id: F1Q885 gene_symbol: mitfb product_type: PROTEIN status: IN_PROGRESS taxon: id: NCBITaxon:7955 label: Danio rerio description: >- mitfb encodes microphthalmia-associated transcription factor b, a basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor of the MiT/TFE family and the second zebrafish co-ortholog of human MITF, retained from the teleost genome duplication alongside mitfa. The 500-residue protein has the MiT/TFE N-terminal region, a bHLH-LZ DNA-binding and dimerization domain and the MiT/TFE C-terminal region, with an N-terminal extension that resembles the RPE-type (A/H) isoforms of mammalian MITF rather than the melanocyte M isoform. mitfb is co-expressed with mitfa in the retinal pigment epithelium (RPE) and is also expressed in the epiphysis and olfactory bulb, but is not expressed in neural crest melanoblasts. The protein keeps the melanogenic activity of the family: expressed from the mitfa promoter it rescues neural crest melanophores in nacre/mitfa mutants. Endogenously, mitfb null fish have no obvious phenotype, mitfa;mitfb double mutants still have a normal RPE (RPE pigmentation requires mitfa, mitfb and tfec together), and loss of mitfb enhances the xanthophore deficit of mitfa mutants, most clearly in adult fins. mitfb therefore acts mainly as a partially redundant MiT factor in zebrafish; in medaka the mitfb co-ortholog has the more central role in melanophore development. existing_annotations: - 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:103270 - MGI:MGI:104554 - MGI:MGI:98511 - PANTHER:PTN005248237 - RGD:3846 - UniProtKB:O75030 review: summary: >- Phylogenetic inference of cis-regulatory DNA binding from the MiT/TFE node. mitfb keeps an intact bHLH-LZ domain (the hu3561 nonsense allele lies in it), and its protein can replace mitfa in melanophore development, which requires DNA binding at melanogenic targets. action: ACCEPT reason: >- mitfb is inside the clade that inherited DNA binding and there is no evidence of loss; the cross-rescue shows the protein retains the ancestral activity. supported_by: - reference_id: PMID:11543618 supporting_text: mitfb, but not a zebrafish ortholog of the closely related gene tfe3, can rescue neural crest melanophore development in nacre/mitfa mutant embryos when expressed via the mitfa promoter - 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:FBgn0263112 - MGI:MGI:103270 - MGI:MGI:104554 - PANTHER:PTN005248237 - RGD:3846 - SGD:S000000199 - UniProtKB:O14948 - UniProtKB:O75030 - UniProtKB:P19532 - ZFIN:ZDB-GENE-010919-1 - ZFIN:ZDB-GENE-010919-2 - ZFIN:ZDB-GENE-990910-11 review: summary: >- Core molecular function inferred for the MiT/TFE family; mitfb itself (ZFIN:ZDB-GENE-010919-1) is a descendant evidence through its own IDA (PMID:11543618), which is expected and not circular. action: ACCEPT reason: Protein-level function is conserved between the two zebrafish copies. supported_by: - reference_id: PMID:11543618 supporting_text: These data suggest that mitfa and mitfb together may recapitulate the expression and functions of a single ancestral Mitf gene - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IDA original_reference_id: PMID:11543618 qualifier: enables review: summary: >- Direct assay from Lister et al. 2001 (abstract-only in cache). The abstract establishes conserved melanogenic potential of mitfb; the transcriptional assay details are in the full text read by the curator. action: ACCEPT reason: Consistent with the family function, the IBA and the in vivo cross-rescue. supported_by: - reference_id: PMID:11543618 supporting_text: mitfb, but not a zebrafish ortholog of the closely related gene tfe3, can rescue neural crest melanophore development in nacre/mitfa mutant embryos when expressed via the mitfa promoter - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:104554 - MGI:MGI:98511 - PANTHER:PTN005248237 - SGD:S000000199 - UniProtKB:O14948 - UniProtKB:O75030 - UniProtKB:P19484 - UniProtKB:P19532 review: summary: Nuclear site of action for a MiT/TFE transcription factor. action: ACCEPT reason: A DNA-binding transcription factor acts in the nucleus; no evidence of divergence. - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0191 - UniRule:UR000414447 review: summary: Automated nuclear localization, consistent with the IBA. action: ACCEPT reason: Consistent with the IBA nucleus annotation and transcription factor activity. - term: id: GO:0005654 label: nucleoplasm evidence_type: IC original_reference_id: PMID:11543618 qualifier: located_in supporting_entities: - GO:0000981 review: summary: Curator inference from the directly assayed transcription factor activity. action: ACCEPT reason: Reasonable IC; same annotation as on mitfa. - 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: >- Family-level (ARBA) subcellular-location mapping; no mitfb-specific localization data exist. action: KEEP_AS_NON_CORE reason: >- Plausible for a MiT/TFE factor regulated by nuclear entry, but not demonstrated for mitfb; kept as non-core, as for mitfa. - term: id: GO:0006351 label: DNA-templated transcription evidence_type: IDA original_reference_id: PMID:11543618 qualifier: acts_upstream_of_or_within review: summary: >- Companion BP to the IDA transcription factor activity. A sequence-specific transcription factor regulates RNA polymerase II transcription rather than executing it. action: MODIFY reason: >- The regulatory term matches the molecular function; the same change is made on mitfa to keep the pair consistent. proposed_replacement_terms: - id: GO:0006357 label: regulation of transcription by RNA polymerase II supported_by: - reference_id: PMID:11543618 supporting_text: These data suggest that mitfa and mitfb together may recapitulate the expression and functions of a single ancestral Mitf gene - 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:IPR021802 review: summary: InterPro2GO mapping from the MiT/TFE C-terminal domain; broad but correct. action: ACCEPT reason: Correct general parent of the RNA polymerase II-specific regulation term. - 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:FBgn0263112 - MGI:MGI:103270 - MGI:MGI:104554 - MGI:MGI:98511 - PANTHER:PTN005248237 - RGD:3846 - SGD:S000000199 - UniProtKB:O14948 - UniProtKB:O75030 - UniProtKB:P19484 - UniProtKB:P19532 - WB:WBGene00020930 review: summary: Family-level process for an RNA polymerase II transcription factor. action: ACCEPT reason: Correct and at an appropriate level of generality. - term: id: GO:0030318 label: melanocyte differentiation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - PANTHER:PTN000000863 - ZFIN:ZDB-GENE-010919-1 - ZFIN:ZDB-GENE-990910-11 review: summary: >- Inference from the MITF node (PTN000000863), which is ancestral to both zebrafish copies. The ancestral melanogenic function is real and the mitfb protein retains it, and in medaka the mitfb co-ortholog is the main melanophore regulator. In zebrafish, however, mitfb is not expressed in neural crest melanoblasts and mitfb null fish have normal melanophores, so the endogenous zebrafish contribution is small. action: KEEP_AS_NON_CORE reason: >- The node placement is sound (both copies inherit the ancestral function, and the protein keeps it), so the IBA is not removed. For zebrafish mitfb the process was partitioned away at the expression level, so it is not a core function of this copy. supported_by: - reference_id: PMID:11543618 supporting_text: mitfb is coexpressed with mitfa in the RPE at an appropriate time to compensate for loss of mitfa function in the nacre mutant but is not expressed in neural crest melanoblasts - reference_id: PMID:37823232 supporting_text: suggesting that mitfb, but not mitfa, plays the more central role in melanophore development in medaka - reference_id: PMID:40123122 supporting_text: Only in zebrafish has one Mitf locus, mitfb, undergone a substantial, though not complete (Figure 5b) reduction in pigmentary function - term: id: GO:0030318 label: melanocyte differentiation evidence_type: IGI original_reference_id: PMID:11543618 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENE-990910-11 review: summary: >- Genetic interaction with mitfa: mitfb driven by the mitfa promoter rescues neural crest melanophores in nacre mutants. This shows that the mitfb protein can drive melanocyte differentiation, not that endogenous mitfb does so. action: KEEP_AS_NON_CORE reason: >- Valid evidence of retained protein capacity (the key protein-level result for the pair), but mitfb is not expressed in neural crest melanoblasts and mitfb nulls have normal melanophores. Kept, as non-core. supported_by: - reference_id: PMID:11543618 supporting_text: mitfb, but not a zebrafish ortholog of the closely related gene tfe3, can rescue neural crest melanophore development in nacre/mitfa mutant embryos when expressed via the mitfa promoter - reference_id: PMID:23139843 supporting_text: no obvious abnormalities in homozygous mitfb embryos or larvae were observed - term: id: GO:0046983 label: protein dimerization activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR011598 - InterPro:IPR036638 review: summary: InterPro2GO mapping from the HLH domain; correct but subsidiary to TF activity. action: KEEP_AS_NON_CORE reason: Correct domain-based inference; part of the TF mechanism. Same action as for mitfa. - term: id: GO:0050936 label: xanthophore differentiation evidence_type: IGI original_reference_id: PMID:37823232 review: summary: >- NEW (proposed). Loss of mitfb in a mitfa mutant background reduces xanthophores beyond the mitfa single mutant, found independently by two groups (CRISPR bHLH-domain allele; premature-termination allele), with the strongest effect in adult fin xanthophores. action: NEW reason: >- Participation: MiT factors directly activate xanthophore pigment-synthesis genes (gch2) in this lineage, so mitfb acts as a partially redundant transcription factor there, not merely as a prerequisite. The evidence comes from double mutants, so the same term is proposed for mitfa. supported_by: - reference_id: PMID:37823232 supporting_text: Compared with a single mitfa mutant, mitfa−/−; mitfb−/− double mutants showed a slightly more severe reduction of xanthophores, with fewer fluorescent xanthophores on the trunk - reference_id: PMID:40123122 supporting_text: These phenotypes suggest that mitfb partially compensates for the loss of mitfa (though not tfec) in xanthophores and especially so in the fins. 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:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:11543618 title: 'Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential.' findings: - statement: mitfb is expressed in the RPE, epiphysis and olfactory bulb, but not in neural crest melanoblasts. supporting_text: mitfb is expressed in the epiphysis and olfactory bulb where mitfa is not - statement: The mitfb protein rescues nacre melanophores when expressed from the mitfa promoter. supporting_text: mitfb, but not a zebrafish ortholog of the closely related gene tfe3, can rescue neural crest melanophore development in nacre/mitfa mutant embryos when expressed via the mitfa promoter - id: PMID:12019239 title: Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. findings: - statement: Each fish Mitf protein corresponds to one tetrapod MITF isoform, with degeneration of alternative exons. supporting_text: In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons - id: PMID:20333216 title: Pigmentation pathway evolution after whole-genome duplication in fish. findings: - statement: mitf paralogs are cited as a case of subfunctionalization of ancestral RPE and melanophore functions. supporting_text: The ancestral functions in RPE - id: PMID:23139843 title: Otx but not Mitf transcription factors are required for zebrafish retinal pigment epithelium development. findings: - statement: mitfb nonsense mutants have no obvious phenotype. supporting_text: no obvious abnormalities in homozygous mitfb embryos or larvae were observed - id: PMID:37823232 title: A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish. findings: - statement: In medaka mitfb has the more central role in melanophore development. supporting_text: suggesting that mitfb, but not mitfa, plays the more central role in melanophore development in medaka - id: PMID:40123122 title: Dominant Negative Mitf Allele Impacts Melanophore and Xanthophore Development and Reveals Collaborative Interactions With Tfec in Zebrafish Chromatophore Lineages. findings: - statement: mitfb partially compensates for loss of mitfa in xanthophores, especially in fins. supporting_text: These phenotypes suggest that mitfb partially compensates for the loss of mitfa (though not tfec) in xanthophores and especially so in the fins. - id: PMID:42663426 title: MIT/TFE family transcription factors, Mitf and Tfec, redundantly promote pigment cell differentiation and retinal epithelium pigmentation in teleosts. findings: - statement: mitfa, mitfb and tfec are jointly required for RPE pigmentation. supporting_text: These findings indicate that the redundant functions of Mitfa, Mitfb, and Tfec are not only essential for the specification of diverse pigment cell types but also critical for RPE pigmentation. core_functions: - description: >- mitfb is a MiT/TFE bHLH-LZ transcription factor that keeps the melanogenic DNA-binding transcription factor activity of the ancestral Mitf (it can replace mitfa in melanophores). Its endogenous zebrafish roles are partially redundant: with mitfa it supports xanthophore development, and with mitfa and tfec it supports RPE pigmentation. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0050936 label: xanthophore differentiation locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:11543618 supporting_text: mitfb, but not a zebrafish ortholog of the closely related gene tfe3, can rescue neural crest melanophore development in nacre/mitfa mutant embryos when expressed via the mitfa promoter - reference_id: PMID:40123122 supporting_text: These phenotypes suggest that mitfb partially compensates for the loss of mitfa (though not tfec) in xanthophores and especially so in the fins. suggested_questions: - question: >- What does mitfb do in the epiphysis and olfactory bulb, where it is expressed without mitfa? Is this expression ancestral (present in the spotted gar mitf or in tetrapod Mitf isoforms) or a zebrafish-lineage gain? - question: >- Does the N-terminal (A/H-isoform-like) region of mitfb confer target specificity that differs from mitfa, or are the two proteins fully interchangeable at RPE and xanthophore targets as they are in melanophores? - question: >- Are the mitfb nonsense alleles (hu3857, hu3561) subject to nonsense-mediated decay with transcriptional adaptation (e.g. upregulation of mitfa or tfec) that could mask a single mutant phenotype? suggested_experiments: - hypothesis: mitfb has a mitfa-independent role in the pineal gland (epiphysis) or olfactory bulb. description: >- Generate an RNA-less (promoter-deletion) mitfb allele to avoid transcriptional adaptation, and profile pineal and olfactory bulb gene expression (single-cell RNA-seq) in mitfb and mitfb;tfec mutants. experiment_type: genetic and genomics - hypothesis: The spotted gar mitf expression pattern is the union of zebrafish mitfa and mitfb expression. description: >- In situ hybridization of gar mitf (all isoforms and isoform-specific probes) in embryos for neural crest melanoblasts, RPE, epiphysis and olfactory bulb, to test whether the zebrafish expression partition is ancestral subfunctionalization or includes gains. experiment_type: comparative expression