identifier: traitmech:000377
label: Rst TIR-NLR system
definition: A phage defense system in which an organism possesses a P4-like TIR-NLR
  locus represented by DefenseFinder as the Rst_TIR-NLR single-profile model and experimentally
  linked to broad virulent-phage and P2-like phage restriction.
definition_source: DOI:10.1016/j.chom.2022.02.018
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: TIR-NLR system
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1016/j.chom.2022.02.018
- synonym_text: Rst_TIR-NLR
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
- synonym_text: Rst_TIR-NLR__TIR
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1016/j.chom.2022.02.018
  snippet: Here, we show that hotspots of genetic diversity within the P2-like phage
    and P4-like satellite families constitute large reservoirs of anti-phage systems.
  notes: Rousset et al. establish that P2-like phage and P4-like satellite hotspots
    are large reservoirs of anti-phage systems.
- reference: DOI:10.1016/j.chom.2022.02.018
  snippet: Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like)
    domain protein.
  notes: Rousset et al. describe one validated P4 hotspot system as a single-gene
    TIR-domain system.
- reference: DOI:10.1016/j.chom.2022.02.018
  snippet: Out of the 18 tested systems, only the TIR-NLR system provided protection
  notes: Rousset et al. report that TIR-NLR was the only P4 system in their tested
    cohort that protected against P2-like phages.
- reference: DOI:10.1016/j.chom.2022.02.018
  snippet: This shows that while the TIR-NLR system protects against a broad range
    of virulent phages, this comes at the cost of limiting the transduction of P4
    by P2.
  notes: Rousset et al. summarize broad virulent-phage protection by the TIR-NLR system
    in the context of P4 transduction costs.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: Rst_TIR-NLR | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots
    of bacterial immune systems
  notes: The DefenseFinder article registry maps the named Rst_TIR-NLR system to the
    Rousset et al. preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "Rst_TIR-NLR\tRst_TIR-NLR\t1\t1\tRst_TIR-NLR__TIR\t\t\t"
  notes: The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system
    requiring the Rst_TIR-NLR__TIR profile.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR__TIR                                 |
    Rst_TIR-NLR            | Custom                  | 70     |'
  notes: The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR
    system namespace.
causal_graphs:
- graph_id: rst_tir_nlr_locus_restricts_phages
  title: Rst TIR-NLR loci restrict virulent and P2-like phages
  description: Conservative system-level sketch linking a P4-like Rst TIR-NLR locus
    to phage restriction.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures Rst_TIR-NLR as a named DefenseFinder single-profile
    phage-defense system while leaving source locus breadth, the phage trigger, TIR/STAND
    activation, and exact Rst_TIR-NLR__TIR profile-to-gene correspondence unresolved.
  nodes:
  - node_id: rst_tir_nlr_locus
    label: Rst TIR-NLR locus
    node_type: GENETIC_ELEMENT
    description: A P4-like TIR-NLR phage-defense locus represented by the Rst_TIR-NLR
      DefenseFinder profile.
  - node_id: virulent_and_p2_like_phage_restriction
    label: virulent and P2-like phage restriction
    node_type: BIOLOGICAL_PROCESS
    description: Restriction of broad virulent phages and P2-like phages by the TIR-NLR
      locus.
  - node_id: rst_tir_nlr_system_trait
    label: Rst TIR-NLR system
    node_type: TRAIT
    grounding: traitmech:000377
    description: Possession of a genome-encoded TIR-NLR phage-defense system.
  - node_id: phage_defense_system
    label: phage defense system
    node_type: TRAIT
    grounding: traitmech:000209
    description: Possession of one or more genome-encoded immune systems that inhibit
      bacteriophage infection.
  edges:
  - subject: rst_tir_nlr_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: virulent_and_p2_like_phage_restriction
    description: Rousset et al. linked the TIR-NLR system to virulent and P2-like
      phage protection, and DefenseFinder models Rst_TIR-NLR as a single-profile system.
    evidence:
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like)
        domain protein.
      notes: Rousset et al. describe one validated P4 hotspot system as a single-gene
        TIR-domain system.
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: Out of the 18 tested systems, only the TIR-NLR system provided protection
      notes: Rousset et al. report that TIR-NLR was the only P4 system in their tested
        cohort that protected against P2-like phages.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "Rst_TIR-NLR\tRst_TIR-NLR\t1\t1\tRst_TIR-NLR__TIR\t\t\t"
      notes: The DefenseFinder rules table models Rst_TIR-NLR as a single-profile
        system requiring the Rst_TIR-NLR__TIR profile.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR__TIR                                 |
        Rst_TIR-NLR            | Custom                  | 70     |'
      notes: The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR
        system namespace.
  - subject: virulent_and_p2_like_phage_restriction
    predicate: confers
    predicate_id: METPO:2007700
    object: rst_tir_nlr_system_trait
    description: Restriction of virulent and P2-like phages realizes the Rst TIR-NLR
      system trait.
    evidence:
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: This shows that while the TIR-NLR system protects against a broad range
        of virulent phages, this comes at the cost of limiting the transduction of
        P4 by P2.
      notes: Rousset et al. summarize broad virulent-phage protection by the TIR-NLR
        system in the context of P4 transduction costs.
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: Out of the 18 tested systems, only the TIR-NLR system provided protection
      notes: Rousset et al. report that TIR-NLR was the only P4 system in their tested
        cohort that protected against P2-like phages.
  - subject: rst_tir_nlr_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Rst TIR-NLR system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: Here, we show that hotspots of genetic diversity within the P2-like
        phage and P4-like satellite families constitute large reservoirs of anti-phage
        systems.
      notes: Rousset et al. establish that P2-like phage and P4-like satellite hotspots
        are large reservoirs of anti-phage systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Rst_TIR-NLR | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots
        of bacterial immune systems
      notes: The DefenseFinder article registry maps the named Rst_TIR-NLR system
        to the Rousset et al. preprint.
discussions:
- discussion_id: rst-tir-nlr-mechanism-gap
  prompt: Resolve Rst_TIR-NLR natural host breadth, exact profile-to-gene correspondence,
    direct phage trigger, and TIR/STAND activation before minting narrower Rst TIR-NLR
    mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Rousset et al. support a P4-like TIR-NLR system that protects against
    virulent and P2-like phages, and DefenseFinder represents Rst_TIR-NLR as a single-profile
    model. This first system-level record leaves natural host breadth, profile-to-gene
    mapping, the direct phage trigger, and TIR/STAND effector logic unresolved.
  evidence:
  - reference: DOI:10.1016/j.chom.2022.02.018
    snippet: Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like)
      domain protein.
    notes: Rousset et al. describe one validated P4 hotspot system as a single-gene
      TIR-domain system.
  - reference: DOI:10.1016/j.chom.2022.02.018
    snippet: Out of the 18 tested systems, only the TIR-NLR system provided protection
    notes: Rousset et al. report that TIR-NLR was the only P4 system in their tested
      cohort that protected against P2-like phages.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "Rst_TIR-NLR\tRst_TIR-NLR\t1\t1\tRst_TIR-NLR__TIR\t\t\t"
    notes: The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system
      requiring the Rst_TIR-NLR__TIR profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR__TIR                                 |
      Rst_TIR-NLR            | Custom                  | 70     |'
    notes: The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR
      system namespace.
  attaches_to:
  - causal_graphs#rst_tir_nlr_locus_restricts_phages
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T09:17:05Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted Rst TIR-NLR system as a DOI-backed GENOMICS TraitRecord under phage
    defense system after an ignored-and-hidden duplicate review found no exact live
    TraitMech, METPO, history, or prior proposal record; the replacement placeholder
    is reserved in proposals/metpo_traitmech_v254.
  llm_assisted: true
- timestamp: '2026-09-26T09:17:06Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed Rst TIR-NLR system during canonical-example issue 444 enforcement
    and left canonical_examples empty because the sources support cloned P4-like TIR-NLR
    system assays and a DefenseFinder system model, but not a direct native microbial
    isolate exemplar with experimentally verified Rst_TIR-NLR activity. No paid research
    was used.
  llm_assisted: true