identifier: traitmech:000416 label: lanthivirin system definition: A phage defense system in which an organism possesses a lanthivirin lanthipeptide biosynthetic gene cluster that can confer anti-phage activity in a native Streptomyces context and after heterologous expression of complete lanthivirin systems. definition_source: DOI:10.1016/j.chom.2026.06.017 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: lanthivirin BGC synonym_type: RELATED_SYNONYM source: DOI:10.1016/j.chom.2026.06.017 - synonym_text: Lanthiphage synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1016/j.chom.2026.06.017 snippet: We demonstrate anti-phage activity both in a native Streptomyces context and through heterologous expression of six distinct lanthivirin systems. notes: Serra et al. support native Streptomyces anti-phage activity and activity from multiple heterologously expressed lanthivirin systems. - reference: DOI:10.1016/j.chom.2026.06.017 snippet: lanthivirin maturation is required for anti-phage activity notes: Serra et al. support the requirement for lanthivirin maturation in anti-phage activity. - reference: DOI:10.1016/j.chom.2026.06.017 snippet: phage-protein-dependent inhibition of phage DNA replication notes: Serra et al. link lanthivirins to inhibition of phage DNA replication. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Lanthiphage | 10\.1101/2024\.06\.26\.600839 | A family of lanthipeptides with anti-phage function |' notes: The pinned DefenseFinder article registry maps the Lanthiphage source key to the lanthipeptide anti-phage preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lanthiphage__LphA |' notes: The pinned DefenseFinder HMM inventory records Lanthiphage__LphA as a custom Lanthiphage profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lanthiphage__LphB1 |' notes: The pinned DefenseFinder HMM inventory records Lanthiphage__LphB1 as a custom Lanthiphage profile. causal_graphs: - graph_id: lanthivirin_bgc_inhibits_phage_dna_replication title: Lanthivirin BGCs mediate anti-phage activity description: Conservative system-level sketch linking possession of a lanthivirin biosynthetic gene cluster to anti-phage activity and lanthivirin system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures lanthivirins at the biosynthetic gene cluster and anti-phage-output level without asserting the full native host range, exact Lanthiphage profile-to-component model, complete phage target breadth, or a DefenseFinder detection rule absent from the pinned rules table. nodes: - node_id: lanthivirin_bgc label: lanthivirin biosynthetic gene cluster node_type: GENETIC_ELEMENT description: A lanthivirin biosynthetic gene cluster represented in the pinned DefenseFinder HMM inventory by Lanthiphage custom profiles. - node_id: lanthivirin_maturation label: lanthivirin maturation node_type: BIOLOGICAL_PROCESS description: Maturation of a lanthivirin lanthipeptide by its biosynthetic gene cluster. - node_id: phage_dna_replication label: phage DNA replication node_type: BIOLOGICAL_PROCESS description: Replication of infecting bacteriophage DNA. - node_id: lanthivirin_system_trait label: lanthivirin system node_type: TRAIT grounding: traitmech:000416 description: Possession of a genome-encoded lanthivirin anti-phage 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: lanthivirin_bgc predicate: enables predicate_id: RO:0002327 object: lanthivirin_maturation description: A lanthivirin biosynthetic gene cluster encodes the machinery required for lanthivirin maturation. evidence: - reference: DOI:10.1016/j.chom.2026.06.017 snippet: lanthivirin maturation is required for anti-phage activity notes: Serra et al. support the requirement for lanthivirin maturation in anti-phage activity. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lanthiphage__LphA |' notes: The pinned DefenseFinder HMM inventory records Lanthiphage__LphA as a custom Lanthiphage profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lanthiphage__LphB1 |' notes: The pinned DefenseFinder HMM inventory records Lanthiphage__LphB1 as a custom Lanthiphage profile. - subject: lanthivirin_maturation predicate: mitigates predicate_id: METPO:2007407 object: phage_dna_replication description: Mature lanthivirins are associated with a phage-protein-dependent inhibition of phage DNA replication. evidence: - reference: DOI:10.1016/j.chom.2026.06.017 snippet: phage-protein-dependent inhibition of phage DNA replication notes: Serra et al. link lanthivirins to inhibition of phage DNA replication. - subject: lanthivirin_maturation predicate: confers predicate_id: METPO:2007700 object: lanthivirin_system_trait description: Lanthivirin maturation realizes the anti-phage activity of the lanthivirin system. evidence: - reference: DOI:10.1016/j.chom.2026.06.017 snippet: We demonstrate anti-phage activity both in a native Streptomyces context and through heterologous expression of six distinct lanthivirin systems. notes: Serra et al. support native Streptomyces anti-phage activity and activity from multiple heterologously expressed lanthivirin systems. - subject: lanthivirin_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Lanthivirin system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Lanthiphage | 10\.1101/2024\.06\.26\.600839 | A family of lanthipeptides with anti-phage function |' notes: The pinned DefenseFinder article registry maps the Lanthiphage source key to the lanthipeptide anti-phage preprint. discussions: - discussion_id: lanthivirin-defensefinder-model-gap prompt: Resolve Lanthiphage HMM-to-component coverage, rule-level detection criteria, sensitive-phage breadth, and exact lanthivirin effector identity before minting narrower lanthivirin mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Serra et al. support lanthivirin biosynthetic gene clusters as anti-phage systems, and the pinned DefenseFinder HMM inventory records Lanthiphage profile rows. The pinned rules table has no Lanthiphage row, and the first-pass record does not yet resolve exact profile-to-component mapping, full native host breadth, phage target breadth, or the direct mature lanthivirin effector. evidence: - reference: DOI:10.1016/j.chom.2026.06.017 snippet: We demonstrate anti-phage activity both in a native Streptomyces context and through heterologous expression of six distinct lanthivirin systems. notes: Serra et al. support native Streptomyces anti-phage activity and activity from multiple heterologously expressed lanthivirin systems. - reference: DOI:10.1016/j.chom.2026.06.017 snippet: lanthivirin maturation is required for anti-phage activity notes: Serra et al. support the requirement for lanthivirin maturation in anti-phage activity. - reference: DOI:10.1016/j.chom.2026.06.017 snippet: phage-protein-dependent inhibition of phage DNA replication notes: Serra et al. link lanthivirins to inhibition of phage DNA replication. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Lanthiphage | 10\.1101/2024\.06\.26\.600839 | A family of lanthipeptides with anti-phage function |' notes: The pinned DefenseFinder article registry maps the Lanthiphage source key to the lanthipeptide anti-phage preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lanthiphage__LphA |' notes: The pinned DefenseFinder HMM inventory records Lanthiphage__LphA as a custom Lanthiphage profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lanthiphage__LphB1 |' notes: The pinned DefenseFinder HMM inventory records Lanthiphage__LphB1 as a custom Lanthiphage profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list Lanthiphage, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#lanthivirin_bgc_inhibits_phage_dna_replication posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T20:02:44Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted lanthivirin 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; kept the graph at lanthipeptide biosynthetic-gene-cluster level because the pinned DefenseFinder HMM rows are not backed by pinned rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v293. llm_assisted: true - timestamp: '2026-09-27T20:02:45Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed lanthivirin system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support Streptomyces-context and heterologous expression assays, plus DefenseFinder Lanthiphage HMM rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous lanthivirin activity. No paid research was used. llm_assisted: true