identifier: traitmech:000306 label: AbiG system definition: An abortive infection system in which an organism possesses a two-gene abiG locus with abiGi and abiGii open reading frames, exemplified by the Lactococcus lactis subsp. cremoris UC653 plasmid pCI750 locus that restricts lactococcal phages without blocking phage DNA replication and is represented by the DefenseFinder AbiG__AbiGi and AbiG__AbiGii profiles. definition_source: DOI:10.1128/aem.62.9.3075-3082.1996 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiG synonym_type: RELATED_SYNONYM source: DOI:10.1128/aem.62.9.3075-3082.1996 evidence: - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: AbiG is an abortive infection (Abi) mechanism encoded by the conjugative plasmid pCI750 originally isolated from Lactococcus lactis subsp. cremoris UC653 notes: O'Connor et al. identify AbiG as an abortive-infection mechanism encoded by the UC653 pCI750 plasmid. - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: Insensitivity conferred by this Abi manifested itself as complete resistance to phi 712 (936 phage species) with only partial resistance to phi c2 (c2 species) notes: O'Connor et al. show that AbiG restricts tested lactococcal phages with species-dependent strength. - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: The smallest subclone of pCI750 which expressed the Abi phenotype contained a 3.5-kb insert which encoded two potential open reading frames notes: O'Connor et al. localize AbiG activity to a pCI750 subclone carrying two predicted coding sequences. - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: abiGi (750 bp) and abiGii (1,194 bp) were separated by 2 bp and appeared to share a single promoter upstream of abiGi notes: O'Connor et al. support abiGi and abiGii as the paired open reading frames of the AbiG locus. - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: The mechanism did not inhibit phage DNA replication notes: O'Connor et al. rule out phage DNA replication as the blocked step in the original AbiG characterization. - reference: DOI:10.1128/aem.65.1.330-335.1999 snippet: The abortive infection system AbiG is encoded by the lactococcal plasmid pCI750 notes: The follow-up O'Connor et al. study reiterates AbiG as a pCI750-encoded lactococcal abortive-infection system. - reference: DOI:10.1128/aem.65.1.330-335.1999 snippet: The abiG locus (consisting of two genes, abiGi and abiGii) was examined by Northern blot analysis, revealing two transcripts of approximately 2.8 and 1.5 kb which were homologous to the two gene-specific probes notes: O'Connor et al. confirm the abiGi/abiGii two-gene locus at the transcript level. - reference: DOI:10.1128/aem.65.1.330-335.1999 snippet: Examination of phage sk1 RNA synthesis demonstrated that both the subcloned AbiG and, to a greater extent, pCI750 inhibited this process notes: O'Connor et al. connect the AbiG subclone to inhibited sk1 phage RNA synthesis. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiG | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiG model namespace to a lactococcal abortive-infection review. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiG\tAbiG\t2\t2\tAbiG__AbiGi, AbiG__AbiGii" notes: The DefenseFinder rules table models AbiG as a two-component system requiring the AbiG__AbiGi and AbiG__AbiGii profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiG__AbiGi | AbiG__AbiGi | AbiG | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiG__AbiGi under the AbiG model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiG__AbiGii | AbiG__AbiGii | AbiG | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiG__AbiGii under the AbiG model namespace. canonical_examples: - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: O'Connor et al. characterized AbiG from conjugative plasmid pCI750, originally isolated from Lactococcus lactis subsp. cremoris UC653, and localized the abortive-infection phenotype to the abiGi/abiGii locus. reference: DOI:10.1128/aem.62.9.3075-3082.1996 causal_graphs: - graph_id: abig_inhibits_lactococcal_phage_rna_synthesis title: AbiG inhibits lactococcal phage RNA synthesis description: Conservative system-level sketch linking an abiGi/abiGii locus to AbiG antiphage activity, inhibited phage RNA synthesis, restricted lactococcal phage propagation, and abortive-infection system possession without asserting AbiG's unresolved primary target. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiG as a named DefenseFinder two-profile abortive-infection system whose pCI750 prototype restricts phi 712, partially restricts phi c2, and inhibits phage sk1 and late c2 RNA synthesis while leaving the phage trigger, AbiGi and AbiGii molecular functions, cellular target, growth-arrest or cell-death route, and phage escape routes unresolved. nodes: - node_id: abig_locus label: abiG locus node_type: GENETIC_ELEMENT description: A two-gene abiGi/abiGii abortive-infection locus represented by the DefenseFinder AbiG rule. - node_id: abig_antiphage_activity label: AbiG antiphage activity node_type: BIOLOGICAL_PROCESS description: Abortive-infection phage resistance mediated by the AbiG system. - node_id: phage_rna_synthesis label: phage RNA synthesis node_type: BIOLOGICAL_PROCESS description: Synthesis of sensitive lactococcal phage RNA during infection. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced completion of lactococcal phage propagation in an AbiG-containing infected host cell. - node_id: abig_system_trait label: AbiG system node_type: TRAIT grounding: traitmech:000306 description: Possession of a genome-encoded AbiG 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: abig_locus predicate: contributes to predicate_id: RO:0002326 object: abig_antiphage_activity description: The pCI750 abiG locus carries abiGi and abiGii open reading frames, and DefenseFinder models AbiG as a two-profile system requiring both AbiG components. evidence: - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: The smallest subclone of pCI750 which expressed the Abi phenotype contained a 3.5-kb insert which encoded two potential open reading frames notes: O'Connor et al. localize the AbiG phenotype to a two-ORF pCI750 subclone. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiG\tAbiG\t2\t2\tAbiG__AbiGi, AbiG__AbiGii" notes: The DefenseFinder rules table models AbiG as a two-component system requiring the AbiG__AbiGi and AbiG__AbiGii profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiG__AbiGi | AbiG__AbiGi | AbiG | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiG__AbiGi under the AbiG model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiG__AbiGii | AbiG__AbiGii | AbiG | Custom | 20 |' notes: The DefenseFinder HMM inventory records AbiG__AbiGii under the AbiG model namespace. - subject: abig_antiphage_activity predicate: mitigates predicate_id: METPO:2007407 object: phage_rna_synthesis description: AbiG antiphage activity inhibits RNA synthesis by tested sensitive lactococcal phages. evidence: - reference: DOI:10.1128/aem.65.1.330-335.1999 snippet: Examination of phage sk1 RNA synthesis demonstrated that both the subcloned AbiG and, to a greater extent, pCI750 inhibited this process notes: O'Connor et al. show that the AbiG subclone inhibits phage sk1 RNA synthesis. - subject: abig_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: AbiG activity restricts propagation by phi 712 and partially restricts phi c2. evidence: - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: Insensitivity conferred by this Abi manifested itself as complete resistance to phi 712 (936 phage species) with only partial resistance to phi c2 (c2 species) notes: O'Connor et al. measure complete or partial resistance from the AbiG mechanism for tested lactococcal phages. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abig_system_trait description: Restriction of lactococcal phage propagation realizes the AbiG abortive-infection trait. evidence: - reference: DOI:10.1128/aem.62.9.3075-3082.1996 snippet: AbiG is an abortive infection (Abi) mechanism encoded by the conjugative plasmid pCI750 notes: O'Connor et al. classify AbiG as a pCI750 abortive-infection mechanism. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'AbiG | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme' notes: The DefenseFinder article registry maps the named AbiG model namespace to a lactococcal abortive-infection review. - subject: abig_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiG system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1128/aem.65.1.330-335.1999 snippet: The abortive infection system AbiG is encoded by the lactococcal plasmid pCI750 notes: O'Connor et al. explicitly place AbiG in the abortive-infection class of phage defense. discussions: - discussion_id: abig-primary-target-gap prompt: Resolve the AbiG phage trigger, AbiGi and AbiGii molecular functions, and primary arrest target before minting narrower AbiG mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: O'Connor et al. support AbiG as a named lactococcal abortive-infection system encoded by two adjacent pCI750 open reading frames, and DefenseFinder represents AbiG with a two-profile rule. The 1999 transcription study connects AbiG to inhibited phage sk1 and late c2 RNA synthesis, but it explicitly leaves unresolved whether transcription is the system's primary target or a secondary effect. evidence: - reference: DOI:10.1128/aem.65.1.330-335.1999 snippet: AbiG inhibits phage sk1 and late c2 RNA synthesis; however, whether this process of transcription is the primary target of the system or a secondary effect remains to be determined notes: O'Connor et al. identify phage RNA-synthesis inhibition as a downstream AbiG effect while leaving the direct target unresolved. attaches_to: - causal_graphs#abig_inhibits_lactococcal_phage_rna_synthesis posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T09:16:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiG 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, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v183. llm_assisted: true - timestamp: '2026-09-20T10:19:00Z' curator: codex action: STANDARDIZED_CAUSAL_NODE_LABEL changes: Reused the existing restricted phage propagation causal-node label after PR review found that the lactococcal-specific label duplicated the taxon-neutral GENOMICS phage-defense node. llm_assisted: true