id: E3W6T6 gene_symbol: tbx5b product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: >- T-box transcription factor 5b, the second zebrafish co-ortholog of human TBX5. It was retained from the teleost genome duplication and is paralogous to tbx5a (heartstrings). It has a T-box DNA-binding domain about 83% identical to that of tbx5a, while the rest of the protein, including a shorter C-terminal region (422 aa), is poorly conserved. It is expressed in the heart field and heart, becoming restricted to the ventricle from about 36 hpf, and in the dorsal retina. Expression starts later and is lower than tbx5a, and expression in the pectoral fin bud is weak or undetected. tbx5b is required in the heart: morphants and a frameshift mutant fail to complete cardiac looping, develop cardiac edema and die by about 6 dpf. It is also required for timely pectoral fin outgrowth and the medio-lateral migration of fin-field cells, but not for fin bud initiation, which depends on tbx5a. With tbx5a it contributes to dorsoventral patterning of the retina. Its roles are not interchangeable with those of tbx5a: tbx5a mRNA does not rescue tbx5b loss, and the reverse also fails. existing_annotations: - term: id: GO:0000785 label: chromatin evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:102539 - MGI:MGI:1201683 - MGI:MGI:98472 - PANTHER:PTN004251338 - UniProtKB:O15178 - ZFIN:ZDB-GENE-020416-5 - ZFIN:ZDB-GENE-980526-437 - ZFIN:ZDB-GENE-990615-5 review: summary: Active in chromatin (IBA). action: ACCEPT reason: >- Expected of a T-box transcription factor; inherited from the Tbx2/3/4/5 node. tbx5b keeps a T-box domain (UniProt 57-237) that is 83% identical to the tbx5a T-box (PMID:39079985), and the IBA node covers the Tbx2/3/4/5 subfamily. No direct DNA-binding or reporter assay has been published for Tbx5b. But tbx5b mRNA rescues its own morphant (PMID:24759614), and an intronic frameshift allele that truncates the protein before the T-box phenocopies the morphant (PMID:30532148). Together these point to a functional T-box transcription factor. The UniProt caution that some PROSITE T-box residues are not conserved is noted, but there is no evidence of lost DNA binding. Kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - MGI:MGI:102539 - MGI:MGI:102541 - MGI:MGI:107404 - MGI:MGI:1277234 - MGI:MGI:1888496 - MGI:MGI:1891158 - MGI:MGI:1923615 - MGI:MGI:98472 - MGI:MGI:98494 - MGI:MGI:98495 - PANTHER:PTN004251338 - UniProtKB:O15119 - UniProtKB:O15178 - UniProtKB:Q13207 - UniProtKB:Q99593 review: summary: RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA). action: ACCEPT reason: >- tbx5b keeps a T-box domain (UniProt 57-237) that is 83% identical to the tbx5a T-box (PMID:39079985), and the IBA node covers the Tbx2/3/4/5 subfamily. No direct DNA-binding or reporter assay has been published for Tbx5b. But tbx5b mRNA rescues its own morphant (PMID:24759614), and an intronic frameshift allele that truncates the protein before the T-box phenocopies the morphant (PMID:30532148). Together these point to a functional T-box transcription factor. The UniProt caution that some PROSITE T-box residues are not conserved is noted, but there is no evidence of lost DNA binding. Kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - reference_id: PMID:30532148 supporting_text: >- There are high levels of conservation at the amino acid level in the Tbox domain between the two paralogues but there are low levels of conservation throughout the rest of the protein [10]. - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR001699 review: summary: >- RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA, InterPro T-box). action: ACCEPT reason: >- tbx5b keeps a T-box domain (UniProt 57-237) that is 83% identical to the tbx5a T-box (PMID:39079985), and the IBA node covers the Tbx2/3/4/5 subfamily. No direct DNA-binding or reporter assay has been published for Tbx5b. But tbx5b mRNA rescues its own morphant (PMID:24759614), and an intronic frameshift allele that truncates the protein before the T-box phenocopies the morphant (PMID:30532148). Together these point to a functional T-box transcription factor. The UniProt caution that some PROSITE T-box residues are not conserved is noted, but there is no evidence of lost DNA binding. Kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - FB:FBgn0011723 - FB:FBgn0028789 - FB:FBgn0035956 - FB:FBgn0261963 - MGI:MGI:102541 - MGI:MGI:1277234 - MGI:MGI:1352483 - MGI:MGI:1888496 - MGI:MGI:1888984 - MGI:MGI:1891158 - MGI:MGI:1923615 - MGI:MGI:98472 - MGI:MGI:98493 - PANTHER:PTN004251338 - UniProtKB:O15119 - UniProtKB:O15178 - UniProtKB:Q13207 - UniProtKB:Q99593 - UniProtKB:Q9UL17 - UniProtKB:Q9UMR3 - ZFIN:ZDB-GENE-001228-1 review: summary: DNA-binding transcription factor activity, RNA polymerase II-specific (IBA). action: ACCEPT reason: >- tbx5b keeps a T-box domain (UniProt 57-237) that is 83% identical to the tbx5a T-box (PMID:39079985), and the IBA node covers the Tbx2/3/4/5 subfamily. No direct DNA-binding or reporter assay has been published for Tbx5b. But tbx5b mRNA rescues its own morphant (PMID:24759614), and an intronic frameshift allele that truncates the protein before the T-box phenocopies the morphant (PMID:30532148). Together these point to a functional T-box transcription factor. The UniProt caution that some PROSITE T-box residues are not conserved is noted, but there is no evidence of lost DNA binding. Kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - reference_id: PMID:24759614 supporting_text: >- Similarly, a full-length tbx5b form was able to rescue the jogging phenotype of tbx5b morphants when co-injected with our tbx5b MO (figure 3b; n = 117). - reference_id: PMID:30532148 supporting_text: >- This mutation would result in a splicing error such that the first intron is not spliced from the protein, leading to a frameshift starting at amino acid 53 and a premature stop codon after 16 incorrect amino acids (Fig 1C). - term: id: GO:0001708 label: cell fate specification evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0261963 - MGI:MGI:102539 - MGI:MGI:1201683 - MGI:MGI:98493 - PANTHER:PTN000137774 - WB:WBGene00003106 - WB:WBGene00003376 - WB:WBGene00006543 - WB:WBGene00006554 - ZFIN:ZDB-GENE-001228-1 - ZFIN:ZDB-GENE-990726-27 review: summary: Cell fate specification (IBA, T-box family node). action: KEEP_AS_NON_CORE reason: >- A broad, family-wide T-box function. No tbx5b-specific fate-specification data exist; the related tbx5a roles are in proepicardium and cardiac precursor specification. Kept as non-core, as for tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0001947 label: heart looping evidence_type: IGI original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-060328-2 - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Heart looping (IGI, tbx5a + tbx5b double morphants). action: ACCEPT reason: >- tbx5b morphants fail to complete looping, and sub-threshold double knockdown also blocks looping (PMID:24759614). The tbx5b CRISPR mutant confirms it: the heart fails to loop (PMID:30532148). Shared with tbx5a and non-redundant, since each single loss is enough. supported_by: - reference_id: PMID:24759614 supporting_text: >- Similarly, injection of tbx5b MO also caused heart looping defects (81%, n = 108), and these embryos displayed D-looped (52%), L-looped (16%) and no-looped (34%) cardiac morphologies - reference_id: PMID:24759614 supporting_text: >- Although, in agreement with a previous report [17], the severity of the phenotype was not enhanced by double knock-down, downregulation of both genes increased the penetrance of the phenotype (figure 1i). - reference_id: PMID:30532148 supporting_text: >- The heart fails to loop and a fluid filled edema forms surrounding the heart (Fig 1E and 1F). - term: id: GO:0001947 label: heart looping evidence_type: IMP original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Heart looping (IMP, tbx5b morpholino). action: ACCEPT reason: >- Seen in tbx5b morphants (PMID:24759614) and confirmed in a tbx5b frameshift mutant (PMID:30532148). supported_by: - reference_id: PMID:24759614 supporting_text: >- Similarly, injection of tbx5b MO also caused heart looping defects (81%, n = 108), and these embryos displayed D-looped (52%), L-looped (16%) and no-looped (34%) cardiac morphologies - reference_id: PMID:30532148 supporting_text: >- The heart fails to loop and a fluid filled edema forms surrounding the heart (Fig 1E and 1F). - reference_id: PMID:30532148 supporting_text: Tbx5b-/- mutants fully phenocopy the reported Tbx5b morphants[10,13]. - term: id: GO:0003007 label: heart morphogenesis evidence_type: IMP original_reference_id: PMID:23226307 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Heart morphogenesis (IMP, tbx5b morpholino). action: ACCEPT reason: >- tbx5b morphants have looping defects and stretched cardiac chambers. Unlike tbx5a morphants, the fins still form (PMID:23226307). supported_by: - reference_id: PMID:23226307 supporting_text: >- MO-Tbx5b injection caused looping defects and stretched cardiac chambers, but it did not induce Tie-2 mis-expression and lack of fins - term: id: GO:0003146 label: heart jogging evidence_type: IGI original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-060328-2 - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Heart jogging (IGI, tbx5a + tbx5b double morphants). action: KEEP_AS_NON_CORE reason: >- Jogging defects are reported only in morphants (PMID:24759614), and the tbx5b mRNA rescue supports morpholino specificity. No tbx5b mutant has been scored for jogging. For tbx5a, mutants (hst and the T-box-truncating oug) jog normally (PMID:34372968), so that row is UNDECIDED in the tbx5a review. For tbx5b there is no contradicting mutant yet, so the term is kept as non-core with a morpholino-only caveat. supported_by: - reference_id: PMID:24759614 supporting_text: >- Similarly, tbx5b morphants displayed left as well as right and middle jogging of their linear heart tubes - reference_id: PMID:24759614 supporting_text: >- Similarly, a full-length tbx5b form was able to rescue the jogging phenotype of tbx5b morphants when co-injected with our tbx5b MO (figure 3b; n = 117). - reference_id: PMID:34372968 supporting_text: >- In such a screen we identified the oudegracht (oug) mutant in which cardiac jogging was unaffected while cardiac looping was compromised. - term: id: GO:0003146 label: heart jogging evidence_type: IMP original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Heart jogging (IMP, tbx5b morpholino). action: KEEP_AS_NON_CORE reason: >- As for the IGI row: morpholino-only, with rescue by tbx5b mRNA (PMID:24759614). Not yet tested in the tbx5b mutant. supported_by: - reference_id: PMID:24759614 supporting_text: >- Similarly, tbx5b morphants displayed left as well as right and middle jogging of their linear heart tubes - reference_id: PMID:24759614 supporting_text: >- Similarly, a full-length tbx5b form was able to rescue the jogging phenotype of tbx5b morphants when co-injected with our tbx5b MO (figure 3b; n = 117). - term: id: GO:0003218 label: cardiac left ventricle formation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:102541 - PANTHER:PTN002601200 - UniProtKB:Q9PWE8 review: summary: Cardiac left ventricle formation (IBA). action: MARK_AS_OVER_ANNOTATED reason: >- Inherited from the Tbx5 clade node, which rests on mammalian left-ventricle data. Zebrafish has a single ventricle. tbx5b is expressed in the ventricle from 36 hpf (PMID:30532148) and is needed for looping, but "left ventricle formation" does not apply to a teleost heart. The same action is taken for tbx5a. supported_by: - reference_id: PMID:30532148 supporting_text: >- Expression in the heart is similar for both paralogues until 36 hpf, when tbx5b expression is restricted to the ventricle, whereas tbx5a expression remains in both chambers of the heart [9]. propagation_review: root_cause: TERM_SCOPING_PROBLEM failure_modes: - LINEAGE_OR_TAXON_MISMATCH source_entities: - source_id: PANTHER:PTN002601200 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: >- The Tbx5-clade node is sound for amniote hearts, which have a left ventricle; teleost hearts have a single ventricle, so the left-ventricle-specific term does not apply to the zebrafish descendants. - source_id: MGI:MGI:102541 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: >- Mouse experimental evidence for left ventricle formation; the anatomy is absent in zebrafish. - term: id: GO:0003677 label: DNA binding evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: enables supporting_entities: - UniRule:UR000400702 review: summary: DNA binding (IEA, UniRule). action: ACCEPT reason: >- Correct but general; GO:0000978 is more informative. tbx5b keeps a T-box domain (UniProt 57-237) that is 83% identical to the tbx5a T-box (PMID:39079985), and the IBA node covers the Tbx2/3/4/5 subfamily. No direct DNA-binding or reporter assay has been published for Tbx5b. But tbx5b mRNA rescues its own morphant (PMID:24759614), and an intronic frameshift allele that truncates the protein before the T-box phenocopies the morphant (PMID:30532148). Together these point to a functional T-box transcription factor. The UniProt caution that some PROSITE T-box residues are not conserved is noted, but there is no evidence of lost DNA binding. Kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0003700 label: DNA-binding transcription factor activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR001699 - InterPro:IPR008967 - InterPro:IPR018186 - InterPro:IPR036960 - InterPro:IPR046360 review: summary: DNA-binding transcription factor activity (IEA, InterPro). action: ACCEPT reason: >- tbx5b keeps a T-box domain (UniProt 57-237) that is 83% identical to the tbx5a T-box (PMID:39079985), and the IBA node covers the Tbx2/3/4/5 subfamily. No direct DNA-binding or reporter assay has been published for Tbx5b. But tbx5b mRNA rescues its own morphant (PMID:24759614), and an intronic frameshift allele that truncates the protein before the T-box phenocopies the morphant (PMID:30532148). Together these point to a functional T-box transcription factor. The UniProt caution that some PROSITE T-box residues are not conserved is noted, but there is no evidence of lost DNA binding. Kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - FB:FBgn0000179 - FB:FBgn0011723 - FB:FBgn0035954 - FB:FBgn0035956 - FB:FBgn0266083 - MGI:MGI:102539 - MGI:MGI:102541 - MGI:MGI:107404 - MGI:MGI:1201683 - MGI:MGI:1277234 - MGI:MGI:1888496 - MGI:MGI:1888984 - MGI:MGI:1923615 - MGI:MGI:98472 - MGI:MGI:98493 - MGI:MGI:98494 - MGI:MGI:98495 - PANTHER:PTN004251338 - RGD:1308264 - UniProtKB:O15119 - UniProtKB:O15178 - UniProtKB:O93288 - UniProtKB:O95935 - UniProtKB:P87377 - UniProtKB:Q13207 - UniProtKB:Q16650 - UniProtKB:Q8IWI9 - UniProtKB:Q8UW76 - UniProtKB:Q99593 - UniProtKB:Q9PWE8 - UniProtKB:Q9UL17 - UniProtKB:Q9Y458 - WB:WBGene00003106 - WB:WBGene00003376 - WB:WBGene00004750 - WB:WBGene00006543 - WB:WBGene00006545 - WB:WBGene00006546 - WB:WBGene00006556 - WB:WBGene00006557 - ZFIN:ZDB-GENE-001228-1 - ZFIN:ZDB-GENE-980526-437 - ZFIN:ZDB-GENE-990615-5 - ZFIN:ZDB-GENE-991124-7 review: summary: Nucleus (IBA). action: ACCEPT reason: >- Expected location of a T-box transcription factor. There is no Tbx5b-specific localization data; kept consistent with tbx5a. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - InterPro:IPR018186 - InterPro:IPR036960 - UniProtKB-SubCell:SL-0191 - UniRule:UR000400702 review: summary: Nucleus (IEA). action: ACCEPT reason: As for the IBA row. - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0086 review: summary: Cytoplasm (IEA, SubCell/ARBA). action: KEEP_AS_NON_CORE reason: >- The inference comes from TBX5 shuttling. Pdlim7 holds zebrafish Tbx5(a) on cytoplasmic actin (PMID:19895804), but this has not been tested for Tbx5b, whose C-terminal region differs from tbx5a's. Kept as non-core, as for tbx5a. supported_by: - reference_id: PMID:19895804 supporting_text: >- As expected, comparable to the chicken protein, full-length Tbx5 was detected in the nucleus but also in the cytoplasm colocalized with Pdlim7 along the actin cytoskeleton - reference_id: PMID:30532148 supporting_text: >- There are high levels of conservation at the amino acid level in the Tbox domain between the two paralogues but there are low levels of conservation throughout the rest of the protein [10]. - term: id: GO:0006355 label: regulation of DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in supporting_entities: - InterPro:IPR001699 - InterPro:IPR008967 - InterPro:IPR018186 - InterPro:IPR036960 review: summary: Regulation of DNA-templated transcription (IEA, InterPro). action: ACCEPT reason: >- A T-box transcription factor. Knocking down tbx5b changes the expression of many genes (PMID:30532148). supported_by: - reference_id: PMID:30532148 supporting_text: >- Specifically, knockdown of tbx5b results in changes in somite size, in the differentiation of vasculature progenitors and in later patterning of trunk blood vessels. - term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0000179 - FB:FBgn0011723 - FB:FBgn0016660 - FB:FBgn0021767 - FB:FBgn0028789 - FB:FBgn0035954 - FB:FBgn0035956 - FB:FBgn0261963 - MGI:MGI:102539 - MGI:MGI:102541 - MGI:MGI:107404 - MGI:MGI:1201683 - MGI:MGI:1277234 - MGI:MGI:1352483 - MGI:MGI:1888496 - MGI:MGI:1888984 - MGI:MGI:1891158 - MGI:MGI:1923615 - MGI:MGI:98472 - MGI:MGI:98493 - MGI:MGI:98494 - MGI:MGI:98495 - PANTHER:PTN004251338 - RGD:735203 - UniProtKB:O15119 - UniProtKB:O15178 - UniProtKB:O95936 - UniProtKB:P24781 - UniProtKB:P87377 - UniProtKB:Q13207 - UniProtKB:Q8AV66 - UniProtKB:Q8AX98 - UniProtKB:Q99593 - UniProtKB:Q9UL17 - UniProtKB:Q9Y458 - WB:WBGene00003106 - WB:WBGene00004750 - WB:WBGene00006554 - ZFIN:ZDB-GENE-991124-7 review: summary: Regulation of transcription by RNA polymerase II (IBA). action: ACCEPT reason: >- As above. tbx5a and tbx5b loss affect partly different target sets (for example bmp4 changes only after tbx5a loss), which suggests different transcriptional networks (PMID:30532148). supported_by: - reference_id: PMID:30532148 supporting_text: >- In the heart, expression of vcana is expanded in embryos deficient in either Tbx5a or Tbx5b, but expression of bmp4 is only restricted in embryos deficient in Tbx5a, not in embryos deficient in Tbx5b[10]. - reference_id: PMID:30532148 supporting_text: >- Specifically, knockdown of tbx5b results in changes in somite size, in the differentiation of vasculature progenitors and in later patterning of trunk blood vessels. - term: id: GO:0007389 label: pattern specification process evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:102541 - PANTHER:PTN002601200 - ZFIN:ZDB-GENE-991124-7 review: summary: Pattern specification process (IBA). action: KEEP_AS_NON_CORE reason: >- tbx5b helps pattern the dorsal retina (with tbx5a) and the medio-lateral migration of fin-field cells (PMID:24759614, PMID:34756968). Broad but correct. supported_by: - reference_id: PMID:24759614 supporting_text: >- suggesting that tbx5 paralogues act redundantly in the dorsal retina to ensure efnb2a expression in this territory. - reference_id: PMID:34756968 supporting_text: >- We show here that loss of Tbx5b function affects initial ML directed movements so that fin field cells fail to migrate laterally but continue to converge along the AP axis. - term: id: GO:0007507 label: heart development evidence_type: IMP original_reference_id: PMID:23441045 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Heart development (IMP, tbx5b morpholino). action: ACCEPT reason: >- tbx5b is needed in the heart for embryonic survival (PMID:23441045). This is confirmed genetically: tbx5b frameshift mutants fail to loop, develop cardiac edema and die by 6 dpf (PMID:30532148). supported_by: - reference_id: PMID:23441045 supporting_text: >- Using morpholino depletion studies, we find that tbx5b is required in the heart for embryonic survival, and influences the timing and morphogenesis of pectoral fin development. - reference_id: PMID:30532148 supporting_text: >- The heart fails to loop and a fluid filled edema forms surrounding the heart (Fig 1E and 1F). - reference_id: PMID:30532148 supporting_text: >- By 6 days, both mutants and morphant embryos die, possibly as a result of the severe heart defects. - term: id: GO:0007507 label: heart development evidence_type: IMP original_reference_id: PMID:23441045 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130702-2 review: summary: Heart development (IMP, second tbx5b morpholino). action: ACCEPT reason: >- As for the first morpholino. Two morpholinos and a mutant agree (PMID:23441045, PMID:30532148). supported_by: - reference_id: PMID:23441045 supporting_text: >- Using morpholino depletion studies, we find that tbx5b is required in the heart for embryonic survival, and influences the timing and morphogenesis of pectoral fin development. - reference_id: PMID:30532148 supporting_text: Tbx5b-/- mutants fully phenocopy the reported Tbx5b morphants[10,13]. - term: id: GO:0009653 label: anatomical structure morphogenesis evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00026583 review: summary: Anatomical structure morphogenesis (IEA, ARBA). action: ACCEPT reason: >- Broad but true: tbx5b is needed for heart and pectoral fin morphogenesis (PMID:30532148). supported_by: - reference_id: PMID:30532148 supporting_text: >- The heart fails to loop and a fluid filled edema forms surrounding the heart (Fig 1E and 1F). - reference_id: PMID:30532148 supporting_text: Tbx5b-/- mutants also exhibit similar fin defects to the Tbx5b morphants. - term: id: GO:0021554 label: optic nerve development evidence_type: IGI original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-060328-2 - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Optic nerve development (IGI, tbx5a + tbx5b double morphants). action: KEEP_AS_NON_CORE reason: >- Only double morphants have a thinner optic nerve (PMID:24759614). A shared, additive, morpholino-only retinal role, the same as for tbx5a. supported_by: - reference_id: PMID:24759614 supporting_text: >- Moreover, and in agreement with both tbx5 genes acting redundantly to ensure proper optic nerve formation, double-morphant embryos showed a significantly thinner optic nerve (figure 4n). - term: id: GO:0033339 label: pectoral fin development evidence_type: IMP original_reference_id: PMID:23441045 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Pectoral fin development (IMP, tbx5b morpholino). action: ACCEPT reason: >- tbx5b is needed for normal pectoral fin outgrowth and shape, but not for fin bud initiation (which needs tbx5a). tbx5b morphants have small, delayed fins, and fin-field cells fail to migrate medio-laterally (PMID:24759614, PMID:34756968). A tbx5b frameshift mutant reproduces the fin defect (PMID:30532148). Whether tbx5b is expressed in the fin at all is disputed (not detected in PMID:19925885; low levels in PMID:23441045), so this role may be partly non-cell-autonomous. This asymmetry in fin roles is copy-specific and should be kept. supported_by: - reference_id: PMID:23441045 supporting_text: >- Using morpholino depletion studies, we find that tbx5b is required in the heart for embryonic survival, and influences the timing and morphogenesis of pectoral fin development. - reference_id: PMID:30532148 supporting_text: Tbx5b-/- mutants also exhibit similar fin defects to the Tbx5b morphants. - term: id: GO:0033339 label: pectoral fin development evidence_type: IMP original_reference_id: PMID:23441045 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130702-2 review: summary: Pectoral fin development (IMP, second tbx5b morpholino). action: ACCEPT reason: >- tbx5b is needed for normal pectoral fin outgrowth and shape, but not for fin bud initiation (which needs tbx5a). tbx5b morphants have small, delayed fins, and fin-field cells fail to migrate medio-laterally (PMID:24759614, PMID:34756968). A tbx5b frameshift mutant reproduces the fin defect (PMID:30532148). Whether tbx5b is expressed in the fin at all is disputed (not detected in PMID:19925885; low levels in PMID:23441045), so this role may be partly non-cell-autonomous. This asymmetry in fin roles is copy-specific and should be kept. supported_by: - reference_id: PMID:23441045 supporting_text: >- Using morpholino depletion studies, we find that tbx5b is required in the heart for embryonic survival, and influences the timing and morphogenesis of pectoral fin development. - reference_id: PMID:34756968 supporting_text: >- Zebrafish deficient in tbx5a lack pectoral fin buds, whereas zebrafish deficient in tbx5b exhibit misshapen pectoral fins, showing that both paralogues function in fin development. - term: id: GO:0033339 label: pectoral fin development evidence_type: IMP original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Pectoral fin development (IMP, tbx5b morpholino, PMID:24759614). action: ACCEPT reason: >- tbx5b is needed for normal pectoral fin outgrowth and shape, but not for fin bud initiation (which needs tbx5a). tbx5b morphants have small, delayed fins, and fin-field cells fail to migrate medio-laterally (PMID:24759614, PMID:34756968). A tbx5b frameshift mutant reproduces the fin defect (PMID:30532148). Whether tbx5b is expressed in the fin at all is disputed (not detected in PMID:19925885; low levels in PMID:23441045), so this role may be partly non-cell-autonomous. This asymmetry in fin roles is copy-specific and should be kept. supported_by: - reference_id: PMID:24759614 supporting_text: >- In agreement with tbx5b playing a role during zebrafish pectoral fin morphogenesis, tbx5b morphants had smaller pectoral fins when compared with control embryos at 3 dpf - reference_id: PMID:24759614 supporting_text: >- Taken together, we show that pectoral fin development has a different requirement for each of the tbx5 paralogues: tbx5a function is required for the earliest steps of initiation of fin outgrowth, whereas tbx5b functions later to ensure properly timed and sustained fin outgrowth. - reference_id: PMID:30532148 supporting_text: Tbx5b-/- mutants also exhibit similar fin defects to the Tbx5b morphants. - term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in supporting_entities: - InterPro:IPR046360 review: summary: Positive regulation of DNA-templated transcription (IEA, InterPro). action: ACCEPT reason: >- Tbx5 proteins act as activators, and tbx5b is a functional T-box factor (see MF rows). There is no tbx5b-specific reporter data. supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - term: id: GO:0048794 label: swim bladder development evidence_type: IGI original_reference_id: PMID:30352852 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-060328-3 - ZFIN:ZDB-MRPHLNO-130123-3 negated: true review: summary: NOT swim bladder development (negated). action: ACCEPT reason: >- tbx5a/tbx5b single and double morphants form a swim bladder, so the pair is not required for swim bladder specification (PMID:30352852). Accepted as a negative result. tbx5b mutants do fail to inflate the swim bladder (PMID:30532148). Inflation is a later, physiological step that is probably secondary to heart failure, so it does not contradict the NOT. Morpholino-only for the formation claim. supported_by: - reference_id: PMID:30352852 supporting_text: >- However, we find that although Tbx5 is required for lung formation, tbx5a / b is not required for SB formation in the zebrafish. - reference_id: PMID:30352852 supporting_text: >- To address potential redundancy, we utilized published MOs designed to target tbx5a , tbx5b , or tbx5a and tbx5b ( 47 , 48 ). - reference_id: PMID:30532148 supporting_text: >- Additionally, unlike their wildtype siblings, the swim bladder of Tbx5b-deficient embryos does not inflate. - term: id: GO:0048794 label: swim bladder development evidence_type: IMP original_reference_id: PMID:30352852 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-130123-3 negated: true review: summary: NOT swim bladder development (negated). action: ACCEPT reason: >- tbx5a/tbx5b single and double morphants form a swim bladder, so the pair is not required for swim bladder specification (PMID:30352852). Accepted as a negative result. tbx5b mutants do fail to inflate the swim bladder (PMID:30532148). Inflation is a later, physiological step that is probably secondary to heart failure, so it does not contradict the NOT. Morpholino-only for the formation claim. supported_by: - reference_id: PMID:30352852 supporting_text: >- However, we find that although Tbx5 is required for lung formation, tbx5a / b is not required for SB formation in the zebrafish. - reference_id: PMID:30352852 supporting_text: >- To address potential redundancy, we utilized published MOs designed to target tbx5a , tbx5b , or tbx5a and tbx5b ( 47 , 48 ). - reference_id: PMID:30532148 supporting_text: >- Additionally, unlike their wildtype siblings, the swim bladder of Tbx5b-deficient embryos does not inflate. - term: id: GO:0060042 label: retina morphogenesis in camera-type eye evidence_type: IGI original_reference_id: PMID:24759614 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-060328-2 - ZFIN:ZDB-MRPHLNO-130123-3 review: summary: Retina morphogenesis in camera-type eye (IGI, double morphants). action: KEEP_AS_NON_CORE reason: >- Dorsal efnb2a shrinks significantly only in tbx5a + tbx5b double morphants (PMID:24759614). This is shared dorsoventral patterning of the retina, the same as for tbx5a, and morpholino-only. supported_by: - reference_id: PMID:24759614 supporting_text: >- suggesting that tbx5 paralogues act redundantly in the dorsal retina to ensure efnb2a expression in this territory. - term: id: GO:0060429 label: epithelium development evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027680 review: summary: Epithelium development (IEA, ARBA). action: MARK_AS_OVER_ANNOTATED reason: >- No zebrafish evidence; an ARBA machine-learning generalization. Treated the same way in tbx5a. 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: GO_REF:0000104 title: >- Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:23226307 title: >- MicroRNA 218 mediates the effects of Tbx5a over-expression on zebrafish heart development. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text; tbx5b morphants loop poorly but keep fins. - id: PMID:23441045 title: >- Zebrafish tbx5 paralogs demonstrate independent essential requirements in cardiac and pectoral fin development. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Abstract only; key pair paper: tbx5b morphant heart/fin phenotypes, no reciprocal mRNA cross-rescue. - id: PMID:24759614 title: >- Distinct tissue-specific requirements for the zebrafish tbx5 genes during heart, retina and pectoral fin development. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; single and double morphants; tbx5b mRNA rescues tbx5b MO. - id: PMID:30352852 title: >- Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text; tbx5a/b morphants form swim bladder. - id: PMID:19925885 title: >- Identification and characterisation of the developmental expression pattern of tbx5b, a novel tbx5 gene in zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Abstract only. First description of tbx5b; proposes TGD origin; no fin expression detected. - id: PMID:30532148 title: A transcriptomics analysis of the Tbx5 paralogues in zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Full text. tbx5b CRISPR allele: 4-bp intron-1 insertion, splicing defect, frameshift at aa 53, PTC; phenocopies morphants. - id: PMID:34756968 title: >- Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Full text. Separate AP (tbx5a) and ML (tbx5b) migration vectors in the fin field; uses tbx5b mutants and morphants. - id: PMID:39079985 title: 'Zebrafish: unraveling genetic complexity through duplicated genes.' findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Review; 83% T-box identity between Tbx5a and Tbx5b. - id: PMID:34372968 title: >- Twisting of the zebrafish heart tube during cardiac looping is a tbx5-dependent and tissue-intrinsic process. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Full text; tbx5a oug allele jogs normally; used as a comparator for morphant jogging claims. - id: PMID:19895804 title: >- Pdlim7 (LMP4) regulation of Tbx5 specifies zebrafish heart atrio-ventricular boundary and valve formation. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text; Tbx5(a) cytoplasmic sequestration by Pdlim7; not tested for Tbx5b. - id: PMID:12223419 title: >- The heartstrings mutation in zebrafish causes heart/fin Tbx5 deficiency syndrome. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Abstract only; tbx5a paralog context. core_functions: - description: >- T-box DNA-binding transcription factor (T-box 83% identical to tbx5a; activity inferred, not assayed directly). molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0006357 label: regulation of transcription by RNA polymerase II locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:39079985 supporting_text: >- The T-box domain of Tbx5b shares only 83% sequence identity with its Tbx5a counterpart - reference_id: PMID:24759614 supporting_text: >- Similarly, a full-length tbx5b form was able to rescue the jogging phenotype of tbx5b morphants when co-injected with our tbx5b MO (figure 3b; n = 117). - description: >- Cardiac looping and embryonic heart function. Required together with tbx5a and not redundant with it; loss is lethal by 6 dpf. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0001947 label: heart looping - id: GO:0007507 label: heart development locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:23441045 supporting_text: >- Using morpholino depletion studies, we find that tbx5b is required in the heart for embryonic survival, and influences the timing and morphogenesis of pectoral fin development. - reference_id: PMID:23441045 supporting_text: >- Because tbx5a hypomorphic mutations are embryonic lethal, tbx5a and tbx5b functions in the heart must not be completely redundant. - reference_id: PMID:30532148 supporting_text: >- The heart fails to loop and a fluid filled edema forms surrounding the heart (Fig 1E and 1F). - reference_id: PMID:30532148 supporting_text: >- By 6 days, both mutants and morphant embryos die, possibly as a result of the severe heart defects. - description: >- Timely pectoral fin outgrowth and medio-lateral migration of fin-field cells (after initiation, which needs tbx5a). molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0033339 label: pectoral fin development locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:24759614 supporting_text: >- Taken together, we show that pectoral fin development has a different requirement for each of the tbx5 paralogues: tbx5a function is required for the earliest steps of initiation of fin outgrowth, whereas tbx5b functions later to ensure properly timed and sustained fin outgrowth. - reference_id: PMID:34756968 supporting_text: >- We show here that loss of Tbx5b function affects initial ML directed movements so that fin field cells fail to migrate laterally but continue to converge along the AP axis. - reference_id: PMID:30532148 supporting_text: Tbx5b-/- mutants also exhibit similar fin defects to the Tbx5b morphants. suggested_questions: - question: >- Is tbx5b expressed in pectoral fin-field cells at all? If not, does it act on fin-field migration non-cell-autonomously, for example from the adjacent heart field or somites? - question: >- Is the failure of tbx5a mRNA to rescue tbx5b morphants due to protein divergence (the C-terminal region, T-box substitutions) or to dose, timing and ubiquitous expression of injected mRNA? - question: >- Does the tbx5b frameshift allele (intron-1 insertion, PTC) trigger nonsense-mediated decay and upregulation of tbx5a? suggested_experiments: - hypothesis: Tbx5b has diverged at the protein level from Tbx5a. description: >- Compare DNA-binding specificity (SELEX or CUT&RUN) and transactivation of Tbx5a and Tbx5b on the same T-box reporters, and swap the coding sequences between the loci by knock-in. experiment_type: biochemical comparison and coding-sequence swap - hypothesis: tbx5b is required for heart jogging. description: >- Score jogging (myl7, 26 hpf) in tbx5b mutants and in a promoter-less tbx5b allele, with measurement of tbx5a transcript levels. experiment_type: mutant phenotyping