A0A3B6RKV1

UniProt ID: A0A3B6RKV1
Organism: Triticum aestivum
Review Status: COMPLETE
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Gene Description

A0A3B6RKV1 (LOC123148885) is a JmjC domain-containing protein in Triticum aestivum (wheat) that belongs to the JMJD6 subfamily of JmjC domain-containing proteins, orthologous to Arabidopsis JMJ22 (At5g06550). The protein contains an F-box domain (residues 89-135) and a JmjC catalytic domain (residues 285-445) within a compact 511-amino-acid frame; this F-box + JmjC architecture is incompatible with KDM5/JARID1 proteins, which require JmjN, ARID, PHD finger, and FYR domains and are typically 800-1200+ amino acids. Multiple independent lines of evidence (PANTHER PTHR12480:SF21, InterPro IPR050910, NCBI orthology, domain architecture) consistently place this protein in the JMJD6 family, not KDM5/JARID1. Based on orthology to AtJMJ22, which is an experimentally characterized H4R3me2 arginine demethylase (PMID:22483719), A0A3B6RKV1 is predicted to catalyze Fe(II)- and 2-oxoglutarate-dependent oxidative demethylation of histone H4 arginine 3 dimethyl marks (H4R3me2), thereby modulating chromatin state and gene expression. The protein is predicted to localize to the nucleus, consistent with its chromatin-associated function; 18 of 24 wheat JmjC family members show predicted nuclear localization. The additional F-box domain suggests potential involvement in SCF (Skp1-Cullin1-F-box) E3 ubiquitin ligase complex-mediated protein turnover, though the substrates for this domain remain uncharacterized. In Arabidopsis, JMJ22 participates in photomorphogenesis, gibberellin-mediated signaling, and seed germination through removal of repressive H4R3me2 marks at GA biosynthesis gene loci (GA3ox1/GA3ox2). A0A3B6RKV1 exists as part of a complete homeologous triad in hexaploid wheat: 7A (A0A3B6RKV1), 7B (A0A3B6SQ95), and 7D (A0A3B6TWS8), all 511 amino acids with 96-98% sequence identity and perfectly conserved catalytic triad, indicating strong purifying selection. Wheat JmjC family members show dynamic expression patterns under drought stress and carry hormone-responsive cis-elements in their promoters. This is an unreviewed TrEMBL entry with protein existence level 3 (inferred from homology); no direct experimental characterization of LOC123148885 has been published. Note: the UniProt "Similarity" field incorrectly states "Belongs to the JARID1 histone demethylase family"; this is contradicted by the PANTHER, InterPro, and NCBI classifications and by the domain architecture.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005634 nucleus
IBA
GO_REF:0000033 		ACCEPT
Summary: Nuclear localization is strongly supported for this protein. The IBA annotation is based on phylogenetic inference from orthologs including AT5G06550 (Arabidopsis JMJ22), Q386V9, and Q96S16 via PANTHER. JmjC domain-containing histone demethylases require nuclear localization to access their chromatin substrates. Wang et al. (2022) found that 18 of 24 wheat JmjC family members are predicted to be nuclear. The UniProt entry independently annotates this protein to the nucleus via ARBA (ECO:0000256). The is_active_in qualifier is appropriate since the protein is expected to carry out its demethylase function on chromatin within the nucleus.
GO:0000987 cis-regulatory region sequence-specific DNA binding
IBA
GO_REF:0000033 		UNDECIDED
Summary: This IBA annotation is transferred from Arabidopsis AT5G06550 (JMJ22) and PANTHER:PTN001753861 via phylogenetic inference. JMJD6 subfamily demethylases are primarily characterized as chromatin-modifying enzymes rather than sequence-specific DNA-binding proteins. JMJD6 subfamily members may associate with specific genomic loci through interactions with other transcription factors or chromatin readers, but direct sequence-specific DNA binding is not the established primary function of this protein family. The deep research report describes the protein as an epigenetic regulator acting on histones rather than a sequence-specific DNA-binding factor. However, this is a phylogenetically inferred annotation from a characterized ortholog, and the full evidence supporting the original annotation for AT5G06550 is not available in the cache. The annotation may reflect a genuine functional property of JMJ22 orthologs that has been experimentally demonstrated in Arabidopsis.
Reason: Cannot verify whether the Arabidopsis ortholog AT5G06550 (JMJ22) has been experimentally demonstrated to have cis-regulatory region sequence-specific DNA binding. This function would be atypical for the JMJD6 family but cannot be ruled out without access to the primary literature. The IBA evidence is based on phylogenetic transfer, which should not be overruled without clear contradictory evidence.
GO:0005634 nucleus
IEA
GO_REF:0000044 		ACCEPT
Summary: This IEA annotation is derived from UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping (ARBA:ARBA00004123). Nuclear localization is consistent with the protein's predicted function as a histone demethylase that must access chromatin. This is concordant with the IBA annotation above and represents an independent line of evidence supporting nuclear localization.
GO:0046872 metal ion binding
IEA
GO_REF:0000104 		MODIFY
Summary: Metal ion binding is consistent with the JmjC domain catalytic mechanism, which requires Fe(II) coordination by conserved His/Glu(or Asp)/His residues for oxidative demethylation. The deep research report confirms that JmjC catalytic residues coordinate Fe(II) as a cofactor. However, GO:0046872 is a very general term. The more informative annotation would be to a specific molecular function term such as histone demethylase activity (GO:0032452), which inherently implies the metal-binding requirement. As an IEA annotation derived from UniRule (UR000416814) based on shared sequence features, it correctly captures that the protein binds metal ions, but is less informative than the actual catalytic activity.
Reason: While metal ion binding is technically correct for the JmjC domain (Fe(II) is a required cofactor), GO:0046872 is overly general and uninformative. The protein's primary molecular function is histone demethylase activity, which subsumes the metal-binding requirement. A more specific term better captures the biological role.
Proposed replacements: histone demethylase activity

Core Functions

Putative histone arginine demethylase of the JMJD6 subfamily that catalyzes Fe(II)- and 2-oxoglutarate-dependent oxidative removal of methyl groups from histone H4 arginine 3 (H4R3me2), functioning in the nucleus to regulate gene expression epigenetically. Inferred from orthology to Arabidopsis JMJ22 (At5g06550, PMID:22483719), which experimentally demethylates H4R3me2 at GA biosynthesis loci. GO:0033749 (histone H4R3 demethylase activity) would be the ideal more specific term but is not available in the local GO cache; GO:0032452 is used as the validated parent term. The protein exists as a homeologous triad in hexaploid wheat: 7A (A0A3B6RKV1), 7B (A0A3B6SQ95), 7D (A0A3B6TWS8), all 511 aa with 96-98% identity and perfectly conserved catalytic triad.

Molecular Function:
histone demethylase activity
Directly Involved In:
epigenetic regulation of gene expression
Cellular Locations:
nucleus
Supporting Evidence:
  • PMID:22483719
    the histone arginine demethylases, JMJ20 and JMJ22, act redundantly as positive regulators of seed germination
  • file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-hypotheses/core-function-1-go-0032452/openscientist.md
    A0A3B6RKV1 belongs to the JMJD6 subfamily (PANTHER PTHR12480:SF21, InterPro IPR050910), orthologous to Arabidopsis JMJ22 (At5g06550), an experimentally characterized H4R3me2 arginine demethylase. Domain architecture (F-box 89-135 + JmjC 285-445, 511 aa) is incompatible with KDM5/JARID1 (requires JmjN, ARID, PHD, FYR; 800-1200+ aa). JmjC domain identity to AtJMJ22 is approximately 77%.
  • file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-deep-research-falcon.md
    The protein contains both a JmjC histone demethylase domain and an F-box domain, and is predicted to localize to the nucleus, consistent with its chromatin-associated function.

References

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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.

ProtNLM2 External predictions

View prediction review YAML · A0A3B6RKV1-protnlm-predictions-review.yaml · Review status: COMPLETE

Sequence similarity to experimentally characterized Arabidopsis JMJ22 and matching F-box/JmjC architecture support inferred epigenetic regulation. Conservation of specific light, hormone, and germination roles remains unresolved.

Source documents: genes/WHEAT/A0A3B6RKV1/A0A3B6RKV1-uniprot.txt · genes/WHEAT/A0A3B6RKV1/A0A3B6RKV1-goa.tsv · publications/PMID_22483719.md · genes/WHEAT/A0A3B6RKV1/A0A3B6RKV1-prediction-evidence/protnlm.json · genes/WHEAT/A0A3B6RKV1/A0A3B6RKV1-prediction-evidence/Q67XX3-uniprot.txt · genes/WHEAT/A0A3B6RKV1/A0A3B6RKV1-hypotheses/prediction-jmj22-developmental-roles/openscientist.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0010099 regulation of photomorphogenesis GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target shares F-box/JmjC architecture with Arabidopsis JMJ22, and the raw ProtNLM evidence record reports a phmmer match to reviewed JMJ22 Q67XX3 with score 689.2. Primary JMJ20/22 experiments establish a role in light-controlled germination (PMID:22483719), making a related developmental function plausible. This similarity does not resolve conservation of the broader photomorphogenic program in wheat. The exact process is absent from the cached target annotations and remains uncertain pending pathway-level evidence.
Supporting Evidence:
GO:0010476 gibberellin mediated signaling pathway GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target has matching F-box/JmjC architecture and a strong reported phmmer match to characterized Arabidopsis JMJ22. JMJ20/22 affect gibberellin levels by modifying chromatin at biosynthetic genes (PMID:22483719), while gibberellin-mediated signaling is a distinct claim. Sequence similarity supports a related chromatin enzyme but does not establish the target's place in a hormone-signaling pathway. The exact process is absent from the cached target annotations and remains uncertain.
Supporting Evidence:
GO:0040029 epigenetic regulation of gene expression GO_BP
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target shares F-box/JmjC architecture with reviewed Arabidopsis JMJ22 Q67XX3, the phmmer match reported in the raw prediction evidence with score 689.2. Primary experiments establish histone arginine demethylation by JMJ20/22 and regulation of chromatin at gibberellin-biosynthetic genes (PMID:22483719). Together, the sequence relationship, domain architecture, and characterized relative support transfer of broad epigenetic regulation; this is a family-based inference, not an assay on wheat or a claim of H3K4 lysine demethylation. The process is absent from the cached target annotations.
Supporting Evidence:
  • file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-uniprot.txt: "ID A0A3B6RKV1_WHEAT Unreviewed; 511 AA. ... DR GO; GO:0005634; C:nucleus; IBA:GO_Central. ... DR GO; GO:0000987; F:cis-regulatory region sequence-specific DNA binding; IBA:GO_Central. ... DR InterPro; IPR003347; JmjC_dom. ... DR InterPro; IPR050910; JMJD6_ArgDemeth/LysHydrox. ... DR PANTHER; PTHR12480:SF21; JMJC DOMAIN-CONTAINING PROTEIN 8; 1. ... FT DOMAIN 89..135 ... FT /note="F-box" ... FT DOMAIN 285..445 ... FT /note="JmjC""
  • PMID:22483719: "histone arginine demethylases, JMJ20 and JMJ22"
  • file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-prediction-evidence/protnlm.json: ""key": "phmmer_accession", "value": "Q67XX3""
  • file:WHEAT/A0A3B6RKV1/A0A3B6RKV1-prediction-evidence/Q67XX3-uniprot.txt: "ID JMJ22_ARATH Reviewed; 502 AA. ... GN Name=JMJ22 {ECO:0000303|PubMed:18713399}; ... DR GO; GO:0040029; P:epigenetic regulation of gene expression; IDA:UniProtKB. ... DR InterPro; IPR050910; JMJD6_ArgDemeth/LysHydrox. ... DR PANTHER; PTHR12480:SF21; JMJC DOMAIN-CONTAINING PROTEIN 8; 1. ... FT DOMAIN 80..126 ... FT /note="F-box" ... FT DOMAIN 279..439 ... FT /note="JmjC""
GO:0010114 response to red light GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target has a strong reported sequence match to Arabidopsis JMJ22 and matching F-box/JmjC architecture. JMJ20/22 are derepressed following phytochrome B activation (PMID:22483719), establishing a red-light-related regulatory context in Arabidopsis. The target's catalytic-family relationship does not establish conservation of that light-dependent regulation in wheat. The response term is absent from the cached target annotations and remains uncertain pending regulatory or expression evidence.
Supporting Evidence:
GO:0010030 positive regulation of seed germination GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target shares domain architecture and a strong reported sequence match with Arabidopsis JMJ22. JMJ20/22 redundantly promote germination by affecting chromatin at gibberellin-biosynthetic genes (PMID:22483719), supporting a relevant developmental hypothesis. The wheat protein's expression context, target loci, and regulatory direction during germination are not established by this sequence relationship. The exact process is absent from the cached target annotations and remains uncertain.
Supporting Evidence:

Deep Research

Falcon

(A0A3B6RKV1-deep-research-falcon.md)

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OpenScientist

(A0A3B6RKV1-hypotheses/core-function-1-go-0032452/openscientist.md)

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OpenScientist

(A0A3B6RKV1-hypotheses/prediction-jmj22-developmental-roles/openscientist.md)

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