id: Q9CQ66 gene_symbol: Dynlt2b product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:10090 label: Mus musculus description: Dynlt2b (Tctex1d2) encodes a 144-residue non-catalytic Tctex-type dynein light chain (Pfam Tctex-1 domain) and is the mouse ortholog of human DYNLT2B, the only Tctex light chain specific to cytoplasmic dynein-2, the minus-end-directed motor of retrograde intraflagellar transport (IFT). In mouse testis the protein co-immunoprecipitates with the dynein-2 intermediate chains WDR34 and WDR60 and with the Tctex light chain DYNLT1, and also with the inner-dynein-arm intermediate chains WDR63 and WDR78. It is most abundant in testis, where it lies along the developing flagellum from round to elongated spermatids, in the manchette, and in the axonemal fraction of mature sperm; it is also detected in motile cilia of brain ventricles, trachea and oviduct. Knockout males are infertile with short, coiled, immotile sperm tails whose axonemes are disorganized from step-4 spermatids onward, and dynein-2 subunits and IFT88 are mislocalized in knockout spermatid flagella, whereas motile cilia of somatic tissues appear normal. Its role in retrograde IFT itself and its ciliary-base and centrosomal localization are inferred from the human ortholog rather than shown in mouse. existing_annotations: - term: id: GO:0000922 label: spindle pole evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Ensembl Compara transfer of a human IDA colocalization of DYNLT2B with WDR60 at mitotic spindle poles. Not examined in mouse; a secondary localization of the dynein-2 light chain. action: KEEP_AS_NON_CORE reason: The human ortholog (same PANTHER subfamily PTHR21255:SF7) was observed at spindle poles during cell division together with WDR60. The transfer within a one-to-one ortholog pair is reasonable, but this location is peripheral to the ciliary dynein-2 role and has no mouse-specific support. supported_by: - reference_id: PMID:25830415 supporting_text: Tctex1d2 associates with Wdr34, Wdr60, and other subunits of Dync1 and Dync2 and colocalizes with Wdr60 to microtubule organizing centers during interphase, the mitotic spindle poles during cell division, and the base of the cilium in ciliated cells. - term: id: GO:0005737 label: cytoplasm evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:3045358 - MGI:MGI:98642 - MGI:MGI:98643 - PANTHER:PTN000478852 - PomBase:SPAC1805.08 - RGD:1549755 - UniProtKB:O04355 - UniProtKB:P63172 - UniProtKB:Q388R0 - UniProtKB:Q389U5 - UniProtKB:Q5JR98 - UniProtKB:Q8WW35 - WB:WBGene00017014 review: summary: Family-level IBA from the Tctex light-chain node PTN000478852; correct, but the defining locations of this protein are the cilium/flagellum and its axoneme. action: KEEP_AS_NON_CORE reason: PTN000478852 covers dynein-1 and dynein-2 Tctex light chains, so cytoplasm is the generality at which the PAINT curator placed the claim. Mouse TCTEX1D2 is in the cytoplasmic manchette and the flagellar compartment, so the claim holds, but more specific location rows carry the functionally relevant information. supported_by: - reference_id: PMID:39827215 supporting_text: "TCTEX1D2 was also localized in the manchette, which are transiently formed in step 10–14\ \ spermatids (Fig. 1C)." propagation_review: root_cause: NO_FAILURE_NON_CORE failure_modes: [] source_entities: - source_id: PANTHER:PTN000478852 comment: Tctex light-chain family node spanning dynein-1 and dynein-2 members; mouse Dynlt2b is inside the clade and the family-wide cytoplasmic claim holds. source_status: SUPPORTS_TRANSFER - term: id: GO:0005813 label: centrosome evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Ensembl Compara transfer of human centrosomal/MTOC colocalization with WDR60; not examined in mouse, secondary to the ciliary role. action: KEEP_AS_NON_CORE reason: The human ortholog colocalizes with WDR60 at interphase MTOCs, consistent with dynein-2 recruitment near the basal body. The ortholog transfer is reasonable but this is not the functionally defining location, and no mouse experiment tested it. supported_by: - reference_id: PMID:25830415 supporting_text: Tctex1d2 associates with Wdr34, Wdr60, and other subunits of Dync1 and Dync2 and colocalizes with Wdr60 to microtubule organizing centers during interphase, the mitotic spindle poles during cell division, and the base of the cilium in ciliated cells. - term: id: GO:0005868 label: cytoplasmic dynein complex evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: part_of supporting_entities: - MGI:MGI:98642 - PANTHER:PTN000478852 - RGD:1549755 - UniProtKB:P51808 - UniProtKB:P63171 - UniProtKB:P63172 - UniProtKB:Q8WW35 review: summary: Membership in cytoplasmic dynein (dynein-2) is supported directly in mouse by co-immunoprecipitation from testis with WDR34, WDR60 and DYNLT1, as well as by the inherited family-level IBA. action: ACCEPT reason: FLAG-tagged endogenous TCTEX1D2 from knock-in testis pulled down the dynein-2 intermediate chains WDR34 and WDR60 and the light chain DYNLT1, and dynein-2 subunits were mislocalized in knockout spermatid flagella. This is mouse experimental support for the complex membership that PAINT placed at PTN000478852 and that human biochemistry established. supported_by: - reference_id: PMID:39827215 supporting_text: In the testes, TCTEX1D2 interacted not only with WDR60 and DYNLT1, but also with WDR34 (Fig. 2A). - reference_id: PMID:39827215 supporting_text: These results indicate that TCTEX1D2 is one of the components of cytoplasmic dynein 2 in germ cells. - reference_id: PMID:25205765 supporting_text: Here, we now also identify the TCTEX1D2 light chain (Tctex-2) as a light chain for dynein-2, not present in dynein-1. propagation_review: root_cause: NO_FAILURE_CORE failure_modes: [] source_entities: - source_id: PANTHER:PTN000478852 comment: Tctex light-chain node; complex membership is inherited by all members and confirmed for mouse Dynlt2b by testis co-IP with dynein-2 subunits. source_status: SUPPORTS_TRANSFER - term: id: GO:0005868 label: cytoplasmic dynein complex evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: part_of supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Ortholog transfer of dynein-2 membership from human; independently confirmed by mouse testis co-IP with dynein-2 subunits. action: ACCEPT reason: Same claim as the IBA row, supported in mouse by co-immunoprecipitation of TCTEX1D2 with WDR34, WDR60 and DYNLT1. supported_by: - reference_id: PMID:39827215 supporting_text: In the testes, TCTEX1D2 interacted not only with WDR60 and DYNLT1, but also with WDR34 (Fig. 2A). - term: id: GO:0005929 label: cilium evidence_type: IEA original_reference_id: GO_REF:0000108 qualifier: located_in supporting_entities: - GO:0035721 review: summary: Inferred from the retrograde IFT annotation; supported directly in mouse, where TCTEX1D2 localizes along spermatid flagella and in motile cilia of ventricle, trachea and oviduct. action: ACCEPT reason: The FLAG knock-in mouse shows TCTEX1D2 along developing sperm flagella and in motile cilia of several somatic tissues. The sperm flagellum is a specialized motile cilium; a more specific sperm-flagellum location is proposed as a new annotation, but the general cilium term is also directly observed for somatic motile cilia and is retained. supported_by: - reference_id: PMID:39827215 supporting_text: "TCTEX1D2 was also expressed in cilia of these tissues (Fig. S2A–C)." - reference_id: PMID:39827215 supporting_text: We found that TCTEX1D2 was localized along the flagella from round spermatids to elongated spermatids. - term: id: GO:0005930 label: axoneme evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Transferred from human (tagged-protein axonemal signal); mouse sperm fractionation directly places TCTEX1D2 in the axonemal (SDS-soluble) fraction along the flagellum. action: ACCEPT reason: In mouse, cauda epididymal sperm fractionation recovered TCTEX1D2 in the SDS-soluble axonemal fraction and immunostaining showed it along the flagellum; the authors conclude it is an axoneme component. The human source (overexpressed tagged protein in ciliary axonemes) is weaker, but the mouse data independently support axonemal localization. supported_by: - reference_id: PMID:39827215 supporting_text: These results showed that TCTEX1D2 is an axoneme component in mice. - term: id: GO:0007018 label: microtubule-based movement evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0024432 - MGI:MGI:98642 - PANTHER:PTN000478852 - PomBase:SPAC1805.08 - UniProtKB:Q8WW35 review: summary: Correct family-level IBA; for this dynein-2-specific light chain the specific process is intraciliary retrograde transport, a descendant term the gene already carries. action: MODIFY reason: PTN000478852 spans dynein-1 and dynein-2 Tctex light chains, so microtubule-based movement is the right generality for the node. Dynlt2b is in the dynein-2-specific subfamily PTHR21255:SF7, and its human ortholog in that subfamily is required for retrograde IFT; GO:0035721 is a descendant of microtubule-based movement and is already on this gene by ISS/ISO/IEA. Same action as on the human ortholog review. supported_by: - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. proposed_replacement_terms: - id: GO:0035721 label: intraciliary retrograde transport propagation_review: root_cause: NO_FAILURE_NON_CORE failure_modes: [] source_entities: - source_id: PANTHER:PTN000478852 comment: Family node spanning dynein-1 and dynein-2 light chains; the term is correct for Dynlt2b but less specific than the retrograde IFT role of the SF7 subfamily. source_status: SUPPORTS_TRANSFER - term: id: GO:0031021 label: interphase microtubule organizing center evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Ortholog transfer of human interphase MTOC colocalization with WDR60; not tested in mouse, secondary. action: KEEP_AS_NON_CORE reason: Directly observed for the human ortholog; plausible for mouse by one-to-one orthology but peripheral to the ciliary dynein-2 function. supported_by: - reference_id: PMID:25830415 supporting_text: Tctex1d2 associates with Wdr34, Wdr60, and other subunits of Dync1 and Dync2 and colocalizes with Wdr60 to microtubule organizing centers during interphase, the mitotic spindle poles during cell division, and the base of the cilium in ciliated cells. - term: id: GO:0035721 label: intraciliary retrograde transport evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Core process, inferred from the human ortholog in the same dynein-2-specific PANTHER subfamily (SF7); retrograde IFT itself has not been measured in mouse. action: ACCEPT reason: Human TCTEX1D2-deficient fibroblasts and knockout cells show retrograde IFT and ciliary trafficking defects. Mouse and human Dynlt2b/DYNLT2B are one-to-one orthologs in PTHR21255:SF7. The mouse knockout is consistent (dynein-2 subunits, DYNC2LI1 and IFT88 mislocalized in spermatid flagella), but no mouse experiment measured retrograde transport directly, so this remains an inferred rather than mouse-established function. supported_by: - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. - reference_id: PMID:39827215 supporting_text: Therefore, cytoplasmic dynein 2 complexes were disrupted in Tctex1d2−/− mice elongated spermatids. - term: id: GO:0035721 label: intraciliary retrograde transport evidence_type: ISO original_reference_id: GO_REF:0000119 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 review: summary: Mouse-human ortholog transfer of the retrograde IFT role; core, inferred. action: ACCEPT reason: Same claim as the IEA row; the donor annotation on human DYNLT2B rests on knockout and patient-fibroblast retrograde IFT defects and was accepted in the human review. supported_by: - reference_id: PMID:29742051 supporting_text: 'We established cell lines lacking WDR60 or TCTEX1D2, both of which are dynein-2-specific subunits encoded by ciliopathy-causing genes, and found that both WDR60-knockout (KO) and TCTEX1D2-KO cells show defects in retrograde ciliary protein trafficking, with WDR60-KO cells demonstrating more severe defects probably due to failed assembly of the dynein-2 complex.' propagation_review: root_cause: NO_FAILURE_CORE failure_modes: [] source_entities: - source_id: UniProtKB:Q8WW35 comment: Human DYNLT2B, one-to-one ortholog in PTHR21255:SF7, with experimental retrograde IFT evidence. source_status: SUPPORTS_TRANSFER - term: id: GO:0035721 label: intraciliary retrograde transport evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 review: summary: UniProt curator transfer of the retrograde IFT role from human DYNLT2B; core, inferred. action: ACCEPT reason: Same claim as the IEA and ISO rows, from the same human ortholog. supported_by: - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. - term: id: GO:0045505 label: dynein intermediate chain binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - FB:FBgn0024432 - PANTHER:PTN000478852 - UniProtKB:Q8WW35 review: summary: Core activity. Mouse TCTEX1D2 co-immunoprecipitates from testis with the dynein-2 intermediate chains WDR34 and WDR60 and with the inner-arm intermediate chains WDR63 and WDR78. action: ACCEPT reason: The family-level IBA is directly supported in mouse by co-IP of endogenous FLAG-tagged TCTEX1D2 with four dynein intermediate chains. In human, the TCTEX1D2-DYNLT1/DYNLT3 dimer was mapped onto WDR60. Co-IP from tissue does not establish which contact is direct, but binding to dynein intermediate chains is the established mode of Tctex light chains. supported_by: - reference_id: PMID:39827215 supporting_text: In the testes, TCTEX1D2 interacted not only with WDR60 and DYNLT1, but also with WDR34 (Fig. 2A). - reference_id: PMID:39827215 supporting_text: Further, co-immunoprecipitation studies revealed that TCTEX1D2 interacted with WDR63 and WDR78 (Fig. 2D). propagation_review: root_cause: NO_FAILURE_CORE failure_modes: [] source_entities: - source_id: PANTHER:PTN000478852 comment: Tctex light-chain node; intermediate-chain binding is the family's conserved activity and is confirmed for mouse Dynlt2b by testis co-IP. source_status: SUPPORTS_TRANSFER - term: id: GO:0045505 label: dynein intermediate chain binding evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Ortholog transfer of intermediate-chain binding from human; confirmed by mouse co-IP data. action: ACCEPT reason: Same claim as the IBA row, with direct mouse co-immunoprecipitation support. supported_by: - reference_id: PMID:39827215 supporting_text: Further, co-immunoprecipitation studies revealed that TCTEX1D2 interacted with WDR63 and WDR78 (Fig. 2D). - term: id: GO:0060271 label: cilium assembly evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Correct but general for mouse. The knockout shows a cell-type-specific requirement in assembling the sperm flagellum (disorganized axoneme from step-4 spermatids), whereas somatic motile cilia are normal. action: MODIFY reason: In mouse the supported descendant is sperm flagellum assembly (GO:0120316, is_a motile cilium assembly, under cilium assembly). Knockout spermatids fail to elongate the axoneme, lack doublet microtubules and show disorganized 9+2, dynein arm, outer dense fiber and fibrous sheath structures, while ventricle, tracheal and oviduct cilia are normal. Participation test - the protein is a structural light chain of the dynein-2 IFT motor whose subunits fail to assemble in knockout spermatid flagella, and IFT is part of cilium assembly, so it contributes structure to the machinery that builds the axoneme rather than being a downstream requirement only. Comparator check - other mouse IFT and axonemal-dynein components such as Ift81, Bbs4 and the inner-arm light chain Dnali1 carry GO:0120316 by IMP. The human evidence for primary-cilium assembly is a separate, milder effect captured by the regulation of cilium assembly row. supported_by: - reference_id: PMID:39827215 supporting_text: Thus, the cause of the failure of flagellar elongation in Tctex1d2−/− mice was disruption of the axonemal structure. - reference_id: PMID:39827215 supporting_text: "In contrast to the severe defects in sperm flagella, cilia of the ventricles, trachea, and oviducts\ \ showed no abnormal morphology in Tctex1d2−/− mice (Fig. S3A–C)." - reference_id: PMID:39827215 supporting_text: From the above, TCTEX1D2 functions in the assembly and structural stability of the cytoplasmic dynein 2 subunits in sperm flagellum formation. proposed_replacement_terms: - id: GO:0120316 label: sperm flagellum assembly - term: id: GO:0097546 label: ciliary base evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Ortholog transfer of the human ciliary-base localization, consistent with dynein-2 recruitment to the basal body; not tested in mouse. action: ACCEPT reason: Endogenous human TCTEX1D2 is at the ciliary base, where IFT dynein is loaded onto trains; the location is part of the core retrograde IFT context and the one-to-one ortholog transfer is reasonable. supported_by: - reference_id: PMID:25830415 supporting_text: Tctex1d2 associates with Wdr34, Wdr60, and other subunits of Dync1 and Dync2 and colocalizes with Wdr60 to microtubule organizing centers during interphase, the mitotic spindle poles during cell division, and the base of the cilium in ciliated cells. - term: id: GO:0120293 label: dynein axonemal particle evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0542 review: summary: SubCell mapping of a UniProt location transferred from human, where it was itself curator-inferred. No experiment places mouse or human DYNLT2B in dynein axonemal particles. action: UNDECIDED reason: Dynein axonemal particles are cytoplasmic preassembly foci for axonemal dyneins. The mouse association with inner-arm intermediate chains WDR63/WDR78 and axonemal localization make passage through these particles plausible, but this has not been tested; the call is left open, matching the human review. supported_by: - reference_id: PMID:39827215 supporting_text: Further, co-immunoprecipitation studies revealed that TCTEX1D2 interacted with WDR63 and WDR78 (Fig. 2D). - term: id: GO:0120293 label: dynein axonemal particle evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in supporting_entities: - UniProtKB:Q8WW35 review: summary: ISS from human DYNLT2B, whose own dynein axonemal particle annotation lacks experimental support. action: UNDECIDED reason: Same claim as the SubCell row; the donor-side localization is not experimentally established, so the transfer is unverified rather than wrong. supported_by: - reference_id: PMID:39827215 supporting_text: These results showed that TCTEX1D2 is an axoneme component in mice. - term: id: GO:1902017 label: regulation of cilium assembly evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: Transferred from a human IMP in which TCTEX1D2 depletion lengthened primary cilia; a downstream consequence of impaired retrograde IFT, not tested in mouse. action: KEEP_AS_NON_CORE reason: The human donor shows that depleted cells still form cilia but they are longer, a typical retrograde IFT phenotype. Mouse somatic motile cilia appear normal in the knockout and primary cilia were not examined. Kept as non-core, consistent with the human review. supported_by: - reference_id: PMID:25205765 supporting_text: In all cases, we can detect a statistically significant increase in cilia length following TCTEX1D2 depletion. - term: id: GO:1905799 label: regulation of intraciliary retrograde transport evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 - ensembl:ENSP00000324323 review: summary: The protein is a subunit of the motor that performs retrograde IFT, so participation rather than regulation is the appropriate claim. action: MODIFY reason: Loss of TCTEX1D2 impairs retrograde IFT and destabilizes the IFT dynein motor, which is evidence that the protein is part of the machinery executing the process, not a modulator of a process executed by others. Lateral correction to GO:0035721, which the gene already carries; same action as on the human ortholog. supported_by: - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. proposed_replacement_terms: - id: GO:0035721 label: intraciliary retrograde transport - term: id: GO:1905799 label: regulation of intraciliary retrograde transport evidence_type: ISO original_reference_id: GO_REF:0000119 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 review: summary: Ortholog transfer of a human regulation term; better captured as participation in retrograde IFT. action: MODIFY reason: Same claim as the IEA row; the donor human annotation was itself modified to intraciliary retrograde transport in the human review. supported_by: - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. proposed_replacement_terms: - id: GO:0035721 label: intraciliary retrograde transport propagation_review: root_cause: NO_FAILURE_CORE failure_modes: [] source_entities: - source_id: UniProtKB:Q8WW35 comment: Human donor's regulation term was itself modified to participation in retrograde IFT; the underlying biology transfers, the term choice does not. source_status: SUPPORTS_TRANSFER - term: id: GO:1905799 label: regulation of intraciliary retrograde transport evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in supporting_entities: - UniProtKB:Q8WW35 review: summary: UniProt ISS of the human regulation term; better captured as participation in retrograde IFT. action: MODIFY reason: Same claim and correction as the IEA and ISO rows. supported_by: - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. proposed_replacement_terms: - id: GO:0035721 label: intraciliary retrograde transport - term: id: GO:0036126 label: sperm flagellum evidence_type: IDA original_reference_id: PMID:39827215 qualifier: located_in review: summary: FLAG knock-in TCTEX1D2 localizes along the flagellum from round to elongated spermatids and along mature epididymal sperm flagella. action: NEW reason: Direct mouse localization evidence (immunostaining of an endogenous 3xFLAG knock-in that does not perturb spermatogenesis), not yet in GOA. More specific than cilium for the cell type where the gene's requirement is shown. supported_by: - reference_id: PMID:39827215 supporting_text: We found that TCTEX1D2 was localized along the flagella from round spermatids to elongated spermatids. - reference_id: PMID:39827215 supporting_text: These results showed that TCTEX1D2 is an axoneme component in mice. - term: id: GO:0002177 label: manchette evidence_type: IDA original_reference_id: PMID:39827215 qualifier: located_in review: summary: TCTEX1D2 is also seen on the manchette of step 10-14 spermatids. action: NEW reason: Direct mouse immunolocalization of the endogenous tagged protein. The manchette is a microtubule-based transport platform used for intramanchette transport of flagellar components; the localization is observed but its functional significance is untested, so it is non-core. supported_by: - reference_id: PMID:39827215 supporting_text: "TCTEX1D2 was also localized in the manchette, which are transiently formed in step 10–14\ \ spermatids (Fig. 1C)." - term: id: GO:0045503 label: dynein light chain binding evidence_type: IPI original_reference_id: PMID:39827215 qualifier: enables review: summary: TCTEX1D2 co-immunoprecipitates DYNLT1 from mouse testis; for the human ortholog the DYNLT1-DYNLT2B heterodimer is solved crystallographically. action: NEW reason: Heterodimerization with the Tctex light chain DYNLT1 (or DYNLT3) is how DYNLT2B sits in the dynein-2 tail. Mouse testis co-IP recovers DYNLT1, and the human ortholog in the same PANTHER subfamily forms a structurally defined DYNLT1-DYNLT2B heterodimer. The human review replaced protein-binding rows with this term; it is absent from mouse GOA. supported_by: - reference_id: PMID:39827215 supporting_text: In the testes, TCTEX1D2 interacted not only with WDR60 and DYNLT1, but also with WDR34 (Fig. 2A). - reference_id: PMID:38454149 supporting_text: X-ray crystallography structure of DYNLT1-DYNLT2B heterodimer. references: - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity 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: GO_REF:0000107 title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara findings: [] - id: GO_REF:0000108 title: Automatic assignment of GO terms using logical inference, based on on inter-ontology links findings: [] - id: GO_REF:0000119 title: Automated transfer of experimentally-verified manual GO annotation data to mouse-human orthologs findings: [] - id: PMID:39827215 title: TCTEX1D2 is essential for sperm flagellum formation in mice. findings: - statement: Endogenous FLAG-tagged TCTEX1D2 co-immunoprecipitates from mouse testis with dynein-2 subunits WDR34, WDR60 and DYNLT1. supporting_text: In the testes, TCTEX1D2 interacted not only with WDR60 and DYNLT1, but also with WDR34 (Fig. 2A). - statement: TCTEX1D2 co-immunoprecipitates with inner-dynein-arm intermediate chains WDR63 and WDR78. supporting_text: Further, co-immunoprecipitation studies revealed that TCTEX1D2 interacted with WDR63 and WDR78 (Fig. 2D). - statement: TCTEX1D2 is in the axonemal fraction of mouse sperm. supporting_text: These results showed that TCTEX1D2 is an axoneme component in mice. - statement: Knockout spermatids show disrupted axonemes; somatic motile cilia are normal. supporting_text: Thus, the cause of the failure of flagellar elongation in Tctex1d2−/− mice was disruption of the axonemal structure. - statement: Dynein-2 subunits fail to assemble in knockout spermatid flagella. supporting_text: Therefore, cytoplasmic dynein 2 complexes were disrupted in Tctex1d2−/− mice elongated spermatids. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached (PMC11743150). The only mouse experimental study of Dynlt2b; CRISPR knockout plus 3xFLAG knock-in. Not yet curated into GOA (no mouse experimental rows as of this review). - id: PMID:26044572 title: TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Human patient fibroblast and Chlamydomonas Tctex2b retrograde IFT data. Used here only for the human ortholog (same PANTHER subfamily SF7). The Chlamydomonas Tctex2b relationship is stated in the paper as a reciprocal best BLAST match; its PANTHER subfamily placement was not verified, so no function is transferred to mouse from the algal protein alone. - id: PMID:25830415 title: Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Human cell localization (MTOC, spindle poles, ciliary base) that underlies the Ensembl Compara transfers. - id: PMID:25205765 title: Subunit composition of the human cytoplasmic dynein-2 complex. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Human dynein-2 proteomics identifying TCTEX1D2 as the dynein-2-specific light chain; cilia length phenotype. - id: PMID:29742051 title: Interaction of WDR60 intermediate chain with TCTEX1D2 light chain of the dynein-2 complex is crucial for ciliary protein trafficking. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Human KO cells; WDR60-TCTEX1D2-DYNLT1/DYNLT3 subcomplex mapping. - id: PMID:38454149 title: Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Structural basis of the DYNLT1-DYNLT2B heterodimer (human proteins). core_functions: - description: Structural Tctex-type light chain of cytoplasmic dynein-2. Mouse testis co-IP shows association with the dynein-2 intermediate chains WDR34/WDR60 and the light chain DYNLT1; its role in retrograde intraflagellar transport is inferred from the human ortholog in the same PANTHER subfamily. molecular_function: id: GO:0045505 label: dynein intermediate chain binding in_complex: id: GO:0005868 label: cytoplasmic dynein complex directly_involved_in: - id: GO:0035721 label: intraciliary retrograde transport locations: - id: GO:0005929 label: cilium - id: GO:0097546 label: ciliary base supported_by: - reference_id: PMID:39827215 supporting_text: In the testes, TCTEX1D2 interacted not only with WDR60 and DYNLT1, but also with WDR34 (Fig. 2A). - reference_id: PMID:26044572 supporting_text: Affinity proteomics indicates that TCTEX1D2/Tctex2b is an integral component of IFT dynein. We demonstrate a retrograde IFT defect in TCTEX1D2-deficient human fibroblasts and Tctex2b-deficient Chlamydomonas cells, and find that IFT dynein is partially destabilized by loss of Tctex2b in Chlamydomonas. - description: Required in mouse for sperm flagellum assembly - an axonemal component of developing and mature sperm flagella, associated with inner-dynein-arm intermediate chains WDR63/WDR78, whose loss disorganizes the spermatid axoneme and the localization of dynein-2 and IFT88 while sparing somatic motile cilia (mouse-experimental). molecular_function: id: GO:0045505 label: dynein intermediate chain binding directly_involved_in: - id: GO:0120316 label: sperm flagellum assembly locations: - id: GO:0036126 label: sperm flagellum - id: GO:0005930 label: axoneme supported_by: - reference_id: PMID:39827215 supporting_text: Further, co-immunoprecipitation studies revealed that TCTEX1D2 interacted with WDR63 and WDR78 (Fig. 2D). - reference_id: PMID:39827215 supporting_text: Thus, the cause of the failure of flagellar elongation in Tctex1d2−/− mice was disruption of the axonemal structure. suggested_questions: - question: Is mouse TCTEX1D2 a stoichiometric light chain of an inner-arm axonemal dynein (the WDR63/WDR78-containing species), or does the co-IP reflect transient association during dynein-2/IFT transport of axonemal cargo? Answering this decides whether an inner dynein arm (GO:0036156) or axonemal dynein complex annotation is warranted. - question: Why does loss of Dynlt2b disrupt sperm flagellum assembly but not somatic motile cilia - is there a testis-biased paralog compensation, or does the long sperm axoneme have a stricter requirement for full dynein-2 stability? suggested_experiments: - description: Live imaging of retrograde IFT (e.g. fluorescent IFT88 or DYNC2LI1) in Dynlt2b-/- mouse fibroblast or tracheal cultures to establish directly in mouse whether retrograde IFT frequency and velocity are reduced, as in human and Chlamydomonas. - description: Cryo-ET subtomogram averaging of wild-type versus Dynlt2b-/- spermatid or tracheal axonemes to test whether a light-chain density is missing from specific inner dynein arms.