RGA (REPRESSOR OF ga1-3 / RGA1 / GRS; AT2G01570; UniProt Q9SLH3) — curation notes

Identity and structure

• One of five Arabidopsis DELLA proteins (GAI, RGA, RGL1, RGL2, RGL3); DELLA subfamily of the plant-specific GRAS family of putative transcriptional regulators PMID:9490740.
• 587 aa. N-terminal DELLA/VHYNP regulatory region (DELLA motif 44–48, VHYNP 89–93) + C-terminal GRAS domain (212–581: LRI, VHIID, LRII, PFYRE, SAW subdomains) (UniProt features).
• DELLA motif required for GA-induced degradation but NOT for SLY1 binding PMID:15155881.

Core function: nuclear repressor of GA signaling

• Negative regulator of GA signal transduction; recessive rga partially suppresses GA-deficient ga1-3 PMID:9490740.
• RGA + GAI partially redundant; RGA dominant PMID:11606552.
• Nuclear localized (GFP-RGA in onion epidermis and transgenic Arabidopsis) [PMID:9490740 "green fluorescent protein-RGA fusion protein is localized to the nucleus in onion epidermal cells"; PMID:11449051 "The green fluorescent protein (GFP)-RGA fusion protein was localized to nuclei in transgenic Arabidopsis"]. Accumulates in nucleus on cold PMID:28412546.

Regulatory switch: GA-GID1-SCF(SLY1) degradation

• GA-bound GID1 receptors bind RGA DELLA region [PMID:16709201 "in vivo interaction in the presence of GA(4) between each AtGID1 and the Arabidopsis DELLA proteins"; PMID:17416730 "the DELLA domain functions as a receiver domain for activated GA receptors"].
• GA-GID1 promotes RGA-SLY1 binding -> SCF(SLY1) ubiquitination -> 26S degradation [PMID:17194763 "the GA-GID1 complex promotes the interaction between RGA and the F-box protein SLY1, a component of the SCF(SLY1) E3 ubiquitin ligase that targets the DELLA protein for degradation"; PMID:15155881; PMID:15161962].
• GA rapidly reduces RGA protein -> derepression PMID:11449051.
• Lys-29-linked ubiquitin chains dominant for RGA degradation; RGA is the SUBSTRATE here (relevant to rejecting GO:0042176 "regulation of protein catabolic process") PMID:19717618.
• Proteolysis-independent inactivation also possible via GID1 binding PMID:18827182.

KEY mechanistic point: RGA has NO DNA-binding domain — acts as transcriptional cofactor

This is decisive for MF curation. RGA/DELLA cannot be a sequence-specific DNA-binding transcription factor.
- PMID:24821766.
- PMID:25035403.
- PMID:21245327.

Therefore GO:0003700 (DNA-binding transcription factor activity, from PMID:17933900 IDA, PMID:11449051 TAS, PMID:11118137 ISS) -> MODIFY to GO:0003712 transcription coregulator activity.
And GO:0000976 (transcription cis-regulatory region binding) from Y1H/eY1H screens (PMID:22037706, 25352272, 25533953, 31806676) -> REMOVE (RGA has no DBD; promoter binding is indirect/artifactual in Y1H).
GO:1990841 (promoter-specific chromatin binding, PMID:29255112) -> MARK_AS_OVER_ANNOTATED (in vivo occupancy real but mediated by CCA1).

Two arms of transcriptional cofactor activity

1. INHIBITION/titration of DNA-binding TFs (the classic "sequestration" model):
2. PIFs (bHLH): PMID:18216857; also PIF1/PIF6/SPT PMID:20093430.
3. BZR1 (BR): PMID:22820377.
4. SPL (flowering): PMID:22942378.
5. CCA1 (clock/MYB): PMID:29255112.
6. ATML1/PDF2 (HD-ZIP): PMID:24989044.
7. CO (photoperiod): PMID:26801684.
8. ANAC106 (NAC): PMID:40755058.
   -> Supports NEW GO:0140297 (DNA-binding transcription factor binding) and GO:0140416 (transcription regulator inhibitor activity).
9. COACTIVATION via IDD scaffolds (the newer "DELLA as coactivator" model):
10. IDDs bridge DELLA to DNA: PMID:24821766.
11. GAF1/IDD2: PMID:25035403.
12. SCL3 (GRAS, attenuator of DELLA): PMID:21245327.
    -> Supports ACCEPT of GO:0045893 (positive regulation of DNA-templated transcription, PMID:24821766 IDA) and NEW GO:0003712.
13. DELLAs do both simultaneously: PMID:25035403.

Pleiotropy (KEEP_AS_NON_CORE for downstream developmental processes)

• Vegetative growth / leaf / trichome / stem (rga gai rescue ga1-3): PMID:11606552. Note: "negative regulation of developmental vegetative growth" (GO:1905614) is the correctly-signed CORE vegetative annotation; the negated unsigned GO:1905613 is contradictory -> REMOVE.
• Seed germination/dormancy: RGA minor/redundant vs RGL2 PMID:24989044. Note PMID:11606552 NOT-annotations: rga gai does NOT rescue germination or flower development defects of ga1-3 -> these negated annotations are correctly ACCEPTed PMID:11606552.
• Anther/pollen (meiotic cytokinesis, tapetum): [PMID:27621423; PMID:33660280 RGAT1; PMID:40755058 ANAC106].
• Cold: PMID:28412546.
• Far-red/red light: RGA transcription controlled by PIL5 PMID:17449805.

Action summary rationale

• Generic GO:0005515 protein binding entries -> mostly MARK_AS_OVER_ANNOTATED (genuine interactions but uninformative term), captured instead by NEW GO:0140297 / GO:0140416 / GO:0003712. Two REMOVE: PMID:19429606 (FRIGIDA paper, not about RGA) and the GO:0042176 misassignment.
• GO:0000976 cis-regulatory binding (4x Y1H screens) -> REMOVE (no DBD).
• GO:0003700 DNA-binding TF activity (3x) -> MODIFY to GO:0003712.
• Nucleus (many) -> ACCEPT.
• GA signaling / negative regulation of GA signaling / response to GA -> ACCEPT (core).

Deep research synthesis (Falcon / Edison Scientific, file:ARATH/RGA/RGA-deep-research-falcon.md)

The Falcon deep-research report (2026) corroborates and extends the core curation calls; it adds no GO IDs but supports several load-bearing decisions:
- Confirms RGA is a nuclear, non-catalytic transcriptional regulator that acts via protein-protein interactions, not direct DNA binding [falcon "RGA does not bind DNA directly; instead, it acts through protein–protein interactions with transcription factors (TFs) and chromatin components, including histone H2A, to reprogram gene expression."; "DELLAs are nucleus-localized regulators that generally do not bind DNA directly and instead control transcription by interacting with many TFs and transcriptional regulators, with chromatin association detectable by ChIP/ChIP-seq"]. This independently supports MODIFY of GO:0003700 -> GO:0003712, the NEW GO:0140297/GO:0003712, and REMOVE of the GO:0000976 Y1H cis-regulatory-region-binding annotations.
- Confirms the canonical GA-GID1-SCF(SLY1) degradation switch [falcon "GA–GID1 signaling inactivates RGA primarily via SCF^SLY1-dependent ubiquitination and proteasomal degradation"; "GA–GID1 binds the DELLA domain of RGA (conserved DELLA/LExLE/VHYNP motifs) to form a GA–GID1–RGA complex"]. Supports the GA-signaling ACCEPTs and the receptor-binding proposed term.
- Supports DELLA as a dual coactivator/corepressor (titration + coactivation), consistent with ACCEPT of GO:0045893 and the coregulator MF [falcon "This supports a modern view of DELLAs as context-dependent transcriptional regulators (coactivator/corepressor roles) rather than simple repressors."]. ChIP-seq/RNA-seq: RGA is a direct repressor of 129 genes and direct activator of 280 genes (huang2023).
- New mechanistic context (not yet a GO call): RGA is recruited to promoters by TFs via the GRAS LHR1 subdomain and stabilized on chromatin via histone-H2A binding through the PFYRE subdomain (TF-RGA-H2A complex; huang2023 Nature Plants, huang2024 Nat Commun). Phosphorylation in PolyS/PolyS-T regions enhances H2A binding without changing nuclear localization or GA-induced degradation; O-fucosylation enhances and O-GlcNAcylation inhibits DELLA-TF interactions. Structural work (Dahal 2025 PNAS; Islam 2025) supports a proteolysis-independent suppression arm in which GID1 binding blocks RGA-IDD TF interactions. These could motivate future MF terms (histone binding / chromatin) but lack a verifiable GO ID in the current GOA/UniProt, so no NEW annotation was added.

No UNDECIDED actions existed in the review (all annotations already adjudicated), and the new evidence does not warrant weakening any existing decision.

Validation

uv run ai-gene-review validate genes/ARATH/RGA/RGA-ai-review.yaml -> Valid (1 non-blocking warning about mixed actions on GO:0010029, which reflects the genuine distinction between negated NOT-annotations and the positive non-core germination role).