Rst TIR-NLR system

traitmech:000377 · CLASS · PROPOSED

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.

Trait evidence (7)

DOI:10.1016/j.chom.2022.02.018
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.

Rousset et al. establish that P2-like phage and P4-like satellite hotspots are large reservoirs of anti-phage systems.
DOI:10.1016/j.chom.2022.02.018
Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like) domain protein.

Rousset et al. describe one validated P4 hotspot system as a single-gene TIR-domain system.
DOI:10.1016/j.chom.2022.02.018
Out of the 18 tested systems, only the TIR-NLR system provided protection

Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages.
DOI:10.1016/j.chom.2022.02.018
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.

Rousset et al. summarize broad virulent-phage protection by the TIR-NLR system in the context of P4 transduction costs.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Rst_TIR-NLR | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems

The DefenseFinder article registry maps the named Rst_TIR-NLR system to the Rousset et al. preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Rst_TIR-NLR Rst_TIR-NLR 1 1 Rst_TIR-NLR__TIR

The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system requiring the Rst_TIR-NLR__TIR profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Rst_TIR-NLR__TIR | Rst_TIR-NLR__TIR | Rst_TIR-NLR | Custom | 70 |

The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR system namespace.

Rst TIR-NLR loci restrict virulent and P2-like phages

Conservative system-level sketch linking a P4-like Rst TIR-NLR locus to phage restriction.

NONMECHANISTIC · 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.

Edge evidence

Rst TIR-NLR locus contributes to virulent and P2-like phage restriction RO:0002326
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.
- DOI:10.1016/j.chom.2022.02.018 Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like) domain protein. Rousset et al. describe one validated P4 hotspot system as a single-gene TIR-domain system.
- DOI:10.1016/j.chom.2022.02.018 Out of the 18 tested systems, only the TIR-NLR system provided protection Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Rst_TIR-NLR Rst_TIR-NLR 1 1 Rst_TIR-NLR__TIR The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system requiring the Rst_TIR-NLR__TIR profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Rst_TIR-NLR__TIR | Rst_TIR-NLR__TIR | Rst_TIR-NLR | Custom | 70 | The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR system namespace.
virulent and P2-like phage restriction confers Rst TIR-NLR system METPO:2007700
Restriction of virulent and P2-like phages realizes the Rst TIR-NLR system trait.
- DOI:10.1016/j.chom.2022.02.018 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. Rousset et al. summarize broad virulent-phage protection by the TIR-NLR system in the context of P4 transduction costs.
- DOI:10.1016/j.chom.2022.02.018 Out of the 18 tested systems, only the TIR-NLR system provided protection Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages.
Rst TIR-NLR system is a phage defense system rdfs:subClassOf
Rst TIR-NLR system possession is a phage-defense-system trait.
- DOI:10.1016/j.chom.2022.02.018 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. Rousset et al. establish that P2-like phage and P4-like satellite hotspots are large reservoirs of anti-phage systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Rst_TIR-NLR | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems The DefenseFinder article registry maps the named Rst_TIR-NLR system to the Rousset et al. preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.chom.2022.02.018

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

TIR-NLR system RELATED_SYNONYM · DOI:10.1016/j.chom.2022.02.018
Rst_TIR-NLR RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Rst_TIR-NLR__TIR RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN rst-tir-nlr-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#rst_tir_nlr_locus_restricts_phages

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

DOI:10.1016/j.chom.2022.02.018
Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like) domain protein.
DOI:10.1016/j.chom.2022.02.018
Out of the 18 tested systems, only the TIR-NLR system provided protection
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Rst_TIR-NLR Rst_TIR-NLR 1 1 Rst_TIR-NLR__TIR
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Rst_TIR-NLR__TIR | Rst_TIR-NLR__TIR | Rst_TIR-NLR | Custom | 70 |

Curation history

2026-09-26T09:17:05Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-26T09:17:06Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.