id: A0A8M9Q0D6 gene_symbol: mapre3b product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: mapre3b (microtubule-associated protein, RP/EB family, member 3b) is one of two zebrafish co-orthologs of vertebrate MAPRE3 (end-binding protein 3, EB3), retained from the teleost genome duplication; its paralog is mapre3a. It encodes a microtubule plus-end tracking protein (+TIP) with an N-terminal calponin-homology (CH) domain that binds growing microtubule ends, a flexible linker, a C-terminal EB-homology coiled-coil domain that mediates dimerization and binding of partner +TIPs, and an acidic tail ending in an aromatic residue. In mammals EB3 is enriched in neurons, tracks growing microtubule ends and, with EB1, promotes persistent microtubule growth by suppressing catastrophes. The zebrafish protein keeps all of these features. mapre3b transcripts are maternally supplied and present at every embryonic stage, and adult RNA-seq detects it broadly (brain, retina, muscle, heart, gill, intestine, liver and other tissues). No functional study of the zebrafish gene has been published. existing_annotations: - term: id: GO:0005815 label: microtubule organizing center evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - AGI_LocusCode:AT3G47690 - AGI_LocusCode:AT5G62500 - MGI:MGI:891995 - PANTHER:PTN000065701 - PomBase:SPAC18G6.15 - UniProtKB:Q15691 - WB:WBGene00012156 - WB:WBGene00013344 - dictyBase:DDB_G0283607 review: summary: Microtubule organizing center (IBA) from the RP/EB family node PTN000065701. action: ACCEPT reason: EB proteins concentrate at centrosomes and the Golgi-associated MTOC as well as at plus ends; UniProt's family-level function text for mapre3b notes anchoring of microtubules at centrosomes. mapre3b keeps every conserved EB domain, so it is inside the clade that inherited this localization. Non-core location; no zebrafish data. Same call for mapre3a. supported_by: - reference_id: PMID:19255245 supporting_text: End binding proteins (EBs) are highly conserved core components of microtubule plus-end tracking protein networks. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0005856 label: cytoskeleton evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0090 review: summary: Cytoskeleton, from the UniProt 'Cytoplasm, cytoskeleton' subcellular location (ARBA rule). action: ACCEPT reason: Correct but general; the protein decorates microtubules. The more specific microtubule plus-end and cytoplasmic microtubule rows carry the informative location. supported_by: - reference_id: PMID:10644998 supporting_text: Confocal microscopy demonstrated that exogenous EB3, like EB1, is associated with the cytoplasmic microtubule network. - term: id: GO:0005881 label: cytoplasmic microtubule evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - AGI_LocusCode:AT3G47690 - AGI_LocusCode:AT5G62500 - PANTHER:PTN000065701 - PomBase:SPAC18G6.15 - SGD:S000000818 - UniProtKB:Q15691 - UniProtKB:Q9UPY8 - WB:WBGene00013344 - dictyBase:DDB_G0283607 review: summary: Cytoplasmic microtubule (IBA) from the RP/EB family node. action: ACCEPT reason: Mammalian EB3 associates with the cytoplasmic microtubule network, and mapre3b keeps the CH domain that mediates microtubule binding. supported_by: - reference_id: PMID:10644998 supporting_text: Confocal microscopy demonstrated that exogenous EB3, like EB1, is associated with the cytoplasmic microtubule network. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0008017 label: microtubule binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR004953 - InterPro:IPR027328 - InterPro:IPR036133 review: summary: Microtubule binding from InterPro EB1 C-terminal / MAPRE family signatures. action: ACCEPT reason: Correct parent of the more specific microtubule plus-end binding (IBA). The CH domain responsible for microtubule binding is conserved in this copy. supported_by: - reference_id: PMID:19255245 supporting_text: Furthermore, we demonstrated in vitro and in cells that the EB plus-end tracking behavior depends on the calponin homology domain but does not require dimer formation. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0031110 label: regulation of microtubule polymerization or depolymerization evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - PANTHER:PTN000065701 - SGD:S000000818 - UniProtKB:Q15691 - UniProtKB:Q9UPY8 review: summary: Regulation of microtubule polymerization or depolymerization (IBA), donors include human MAPRE1 and MAPRE3 and yeast Bim1. action: ACCEPT reason: The main activity of mammalian EB1 and EB3 in cells is suppression of catastrophes, which promotes persistent microtubule growth; dimerization through the EBH domain is required. mapre3b keeps both the CH and EBH domains. Core process, shared with mapre3a. No zebrafish measurement exists. supported_by: - reference_id: PMID:19255245 supporting_text: Protein depletion and rescue experiments showed that EB1 and EB3, but not EB2, promote persistent microtubule growth by suppressing catastrophes. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0035371 label: microtubule plus-end evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:2140967 - MGI:MGI:891995 - PANTHER:PTN000065701 - PomBase:SPAC18G6.15 - SGD:S000000818 - UniProtKB:E2RU10 - WB:WBGene00012156 - WB:WBGene00013344 review: summary: Microtubule plus-end (IBA), family node PTN000065701. action: ACCEPT reason: Plus-end tracking is the defining behaviour of EB proteins and depends on the CH domain, which mapre3b keeps. Core location. supported_by: - reference_id: PMID:19255245 supporting_text: Furthermore, we demonstrated in vitro and in cells that the EB plus-end tracking behavior depends on the calponin homology domain but does not require dimer formation. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0035372 label: protein localization to microtubule evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:891995 - PANTHER:PTN000065701 - PomBase:SPAC18G6.15 - SGD:S000000818 - UniProtKB:E2RU10 - UniProtKB:Q15691 review: summary: Protein localization to microtubule (IBA); EBs recruit other +TIPs to plus ends. action: ACCEPT reason: 'EBs are the hub of plus-end tracking networks: the EBH domain and C-terminal EEY/F tail bind partner +TIPs, which the EBs recruit to growing ends. mapre3b keeps the EBH domain and the aromatic C-terminal tail. Accepted as a core process for the family; not tested in zebrafish.' supported_by: - reference_id: PMID:19255245 supporting_text: End binding proteins (EBs) are highly conserved core components of microtubule plus-end tracking protein networks. - reference_id: PMID:19255245 supporting_text: EBs terminate with a flexible acidic tail containing the C-terminal EEY/F sequence, which is important for self-inhibition and binding to various partners - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0051010 label: microtubule plus-end binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - FB:FBgn0027066 - FB:FBgn0034403 - MGI:MGI:106271 - MGI:MGI:2140967 - MGI:MGI:891995 - PANTHER:PTN000065701 - PomBase:SPAC18G6.15 - RGD:621781 - SGD:S000000818 - UniProtKB:E2RU10 - UniProtKB:Q15691 review: summary: Microtubule plus-end binding (IBA); many donors across eukaryotes including human MAPRE1/MAPRE3. action: ACCEPT reason: Core molecular function of EB proteins, conferred by the CH domain; mapre3b keeps it (CH domain about 90% identical to human MAPRE3). Shared with mapre3a. supported_by: - reference_id: PMID:19255245 supporting_text: Furthermore, we demonstrated in vitro and in cells that the EB plus-end tracking behavior depends on the calponin homology domain but does not require dimer formation. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0051225 label: spindle assembly evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0027066 - PANTHER:PTN000065701 - dictyBase:DDB_G0283607 review: summary: Spindle assembly (IBA), donors fly EB1 and Dictyostelium EB1. action: KEEP_AS_NON_CORE reason: The node is placed deep in the RP/EB family and the domains are conserved in mapre3b, so there is no sequence-based reason to reject it. However, the vertebrate evidence for a mitotic spindle role concerns mainly EB1 (MAPRE1), and mammalian EB3 is best known as a neuron-enriched +TIP. Kept as a plausible, non-core family role; no zebrafish data. Same call for mapre3a. supported_by: - reference_id: PMID:12684451 supporting_text: Using EB3-GFP as a marker of microtubule growth in live cells, we subsequently analyze microtubule dynamics in neurons. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. - term: id: GO:0051233 label: spindle midzone evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - PANTHER:PTN000065701 - PomBase:SPAC18G6.15 - SGD:S000000818 review: summary: Spindle midzone (IBA), donors yeast Mal3 and Bim1. action: KEEP_AS_NON_CORE reason: Seeded by the fungal EB orthologues. The family function (plus-end binding) is conserved in mapre3b, and EBs decorate growing spindle microtubules, but no vertebrate EB3 data address the midzone specifically. Kept as a non-core location. Same call for mapre3a. supported_by: - reference_id: PMID:19255245 supporting_text: End binding proteins (EBs) are highly conserved core components of microtubule plus-end tracking protein networks. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: PMID:10644998 title: EB3, a novel member of the EB1 family preferentially expressed in the central nervous system, binds to a CNS-specific APC homologue. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only; identification of human EB3, brain-enriched expression, microtubule association. - id: PMID:12684451 title: Visualization of microtubule growth in cultured neurons via the use of EB3-GFP (end-binding protein 3-green fluorescent protein). findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Mouse EB3 at growing microtubule ends in neurons; EB3 enriched in brain extracts. - id: PMID:19255245 title: Mammalian end binding proteins control persistent microtubule growth. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: EB1/EB3 suppress catastrophes; CH domain for tip tracking, dimerization for activity. - id: PMID:39939668 title: Piggyback knockdown screening of unique genes of zebrafish young thrombocytes identifies eight novel genes in thrombopoiesis. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Zebrafish; mapre3b is among 394 young-thrombocyte genes screened by knockdown but is not one of the eight hits. - id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md title: mapre3a / mapre3b protein, expression and synteny comparison reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified the sidecar supports both copies as MAPRE3 ohnologs retaining the CH domain, EBH domain and C-terminal aromatic tail, with expression differences but no protein-level divergence detected. findings: [] core_functions: - description: 'Microtubule plus-end tracking protein of the EB family (EB3 orthologue): binds growing microtubule plus ends through its CH domain, dimerizes through the EBH domain and, by homology with mammalian EB1/EB3, suppresses catastrophes and recruits other +TIPs. Inferred from conserved domains; no zebrafish measurement. Protein features shared with mapre3a.' molecular_function: id: GO:0051010 label: microtubule plus-end binding directly_involved_in: - id: GO:0031110 label: regulation of microtubule polymerization or depolymerization - id: GO:0035372 label: protein localization to microtubule locations: - id: GO:0035371 label: microtubule plus-end - id: GO:0005881 label: cytoplasmic microtubule supported_by: - reference_id: PMID:19255245 supporting_text: Protein depletion and rescue experiments showed that EB1 and EB3, but not EB2, promote persistent microtubule growth by suppressing catastrophes. - reference_id: PMID:19255245 supporting_text: Furthermore, we demonstrated in vitro and in cells that the EB plus-end tracking behavior depends on the calponin homology domain but does not require dimer formation. - reference_id: file:DANRE/mapre3a/mapre3a-bioinformatics/RESULTS.md supporting_text: Both copies keep the microtubule-binding CH domain, the EBH dimerization/partner-binding domain and the C-terminal aromatic tail. suggested_questions: - question: Where are mapre3a and mapre3b expressed at cellular resolution in larval retina and brain, and does mapre3a mark a neuronal subset that mapre3b lacks? - question: Is gar MAPRE3 maternally deposited like mapre3b, which would make the zygotic-only onset of mapre3a a derived state? suggested_experiments: - hypothesis: mapre3a and mapre3b encode equivalent plus-end tracking proteins. description: Express tagged Mapre3a and Mapre3b in zebrafish cells or embryos and compare comet velocity, lifetime and catastrophe frequency; test whether either rescues EB3 depletion in mammalian cells. experiment_type: biochemical/cell-biological comparison - hypothesis: The copies are partly redundant in neurons. description: Generate mapre3a and mapre3b single and double mutants (including promoter-less or RNA-less alleles to avoid transcriptional adaptation) and assay axon growth and retinal lamination. experiment_type: genetic interaction