identifier: traitmech:000339 label: AbiJ system definition: An abortive infection system in which an organism possesses an AbiJ-family locus represented by the DefenseFinder AbiJ model namespace and mandatory AbiJ__AbiJ profile. definition_source: DOI:10.1111/j.1574-6968.1997.tb10185.x trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiJ synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: AbiJ__AbiJ synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: abi-859 synonym_type: RELATED_SYNONYM source: DOI:10.1093/femsre/fuag009 evidence: - reference: DOI:10.1111/j.1574-6968.1997.tb10185.x snippet: A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis notes: Europe PMC metadata verifies the Deng et al. 1997 AbiJ primary paper title and PMID:8997719; the DOI landing page was Cloudflare-blocked and Europe PMC exposed no abstract or full text, so this record cites Deng et al. for the primary AbiJ identity and uses later accessible sources for snippet-backed system details. - reference: DOI:10.1093/femsre/fuag009 snippet: Experimentally confirmed lactococcal Abi-like systems, as well as information on their antiphage activity range notes: The FEMS review frames Table 1 as a curated set of experimentally confirmed lactococcal Abi-like systems. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiJ (Also abi-859) notes: The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems. - reference: DOI:10.1073/pnas.2426508122 snippet: we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP) notes: Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiA escape mutants also circumvent AbiJ, which was not observed for other combinations notes: The FEMS review summarizes Mosterd et al.'s escape-mutant evidence linking AbiA escape mutations to AbiJ bypass while not yet identifying AbiJ's direct molecular trigger. - reference: DOI:10.1093/femsre/fuag009 snippet: Although no particular mechanistic information is currently available for AbiJ notes: The FEMS review explicitly keeps AbiJ mechanism unresolved; this record therefore avoids protein-level chemistry and TA-system mechanism claims. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiJ | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiJ model namespace to the Chopin et al. lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiJ\tAbiJ\t1\t1\tAbiJ__AbiJ\t\t\t" notes: The DefenseFinder rules table models AbiJ as a one-component system requiring the AbiJ__AbiJ profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiJ__AbiJ | AbiJ__AbiJ | AbiJ | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiJ__AbiJ under the AbiJ model namespace. causal_graphs: - graph_id: abij_locus_restricts_lactococcal_phage title: AbiJ loci confer abortive-infection phage defense description: Conservative system-level sketch linking possession of a DefenseFinder AbiJ locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, molecular activity, or arrest route. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiJ as a named single-profile lactococcal abortive-infection system with a DefenseFinder AbiJ__AbiJ HMM profile while leaving its direct phage trigger, AbiJ molecular function, exact relationship to AbiA escape routes, natural locus breadth, and cell-arrest or death route unresolved. nodes: - node_id: abij_locus label: AbiJ locus node_type: GENETIC_ELEMENT description: An AbiJ-family abortive-infection locus represented by the DefenseFinder AbiJ__AbiJ profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage propagation in cells carrying an AbiJ-family abortive-infection system. - node_id: abij_system_trait label: AbiJ system node_type: TRAIT grounding: traitmech:000339 description: Possession of a genome-encoded AbiJ abortive-infection phage-defense system. - node_id: abortive_infection_system_trait label: abortive infection system node_type: TRAIT grounding: traitmech:000214 description: Possession of a genome-encoded abortive-infection phage-defense system. edges: - subject: abij_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The DefenseFinder AbiJ namespace is modeled as a one-profile AbiJ__AbiJ system, and AbiJ is a plasmid-encoded lactococcal phage-resistance system. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiJ\tAbiJ\t1\t1\tAbiJ__AbiJ\t\t\t" notes: The DefenseFinder rules table models AbiJ as a one-component system requiring the AbiJ__AbiJ profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiJ__AbiJ | AbiJ__AbiJ | AbiJ | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiJ__AbiJ under the AbiJ model namespace. - reference: DOI:10.1073/pnas.2426508122 snippet: we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP) notes: Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abij_system_trait description: Restriction of phage propagation realizes the AbiJ abortive-infection system possession trait. evidence: - reference: DOI:10.1093/femsre/fuag009 snippet: AbiJ (Also abi-859) notes: The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems. - reference: DOI:10.1073/pnas.2426508122 snippet: we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP) notes: Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation. - subject: abij_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiJ system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1093/femsre/fuag009 snippet: AbiJ (Also abi-859) notes: The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiJ | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiJ model namespace to the Chopin et al. lactococcal abortive-infection review. discussions: - discussion_id: abij-trigger-and-effector-gap prompt: Resolve the AbiJ phage trigger, molecular activity, and exact AbiA escape-mutant overlap before minting narrower AbiJ mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Deng et al. support AbiJ as a lactococcal plasmid-encoded abortive-infection system, and DefenseFinder represents AbiJ with a one-profile rule. Mosterd et al. show that AbiJ escape behavior overlaps with AbiA escape mutants, but the FEMS review notes that AbiJ still lacks a resolved mechanism. This first system-level record therefore leaves AbiJ's direct phage trigger, molecular effector activity, natural locus breadth, exact HEPN-domain interpretation, growth-arrest or cell-death route, and phage escape routes unresolved. evidence: - reference: DOI:10.1093/femsre/fuag009 snippet: While AbiB and AbiJ show only weak predictions (HHpred hits for HEPN domain containing-proteins with E-values > 0.1) or lack identifiable functional domains based on InterPro and HHpred notes: The FEMS review notes that AbiJ HEPN-domain evidence remains weak in sequence/domain-prediction analyses. - reference: DOI:10.1093/femsre/fuag009 snippet: Although no particular mechanistic information is currently available for AbiJ notes: The FEMS review leaves AbiJ's mechanism unresolved. attaches_to: - causal_graphs#abij_locus_restricts_lactococcal_phage posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T16:24:09Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiJ system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent 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_v216. llm_assisted: true - timestamp: '2026-09-21T16:48:47Z' curator: codex action: FIX_EVIDENCE_SNIPPET changes: Replaced the AbiJ subclass-edge FEMS table-heading evidence with the AbiJ-specific table row after PR 1208 review issue 1209 found that the original snippet did not itself mention AbiJ. llm_assisted: true