Pi-ta (LOC_Os12g18360) is a 928-residue coiled-coil, nucleotide-binding (NB-ARC), leucine-rich repeat (CC-NB-LRR, CNL) protein of rice, encoded near the centromere of chromosome 12 in a blast resistance cluster that also contains the unrelated armadillo-repeat resistance gene Ptr. It has an N-terminal Rx-type coiled coil, an NB-ARC domain with an intact P-loop, a winged-helix domain and a C-terminal LRR region. The NB-ARC domain is expected to bind ADP in the resting state, as in other plant NLRs, but this has not been measured. Pi-ta was cloned as the receptor for the Pyricularia (Magnaporthe) oryzae effector AVR-Pita: the AVR-Pita176 fragment was reported to bind the Pi-ta LRR region in yeast and in vitro, and resistant and susceptible alleles differ only at residue 918 (Ala in resistant alleles, Ser in susceptible pi-ta alleles). The sequence of this record (cultivar Tsuyake) carries Ser918 and is a susceptible allele. Later knockdown and knockout genetics showed that AVR-Pita recognition and the classical Pi-ta and Pi-ta2 resistance specificities are conferred by alleles of Ptr, and that the NLR is not needed for them. One study found that knocking out the Pi-ta allele of cultivar Fuhui 2663 abolished resistance to one blast isolate. The physiological function of the Pi-ta NLR, including any ligand, immune output or subcellular location, is therefore unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002758 innate immune response-activating signaling pathway | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA machine-learning transfer applied to plant CNL proteins. The only Pi-ta-specific support for immune signalling was the AVR-Pita recognition model (direct binding to the LRR region and transient co-expression), which locus-resolved genetics have since contradicted. Reason: Many CNLs do activate immune signalling, so the term is not absurd for this protein family. For Pi-ta, however, Xiao et al. 2024 showed that AVR-Pita recognition relies on Ptr and that the NLR plays no part in it. No other immune pathway has been shown to signal through the Pi-ta NLR. The record is also a Ser918 susceptible allele. The term asserts more than the gene-specific evidence supports. Supporting Evidence: PMID:38834685 we found that AVR-Pita recognition relies solely on Ptr and that the NLR Pi-ta has no role in it, indicating that it is not the Pi-ta resistance gene. file:ORYSJ/Pi-ta/Pi-ta-deep-research-falcon.md Xiao and colleagues could not reproduce the reported AVR-Pita interaction with Pi-ta short/long constructs or their tested regions. PMID:10921881 These data suggest that the AVR-Pita 176 protein binds directly to the Pi-ta LRD region inside the plant cell to initiate a Pi-ta -mediated defense response. |
| GO:0006952 defense response | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the plant disease resistance protein family (IPR044974). Pi-ta has the full CC-NB-ARC-LRR architecture of this family. Reason: The general defense response term is a fair family-level inference for an intact CNL. Gene-specific evidence is split: one CRISPR study links the Fuhui 2663 Pi-ta allele to blast resistance, while locus-resolved genetics show the NLR is not needed for AVR-Pita-dependent resistance. The term is kept at this general level but not treated as an established core function. Supporting Evidence: PMID:10921881 Pi-ta encodes a putative cytoplasmic receptor with a centrally localized nucleotide-binding site and leucine-rich domain (LRD) at the C-terminus. PMID:36050368 Using CRISPR/Cas9 genome editing technology, we knocked out Pita-Fuhui2663 in Fuhui 2663 and found that the knockout mutants lost its resistance, indicating that Pita-Fuhui2663 confers blast resistance. |
| GO:0006952 defense response | IMP PMID:11090207 tA single amino acid difference distinguishes resistant and ... | KEEP AS NON CORE | Summary: Bryan et al. 2000 cloned Pi-ta by map-based cloning. They reported that co-expressing a Pi-ta(+) allele with AVR-Pita in rice cells induced a resistance response, whereas the Ser918 pi-ta(-) allele did not. Gramene attached this IMP to both the resistant (Q9AY26) and susceptible (Q84UB1, Ser918) UniProt records. Reason: The curator read the full text, which is not cached here. The paper's conclusion has since been directly contradicted: Xiao et al. 2024 used RNAi and CRISPR lines to show that Pi-ta resistance and AVR-Pita recognition depend on Ptr, a separate gene in the same cluster, and not on the NLR. Zhao et al. 2018 had already shown that Ptr is required for Pi-ta-type resistance. On the other side, He et al. 2022 found that two CRISPR knockout lines of the Fuhui 2663 Pi-ta allele became susceptible to isolate KJ201, which supports some defense role for the NLR in that background. With the evidence in conflict, the general defense response term is kept, deferring to the curator and to the 2022 knockout data, but it is not treated as a core function. It is not removed because necessity in Fuhui 2663 has not been refuted. Note also that this UniProt record is the Ser918 allele, which the original paper found unable to trigger the response. Supporting Evidence: PMID:11090207 Transient expression in rice cells of a Pi-ta(+) R gene together with AVR-Pita(+) induces a resistance response. PMID:11090207 No resistance response is induced in transient assays that use a naturally occurring pi-ta(-) allele differing only by the serine at position 918. PMID:38834685 Taken together, our work establishes that the M. oryzae effector AVR-Pita is detected in an allele-specific manner by the unconventional rice resistance protein Ptr and that the NLR Pi-ta has no function in Pi-ta resistance and the recognition of AVR-Pita. PMID:36050368 Inoculation of rice blast fungus showed that the two knockout lines generated by CRISPR/Cas9 were susceptible to KJ201, while their parent Fuhui2663 was resistant to KJ201. |
| GO:0009626 plant-type hypersensitive response | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA transfer of HR from characterised CNLs. The only Pi-ta-linked cell death data come from transient assays in Jia et al. 2000, interpreted under the AVR-Pita-Pi-ta recognition model. Reason: Cell death has never been shown to be executed by the Pi-ta NLR itself. For example, no autoactive mutant or Pi-ta-dependent cell death assay in a Ptr-null background has been reported. The AVR-Pita-triggered response once attributed to Pi-ta is now attributed to Ptr. HR is plausible for the family but not established for this gene. Supporting Evidence: PMID:10921881 The absence of AVR-Pita 176 transcripts in Pi-ta -containing plant cells is consistent with the occurrence of HR-associated cell death in transformed cells. PMID:38834685 we found that AVR-Pita recognition relies solely on Ptr and that the NLR Pi-ta has no role in it |
| GO:0042742 defense response to bacterium | IEA GO_REF:0000117 | REMOVE | Summary: ARBA transfer of a bacterial defense term to a rice blast CNL. No bacterial infection, recognition or resistance data exist for Pi-ta. Reason: All Pi-ta literature concerns the fungal blast pathogen. The term comes from over-propagation of bacterial-resistance annotations of other NB-LRR proteins (for example Arabidopsis RPS/RPM CNLs). There is no biological basis for it in this gene. Supporting Evidence: PMID:11090207 The rice blast resistance (R) gene Pi-ta mediates gene-for-gene resistance against strains of the fungus Magnaporthe grisea that express avirulent alleles of AVR-Pita. |
| GO:0043531 ADP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the NB-ARC domain (IPR002182, residues 214-385). The Pi-ta sequence keeps the Walker A/P-loop (GSGGVGKTT), kinase-2 (FIIIEDLW) and GLPL (GGLPLAI) motifs that form the nucleotide pocket. Reason: Plant NLR NB-ARC domains bind ADP in their resting state, and the motifs needed for nucleotide binding are intact in Pi-ta. This is the only molecular activity that can be inferred with reasonable confidence for Pi-ta. It is a structural inference; nucleotide binding has not been measured for Pi-ta itself. Supporting Evidence: PMID:10921881 Pi-ta encodes a putative cytoplasmic receptor with a centrally localized nucleotide-binding site and leucine-rich domain (LRD) at the C-terminus. PMID:11090207 Pi-ta encodes a predicted 928-amino acid cytoplasmic receptor with a centrally localized nucleotide binding site. |
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Download this section (compressed HTML)Q: Xiao et al. 2024 attribute Pi-ta and Pi-ta2 resistance to Ptr alleles. Should the fungal-defense annotations historically attached to the Pi-ta NLR (and the AVR-Pita recognition model) be re-curated onto Ptr (LOC_Os12g18729), leaving the NLR without a process annotation until its own function is shown?
Q: Gramene attached the same IMP defense response annotation (PMID:11090207) to both the resistant Ala918 record (Q9AY26) and this susceptible Ser918 record (Q84UB1). The original paper showed that the Ser918 allele does not trigger resistance. Which UniProt record should carry gene-level annotations for the Pi-ta locus?
Q: How can the He et al. 2022 result (Pi-ta knockout in Fuhui 2663 abolishes resistance to isolate KJ201) be reconciled with the Xiao et al. 2024 finding that the NLR is dispensable? Is KJ201 resistance AVR-Pita dependent, and which Ptr allele does Fuhui 2663 carry?
Experiment: Complement the Fuhui 2663 Pi-ta knockout lines with the wild-type Pi-ta allele. Genotype their Ptr allele and test the AVR-Pita status of isolate KJ201. This would decide whether the Pi-ta NLR has an independent resistance role in that background.
Experiment: Express Pi-ta (Ala918 and Ser918) alone and with AVR-Pita, Ptr alleles or candidate effectors in Nicotiana benthamiana and Ptr-null rice protoplasts. Include P-loop (K243) and MHD-type mutants to test whether the NLR can trigger cell death on its own.
Experiment: Determine the subcellular localisation of tagged Pi-ta in rice cells and test co-immunoprecipitation with PTR, to see whether the NLR and PTR physically or functionally interact.
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