id: A0A3B6RKV1 gene_symbol: A0A3B6RKV1 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:4565 label: Triticum aestivum description: >- A0A3B6RKV1 (LOC123148885, TraesCS7A02G443400, chromosome 7A) encodes a 511-residue F-box/JmjC domain protein of bread wheat. It belongs to PANTHER subfamily PTHR12480:SF21 (the JMJD8-related subfamily of the JMJD4/JMJD6/JMJD8 JmjC oxygenase family), which it shares with Arabidopsis JMJ22 (At5g06550) and animal JMJD8. Its closest characterised relative is Arabidopsis JMJ22, with which it shares the N-terminal F-box (residues 89-135) and C-terminal JmjC domain (residues 285-445; about 77% identity in the JmjC domain) and the Fe(II)-binding His330-Asp332-His413 triad. These features indicate an Fe(II)- and 2-oxoglutarate-dependent oxygenase. JMJ22 is a nuclear histone H4 arginine-3 (H4R3me2) demethylase that, redundantly with JMJ20, promotes light (phytochrome B)-induced seed germination by removing repressive H4R3me2 at gibberellin biosynthesis genes GA3ox1 and GA3ox2. The wheat protein is therefore expected to act in the nucleus as a JmjC demethylase, possibly of methylarginine on histones, but neither its activity, substrate, the role of its F-box, nor any developmental function has been tested experimentally. Homeologous copies are encoded on chromosomes 7B and 7D. existing_annotations: - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: >- PAINT node PTN001753861 (PTHR12480 SF21 clade) carries an IBD for nucleus seeded by Arabidopsis JMJ22 (AT5G06550), Trypanosoma Q386V9 and human JMJD8 (Q96S16). The wheat protein is a same-subfamily plant ortholog of JMJ22, whose nuclear localization was shown directly (UniProt Swiss-Prot, ECO:0000269 PubMed:22483719). The human donor JMJD8 is now curated by UniProt as ER-lumenal/cytoplasmic, so the deep node placement may be broader than warranted for animals, but for the plant F-box/JmjC branch, which includes the wheat target, nucleus is well supported. action: ACCEPT reason: >- Target sits inside the plant JMJ22 branch of the SF21 clade, and the nearest donor (JMJ22) has direct experimental nuclear localization; a chromatin-acting JmjC enzyme is expected to be nuclear. supported_by: - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q67XX3-JMJ22-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: 'SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22483719}.' - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/RESULTS-rereview.md supporting_text: A0A3B6RKV1, Arabidopsis JMJ22 (Q67XX3, At5g06550) and human JMJD8 (Q96S16) are all - term: id: GO:0000987 label: cis-regulatory region sequence-specific DNA binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- This IBA rests on a single donor, an IDA by TAIR for Arabidopsis JMJ22 from Cho et al. 2012 (PMID:22483719), placed at the eukaryote-level node PTN001753861. Only the abstract of that paper is cached. The abstract reports that SOMNUS, a zinc-finger protein, directly represses JMJ20/JMJ22, and that JMJ20/JMJ22 remove histone arginine methylation at GA3ox1/GA3ox2. The DNA-binding assay that underlies the TAIR IDA cannot be identified from the abstract, and it could have been the SOMNUS-promoter EMSA. JMJ22 was also recovered as a promoter-binding protein in an Arabidopsis yeast one-hybrid screen (PMID:25533953, GO:0000976 IPI). JmjC demethylases are usually recruited to loci by other factors and have no known sequence-specific DNA-binding domain, and the wheat protein has no recognisable DNA-binding domain apart from the F-box and JmjC domain. The annotation is therefore neither confirmed nor refuted. action: UNDECIDED reason: >- The donor experimental annotation cannot be checked against full text, and the function is atypical for a JmjC/F-box protein without a DNA-binding domain. A curator-made IDA should not be overruled from an abstract, so this is left undecided rather than removed. The eukaryote-wide node placement on a single plant donor is also questionable, because animal JMJD8 is ER-lumenal. propagation_review: root_cause: UNRESOLVED source_entities: - source_id: PANTHER:PTN001753861 source_label: PTN001753861 source_status: UNRESOLVED comment: >- Eukaryote-level SF21 node with a single donor for this term, the JMJ22 IDA from PMID:22483719, which is abstract-only in cache. The wheat target is inside the plant JMJ22 branch, so the open question is whether the donor annotation is sound, not whether the target inherits from it. supported_by: - reference_id: PMID:22483719 supporting_text: When PHYB is inactive, JMJ20/JMJ22 are directly repressed by the zinc-finger protein SOMNUS. - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q96S16-JMJD8-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum lumen' - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: >- Electronic mapping of the UniProt subcellular-location statement (itself an ARBA prediction). The ARBA prediction is not independent evidence, but the same claim is supported by the IBA above and by direct nuclear localization of the same-subfamily ortholog JMJ22. The two rows agree. action: ACCEPT reason: >- Consistent with the accepted IBA row for the same term, which is grounded in the experimentally localized ortholog JMJ22. supported_by: - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q67XX3-JMJ22-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: 'SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22483719}.' - term: id: GO:0046872 label: metal ion binding evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: enables review: summary: >- The JmjC domain (PROSITE PS51184) coordinates a catalytic Fe(II) through an HxD...H triad. In the wheat protein all three ligands are conserved (His330, Asp332, His413, mapped by alignment from JMJ22 His324, Asp326, His407). JMJ22 is annotated by UniProt to bind one Fe(2+) per subunit. The term is correct but general, and the supported specific metal is ferrous iron. The earlier review's replacement (histone demethylase activity) changed the claim rather than refining it, and PAINT did not propagate the JMJ22 histone demethylase activity to this clade. action: MODIFY reason: >- Correct but less specific than the evidence supports. The JmjC Fe(II) site is fully conserved, so the precise is_a descendant is ferrous iron binding. proposed_replacement_terms: - id: GO:0008198 label: ferrous iron binding supported_by: - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/RESULTS-rereview.md supporting_text: AtJMJ22 Fe(II) ligands H324, D326, H407 map to wheat H330, D332, H413 (all conserved). - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-uniprot.txt record_section: ["DR:PROSITE"] supporting_text: DR PROSITE; PS51184; JMJC; 1. - term: id: GO:0016706 label: 2-oxoglutarate-dependent dioxygenase activity evidence_type: ISS original_reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/RESULTS-rereview.md qualifier: enables review: summary: >- The protein has a complete JmjC domain with the Fe(II)-binding HxD...H triad (His330, Asp332, His413) conserved with its same-subfamily ortholog JMJ22, whose Fe(II)/2-oxoglutarate-dependent methylarginine demethylase reaction is experimentally established. The general dioxygenase activity is the level that holds across the PTHR12480 family (JMJD4, JMJD6, JMJD8, JMJ22) without assuming a substrate. action: NEW reason: >- Catalytic Fe(II)/2OG oxygenase activity is supported by conserved active-site residues and orthology to an enzyme with demonstrated 2OG-dependent activity. The substrate (histone H4R3me2 for JMJ22) is not asserted, because PAINT did not propagate JMJ22's histone demethylase activity and nothing has been tested for the wheat protein. supported_by: - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/RESULTS-rereview.md supporting_text: AtJMJ22 Fe(II) ligands H324, D326, H407 map to wheat H330, D332, H413 (all conserved). - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q67XX3-JMJ22-uniprot.txt supporting_text: 'Evidence={ECO:0000269|PubMed:22483719};' references: - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: - statement: >- IBA annotations for A0A3B6RKV1 come from PAINT node PANTHER:PTN001753861 (PTHR12480). Nucleus is seeded by AT5G06550 (JMJ22), Q386V9 and Q96S16 (JMJD8); cis-regulatory region sequence-specific DNA binding is seeded by AT5G06550 alone. JMJ22's histone demethylase activity (IGI) and its process annotations were not propagated. - 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:0000104 title: >- Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features findings: [] - id: PMID:22483719 title: Control of seed germination by light-induced histone arginine demethylation activity. findings: - statement: >- JMJ20 and JMJ22 act redundantly as positive regulators of seed germination. Upon PHYB activation, JMJ20/JMJ22 are derepressed, resulting in increased gibberellic acid levels through the removal of repressive histone arginine methylations (H4R3me2) at GA3ox1/GA3ox2, which in turn promotes seed germination. supporting_text: >- the histone arginine demethylases, JMJ20 and JMJ22, act redundantly as positive regulators of seed germination reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Abstract-only in cache. Characterises the Arabidopsis ortholog JMJ22 (same PANTHER subfamily SF21); JMJ20 is a paralog in subfamily SF6. Not a study of the wheat protein. - id: PMID:25533953 title: An Arabidopsis gene regulatory network for secondary cell wall synthesis. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: >- Yeast one-hybrid network study that is the source of a TAIR GO:0000976 IPI on JMJ22. Cited only as context for the DNA-binding question; it does not address the wheat protein. - id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-deep-research-falcon.md title: Deep research report for A0A3B6RKV1 (LOC123148885) in Triticum aestivum findings: - statement: >- The falcon report places LOC123148885 in the KDM5/JARID1 (H3K4 demethylase) subfamily. This is contradicted by PANTHER (PTHR12480:SF21), InterPro IPR050910 and the F-box/JmjC domain architecture, which lacks JmjN, ARID, PHD and FYR domains. supporting_text: >- The primary function of LOC123148885 can be inferred from its membership in the KDM5/JARID1 subfamily of JmjC domain-containing histone demethylases. reference_review: relevance: LOW correctness: MISCITED review_notes: >- Generated report; its central subfamily assignment (KDM5/JARID1, H3K4) is wrong, apparently driven by the UniProt "JARID1 histone demethylase family" similarity text. Kept for provenance; no longer used as support for any function claim. Its wheat JmjC-family statements (24 genes, 18 nuclear) concern KDM4/KDM5 members and are not specific to this protein. - id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-hypotheses/core-function-1-go-0032452/openscientist.md title: >- OpenScientist deep research report on core function hypothesis for A0A3B6RKV1 histone demethylase activity findings: - statement: >- Corrected the KDM5/JARID1 call to a JMJ22-like assignment based on PANTHER, InterPro and domain architecture. reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: >- Generated report. Its orthology call (JMJ22) is confirmed by this re-review, but it labels SF21 as the "JMJD6 subfamily" (SF21 is JMJD8-related; JMJD6 is SF32) and the earlier review derived from it gave the third Fe(II) ligand as His362 (it is His413). No longer used as quoted support; replaced by the re-review alignment. - id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-uniprot.txt title: UniProtKB A0A3B6RKV1 record findings: [] - id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/RESULTS-rereview.md title: A0A3B6RKV1 vs Arabidopsis JMJ22 and human JMJD8 alignment and residue mapping findings: - statement: >- Wheat, JMJ22 and JMJD8 share PANTHER SF21; JMJ20 is in SF6. Wheat vs JMJ22 global identity is 62.6% (JmjC 77%), with conserved F-box and conserved Fe(II) ligands H330/D332/H413. supporting_text: AtJMJ22 JmjC 279-439 maps to wheat 285-445 (77.0% identity). - id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q67XX3-JMJ22-uniprot.txt title: UniProtKB Q67XX3 (Arabidopsis JMJ22) record, fetched 2026-10-20 findings: [] - id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q96S16-JMJD8-uniprot.txt title: UniProtKB Q96S16 (human JMJD8) record, fetched 2026-10-20 findings: [] core_functions: - description: >- Nuclear Fe(II)- and 2-oxoglutarate-dependent JmjC oxygenase of the plant F-box/JmjC (JMJ22-like) branch of PANTHER subfamily PTHR12480:SF21, with a fully conserved HxD...H iron-binding triad. By orthology to Arabidopsis JMJ22, the most likely activity is histone H4R3me2 arginine demethylation. That substrate-specific activity was not propagated by PAINT and has not been tested for the wheat protein, so it is not asserted here. supported_by: - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/RESULTS-rereview.md supporting_text: AtJMJ22 Fe(II) ligands H324, D326, H407 map to wheat H330, D332, H413 (all conserved). - reference_id: file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-bioinformatics/Q67XX3-JMJ22-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: >- Histone demethylase that demethylates 'Arg-3' (H4R3me) of histone H4 with a specific activity for H4R3me2 (PubMed:22483719). - reference_id: PMID:22483719 supporting_text: >- the histone arginine demethylases, JMJ20 and JMJ22, act redundantly as positive regulators of seed germination molecular_function: id: GO:0016706 label: 2-oxoglutarate-dependent dioxygenase activity locations: - id: GO:0005634 label: nucleus suggested_questions: - question: >- Does the wheat JMJ22 ortholog demethylate H4R3me2 (or other methylarginine/lysine marks) in vitro, and is the activity shared by the 7A, 7B and 7D homeologs? - question: >- What is the evidential basis of the TAIR IDA for GO:0000987 on JMJ22 in PMID:22483719, and is the PAINT placement of that term at eukaryote-level node PTN001753861 (which includes ER-lumenal animal JMJD8) appropriate? - question: >- Does the F-box domain of plant JMJ22-like proteins assemble into SCF complexes, or is it a degenerate structural module? suggested_experiments: - description: >- Express recombinant A0A3B6RKV1 (wild type and H330A/H413A Fe-site mutants) and assay demethylation of H4R3me2 peptides and nucleosomes by mass spectrometry, with formaldehyde release as readout. - description: >- Test whether the wheat gene complements the Arabidopsis jmj20 jmj22 double mutant's red-light seed germination defect. - description: >- Co-immunoprecipitation with wheat SKP1/ASK homologs to test whether the F-box is functional.