mksr-1 (K03E6.4 / WBGene00019364 / Q21191) — research notes

Identity

UniProt Q21191 (Q21191_CAEEL), Caenorhabditis elegans, 229 aa.
RecName: B9 domain-containing protein 1 (i.e. B9D1 ortholog) [UniProt Q21191, "RecName: Full=B9 domain-containing protein 1"].
Gene: mksr-1 ("MKS-1-related protein 1"); ORF K03E6.4; WormBase WBGene00019364; on Chromosome X.
Domain content: a single B9 (C2-B9-type) domain (InterPro IPR010796 "C2_B9-type_dom"; Pfam PF07162 "B9-C2"; PROSITE PS51381 C2_B9). PANTHER PTHR12968:SF1 "B9 DOMAIN-CONTAINING PROTEIN 1".
Belongs to the B9D family [UniProt Q21191, "Belongs to the B9D family."].
NOT an integral membrane protein: no signal peptide, no transmembrane keyword. This distinguishes it from mks-2 (TMEM216, multi-pass membrane). mksr-1 is a peripheral B9/C2-domain component of the MKS module. (UniProt keywords: Cell projection, Cilium biogenesis/degradation, Cytoplasm, Cytoskeleton.)
UniProt subcellular location: "Cytoplasm, cytoskeleton, cilium basal body" (ARBA electronic).
UniProt binary interaction: Q21191; Q9N423: mksr-2; NbExp=3; IntAct=EBI-330284, EBI-330279 — i.e. MKSR-1 binds MKSR-2 (B9D2, Q9N423).

Nomenclature caution

Older literature uses conflicting names for the three worm B9 proteins. Williams et al. 2008 (PMID:18337471) named them XBX-7 (MKS1), TZA-1 (B9D2), TZA-2 (B9D1). Bialas et al. 2009 (PMID:19208769) and Williams et al. 2011 (PMID:21422230) use the now-standard MKS-1, MKSR-1/B9D1, MKSR-2/B9D2. UniProt, WormBase and the CAEEL_CILIOPATHY project all use mksr-1 = B9D1, mksr-2 = B9D2. I use the standard naming; where a paper uses other names I note the correspondence.

What is KNOWN

Family, domain, evolution

The B9 domain occurs "exclusively within a family of three proteins distributed widely in ciliated organisms" [PMID:19208769 abstract, "this domain occurs exclusively within a family of three proteins distributed widely in ciliated organisms"].
Structure/fold predictions relate the B9 domain to a C2 domain (Ca2+/lipid-binding, synaptotagmin-like) [PMID:21422230, "B9 domains of MKS-1, MKSR-1, and MKSR-2 may be structurally related to C2 domains"; "This motif is predicted to bind Ca2+/lipids and participate—similar to synaptotagmin—in membrane/vesicle trafficking and fusion"]. This is a predicted biochemical property; no direct Ca2+/lipid-binding assay for MKSR-1 exists in these papers.

Localization (experimental)

All three C. elegans B9 proteins (MKS-1, MKSR-1, MKSR-2) "localize to transition zones/basal bodies of sensory cilia" [PMID:19208769 abstract].
Direct imaging: MKSR-1/B9D1 localizes to the ciliary transition zone in C. elegans sensory neurons [PMID:21422230, "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"; GFP-MKSR-1 imaged at TZ, Fig 1–2, Fig 8G]. This is the basis of the WormBase IDA GO:0035869 (ciliary transition zone) annotation (PMID:21422230).
Localization is co-dependent among the B9 proteins: "Their subcellular localization is largely co-dependent, pointing to a functional relationship between the proteins" [PMID:19208769 abstract].
MKSR-1 TZ localization depends on upstream MKS-5: "mks-5 mutants failed to properly localize MKS-1, MKSR-1, and MKSR-2" PMID:21422230.
MKSR-1::tdTomato is used as a TZ comarker [mks-2 review cites PMID:26982032, "MKSR-1::tdTomato and MKS-2::GFP are TZ protein comarkers"].

The MKS module / complex

MKSR-1 is a member of the MKS/MKSR module together with MKS-1, MKSR-2, MKS-3, MKS-6: "MKS/MKSR module ... consisting of MKS-1/MKSR-1/MKSR-2/MKS-3/MKS-6" PMID:21422230. Modeled in GO as the MKS complex (GO:0036038).
The MKS module and the NPHP module (NPHP-1/NPHP-4) are recruited/anchored by the central scaffold MKS-5/RPGRIP1L.

Function: transition-zone assembly / Y-links / membrane anchoring

MKSR-1 acts, redundantly with the NPHP module, in building the TZ. The mksr-1;nphp-4 double mutant has severe TZ ultrastructure defects — TZ not anchored to membrane, missing Y-links: "Phenotypes nearly identical to mks-6;nphp-4 mutants were observed in the mksr-1;nphp-4 strain" PMID:21422230. (Table I: mksr-1;nphp-4 shows enlarged TZ membrane diameter and 0% of TZs with Y-links.)
MKSR-1 is required for the TZ localization of other MKS-module proteins (MKS-6, MKS-3): "disrupting MKSR-1, MKSR-2, or MKS-5 results in TZ delocalization of MKS-6 ... and MKS-3" PMID:21422230. This underlies the IMP GO:1904491 (protein localization to ciliary transition zone) and GO:0008104 (intracellular protein localization) annotations.

Function: ciliary gate / diffusion barrier

MKSR-1 is required to restrict membrane-associated proteins from entering the cilium (ciliary gate). In the mksr-1 single mutant, three normally-excluded proteins accumulate inside cilia:
MKS-3: "accumulates abnormally inside cilia (cil) and at dendritic tips (DT) in mks-5, mksr-1, and mksr-2 mutants" [PMID:21422230, Fig 9L].
RPI-2 (RP2 ortholog): "accumulates within cilia of ... mksr-1, mksr-2, mks-5, mks-6, and nphp-4 single mutants" [PMID:21422230, Fig 9M].
TRAM-1a: "accumulates within cilia of mksr-1, mksr-2, mks-5, mks-6, nphp-1, and nphp-4 mutants" [PMID:21422230, Fig 9N].
General model: "TZ proteins normally function to maintain a boundary at the cilium base, establishing the TZ as a bona fide ciliary gate" PMID:21422230. This supports a NEW GO:1903565 (negative regulation of protein localization to cilium) annotation, mirroring the mks-2 review.
Notably, the mksr-1 single mutant already shows the gate defect (RPI-2, TRAM-1a, MKS-3 mislocalization) even though gross cilium structure is normal — the gate phenotype is more sensitive than the structural phenotype.

Redundancy / single-mutant subtlety

Single, double and triple mks/mksr mutants "do not display overt defects in ciliary structure, intraflagellar transport or chemosensation" [PMID:19208769 abstract].
B9-gene mutations "do not overtly affect cilia formation unless they are in combination with a mutation in nph-1 or nph-4" [PMID:18337471 abstract]. → basis of the IGI GO:1905515 (non-motile cilium assembly) annotations (mksr-1 × nphp-1/nphp-4, WITH WBGene00011261=nphp-4, WBGene00007490=nphp-1).

Lifespan / insulin-IGF phenotype

Double mks/mksr mutants have an increased lifespan phenotype due to abnormal insulin-IGF-I signaling: "we find genetic interactions between all double mks/mksr mutant combinations, manifesting as an increased lifespan phenotype, which is due to abnormal insulin-IGF-I signaling" [PMID:19208769 abstract]. → basis of the IGI GO:0008340 (determination of adult lifespan) annotations. This is an indirect, module-redundancy phenotype (a downstream consequence of impaired ciliary signaling), not a direct molecular function of MKSR-1.

Larval foraging behavior

GO:0035177 (larval foraging behavior) IGI annotation from PMID:18337471 (WITH WBGene00011261 = nphp-4). Foraging/roaming behavior in worms depends on functional sensory cilia; a B9×nphp genetic interaction affecting cilia would plausibly affect foraging. The cached record is abstract-only (does not state "foraging" explicitly), so this is a curator judgment from full text — retained (KEEP_AS_NON_CORE), not overruled.

Protein interactions

MKSR-1 binds MKSR-2 (B9D2). UniProt binary interaction Q21191–Q9N423 (NbExp=3); IntAct EBI-330284/EBI-330279; DIP-27480N. GOA has IPI GO:0005515 (protein binding) annotations with WITH/FROM UniProtKB:Q9N423 from PMID:14704431 (Li et al. 2004 worm interactome) and PMID:19123269 (Simonis et al. 2009 empirically-controlled interactome), plus one WB IPI from PMID:18337471 (WITH WBGene00021416 = mksr-2). The interaction is real, but protein binding is uninformative; the biologically meaningful fact is the B9D1–B9D2 (MKSR-1–MKSR-2) heterodimer within the MKS module.

What is NOT known

No molecular-function GO term captures what MKSR-1 does. It is a structural/scaffold subunit of the TZ MKS module (diffusion-barrier / Y-link scaffold). GO has no "structural constituent of the ciliary transition zone" MF term; structural molecule activity (GO:0005198) is the closest placeholder. (Ontology gap — shared across MKS/NPHP-module genes; cf. the mks-2 review.)
Whether the predicted C2/B9 Ca2+/lipid-binding activity is real for MKSR-1 (no direct biochemical assay).
MKSR-1's direct binding partners beyond MKSR-2 in the worm TZ, and its precise position within the MKS-module architecture (super-resolution / proteomics not resolved for MKSR-1 specifically).
Whether MKSR-1 has any non-redundant sub-function distinct from the other core MKS-module proteins (single mutants near-normal structurally; phenotypes emerge in nphp double mutants), though the single-mutant gate leak (RPI-2/TRAM-1a) indicates at least some non-fully-redundant barrier contribution.

Annotation review plan (summary)

GO term	Evid	Ref	Planned action
GO:0036038 MKS complex (part_of)	IBA	GO_REF:0000033	ACCEPT (core; corroborated by direct imaging/genetics)
GO:0060271 cilium assembly (involved_in)	IBA	GO_REF:0000033	MODIFY → GO:1905515 non-motile cilium assembly (worm sensory cilia are non-motile; more specific)
GO:0005929 cilium (located_in)	IEA	GO_REF:0000117	MODIFY → GO:0035869 ciliary transition zone (specific; IDA-supported) / or KEEP_AS_NON_CORE
GO:0005515 protein binding (enables) ×3	IPI	PMID:14704431 / 19123269 / 18337471	KEEP_AS_NON_CORE (real MKSR-1–MKSR-2 interaction; uninformative term; do not remove experimental IPI)
GO:1905515 non-motile cilium assembly (involved_in) ×2	IGI	PMID:18337471 / 21422230	ACCEPT (core, redundant module function)
GO:1904491 protein localization to ciliary transition zone (involved_in) ×2	IMP	PMID:26595381 / 21422230	ACCEPT (PMID:21422230 shows MKSR-1 required for MKS-6/MKS-3 TZ localization; PMID:26595381 abstract-only, defer to curator)
GO:0035869 ciliary transition zone (located_in)	IDA	PMID:21422230	ACCEPT (core CC; direct imaging)
GO:0008340 determination of adult lifespan (involved_in) ×4	IGI	PMID:19208769	KEEP_AS_NON_CORE (indirect insulin-IGF phenotype in double mutants; not a core function)
GO:0008104 intracellular protein localization (involved_in)	IMP	PMID:18337471	MODIFY → GO:1904491 (the specific process is protein localization to the TZ)
GO:0035177 larval foraging behavior (involved_in)	IGI	PMID:18337471	KEEP_AS_NON_CORE (downstream sensory-cilium behavior; curator full-text judgment; abstract-only cache)

Proposed NEW: GO:1903565 negative regulation of protein localization to cilium (ciliary gate; RPI-2/TRAM-1a/MKS-3 exclusion) — mirrors mks-2 review, directly supported in the mksr-1 single mutant.

Deep research

Falcon deep research launched via just deep-research-falcon worm mksr-1 --fallback perplexity-lite. The wrapper reported a 600s timeout and the perplexity-lite fallback failed with a 401 quota error, but the underlying falcon (Edison) client actually completed at 1120s and wrote a genuine 50KB report (mksr-1-deep-research-falcon.md, 32 citations, artifacts folder). I read it: it independently confirms MKSR-1 = B9D1, a soluble single-B9-domain protein, obligate B9 complex with MKS-1/MKSR-2, TZ/basal-body localization and MKS-module/ciliopathy role — fully consistent with this review. It cites some additional non-cached sources (okazaki2020, zhang2010); I did NOT add those as citations since they are not in the publications cache and the review is anchored to verified cached PMIDs. This is a genuine late falcon file (kept per ground rules).
Review grounded primarily on cached primary literature (PMID:21422230 full text; PMID:19208769, 18337471, 26595381 abstracts) and UniProt/GOA.