C6T1A2

UniProt ID: C6T1A2
Organism: Glycine max
Review Status: COMPLETE
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Gene Description

C6T1A2 (soybean ZFP1, NCBI Gene 732609, Glyma17g18110.1) is a 210-residue Q-type C2H2 zinc finger transcription factor from soybean (Glycine max). It contains a single C2H2-type zinc finger domain (residues 79-106) with the diagnostic plant-specific QALGGH DNA-binding motif (residues 92-97), which is the defining feature of Q-type C2H2 zinc finger transcription factors. The protein also carries a C-terminal LxLxL EAR-like motif characteristic of transcriptional repressors, suggesting it functions as a negative regulator of transcription. It was cloned as part of a soybean transcription factor ORFeome effort that identified drought-resistance-associated transcription factors. InterPro classifies it in the Zinc_finger_protein_7 family (IPR053266) and in the C2H2-type zinc finger superfamily (IPR036236, IPR013087), while PANTHER places it in the ZINC FINGER PROTEIN 4-LIKE family (PTHR47593). The closest characterized ortholog is Arabidopsis ZFP7 (Q39266), which shares the same single-C2H2 domain architecture and IPR053266 family membership and has been experimentally shown to regulate ABA signaling. Same-species support comes from GmZAT10-1, a soybean C2H2 zinc finger protein experimentally demonstrated to have transcriptional activation activity, nuclear localization, and DNA-binding capability. No gene-specific experimental studies have been published for C6T1A2 itself; all functional inferences derive from domain architecture, motif analysis, family membership, and analogy to characterized orthologs.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003700 DNA-binding transcription factor activity
ISS
UniProtKB:C6T1A2 		NEW
Summary: Proposed new annotation based on domain architecture. C6T1A2 contains a single C2H2-type zinc finger domain (residues 79-106) and is classified in the Zinc_finger_protein_7 family (IPR053266) and ZINC FINGER PROTEIN 4-LIKE PANTHER family (PTHR47593). It was cloned as part of a soybean transcription factor ORFeome. No direct experimental evidence for transcription factor activity exists; the inference is from domain/family membership and analogy to characterized plant C2H2 zinc finger transcription factors.
Reason: No molecular function annotation exists for C6T1A2 in GOA. The C2H2 zinc finger domain architecture and classification in the Zinc_finger_protein_7 family support DNA-binding transcription factor activity as the most likely molecular function. Evidence code ISS is appropriate given the reliance on sequence similarity to characterized family members.
Supporting Evidence:
UniProtKB:C6T1A2
InterPro; IPR053266; Zinc_finger_protein_7.
UniProtKB:C6T1A2
PANTHER; PTHR47593; ZINC FINGER PROTEIN 4-LIKE; 1.
file:SOYBN/C6T1A2/C6T1A2-deep-research-falcon.md
Based on InterPro domain annotation showing C2H2-type zinc finger domains (IPR013087, IPR036236, IPR053266), this protein is predicted to function as a DNA-binding transcription factor localized to the nucleus.
GO:0005634 nucleus
ISS
UniProtKB:C6T1A2 		NEW
Summary: Proposed new annotation for nuclear localization. As a predicted C2H2-type zinc finger transcription factor, C6T1A2 is expected to localize to the nucleus where it would bind DNA and regulate transcription. Multiple soybean C2H2 zinc finger proteins have been experimentally confirmed as nuclear-localized. ProtNLM2 also predicted this localization with high confidence (0.97), though it was assessed as trivially derivable from the protein's classification.
Reason: No cellular component annotation exists for C6T1A2 in GOA. Nuclear localization is the expected location for a C2H2-type zinc finger transcription factor. Evidence code ISS is appropriate given the reliance on domain architecture and analogy to characterized family members.
Supporting Evidence:
file:SOYBN/C6T1A2/C6T1A2-deep-research-falcon.md
Based on InterPro domain annotation showing C2H2-type zinc finger domains (IPR013087, IPR036236, IPR053266), this protein is predicted to function as a DNA-binding transcription factor localized to the nucleus.
file:SOYBN/C6T1A2/C6T1A2-protnlm-predictions-review.yaml
Nuclear localization is trivially expected for any C2H2-type zinc finger transcription factor.

Core Functions

C6T1A2 is strongly supported as a DNA-binding transcription factor based on convergent evidence: its C2H2-type zinc finger domain (residues 79-106) contains the plant-specific QALGGH DNA-binding motif (residues 92-97), which is the diagnostic marker for Q-type C2H2 zinc finger transcription factors. AlphaFold predicts this domain with very high confidence (pLDDT 91.5 for the zinc finger, 95.8 for the QALGGH motif). The protein also carries a C-terminal EAR-like repression motif, suggesting it functions specifically as a transcriptional repressor. Same-species support comes from GmZAT10-1, a soybean C2H2 zinc finger protein experimentally demonstrated to have nuclear localization and DNA-binding capability (PMID:40158630). OpenScientist investigation confirmed strong support for GO:0003700 at ISS evidence level.

Molecular Function:
DNA-binding transcription factor activity
Cellular Locations:
nucleus
Supporting Evidence:
  • UniProtKB:C6T1A2
    InterPro; IPR053266; Zinc_finger_protein_7.
  • UniProtKB:C6T1A2
    PANTHER; PTHR47593; ZINC FINGER PROTEIN 4-LIKE; 1.
  • file:SOYBN/C6T1A2/C6T1A2-deep-research-falcon.md
    Based on InterPro domain annotation showing C2H2-type zinc finger domains (IPR013087, IPR036236, IPR053266), this protein is predicted to function as a DNA-binding transcription factor localized to the nucleus.
  • file:SOYBN/C6T1A2/C6T1A2-hypotheses/core-function-1-go-0003700/openscientist.md
    QALGGH motif (residues 92-97) is the diagnostic marker for Q-type C2H2 zinc finger transcription factors. AlphaFold pLDDT 91.5 for zinc finger domain. C-terminal EAR-like repression motif present. Same-species evidence from GmZAT10-1 (PMID:40158630) confirms soybean C2H2 ZFPs function as DNA-binding transcription factors.

References

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Suggested Questions for Experts

Q: Does C6T1A2 (Glyma17g18110.1) function as a transcriptional activator or repressor, and what are its DNA-binding target sequences?

Q: Is C6T1A2 functionally orthologous to Arabidopsis ZFP7 (Q39266), and does it play a role in ABA signaling or drought stress responses in soybean?

Suggested experts: Henry T. Nguyen

Suggested Experiments

Experiment: Express C6T1A2 in a yeast or plant protoplast transcription activation assay (e.g., GAL4-AD/BD or LUC reporter system) to determine whether it has transcriptional activator or repressor activity, and perform electrophoretic mobility shift assays (EMSA) to identify DNA-binding sequence specificity.

Hypothesis: C6T1A2 binds specific DNA sequences via its C2H2 zinc finger domain and modulates transcription of target genes.

Type: transcription factor activity assay

Experiment: Generate transgenic soybean lines overexpressing or with CRISPR/Cas9 knockout of Glyma17g18110.1 and phenotype under drought and ABA treatments, measuring germination rate, stomatal conductance, and drought-responsive gene expression to test whether this gene modulates ABA signaling as predicted from its homology to Arabidopsis ZFP7.

Hypothesis: C6T1A2 negatively regulates ABA-activated signaling during germination and drought responses in soybean, analogous to its Arabidopsis homolog ZFP7.

Type: loss-of-function and gain-of-function genetics with stress phenotyping

Experiment: Perform subcellular localization of C6T1A2 fused to GFP in soybean protoplasts or Nicotiana benthamiana leaf epidermal cells to confirm predicted nuclear localization.

Hypothesis: C6T1A2 localizes to the nucleus, consistent with its predicted role as a transcription factor.

Type: subcellular localization by fluorescent protein fusion

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 · C6T1A2-protnlm-predictions-review.yaml · Review status: COMPLETE

The plant ZFP-family protein plausibly acts in the nucleus. A negative role in ABA signaling is supported in related Arabidopsis factors but remains unresolved for this soybean member.

Source documents: genes/SOYBN/C6T1A2/C6T1A2-uniprot.txt · genes/SOYBN/C6T1A2/C6T1A2-goa.tsv · publications/PMID_24808098.md · genes/SOYBN/C6T1A2/C6T1A2-hypotheses/prediction-negative-regulation-aba-signaling/openscientist.md

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

GO:0009788 negative regulation of abscisic acid-activated signaling pathway GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target is a plant C2H2 zinc-finger protein assigned to the ZFP7-like subfamily. Arabidopsis ZFP3 and overexpressed relatives including ZFP7 affect ABA sensitivity during germination (PMID:24808098), providing a relevant family-based hypothesis. However, the experiments do not establish the endogenous regulatory direction of this soybean paralog, and zinc-finger architecture alone cannot do so. The exact process is absent from the cached annotations and remains uncertain pending more resolved orthology or functional evidence.
Supporting Evidence:
GO:0005634 nucleus GO_CC
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target has the plant ZFP-family C2H2 DNA-binding architecture and a ZFP7-like subfamily assignment. Primary work identifies the related Arabidopsis ZFP3 as a nuclear protein (PMID:24808098), supporting broad nuclear localization by transfer within this transcription-factor group. This is a family-based inference rather than a localization experiment on soybean C6T1A2. Nucleus is absent from the cached GOA/UniProt annotations, so it is supported as an additional localization rather than an existing annotation match.
Supporting Evidence:
  • file:SOYBN/C6T1A2/C6T1A2-uniprot.txt: "ID C6T1A2_SOYBN Unreviewed; 210 AA. ... DR InterPro; IPR053266; Zinc_finger_protein_7. ... DR InterPro; IPR013087; Znf_C2H2_type. ... FT DOMAIN 79..106 ... FT /note="C2H2-type""
  • PMID:24808098: "ZFP3, a nuclear C2H2 zinc finger protein"

Deep Research

Falcon

(C6T1A2-deep-research-falcon.md)

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OpenScientist

(C6T1A2-hypotheses/core-function-1-go-0003700/openscientist.md)

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OpenScientist

(C6T1A2-hypotheses/prediction-negative-regulation-aba-signaling/openscientist.md)

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