identifier: traitmech:000342 label: AbiO system definition: An abortive infection system in which an organism possesses a single-component AbiO-family locus represented by DefenseFinder as a mandatory AbiO__AbiO profile. definition_source: DOI:10.3168/jds.S0022-0302(98)75713-3 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiO synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: AbiO__AbiO synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.3168/jds.S0022-0302(98)75713-3 snippet: Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO notes: Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: the majority (18 systems) are each represented by single protein-coding genes notes: The FEMS review lists AbiO among the confirmed lactococcal Abi-like systems in Table 1 and omits AbiO from the named two- and three-component exception lists. - reference: DOI:10.1093/femsre/fuag009 snippet: the AbiO N-terminal domain resembles a restriction endonuclease type II-like domain-containing protein notes: The FEMS review summarizes a predicted nuclease-like AbiO N-terminal domain but does not establish the exact AbiO trigger or effector activity. - reference: DOI:10.1093/femsre/fuag009 snippet: Its C-terminal domain is predicted to encompass a superfamily 1B (SF1B) helicase notes: The FEMS review summarizes a predicted SF1B helicase-like AbiO C-terminal domain without resolving how AbiO arrests infected cells. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector notes: The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiO | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiO 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: "AbiO\tAbiO\t1\t1\tAbiO__AbiO\t\t\t" notes: The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiO__AbiO | AbiO__AbiO | AbiO | Custom | 50 |' notes: The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace. causal_graphs: - graph_id: abio_locus_restricts_lactococcal_phage title: AbiO loci confer abortive-infection phage defense description: Conservative system-level sketch linking possession of a DefenseFinder AbiO locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, predicted nuclease activity, or predicted helicase activity. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiO as a named single-profile lactococcal Abi-like system with the DefenseFinder AbiO__AbiO HMM while leaving its direct phage trigger, restriction-endonuclease interpretation, helicase interpretation, exact molecular activity, phage escape routes, and growth-arrest or cell-death route unresolved. nodes: - node_id: abio_locus label: AbiO locus node_type: GENETIC_ELEMENT description: An AbiO-family abortive-infection locus represented by the DefenseFinder AbiO__AbiO profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage propagation in cells carrying an AbiO-family abortive-infection system. - node_id: abio_system_trait label: AbiO system node_type: TRAIT grounding: traitmech:000342 description: Possession of a genome-encoded AbiO 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: abio_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The DefenseFinder AbiO namespace is modeled as a one-profile AbiO__AbiO system. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiO\tAbiO\t1\t1\tAbiO__AbiO\t\t\t" notes: The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiO__AbiO | AbiO__AbiO | AbiO | Custom | 50 |' notes: The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abio_system_trait description: Restriction of phage propagation realizes the AbiO abortive-infection system possession trait. evidence: - reference: DOI:10.3168/jds.S0022-0302(98)75713-3 snippet: Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO notes: Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector notes: The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype. - subject: abio_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiO system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.3168/jds.S0022-0302(98)75713-3 snippet: Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO notes: Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiO | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiO model namespace to the Chopin et al. lactococcal abortive-infection review. discussions: - discussion_id: abio-trigger-and-effector-gap prompt: Resolve the AbiO phage trigger, restriction-endonuclease and helicase activity, and growth-arrest or cell-death route before minting narrower AbiO mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Prevots and Ritzenthaler support AbiO as a lactococcal abortive phage resistance gene, the FEMS review retains AbiO among confirmed lactococcal Abi-like systems, and DefenseFinder represents AbiO with a mandatory AbiO__AbiO profile. The FEMS table leaves the AbiO effect on the cell and phage escape proteins unknown for the tested phages, and the FEMS structural discussion predicts restriction-endonuclease-like and SF1B-helicase-like domains while not resolving the molecular trigger or effector activity. This first system-level record therefore leaves the direct phage trigger, exact molecular activity, growth-arrest or cell-death route, and phage escape routes unresolved. evidence: - reference: DOI:10.1093/femsre/fuag009 snippet: the AbiO N-terminal domain resembles a restriction endonuclease type II-like domain-containing protein notes: The FEMS review summarizes a predicted nuclease-like AbiO N-terminal domain but does not establish the exact AbiO trigger or effector activity. - reference: DOI:10.1093/femsre/fuag009 snippet: Its C-terminal domain is predicted to encompass a superfamily 1B (SF1B) helicase notes: The FEMS review summarizes a predicted SF1B helicase-like AbiO C-terminal domain without resolving how AbiO arrests infected cells. - reference: DOI:10.1093/femsre/fuag009 snippet: AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector notes: The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiO\tAbiO\t1\t1\tAbiO__AbiO\t\t\t" notes: The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiO__AbiO | AbiO__AbiO | AbiO | Custom | 50 |' notes: The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace. attaches_to: - causal_graphs#abio_locus_restricts_lactococcal_phage posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T18:34:41Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiO 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_v219. llm_assisted: true