id: F1QWN1 gene_symbol: tp53bp2b product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:7955 label: Danio rerio description: 'tp53bp2b is one of two zebrafish co-orthologs of human TP53BP2 (ASPP2), a large cytoplasmic scaffold protein with an N-terminal Ras-associating (ubiquitin-like) domain, a coiled-coil and a long proline-rich, largely disordered middle region, and a C-terminal module of four ankyrin repeats and an SH3 domain. In mammals this C-terminal module binds the p53 DNA-binding domain and enhances p53-dependent apoptosis, and ASPP2 also acts at apical cell junctions, where it binds Par-3 and scaffolds PP1 and YAP. In zebrafish embryos, Aspp2b (like its paralog Aspp2a) binds Irs-1 and restrains embryonic body growth without changing developmental rate, by dampening Akt signaling. tp53bp2b transcripts are maternally provided and present in early embryos, are low during gastrulation and organogenesis, and are found in many larval and adult tissues. A GFP-tagged form expressed in embryos is cytoplasmic, and tp53bp2b is induced by the ciliogenic transcription factor Foxj1.' existing_annotations: - term: id: GO:0002039 label: p53 binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - PANTHER:PTN001538228 - UniProtKB:Q13625 - WB:WBGene00000146 review: summary: p53 binding propagated from the PANTHER ASPP node (human ASPP2 and worm ape-1 donors). action: ACCEPT reason: 'The p53-binding module of ASPP2 is the C-terminal ankyrin repeats plus SH3 domain. The four ankyrin repeats of tp53bp2b are 90.7-97.1% identical to human TP53BP2 and the SH3 domain is intact, so tp53bp2b sits inside the clade that inherited this function with no sign of loss. Binding of zebrafish Aspp2b to Tp53 has not itself been tested.' supported_by: - reference_id: PMID:8875926 supporting_text: the SH3 domain binds the L3 loop of p53 in a manner distinct from that of previously characterized SH3-polyproline peptide complexes, and (ii) an ankyrin repeat, which forms an L-shaped structure consisting of a beta hairpin and two alpha helices, binds the L2 loop of p53 - reference_id: file:DANRE/tp53bp2a/tp53bp2a-bioinformatics/RESULTS.md supporting_text: The four ankyrin repeats are 90.6-100% identical to human TP53BP2 in both copies - term: id: GO:0002039 label: p53 binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR047163 review: summary: p53 binding from the InterPro ASPP1/2 family signature. action: ACCEPT reason: Same claim as the IBA row, reached from the ASPP1/2 family signature; consistent with the conserved ankyrin-SH3 module. supported_by: - reference_id: PMID:11684014 supporting_text: ASPP proteins interact with p53 and specifically enhance p53-induced apoptosis but not cell cycle arrest. - term: id: GO:0003341 label: cilium movement evidence_type: IMP original_reference_id: PMID:25139857 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-141110-25 review: summary: From a morpholino screen of 50 randomly chosen Foxj1-induced genes, scored for motile-cilia phenotypes and, for ten genes, for Kupffer's vesicle cilia motility. action: UNDECIDED reason: 'tp53bp2b is not named in the main text of the paper; its per-gene data are in supplementary Table S3, which is not in the cache, so I cannot see which phenotypes or motility values were recorded for it. The evidence is a single splice-blocking morpholino with no mutant, and no ciliary role is known for ASPP2 in other species. The paper itself notes that most Foxj1 targets are not ciliary proteins and may act indirectly. I defer to the curator but cannot confirm.' supported_by: - reference_id: PMID:25139857 supporting_text: However, upon morpholino-mediated knockdown of nine out of the ten selected genes, the percentage of motile cilia decreased to as low as 2% - reference_id: PMID:25139857 supporting_text: Therefore, it is likely that most of the FIGs encode novel membrane, cytoplasmic or nuclear regulators of cilia formation and function. - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - PANTHER:PTN001538228 - UniProtKB:Q13625 - UniProtKB:Q96KQ4 review: summary: Nuclear activity propagated from human ASPP2 and ASPP1. action: KEEP_AS_NON_CORE reason: Mammalian ASPP proteins act on p53 at pro-apoptotic promoters, so a nuclear pool is plausible, but the best-characterized sites of ASPP2 are cytoplasmic and junctional, and GFP-tagged Aspp2b was scored as cytoplasmic in zebrafish embryos. Kept as a non-core location. supported_by: - reference_id: PMID:11684014 supporting_text: ASPP enhance the DNA binding and transactivation function of p53 on the promoters of proapoptotic genes in vivo. - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0191 review: summary: Nucleus from the UniProt subcellular-location rule (ARBA). action: KEEP_AS_NON_CORE reason: As for the IBA row; a minor location for this largely cytoplasmic and junctional scaffold. supported_by: - reference_id: PMID:11684014 supporting_text: ASPP enhance the DNA binding and transactivation function of p53 on the promoters of proapoptotic genes in vivo. - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:25139857 qualifier: located_in review: summary: GFP-tagged Aspp2b expressed from injected mRNA in zebrafish embryos localized to the cytoplasm (not to cilia). action: ACCEPT reason: Direct localization of the zebrafish protein, consistent with mammalian ASPP2 being a cytoplasmic and junctional scaffold. Per-gene images are in the supplement; the main text describes the non-ciliary class of proteins as cytoplasmic, nuclear or membrane. supported_by: - reference_id: PMID:25139857 supporting_text: Surprisingly, the remaining proteins showed no association with ciliary structures - 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 from the UniProt subcellular-location rule (ARBA). action: ACCEPT reason: Agrees with the IDA row and with mammalian ASPP2. supported_by: - reference_id: PMID:25360797 supporting_text: Here we report that the tumour suppressor ASPP2 forms an apical-lateral polarity complex at the level of tight junctions in polarised epithelial cells - term: id: GO:0005912 label: adherens junction evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - FB:FBgn0034606 - PANTHER:PTN001538228 review: summary: Adherens junction propagated from Drosophila ASPP. action: ACCEPT reason: Junctional localization is a conserved property of ASPP2 (mouse ASPP2 maintains tight/adherens junctions and binds Par-3) and of fly ASPP. tp53bp2b keeps the domains; no zebrafish junction data. supported_by: - reference_id: PMID:20619750 supporting_text: Mechanistically, ASPP2 maintains the integrity of tight/adherens junctions. - term: id: GO:0007165 label: signal transduction evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in supporting_entities: - InterPro:IPR000159 review: summary: Generic signal transduction from the Ras-associating domain InterPro2GO mapping. action: MODIFY reason: Not wrong but uninformative. The zebrafish experiment on this gene shows it dampens Akt signaling downstream of Irs-1, which is captured by the more specific term already carried by experimental evidence. proposed_replacement_terms: - id: GO:0051898 label: negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction supported_by: - reference_id: PMID:24362258 supporting_text: Aspp2a and 2b inhibit Akt signaling. This inhibition was reversed by coinjection of myr-Akt1, a constitutively active form of Akt1. - term: id: GO:0042981 label: regulation of apoptotic process evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in supporting_entities: - InterPro:IPR047163 review: summary: Regulation of apoptosis from the ASPP1/2 family signature. action: ACCEPT reason: Regulation of p53-dependent apoptosis is the defining function of the ASPP family. It is untested for zebrafish Aspp2b, but the p53-binding module is conserved. The broad term is acceptable for an IEA. supported_by: - reference_id: PMID:11684014 supporting_text: Inhibition of endogenous ASPP function suppresses the apoptotic function of endogenous p53 in response to apoptotic stimuli. - term: id: GO:0043009 label: chordate embryonic development evidence_type: IMP original_reference_id: PMID:24362258 qualifier: acts_upstream_of_or_within review: summary: Knockdown of aspp2b altered embryonic growth in zebrafish. action: MODIFY reason: 'The paper''s finding is specific: Aspp2b restrains body growth while developmental rate (timing) is unchanged. "Chordate embryonic development" is broad and implies a developmental-timing role the authors explicitly exclude. Negative regulation of multicellular organism growth states the claim. I have only the abstract; the refinement follows the title and abstract, not a disagreement with the curator.' proposed_replacement_terms: - id: GO:0040015 label: negative regulation of multicellular organism growth supported_by: - reference_id: PMID:24362258 supporting_text: Here, we show that zebrafish Aspp2a and Aspp2b negatively regulate embryonic growth without affecting developmental rate. - term: id: GO:0048471 label: perinuclear region of cytoplasm evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - PANTHER:PTN001538228 - RGD:1304651 review: summary: Perinuclear cytoplasm propagated from rat Tp53bp2. action: KEEP_AS_NON_CORE reason: Consistent with a cytoplasmic protein; not a site of any characterized function and not tested in zebrafish. The best-characterized ASPP2 site is the apical junction. supported_by: - reference_id: PMID:25360797 supporting_text: Here we report that the tumour suppressor ASPP2 forms an apical-lateral polarity complex at the level of tight junctions in polarised epithelial cells - term: id: GO:0051898 label: negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction evidence_type: IMP original_reference_id: PMID:24362258 qualifier: acts_upstream_of_or_within review: summary: Aspp2b inhibits Akt signaling in zebrafish embryos; the effect is reversed by constitutively active Akt1. action: ACCEPT reason: Direct zebrafish evidence on this copy, with an epistasis test (myr-Akt1) and a mechanism (binding to Irs-1). Abstract only in cache; accepted, deferring to the curator who read the full text. supported_by: - reference_id: PMID:24362258 supporting_text: Aspp2a and 2b inhibit Akt signaling. This inhibition was reversed by coinjection of myr-Akt1, a constitutively active form of Akt1. - reference_id: PMID:24362258 supporting_text: Zebrafish Aspp2a and Aspp2b physically bound with Irs-1, and the growth inhibitory effects of ASPP2/Aspp2 depend on the presence of their ankyrin repeats and SH3 domains. - term: id: GO:0072332 label: intrinsic apoptotic signaling pathway by p53 class mediator evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - PANTHER:PTN001538228 - UniProtKB:Q13625 - UniProtKB:Q96KQ4 review: summary: p53-mediated intrinsic apoptosis, propagated from human ASPP2 and ASPP1. action: ACCEPT reason: This is the ancestral ASPP function, and the p53-binding module is conserved in tp53bp2b. Not yet tested in zebrafish. supported_by: - reference_id: PMID:11684014 supporting_text: ASPP enhance the DNA binding and transactivation function of p53 on the promoters of proapoptotic genes in vivo. - term: id: GO:0043560 label: insulin receptor substrate binding evidence_type: IPI original_reference_id: PMID:24362258 review: summary: Zebrafish Aspp2b binds Irs-1. action: NEW reason: Physical interaction with Irs-1 reported for both zebrafish copies, and the growth phenotype needs the ankyrin-SH3 module; this is the only molecular interaction shown for the zebrafish protein and it explains the Akt phenotype. Abstract only; assay details not visible. supported_by: - reference_id: PMID:24362258 supporting_text: Zebrafish Aspp2a and Aspp2b physically bound with Irs-1, and the growth inhibitory effects of ASPP2/Aspp2 depend on the presence of their ankyrin repeats and SH3 domains. core_functions: - description: Binds Irs-1 through its ankyrin-SH3 module and dampens insulin/IGF-Akt signaling, restraining embryonic body growth without affecting developmental timing (shown for both zebrafish copies by knockdown, overexpression and myr-Akt1 epistasis). molecular_function: id: GO:0043560 label: insulin receptor substrate binding directly_involved_in: - id: GO:0051898 label: negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction locations: - id: GO:0005737 label: cytoplasm supported_by: - reference_id: PMID:24362258 supporting_text: Zebrafish Aspp2a and Aspp2b physically bound with Irs-1, and the growth inhibitory effects of ASPP2/Aspp2 depend on the presence of their ankyrin repeats and SH3 domains. - description: p53 cofactor that promotes p53-dependent apoptosis, inferred from the conserved ankyrin-SH3 p53-binding module and mammalian ASPP2; not yet tested in zebrafish. molecular_function: id: GO:0002039 label: p53 binding directly_involved_in: - id: GO:0072332 label: intrinsic apoptotic signaling pathway by p53 class mediator supported_by: - reference_id: PMID:11684014 supporting_text: ASPP proteins interact with p53 and specifically enhance p53-induced apoptosis but not cell cycle arrest. - reference_id: file:DANRE/tp53bp2a/tp53bp2a-bioinformatics/RESULTS.md supporting_text: The four ankyrin repeats are 90.6-100% identical to human TP53BP2 in both copies 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:24362258 title: Aspp2 negatively regulates body growth but not developmental timing by modulating IRS signaling in zebrafish embryos. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only in cache. The only functional study of either zebrafish copy; tests aspp2a and aspp2b side by side (knockdown, overexpression, Irs-1 binding, myr-Akt1 epistasis). - id: PMID:25139857 title: Systematic discovery of novel ciliary genes through functional genomics in the zebrafish. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text cached, but tp53bp2b appears only in supplementary Table S3 (not cached); it is one of 50 randomly chosen Foxj1-induced genes screened by morpholino and GFP-fusion localization. - id: PMID:11684014 title: ASPP proteins specifically stimulate the apoptotic function of p53. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; defines the ASPP family as p53 apoptotic cofactors (human cells). - id: PMID:8875926 title: Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; crystal structure of the p53 core bound to the ASPP2 ankyrin-SH3 module. - id: PMID:20619750 title: ASPP2 binds Par-3 and controls the polarity and proliferation of neural progenitors during CNS development. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; mouse ASPP2 at tight/adherens junctions, Par-3 binding. - id: PMID:25360797 title: ASPP2 links the apical lateral polarity complex to the regulation of YAP activity in epithelial cells. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Mammalian cells and mouse colon; ASPP2 as PP1/YAP scaffold at tight junctions. - id: file:DANRE/tp53bp2a/tp53bp2a-bioinformatics/RESULTS.md title: tp53bp2a / tp53bp2b protein, expression and synteny comparison reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified the sidecar supports both TP53BP2 duplicates retaining the ankyrin-SH3 module and broad expression, with quantitative temporal differences and weaker-than-textbook TGD synteny. findings: [] suggested_questions: - question: Does tp53bp2b have a real role in motile cilia (as the morpholino screen suggested), and would a stable mutant confirm it? - question: Both copies are maternally provided, but only tp53bp2b drops to near background during gastrulation and organogenesis. Is that a loss of zygotic enhancers in tp53bp2b, and does the gar gene show continuous expression? - question: Does Aspp2b bind Tp53 and enhance p53-dependent apoptosis? suggested_experiments: - hypothesis: tp53bp2b is required for Kupffer's vesicle cilia motility. description: Make a stable tp53bp2b mutant (and maternal-zygotic mutant, given maternal expression); score Kupffer's vesicle cilia motility, left-right asymmetry markers and kidney cysts. experiment_type: loss of function - hypothesis: The Aspp2a and Aspp2b proteins are interchangeable. description: Rescue the growth phenotype of each single or double mutant with either coding sequence. experiment_type: cross-rescue