegans.
findings:
- statement: The C. elegans inversin compartment is conserved and distinct from the doublet region.
supporting_text: We show that the InvC is conserved and distinct from the doublet region.
- statement: nphp-2 and doublet-region genes are redundantly required for ciliogenesis.
supporting_text: nphp-2 (the C. elegans Inversin homolog) and the doublet region genes arl-13, klp-11,
and unc-119 are redundantly required for ciliogenesis.
- statement: InvC and doublet-region genes form two modules antagonized by hdac-6.
supporting_text: InvC and doublet region genes can be sorted into two modules-nphp-2+klp-11 and arl-13+unc-119-which
are both antagonized by the hdac-6 deacetylase.
- statement: nphp-2 is required for ciliary microtubule patterning and cilia anchoring.
supporting_text: These defects indicate that nphp-2 is required both for microtubule patterning and
for cilia anchoring.
- statement: NPHP-2 requires its calcium-binding EF-hand domain for InvC targeting.
supporting_text: NPHP-2 does require its calcium binding EF hand domain for targeting to the InvC.
- statement: NPHP-2 marks a ciliary region distinct from the doublet region, analogous to the mammalian
InvC.
supporting_text: We conclude that NPHP-2 marks a region of the cilium distinct from the doublet region,
and propose that this region is analogous to the InvC of mammalian cilia.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified (Warburton-Pitt, Silva, Nguyen, Hall, Barr 2014, PLoS Genet); full text
cached. The most detailed nphp-2 study; provides the InvC-vs-doublet-region distinction, EF-hand
dependence, microtubule-patterning/anchoring role, and explicit field admissions of the open mechanistic
questions used in knowledge_gaps.
- id: PMID:39110529
title: Dimerization activates the Inversin complex in C. elegans.
findings:
- statement: In C. elegans the canonical Inversin complex uses MLT-4 (INVS ortholog) and acts at epithelial
junctions in molting, not in cilia.
supporting_text: the C. elegans homologues colocalize, albeit at epithelial junctions rather than
cilia
- statement: How the Inversin-complex components assemble into a functionally active state is not fundamentally
understood.
supporting_text: we lack fundamental knowledge about how the components might assemble into a functionally
active state
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified (Beyrent et al. 2024, Mol Biol Cell); full text cached. This paper is
about MLT-4/NEKL-2/MLT-2 (the junctional/molting Inversin complex), a DIFFERENT worm protein from
ciliary NPHP-2/Y32G9A.6. Cited only as background for the ortholog-assignment knowledge gap; its
MLT-4 findings are not attributed to nphp-2.
- id: file:worm/nphp-2/nphp-2-deep-research-falcon.md
title: Deep research report on nphp-2 (Edison Scientific Literature)
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Genuine falcon/Edison deep-research report (25 citations, ~25 min run). Corroborates
the primary literature (middle-segment/InvC localization, EF-hand dependence, genetic-modifier role,
non-IFT). Used only for orientation; all load-bearing claims are anchored to PMID-verified verbatim
quotes.
existing_annotations:
- term:
id: GO:0003674
label: molecular_function
evidence_type: ND
original_reference_id: GO_REF:0000015
qualifier: enables
review:
summary: Root molecular_function placeholder (ND = No biological Data). No specific molecular activity
has been experimentally assigned to NPHP-2.
action: ACCEPT
reason: NPHP-2 is a non-catalytic ankyrin-repeat protein and no specific molecular function has been
experimentally determined. Its role is that of a structural organizer/genetic modifier acting through
protein-protein interactions and a calcium-binding EF-hand, but no discrete MF term is supported
by direct evidence. The ND placeholder is appropriate; the MF darkness is captured in knowledge_gaps.
- term:
id: GO:0097543
label: ciliary inversin compartment
evidence_type: IDA
original_reference_id: PMID:25335890
qualifier: located_in
review:
summary: Direct experimental localization of NPHP-2 to the ciliary inversin compartment (InvC), the
proximal/middle segment of the doublet-based ciliary shaft just distal to the transition zone. This
is the core, defining localization of NPHP-2 and distinguishes it from the transition-zone nephrocystins
NPHP-1/NPHP-4.
action: ACCEPT
reason: Core localization, supported by multiple independent C. elegans studies. The InvC is conserved
and distinct from the doublet region, and NPHP-2 marks it specifically. This is the most informative
cellular-component annotation for the gene.
supported_by:
- reference_id: PMID:25501555
supporting_text: We conclude that NPHP-2 marks a region of the cilium distinct from the doublet
region, and propose that this region is analogous to the InvC of mammalian cilia.
- reference_id: PMID:22393243
supporting_text: the C. elegans inversin ortholog, NPHP-2, localizes to the middle segment of sensory
cilia
- term:
id: GO:1904108
label: protein localization to ciliary inversin compartment
evidence_type: IMP
original_reference_id: PMID:25335890
qualifier: involved_in
review:
summary: NPHP-2 is required to anchor/localize signaling components to the proximal ciliary (InvC)
region; in AFD thermosensory neurons it anchors the cGMP-gated channel within the proximal cilium.
This is a core biological process for NPHP-2 and is directly grounded in the source paper.
action: ACCEPT
reason: Well-supported experimental (IMP) annotation. The source reference explicitly shows NPHP-2
is required to anchor a cGMP-gated ion channel in the proximal ciliary region, which is exactly
the InvC subdomain NPHP-2 defines. Represents the best-characterized functional role of the protein.
supported_by:
- reference_id: PMID:25335890
supporting_text: requires NPHP-2 (known as inversin in mammals) to anchor a cGMP-gated ion channel
within the proximal ciliary region
core_functions:
- description: 'Structural organizer of the ciliary inversin compartment: NPHP-2 localizes to and marks
the InvC (proximal/middle doublet region of sensory cilia, distal to the transition zone) and is required
to anchor/localize proximal-ciliary signaling components there, including the cGMP-gated channel subunit
TAX-2.'
directly_involved_in:
- id: GO:1904108
label: protein localization to ciliary inversin compartment
locations:
- id: GO:0097543
label: ciliary inversin compartment
supported_by:
- reference_id: PMID:25335890
supporting_text: requires NPHP-2 (known as inversin in mammals) to anchor a cGMP-gated ion channel
within the proximal ciliary region
- reference_id: PMID:25501555
supporting_text: We conclude that NPHP-2 marks a region of the cilium distinct from the doublet region,
and propose that this region is analogous to the InvC of mammalian cilia.
- description: Contributes to sensory (non-motile) ciliogenesis, cilium placement/anchoring, and ciliary
microtubule ultrastructural patterning, acting redundantly with nphp-1/nphp-4 and with the doublet-region
module (arl-13, klp-11, unc-119) and as a sensillum-dependent modifier of the MKS transition-zone
pathway.
directly_involved_in:
- id: GO:1905515
label: non-motile cilium assembly
locations:
- id: GO:0097543
label: ciliary inversin compartment
supported_by:
- reference_id: PMID:25501555
supporting_text: These defects indicate that nphp-2 is required both for microtubule patterning and
for cilia anchoring.
- reference_id: PMID:22393243
supporting_text: nphp-2 plays an important role in C. elegans cilia by acting as a modifier of the
NPHP and MKS pathways to control cilia formation and development
proposed_new_terms:
- proposed_name: structural constituent of ciliary inversin compartment
proposed_definition: The action of a protein that contributes to the structural organization and integrity
of the ciliary inversin compartment (InvC), a proximal subdomain of the doublet-based ciliary shaft
distal to the transition zone, for example by scaffolding the retention of proximal-ciliary signaling
components without itself catalyzing a biochemical reaction.
proposed_parent:
id: GO:0005198
label: structural molecule activity
knowledge_gaps:
- gap_statement: NPHP-2 has no assigned molecular function and no adequate GO molecular-function term
to express one. It is a non-catalytic ankyrin-repeat protein whose role is to organize the ciliary
inversin compartment and anchor proximal-ciliary signaling components, but GO has no structural-constituent-of-the-ciliary-inversin-compartment
activity, so the gene reads as MF-dark despite a well-defined cellular and process-level role.
boundary: 'It is firmly established that NPHP-2 = inversin localizes to and marks the InvC, is required
for microtubule patterning, cilia anchoring/placement and ciliogenesis, and anchors the proximal-cilium
cGMP-gated channel. What is missing is a molecular-function representation: the worm GOA record carries
only a cellular-component and a biological-process term plus the ND molecular_function root.'
gap_kind:
- ONTOLOGY
- CURATION
dark_aspect: MF_DARK
status: OPEN
significance: 'This is the canonical structural/scaffold-subunit ontology gap shared across the ciliary
inversin/nephrocystin gene set: a mechanistically well-understood organizer that cannot be annotated
with an informative MF term, contributing to apparent molecular-function darkness.'
resolution: Develop/adopt a molecular-function term for a structural constituent of the ciliary inversin
compartment (analogous to structural constituent of ribosome) and annotate NPHP-2 to it; see proposed_new_terms.
provenance:
- reference_id: PMID:25501555
supporting_text: We conclude that NPHP-2 marks a region of the cilium distinct from the doublet region,
and propose that this region is analogous to the InvC of mammalian cilia.
proposed_terms:
- proposed_name: structural constituent of ciliary inversin compartment
proposed_definition: The action of a protein that contributes to the structural organization and integrity
of the ciliary inversin compartment (InvC), for example by scaffolding the retention of proximal-ciliary
signaling components without itself catalyzing a biochemical reaction.
proposed_parent:
id: GO:0005198
label: structural molecule activity
- gap_statement: How the ciliary inversin compartment is initially established and maintained, and which
direct molecular partners recruit and retain NPHP-2 there, is unknown. NPHP-2 reaches and is restricted
to the InvC independently of transition-zone, doublet-region and other InvC genes, so the factor(s)
that pattern the compartment and the NPHP-2 interactome that executes its scaffolding function have
not been identified.
boundary: 'Established: NPHP-2 marks the InvC and is required for microtubule patterning and cilia anchoring;
its ciliary targeting/restriction does not require the tested TZ, doublet-region or InvC genes; the
InvC is set up early in development. Not established: the upstream cue that patterns the InvC and
the direct binding partners through which NPHP-2 organizes it.'
gap_kind:
- BIOLOGY
dark_aspect: RESIDUAL_SUBGAP
status: OPEN
significance: Identifying the InvC-patterning cue and the NPHP-2 interactome would convert a marks-a-region,
required-for-patterning description into a mechanism, and would explain how nephronophthisis (inversin)
mutations disrupt proximal-ciliary signaling.
resolution: Unbiased proximity-labeling/immunoprecipitation of tagged NPHP-2 in ciliated neurons, plus
forward/candidate genetic screens for factors required for InvC establishment, with InvC-marker and
channel-anchoring readouts.
provenance:
- reference_id: PMID:25501555
supporting_text: The mechanisms that establish and maintain the InvC are unknown.
- reference_id: PMID:25501555
supporting_text: The next challenge is to determine what initially patterns the doublet region and
InvC, and to understand the function of these cilia regions.
- gap_statement: Whether the NPHP-2 EF-hand actually binds calcium and, if so, whether the calcium signal
specifies NPHP-2 localization, modulates its activity, or both, is undetermined. The EF-hand is only
a predicted calcium-binding motif; it is required for InvC targeting and function, but the biochemical
calcium binding and the origin of any calcium cue are unproven.
boundary: 'Established: deletion of the EF-hand abolishes NPHP-2 localization to amphid/phasmid cilia
and impairs rescue, so the domain is functionally essential in those cells. Not established: direct
Ca2+ binding by the domain, and the source/nature of the calcium signal it would sense.'
gap_kind:
- BIOLOGY
dark_aspect: MF_DARK
status: OPEN
significance: If the EF-hand is a bona fide calcium sensor, NPHP-2 would gain a concrete molecular activity
(calcium ion binding) linking ciliary calcium signaling to InvC organization; resolving this would
also inform the conserved requirement for a calcium-binding domain in vertebrate inversin.
resolution: In vitro calcium-binding assays on the isolated EF-hand, and separation-of-function EF-hand
point mutants (binding-dead vs structural) tested for InvC targeting and channel anchoring in vivo.
provenance:
- reference_id: PMID:25501555
supporting_text: the origin and nature of the calcium signal these domains detect is unknown
- reference_id: PMID:25501555
supporting_text: 'Two possibilities arise for the function of these domains: Ca2+ specifies the localization
of NPHP-2, modulates the activity of the protein, or both.'
- gap_statement: The relationship between the ciliary NPHP-2/Y32G9A.6 and the canonical vertebrate-style
Inversin complex is unresolved. In C. elegans the classical Inversin complex is built from MLT-4 (INVS),
NEKL-2 (NEK8) and MLT-2 (ANKS6) and functions at epithelial junctions during molting rather than in
cilia; whether ciliary NPHP-2 assembles an analogous NEK8/ANKS6-type module in the InvC, or acts independently,
is not known.
boundary: 'Established: nphp-2/Y32G9A.6 is the ciliary inversin ortholog in the sensory-cilia literature,
while the MLT-4/NEKL-2/MLT-2 complex acts at junctions in molting. Not established: whether the two
systems share components or mechanism, and which worm protein is the true functional inversin ortholog
in each context.'
gap_kind:
- BIOLOGY
dark_aspect: RESIDUAL_SUBGAP
status: OPEN
significance: Clarifying the ortholog relationship determines how findings about the junctional Inversin
complex (e.g. dimerization-dependent activation) transfer to ciliary NPHP-2 function and to human
inversin/nephronophthisis biology.
resolution: Systematic tagging/interaction mapping of NPHP-2, MLT-4, NEKL-2 and MLT-2 across ciliated
and epithelial tissues, with cross-rescue and complex-composition assays.
provenance:
- reference_id: PMID:39110529
supporting_text: the C. elegans homologues colocalize, albeit at epithelial junctions rather than
cilia
- reference_id: PMID:39110529
supporting_text: we lack fundamental knowledge about how the components might assemble into a functionally
active state
suggested_questions:
- question: Does the NPHP-2 EF-hand bind calcium biochemically, and does calcium specify InvC localization,
modulate NPHP-2 activity, or both?
- question: What are the direct binding partners of NPHP-2 in the ciliary inversin compartment, and do
they include NEK8/ANKS6-type proteins?
- question: What upstream cue initially patterns the inversin compartment independently of the transition
zone, doublet-region and IFT machinery?
suggested_experiments:
- description: Proximity-labeling (TurboID) or immunoprecipitation of endogenously tagged NPHP-2 in ciliated
sensory neurons to identify the InvC interactome.
hypothesis: NPHP-2 scaffolds a defined set of proximal-ciliary proteins that retain signaling components
(e.g. TAX-2/TAX-4) in the InvC.
- description: In vitro calcium-binding assays on the isolated EF-hand plus binding-dead point mutants
assayed in vivo for InvC targeting and cGMP-gated channel anchoring.
hypothesis: The EF-hand is a functional calcium sensor whose calcium binding is required for InvC targeting
and/or NPHP-2 activity.
- description: Candidate and forward genetic screens for factors required to establish the InvC, using
an InvC marker (NPHP-2 GFP territory) and channel-anchoring readouts.
hypothesis: A dedicated patterning cue, distinct from TZ/doublet-region/IFT genes, defines the proximal
InvC subdomain.
tags:
- caeel-ciliopathy