RGA4 (ORYSJ, F7J0M4) curation notes

2026-10-02 — initial review (claude-code)

Sources: UniProt F7J0M4, GOA (14 rows), falcon deep research, cached publications
PMID:25024433 (full text), PMID:23548743, PMID:21251109, PMID:27289079 (abstract only).
Full text of PMID:23548743 was not retrievable via PMC (PubMed MCP returned abstract only).

Identity

• CC-NB-ARC-LRR (CNL) protein, 996 aa; Pia / Pi-CO39 locus on chr 11, paired head-to-head with RGA5.
• Both genes required for Pia: PMID:21251109; PMID:21251109.
• Pair recognises two unrelated M. oryzae effectors, but binding is to RGA5 only: PMID:23548743.

Executor function (key paper PMID:25024433, full text)

• Autoactive cell death: PMID:25024433
• Repressed by RGA5, de-repressed by AVR-Pia binding to RGA5: PMID:25024433.
• Physiological, not overexpression artefact: RGA5 RNAi in Sasanishiki protoplasts triggers death that requires RGA4 PMID:25024433.
• P-loop K209R abolishes RGA4 activity; RGA5 P-loop dispensable: PMID:25024433.
• Degenerate MHD (TYG500-502) underlies autoactivity; G502D (TYD) kills it.
• Model: PMID:25024433
• Homo- and hetero-complexes via CC domains (Y2H on CC fragments + co-IP in rice protoplasts and N. benthamiana); AVR-Pia does not disrupt hetero-complex.
• Localisation: PMID:25024433 — no nuclear relocalisation on AVR-Pia.

Bacterial resistance

• Only via engineering: PMID:27289079 and TAL-induced AVR1-CO39 in Pi-CO39 lines. Not a natural recognition specificity, so non-core.

Mechanism unknowns (deep research)

• No resistosome / Ca2+ channel data for RGA4; downstream partners unknown.

Decisions

• protein binding (IPI, RGA5) -> MODIFY to protein heterodimerization activity (+ homodimerization).
• regulation of PRR signaling pathway (EXP, PHI-base) -> MODIFY: RGA4 is an intracellular NLR, not a PRR-pathway regulator; the paper contains no PRR work. Replace with innate immune response-activating signaling pathway.
• defense response to bacterium IDA from PMID:23548743: abstract is purely about the fungal effectors; bacterial evidence lives in PMID:27289079. Kept as non-core rather than removed (cannot see 2013 full text).
• NEW: defense response to fungus (GO:0050832) — RGA4 is the executor of resistance to M. oryzae; absent from GOA. Participation: RGA4 itself generates the immune/cell-death signal.
• Notably no receptor MF for RGA4 (RGA5 carries innate immune receptor activity EXP). RGA4 must NOT get effector binding / receptor terms.

Project Q5 (sensor vs executor)

GOA rows for RGA4 and RGA5 are nearly identical (same IDA/IMP/EXP set from the same two papers, same ARBA/InterPro IEAs). Only difference: RGA5 has innate immune receptor activity (EXP) and metal ion binding (IEA, HMA). After review, RGA4 distinctive terms: HR execution (core), heterodimerization with RGA5, nucleotide-binding-dependent signalling; RGA5's PRR-regulation row would map to negative regulation of RGA4 signalling instead.