C6T1A2

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

C6T1A2 is the 210-residue product of soybean GLYMA_17G165600 (Glyma17g18110; NCBI Gene 732609, also recorded as ZFP1). It is a plant Q-type C2H2 zinc-finger protein. It has a single C2H2 zinc finger (residues 79-106) carrying the plant-specific QALGGH motif (residues 92-97), disordered N-terminal and central regions with an acidic N-terminus, and a C-terminal LDLRL sequence that matches the LxLxL EAR-like transcriptional repression motif. This domain organisation is typical of single-finger plant C2H2 transcription factors, so the protein most likely acts as a nuclear, sequence-specific DNA-binding transcription factor, possibly a repressor. In PANTHER it belongs to subfamily SF9 of PTHR47593. SF9 is a lineage that arose by a duplication in the core eudicots (Pentapetalae) and contains no experimentally characterised member. The Arabidopsis ZFP proteins that regulate ABA responses during germination (ZFP3, ZFP4, ZFP7) are only about 35% identical to it and are placed in a different PANTHER tree. No gene-specific experimental study of C6T1A2 has been published. Its transcript was cloned in a soybean drought-associated transcription factor ORFeome.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003700 DNA-binding transcription factor activity
ISS
UniProtKB:C6T1A2 		NEW
Summary: Proposed annotation. GOA has no annotation for C6T1A2. The protein has one C2H2 zinc finger with the plant Q-type QALGGH motif, the signature of single-finger plant C2H2 transcription factors, and its transcript was cloned in a soybean transcription factor ORFeome. No experimental assay of C6T1A2 or of any PTHR47593:SF9 member exists, so this is a domain-level inference.
Reason: The Q-type C2H2 zinc finger is a DNA-binding domain, and the QALGGH helix is conserved across the plant single-finger transcription factors (the Arabidopsis ZFP proteins and soybean SF8/SF9 paralogs; see RESULTS-rereview.md). This makes DNA-binding transcription factor activity the best-supported molecular function. The inference does not come from a PAINT node: the PAINT GO:0000976 node (PTN009184003) is in the PANTHER PTHR45730 tree, which does not contain C6T1A2. A more specific term (e.g. repressor activity, implied by the EAR-like motif) is not asserted, because no repression assay exists.
Supporting Evidence:
UniProtKB:C6T1A2
FT DOMAIN 79..106
UniProtKB:C6T1A2
PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.
file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md
The QALGGH motif of plant Q-type C2H2 zinc fingers is present at residues 92-97.
PMID:26268547
Cys2(C2)His2(H2)-type zinc fingers (ZFs), constituting
GO:0005634 nucleus
ISS
UniProtKB:C6T1A2 		NEW
Summary: Proposed annotation. A protein whose only folded domain is a DNA-binding C2H2 zinc finger and that is predicted to act as a transcription factor is expected in the nucleus. The location has not been tested for C6T1A2 or any SF9 member. Related Arabidopsis single-finger ZFPs in a different PANTHER family are nuclear (e.g. ZFP3).
Reason: The nuclear location follows from the inferred transcription factor activity. Arabidopsis ZFP3 is a nuclear C2H2 zinc-finger protein, but it sits in another PANTHER family, so it is cited only as class-level context, not as an ortholog transfer. Earlier support taken from a ProtNLM2 prediction review has been removed.
Supporting Evidence:
file:SOYBN/C6T1A2/C6T1A2-deep-research-falcon.md
this protein is predicted to function as a DNA-binding transcription factor localized to the nucleus
PMID:24808098
ZFP3, a nuclear C2H2 zinc finger protein

Core Functions

Predicted sequence-specific DNA-binding transcription factor, acting in the nucleus through a single plant Q-type (QALGGH) C2H2 zinc finger. A C-terminal EAR-like LxLxL motif suggests it may act as a repressor. This is inferred from domain architecture only. No member of its PANTHER subfamily (PTHR47593:SF9) has been characterised experimentally.

Molecular Function:
DNA-binding transcription factor activity
Cellular Locations:
nucleus
Supporting Evidence:
  • UniProtKB:C6T1A2
    FT DOMAIN 79..106
  • file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md
    The QALGGH motif of plant Q-type C2H2 zinc fingers is present at residues 92-97.
  • file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md
    C-terminal LDLRL at residues 206-210 matches the LxLxL EAR-like repression motif

References

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Suggested Questions for Experts

Q: Does C6T1A2 bind DNA through its QALGGH zinc finger (and if so, which sequence, for example the AGT core bound by other Q-type ZFPs)? Does its EAR-like C-terminus make it a transcriptional repressor?

Q: The PAINT nodes listed in interpro/panther/PTHR47593/PTHR47593-paint.tsv (PTN008158895, PTN009184003) belong to the PANTHER 19 PTHR45730 tree. Should PTHR47593 (which contains C6T1A2) receive its own PAINT review? Did the Pentapetalae SF8/SF9 duplication separate functionally distinct lineages?

Q: Does any PTHR47593:SF9 member act in ABA or drought responses, given that the ABA role is established only for Arabidopsis ZFPs in a different PANTHER tree?

Suggested experts: Henry T. Nguyen

Suggested Experiments

Experiment: Test C6T1A2 in a yeast GAL4-BD or plant protoplast LUC reporter assay, with and without the C-terminal LDLRL motif, for activation or repression activity. Define its DNA-binding specificity by EMSA or DAP-seq.

Hypothesis: C6T1A2 binds specific DNA sequences via its Q-type C2H2 zinc finger and represses transcription through its EAR-like motif.

Type: transcription factor activity assay

Experiment: Localise a C6T1A2-GFP fusion in soybean protoplasts or Nicotiana benthamiana leaf epidermis.

Hypothesis: C6T1A2 localizes to the nucleus.

Type: subcellular localization by fluorescent protein fusion

Experiment: Phenotype CRISPR/Cas9 mutants of the SF9 paralogs (GLYMA_17G165600 together with the GLYMA_05G100900 homeolog) under ABA and drought treatments, measuring germination and stress-responsive gene expression.

Hypothesis: SF9 ZFPs modulate ABA or drought responses in soybean, as the paralogous Arabidopsis ZFPs do.

Type: loss-of-function genetics with stress phenotyping

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

C6T1A2 (soybean GLYMA_17G165600) is a single-finger plant Q-type C2H2 zinc-finger protein in PTHR47593:SF9, a lineage with no experimentally characterised member and no PAINT annotation. Its domain architecture suggests a nuclear transcription factor, but neither nuclear localization nor a role in ABA signaling has been tested for C6T1A2 or any SF9 member; the Arabidopsis ZFP proteins with ABA phenotypes lie in a different PANTHER tree.

Source documents: genes/SOYBN/C6T1A2/C6T1A2-uniprot.txt · genes/SOYBN/C6T1A2/C6T1A2-goa.tsv · genes/SOYBN/C6T1A2/C6T1A2-ai-review.yaml · genes/SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md · interpro/panther/PTHR47593/PTHR47593-review.yaml · publications/PMID_24808098.md · publications/PMID_27047508.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: C6T1A2 is a single-finger Q-type C2H2 zinc-finger protein in PTHR47593:SF9. Arabidopsis ZFP3 and related ZFPs confer ABA insensitivity at germination when overexpressed (PMID:24808098), and the PAINT GO:0009788 node covering Arabidopsis ZFP4/ZFP7 lies in the PTHR45730 tree, which does not contain C6T1A2; those proteins are only about 34-37% identical to it. The soybean QALGGH protein GmZFP3 (a chromosome 7 locus, not C6T1A2) acts negatively in drought tolerance and may act through an ABA-dependent pathway (PMID:27047508), which is not evidence for this gene. No experiment on C6T1A2 or any SF9 member tests ABA signaling, and no rows exist in GOA, so the prediction is plausible as a family-class hypothesis but cannot be validated or refuted.
Supporting Evidence:
GO:0005634 nucleus GO_CC
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: C6T1A2 has one Q-type C2H2 zinc finger (QALGGH, residues 92-97) and was cloned in a soybean transcription-factor ORFeome, so a nuclear location is expected from domain architecture. It has not been tested for C6T1A2 or any PTHR47593:SF9 member. Arabidopsis ZFP3 is nuclear (PMID:24808098) but lies in a different PANTHER tree, so this is class-level context rather than a phylogenetic transfer, and the PAINT nucleus node (PTN009184003) is likewise outside the C6T1A2 tree. A soybean QALGGH relative, GmZFP3, was distributed throughout the cell rather than confined to the nucleus (PMID:27047508), so domain class alone does not fix the localization. Nucleus is absent from GOA for this gene. The prediction is plausible but supported only by domain inference.
Supporting Evidence:

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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📚 Additional Documentation

Notes

(C6T1A2-notes.md)

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📄 View Raw YAML

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