id: F1QZE9 gene_symbol: tmc2b product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: 'tmc2b (transmembrane channel-like 2b) is one of two zebrafish co-orthologs of vertebrate TMC2, the other being tmc2a; it lies on chromosome 5 about 5 kb from tmc1. Tmc2b is a multi-pass membrane protein of the TMC family and a pore-forming subunit of the hair-cell mechanoelectrical transduction (MET) channel, a non-selective, calcium-permeable cation channel opened by tip-link tension. GFP-tagged Tmc2b localizes to the tips of stereocilia, and its delivery to the hair bundle requires Tomt and Tmie. tmc2b is expressed only in sensory hair cells: it is the dominant Tmc transcript in lateral-line neuromasts and, in the inner ear, is expressed with tmc1 in peripheral (extrastriolar) hair cells. Tmc2b is required for mechanotransduction in most lateral-line hair cells, with Tmc2a supplying the rest, and is the main contributor to utricular (vestibular) function at low frequencies; in the saccule it contributes to hearing behind Tmc2a. A hair-cell Tmc2b transgene restores transduction, hearing and balance in larvae lacking tmc1, tmc2a and tmc2b.' existing_annotations: - term: id: GO:0005245 label: voltage-gated calcium channel activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - MGI:MGI:2151017 - PANTHER:PTN002761430 review: summary: Voltage-gated calcium channel activity, propagated from the PANTHER TMC2 node (mouse Tmc2 donor). action: MODIFY reason: 'Same assessment as for tmc2a: TMC channels are gated by tip-link tension, not membrane voltage, and are non-selective, calcium-permeable cation channels. Tmc2b sits at stereocilia tips and is required for lateral-line transduction, consistent with a mechanically gated channel subunit.' proposed_replacement_terms: - id: GO:0140135 label: mechanosensitive monoatomic cation channel activity supported_by: - &id001 reference_id: PMID:29269857 supporting_text: First, by transgenesis, we showed that full-length Tmc2b fused to GFP localizes to the tips of neuromast stereocilia (Fig. 2a, b), fulfilling a key requirement of being a component of the mechanotransduction apparatus in zebrafish hair cells. - &id002 reference_id: PMID:39773557 supporting_text: Significant progress in our understanding of MET has been recently made by identifying the transmembrane channel-like proteins 1 and 2 (TMC1 and TMC2) as the pore-forming subunits of the MET channel (Kawashima et al., 2011; Pan et al., 2018). propagation_review: root_cause: TERM_SCOPING_PROBLEM failure_modes: - GRANULARITY_MISMATCH source_entities: - source_id: MGI:MGI:2151017 source_label: Tmc2 (mouse) source_status: SOURCE_BAD comment: QuickGO shows mouse Tmc2 carries GO:0005245 by IMP/IGI from PMID:23871232, a study of calcium permeability and single-channel currents of the mechanically gated hair-cell channel, not of voltage gating (as traced in the human TMC1 review). - source_id: PANTHER:PTN002761430 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: The node correctly groups vertebrate TMC2 orthologs including both zebrafish copies; only the gating mechanism in the chosen term is wrong. - term: id: GO:0005886 label: plasma membrane evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:2151016 - PANTHER:PTN001151822 - WB:WBGene00020490 - ZFIN:ZDB-GENE-060526-280 review: summary: Plasma membrane location propagated across the TMC family. action: ACCEPT reason: Tmc2b-GFP localizes to the tips of stereocilia, which are plasma-membrane protrusions. Correct but general. supported_by: - *id001 - term: id: GO:0005886 label: plasma membrane evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: located_in supporting_entities: - InterPro:IPR038900 review: summary: Plasma membrane from the InterPro TMC family signature. action: ACCEPT reason: Consistent with the IBA row and with stereocilia-tip localization of Tmc2b-GFP. - term: id: GO:0008381 label: mechanosensitive monoatomic ion channel activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - MGI:MGI:2151017 - PANTHER:PTN001151822 review: summary: Mechanosensitive ion channel activity asserted at the PANTHER TMC node. action: ACCEPT reason: Core function. Tmc2b is required for mechanotransduction in most lateral-line hair cells, and a hair-cell Tmc2b transgene restores transduction in all end organs of tmc1/tmc2a/tmc2b triple mutants, showing that Tmc2b alone can support the channel. The more precise child GO:0140135 is recorded in core_functions. supported_by: - &id007 reference_id: PMID:29269857 supporting_text: 94 ± 1.2% (n = 55) of control hair cells loaded fluorophore; in contrast, 35 ± 1.8% (n = 48) of tmc2b −/− hair cells loaded (Fig. 3d), confirming Tmc2b is absolutely required for a subpopulation of hair cells within a single neuromast. - &id005 reference_id: PMID:32371604 supporting_text: The results described above (1) confirm the expectation that concurrent disruption of tmc1/2a/2b leads to complete loss of MET activity and (2) reveal that exogenous Tmc2b-mEGFP can rescue auditory/vestibular deficits and restore FM labeling in all mechanosensory end organs. - *id002 - term: id: GO:0016020 label: membrane evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - InterPro:IPR012496 - UniProtKB-SubCell:SL-0162 review: summary: Membrane, from InterPro and UniProt subcellular location. action: ACCEPT reason: Correct; less specific than plasma membrane. - term: id: GO:0034220 label: monoatomic ion transmembrane transport evidence_type: IEA original_reference_id: GO_REF:0000108 qualifier: involved_in supporting_entities: - GO:0008381 review: summary: Ion transmembrane transport inferred from the mechanosensitive ion channel activity. action: MODIFY reason: 'Correct in kind but under-specific: the MET channel conducts cations. Same modification as for tmc2a and human TMC1.' proposed_replacement_terms: - id: GO:0098655 label: monoatomic cation transmembrane transport - term: id: GO:0042472 label: inner ear morphogenesis evidence_type: IEP original_reference_id: PMID:25114259 qualifier: involved_in review: summary: Inner ear morphogenesis, inferred from tmc2b expression in the ear. action: REMOVE reason: Expression in otic hair cells does not show a role in shaping the ear. tmc2b is expressed only in hair cells, the protein is a transduction channel subunit, and hair bundles and other MET components are intact in tmc triple mutants. supported_by: - &id003 reference_id: PMID:25114259 supporting_text: In contrast to the broad expression pattern of pcdh15a in the larval brain and sensory hair cells ( 5 ), expression of tmc1 , tmc2a , and tmc2b genes was restricted to hair cells of the inner ear and lateral line organ - &id004 reference_id: PMID:32371604 supporting_text: Together, these results suggest that hair bundles are intact and central components of the MET complex are properly localized in tmc triple mutants. - term: id: GO:0048839 label: inner ear development evidence_type: IEP original_reference_id: PMID:25114259 qualifier: involved_in review: summary: Inner ear development, inferred from tmc2b expression in the ear. action: REMOVE reason: 'Same as inner ear morphogenesis: an expression pattern, not evidence of a developmental role; tmc mutant hair bundles form normally.' supported_by: - *id003 - *id004 - term: id: GO:0048884 label: neuromast development evidence_type: IEP original_reference_id: PMID:25114259 qualifier: involved_in review: summary: Neuromast development, inferred from tmc2b expression in neuromast hair cells. action: REMOVE reason: The annotation rests on expression. tmc2b mutants have normal hair bundles; their posterior neuromasts have about one-third fewer hair cells, a reduction also seen in other transduction mutants and most simply read as a consequence of lost transduction rather than a role of the channel subunit in building the organ. supported_by: - reference_id: PMID:25114259 supporting_text: In the lateral-line neuromasts, only tmc2b was robustly detected by in situ hybridization - &id006 reference_id: PMID:29269857 supporting_text: In mutants, no defects in hair bundle morphology (Supplementary Fig. 2a–d) or hearing (Supplementary Fig. 2f, g) were observed. - reference_id: PMID:29269857 supporting_text: However, posterior neuromasts of mutants had a mild reduction in hair cell numbers (approximately one-third decrease, 6 dpf; Supplementary Fig. 2c–e; Supplementary Fig. 3 ). - term: id: GO:0050910 label: detection of mechanical stimulus involved in sensory perception of sound evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:2151017 - PANTHER:PTN002761430 - UniProtKB:Q8TDI7 - ZFIN:ZDB-GENE-060526-262 - ZFIN:ZDB-GENE-060526-280 review: summary: Detection of mechanical stimulus involved in sensory perception of sound, from the PANTHER TMC2 node. action: ACCEPT reason: 'Tmc2b contributes to hearing, although less than Tmc2a: tmc2b single mutants hear, but tmc2a/tmc2b double mutants have lower saccular microphonics than tmc2a single mutants, and in the absence of Tmc2a most of the remaining current is carried by Tmc2b. A Tmc2b transgene restores hearing in triple mutants.' supported_by: - reference_id: PMID:32371604 supporting_text: These results suggest that Tmc2b makes some contribution to macular hair-cell activity. - reference_id: PMID:32167554 supporting_text: However, in the absence of Tmc2a, most of the remaining current is carried by Tmc2b. - *id005 - term: id: GO:0050910 label: detection of mechanical stimulus involved in sensory perception of sound evidence_type: IGI original_reference_id: PMID:29269857 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-190604-15 review: summary: Sound-detection term from the tmc2a/tmc2b double mutant of Chou et al. 2017. action: MODIFY reason: The double mutant was assayed in the lateral line in this paper, where transduction was abolished; the lateral line detects water motion, not sound. The finding belongs under the general mechanosensory detection term (same change as on the tmc2a row). Hearing is covered by the IBA row. proposed_replacement_terms: - id: GO:0050974 label: detection of mechanical stimulus involved in sensory perception supported_by: - reference_id: PMID:29269857 supporting_text: Stimulus-evoked microphonic potentials were not detectable in neuromasts with A–P orientations in the PLL of tmc2a −/− /tmc2b −/− larvae (Fig. 8a, b) at 6 dpf, yet robust signatures were apparent in controls. - term: id: GO:0050910 label: detection of mechanical stimulus involved in sensory perception of sound evidence_type: IMP original_reference_id: PMID:29269857 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-190604-1 review: summary: Sound-detection term from the tmc2b single mutant of Chou et al. 2017. action: MODIFY reason: The paper reports that tmc2b single mutants have no hearing defect; the phenotype is loss of transduction in most lateral-line hair cells. The mechanosensory role is real, but the sound-perception child is contradicted for this genotype, so the row should move to the general detection term. proposed_replacement_terms: - id: GO:0050974 label: detection of mechanical stimulus involved in sensory perception supported_by: - *id006 - *id007 - term: id: GO:0060005 label: vestibular reflex evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:2151017 - PANTHER:PTN002761430 review: summary: Vestibular reflex, from the PANTHER TMC2 node. action: KEEP_AS_NON_CORE reason: Organism-level reflex downstream of utricular transduction. Both double-mutant combinations that reduce vestibular-induced eye movements include the tmc2b allele, and Tmc2b suffices for low-frequency responses; correct, but a consequence of the channel function. supported_by: - &id008 reference_id: PMID:32371604 supporting_text: The two double-mutant combinations that gave rise to a deficit included the tmc2b sa8817 allele, suggesting that Tmc2b is the primary contributor to vestibular end organ function. - reference_id: PMID:37952940 supporting_text: In contrast, tmc1/2a mutants were comparable to WT siblings, suggesting that tmc2b was sufficient to mediate responses at sub-Hz frequencies. - term: id: GO:0070588 label: calcium ion transmembrane transport evidence_type: IEA original_reference_id: GO_REF:0000108 qualifier: involved_in supporting_entities: - GO:0005245 review: summary: Calcium ion transmembrane transport inferred from the channel activity terms. action: ACCEPT reason: Calcium entry through the MET channel follows from the channel activity; Tmc2b-only neuromast bundles show mechanically evoked calcium signals. supported_by: - reference_id: PMID:36905930 supporting_text: This idea is supported by our results, as we show that the calcium signals in hair bundles expressing both Tmc2b and Tmc2a are larger compared to those expressing just Tmc2b (Figure 6). - term: id: GO:0032426 label: stereocilium tip evidence_type: IDA original_reference_id: PMID:29269857 review: summary: Full-length Tmc2b-GFP localizes to the tips of stereocilia in neuromast hair cells, and Tmc2b-GFP is present in inner-ear hair bundles. action: NEW reason: Direct localization of the full-length tagged protein, reproduced by several groups, with the hair-bundle signal lost in tomt and tmie mutants that block its trafficking. This is the site where the channel works and is more informative than the plasma membrane rows. No equivalent data exist for Tmc2a (its transgene did not express), so the term is proposed for tmc2b only. supported_by: - *id001 - reference_id: PMID:28534737 supporting_text: We find that GFP-tagged Tmc1 and Tmc2b fail to localize to the hair bundle in mercury mutants, and that Tomt can rescue this trafficking defect. - reference_id: PMID:30726219 supporting_text: In tmie zebrafish mutants, we observed that GFP-tagged Tmc1 and Tmc2b, which are subunits of the MET channel, fail to target to the hair bundle. 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:0000108 title: Automatic assignment of GO terms using logical inference, based on on inter-ontology links findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:25114259 title: Tip-link protein protocadherin 15 interacts with transmembrane channel-like proteins TMC1 and TMC2. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. Names the pair; tmc2b is the tmc transcript robustly detected in neuromasts by in situ hybridization; tmc1 and tmc2b are adjacent on chr5. - id: PMID:29269857 title: A molecular basis for water motion detection by the mechanosensory lateral line of zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: 'Full text. tmc2b TALEN mutant: lateral-line transduction lost in most hair cells, hearing normal; Tmc2b-GFP at stereocilia tips; double mutant abolishes lateral-line transduction.' - id: PMID:32167554 title: Tmc proteins are essential for zebrafish hearing where Tmc1 is not obligatory. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text. Tmc2b carries most saccular current when Tmc2a is absent. - id: PMID:32371604 title: Disruption of tmc1/2a/2b Genes in Zebrafish Reveals Subunit Requirements in Subtypes of Inner Ear Hair Cells. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text. Tmc2b-mEGFP rescues tmc triple mutants in all end organs; Tmc2b primary for vestibular function; tmc2b sa8817 allele. - id: PMID:37952940 title: Transmembrane Channel-Like (Tmc) Subunits Contribute to Frequency Sensitivity in the Zebrafish Utricle. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. tmc2b co-expressed with tmc1 in extrastriola; sufficient for low-frequency utricular responses. - id: PMID:38035267 title: Differential expression of mechanotransduction complex genes in auditory/vestibular hair cells in zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: 'Full text. HCR maps: tmc2b peripheral/extrastriolar with tmc1.' - id: PMID:36905930 title: Asymmetric mechanotransduction by hair cells of the zebrafish lateral line. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. Tmc2b in all neuromast hair cells, Tmc2a only in one orientation. - id: PMID:28534737 title: Integration of Tmc1/2 into the mechanotransduction complex in zebrafish hair cells is regulated by Transmembrane O-methyltransferase (Tomt). findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. Tmc2b-GFP bundle localization requires Tomt; Tmc2b-GFP rescues tmc2b sa8817. - id: PMID:30726219 title: Subunits of the mechano-electrical transduction channel, Tmc1/2b, require Tmie to localize in zebrafish sensory hair cells. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. Tmc2b-GFP bundle localization requires Tmie. - id: PMID:39773557 title: Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. Family-level statement that TMC1/2 are pore-forming MET subunits. - id: file:DANRE/tmc2a/tmc2a-bioinformatics/RESULTS.md title: tmc2a / tmc2b identity, conserved synteny and expression records reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified the sidecar supports a TGD-consistent origin and public hair-cell expression records for both copies; it does not distinguish TGD from segmental duplication by synteny alone. findings: [] core_functions: - description: Pore-forming subunit of the hair-cell mechanoelectrical transduction channel at stereocilia tips; the main Tmc subunit of lateral-line and extrastriolar inner-ear hair cells. Recorded as a contribution because the channel also needs other subunits (Tmie, Lhfpl5, Cib2/3). contributes_to_molecular_function: id: GO:0140135 label: mechanosensitive monoatomic cation channel activity directly_involved_in: - id: GO:0050974 label: detection of mechanical stimulus involved in sensory perception - id: GO:0050910 label: detection of mechanical stimulus involved in sensory perception of sound - id: GO:0098655 label: monoatomic cation transmembrane transport locations: - id: GO:0032426 label: stereocilium tip supported_by: - *id001 - *id007 - *id005 - *id008 suggested_questions: - question: Can Tmc2a substitute for Tmc2b in the lateral-line hair cells that depend absolutely on Tmc2b (e.g. anterior-facing cells of posterior neuromasts) if it is expressed there? This would decide whether the pair split by expression only. - question: What sets the Tmc2b-independent residual transduction in neuromasts IO4, SO1 and SO3, given that tmc2a is barely detectable in the lateral line by in situ hybridization? - question: Is the reduced neuromast hair-cell number in tmc2b mutants a general consequence of lost transduction, or a Tmc2b-specific role in hair-cell maintenance? suggested_experiments: - hypothesis: Tmc2a and Tmc2b proteins are interchangeable and the pair differs only in expression. description: Express Tmc2a under the tmc2b regulatory region (or a lateral-line-specific driver) in tmc2b mutants and score dye uptake and microphonics in posterior neuromasts. experiment_type: cross-rescue - hypothesis: The utricular low-frequency role of Tmc2b reflects its extrastriolar expression rather than channel properties. description: Compare MET current kinetics and adaptation in extrastriolar hair cells of tmc1/tmc2a double mutants (Tmc2b only) and striolar cells of tmc1/tmc2b double mutants (Tmc2a only). experiment_type: electrophysiology