id: Q19119
gene_symbol: xbx-1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: >-
  xbx-1 encodes the Caenorhabditis elegans cytoplasmic dynein-2 light intermediate
  chain, the ortholog of mammalian DYNC2LI1/D2LIC. It is a non-catalytic subunit of
  the dynein-2 (IFT-dynein) motor, which also contains the CHE-3 heavy chain.
  Dynein-2 is the minus-end-directed microtubule motor that powers retrograde
  intraflagellar transport (IFT), returning IFT trains and turned-over cargo from
  the ciliary tip back to the base. XBX-1 binds the dynein heavy chain and is
  required to build and maintain the sensory cilia of C. elegans: it localizes to
  the ciliary base and basal body and moves bidirectionally along the axoneme
  (carried anterogradely as inactive cargo by kinesin-2, then powering the
  retrograde run). Loss of xbx-1 gives short, malformed cilia with a distal bulb in
  which IFT proteins accumulate, together with the sensory-behaviour defects typical
  of ciliary mutants. xbx-1 belongs to the DAF-19 (RFX) X-box-regulated ciliary gene
  battery, from which it takes its name.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: PMID:12802075
  title: XBX-1 encodes a dynein light intermediate chain required for retrograde intraflagellar
    transport and cilia assembly in Caenorhabditis elegans.
  findings:
  - statement: >-
      xbx-1 is required for retrograde IFT and is homologous to the mammalian dynein
      light intermediate chain D2LIC.
    supporting_text: >-
      xbx-1, that is required for retrograde IFT and shares homology with a mammalian
      dynein light intermediate chain (D2LIC)
  - statement: >-
      XBX-1 functions together with the CHE-3 dynein heavy chain in retrograde IFT,
      downstream of the IFT-A (complex A) proteins.
    supporting_text: >-
      the DLIC protein XBX-1 functions together with the CHE-3 dynein in retrograde
      IFT, downstream of the complex A proteins
  - statement: >-
      XBX-1 localizes to the ciliary base and moves bidirectionally (anterograde and
      retrograde) along the axoneme.
    supporting_text: >-
      XBX-1 localizes to the base of the cilia and undergoes anterograde and
      retrograde movement along the axoneme
  - statement: >-
      Loss of xbx-1 produces short cilia with a distal bulb in which IFT proteins
      accumulate, the hallmark of retrograde IFT failure.
    supporting_text: >-
      they are shortened and have a bulb like structure in which IFT proteins
      accumulate
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary characterization of XBX-1. PubMed-verified; abstract-only in cache but
      the abstract directly supports the dynein light intermediate chain identity,
      D2LIC homology, requirement for retrograde IFT, cilium assembly phenotype
      (short cilia with a distal IFT-protein bulb), base/axoneme localization with
      bidirectional movement, and functional partnership with the CHE-3 dynein
      downstream of IFT-A.
- id: PMID:17420466
  title: Mutation of the MAP kinase DYF-5 affects docking and undocking of kinesin-2
    motors and reduces their speed in the cilia of Caenorhabditis elegans.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Paper is about DYF-5/kinesin-2; the cached abstract does not mention xbx-1.
      XBX-1 is used in the full text as a ciliary/IFT marker, which is the basis of
      the IDA non-motile cilium localization annotation. Contextual for xbx-1.
- id: PMID:22922713
  title: The BBSome controls IFT assembly and turnaround in cilia.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Full text refers to XBX-1 explicitly as the retrograde IFT motor dynein light
      chain and D2LIC ortholog; the basis of the IDA basal body localization. The
      cached abstract does not mention xbx-1.
- id: PMID:25335890
  title: Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans
    thermosensory neuron.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Paper concerns the AFD bipartite signaling compartment; cached abstract does
      not mention xbx-1. XBX-1 is used in the full text as an axoneme/ciliary-base
      marker, the basis of the IDA localization annotations.
- id: PMID:27623382
  title: A Conserved Role for Girdin in Basal Body Positioning and Ciliogenesis.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Paper concerns GRDN-1/Girdin and basal body positioning; cached abstract does
      not mention xbx-1. XBX-1 is used in the full text as a cilium marker, the basis
      of the IDA cilium localization annotation.
- id: PMID:27930654
  title: Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a
    Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Full text uses tdTomato-tagged XBX-1 as the reference IFT marker localizing to
      the ciliary base and axoneme; the basis of the IDA axoneme, ciliary base and
      transition-zone annotations. The cached abstract does not mention xbx-1.
- id: PMID:33460640
  title: GRDN-1/Girdin regulates dendrite morphogenesis and cilium position in two
    specialized sensory neuron types in C. elegans.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Full text restates that the dynein light intermediate chain XBX-1 localizes to
      the basal body and moves bidirectionally along the ciliary axoneme (citing
      Schafer et al., 2003); the basis of the IDA basal body annotation. The cached
      abstract does not mention xbx-1.
existing_annotations:
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      XBX-1 localizes to the ciliary base/basal body, where dynein-2 is loaded onto
      IFT trains. Phylogenetically inferred and corroborated by multiple IDA calls
      (PMID:33460640, PMID:22922713).
    action: ACCEPT
    reason: >-
      Consistent with experimentally observed base/basal body localization of XBX-1
      and with the known site of dynein-2 loading. A non-core location term but
      correct.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0045504
    label: dynein heavy chain binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Core molecular function: as the dynein-2 light intermediate chain, XBX-1 binds
      the dynein-2 heavy chain (CHE-3) within the retrograde IFT motor.
    action: ACCEPT
    reason: >-
      This is the defining, informative molecular function of a dynein light
      intermediate chain. Supported by orthology to D2LIC and by the functional
      partnership with CHE-3 in retrograde IFT. Retained as core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        the DLIC protein XBX-1 functions together with the CHE-3 dynein in
        retrograde IFT, downstream of the complex A proteins
- term:
    id: GO:0005868
    label: cytoplasmic dynein complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  review:
    summary: >-
      Core complex membership: XBX-1 is a subunit of the cytoplasmic dynein-2
      (IFT-dynein) motor complex.
    action: ACCEPT
    reason: >-
      Well supported; XBX-1 is the light intermediate chain of dynein-2. GO:0005868
      is the most specific available term (GO lacks a dedicated "cytoplasmic
      dynein 2 complex" cellular-component class; see knowledge_gaps). Retained as
      core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        the DLIC protein XBX-1 functions together with the CHE-3 dynein in
        retrograde IFT, downstream of the complex A proteins
- term:
    id: GO:0035721
    label: intraciliary retrograde transport
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Core biological process: XBX-1 is part of the dynein-2 motor that drives
      retrograde IFT (tip-to-base) in cilia.
    action: ACCEPT
    reason: >-
      Directly supported by IMP evidence (PMID:12802075) and orthology; this is the
      central process for the gene. Retained as core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        xbx-1, that is required for retrograde IFT and shares homology with a
        mammalian dynein light intermediate chain (D2LIC)
- term:
    id: GO:0035735
    label: intraciliary transport involved in cilium assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      IFT (including the retrograde arm powered by dynein-2/XBX-1) is required for
      cilium assembly and maintenance.
    action: ACCEPT
    reason: >-
      Consistent with the xbx-1 loss-of-function cilium-assembly phenotype and with
      the established role of IFT in ciliogenesis. Broader BP framing complementary
      to the more specific retrograde-transport and non-motile-cilium-assembly terms.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        they are shortened and have a bulb like structure in which IFT proteins
        accumulate
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      XBX-1 moves along the ciliary axoneme as part of IFT, where the dynein-2 motor
      operates during retrograde transport.
    action: ACCEPT
    reason: >-
      Phylogenetically inferred and corroborated by IDA axoneme localization
      (PMID:12802075, PMID:27930654, PMID:25335890). Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0005813
    label: centrosome
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic annotation transferred from the UniProt Subcellular Location
      "microtubule organizing center, centrosome" mapping. In C. elegans ciliated
      sensory neurons the relevant MTOC is the centriole-derived ciliary basal body,
      already captured by IDA basal body annotations.
    action: KEEP_AS_NON_CORE
    reason: >-
      Dynein-2 is the ciliary/IFT dynein, not the mitotic-spindle dynein; there is no
      direct evidence for a canonical mitotic centrosome role for XBX-1. The
      "centrosome" call over-generalizes the basal-body/MTOC localization. Kept
      (basal bodies are centriole-derived MTOCs) but flagged non-core.
- term:
    id: GO:0005868
    label: cytoplasmic dynein complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: part_of
  review:
    summary: >-
      InterPro-based electronic support for dynein-2 complex membership, redundant
      with the IBA part_of annotation.
    action: ACCEPT
    reason: >-
      Consistent electronic corroboration of the experimentally/phylogenetically
      supported dynein complex membership.
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic (Subcellular Location) support for axoneme localization, redundant
      with IDA axoneme annotations.
    action: ACCEPT
    reason: >-
      Consistent with experimentally observed axoneme localization.
- term:
    id: GO:0035721
    label: intraciliary retrograde transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro-based electronic support for the core retrograde IFT process,
      redundant with IMP/IBA annotations.
    action: ACCEPT
    reason: >-
      Consistent electronic corroboration of the central biological process.
- term:
    id: GO:0035735
    label: intraciliary transport involved in cilium assembly
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro-based electronic support for the role of IFT in cilium assembly,
      redundant with the IBA annotation.
    action: ACCEPT
    reason: >-
      Consistent with the gene's established role in ciliogenesis via IFT.
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: IDA
  original_reference_id: PMID:33460640
  qualifier: located_in
  review:
    summary: >-
      Direct observation that XBX-1 localizes to the basal body and moves
      bidirectionally along the axoneme.
    action: ACCEPT
    reason: >-
      Experimentally supported basal body localization (curator read full text); the
      site where dynein-2 is loaded onto IFT trains. Corroborated by the primary
      characterization (PMID:12802075). Correct non-core location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IDA
  original_reference_id: PMID:27930654
  qualifier: located_in
  review:
    summary: >-
      XBX-1::tdTomato was used as an IFT marker localizing to the ciliary base and
      axoneme.
    action: ACCEPT
    reason: >-
      Experimentally supported axoneme localization (curator read full text),
      corroborated by the primary characterization (PMID:12802075). Consistent with
      IFT movement of the dynein-2 motor.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0035869
    label: ciliary transition zone
  evidence_type: IDA
  original_reference_id: PMID:27930654
  qualifier: located_in
  review:
    summary: >-
      XBX-1 traverses the ciliary base/transition zone during IFT, where the dynein-2
      motor enters and exits the ciliary compartment.
    action: ACCEPT
    reason: >-
      IDA annotation from a study using XBX-1 as a ciliary marker; the curator read
      the full text. XBX-1 passes through the transition zone as part of IFT, so the
      localization is biologically consistent. Non-core location.
- term:
    id: GO:0097546
    label: ciliary base
  evidence_type: IDA
  original_reference_id: PMID:27930654
  qualifier: located_in
  review:
    summary: >-
      Direct observation of XBX-1 at the ciliary base, the site of dynein-2 loading
      and IFT-train assembly/turnaround.
    action: ACCEPT
    reason: >-
      Experimentally supported and central to dynein-2 function (loading/unloading);
      corroborated by the primary characterization (PMID:12802075). Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IDA
  original_reference_id: PMID:27623382
  qualifier: located_in
  review:
    summary: >-
      XBX-1 localizes to cilia (general ciliary compartment), consistent with its
      role in IFT.
    action: ACCEPT
    reason: >-
      Experimentally supported general ciliary localization (curator read full text);
      a parent of the more specific non-motile cilium term also annotated.
      Corroborated by the primary characterization (PMID:12802075). Correct but
      non-core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0097730
    label: non-motile cilium
  evidence_type: IDA
  original_reference_id: PMID:17420466
  qualifier: located_in
  review:
    summary: >-
      XBX-1 localizes to the non-motile sensory cilia of C. elegans, where it
      operates in IFT.
    action: ACCEPT
    reason: >-
      IDA from a study using XBX-1 as a ciliary/IFT marker (curator read full text);
      C. elegans sensory cilia are non-motile. Corroborated by the primary
      characterization (PMID:12802075). Correct location for the cell type. Non-core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IDA
  original_reference_id: PMID:25335890
  qualifier: located_in
  review:
    summary: >-
      XBX-1 used as an axoneme/ciliary marker in AFD sensory neurons.
    action: ACCEPT
    reason: >-
      Experimentally supported axoneme localization (curator read full text),
      redundant with other IDA axoneme calls and corroborated by the primary
      characterization (PMID:12802075). Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0035721
    label: intraciliary retrograde transport
  evidence_type: IMP
  original_reference_id: PMID:12802075
  qualifier: involved_in
  review:
    summary: >-
      Loss of xbx-1 disrupts retrograde IFT, causing IFT proteins to accumulate in a
      distal ciliary bulb; XBX-1 functions with the CHE-3 dynein downstream of IFT-A.
    action: ACCEPT
    reason: >-
      Primary experimental (IMP) evidence for the gene's central biological process.
      Retained as core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        the DLIC protein XBX-1 functions together with the CHE-3 dynein in
        retrograde IFT, downstream of the complex A proteins
    - reference_id: PMID:12802075
      supporting_text: >-
        they are shortened and have a bulb like structure in which IFT proteins
        accumulate
- term:
    id: GO:0045504
    label: dynein heavy chain binding
  evidence_type: ISS
  original_reference_id: PMID:12802075
  qualifier: enables
  review:
    summary: >-
      By sequence similarity to mammalian D2LIC, XBX-1 binds the dynein-2 heavy
      chain within the retrograde IFT motor.
    action: ACCEPT
    reason: >-
      Informative, specific molecular function (not generic protein binding).
      Supported by orthology to D2LIC (with/from rat D2LIC) and by the functional
      partnership with CHE-3. Retained as core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        xbx-1, that is required for retrograde IFT and shares homology with a
        mammalian dynein light intermediate chain (D2LIC)
- term:
    id: GO:0097546
    label: ciliary base
  evidence_type: IDA
  original_reference_id: PMID:25335890
  qualifier: located_in
  review:
    summary: >-
      XBX-1 localizes to the ciliary base in AFD sensory neurons.
    action: ACCEPT
    reason: >-
      Experimentally supported ciliary base localization (curator read full text),
      redundant with other IDA base calls and corroborated by the primary
      characterization (PMID:12802075). Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:1905515
    label: non-motile cilium assembly
  evidence_type: IMP
  original_reference_id: PMID:12802075
  qualifier: involved_in
  review:
    summary: >-
      xbx-1 mutants have short, malformed sensory cilia with a distal IFT-protein
      bulb, showing XBX-1 is required for assembly of non-motile cilia.
    action: ACCEPT
    reason: >-
      Primary experimental (IMP) evidence for the cilium-assembly requirement; C.
      elegans sensory cilia are non-motile. Retained as core.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        they are shortened and have a bulb like structure in which IFT proteins
        accumulate
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: IDA
  original_reference_id: PMID:22922713
  qualifier: located_in
  review:
    summary: >-
      XBX-1 (dynein-2 light chain, D2LIC ortholog) used as a retrograde IFT motor
      marker localizing to cilia/basal body.
    action: ACCEPT
    reason: >-
      Experimentally supported basal body localization (curator read full text),
      redundant with the PMID:33460640 IDA call and corroborated by the primary
      characterization (PMID:12802075). Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0097730
    label: non-motile cilium
  evidence_type: IDA
  original_reference_id: PMID:12802075
  qualifier: located_in
  review:
    summary: >-
      XBX-1 localizes within the non-motile sensory cilia, moving between the base
      and the axoneme.
    action: ACCEPT
    reason: >-
      Experimentally supported localization to C. elegans (non-motile) sensory cilia.
      Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IDA
  original_reference_id: PMID:12802075
  qualifier: located_in
  review:
    summary: >-
      XBX-1 undergoes bidirectional movement along the ciliary axoneme.
    action: ACCEPT
    reason: >-
      Primary experimental evidence for axoneme localization/movement of the
      dynein-2 motor. Correct location.
    supported_by:
    - reference_id: PMID:12802075
      supporting_text: >-
        XBX-1 localizes to the base of the cilia and undergoes anterograde and
        retrograde movement along the axoneme
core_functions:
- description: >-
    Cytoplasmic dynein-2 light intermediate chain: a non-catalytic subunit of the
    dynein-2 (IFT-dynein) motor that binds the CHE-3 dynein heavy chain and
    contributes to the complex's minus-end-directed microtubule motor activity,
    powering retrograde intraflagellar transport required for sensory cilium
    assembly and maintenance.
  molecular_function:
    id: GO:0045504
    label: dynein heavy chain binding
  contributes_to_molecular_function:
    id: GO:0008569
    label: minus-end-directed microtubule motor activity
  directly_involved_in:
  - id: GO:0035721
    label: intraciliary retrograde transport
  - id: GO:1905515
    label: non-motile cilium assembly
  locations:
  - id: GO:0005930
    label: axoneme
  - id: GO:0097730
    label: non-motile cilium
  in_complex:
    id: GO:0005868
    label: cytoplasmic dynein complex
  supported_by:
  - reference_id: PMID:12802075
    supporting_text: >-
      the DLIC protein XBX-1 functions together with the CHE-3 dynein in retrograde
      IFT, downstream of the complex A proteins
  - reference_id: PMID:12802075
    supporting_text: >-
      xbx-1, that is required for retrograde IFT and shares homology with a mammalian
      dynein light intermediate chain (D2LIC)
proposed_new_terms:
- proposed_name: cytoplasmic dynein 2 complex
  proposed_definition: >-
    A cytoplasmic dynein complex, distinct from the cytoplasmic dynein 1 complex,
    that is specialized for retrograde intraflagellar transport within cilia and
    flagella. It is built around the dynein-2 heavy chain (DYNC2H1/CHE-3) together
    with dynein-2-specific light intermediate (DYNC2LI1/D2LIC/XBX-1), intermediate,
    light and associated chains, and generates minus-end-directed (tip-to-base)
    movement along the ciliary axoneme.
  justification: >-
    GO has a single cellular-component term GO:0005868 "cytoplasmic dynein complex"
    that conflates the functionally and compositionally distinct dynein-1 (mitotic/
    trafficking) and dynein-2 (ciliary/IFT) motors. A dynein-2-specific term would
    let XBX-1 and its partners be annotated to their actual complex. This benefits
    dynein-2 subunit annotation across species, not just XBX-1 — e.g. the heavy chain
    CHE-3/DYNC2H1, the intermediate chains WDR60/WDR34, and the dynein-2 light chains
    — and would separate IFT-dynein from dynein-1 in enrichment analyses and GO-CAM
    models.
  proposed_parent:
    id: GO:0005868
    label: cytoplasmic dynein complex
knowledge_gaps:
- gap_statement: >-
    The specific molecular contribution of the XBX-1 light intermediate chain to
    dynein-2 function in C. elegans is undetermined: whether it is chiefly required
    for dynein-2 complex assembly/stability, for coupling the motor to IFT trains as
    a cargo adaptor, or for regulating motor activation/autoinhibition at the ciliary
    tip.
  boundary: >-
    It is firmly established that XBX-1 is the dynein-2 LIC (D2LIC ortholog), binds
    the CHE-3 heavy chain, localizes to the ciliary base/axoneme, and is required for
    retrograde IFT and cilium assembly. The light intermediate chain itself has no
    demonstrated enzymatic activity; the ATP-dependent minus-end-directed motor
    activity is a property of the CHE-3 heavy chain/dynein-2 complex.
  gap_kind:
  - BIOLOGY
  dark_aspect: RESIDUAL_SUBGAP
  status: OPEN
  significance: >-
    DYNC2LI1 mutations cause skeletal ciliopathies (short-rib thoracic dysplasia);
    understanding the LIC's mechanistic role would clarify how dynein-2 assembly and
    IFT-train coupling are controlled and how they fail in disease.
  resolution: >-
    Structure-function dissection of XBX-1 (domain/point mutants) with biochemical
    assays of dynein-2 assembly and heavy-chain binding, plus live IFT imaging of
    train coupling and velocities in xbx-1 alleles.
  provenance:
  - reference_id: PMID:12802075
    supporting_text: >-
      the DLIC protein XBX-1 functions together with the CHE-3 dynein in retrograde
      IFT, downstream of the complex A proteins
- gap_statement: >-
    No GO cellular-component term expresses the cytoplasmic dynein-2 (IFT-dynein)
    complex distinctly from cytoplasmic dynein-1, so XBX-1's actual complex
    membership can only be annotated with the conflated parent term GO:0005868.
  boundary: >-
    XBX-1 is unambiguously a subunit of the ciliary retrograde IFT dynein-2 motor
    (with CHE-3/DYNC2H1); the only available GO CC term, GO:0005868 "cytoplasmic
    dynein complex", also covers dynein-1.
  gap_kind:
  - ONTOLOGY
  dark_aspect: CC_DARK
  status: OPEN
  significance: >-
    A dynein-2-specific complex term would let IFT-dynein subunits be annotated to
    their true complex and separated from dynein-1 in enrichment and model building.
  resolution: >-
    Add a "cytoplasmic dynein 2 complex" cellular-component term as a child of
    GO:0005868 (see proposed_new_terms).
suggested_questions:
- question: >-
    Does XBX-1 act mainly to stabilize/assemble the dynein-2 motor, to couple it to
    IFT trains, or to regulate its activation during ciliary turnaround?
  experts:
  - Intraflagellar transport / dynein-2 motor biologists
- question: >-
    Does XBX-1 have any dynein-2-independent role at the basal body/centriole?
  experts:
  - C. elegans ciliary cell biologists
suggested_experiments:
- hypothesis: >-
    XBX-1 is required for dynein-2 complex stability and for coupling the motor to
    IFT trains.
  description: >-
    Structure-function analysis of XBX-1 (targeted deletions/point mutations of the
    DLIC fold) combined with co-immunoprecipitation of CHE-3 and live imaging of
    IFT-train velocities and turnaround in the mutant alleles.
  experiment_type: structure-function / live imaging
- hypothesis: >-
    XBX-1 loss selectively impairs the retrograde (dynein-2) IFT arm.
  description: >-
    Dual-color live imaging of anterograde (kinesin-2/IFT-B) and retrograde
    (XBX-1/CHE-3) markers in xbx-1 mutants to quantify which transport arm and which
    ciliary segment are affected.
  experiment_type: live imaging
tags:
- caeel-ciliopathy