identifier: traitmech:000317 label: AbiR system definition: An abortive infection system in which an organism possesses a multicomponent AbiR determinant represented by the DefenseFinder AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles and capable of restricting lactococcal phage propagation by an early abortive-infection mechanism that impedes phage DNA replication, as exemplified by the two pKR223 loci from Lactococcus lactis subsp. lactis KR2 separated by the LlaKR2I restriction-modification genes. definition_source: DOI:10.1128/AEM.66.6.2647-2651.2000 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiR synonym_type: RELATED_SYNONYM source: DOI:10.1128/AEM.66.6.2647-2651.2000 evidence: - reference: PMID:10831451 snippet: The native lactococcal plasmid pKR223 encodes two distinct phage resistance mechanisms, a restriction and modification (R/M) system designated LlaKR2I and an abortive infection mechanism (Abi) which affects prolate-headed-phage proliferation notes: Twomey et al. identify native Lactococcus lactis plasmid pKR223 as the source of a restriction-modification system and a separate abortive-infection determinant. - reference: PMID:10831451 snippet: sequence analysis has validated the novelty of the Abi system, which has now been designated AbiR notes: Twomey et al. name AbiR as the novel abortive-infection system from pKR223. - reference: PMID:10831451 snippet: Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes notes: Twomey et al. show that the AbiR phenotype requires two pKR223 loci separated by the LlaKR2I restriction-modification genes. - reference: PMID:10831451 snippet: Mechanistic studies on the AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication notes: Twomey et al. connect AbiR activity to a heat-sensitive abortive-infection phenotype that impedes phage DNA replication. - reference: PMID:10831451 snippet: These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning Abi system notes: Twomey et al. classify AbiR as a multicomponent early abortive-infection system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiR | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiR model namespace to a lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiR\tAbiR\t3\t3\tAbiR__AbiRa, AbiR__AbiRb, AbiR__AbiRc" notes: The DefenseFinder rules table models AbiR as a three-component system requiring the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiR__AbiRa | AbiR__AbiRa | AbiR | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiR__AbiRa under the AbiR model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiR__AbiRb | AbiR__AbiRb | AbiR | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiR__AbiRb under the AbiR model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiR__AbiRc | AbiR__AbiRc | AbiR | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiR__AbiRc under the AbiR model namespace. canonical_examples: - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: Twomey et al. characterized AbiR from native plasmid pKR223 of Lactococcus lactis subsp. lactis KR2 and showed a multicomponent, two-locus Abi phenotype that impeded phage DNA replication. reference: DOI:10.1128/AEM.66.6.2647-2651.2000 causal_graphs: - graph_id: abir_loci_impede_phage_dna_replication title: AbiR activity impedes lactococcal phage DNA replication description: Conservative system-level sketch linking the separated pKR223 AbiR loci to AbiR antiphage activity, impeded phage DNA replication, restricted lactococcal phage propagation, and abortive-infection system possession without resolving the phage trigger or individual component activities. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiR as a named DefenseFinder three-profile abortive-infection system whose pKR223 prototype is encoded by two genetic loci and impedes phage DNA replication. It leaves the direct phage trigger, the profile-to-locus mapping, AbiRa, AbiRb, and AbiRc molecular functions, the reason the R/M genes interrupt the two AbiR loci, and phage escape routes unresolved. nodes: - node_id: abir_loci label: AbiR loci node_type: GENETIC_ELEMENT description: A multicomponent abortive-infection determinant encoded by two separated pKR223 loci and represented by the DefenseFinder AbiR rule. - node_id: abir_antiphage_activity label: AbiR antiphage activity node_type: BIOLOGICAL_PROCESS description: Abortive-infection phage resistance mediated by the AbiR system. - node_id: phage_dna_replication label: phage DNA replication node_type: BIOLOGICAL_PROCESS description: Replication of lactococcal bacteriophage DNA during sensitive-host infection. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced completion of lactococcal phage propagation in an AbiR-containing infected host cell. - node_id: abir_system_trait label: AbiR system node_type: TRAIT grounding: traitmech:000317 description: Possession of a genome-encoded AbiR 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: abir_loci predicate: contributes to predicate_id: RO:0002326 object: abir_antiphage_activity description: The pKR223 AbiR determinant is encoded by two genetic loci separated by LlaKR2I genes, and DefenseFinder models AbiR as a three-profile system requiring AbiRa, AbiRb, and AbiRc components. evidence: - reference: PMID:10831451 snippet: Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes notes: Twomey et al. show that the AbiR phenotype requires two separated pKR223 genetic loci. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiR\tAbiR\t3\t3\tAbiR__AbiRa, AbiR__AbiRb, AbiR__AbiRc" notes: The DefenseFinder rules table models AbiR as a three-component system requiring the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiR__AbiRa | AbiR__AbiRa | AbiR | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiR__AbiRa under the AbiR model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiR__AbiRb | AbiR__AbiRb | AbiR | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiR__AbiRb under the AbiR model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiR__AbiRc | AbiR__AbiRc | AbiR | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiR__AbiRc under the AbiR model namespace. - subject: abir_antiphage_activity predicate: mitigates predicate_id: METPO:2007407 object: phage_dna_replication description: AbiR antiphage activity impedes sensitive phage DNA replication as an early abortive-infection output. evidence: - reference: PMID:10831451 snippet: Mechanistic studies on the AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication notes: Twomey et al. classify the AbiR phenotype as heat-sensitive and DNA-replication impeding. - subject: abir_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: AbiR antiphage activity affects prolate-headed-phage proliferation through a multicomponent early Abi mechanism. evidence: - reference: PMID:10831451 snippet: These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning Abi system notes: Twomey et al. summarize the AbiR phenotype as multicomponent, heat-sensitive, and early functioning. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abir_system_trait description: Restriction of lactococcal phage propagation realizes the AbiR abortive-infection trait. evidence: - reference: PMID:10831451 snippet: sequence analysis has validated the novelty of the Abi system, which has now been designated AbiR notes: Twomey et al. name AbiR as the novel pKR223 abortive-infection system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiR | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiR model namespace to a lactococcal abortive-infection review. - subject: abir_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiR system possession is an abortive-infection-system trait. evidence: - reference: PMID:10831451 snippet: These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning Abi system notes: Twomey et al. classify AbiR in the abortive-infection class of phage defense. discussions: - discussion_id: abir-component-activity-gap prompt: Resolve the AbiR phage trigger, profile-to-locus mapping, and AbiRa, AbiRb, and AbiRc molecular functions before minting narrower AbiR mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Twomey et al. support AbiR as a multicomponent abortive-infection system encoded by two separated pKR223 loci, and DefenseFinder represents AbiR with a three-profile rule. This first system-level record leaves the phage trigger, the mapping from the two original genetic loci to AbiRa, AbiRb, and AbiRc profiles, the component molecular activities, and the direct reason that AbiR impedes phage DNA replication unresolved. evidence: - reference: PMID:10831451 snippet: Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes notes: Twomey et al. localize AbiR to two separated pKR223 loci rather than to the three-component DefenseFinder profile scheme. attaches_to: - causal_graphs#abir_loci_impede_phage_dna_replication posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T19:30:10Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiR 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_v194. llm_assisted: true - timestamp: '2026-09-20T20:02:22Z' curator: codex action: REVISED_SCOPE changes: Addressed PR 1154 review issue 1155 by narrowing the AbiR definition to the DefenseFinder AbiR determinant and treating the two separated pKR223 loci from Lactococcus lactis subsp. lactis KR2 as exemplar evidence rather than a constitutive class restriction. llm_assisted: true