id: E1BL04 gene_symbol: E1BL04 product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:9913 label: Bos taurus description: >- E1BL04 is the bovine XIRP2 gene product (Xin actin-binding repeat-containing protein 2, also called CMYA3, myomaxin or mXinbeta in mouse), a 3561-residue member of the Xin family (PANTHER PTHR22591, XIRP2 subfamily SF1). Its central region carries an array of 16-residue Xin repeats (26 PROSITE Xin repeats), a motif that binds actin filaments directly, stabilizes them and can cross-link them into networks; the rest of the protein is largely disordered. The protein has no LIM domain, so it corresponds to the long Xin-repeat class of XIRP2 products rather than to the LIM-containing isoforms. By orthology with mouse and human XIRP2, it is a striated-muscle protein of the Z disc/costamere region and of the cardiac intercalated disc, where it binds alpha-actinin-2 and anchors and stabilizes actin filaments. Mouse Xirp2 is required for intercalated disc maturation and for postnatal heart growth. In inner-ear hair cells, long XIRP2 isoforms sit in stereocilia and the cuticular plate and keep the paracrystalline actin arrays organized. No experimental work has been done on the bovine protein itself. existing_annotations: - term: id: GO:0001725 label: stress fiber evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: colocalizes_with review: summary: >- PAINT node PTN000502290 (family-level Xin node spanning XIRP1 SF2 and XIRP2 SF1) seeded by human XIRP2 (A4UGR9) and human XIRP1 (Q702N8). Human XIRP2 Xin repeats expressed in cultured non-muscle cells decorate and stabilize stress fibers. E1BL04 lies inside the clade and retains the Xin-repeat array. action: KEEP_AS_NON_CORE reason: >- The colocalization is real but comes from overexpression in non-muscle cells; stress fibers are not the physiological site of this striated-muscle protein. The force-dependent recruitment of XIRP2 to stress-fiber strain sites (PMID:37294664) maps to the C-terminal LIM/CTD region, which E1BL04 lacks, so it does not add support for this accession. supported_by: - reference_id: PMID:15454575 supporting_text: upon expression in cultured cells, these repeats bind to and stabilize the actin-based cytoskeleton - reference_id: PMID:15454575 supporting_text: Human XIRP2 contains 28 Xin repeats with properties identical to those of Xin - term: id: GO:0005925 label: focal adhesion evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: colocalizes_with review: summary: >- Same PAINT node (PTN000502290; seeds human XIRP2 and human XIRP1). Overexpressed Xin-repeat constructs associate with the ends of actin stress fibers at focal adhesions in cultured cells. action: KEEP_AS_NON_CORE reason: >- Consistent with the actin-binding repeats, but this is a cultured non-muscle context. In muscle, the corresponding attachment sites are the costameres, the myotendinous junction and the intercalated disc. The qualifier colocalizes_with is appropriate. supported_by: - reference_id: PMID:15454575 supporting_text: upon expression in cultured cells, these repeats bind to and stabilize the actin-based cytoskeleton - term: id: GO:0007015 label: actin filament organization evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: >- PAINT placed this process at the family-level node PTN000502290 with human XIRP1 (Q702N8, SF2) as the only seed, so for XIRP2 it is an ancestral-node inference rather than a direct XIRP2 transfer. It is nonetheless independently supported for XIRP2. Xin repeats bind actin filaments directly and arrange them into networks. Human XIRP2 repeats have the same properties. Loss of mouse Xirp2 disorganizes the paracrystalline actin arrays of hair-cell stereocilia. action: ACCEPT reason: >- The product does part of the work: its Xin-repeat array binds, stabilizes and cross-links actin filaments. E1BL04 keeps the full repeat array (RESULTS.md), and the family-level PAINT node is consistent with a conserved repeat-mediated mechanism. supported_by: - reference_id: PMID:15454575 supporting_text: they not only directly bind actin filaments, but also have the capability of arranging microfilaments into networks - reference_id: PMID:25772365 supporting_text: At an ultrastructural level, the paracrystalline actin filaments became disorganized. - reference_id: file:BOVIN/E1BL04/E1BL04-bioinformatics/RESULTS.md supporting_text: E1BL04 is a full-length XIRP2 long (Xin-repeat) product - term: id: GO:0051015 label: actin filament binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- PAINT node PTN000502290 seeded by human XIRP2 (A4UGR9, IMP for this term from PMID:15454575) and human XIRP1 (Q702N8). Xin repeats bind actin filaments directly in co-sedimentation assays. E1BL04 has 26 PROSITE Xin repeats and 18 Pfam Xin domains. action: ACCEPT reason: >- This is the defining molecular function of the Xin family and is carried by the repeat array that E1BL04 retains. A4UGR9 appearing among the seeds reflects experimental grounding on the orthologous gene, which is expected for an IBA. supported_by: - reference_id: PMID:15454575 supporting_text: they not only directly bind actin filaments - reference_id: PMID:15454575 supporting_text: Human XIRP2 contains 28 Xin repeats with properties identical to those of Xin - reference_id: file:BOVIN/E1BL04/E1BL04-uniprot.txt record_section: ["CC:DOMAIN"] supporting_text: Xin repeats bind F-actin - term: id: GO:0003779 label: actin binding evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: >- Combined automated annotation from the Xin repeat (IPR012510) and XIRP1/XIRP2 family (IPR030072) signatures. It is correct, but less specific than the evidence supports. action: MODIFY reason: >- Xin repeats bind actin filaments specifically. The term should be refined to GO:0051015 actin filament binding, which the gene already carries by IBA and Ensembl Compara. proposed_replacement_terms: - id: GO:0051015 label: actin filament binding supported_by: - reference_id: file:BOVIN/E1BL04/E1BL04-uniprot.txt record_section: ["CC:DOMAIN"] supporting_text: Xin repeats bind F-actin - reference_id: PMID:15454575 supporting_text: they not only directly bind actin filaments - term: id: GO:0030036 label: actin cytoskeleton organization evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: >- InterPro2GO mapping from IPR012510/IPR030072. Correct, but the evidence supports the more specific process of organizing actin filaments. action: MODIFY reason: >- The term should be refined to GO:0007015 actin filament organization (an is_a descendant), which the gene already carries by IBA. The repeats act directly on actin filaments, binding, stabilizing and cross-linking them. proposed_replacement_terms: - id: GO:0007015 label: actin filament organization supported_by: - reference_id: PMID:15454575 supporting_text: they not only directly bind actin filaments, but also have the capability of arranging microfilaments into networks - term: id: GO:0030054 label: cell junction evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: located_in review: summary: >- InterPro2GO mapping from IPR012510. XIRP2 is at the intercalated disc in cardiomyocytes, a cell-cell junction. The term is correct but very general. action: MODIFY reason: >- The term should be refined to GO:0005911 cell-cell junction, which the gene already carries (from mouse Xirp2 IDA via Ensembl Compara). Intercalated disc (GO:0014704) is the more precise muscle location and is recorded in core_functions. proposed_replacement_terms: - id: GO:0005911 label: cell-cell junction supported_by: - reference_id: PMID:20360251 supporting_text: The Xin repeat-containing proteins mXinalpha and mXinbeta localize to the intercalated disc of mouse heart - term: id: GO:0070161 label: anchoring junction evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: >- UniProt subcellular-location mapping (SL-0038 Cell junction). The bovine UniProt subcellular location statement is ARBA-derived, so it is not independent support. The location agrees with ortholog data, since the intercalated disc is an anchoring cell-cell junction. action: MODIFY reason: >- The term is correct but general. GO:0005911 cell-cell junction is an is_a descendant of anchoring junction, and the gene already carries it. The intercalated disc (GO:0014704, also a descendant) is the specific site in heart. proposed_replacement_terms: - id: GO:0005911 label: cell-cell junction supported_by: - reference_id: PMID:20360251 supporting_text: The Xin repeat-containing proteins mXinalpha and mXinbeta localize to the intercalated disc of mouse heart - term: id: GO:0001725 label: stress fiber evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with review: summary: >- Ensembl Compara transfer of the same claim from human XIRP2 (A4UGR9; IMP, PMID:15454575). action: KEEP_AS_NON_CORE reason: >- Consistent with the IBA row for the same term. The colocalization is seen with overexpression in cultured cells and is not the physiological muscle location. supported_by: - reference_id: PMID:15454575 supporting_text: upon expression in cultured cells, these repeats bind to and stabilize the actin-based cytoskeleton - term: id: GO:0005911 label: cell-cell junction evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: located_in review: summary: >- Ensembl Compara transfer from mouse Xirp2 (Q4U4S6), which carries IDA from PMID:37294664. Long XIRP2 isoforms localize to cell junctions in hair cells, and mouse Xirp2 is an intercalated disc protein in heart. action: ACCEPT reason: >- Cell-cell junction residence is documented for XIRP2 long isoforms, the class E1BL04 belongs to, in both hair cells and cardiomyocytes. This is the appropriate general CC term. Intercalated disc is the precise cardiac site. supported_by: - reference_id: PMID:37294664 supporting_text: The long isoform primarily localizes to the cuticular plate and cell junctions, while the short isoform is enriched in stereocilia - reference_id: PMID:20360251 supporting_text: The Xin repeat-containing proteins mXinalpha and mXinbeta localize to the intercalated disc of mouse heart - term: id: GO:0005925 label: focal adhesion evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: colocalizes_with review: summary: >- Ensembl Compara transfer of the human XIRP2 (A4UGR9) focal adhesion colocalization (IMP, PMID:15454575). action: KEEP_AS_NON_CORE reason: >- Consistent with the IBA row for the same term. The evidence comes from a cultured non-muscle context. supported_by: - reference_id: PMID:15454575 supporting_text: upon expression in cultured cells, these repeats bind to and stabilize the actin-based cytoskeleton - term: id: GO:0030018 label: Z disc evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: located_in review: summary: >- Ensembl Compara transfer from mouse Xirp2 (Q4U4S6). Mouse myomaxin (Xirp2) localizes to the Z-disc/costameric region of striated muscle (IDA, PMID:17046827). action: ACCEPT reason: >- Z disc/costamere localization is a core muscle location of XIRP2 and agrees with its alpha-actinin-2 interaction. E1BL04 is a full-length long XIRP2 product in the same PANTHER subfamily (SF1) as the mouse donor. supported_by: - reference_id: PMID:17046827 supporting_text: localizes to the Z-disc/costameric region in striated muscle - term: id: GO:0051015 label: actin filament binding evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables review: summary: >- Ensembl Compara transfer from human XIRP2 (A4UGR9; IMP, PMID:15454575). Same claim as the IBA row. action: ACCEPT reason: >- This is the core molecular function, carried by the Xin repeat array that E1BL04 retains. It is consistent with the IBA row. supported_by: - reference_id: PMID:15454575 supporting_text: Human XIRP2 contains 28 Xin repeats with properties identical to those of Xin - reference_id: file:BOVIN/E1BL04/E1BL04-uniprot.txt record_section: ["CC:DOMAIN"] supporting_text: Xin repeats bind F-actin - term: id: GO:0051393 label: alpha-actinin binding evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables review: summary: >- Ensembl Compara transfer from mouse Xirp2 (Q4U4S6; IDA, PMID:17046827). Myomaxin interacts with the sarcomeric Z-disc protein alpha-actinin-2. action: ACCEPT reason: >- Alpha-actinin binding is an experimentally supported XIRP2 activity that explains its Z-disc targeting. The ortholog relationship (same PANTHER SF1 subfamily, full-length long product) supports the transfer. The binding region has not been mapped, so retention cannot be checked at residue level. supported_by: - reference_id: PMID:17046827 supporting_text: interacts with the sarcomeric Z-disc protein, alpha-actinin-2 - term: id: GO:0110053 label: regulation of actin filament organization evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: summary: >- Ensembl Compara transfer from mouse Xirp2 (Q4U4S6; IMP, PMID:25772365). In Xirp2-null hair cells, stereocilia degenerate and their paracrystalline actin arrays become disorganized. action: KEEP_AS_NON_CORE reason: >- The phenotype is a requirement for the organization of actin arrays. Mechanistically it is better described by the direct process GO:0007015 actin filament organization (accepted), in which the Xin repeats bind and stabilize the filaments. The regulatory framing is defensible because the protein protects filaments, but it is peripheral to the direct activity and rests on a knockout phenotype in a hair-cell context. supported_by: - reference_id: PMID:25772365 supporting_text: XIRP2 is notable for its 28 Xin repeats, which bind and stabilize actin bundles - reference_id: PMID:25772365 supporting_text: At an ultrastructural level, the paracrystalline actin filaments became disorganized. - term: id: GO:1903829 label: positive regulation of protein localization evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: summary: >- Ensembl Compara transfer from mouse Xirp2 (Q4U4S6; IMP, PMID:37294664). The underlying finding is that XIRP2 is required to enrich monomeric gamma-actin at noise-induced stereocilia gaps. This activity maps to the short stereocilia isoform and to its C-terminal LIM domain and CTD, and the CTD alone pulls down monomeric gamma-actin. action: MARK_AS_OVER_ANNOTATED reason: >- E1BL04 lacks the LIM domain and C-terminal domain that carry this activity (RESULTS.md: no LIM match, and the mouse isoform-1 C-terminal region is not covered). The annotated sequence therefore lacks the region responsible, a domain-architecture mismatch. The term is also vague, since it does not name the protein whose localization is affected. Other bovine XIRP2 gene models (A0AAA9SWG7, A0AAA9SUE1) may represent short isoforms to which this would apply better. supported_by: - reference_id: PMID:37294664 supporting_text: Because the short isoform of XIRP2 contains a LIM domain, we hypothesized that it was recognizing strained actin in the stereocilia and facilitating repair. - reference_id: PMID:37294664 supporting_text: The C-terminal domain (CTD) of XIRP2 is sufficient to pull down monomeric γ-actin. - reference_id: file:BOVIN/E1BL04/E1BL04-bioinformatics/RESULTS.md supporting_text: E1BL04 lacks the C-terminal LIM domain / C-terminal domain (CTD) - term: id: GO:0014704 label: intercalated disc evidence_type: ISS original_reference_id: PMID:20360251 qualifier: located_in review: summary: >- Proposed location. Mouse Xirp2 (mXinbeta), in the same PANTHER subfamily (SF1) as E1BL04, localizes to the cardiac intercalated disc and is required for intercalated disc maturation. E1BL04 is a full-length long XIRP2 product and keeps the Xin-repeat array. action: NEW reason: >- This is the specific cardiac site of XIRP2. It refines the accepted cell-cell junction term (GO:0014704 is_a GO:0005911). It is a location claim and does not imply that the protein takes part in a process. supported_by: - reference_id: PMID:20360251 supporting_text: The Xin repeat-containing proteins mXinalpha and mXinbeta localize to the intercalated disc of mouse heart - reference_id: file:BOVIN/E1BL04/E1BL04-bioinformatics/RESULTS.md supporting_text: E1BL04 is a full-length XIRP2 long (Xin-repeat) product references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: - statement: >- InterPro identifies the Xin repeat domain (IPR012510) and the XIRP1/XIRP2 family (IPR030072), giving actin binding, actin cytoskeleton organization and cell junction mappings; all are correct but general. - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: - statement: >- PAINT node PTN000502290 is a family-level Xin node seeded by human XIRP2 (A4UGR9) and human XIRP1 (Q702N8). The actin filament organization IBD is seeded by XIRP1 alone. (The earlier version of this review mislabelled Q702N8 as mouse Xirp2; it is human XIRP1, PANTHER SF2.) - 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: - statement: >- The mapping of SL-0038 Cell junction gives anchoring junction. The bovine subcellular location statement is ARBA-derived. - id: GO_REF:0000107 title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara findings: - statement: >- These transfers are from human XIRP2 (A4UGR9) and mouse Xirp2 (Q4U4S6). They are the most informative annotations for this entry, but one, positive regulation of protein localization, derives from an isoform-specific (LIM/CTD) activity that E1BL04 lacks. - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: - statement: >- The combined IEA methods assign the general term actin binding, which is better refined to actin filament binding. - id: file:BOVIN/E1BL04/E1BL04-uniprot.txt title: UniProt entry E1BL04 findings: - statement: >- This is an unreviewed (PE 3) 3561-aa XIRP2 entry with 26 PROSITE Xin repeats and 18 Pfam Xin domains. It is placed in PANTHER PTHR22591:SF1 (XIRP2) and has no LIM domain. - id: file:BOVIN/E1BL04/E1BL04-bioinformatics/RESULTS.md title: E1BL04 comparison with characterized Xin-family proteins findings: - statement: >- E1BL04 aligns over 99% of human XIRP2 at 80.5% identity, against 36-38% identity to XIRP1. It lacks the LIM/CTD region of mouse Xirp2 isoform 1 and the short isoform. - id: PMID:15454575 title: Xin repeats define a novel actin-binding motif. findings: - statement: Xin repeats bind actin filaments directly, stabilize them and arrange them into networks. Human XIRP2 repeats share these properties. supporting_text: they not only directly bind actin filaments, but also have the capability of arranging microfilaments into networks reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract-only cache. The paper defines the Xin repeat as an actin-binding motif, and its abstract states that the XIRP2 repeats behave like those of Xin. It is the source of the human XIRP2 IMP rows. - id: PMID:17046827 title: Myomaxin is a novel transcriptional target of MEF2A that encodes a Xin-related alpha-actinin-interacting protein. findings: - statement: Mouse Xirp2 (myomaxin) localizes to the Z-disc/costamere and interacts with alpha-actinin-2. supporting_text: interacts with the sarcomeric Z-disc protein, alpha-actinin-2 reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract-only cache. Source of the mouse IDA rows for Z disc and alpha-actinin binding. - id: PMID:20360251 title: Essential roles of an intercalated disc protein, mXinbeta, in postnatal heart growth and survival. findings: - statement: Mouse Xirp2 localizes to the intercalated disc and is required for intercalated disc maturation and for the localization of Xirp1 and N-cadherin there. supporting_text: Loss of mXinbeta resulted in the failure of forming mature intercalated discs and the mislocalization of mXinalpha and N-cadherin. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached. This is knockout and necessity evidence. It is used for location (intercalated disc) and not to propose new process terms. - id: PMID:25772365 title: XIRP2, an actin-binding protein essential for inner ear hair-cell stereocilia. findings: - statement: Long XIRP2 isoforms with Xin repeats occur in stereocilia and cuticular plates. Loss of Xirp2 disorganizes the paracrystalline actin of stereocilia. supporting_text: XIRP2 is notable for its 28 Xin repeats, which bind and stabilize actin bundles reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached. Source of the mouse IMP for regulation of actin filament organization. - id: PMID:37294664 title: Repair of noise-induced damage to stereocilia F-actin cores is facilitated by XIRP2 and its novel mechanosensor domain. findings: - statement: The repair of stereocilia gaps and the gamma-actin recruitment depend on the LIM/CTD of the short XIRP2 isoform. The long isoform is at the cuticular plate and cell junctions. supporting_text: The long isoform primarily localizes to the cuticular plate and cell junctions, while the short isoform is enriched in stereocilia reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text cached. The functional findings are isoform-specific and map to a region that is absent from E1BL04. - id: PMID:17766470 title: Loss of mXinalpha, an intercalated disk protein, results in cardiac hypertrophy and cardiomyopathy with conduction defects. reference_review: relevance: LOW correctness: VERIFIED review_notes: Abstract-only cache. The paper is about mouse Xirp1 (mXinalpha); the abstract mentions Xirp2 only as compensatorily upregulated. It is cited by MGI for a mouse Xirp2 anchoring junction EXP row. It is not used as support here. core_functions: - description: >- Binds actin filaments directly through its central array of Xin repeats, and stabilizes and cross-links them. In striated muscle this anchors and organizes actin at the Z disc/costamere and at the cardiac intercalated disc. molecular_function: id: GO:0051015 label: actin filament binding locations: - id: GO:0030018 label: Z disc - id: GO:0014704 label: intercalated disc directly_involved_in: - id: GO:0007015 label: actin filament organization supported_by: - reference_id: PMID:15454575 supporting_text: they not only directly bind actin filaments, but also have the capability of arranging microfilaments into networks - reference_id: PMID:20360251 supporting_text: The Xin repeat-containing proteins mXinalpha and mXinbeta localize to the intercalated disc of mouse heart - reference_id: file:BOVIN/E1BL04/E1BL04-uniprot.txt record_section: ["CC:DOMAIN"] supporting_text: Xin repeats bind F-actin - description: >- Binds the Z-disc cross-linker alpha-actinin-2, which targets the protein to the peripheral Z-disc complex of striated muscle. molecular_function: id: GO:0051393 label: alpha-actinin binding locations: - id: GO:0030018 label: Z disc supported_by: - reference_id: PMID:17046827 supporting_text: interacts with the sarcomeric Z-disc protein, alpha-actinin-2 suggested_questions: - question: >- Do the short bovine XIRP2 gene models (A0AAA9SWG7, A0AAA9SUE1) encode the LIM/CTD-containing stereocilia isoform? If so, should the stereocilia-repair and gamma-actin recruitment annotations be attached to them rather than to E1BL04? - question: >- Which region of XIRP2 binds alpha-actinin-2, and is it conserved in the bovine long product? - question: >- Does bovine XIRP2 localize to the intercalated disc and Z disc of cattle cardiomyocytes, as the mouse ortholog does? suggested_experiments: - hypothesis: >- Bovine XIRP2 localizes to Z discs and intercalated discs in cattle cardiomyocytes. description: >- Immunofluorescence on bovine cardiac and skeletal muscle sections, co-stained for alpha-actinin (Z disc) and N-cadherin (intercalated disc). experiment_type: immunofluorescence microscopy - hypothesis: >- The Xin-repeat region of bovine XIRP2 binds and bundles F-actin. description: >- Express recombinant Xin-repeat fragments and assay high- and low-speed F-actin co-sedimentation. experiment_type: actin co-sedimentation assay