identifier: traitmech:000316 label: AbiI system definition: An abortive infection system in which an organism possesses an abiI-family locus represented by the DefenseFinder AbiI__AbiI profile and exemplified by the Lactococcus lactis M138 pND852 locus whose single abiI open reading frame restricts lactococcal phage propagation by an abortive-infection mechanism. definition_source: DOI:10.1016/S0168-1656(97)01692-1 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiI synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: PMID:9195753 snippet: Plasmid pND852 (56 kb) encodes nisin resistance and was isolated from Lactococcus lactis ssp lactis (L. lactis) M138 by conjugation to L. lactis LM0230 notes: Su et al. identified plasmid pND852 from Lactococcus lactis M138 as the source of the abiI-associated phage resistance locus. - reference: PMID:9195753 snippet: It conferred strong resistance to the isometric-headed phage phi 712 and partial resistance to the prolate-headed phage phi c2 notes: Su et al. show that pND852 confers resistance to tested lactococcal phages. - reference: PMID:9195753 snippet: A 2.6 kb HpaII fragment encoding phage resistance was cloned into the streptococcal/Bacillus hybrid vector pGB301 to generate pND817 notes: Su et al. localized phage resistance from pND852 to the 2.6 kb fragment in pND817. - reference: PMID:9195753 snippet: The mechanism of phage resistance encoded by pND817 involved abortive infection notes: Su et al. classified the pND817 phage-resistance mechanism as abortive infection. - reference: PMID:9195753 snippet: reduction in burst size from 166 to 6 at 30 degrees C and from 160 to 90 at 37 degrees C notes: Su et al. measured reduced phage burst size from the cloned pND817 abortive-infection locus. - reference: PMID:9195753 snippet: DNA sequencing revealed that the abortive infection was encoded by a single open reading frame (ORF), designated abiI, encoding a 332 amino acid protein notes: Su et al. support a single abiI open reading frame as the coding sequence for the pND817 abortive-infection locus. - reference: PMID:9195753 snippet: Frame shift mutation at the unique EcoRI site within the ORF resulted in loss of the Abi+ phenotype notes: Su et al. verified that the abiI open reading frame is required for the phage-resistance phenotype. - reference: PMID:9195753 snippet: Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database notes: Su et al. did not resolve AbiI molecular activity or homology during the original characterization. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiI | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiI model namespace to a lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiI\tAbiI\t1\t1\tAbiI__AbiI" notes: The DefenseFinder rules table models AbiI as a one-component system requiring the AbiI__AbiI profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiI__AbiI | AbiI__AbiI | AbiI | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiI__AbiI under the AbiI model namespace. canonical_examples: - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: Su et al. cloned the abiI determinant from Lactococcus lactis M138 plasmid pND852 into pND817 and showed abortive-infection phage resistance from a single abiI open reading frame. reference: DOI:10.1016/S0168-1656(97)01692-1 causal_graphs: - graph_id: abii_locus_reduces_lactococcal_phage_burst title: AbiI activity restricts lactococcal phage burst size description: Conservative system-level sketch linking an abiI-family locus to AbiI antiphage activity, reduced lactococcal phage burst size, restricted phage propagation, and abortive-infection system possession without asserting the unresolved molecular target. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiI as a named DefenseFinder single-profile abortive-infection system whose pND852 prototype restricts phi 712 and partially restricts phi c2. It leaves the direct phage trigger, AbiI molecular function, cell-death or packaging route, natural locus breadth, and phage escape routes unresolved. nodes: - node_id: abii_locus label: abiI locus node_type: GENETIC_ELEMENT description: An abiI-family abortive-infection locus represented by the DefenseFinder AbiI__AbiI profile. - node_id: abii_antiphage_activity label: AbiI antiphage activity node_type: BIOLOGICAL_PROCESS description: Abortive-infection phage resistance mediated by the AbiI system. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced completion of lactococcal phage propagation in an AbiI-containing infected host cell. - node_id: abii_system_trait label: AbiI system node_type: TRAIT grounding: traitmech:000316 description: Possession of a genome-encoded AbiI 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: abii_locus predicate: contributes to predicate_id: RO:0002326 object: abii_antiphage_activity description: The abiI-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiI as a one-profile system. evidence: - reference: PMID:9195753 snippet: DNA sequencing revealed that the abortive infection was encoded by a single open reading frame (ORF), designated abiI, encoding a 332 amino acid protein notes: Su et al. identify abiI as the single ORF encoding the pND817 abortive-infection phenotype. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiI\tAbiI\t1\t1\tAbiI__AbiI" notes: The DefenseFinder rules table models AbiI as a one-component system requiring the AbiI__AbiI profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiI__AbiI | AbiI__AbiI | AbiI | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiI__AbiI under the AbiI model namespace. - subject: abii_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: AbiI activity strongly restricts phi 712 and partially restricts phi c2 propagation in Lactococcus lactis. evidence: - reference: PMID:9195753 snippet: It conferred strong resistance to the isometric-headed phage phi 712 and partial resistance to the prolate-headed phage phi c2 notes: Su et al. measured strong or partial resistance from the AbiI-containing pND852 plasmid for two tested lactococcal phages. - reference: PMID:9195753 snippet: reduction in burst size from 166 to 6 at 30 degrees C and from 160 to 90 at 37 degrees C notes: Su et al. connect pND817 to sharply reduced phi 712 burst size. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abii_system_trait description: Restriction of lactococcal phage propagation realizes the AbiI abortive-infection trait. evidence: - reference: PMID:9195753 snippet: The mechanism of phage resistance encoded by pND817 involved abortive infection notes: Su et al. classify the pND817 mechanism as abortive infection. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiI | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiI model namespace to a lactococcal abortive-infection review. - subject: abii_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiI system possession is an abortive-infection-system trait. evidence: - reference: PMID:9195753 snippet: The mechanism of phage resistance encoded by pND817 involved abortive infection notes: Su et al. place AbiI in the abortive infection class of phage defense. discussions: - discussion_id: abii-trigger-and-effector-gap prompt: Resolve the AbiI phage trigger, molecular activity, and direct arrest target before minting narrower AbiI mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Su et al. support AbiI as a named lactococcal abortive-infection locus whose cloned pND852 fragment reduces phi 712 burst size and whose abiI frameshift abolishes phage resistance. DefenseFinder represents AbiI with a one-profile rule, but this first system-level record leaves the phage trigger, AbiI molecular function, direct host or phage target, growth-arrest or cell-death route, and phage escape routes unresolved. evidence: - reference: PMID:9195753 snippet: Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database notes: Su et al. report no informative sequence homology for AbiI in the original characterization. attaches_to: - causal_graphs#abii_locus_reduces_lactococcal_phage_burst posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T18:33:34Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiI 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_v193. llm_assisted: true