RGA4 (Os11gRGA4, SasRGA4) is a 996-residue coiled-coil, nucleotide-binding (NB-ARC), leucine-rich repeat (CC-NB-LRR, CNL) immune receptor of rice that, together with the adjacent and inversely oriented CNL gene RGA5, constitutes the Pia / Pi-CO39 blast resistance locus. The two proteins act as an obligate sensor/executor heteropair conferring recognition of the unrelated Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39. RGA4 is the executor: it is an intrinsically (constitutively) active inducer of hypersensitive-response cell death, and this activity is held in check by RGA5, with which it forms hetero-complexes through its N-terminal coiled-coil domain; RGA4 also self-associates. RGA4 itself does not bind the effectors. Binding of AVR-Pia or AVR1-CO39 to the integrated heavy-metal-associated (HMA/RATX1) domain of RGA5 relieves the repression and RGA4 triggers cell death and resistance. RGA4 activity requires an intact P-loop (K209) in its NB-ARC domain, and its autoactivity depends on a degenerate MHD motif (TYG) in the ARC2 subdomain. RGA4 resides mainly in the cytosol and does not relocalise to the nucleus on effector recognition. When ectopically activated it also restricts Xanthomonas oryzae, showing that its immune output is not pathogen-specific.
The preferred accession for this review is F7J0M4. These relationships are manually assessed.
REFERENCE PROTEOME LOCUS COUNTERPART · Reviewed 2026-10-19
Reference proteome: UP000059680
Retain F7J0M4 as the primary Swiss-Prot accession. Both reviewed records represent RGA4 in different rice cultivars, and the reference entry is the leading full-length match. UniProt contrasts AVR-Pia recognition in Aichi asahi/Sasanishiki with its absence in Nipponbare. Record this as a reference-cultivar locus counterpart, not equivalent resistance function; loss of recognition by the RGA4/RGA5 system does not establish that RGA4 alone is inactive.
MMseqs2 searched 48,896 sequences across UP000059680 at E <= 1e-5 and sensitivity 7.5, returning 358 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 358 returned candidates are retained, with 10 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity.
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
target_sequence_count: 48896
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
candidate_count: 358
F7J0M6: 951 identities across 1017 global-alignment columns (93.5103% identity including gaps), 42 substitutions and 24 gap columns. Query coverage is 99.6988%; target coverage is 97.929%. Sequence similarity is interpreted in the manual rationale. Identity over paired residues is 95.7704% (951/993); gap columns are excluded from this denominator.
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
query_length: 996 target_length: 1014 alignment_columns: 1017 identities: 951 mismatches: 42 gap_columns: 24 identity_percent: 93.5103 query_coverage_percent: 99.6988 target_coverage_percent: 97.929
The primary accession is outside every searched exact-taxon reference proteome. Current UniProt records place F7J0M6 in UP000059680 and give it the same taxon as the primary.
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
primary_in_any_reference_proteome: false
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
alternative_in_reference_proteome: true
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
same_taxon: true
Sampled UniSave observations: 09-DEC-2015, entry version 17.: no Proteomes cross-reference; 12-AUG-2020, entry version 38.: no Proteomes cross-reference; 27-NOV-2024, entry version 48.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt's motivation.
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
entry_date: 09-DEC-2015, entry version 17. proteomes: []
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
entry_date: 12-AUG-2020, entry version 38. proteomes: []
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
entry_date: 27-NOV-2024, entry version 48. proteomes: []
The reviewed reference entry explicitly contrasts cultivar-dependent recognition of AVR-Pia. This concerns the resistance system and does not prove that RGA4 alone is inactive.
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
cultivars Nipponbare, Mokoto and Hitomebore
The reviewed reference record F7J0M6 assigns RGA4 to Os11g0225100 / LOC_Os11g11790. Both F7J0M4 and F7J0M6 use the RGA4 name attributed to PMID:21251109, the study of the chromosome-11 Pia locus across rice cultivars. Together with the leading full-length sequence match and the study's identification of the Sasanishiki Os11gRGA4 allele, this supports a curated locus correspondence. This is not an independent genomic coordinate alignment and does not establish equivalent resistance activity.
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
value: Os11g0225100
file:ORYSJ/RGA4/RGA4-record-evidence.yaml
value: LOC_Os11g11790
The wild-type 'Sasanishiki' allele of Os11gRGA4 (SasRGA4) complemented Pia function in both mutants
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002758 innate immune response-activating signaling pathway | IDA PMID:23548743 The rice resistance protein pair RGA4/RGA5 recognizes the Ma... | ACCEPT | Summary: RGA4 and RGA5 together are required for recognition of AVR1-CO39 and AVR-Pia and for triggering the immune response. Later work showed RGA4 is the component that generates the immune/cell-death signal once RGA5 repression is lifted. Reason: RGA4 is the signalling executor of the RGA4/RGA5 pair, so it directly participates in the effector-triggered signalling pathway that activates innate immunity. GO has no host-side effector-triggered immunity signalling term, so this is the appropriate process term. Supporting Evidence: PMID:23548743 Two NB-LRR protein-coding genes from rice (Oryza sativa), RGA4 and RGA5, were found to be required for the recognition of the Magnaporthe oryzae effector AVR1-CO39. PMID:25024433 RGA4 mediates cell death activation, while RGA5 acts as a repressor of RGA4 and as an AVR receptor. |
| GO:0002758 innate immune response-activating signaling pathway | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning prediction for CNL proteins; consistent with the experimental IDA annotation for the same term. Reason: Correct and experimentally corroborated for RGA4 as the signalling executor of the pair. Supporting Evidence: PMID:25024433 These results support the conclusion that cell death signaling is activated exclusively by RGA4 and that AVR-Pia binding does not lead to RGA5 activation but solely to RGA4 de-repression. |
| GO:0005515 protein binding | IPI PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | MODIFY | Summary: RGA4 co-immunoprecipitates with RGA5 in rice protoplasts and N. benthamiana, and the CC domains of the two proteins interact in yeast two-hybrid assays. RGA4 also self-associates. Reason: The interaction is real but "protein binding" is uninformative. The interaction is a CC-domain-mediated hetero-complex with RGA5 (and a homo-complex with RGA4 itself), better captured by protein heterodimerization activity, with homodimerization as a secondary term. Dimer stoichiometry is not formally established, so these remain approximations of "hetero-/homo-complex formation". Proposed replacements: protein heterodimerization activity protein homodimerization activity Supporting Evidence: PMID:25024433 RGA4 and RGA5 form homo- and hetero-complexes and interact through their coiled-coil domains. PMID:25024433 CC-RGA4 1–130 and CC-RGA5 1–133 showed homo- and hetero-interactions |
| GO:0005737 cytoplasm | IDA PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | ACCEPT | Summary: RGA4:GFP is observed mainly in the cytosol of rice protoplasts, with little or no nuclear signal. Reason: Directly observed; the cytosol annotation from the same paper is the more specific term, but cytoplasm is correct. Supporting Evidence: PMID:25024433 Green fluorescence of RGA4:GFP was observed mainly in the cytosol labeled by mCherry |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Mapped from the UniProt subcellular location (Cytoplasm), which is itself based on PMID:25024433. Reason: Consistent with the experimental localisation data. Supporting Evidence: PMID:25024433 These results suggest that RGA4 and RGA5 localize to the cytosol and are excluded from the nucleus. |
| GO:0005829 cytosol | EXP PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | ACCEPT | Summary: RGA4 co-localises with a cytosolic mCherry marker in rice protoplasts and is not relocalised to the nucleus upon AVR-Pia recognition. Reason: Most specific localisation supported by direct experimental data. Supporting Evidence: PMID:25024433 Upon recognition of AVR-Pia, neither RGA4 nor RGA5 is re-localized to the nucleus. |
| GO:0006952 defense response | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO mapping from the plant disease resistance protein family (IPR044974). Correct but very general. Reason: True but uninformative; RGA4 already carries the more specific plant-type hypersensitive response and innate immune signalling terms, and a defense response to fungus annotation is proposed. Supporting Evidence: PMID:25024433 RGA4 and RGA5, two NB-LRRs from rice, interact functionally and physically to mediate resistance to the fungal pathogen Magnaporthe oryzae |
| GO:0009626 plant-type hypersensitive response | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction; strongly corroborated by experimental data showing RGA4 is the executor of HR-like cell death. Reason: Correct and core for RGA4. Supporting Evidence: PMID:25024433 Taken together, these results suggest that RGA4 acts as an HR executer which is regulated in its activity by RGA5. |
| GO:0009626 plant-type hypersensitive response | IMP PMID:23548743 The rice resistance protein pair RGA4/RGA5 recognizes the Ma... | ACCEPT | Summary: Loss of RGA4 (and RGA5) abolishes AVR1-CO39/AVR-Pia-triggered resistance. The full text was not accessible; the abstract reports that both genes are required for effector recognition. Reason: Consistent with the later demonstration that RGA4 is the HR executor; deferred to the curator who read the full text. Supporting Evidence: PMID:23548743 RGA4 and RGA5 also mediate recognition of the unrelated M. oryzae effector AVR-Pia, indicating that the corresponding R proteins possess dual recognition specificity. PMID:25024433 RGA4 triggers an AVR-independent cell death that is repressed in the presence of RGA5 in both rice protoplasts and Nicotiana benthamiana. |
| GO:0009626 plant-type hypersensitive response | IMP PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | ACCEPT | Summary: RGA4 P-loop (K209R) and MHD-restoring/TYD mutants lose cell-death activity both alone and in the presence of RGA5 plus AVR-Pia; RGA5 silencing triggers cell death that depends entirely on RGA4. Reason: Core function. RGA4 itself generates the HR cell death signal; this is the key executor annotation that distinguishes RGA4 from its sensor partner RGA5, which has no cell-death-inducing activity. Supporting Evidence: PMID:25024433 Thus, an intact RGA4 nucleotide-binding pocket is required for cell death induction by RGA4, either on its own or in the presence of RGA5 and AVR-Pia. PMID:25024433 In the rga4 loss-of-function-mutant line Sas1493 (Okuyama et al , 2011 ), RGA5 depletion had no effect indicating that the cell death induced by RGA5 depletion relies entirely on RGA4. |
| GO:0042742 defense response to bacterium | IDA PMID:23548743 The rice resistance protein pair RGA4/RGA5 recognizes the Ma... | MARK AS OVER ANNOTATED | Summary: The cached abstract of PMID:23548743 only addresses recognition of the fungal effectors AVR-Pia and AVR1-CO39, and full text could not be retrieved. Bacterial (Xanthomonas oryzae) resistance mediated by the RGA4/RGA5 pair was shown later, in engineered systems (PMID:27289079). Reason: Not removed, because the supporting full text was not available to check. Biologically, RGA4 activation can restrict Xanthomonas oryzae, but only when AVR1-CO39 or an NLR is artificially induced by designer TAL effectors. There is no natural bacterial recognition specificity, so a bacterial defense term overstates RGA4's biological role. The same call is made for the sensor RGA5. The reference attribution may be worth rechecking against PMID:27289079. Supporting Evidence: PMID:27289079 This induced AVR1-CO39 expression and triggered BB and BLS resistance when the corresponding Pi-CO39 resistance locus was present. |
| GO:0042742 defense response to bacterium | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA prediction from the CNL family, many of whose characterised members recognise bacterial effectors. Reason: The only support is engineered Xanthomonas resistance through the RGA4/RGA5 pair. The natural function of RGA4 is resistance to the blast fungus, so this is an over-annotation (consistent with the RGA5 review). Supporting Evidence: PMID:27289079 demonstrating that NLR-triggered immune responses efficiently control Xoo |
| GO:0043531 ADP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the NB-ARC domain. Nucleotide binding has not been measured for RGA4, but the P-loop lysine K209 is required for all RGA4 activity, implying a functional nucleotide-binding pocket. Reason: The NB-ARC ADP-binding mapping is the standard family-level representation of the nucleotide-dependent switch in NLRs, and RGA4 is the partner in which that pocket is functionally required (unlike RGA5). RGA4's degenerate MHD motif is thought to keep it out of the ADP-bound, resting state. ATP binding may therefore describe the active form better, but neither nucleotide has been measured. Supporting Evidence: PMID:25024433 This finding suggests that RGA4 activity is likely to be dependent on nucleotide binding and exchange while RGA5 activity is not. file:ORYSJ/RGA4/RGA4-deep-research-falcon.md eliminated its spontaneous and AVR-Pia-associated cell-death activity |
| GO:0062207 regulation of pattern recognition receptor signaling pathway | EXP PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | MODIFY | Summary: PHI-base EXP annotation. PMID:25024433 (full text read) concerns effector recognition and cell-death activation by the intracellular CNL pair RGA4/RGA5. It contains no experiments on pattern recognition receptors or PRR signalling, which the paper explicitly distinguishes as the separate first layer of immunity. Reason: The term does not describe what RGA4 does. RGA4 is not a regulator of PRR (pattern-triggered) signalling. It is the executor of effector-triggered NLR signalling and HR. The essence of the annotation (an immune signalling role shown in this paper) is better captured by innate immune response-activating signaling pathway. That would also keep it distinct from the sensor RGA5, whose role in the same paper is repression of RGA4. Proposed replacements: innate immune response-activating signaling pathway Supporting Evidence: PMID:25024433 The first layer of defense relies on the recognition of conserved microbe-associated molecular patterns (MAMPs) by the so-called pattern recognition receptors (PRRs). PMID:25024433 These results establish a model for the interaction of hetero-pairs of NB-LRRs in plants |
| GO:0050832 defense response to fungus | IMP PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | NEW | Summary: RGA4 is required for Pia / Pi-CO39 resistance to Magnaporthe oryzae carrying AVR-Pia or AVR1-CO39. RGA4 loss-of-function mutants and P-loop or MHD mutants lose resistance or cell-death activity. No fungal defense term is present in GOA. Reason: Participation test passed. RGA4 is not a substrate or a passive requirement: it is the component that itself produces the immune and cell-death signal that restricts the fungus, while RGA5 does the sensing. This is the natural, primary biological context of RGA4, and it is better supported than the bacterial defense terms already in GOA. Supporting Evidence: PMID:25024433 We show that RGA4 and RGA5, two NB-LRRs from rice, interact functionally and physically to mediate resistance to the fungal pathogen Magnaporthe oryzae PMID:21251109 suggesting that SasRGA4 is necessary for Pia function |
Loading supporting content…
Download this section (compressed HTML)Q: GOA currently gives RGA4 (executor) and RGA5 (sensor) an almost identical set of annotations, drawn from the same two papers. Should RGA5's role be captured as negative regulation of RGA4-driven HR/immune signalling plus effector binding (innate immune receptor activity), and RGA4's as the positive executor of HR, so that the division of labour is machine-readable?
Q: Does activated RGA4 form an oligomeric resistosome with Ca2+-permeable channel activity, as shown for other CC-NLRs such as ZAR1 and Sr35? If so, what is the appropriate executor molecular function term?
Q: Is the defense response to bacterium IDA attributed to PMID:23548743 intended to reference PMID:27289079, the paper that tests Xanthomonas oryzae resistance?
Experiment: Purify full-length or CC-domain RGA4, test oligomerisation and membrane association after RGA5 removal or effector addition, and measure Ca2+-permeable channel activity (for example by electrophysiology in Xenopus oocytes or HEK cells) to define the executor biochemistry.
Experiment: Measure nucleotide binding of RGA4 (wild type, K209R and the MHD-restored and TYD variants) to determine whether its autoactive state is ATP-bound, which would decide between ADP binding and ATP binding as the correct molecular function term.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)