RPM1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0006952 defense response	TAS PMID:7638602 Structure of the Arabidopsis RPM1 gene enabling dual specifi...	MODIFY	Summary: RPM1 mediates effector-triggered defense against Pseudomonas strains expressing AvrB or AvrRpm1, but the existing defense response term is broad. Reason: Defense response to bacterium better captures the experimentally supported RPM1 output than generic defense response. Proposed replacements: defense response to bacterium
GO:0009626 plant-type hypersensitive response	IDA PMID:8768370 Expression of the Pseudomonas syringae avirulence protein Av...	ACCEPT	Summary: RPM1 activation by AvrB/AvrRpm1-triggered RIN4 modification elicits hypersensitive-response cell death. Reason: Hypersensitive response is a canonical output of RPM1-mediated effector-triggered immunity and is supported by AvrB/RPM1 experiments.
GO:0000166 nucleotide binding	ISS PMID:7638602 Structure of the Arabidopsis RPM1 gene enabling dual specifi...	MODIFY	Summary: RPM1 has an NB-ARC nucleotide-binding module, but generic nucleotide binding is less precise than the ADP/ATP switch used by NLRs. Reason: Use ADP binding or ATP binding for the NB-ARC molecular switch rather than a broad nucleotide-binding term. Proposed replacements: ADP binding ATP binding
GO:0005515 protein binding	IPI PMID:11955429 RIN4 interacts with Pseudomonas syringae type III effector m...	MARK AS OVER ANNOTATED	Summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism. Reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
GO:0005515 protein binding	IPI PMID:15722472 RIN13 is a positive regulator of the plant disease resistanc...	MARK AS OVER ANNOTATED	Summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism. Reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
GO:0005515 protein binding	IPI PMID:16212605 A duplicated pair of Arabidopsis RING-finger E3 ligases cont...	MARK AS OVER ANNOTATED	Summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism. Reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
GO:0005515 protein binding	IPI PMID:20332379 Endosome-associated CRT1 functions early in resistance gene-...	MARK AS OVER ANNOTATED	Summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism. Reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
GO:0005515 protein binding	IPI PMID:38358510 The RIN4-like/NOI proteins NOI10 and NOI11 modulate the resp...	MARK AS OVER ANNOTATED	Summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism. Reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
GO:0043531 ADP binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: RPM1 contains an NB-ARC module expected to bind ADP/ATP as part of NLR molecular switching. Reason: ADP binding is mechanistically relevant, but RPM1's core gene-level role is immune receptor signaling rather than nucleotide binding alone.
GO:0006952 defense response	IEA GO_REF:0000002	MODIFY	Summary: RPM1 mediates effector-triggered defense against Pseudomonas strains expressing AvrB or AvrRpm1, but the existing defense response term is broad. Reason: Defense response to bacterium better captures the experimentally supported RPM1 output than generic defense response. Proposed replacements: defense response to bacterium
GO:0009626 plant-type hypersensitive response	IEA GO_REF:0000117	ACCEPT	Summary: RPM1 activation by AvrB/AvrRpm1-triggered RIN4 modification elicits hypersensitive-response cell death. Reason: Hypersensitive response is a canonical output of RPM1-mediated effector-triggered immunity and is supported by AvrB/RPM1 experiments.
GO:0005886 plasma membrane	IEA GO_REF:0000044	ACCEPT	Summary: RPM1 is a peripheral protein enriched at the plasma membrane. Reason: Plasma membrane localization is central to RPM1 function because RPM1 guards RIN4 at the cytoplasmic face of the plasma membrane.
GO:0005886 plasma membrane	IEA GO_REF:0000117	ACCEPT	Summary: RPM1 is a peripheral protein enriched at the plasma membrane. Reason: Plasma membrane localization is central to RPM1 function because RPM1 guards RIN4 at the cytoplasmic face of the plasma membrane.
GO:0005886 plasma membrane	IDA PMID:9861059 The Arabidopsis thaliana RPM1 disease resistance gene produc...	ACCEPT	Summary: RPM1 is a peripheral protein enriched at the plasma membrane. Reason: Plasma membrane localization is central to RPM1 function because RPM1 guards RIN4 at the cytoplasmic face of the plasma membrane.
GO:0012505 endomembrane system	IEA GO_REF:0000044	MODIFY	Summary: The cited localization evidence points to plasma-membrane/microsomal association and is better captured by a plasma-membrane cytoplasmic-face term than by broad endomembrane system. Reason: RPM1 is specifically a peripheral/extrinsic protein at the cytoplasmic side of the plasma membrane; endomembrane system is less precise. Proposed replacements: extrinsic component of cytoplasmic side of plasma membrane
GO:0012505 endomembrane system	EXP PMID:9861059 The Arabidopsis thaliana RPM1 disease resistance gene produc...	MODIFY	Summary: The cited localization evidence points to plasma-membrane/microsomal association and is better captured by a plasma-membrane cytoplasmic-face term than by broad endomembrane system. Reason: RPM1 is specifically a peripheral/extrinsic protein at the cytoplasmic side of the plasma membrane; endomembrane system is less precise. Proposed replacements: extrinsic component of cytoplasmic side of plasma membrane
GO:0031234 extrinsic component of cytoplasmic side of plasma membrane	IDA PMID:9861059 The Arabidopsis thaliana RPM1 disease resistance gene produc...	ACCEPT	Summary: RPM1 resides on the cytoplasmic face of the plasma membrane as a peripheral membrane-associated immune receptor. Reason: This is the most precise existing localization annotation for the site of RPM1-RIN4 guard signaling.
GO:0140375 immune receptor activity	IC file:ARATH/RPM1/RPM1-deep-research-falcon.md	NEW	Summary: RPM1 functions as a CNL immune receptor that monitors effector-induced RIN4 modification. Reason: GOA captures defense outputs and nucleotide binding but omits the core molecular role of RPM1 as an immune receptor. Supporting Evidence: file:ARATH/RPM1/RPM1-deep-research-falcon.md RPM1 is a canonical example of indirect effector recognition PMID:7638602 The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes. PMID:8768370 both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent necrosis
GO:0002218 activation of innate immune response	IC file:ARATH/RPM1/RPM1-deep-research-falcon.md	NEW	Summary: RPM1 activates intracellular effector-triggered immune signaling after effector-induced RIN4 modification. Reason: This broader innate-immune activation term avoids incorrectly treating RPM1 guarded effector recognition as PAMP pattern-recognition receptor signaling. Supporting Evidence: file:ARATH/RPM1/RPM1-deep-research-falcon.md mediating effector-triggered immunity (ETI) to Pseudomonas syringae effectors AvrRpm1 and AvrB PMID:7638602 The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes. PMID:8768370 both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent necrosis
GO:0042742 defense response to bacterium	IC file:ARATH/RPM1/RPM1-deep-research-falcon.md	NEW	Summary: RPM1 confers resistance to Pseudomonas syringae strains expressing AvrB or AvrRpm1. Reason: This is the precise antibacterial defense output missing from current RPM1 GOA rows. Supporting Evidence: file:ARATH/RPM1/RPM1-deep-research-falcon.md RPM1 mediates race-specific resistance to P. syringae strains delivering AvrB or AvrRpm1 PMID:7638602 The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes. PMID:8768370 Both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent necrosis.

Core Functions

Plasma-membrane CNL immune receptor guarding RIN4. RPM1 monitors effector-induced RIN4 modification, especially AvrB/AvrRpm1-associated RIN4 Thr166 phosphorylation, at the cytoplasmic face of the plasma membrane and activates effector-triggered antibacterial defense and hypersensitive response.

Molecular Function:

immune receptor activity

Directly Involved In:

activation of innate immune response defense response to bacterium

Cellular Locations:

extrinsic component of cytoplasmic side of plasma membrane plasma membrane

Supporting Evidence:

file:ARATH/RPM1/RPM1-deep-research-falcon.md
RPM1 is a canonical example of **indirect effector recognition**
file:ARATH/RPM1/RPM1-deep-research-falcon.md
RPM1 is a peripheral protein on the cytoplasmic face of the plasma membrane
PMID:7638602
The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes.
PMID:8768370
Both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent necrosis.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

InterPro2GO mapping electronically transfers GO terms (e.g. nucleotide binding, defense response) onto RPM1 from its NB-ARC and LRR InterPro signatures; useful for breadth but not RPM1-specific function.

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

UniProt SubcellularLocation-to-GO mapping yields plasma membrane localization for RPM1, consistent with peripheral plasma-membrane localization reported experimentally.

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

ARBA machine-learning rules propagate broad NLR-family annotations to RPM1; treated as supporting context rather than as primary evidence of the RIN4-guard mechanism.

PMID:11955429

RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis.

RIN4 interacts with AvrB, AvrRpm1, and RPM1 and is required for RPM1-mediated resistance.

PMID:15722472

RIN13 is a positive regulator of the plant disease resistance protein RPM1.

RIN13 is a positive regulator of RPM1-mediated immunity but does not define RPM1 core molecular activity.

PMID:16212605

A duplicated pair of Arabidopsis RING-finger E3 ligases contribute to the RPM1- and RPS2-mediated hypersensitive response.

RING-finger E3 ligases contribute to RPM1- and RPS2-mediated hypersensitive response outputs.

PMID:20332379

Endosome-associated CRT1 functions early in resistance gene-mediated defense signaling in Arabidopsis and tobacco.

CRT1 functions early in resistance-gene-mediated defense signaling and is an RPM1-associated immune regulator.

PMID:38358510

The RIN4-like/NOI proteins NOI10 and NOI11 modulate the response to biotic stresses mediated by RIN4 in Arabidopsis.

RIN4-like/NOI proteins modulate RIN4-mediated biotic stress responses relevant to RPM1 signaling context.

PMID:7638602

Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance.

RPM1 encodes an NB-LRR disease-resistance protein enabling dual specificity to Pseudomonas syringae avrRpm1 and avrB.

PMID:8768370

Expression of the Pseudomonas syringae avirulence protein AvrB in plant cells alleviates its dependence on the hypersensitive response and pathogenicity (Hrp) secretion system in eliciting genotype-specific hypersensitive cell death.

Intracellular AvrB expression triggers RPM1-dependent hypersensitive cell death.

PMID:9861059

The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response.

RPM1 is a peripheral plasma membrane protein likely residing on the cytoplasmic face of the plasma membrane and degraded coincident with HR.

file:ARATH/RPM1/RPM1-deep-research-falcon.md

Falcon deep research for Arabidopsis RPM1

RPM1 is a plasma-membrane-associated CNL immune receptor that guards RIN4 and is activated by effector-induced RIN4 modification.
RPM1 localization and immune recognition are organized at the cytoplasmic face of the plasma membrane.

file:ARATH/RPM1/RPM1-uniprot.txt

UniProt record for Arabidopsis RPM1

UniProt identifies RPM1/Q39214 as a disease resistance NB-LRR protein with plasma membrane, ADP/ATP binding, and hypersensitive response annotations.

file:interpro/panther/PTHR23155/PTHR23155-entries.csv

PANTHER PTHR23155 disease resistance protein RP family entries

PTHR23155 places Arabidopsis Q39214/RPM1 in disease resistance protein RPM1 subfamily SF1205.

Suggested Experiments

Experiment: Reconstitute RPM1 with RIN4 phosphorylation or ADP-ribosylation states in plasma-membrane fractions to quantify receptor activation and nucleotide exchange.

Experiment: Measure RPM1 ADP/ATP binding and hydrolysis states before and after RIN4 phosphomimic activation to connect NB-ARC switching with guardee modification sensing.

Deep Research

Falcon

(RPM1-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 30 citations 2026-05-07T02:43:10.286725

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Functional annotation of Arabidopsis RPM1 (AT3G07040; UniProt Q39214)

1) Target identity verification (critical)

The literature assembled here matches Arabidopsis thaliana RPM1 (locus AT3G07040; UniProt Q39214), a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR; CNL/NLR) disease resistance protein mediating effector-triggered immunity (ETI) to Pseudomonas syringae effectors AvrRpm1 and AvrB (Boyes et al., 1998-12, https://doi.org/10.1073/pnas.95.26.15849; Chiang & Coaker, 2015-10, https://doi.org/10.1199/tab.0183) (boyes1998thearabidopsisthaliana pages 1-2, chiang2015effectortriggeredimmunity pages 3-5).

2) Key concepts and definitions (current understanding)

Plant ETI and the “guard” model

RPM1 is a canonical example of indirect effector recognition: rather than binding effectors directly, RPM1 monitors (“guards”) the host protein RIN4 (RPM1-INTERACTING PROTEIN 4) and becomes activated when bacterial effectors alter RIN4 (chiang2015effectortriggeredimmunity pages 3-5, cunha2009structuralinsightsinto pages 103-107). This fits the broader concept that NLRs sense effector-induced perturbations of host targets and then trigger a robust defense program (chiang2015effectortriggeredimmunity pages 3-5).

NLRs as nucleotide-dependent molecular switches

NLRs such as RPM1 contain an NB-ARC module and are commonly modeled as nucleotide-dependent molecular switches, with pathogen perception leading to conformational change and ADP-to-ATP exchange to initiate downstream signaling (chiang2015effectortriggeredimmunity pages 3-5).

3) Primary molecular function of RPM1

3.1 What RPM1 recognizes

RPM1 mediates race-specific resistance to P. syringae strains delivering AvrB or AvrRpm1 into plant cells (Boyes et al., 1998-12; Chiang & Coaker, 2015-10) (boyes1998thearabidopsisthaliana pages 1-2, chiang2015effectortriggeredimmunity pages 3-5). Mechanistically, RPM1 is activated by effector-triggered modification of RIN4, particularly at a key phosphorylation site (below) (chiang2015effectortriggeredimmunity pages 3-5, redditt2019avrrpm1functionsas pages 1-2).

3.2 The guarded host protein (RIN4) and the activating “signal”

Multiple sources converge on RIN4 as the guarded host protein required for RPM1 activation and proper RPM1 function/accumulation (cunha2009structuralinsightsinto pages 103-107, cunha2009structuralinsightsinto pages 98-103, day2006ndr1interactionwith pages 1-2).

A central mechanistic trigger is RIN4 phosphorylation at Thr166 (T166):
- A review in The Arabidopsis Book summarizes that RPM1 activation can be triggered by phosphorylation of RIN4 at T166 (and also by deletion of nearby Pro149) (Chiang & Coaker, 2015-10) (chiang2015effectortriggeredimmunity pages 3-5).
- A mechanistic Plant Cell study reports that AvrRpm1’s enzymatic activity is required for subsequent phosphorylation of RIN4 on Thr166, and that Thr166 phosphorylation is necessary and sufficient to activate RPM1 (Redditt et al., 2019-11, https://doi.org/10.1105/tpc.19.00020r2) (redditt2019avrrpm1functionsas pages 1-2).

3.3 Upstream effector biochemistry and host enzymes (how RIN4 is modified)

AvrRpm1 is an ADP-ribosyl transferase. Redditt et al. demonstrate that AvrRpm1 induces mono-ADP-ribosylation of RIN4 (within two conserved NOI domains) and also modifies ≥10 additional Arabidopsis NOI-domain proteins, establishing a broader biochemical footprint beyond RIN4 alone (redditt2019avrrpm1functionsas pages 1-2). In the same work, AvrRpm1’s ADP-ribosylation activity is reported to be required for the downstream RIN4 T166 phosphorylation event that triggers RPM1 (redditt2019avrrpm1functionsas pages 1-2).

For AvrB, a review synthesis indicates that AvrB promotes host-kinase–dependent phosphorylation of RIN4 (e.g., via RIPK, RPM1-INDUCED PROTEIN KINASE), culminating in RPM1 activation (chiang2015effectortriggeredimmunity pages 3-5).

4) Subcellular localization and where RPM1 acts

4.1 RPM1 is a peripheral plasma membrane protein

Direct biochemical fractionation experiments using functional epitope-tagged RPM1 (RPM1::MYC) show RPM1 is wholly membrane-associated in microsomal pellets, enriched in plasma-membrane fractions, and can be released by treatments that remove peripheral (not integral) membrane proteins, supporting localization to the cytoplasmic face of the plasma membrane (Boyes et al., 1998-12) (boyes1998thearabidopsisthaliana pages 4-5, boyes1998thearabidopsisthaliana pages 2-3). These conclusions are also supported by the corresponding figure evidence from Boyes et al. (Fig. 2 panels) (boyes1998thearabidopsisthaliana media 4e7b4a1b).

A later review likewise characterizes RPM1 (AT3G07040) as a plasma membrane–associated NLR guarding RIN4 (chiang2015effectortriggeredimmunity pages 3-5).

4.2 Activation-linked RPM1 protein loss (negative feedback)

RPM1 protein abundance declines rapidly coincident with hypersensitive response (HR) onset after activation. Boyes et al. report that RPM1::MYC levels “declined sharply” at HR onset, without evidence for global protein destruction or appearance of a stable C-terminal cleavage fragment (boyes1998thearabidopsisthaliana pages 4-5). This activation-associated loss is also visible in their immunoblot time course figures (Boyes et al. Fig. 3/4) (boyes1998thearabidopsisthaliana media 4e7b4a1b).

5) Signaling pathways downstream and genetic requirements

5.1 NDR1 dependence (CNL branch)

RPM1 is in the CNL class, and CNL ETI is generally associated with a requirement for NDR1 (NON-RACE-SPECIFIC DISEASE RESISTANCE 1) rather than the EDS1/PAD4 module that is more characteristic of many TIR-NLR pathways (seto2021recognitionofthe pages 30-33).

Primary genetic evidence indicates that NDR1 is required for RPM1-mediated resistance outputs (bacterial growth restriction). In a structure–function analysis of RPM1, Tornero et al. report that ndr1 mutant plants do not restrict bacterial growth in RPM1-mediated resistance assays, concluding that NDR1 is required for RPM1 function (Tornero et al., 2002-02, https://doi.org/10.1105/tpc.010393) (tornero2002largescalestructure–function pages 1-2). At the mechanistic interface, NDR1 associates with RIN4 in planta, and the RIN4–NDR1 interaction is described as an important node integrating multiple RIN4-guarding resistance pathways (Day et al., 2006-09, https://doi.org/10.1105/tpc.106.044693) (day2006ndr1interactionwith pages 1-2).

5.2 Shared PTI/ETI outputs

RPM1-triggered ETI engages defense outputs that overlap with PTI, including ROS, Ca2+ signaling, and MAPK cascades, with ETI more frequently associated with hypersensitive cell death (HR) (seto2021recognitionofthe pages 30-33). This situates RPM1 as part of the general intracellular NLR layer that amplifies and sustains immune responses.

6) Recent developments (prioritizing 2023–2024) relevant to RPM1 functional annotation

6.1 Spatial regulation of the RIN4 T166 phospho-switch (2024)

A 2024 study/refinement focusing on RIN4 provides a mechanistic update highly relevant to RPM1 activation logic: Zhao & Day (2024-12, Frontiers in Plant Science, https://doi.org/10.3389/fpls.2024.1473944) report that phosphorylation of RIN4 at Thr166 affects RIN4 plasma membrane tethering and can repress defense activation, linking the RPM1-associated phospho-switch to subcellular localization control. They further connect RIN4 PM tethering to Exo70B1-mediated exocytosis and the actin cytoskeleton, and propose that phosphorylation reduces RIN4’s binding affinity for Exo70B1, shifting RIN4 localization and immune output (zhao2024subcellularspatialregulation pages 1-2).

This 2024 work is best interpreted as an update on the context in which RPM1 senses the RIN4 T166 state—i.e., the T166 modification is not only a biochemical “on/off” signal but also intersects with membrane trafficking and spatial organization of immunity (zhao2024subcellularspatialregulation pages 1-2).

7) Applications and real-world implementations

RPM1 itself is primarily a model Arabidopsis ETI receptor used to dissect principles of NLR activation, guardee modification sensing, and membrane organization of intracellular immunity (chiang2015effectortriggeredimmunity pages 3-5, boyes1998thearabidopsisthaliana pages 4-5). While this evidence set does not include 2023–2024 field-deployment papers specifically transferring RPM1 to crops, the RPM1/RIN4/AvrRpm1 system is experimentally leveraged as a tractable ETI module (e.g., inducible effector expression systems in RPM1 backgrounds) to probe immune signaling and regulation (tornero2002largescalestructure–function pages 1-2, boyes1998thearabidopsisthaliana pages 4-5).

8) Expert synthesis and authoritative interpretations

A key authoritative synthesis is The Arabidopsis Book ETI review (Chiang & Coaker, 2015-10), which explicitly frames RPM1 as a plasma membrane-associated NLR activated by RIN4 T166 phosphorylation (and related perturbations such as Pro149 deletion), fitting the guard model and the nucleotide-switch paradigm of NLR activation (chiang2015effectortriggeredimmunity pages 3-5). The 2024 Zhao & Day study adds a contemporary mechanistic layer by connecting the same T166 phospho-switch to RIN4’s spatial distribution and trafficking dependencies, illustrating how ETI-relevant guardee modifications can be integrated with membrane logistics (zhao2024subcellularspatialregulation pages 1-2).

9) Quantitative statistics and recent data from studies

9.1 Population genetics of RPM1 presence/absence polymorphism

RPM1 is a classic case of a presence/absence polymorphism maintained over long evolutionary time.

Stahl et al. (1999-08, Nature, https://doi.org/10.1038/23260) report:
- Worldwide resistance-allele frequency of 0.52 in a random sample of 26 accessions (treated as 27 alleles), with s.e. ≈ 0.098 (stahl1999dynamicsofdisease pages 1-2).
- Strong departure from neutrality at the deletion junction region, including Tajima’s D = 3.06 (P < 0.001) (stahl1999dynamicsofdisease pages 2-2).
- Divergence between resistant and susceptible haplotypes at the junction reaching 11.8%, comparable to 10.5% average divergence between A. thaliana and A. lyrata (stahl1999dynamicsofdisease pages 2-2).
- An estimated polymorphism age of ~9.8 million years, supporting long-term maintenance (balancing selection) (stahl1999dynamicsofdisease pages 2-2).
- Elevated intraclass diversity among resistance haplotypes (e.g., “30 versus 3” polymorphisms overall; conservative counts of 12 resistance vs 3 susceptibility polymorphisms) and geographic structure (generally high resistance allele frequency across the northern hemisphere but low in the US midwest) (stahl1999dynamicsofdisease pages 3-4).

Together, these statistics support an expert conclusion that RPM1 polymorphism is consistent with a long-lived balanced polymorphism (“trench warfare”) rather than rapid sequential sweeps (arms race), and that local demography can still modulate allele retention (stahl1999dynamicsofdisease pages 2-3, stahl1999dynamicsofdisease pages 3-4).

Summary artifact

The following table consolidates the key evidence-backed annotation points (recognition, guardee, activation modifications, localization, signaling requirements, and key statistics):

Aspect	Key findings	Key citations with pqac IDs	URLs / publication dates
Identity / domains	RPM1 in the cited literature is the Arabidopsis thaliana disease-resistance gene AT3G07040, described as a CC-NB-LRR/CNL NLR. Reviews place it in the NB-ARC-containing, plasma membrane–associated NLR class.	(chiang2015effectortriggeredimmunity pages 3-5, boyes1998thearabidopsisthaliana pages 1-2)	Chiang & Coaker 2015-10, https://doi.org/10.1199/tab.0183; Boyes et al. 1998-12, https://doi.org/10.1073/pnas.95.26.15849
Recognition	RPM1 recognizes the Pseudomonas syringae type III effectors AvrB and AvrRpm1 indirectly rather than by stable direct effector binding. Recognition occurs through sensing effector-induced perturbation of the host protein RIN4.	(chiang2015effectortriggeredimmunity pages 3-5, redditt2019avrrpm1functionsas pages 1-2, day2006ndr1interactionwith pages 1-2)	Chiang & Coaker 2015-10, https://doi.org/10.1199/tab.0183; Redditt et al. 2019-11, https://doi.org/10.1105/tpc.19.00020r2; Day et al. 2006-09, https://doi.org/10.1105/tpc.106.044693
Guardee	RIN4 is the guarded host protein central to RPM1 activation. It is a multifunctional, membrane-associated regulator of immunity that also negatively regulates PTI and is required for proper RPM1 function and accumulation.	(cunha2009structuralinsightsinto pages 103-107, cunha2009structuralinsightsinto pages 98-103, day2006ndr1interactionwith pages 1-2)	Day et al. 2006-09, https://doi.org/10.1105/tpc.106.044693
Activating modifications	Phosphorylation of RIN4 at Thr166 is reported as necessary and sufficient for RPM1 activation; deletion of nearby Pro149 can also activate RPM1. AvrB/AvrRpm1-induced phosphorylation is therefore the key molecular trigger in the guard model.	(chiang2015effectortriggeredimmunity pages 3-5, redditt2019avrrpm1functionsas pages 1-2, zhao2024subcellularspatialregulation pages 1-2)	Chiang & Coaker 2015-10, https://doi.org/10.1199/tab.0183; Redditt et al. 2019-11, https://doi.org/10.1105/tpc.19.00020r2; Zhao & Day 2024-12, https://doi.org/10.3389/fpls.2024.1473944
Upstream effectors / enzymes	AvrRpm1 and AvrB are the upstream bacterial effectors. AvrRpm1 functions as an ADP-ribosyl transferase that mono-ADP-ribosylates RIN4/NOI proteins, and this activity is required for subsequent RIN4 Thr166 phosphorylation; AvrB promotes RIPK-mediated phosphorylation of RIN4.	(redditt2019avrrpm1functionsas pages 1-2, chiang2015effectortriggeredimmunity pages 3-5)	Redditt et al. 2019-11, https://doi.org/10.1105/tpc.19.00020r2; Chiang & Coaker 2015-10, https://doi.org/10.1199/tab.0183
Downstream signaling requirements	RPM1 belongs to the CNL branch that generally requires NDR1 rather than EDS1 for signaling. NDR1 is shared by RPM1- and RPS2-mediated pathways, associates with RIN4, and is required for RPM1-mediated bacterial growth restriction; ETI outputs overlap with PTI, including ROS, Ca2+ signaling, MAPKs, and often HR.	(seto2021recognitionofthe pages 30-33, tornero2002largescalestructure–function pages 1-2, day2006ndr1interactionwith pages 1-2)	Tornero et al. 2002-02, https://doi.org/10.1105/tpc.010393; Day et al. 2006-09, https://doi.org/10.1105/tpc.106.044693
Localization	RPM1 is a peripheral protein on the cytoplasmic face of the plasma membrane, enriched in plasma membrane fractions rather than being an integral membrane protein. The associated recognition system is thus organized at the plasma membrane where RIN4 and relevant effectors operate.	(boyes1998thearabidopsisthaliana pages 4-5, boyes1998thearabidopsisthaliana pages 2-3)	Boyes et al. 1998-12, https://doi.org/10.1073/pnas.95.26.15849
Activation-linked degradation	RPM1 protein abundance declines sharply coincident with hypersensitive response onset after activation, and degradation is also observed during RPS4-mediated HR. This was interpreted as possible negative feedback limiting cell death/resistance output.	(boyes1998thearabidopsisthaliana pages 4-5, boyes1998thearabidopsisthaliana pages 1-2, boyes1998thearabidopsisthaliana media 4e7b4a1b)	Boyes et al. 1998-12, https://doi.org/10.1073/pnas.95.26.15849
Population genetics / statistics	Rpm1 shows a classic presence/absence polymorphism: a worldwide resistance-allele frequency of 0.52 in a random sample of 26 accessions (27 alleles), Tajima’s D = 3.06 (P < 0.001), divergence between R and S haplotypes up to 11.8%, and an estimated age of ~9.8 million years. These data support long-term balancing selection (“trench warfare”) rather than rapid turnover by recurrent sweeps.	(stahl1999dynamicsofdisease pages 2-3, stahl1999dynamicsofdisease pages 1-2, stahl1999dynamicsofdisease pages 2-2, stahl1999dynamicsofdisease pages 3-4)	Stahl et al. 1999-08, https://doi.org/10.1038/23260
Recent 2024 updates	A 2024 study links RIN4 Thr166 phosphorylation to altered subcellular localization: phospho-mimic RIN4 disrupts plasma membrane tethering via reduced Exo70B1 interaction and represses defense activation, refining how the RPM1-associated phospho-switch is spatially controlled. A 2024 review also places RPM1/RIN4 within PTI–ETI synergistic signaling.	(zhao2024subcellularspatialregulation pages 1-2)	Zhao & Day 2024-12, https://doi.org/10.3389/fpls.2024.1473944

Table: This table summarizes evidence-backed functional annotation for Arabidopsis RPM1, including recognition mechanism, signaling requirements, localization, and quantitative population-genetic findings. It is useful as a compact reference for the main experimentally supported claims and their source contexts.

Key figure evidence (images)

Boyes et al. provide figure-based experimental support for (i) plasma membrane enrichment/peripheral association of RPM1::MYC and (ii) RPM1 degradation coincident with HR, including immunoblot time courses and fractionation panels (boyes1998thearabidopsisthaliana media 4e7b4a1b).

Evidence gaps (scope limitation)

Within the retrieved full-text evidence, specific 2023–2024 sources directly reporting RPM1 structural (cryo-EM) resistosome formation or deployment/engineering of RPM1 in crops were not available; accordingly, this report does not assert RPM1-specific resistosome architecture or field-validated RPM1 transgenic applications beyond what is supported by the cited sources.

References

(boyes1998thearabidopsisthaliana pages 1-2): Douglas C. Boyes, Jaesung Nam, and Jeffery L. Dangl. The arabidopsis thaliana rpm1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proceedings of the National Academy of Sciences of the United States of America, 95 26:15849-54, Dec 1998. URL: https://doi.org/10.1073/pnas.95.26.15849, doi:10.1073/pnas.95.26.15849. This article has 531 citations and is from a highest quality peer-reviewed journal.
(chiang2015effectortriggeredimmunity pages 3-5): Yi-Hsuan Chiang and Gitta Coaker. Effector triggered immunity: nlr immune perception and downstream defense responses. The Arabidopsis Book, 2015:e0183, Oct 2015. URL: https://doi.org/10.1199/tab.0183, doi:10.1199/tab.0183. This article has 96 citations and is from a peer-reviewed journal.
(cunha2009structuralinsightsinto pages 103-107): LCV Da Cunha. Structural insights into the function of the arabidopsis protein rin4, a multi-regulator of plant resistance against bacterial pathogens. Unknown journal, 2009.
(redditt2019avrrpm1functionsas pages 1-2): Thomas J. Redditt, Eui-Hwan Chung, H. Z. Karimi, N. Rodibaugh, Yixiang Zhang, Jonathan C Trinidad, Jin Hee Kim, Qian Zhou, Mingzhe Shen, Jeffery L Dangl, David Mackey, and R. Innes. Avrrpm1 functions as an adp-ribosyl transferase to modify noi domain-containing proteins, including arabidopsis and soybean rpm1-interacting protein4. The Plant cell, 31 11:2664-2681, Nov 2019. URL: https://doi.org/10.1105/tpc.19.00020r2, doi:10.1105/tpc.19.00020r2. This article has 100 citations.
(cunha2009structuralinsightsinto pages 98-103): LCV Da Cunha. Structural insights into the function of the arabidopsis protein rin4, a multi-regulator of plant resistance against bacterial pathogens. Unknown journal, 2009.
(day2006ndr1interactionwith pages 1-2): Brad Day, Douglas Dahlbeck, and Brian J. Staskawicz. Ndr1 interaction with rin4 mediates the differential activation of multiple disease resistance pathways in arabidopsis. The Plant Cell Online, 18:2782-2791, Sep 2006. URL: https://doi.org/10.1105/tpc.106.044693, doi:10.1105/tpc.106.044693. This article has 203 citations.
(boyes1998thearabidopsisthaliana pages 4-5): Douglas C. Boyes, Jaesung Nam, and Jeffery L. Dangl. The arabidopsis thaliana rpm1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proceedings of the National Academy of Sciences of the United States of America, 95 26:15849-54, Dec 1998. URL: https://doi.org/10.1073/pnas.95.26.15849, doi:10.1073/pnas.95.26.15849. This article has 531 citations and is from a highest quality peer-reviewed journal.
(boyes1998thearabidopsisthaliana pages 2-3): Douglas C. Boyes, Jaesung Nam, and Jeffery L. Dangl. The arabidopsis thaliana rpm1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proceedings of the National Academy of Sciences of the United States of America, 95 26:15849-54, Dec 1998. URL: https://doi.org/10.1073/pnas.95.26.15849, doi:10.1073/pnas.95.26.15849. This article has 531 citations and is from a highest quality peer-reviewed journal.
(boyes1998thearabidopsisthaliana media 4e7b4a1b): Douglas C. Boyes, Jaesung Nam, and Jeffery L. Dangl. The arabidopsis thaliana rpm1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proceedings of the National Academy of Sciences of the United States of America, 95 26:15849-54, Dec 1998. URL: https://doi.org/10.1073/pnas.95.26.15849, doi:10.1073/pnas.95.26.15849. This article has 531 citations and is from a highest quality peer-reviewed journal.
(seto2021recognitionofthe pages 30-33): DJ Seto. Recognition of the pseudomonas syringae type iii effector hopf1r by the arabidopsis nlr zar1. Unknown journal, 2021.
(tornero2002largescalestructure–function pages 1-2): Pablo Tornero, Ryon A. Chao, William N. Luthin, Stephen A. Goff, and Jeffery L. Dangl. Large-scale structure –function analysis of the arabidopsis rpm1 disease resistance protein. The Plant Cell, 14:435-450, Feb 2002. URL: https://doi.org/10.1105/tpc.010393, doi:10.1105/tpc.010393. This article has 216 citations.
(zhao2024subcellularspatialregulation pages 1-2): Yi Zhao and Brad Day. Subcellular spatial regulation of immunity-induced phosphorylation of rin4 links pamp-triggered immunity to exo70b1. Frontiers in Plant Science, Dec 2024. URL: https://doi.org/10.3389/fpls.2024.1473944, doi:10.3389/fpls.2024.1473944. This article has 1 citations.
(stahl1999dynamicsofdisease pages 1-2): Eli A. Stahl, Greg Dwyer, Rodney Mauricio, Martin Kreitman, and Joy Bergelson. Dynamics of disease resistance polymorphism at the rpm1 locus of arabidopsis. Nature, 400:667-671, Aug 1999. URL: https://doi.org/10.1038/23260, doi:10.1038/23260. This article has 699 citations and is from a highest quality peer-reviewed journal.
(stahl1999dynamicsofdisease pages 2-2): Eli A. Stahl, Greg Dwyer, Rodney Mauricio, Martin Kreitman, and Joy Bergelson. Dynamics of disease resistance polymorphism at the rpm1 locus of arabidopsis. Nature, 400:667-671, Aug 1999. URL: https://doi.org/10.1038/23260, doi:10.1038/23260. This article has 699 citations and is from a highest quality peer-reviewed journal.
(stahl1999dynamicsofdisease pages 3-4): Eli A. Stahl, Greg Dwyer, Rodney Mauricio, Martin Kreitman, and Joy Bergelson. Dynamics of disease resistance polymorphism at the rpm1 locus of arabidopsis. Nature, 400:667-671, Aug 1999. URL: https://doi.org/10.1038/23260, doi:10.1038/23260. This article has 699 citations and is from a highest quality peer-reviewed journal.
(stahl1999dynamicsofdisease pages 2-3): Eli A. Stahl, Greg Dwyer, Rodney Mauricio, Martin Kreitman, and Joy Bergelson. Dynamics of disease resistance polymorphism at the rpm1 locus of arabidopsis. Nature, 400:667-671, Aug 1999. URL: https://doi.org/10.1038/23260, doi:10.1038/23260. This article has 699 citations and is from a highest quality peer-reviewed journal.

Citations

chiang2015effectortriggeredimmunity pages 3-5
boyes1998thearabidopsisthaliana pages 4-5
seto2021recognitionofthe pages 30-33
zhao2024subcellularspatialregulation pages 1-2
stahl1999dynamicsofdisease pages 1-2
stahl1999dynamicsofdisease pages 2-2
stahl1999dynamicsofdisease pages 3-4
boyes1998thearabidopsisthaliana pages 1-2
cunha2009structuralinsightsinto pages 103-107
cunha2009structuralinsightsinto pages 98-103
boyes1998thearabidopsisthaliana pages 2-3
stahl1999dynamicsofdisease pages 2-3
https://doi.org/10.1073/pnas.95.26.15849;
https://doi.org/10.1199/tab.0183
https://doi.org/10.1105/tpc.19.00020r2
https://doi.org/10.1105/tpc.010393
https://doi.org/10.1105/tpc.106.044693
https://doi.org/10.3389/fpls.2024.1473944
https://doi.org/10.1038/23260
https://doi.org/10.1199/tab.0183;
https://doi.org/10.1073/pnas.95.26.15849
https://doi.org/10.1105/tpc.19.00020r2;
https://doi.org/10.1105/tpc.010393;
https://doi.org/10.1073/pnas.95.26.15849,
https://doi.org/10.1199/tab.0183,
https://doi.org/10.1105/tpc.19.00020r2,
https://doi.org/10.1105/tpc.106.044693,
https://doi.org/10.1105/tpc.010393,
https://doi.org/10.3389/fpls.2024.1473944,
https://doi.org/10.1038/23260,

📄 View Raw YAML

id: Q39214
gene_symbol: RPM1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:3702
  label: Arabidopsis thaliana
description: 'RPM1 is an Arabidopsis coiled-coil NB-LRR/CNL immune receptor that confers resistance to Pseudomonas syringae strains delivering AvrB or AvrRpm1. RPM1 acts at the cytoplasmic face of the plasma membrane, where it guards the RIN4 immune hub and is activated by effector-induced RIN4 modification, especially Thr166 phosphorylation. Its core role is nucleotide-dependent immune receptor signaling that triggers effector-triggered antibacterial defense and hypersensitive response; generic protein binding and broad defense-response rows should be interpreted through this RPM1-RIN4 plasma-membrane guard mechanism.'
existing_annotations:
- term:
    id: GO:0006952
    label: defense response
  evidence_type: TAS
  original_reference_id: PMID:7638602
  review:
    summary: RPM1 mediates effector-triggered defense against Pseudomonas strains expressing AvrB or AvrRpm1, but the existing defense response term is broad.
    action: MODIFY
    reason: Defense response to bacterium better captures the experimentally supported RPM1 output than generic defense response.
    proposed_replacement_terms:
    - id: GO:0042742
      label: defense response to bacterium
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IDA
  original_reference_id: PMID:8768370
  review:
    summary: RPM1 activation by AvrB/AvrRpm1-triggered RIN4 modification elicits hypersensitive-response cell death.
    action: ACCEPT
    reason: Hypersensitive response is a canonical output of RPM1-mediated effector-triggered immunity and is supported by AvrB/RPM1 experiments.
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: ISS
  original_reference_id: PMID:7638602
  review:
    summary: RPM1 has an NB-ARC nucleotide-binding module, but generic nucleotide binding is less precise than the ADP/ATP switch used by NLRs.
    action: MODIFY
    reason: Use ADP binding or ATP binding for the NB-ARC molecular switch rather than a broad nucleotide-binding term.
    proposed_replacement_terms:
    - id: GO:0043531
      label: ADP binding
    - id: GO:0005524
      label: ATP binding
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11955429
  review:
    summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15722472
  review:
    summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16212605
  review:
    summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20332379
  review:
    summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:38358510
  review:
    summary: RPM1-associated interactions with RIN4, RIN-family proteins, CRT1, and other immune regulators are biologically meaningful, but generic protein binding obscures the receptor mechanism.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is RPM1 immune receptor activity at a RIN4-centered plasma-membrane complex; protein binding alone is too generic for the core function.
- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: RPM1 contains an NB-ARC module expected to bind ADP/ATP as part of NLR molecular switching.
    action: KEEP_AS_NON_CORE
    reason: ADP binding is mechanistically relevant, but RPM1's core gene-level role is immune receptor signaling rather than nucleotide binding alone.
- term:
    id: GO:0006952
    label: defense response
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: RPM1 mediates effector-triggered defense against Pseudomonas strains expressing AvrB or AvrRpm1, but the existing defense response term is broad.
    action: MODIFY
    reason: Defense response to bacterium better captures the experimentally supported RPM1 output than generic defense response.
    proposed_replacement_terms:
    - id: GO:0042742
      label: defense response to bacterium
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: RPM1 activation by AvrB/AvrRpm1-triggered RIN4 modification elicits hypersensitive-response cell death.
    action: ACCEPT
    reason: Hypersensitive response is a canonical output of RPM1-mediated effector-triggered immunity and is supported by AvrB/RPM1 experiments.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: RPM1 is a peripheral protein enriched at the plasma membrane.
    action: ACCEPT
    reason: Plasma membrane localization is central to RPM1 function because RPM1 guards RIN4 at the cytoplasmic face of the plasma membrane.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: RPM1 is a peripheral protein enriched at the plasma membrane.
    action: ACCEPT
    reason: Plasma membrane localization is central to RPM1 function because RPM1 guards RIN4 at the cytoplasmic face of the plasma membrane.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:9861059
  review:
    summary: RPM1 is a peripheral protein enriched at the plasma membrane.
    action: ACCEPT
    reason: Plasma membrane localization is central to RPM1 function because RPM1 guards RIN4 at the cytoplasmic face of the plasma membrane.
- term:
    id: GO:0012505
    label: endomembrane system
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: The cited localization evidence points to plasma-membrane/microsomal association and is better captured by a plasma-membrane cytoplasmic-face term than by broad endomembrane system.
    action: MODIFY
    reason: RPM1 is specifically a peripheral/extrinsic protein at the cytoplasmic side of the plasma membrane; endomembrane system is less precise.
    proposed_replacement_terms:
    - id: GO:0031234
      label: extrinsic component of cytoplasmic side of plasma membrane
- term:
    id: GO:0012505
    label: endomembrane system
  evidence_type: EXP
  original_reference_id: PMID:9861059
  review:
    summary: The cited localization evidence points to plasma-membrane/microsomal association and is better captured by a plasma-membrane cytoplasmic-face term than by broad endomembrane system.
    action: MODIFY
    reason: RPM1 is specifically a peripheral/extrinsic protein at the cytoplasmic side of the plasma membrane; endomembrane system is less precise.
    proposed_replacement_terms:
    - id: GO:0031234
      label: extrinsic component of cytoplasmic side of plasma membrane
- term:
    id: GO:0031234
    label: extrinsic component of cytoplasmic side of plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:9861059
  review:
    summary: RPM1 resides on the cytoplasmic face of the plasma membrane as a peripheral membrane-associated immune receptor.
    action: ACCEPT
    reason: This is the most precise existing localization annotation for the site of RPM1-RIN4 guard signaling.
- term:
    id: GO:0140375
    label: immune receptor activity
  evidence_type: IC
  original_reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
  review:
    summary: RPM1 functions as a CNL immune receptor that monitors effector-induced RIN4 modification.
    action: NEW
    reason: GOA captures defense outputs and nucleotide binding but omits the core molecular role of RPM1 as an immune receptor.
    additional_reference_ids:
    - PMID:7638602
    - PMID:8768370
    supported_by:
    - reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
      supporting_text: RPM1 is a canonical example of **indirect effector recognition**
    - reference_id: PMID:7638602
      supporting_text: The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes.
    - reference_id: PMID:8768370
      supporting_text: both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent necrosis
- term:
    id: GO:0002218
    label: activation of innate immune response
  evidence_type: IC
  original_reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
  review:
    summary: RPM1 activates intracellular effector-triggered immune signaling after effector-induced RIN4 modification.
    action: NEW
    reason: This broader innate-immune activation term avoids incorrectly treating RPM1 guarded effector recognition as PAMP pattern-recognition receptor signaling.
    additional_reference_ids:
    - PMID:7638602
    - PMID:8768370
    supported_by:
    - reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
      supporting_text: mediating effector-triggered immunity (ETI) to *Pseudomonas syringae* effectors **AvrRpm1** and **AvrB**
    - reference_id: PMID:7638602
      supporting_text: The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing either of two unrelated Pseudomonas syringae avr genes.
    - reference_id: PMID:8768370
      supporting_text: both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent necrosis
- term:
    id: GO:0042742
    label: defense response to bacterium
  evidence_type: IC
  original_reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
  review:
    summary: RPM1 confers resistance to Pseudomonas syringae strains expressing AvrB or AvrRpm1.
    action: NEW
    reason: This is the precise antibacterial defense output missing from current RPM1 GOA rows.
    additional_reference_ids:
    - PMID:7638602
    - PMID:8768370
    supported_by:
    - reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
      supporting_text: RPM1 mediates race-specific resistance to *P. syringae* strains delivering **AvrB** or **AvrRpm1**
    - reference_id: PMID:7638602
      supporting_text: The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing
        either of two unrelated Pseudomonas syringae avr genes.
    - reference_id: PMID:8768370
      supporting_text: Both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent
        necrosis.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings:
  - statement: InterPro2GO mapping electronically transfers GO terms (e.g. nucleotide binding, defense response) onto RPM1 from its NB-ARC and LRR InterPro signatures; useful for breadth but not RPM1-specific function.
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings:
  - statement: UniProt SubcellularLocation-to-GO mapping yields plasma membrane localization for RPM1, consistent with peripheral plasma-membrane localization reported experimentally.
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings:
  - statement: ARBA machine-learning rules propagate broad NLR-family annotations to RPM1; treated as supporting context rather than as primary evidence of the RIN4-guard mechanism.
- id: PMID:11955429
  title: RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis.
  findings:
  - statement: RIN4 interacts with AvrB, AvrRpm1, and RPM1 and is required for RPM1-mediated resistance.
- id: PMID:15722472
  title: RIN13 is a positive regulator of the plant disease resistance protein RPM1.
  findings:
  - statement: RIN13 is a positive regulator of RPM1-mediated immunity but does not define RPM1 core molecular activity.
- id: PMID:16212605
  title: A duplicated pair of Arabidopsis RING-finger E3 ligases contribute to the RPM1- and RPS2-mediated hypersensitive response.
  findings:
  - statement: RING-finger E3 ligases contribute to RPM1- and RPS2-mediated hypersensitive response outputs.
- id: PMID:20332379
  title: Endosome-associated CRT1 functions early in resistance gene-mediated defense signaling in Arabidopsis and tobacco.
  findings:
  - statement: CRT1 functions early in resistance-gene-mediated defense signaling and is an RPM1-associated immune regulator.
- id: PMID:38358510
  title: The RIN4-like/NOI proteins NOI10 and NOI11 modulate the response to biotic stresses mediated by RIN4 in Arabidopsis.
  findings:
  - statement: RIN4-like/NOI proteins modulate RIN4-mediated biotic stress responses relevant to RPM1 signaling context.
- id: PMID:7638602
  title: Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance.
  findings:
  - statement: RPM1 encodes an NB-LRR disease-resistance protein enabling dual specificity to Pseudomonas syringae avrRpm1 and avrB.
- id: PMID:8768370
  title: Expression of the Pseudomonas syringae avirulence protein AvrB in plant cells alleviates its dependence on the hypersensitive response and pathogenicity (Hrp) secretion system in eliciting genotype-specific hypersensitive cell death.
  findings:
  - statement: Intracellular AvrB expression triggers RPM1-dependent hypersensitive cell death.
- id: PMID:9861059
  title: The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response.
  findings:
  - statement: RPM1 is a peripheral plasma membrane protein likely residing on the cytoplasmic face of the plasma membrane and degraded coincident with HR.
- id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
  title: Falcon deep research for Arabidopsis RPM1
  findings:
  - statement: RPM1 is a plasma-membrane-associated CNL immune receptor that guards RIN4 and is activated by effector-induced RIN4 modification.
  - statement: RPM1 localization and immune recognition are organized at the cytoplasmic face of the plasma membrane.
- id: file:ARATH/RPM1/RPM1-uniprot.txt
  title: UniProt record for Arabidopsis RPM1
  findings:
  - statement: UniProt identifies RPM1/Q39214 as a disease resistance NB-LRR protein with plasma membrane, ADP/ATP binding, and hypersensitive response annotations.
- id: file:interpro/panther/PTHR23155/PTHR23155-entries.csv
  title: PANTHER PTHR23155 disease resistance protein RP family entries
  findings:
  - statement: PTHR23155 places Arabidopsis Q39214/RPM1 in disease resistance protein RPM1 subfamily SF1205.
core_functions:
- description: Plasma-membrane CNL immune receptor guarding RIN4. RPM1 monitors effector-induced RIN4 modification, especially AvrB/AvrRpm1-associated RIN4 Thr166 phosphorylation, at the cytoplasmic face of the plasma membrane and activates effector-triggered antibacterial defense and hypersensitive response.
  molecular_function:
    id: GO:0140375
    label: immune receptor activity
  directly_involved_in:
  - id: GO:0002218
    label: activation of innate immune response
  - id: GO:0042742
    label: defense response to bacterium
  locations:
  - id: GO:0031234
    label: extrinsic component of cytoplasmic side of plasma membrane
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
    supporting_text: RPM1 is a canonical example of **indirect effector recognition**
  - reference_id: file:ARATH/RPM1/RPM1-deep-research-falcon.md
    supporting_text: RPM1 is a peripheral protein on the cytoplasmic face of the plasma membrane
  - reference_id: PMID:7638602
    supporting_text: The Arabidopsis thaliana RPM1 gene enables dual specificity to pathogens expressing
      either of two unrelated Pseudomonas syringae avr genes.
  - reference_id: PMID:8768370
    supporting_text: Both stable and transient expression of avrB in Arabidopsis resulted in RPM1-dependent
      necrosis.
proposed_new_terms: []
suggested_questions:
- question: Should RPM1 and related CNLs receive immune receptor activity annotations rather than only generic nucleotide/protein binding annotations?
- question: Should broad endomembrane-system annotations for RPM1 be replaced upstream with the cytoplasmic-face plasma membrane term?
suggested_experiments:
- description: Reconstitute RPM1 with RIN4 phosphorylation or ADP-ribosylation states in plasma-membrane fractions to quantify receptor activation and nucleotide exchange.
- description: Measure RPM1 ADP/ATP binding and hydrolysis states before and after RIN4 phosphomimic activation to connect NB-ARC switching with guardee modification sensing.

Gene Description

Existing Annotations Review

Core Functions

Plasma-membrane CNL immune receptor guarding RIN4. RPM1 monitors effector-induced RIN4 modification, especially AvrB/AvrRpm1-associated RIN4 Thr166 phosphorylation, at the cytoplasmic face of the plasma membrane and activates effector-triggered antibacterial defense and hypersensitive response.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research report: Functional annotation of Arabidopsis RPM1 (AT3G07040; UniProt Q39214)

1) Target identity verification (critical)

2) Key concepts and definitions (current understanding)

Plant ETI and the “guard” model

NLRs as nucleotide-dependent molecular switches

3) Primary molecular function of RPM1

3.1 What RPM1 recognizes

3.2 The guarded host protein (RIN4) and the activating “signal”

3.3 Upstream effector biochemistry and host enzymes (how RIN4 is modified)

4) Subcellular localization and where RPM1 acts

4.1 RPM1 is a peripheral plasma membrane protein

4.2 Activation-linked RPM1 protein loss (negative feedback)

5) Signaling pathways downstream and genetic requirements

5.1 NDR1 dependence (CNL branch)

5.2 Shared PTI/ETI outputs

6) Recent developments (prioritizing 2023–2024) relevant to RPM1 functional annotation

6.1 Spatial regulation of the RIN4 T166 phospho-switch (2024)

7) Applications and real-world implementations

8) Expert synthesis and authoritative interpretations

9) Quantitative statistics and recent data from studies

9.1 Population genetics of RPM1 presence/absence polymorphism

Summary artifact

Key figure evidence (images)

Evidence gaps (scope limitation)

Citations

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