identifier: traitmech:000319 label: AbiB system definition: An abortive infection system in which an organism possesses an abiB-family locus represented by the DefenseFinder AbiB__AbiB profile and exemplified by the Lactococcus lactis IL1403 determinant whose AbiB activity blocks sensitive bIL170 phage growth and promotes rapid degradation of sensitive phage transcripts after infection. definition_source: DOI:10.1046/j.1365-2958.1996.371896.x trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiB synonym_type: RELATED_SYNONYM source: DOI:10.1046/j.1365-2958.1996.371896.x evidence: - reference: PMID:8825768 snippet: The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170, but not of the resistant phage bIL41, on Lactococcus lactis strain IL1403 notes: Parreira et al. place AbiB in the abortive-infection class and show that it blocks the sensitive lactococcal phage bIL170 on Lactococcus lactis IL1403. - reference: PMID:8825768 snippet: AbiB promotes a dramatic degradation of sensitive phage transcripts, starting 10-15 min after infection notes: Parreira et al. connect AbiB activity to rapid decay of transcripts from sensitive phages after infection. - reference: PMID:8825768 snippet: The decay of the transcripts is the probable cause of the arrest of the sensitive phage development notes: Parreira et al. infer that phage transcript decay causes arrest of AbiB-sensitive phage development. - reference: PMID:8825768 snippet: Mapping of the 5' end of degradation products established that they result from endonucleolytic cleavage preferentially at U/U, A/U and U/A sites notes: Parreira et al. map AbiB-associated phage transcript decay products to preferential endonucleolytic cleavage sites. - reference: PMID:8825768 snippet: an early product of the sensitive phage either induces the synthesis or stimulates the activity of an RNase in an AbiB+ cell notes: Parreira et al. leave the AbiB trigger and nuclease identity unresolved, favoring an open knowledge gap for narrower mechanism children. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiB | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiB model namespace to a lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiB\tAbiB\t1\t1\tAbiB__AbiB" notes: The DefenseFinder rules table models AbiB as a one-component system requiring the AbiB__AbiB profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiB__AbiB | AbiB__AbiB | AbiB | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiB__AbiB under the AbiB model namespace. canonical_examples: - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: Parreira et al. studied AbiB in Lactococcus lactis IL1403 and showed that it prevented sensitive bIL170 phage growth while promoting sensitive phage transcript decay. reference: DOI:10.1046/j.1365-2958.1996.371896.x causal_graphs: - graph_id: abib_locus_degrades_sensitive_phage_transcripts title: AbiB activity degrades sensitive lactococcal phage transcripts description: Conservative system-level sketch linking an abiB-family locus to AbiB antiphage activity, sensitive-phage transcript degradation, sensitive-phage arrest, and abortive-infection system possession without asserting the unresolved phage trigger or nuclease effector. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiB as a named DefenseFinder single-profile abortive-infection system whose IL1403 prototype restricts bIL170 phage by promoting rapid sensitive-phage transcript degradation. It leaves the direct phage trigger, AbiB molecular function, RNase effector identity, natural locus breadth, and phage escape routes unresolved. nodes: - node_id: abib_locus label: abiB locus node_type: GENETIC_ELEMENT description: An abiB-family abortive-infection locus represented by the DefenseFinder AbiB__AbiB profile. - node_id: abib_antiphage_activity label: AbiB antiphage activity node_type: BIOLOGICAL_PROCESS description: Abortive-infection phage resistance mediated by the AbiB system. - node_id: sensitive_phage_transcript_degradation label: sensitive phage transcript degradation node_type: BIOLOGICAL_PROCESS description: Rapid decay of sensitive lactococcal phage transcripts in an AbiB-containing infected host. - node_id: sensitive_phage_development_arrest label: sensitive phage development arrest node_type: BIOLOGICAL_PROCESS description: Failure of AbiB-sensitive bIL170 phages to complete productive growth on Lactococcus lactis IL1403. - node_id: abib_system_trait label: AbiB system node_type: TRAIT grounding: traitmech:000319 description: Possession of a genome-encoded AbiB 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: abib_locus predicate: contributes to predicate_id: RO:0002326 object: abib_antiphage_activity description: The abiB-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiB as a one-profile system. evidence: - reference: PMID:8825768 snippet: The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170 notes: Parreira et al. identify AbiB as an abortive-infection determinant that blocks sensitive phage growth. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiB\tAbiB\t1\t1\tAbiB__AbiB" notes: The DefenseFinder rules table models AbiB as a one-component system requiring the AbiB__AbiB profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiB__AbiB | AbiB__AbiB | AbiB | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiB__AbiB under the AbiB model namespace. - subject: abib_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: sensitive_phage_transcript_degradation description: AbiB activity promotes rapid degradation of sensitive phage transcripts after infection. evidence: - reference: PMID:8825768 snippet: AbiB promotes a dramatic degradation of sensitive phage transcripts, starting 10-15 min after infection notes: Parreira et al. connect AbiB to rapid decay of sensitive phage transcripts. - subject: sensitive_phage_transcript_degradation predicate: contributes to predicate_id: RO:0002326 object: sensitive_phage_development_arrest description: Transcript decay probably arrests development of AbiB-sensitive phages. evidence: - reference: PMID:8825768 snippet: The decay of the transcripts is the probable cause of the arrest of the sensitive phage development notes: Parreira et al. interpret phage transcript decay as the likely cause of sensitive phage developmental arrest. - subject: sensitive_phage_development_arrest predicate: confers predicate_id: METPO:2007700 object: abib_system_trait description: Arrest of sensitive lactococcal phage development realizes the AbiB abortive-infection trait. evidence: - reference: PMID:8825768 snippet: The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170 notes: Parreira et al. show that AbiB prevents sensitive lactococcal phage growth. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiB | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiB model namespace to a lactococcal abortive-infection review. - subject: abib_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiB system possession is an abortive-infection-system trait. evidence: - reference: PMID:8825768 snippet: The abortive infection determinant AbiB notes: Parreira et al. place AbiB in the abortive-infection class of phage defense. discussions: - discussion_id: abib-trigger-and-rnase-gap prompt: Resolve the AbiB phage trigger, AbiB molecular function, and RNase effector before minting narrower AbiB mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Parreira et al. support AbiB as a named lactococcal abortive-infection determinant that prevents bIL170 growth and promotes sensitive phage transcript degradation. DefenseFinder represents AbiB with a one-profile rule, but this first system-level record leaves the phage trigger, AbiB molecular function, RNase effector identity, natural locus breadth, and phage escape routes unresolved. attaches_to: - causal_graphs#abib_locus_degrades_sensitive_phage_transcripts posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T21:21:12Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiB 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_v196. llm_assisted: true