RGA5 (Os11gRGA5, SasRGA5) is a 1,116-residue intracellular coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR, NLR) immune receptor encoded at the Pia/Pi-CO39 blast-resistance locus on rice chromosome 11, where it lies head-to-head with its partner NLR gene RGA4. RGA5 is the sensor of the pair. Its C-terminal region, after the LRR, carries an integrated heavy-metal-associated (HMA; also called RATX1) domain that directly binds the sequence-unrelated MAX-family effectors AVR-Pia and AVR1-CO39 secreted by the rice blast fungus Magnaporthe oryzae. The HMA domain has a canonical HMA fold, but its metal-binding motif is degenerate, so it acts as an effector-binding decoy rather than as a metal-binding module. In the absence of effector, RGA5 forms homo- and hetero-complexes with RGA4 through their coiled-coil domains and represses the autoactive, cell death-inducing activity of RGA4; the RGA5 CC domain is required for this repression while the HMA domain is dispensable for it. Effector binding to the HMA domain relieves the repression, so that RGA4 triggers a hypersensitive cell death response and resistance. RGA5 does not itself activate cell death, and an intact RGA5 P-loop is not needed for repression or for effector recognition. Only the RGA5-A splice form, which keeps an intact HMA domain, is functional; the intron-retaining RGA5-B form is inactive. Both RGA5 and RGA4 localize mainly to the cytosol and do not move to the nucleus on effector recognition. RGA5 has become a scaffold for engineering new recognition specificities by redesigning its HMA domain.
The preferred accession for this review is F7J0N2. These relationships are manually assessed.
REFERENCE PROTEOME CANDIDATE · Reviewed 2026-10-19
Reference proteome: UP000059680
Retain F7J0N2 as the primary Swiss-Prot accession. Q2R8L1 is a plausible reference-proteome counterpart, but the captured evidence does not independently map the Sasanishiki protein to the Nipponbare locus. The target is named RGA5 at Os11g0225300 / LOC_Os11g11810; those identifiers locate the target only. The sequence is substantially divergent (624 identities over 1105 paired residues, with 207 gap columns), and the cultivar-dependent AVR-Pia recognition statement concerns the resistance system. Retain a candidate pending cross-cultivar locus mapping; do not assert equivalent receptor specificity or protein integrity.
MMseqs2 searched 48,896 sequences across UP000059680 at E <= 1e-5 and sensitivity 7.5, returning 404 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 404 returned candidates are retained, with 10 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity.
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
target_sequence_count: 48896
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
candidate_count: 404
Q2R8L1: 624 identities across 1312 global-alignment columns (47.561% identity including gaps), 481 substitutions and 207 gap columns. Query coverage is 99.0143%; target coverage is 84.9347%. Sequence similarity is interpreted in the manual rationale. Identity over paired residues is 56.4706% (624/1105); gap columns are excluded from this denominator.
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
query_length: 1116 target_length: 1301 alignment_columns: 1312 identities: 624 mismatches: 481 gap_columns: 207 identity_percent: 47.561 query_coverage_percent: 99.0143 target_coverage_percent: 84.9347
The primary accession is outside every searched exact-taxon reference proteome. Current UniProt records place Q2R8L1 in UP000059680 and give it the same taxon as the primary.
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
primary_in_any_reference_proteome: false
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
alternative_in_reference_proteome: true
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
same_taxon: true
Sampled UniSave observations: 09-DEC-2015, entry version 12.: no Proteomes cross-reference; 11-DEC-2019, entry version 31.: no Proteomes cross-reference; 27-NOV-2024, entry version 45.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt's motivation.
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
entry_date: 09-DEC-2015, entry version 12. proteomes: []
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
entry_date: 11-DEC-2019, entry version 31. proteomes: []
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
entry_date: 27-NOV-2024, entry version 45. proteomes: []
The target record names the Nipponbare locus Os11g0225300 / LOC_Os11g11810. These target-only identifiers and the cultivar-dependent AVR-Pia recognition statement do not independently establish correspondence to the Sasanishiki locus.
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
cultivars Nipponbare, Mokoto and Hitomebore
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
value: Os11g0225300
file:ORYSJ/RGA5/RGA5-record-evidence.yaml
value: LOC_Os11g11810
| 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: RGA5 directly binds the M. oryzae effectors AVR-Pia and AVR1-CO39 and, together with RGA4, initiates the effector-triggered immune signaling that leads to resistance. As the receptor that perceives the ligand, RGA5 takes part in this signaling pathway. Reason: RGA5 is the effector-binding receptor that starts the signaling pathway, so it does part of the work of the pathway rather than only being required for it. Direct binding is linked to function because an inactive AVR-Pia allele that does not bind RGA5-A is not recognized. GO:0002758 is the term used for plant NLR immune signaling (e.g. Arabidopsis RPS4). The more specific GO:0035872 (NLR receptor signaling pathway) is not used for any plant gene product, so it is not proposed here. Supporting Evidence: PMID:23548743 revealed direct binding of AVR-Pia and AVR1-CO39 to RGA5-A, providing evidence for the recognition of multiple Avr proteins by direct binding to a single R protein PMID:23548743 Direct binding seems to be required for resistance as an inactive AVR-Pia allele did not bind RGA5-A |
| GO:0002758 innate immune response-activating signaling pathway | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning transfer of innate immune signaling to an NLR protein. The experimental IDA row for the same term supports it. Reason: Consistent with experimental evidence that RGA5 is the effector receptor that starts RGA4-dependent immune signaling. Supporting Evidence: PMID:25024433 RGA4 mediates cell death activation, while RGA5 acts as a repressor of RGA4 and as an AVR receptor |
| GO:0005515 protein binding | IPI PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | MODIFY | Summary: IPI with RGA4 (F7J0M4). RGA5 and RGA4 form hetero-complexes through their coiled-coil domains, and RGA5 uses this association to repress the autoactive cell-death activity of RGA4. The repression is specific: RGA5 does not suppress the autoactive NLRs Orin1 or L6. Reason: Protein binding is uninformative. The same paper shows what the binding does: RGA5 physically associates with RGA4 through the CC domain, and the CC domain is required for inhibiting RGA4-triggered cell death. This fits molecular function inhibitor activity (GO:0140678), which is defined as inhibition of a target's activity through non-covalent binding. This MF is what tells the sensor (RGA5) apart from the executor (RGA4). Proposed replacements: molecular function inhibitor activity Supporting Evidence: PMID:25024433 RGA4 and RGA5 form homo- and hetero-complexes and interact through their coiled-coil domains PMID:25024433 Neither Orin1- nor L6 MHV -mediated cell death was suppressed by RGA5 showing that its inhibition activity is specific PMID:25024433 The RGA5 CC domain is necessary but not sufficient for repression of RGA4-mediated cell death, while its RATX1 domain is dispensable |
| GO:0005737 cytoplasm | IDA PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | ACCEPT | Summary: Functional Venus:RGA5 fusions co-localize with a cytosolic marker in rice protoplasts and are excluded from nuclei. Reason: Directly supported by confocal imaging of a functional fusion protein. Cytosol (GO:0005829) is the more specific term, but cytoplasm is correct. Supporting Evidence: PMID:25024433 Similar results were obtained for Venus:RGA5 which co-localized with Cerulean in the cytosol but not with NLS:Cerulean in the nuclei |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping of the experimentally determined cytoplasmic localization. Reason: Consistent with the IDA evidence from rice protoplasts. Supporting Evidence: PMID:25024433 Localization studies in rice protoplast suggest that RGA4 and RGA5 localize to the cytosol |
| GO:0005829 cytosol | EXP PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | ACCEPT | Summary: RGA5 is mainly cytosolic in rice protoplasts and does not move to the nucleus after AVR-Pia recognition. Reason: The most specific location term with direct experimental support. It is where RGA5 binds effectors and associates with RGA4. 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 | ACCEPT | Summary: InterPro2GO mapping from the plant disease resistance protein family (IPR044974). Broad but correct. Reason: RGA5 is a resistance protein needed for effector-triggered defense against M. oryzae. The term is general but not wrong. Supporting Evidence: PMID:21251109 SasRGA4 and SasRGA5, that are located next to each other and oriented in the opposite direction are necessary for Pia function |
| GO:0009626 plant-type hypersensitive response | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA transfer of the hypersensitive response to an NLR. For RGA5 the hypersensitive cell death depends on its effector recognition, but RGA4 carries it out. Reason: RGA5 does not trigger cell death itself. Autoactive MHD-motif mutants of RGA5 cause no cell death, and the authors conclude that cell death signaling is activated only by RGA4. RGA5 sits upstream of the response as its receptor and gatekeeper, so the term is correct as an involvement but is not a core RGA5 function. It is core for RGA4. 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:0009626 plant-type hypersensitive response | IMP PMID:23548743 The rice resistance protein pair RGA4/RGA5 recognizes the Ma... | KEEP AS NON CORE | Summary: Genetic analysis shows that RGA5-A, but not RGA5-B, is needed with RGA4 for AVR-dependent resistance. Hypersensitive cell death in response to AVR-Pia/AVR1-CO39 needs a functional RGA5. Reason: The mutant evidence shows that RGA5 is necessary for the effector-induced hypersensitive response, which is consistent with its role as the receptor. RGA4 is the protein that actually executes cell death, so for RGA5 this is a downstream outcome rather than a core activity. The annotation is kept as non-core and is not removed. Supporting Evidence: PMID:23548743 Genetic analysis showed that only RGA5-A confers resistance, while RGA5-B is inactive. 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 ... | KEEP AS NON CORE | Summary: In rice protoplasts and N. benthamiana, RGA4 + RGA5 + AVR-Pia gives rapid cell death, and removing RGA5 or the effector changes the outcome. RGA5 gates the hypersensitive response but does not execute it. Reason: Same reasoning as the other hypersensitive response rows. The core RGA5 contribution is captured by innate immune receptor activity, by inhibition of RGA4 activity, and by regulation of the plant-type hypersensitive response (GO:0010363, proposed below as the replacement for the PRR-signaling regulation term). Supporting Evidence: PMID:25024433 Upon recognition of the pathogen effector AVR-Pia by direct binding to RGA5, repression is relieved and cell death occurs. |
| GO:0042742 defense response to bacterium | IDA PMID:23548743 The rice resistance protein pair RGA4/RGA5 recognizes the Ma... | MARK AS OVER ANNOTATED | Summary: Native RGA5 recognizes effectors of the fungus M. oryzae. Resistance to the bacterium Xanthomonas oryzae involving RGA4/RGA5 has been shown only in an engineered system. There, transgenic Xanthomonas strains carrying a designer TAL effector switched on an inducible copy of the fungal AVR1-CO39 gene in transgenic rice (PMID:27289079). The cited 2013 paper is cached as abstract only, and its abstract describes only fungal effector recognition. Reason: I am not disputing what the curator saw in the full text. The objection is biological. RGA5 does not perceive any bacterial molecule. Bacterial resistance needs a fungal effector to be expressed artificially, so it shows that the RGA4/RGA5 output can work against other pathogens. It is not a natural defense response of RGA5 to bacteria. Supporting Evidence: PMID:27289079 transgenic rice lines harboring the AVR1-CO39 effector gene from the rice blast fungus Magnaporthe oryzae, under the control of an inducible promoter, were challenged with transgenic Xoo and Xoc strains carrying a TAL effector designed to transactivate the inducible promoter |
| GO:0042742 defense response to bacterium | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA machine-learning transfer of a defense response to bacterium term, common among NLRs. RGA5 recognizes only fungal effectors. Reason: No native bacterial recognition by RGA5 is known. Its only reported anti-bacterial activity depends on artificial expression of a fungal effector (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:0043531 ADP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the NB-ARC domain. RGA5 has an NB-ARC domain (residues 182-466), but no nucleotide binding has been measured for it. Its P-loop lysine (K210) is not needed for RGA4 repression or for effector-triggered derepression. Reason: ADP binding is plausible from the domain, as NB-ARC domains of resting NLRs bind ADP. However, the K210R P-loop mutant of RGA5 keeps full function, so nucleotide binding is not part of the activity that makes RGA5 a sensor. This differs from RGA4, whose P-loop is essential. Supporting Evidence: PMID:25024433 However, an intact RGA5 P-loop motif is not necessary for repression of RGA4-induced cell death or for removal of this repression after AVR-Pia recognition. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from the HMA domain (IPR006121). The RGA5 integrated HMA domain has the HMA fold, but the crystal structure shows that its metal-binding motif is degenerate: the second cysteine is replaced by serine. The domain works as an effector-binding decoy. Reason: The domain-to-GO mapping assumes the canonical MxCxxC metal-binding motif, which RGA5 lacks. No metal binding has been shown, and the HMA domain's function is binding the AVR-Pia and AVR1-CO39 effectors. Supporting Evidence: PMID:30355769 The metal-binding motif, characteristic of HMAs, is degenerated in RGA5HMA, as only the first Cys is conserved, while the second is replaced by a Ser. file:ORYSJ/RGA5/RGA5-deep-research-falcon.md The RGA5 HMA fold resembles other HMA domains, but its characteristic metal-binding motif is |
| GO:0062207 regulation of pattern recognition receptor signaling pathway | EXP PMID:25024433 The NB-LRR proteins RGA4 and RGA5 interact functionally and ... | MODIFY | Summary: RGA5 represses RGA4-mediated cell death without effector, and effector binding relieves this repression. RGA5 therefore regulates the RGA4-dependent immune response, which is well supported. Reason: The regulatory role is real, but the term is placed oddly. GO counts NLR signaling as a child of pattern recognition receptor signaling (GO:0035872 is_a GO:0002221). In plants, however, "pattern recognition receptor" means cell-surface PAMP receptors, which are distinct from intracellular NLRs. The output that RGA5 is shown to control is RGA4-triggered hypersensitive cell death. The plant-specific term regulation of plant-type hypersensitive response (GO:0010363) fits better and covers both the repression and the effector-triggered release. "Negative regulation" was not chosen, because RGA5 is also what allows the response once it binds effector. Proposed replacements: regulation of plant-type hypersensitive response Supporting Evidence: PMID:25024433 RGA5 can be regarded as an AVR receptor since it physically binds AVR1-CO39 and AVR-Pia (Cesari et al , 2013 ) and transduces AVR signal perception into a relief of RGA4 repression, resulting in resistance induction and HR. |
| GO:0140376 innate immune receptor activity | EXP PMID:28087830 Recognition of the Magnaporthe oryzae Effector AVR-Pia by th... | ACCEPT | Summary: RGA5 directly binds AVR-Pia through its integrated RATX1/HMA domain, and this binding is needed for recognition and resistance. The same domain binds AVR1-CO39 (Kd about 5-7 uM; crystal structure, PMID:30355769). RGA5 is the receptor of the RGA4/RGA5 pair. Reason: This is the core molecular function of RGA5. The ligand is a pathogen effector perceived directly, and binding is coupled to triggering the immune response through derepression of RGA4. This MF should be on the sensor RGA5 and not on the executor RGA4, which does not bind the effectors. Supporting Evidence: PMID:28087830 The Magnaporthe oryzae effector AVR-Pia interacts with the decoy domain of the rice NLR immune receptor RGA5 through a defined surface area, and this interaction is required for effector recognition. PMID:30355769 Mutations in the HMA-binding interface of AVR1-CO39 perturb RGA5HMA-binding, in vitro and in vivo, and affect the recognition of M. oryzae in a rice cultivar containing Pi-CO39 |
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Download this section (compressed HTML)Q: Sensor and executor NLRs in pairs such as RGA5/RGA4 (and RRS1/RPS4) get nearly identical electronic annotations: hypersensitive response, defense response, ADP binding. Should GO practice routinely give innate immune receptor activity and molecular function inhibitor activity to the sensor, and keep cell death execution terms for the executor?
Q: GO:0035872 (NLR signaling pathway) has no plant annotations, and plant NLR signaling is annotated as GO:0002758. Is this a deliberate convention, or should plant NLR pairs move to the NLR-specific term?
Q: Would a more specific MF child of innate immune receptor activity for direct pathogen-effector binding (as opposed to PAMP binding) be useful for sensor NLRs with integrated decoy domains?
Experiment: Cryo-EM structure of the full-length RGA4/RGA5 hetero-complex with and without AVR-Pia, to find out how effector binding to the HMA domain relieves RGA4 repression without the complex dissociating.
Experiment: Metal-binding assays (ICP-MS, ITC with Cu/Zn) on the RGA5 HMA domain, and on a variant with the second cysteine restored, to test directly whether the degenerate motif has lost metal binding.
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