identifier: traitmech:000322 label: AbiAlpha system definition: An abortive infection system in which an organism possesses an abi-alpha-family locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile and exemplified by the Enterococcus faecalis V583 prophage 6 abi-alpha determinant, whose encoded DUF4393/PF14337-family activity perturbs the Idefix lytic cycle and causes premature lysis of infected Enterococcus faecalis. definition_source: DOI:10.3390/v11010048 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiAlpha synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: PMID:30634666 snippet: We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abiα. notes: Lossouarn et al. named a new Abi mechanism from Enterococcus faecalis V583 prophage 6. - reference: PMID:30634666 snippet: It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis notes: Lossouarn et al. connected AbiAlpha to DUF4393 and an infected-cell premature-lysis phenotype. - reference: PMID:30634666 snippet: The abiα gene is widespread among prophages of enterococci and other Gram-positive bacteria. notes: Lossouarn et al. describe AbiAlpha homologs as prophage features rather than a single V583-only gene. - reference: DOI:10.3390/v11010048 snippet: These results confirmed that ef2833 is responsible for the abortive mechanism. notes: Lossouarn et al. experimentally connected ef2833 to the V583 prophage 6 Abi phenotype. - reference: DOI:10.3390/v11010048 snippet: We concluded that Abiα provokes a lysis asynchrony. notes: Lossouarn et al. linked the AbiAlpha mechanism to altered Idefix lysis timing. - reference: DOI:10.3390/v11010048 snippet: Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed notes: Lossouarn et al. summarized the system as infected-cell death with perturbed Idefix lytic-cycle progression. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: AbiAlpha | 10\.3390/v11010048 | Enterococcus faecalis countermeasures defeat a virulent Picovirinae bacteriophage notes: The DefenseFinder article registry maps the named AbiAlpha model namespace to the enterococcal AbiAlpha discovery paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiAlpha__AbiAlpha | | AbiAlpha | PF14337.11 | 27.1 |' notes: The DefenseFinder HMM inventory records AbiAlpha__AbiAlpha under the AbiAlpha model namespace with Pfam PF14337.11. canonical_examples: - taxon_id: NCBITaxon:1351 taxon_label: Enterococcus faecalis note: Lossouarn et al. characterized AbiAlpha from Enterococcus faecalis V583 prophage 6 and showed that it causes premature lysis during Idefix infection. reference: DOI:10.3390/v11010048 causal_graphs: - graph_id: abialpha_locus_causes_enterococcal_premature_lysis title: AbiAlpha perturbs Idefix lysis in Enterococcus faecalis description: Conservative system-level sketch linking an abi-alpha-family locus to AbiAlpha antiphage activity, Idefix lytic-cycle perturbation, premature lysis of infected Enterococcus faecalis, and AbiAlpha-system possession without asserting the direct DUF4393-family molecular target. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiAlpha as a named DefenseFinder single-profile abortive-infection system whose V583 prophage 6 prototype restricts Idefix by perturbing lysis timing. It leaves the direct phage trigger, DUF4393-family molecular function, direct Idefix target, natural host range, and phage escape routes unresolved. nodes: - node_id: abialpha_locus label: abi-alpha locus node_type: GENETIC_ELEMENT description: An abi-alpha-family abortive-infection locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile. - node_id: abialpha_antiphage_activity label: AbiAlpha antiphage activity node_type: BIOLOGICAL_PROCESS description: Enterococcal abortive-infection activity mediated by the AbiAlpha system. - node_id: idefix_lytic_cycle_perturbation label: Idefix lytic-cycle perturbation node_type: BIOLOGICAL_PROCESS description: Perturbation of the Idefix lytic cycle in AbiAlpha-containing Enterococcus faecalis. - node_id: infected_cell_premature_lysis label: infected-cell premature lysis node_type: BIOLOGICAL_PROCESS description: Premature lysis of Idefix-infected Enterococcus faecalis cells that express AbiAlpha. - node_id: abialpha_system_trait label: AbiAlpha system node_type: TRAIT grounding: traitmech:000322 description: Possession of a genome-encoded AbiAlpha 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: abialpha_locus predicate: contributes to predicate_id: RO:0002326 object: abialpha_antiphage_activity description: The abi-alpha-family locus encoded by V583 prophage 6 is responsible for AbiAlpha antiphage activity, and DefenseFinder models AbiAlpha as a single PF14337-family HMM profile. evidence: - reference: PMID:30634666 snippet: We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abiα. notes: Lossouarn et al. localized AbiAlpha to Enterococcus faecalis V583 prophage 6. - reference: DOI:10.3390/v11010048 snippet: These results confirmed that ef2833 is responsible for the abortive mechanism. notes: Lossouarn et al. connected ef2833 with the V583 prophage 6 Abi phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiAlpha__AbiAlpha | | AbiAlpha | PF14337.11 | 27.1 |' notes: The DefenseFinder HMM inventory records AbiAlpha__AbiAlpha under the AbiAlpha model namespace with Pfam PF14337.11. - subject: abialpha_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: idefix_lytic_cycle_perturbation description: AbiAlpha activity perturbs the Idefix lytic cycle in infected Enterococcus faecalis cells. evidence: - reference: DOI:10.3390/v11010048 snippet: Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed notes: Lossouarn et al. summarized the AbiAlpha output as death of infected cells while the Idefix lytic cycle is perturbed. - subject: abialpha_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: infected_cell_premature_lysis description: AbiAlpha activity causes premature lysis of Idefix-infected Enterococcus faecalis. evidence: - reference: PMID:30634666 snippet: conferred a typical Abi phenotype by causing a premature lysis notes: Lossouarn et al. reported premature lysis as the AbiAlpha-infected-cell output. - reference: DOI:10.3390/v11010048 snippet: Based on our results, we can only speculate that Abiα interferes with lysis notes: Lossouarn et al. framed the direct AbiAlpha lysis target as unresolved. - subject: idefix_lytic_cycle_perturbation predicate: contributes to predicate_id: RO:0002326 object: abialpha_system_trait description: Perturbation of Idefix lytic-cycle progression contributes to the AbiAlpha system trait. evidence: - reference: DOI:10.3390/v11010048 snippet: Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed notes: Lossouarn et al. connected AbiAlpha with Idefix lytic-cycle perturbation. - subject: infected_cell_premature_lysis predicate: confers predicate_id: METPO:2007700 object: abialpha_system_trait description: Premature lysis of Idefix-infected Enterococcus faecalis realizes the AbiAlpha abortive-infection trait. evidence: - reference: PMID:30634666 snippet: It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis notes: Lossouarn et al. identified premature lysis as an AbiAlpha Abi phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: AbiAlpha | 10\.3390/v11010048 | Enterococcus faecalis countermeasures defeat a virulent Picovirinae bacteriophage notes: The DefenseFinder article registry maps the named AbiAlpha model namespace to the enterococcal AbiAlpha discovery paper. - subject: abialpha_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiAlpha system possession is an abortive-infection-system trait. evidence: - reference: PMID:30634666 snippet: a new abortive infection (Abi) mechanism, which we designated Abiα notes: Lossouarn et al. place AbiAlpha in the abortive-infection class of phage defense. discussions: - discussion_id: abialpha-lysis-route-gap prompt: Resolve the AbiAlpha direct molecular target, Idefix trigger, lysis route, natural host range, and phage escape routes before minting narrower AbiAlpha mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Lossouarn et al. support AbiAlpha as a prophage-encoded Enterococcus faecalis abortive-infection system that maps to DUF4393/PF14337 and perturbs Idefix lysis timing. DefenseFinder represents AbiAlpha with a one-profile HMM inventory row but does not resolve the direct phage trigger, DUF4393-family molecular function, Idefix lysis target, natural host range, or escape routes. attaches_to: - causal_graphs#abialpha_locus_causes_enterococcal_premature_lysis posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T23:47:17Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiAlpha 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_v199. llm_assisted: true - timestamp: '2026-09-21T00:11:47Z' curator: codex action: EDIT changes: Addressed PR 1163 review issue 1165 by broadening the AbiAlpha class boundary from a prophage locus to an abi-alpha-family locus while keeping Enterococcus faecalis V583 prophage 6 as the characterized example. llm_assisted: true - timestamp: '2026-09-21T00:55:00Z' curator: codex action: EDIT changes: Re-copied the DefenseFinder AbiAlpha HMM registry row byte-exactly from the pinned Liste_hmm_system.md source while confirming the article-registry title casing against List_system_article.md for PR 1163 review issue 1168. llm_assisted: true