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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Summary: InterPro2GO mapping from IPR012510/IPR030072. Correct, but the evidence supports the more specific process of organizing actin filaments.
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.
Summary: InterPro2GO mapping from IPR012510. XIRP2 is at the intercalated disc in cardiomyocytes, a cell-cell junction. The term is correct but very general.
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.
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.
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.
Summary: Ensembl Compara transfer of the same claim from human XIRP2 (A4UGR9; IMP, PMID:15454575).
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.
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.
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.
Summary: Ensembl Compara transfer from mouse Xirp2 (Q4U4S6). Mouse myomaxin (Xirp2) localizes to the Z-disc/costameric region of striated muscle (IDA, PMID:17046827).
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.
Summary: Ensembl Compara transfer from mouse Xirp2 (Q4U4S6; IDA, PMID:17046827). Myomaxin interacts with the sarcomeric Z-disc protein alpha-actinin-2.
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.
interacts with the sarcomeric Z-disc protein, alpha-actinin-2
GO:0110053 regulation of actin filament organization
IEA GO_REF:0000107
KEEP AS NON CORE
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.
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.
At an ultrastructural level, the paracrystalline actin filaments became disorganized.
GO:1903829 positive regulation of protein localization
IEA GO_REF:0000107
MARK AS OVER ANNOTATED
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.
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.
Because the short isoform of XIRP2 contains a LIM domain, we hypothesized that it was recognizing strained actin in the stereocilia and facilitating repair.
ISS PMID:20360251 Essential roles of an intercalated disc protein, mXinbeta, i...
NEW
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.
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.
E1BL04 is a full-length XIRP2 long (Xin-repeat) product
Core Functions
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.
Q: 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?
Q: Which region of XIRP2 binds alpha-actinin-2, and is it conserved in the bovine long product?
Q: Does bovine XIRP2 localize to the intercalated disc and Z disc of cattle cardiomyocytes, as the mouse ortholog does?
Suggested Experiments
Experiment: Immunofluorescence on bovine cardiac and skeletal muscle sections, co-stained for alpha-actinin (Z disc) and N-cadherin (intercalated disc).
Hypothesis: Bovine XIRP2 localizes to Z discs and intercalated discs in cattle cardiomyocytes.
Type: immunofluorescence microscopy
Experiment: Express recombinant Xin-repeat fragments and assay high- and low-speed F-actin co-sedimentation.
Hypothesis: The Xin-repeat region of bovine XIRP2 binds and bundles F-actin.
Type: actin co-sedimentation assay
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
E1BL04 is bovine XIRP2, a Xin-repeat protein of the XIRP2 subfamily (PANTHER PTHR22591:SF1) that binds and organizes actin filaments and localizes to striated-muscle junctions. All three ProtNLM2 predictions (actin cytoskeleton organization, cell junction, actin binding) are biologically correct, and each is already carried by the gene in GOA by automated InterPro-based annotation, so none is novel. The gene review refines each to a more specific descendant the gene also carries.
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: The target carries the Xin actin-binding repeat (IPR012510) and the XIRP2 subfamily assignment (PTHR22591:SF1). Xin repeats, including those of human XIRP2, bind actin filaments directly and arrange them into networks (PMID:15454575), which supports actin cytoskeleton organization by phylogenetic transfer. The exact term is already in GOA for this gene (InterPro2GO), and the gene review refines it to actin filament organization (GO:0007015), which the gene also carries by IBA. The prediction is correct but not novel.
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: Mouse Xirp2 (mXinbeta) localizes to the intercalated disc of the heart (PMID:20360251), a cell-cell junction, and the bovine target is its XIRP2-subfamily ortholog. Cell junction is therefore correct by orthology. The exact term is already in GOA for this gene (InterPro2GO), and the gene review refines it to cell-cell junction (GO:0005911), which the gene also carries by Ensembl Compara transfer. The prediction is correct but not novel.
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: Xin repeats are experimentally established actin-binding modules, and human XIRP2 repeats share this activity (PMID:15454575). The bovine target contains these repeats (PROSITE PRU00721). Actin binding is already in GOA for this gene (combined automated annotation, GO_REF:0000120), and the gene review refines it to actin filament binding (GO:0051015), which the gene also carries by IBA. The prediction is correct but not novel.