TIR-III system

traitmech:000481 · CLASS · PROPOSED

A phage defense system in which an organism possesses a TIR-III locus, represented in the pinned DefenseFinder HMM inventory by TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles, that can inhibit bacteriophage plaquing.

Trait evidence (5)

DOI:10.1038/s41467-024-51738-3
Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX

Wang et al. report that TIR-III belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets.
DOI:10.1038/s41467-024-51738-3
The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control

Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plating reduction against a phage panel.
DOI:10.1038/s41467-024-51738-3
TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form

Wang et al. found that TIR-I, TIR-III, and TIR-IV systems occur in diverse domain contexts, while TIR-VII and TIR-VIII systems were recovered in a single form.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| TIR-III | 10\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |

The pinned DefenseFinder article registry maps the named TIR-III system to the Wang et al. TIR-domain anti-phage system paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| TIR-III__TIR-III_A | | TIR-III | Custom | 100 | | TIR-III__TIR-III_B | | TIR-III | Custom | 300 |

The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles under the TIR-III system namespace.

TIR-III loci inhibit bacteriophage plaquing

Conservative system-level sketch linking a TIR-III locus to inhibited bacteriophage plaquing and TIR-III system possession.

NONMECHANISTIC · The graph captures TIR-III at TIR-system and anti-phage assay level without asserting exact native-host breadth, one universal domain architecture, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table.

Edge evidence

TIR-III locus contributes to inhibited bacteriophage plaquing RO:0002326
Wang et al. linked TIR-III to anti-phage activity, and DefenseFinder records two custom TIR-III system profiles.
- DOI:10.1038/s41467-024-51738-3 Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX Wang et al. report that TIR-III belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | TIR-III__TIR-III_A | | TIR-III | Custom | 100 | | TIR-III__TIR-III_B | | TIR-III | Custom | 300 | The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles under the TIR-III system namespace.
inhibited bacteriophage plaquing confers TIR-III system METPO:2007700
TIR-III-mediated inhibition of bacteriophage plaquing realizes the TIR-III system trait.
- DOI:10.1038/s41467-024-51738-3 The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control.
TIR-III system is a phage defense system rdfs:subClassOf
TIR-III system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | TIR-III | 10\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages | The pinned DefenseFinder article registry maps the named TIR-III system to the Wang et al. TIR-domain anti-phage system paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41467-024-51738-3

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

TIR-III EXACT_SYNONYM · DOI:10.1038/s41467-024-51738-3
TIR-III__TIR-III_A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
TIR-III__TIR-III_B 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 TIR-III native host breadth, the TIR-III__TIR-III_A and TIR-III__TIR-III_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-III mechanism children.

KNOWLEDGE GAP OPEN tir-iii-detection-trigger-gap · raised by codex · 2026-09-30

Attached to causal_graphs#tir_iii_locus_inhibits_phage_plaquing

Wang et al. support TIR-III as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-III occurs in diverse domain contexts. The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-III row. This first record therefore does not assert profile requirement logic, accession-level components, a universal domain architecture, or a direct phage trigger.

Evidence

DOI:10.1038/s41467-024-51738-3
Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX
DOI:10.1038/s41467-024-51738-3
TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| TIR-III__TIR-III_A | | TIR-III | Custom | 100 | | TIR-III__TIR-III_B | | TIR-III | Custom | 300 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-30T03:32:00Z · MINTED_TRAITMECH_ID · codex
Minted TIR-III system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-III direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v358.
2026-09-30T03:32:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed TIR-III system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-III HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-III activity. No paid research was used.