RGA5 (F7J0N2, Oryza sativa subsp. japonica) — curation notes

2026-10-02 — initial review (claude-code, claude-opus-5-5)

Sources: UniProt F7J0N2, GOA (16 rows), RGA5-deep-research-falcon.md, cached papers
PMID:21251109 (abstract), 23548743 (abstract only; PMC full text not retrievable via
PubMed MCP), 25024433 (full text), 27289079 (abstract), 28087830 (full text),
30355769 (full text).

Identity and architecture

• CC-NB-LRR at the Pia locus on chr11 next to RGA4; both are needed for Pia function
  PMID:21251109.
• An integrated HMA/RATX1 domain after the LRR (~997-1069). Only the RGA5-A splice form works
  PMID:23548743.

Sensor function (core)

• Binds AVR-Pia and AVR1-CO39 directly PMID:23548743.
• Binding to the HMA decoy is needed for recognition PMID:28087830.
• Crystal structure of the HMA–AVR1-CO39 complex; Kd 5.4 uM (RGA5_S) PMID:30355769.
• HMA metal motif is degenerate PMID:30355769 -> REMOVE metal ion binding.

Repressor of RGA4 (core, distinguishes sensor from executor)

• PMID:25024433
• CC-domain hetero-complexes; the CC domain is needed for repression and the RATX1 domain is dispensable for it PMID:25024433.
• Repression is specific: Orin1 and L6-MHV cell death are not suppressed PMID:25024433.
• RGA5 never activates cell death itself. MHD mutants are not autoactive, and the K210R P-loop mutant is fully functional PMID:25024433.
• Cytosolic, with no nuclear relocalization after AVR-Pia PMID:25024433.

Bacteria

• Xanthomonas resistance appears only when Xoo/Xoc carrying designer TALEs switch on a transgene encoding the fungal AVR1-CO39 PMID:27289079. This is not native bacterial recognition -> MARK_AS_OVER_ANNOTATED for defense response to bacterium (IDA + IEA). The IDA cites PMID:23548743, whose abstract is fungal only. I did not claim mis-attribution; the argument is biological.

Term decisions / comparator checks

• GO:0035872 (NLR signaling pathway) has 0 annotations in Viridiplantae (QuickGO). Plant NLRs use GO:0002758 (e.g. RPS4), so I kept GO:0002758.
• GO:0062207 (regulation of PRR signaling) -> MODIFY to GO:0010363 regulation of plant-type hypersensitive response. In plants, PRR means surface PAMP receptors.
• protein binding (IPI with RGA4) -> MODIFY to GO:0140678 molecular function inhibitor activity.
• Hypersensitive response rows: KEEP_AS_NON_CORE for RGA5 (RGA4 executes it).
• GO:7770053 "NLR receptor complex" exists in current GO, but I did not use it (new id range; may not validate).

Project Q5 (sensor vs executor)

• GOA for RGA4 is nearly identical to RGA5's: same BP/CC rows, including GO:0062207 EXP and the HR IMPs. The only differences in RGA5's set are GO:0140376 (receptor) and the HMA metal mapping. After this review, RGA5 is distinguished by receptor activity plus MF inhibitor activity and regulation of HR, with HR as non-core.