identifier: traitmech:000300 label: AbiV system definition: An abortive infection system in which an organism possesses an abiV locus whose encoded AbiV protein can restrict 936-like or c2-like lactococcal phages by interacting with phage-encoded SaV and inhibiting phage protein translation. definition_source: DOI:10.1128/AEM.00093-10 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 evidence: - reference: DOI:10.1128/AEM.00780-08 snippet: We report here a novel lactococcal Abi system, designated AbiV, which is chromosomally encoded and effective against virulent phages belonging to the 936 and c2 species notes: Haaber et al. name AbiV as a chromosomal lactococcal abortive-infection system that can defend against 936- and c2-group virulent phages. - reference: DOI:10.1128/AEM.00780-08 snippet: This gene was also found to confer phage resistance to L. lactis MG1363 when it was cloned into an expression vector notes: Haaber et al. show that expressing the AbiV open reading frame is sufficient to confer phage resistance in Lactococcus lactis MG1363. - reference: DOI:10.1128/AEM.00780-08 snippet: A subsequent frameshift mutation in the ORF completely eliminated the phage resistance phenotype, confirming that the ORF was necessary for phage resistance notes: Haaber et al. show that the AbiV open reading frame is necessary for the cloned resistance phenotype. - reference: DOI:10.1128/AEM.00780-08 snippet: the data show that the phage resistance mechanism encoded by orf1 is an abortive infection mechanism notes: Haaber et al. classify the orf1/abiV resistance determinant as an abortive-infection mechanism. - reference: DOI:10.1128/AEM.00780-08 snippet: AbiV prevented cleavage of the replicated phage DNA and thus that it acts at a later stage of the phage infection process notes: Haaber et al. localize AbiV activity after phage DNA replication and connect it to failed DNA cleavage. - reference: DOI:10.1128/AEM.00780-08 snippet: AbiV inhibits proliferation of small isometric phages belonging to the 936 species and of prolate phages belonging to the c2 species notes: Haaber et al. support the observed 936- and c2-species phage sensitivity of the AbiV system. - reference: DOI:10.1128/AEM.02093-08 snippet: The orf was named sav (for sensitivity to AbiV), and the encoded polypeptide was named SaV notes: Haaber et al. name the phage sav gene and encoded SaV protein after AbiV-insensitive phage mutant sequencing. - reference: DOI:10.1128/AEM.02093-08 snippet: Analyses of the sav regions in other AbiV-insensitive phage mutants from both the 936 and c2 groups revealed amino acid changes in the central region of the SaV protein notes: Haaber et al. show that AbiV escape in 936- and c2-group phages maps to the conserved central region of SaV. - reference: DOI:10.1128/AEM.00093-10 snippet: they strongly and specifically interact with each other to form a stable protein complex notes: Haaber et al. demonstrate a strong, specific direct interaction between the host AbiV protein and phage SaV. - reference: DOI:10.1128/AEM.00093-10 snippet: Western blotting showed that translation of both early and late phage proteins was severely inhibited in the presence of AbiV notes: Haaber et al. connect AbiV-SaV activity to a severe block in phage protein translation. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: AbiV | 10\.1128/AEM\.00780-08 | AbiV, a novel antiphage abortive infection mechanism on the chromosome of Lactococcus lactis subsp\. cremoris MG1363 notes: The DefenseFinder article registry maps the named AbiV system to the Haaber et al. AbiV paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiV__AbiV | AbiV__AbiV | AbiV | Custom | 20 |' notes: The DefenseFinder HMM inventory records the custom AbiV profile in the AbiV model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiV\tAbiV\t1\t1\tAbiV__AbiV" notes: The DefenseFinder rules table models AbiV as a single-profile system. canonical_examples: - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: Haaber et al. discovered abiV on the Lactococcus lactis subsp. cremoris MG1363 chromosome, expressed it in Lactococcus lactis MG1363, and showed that its expression conferred abortive-infection phage resistance. reference: DOI:10.1128/AEM.00780-08 causal_graphs: - graph_id: abiv_sav_translation_block title: AbiV-SaV activity blocks phage protein translation description: Evidence-backed process sketch linking an abiV locus to AbiV antiphage activity, phage sav sensitivity determinants, AbiV-SaV complex formation, inhibited host translation, blocked phage protein synthesis, restricted phage propagation, and abortive-infection system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures the SaV-dependent AbiV complex and translation block without asserting the direct host translational target of the complex, the detailed route to late phage-DNA maturation arrest, or why one tested 936 phage and the P335 phages were insensitive. nodes: - node_id: abiv_locus label: abiV locus node_type: GENETIC_ELEMENT description: An abortive-infection locus encoding the AbiV phage resistance determinant. - node_id: abiv_antiphage_activity label: AbiV antiphage activity node_type: BIOLOGICAL_PROCESS description: Abortive-infection antiphage activity mediated by the AbiV protein. - node_id: sav_phage_gene label: sav phage gene node_type: GENETIC_ELEMENT description: A 936-like or c2-like phage gene whose encoded SaV protein is required for AbiV sensitivity. - node_id: abiv_sav_complex_formation label: AbiV-SaV complex formation node_type: BIOLOGICAL_PROCESS description: Direct interaction of AbiV and phage SaV homodimers to form a stable AbiV-SaV complex. - node_id: inhibited_host_translation label: inhibited host translational machinery node_type: BIOLOGICAL_PROCESS description: AbiV-SaV-dependent inhibition of the host translational machinery during phage infection. - node_id: blocked_phage_protein_synthesis label: blocked phage protein synthesis node_type: BIOLOGICAL_PROCESS description: Reduced translation of early and late phage proteins in an AbiV-containing infected host cell. - node_id: stalled_phage_dna_maturation label: stalled phage DNA maturation node_type: BIOLOGICAL_PROCESS description: Late phage DNA maturation block in which replicated concatemeric 936-like phage DNA is not cleaved into mature resolved DNA. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced completion of 936-like or c2-like phage propagation in an AbiV-containing infected host cell. - node_id: abiv_system_trait label: AbiV system node_type: TRAIT grounding: traitmech:000300 description: Possession of a genome-encoded AbiV abortive-infection 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: abiv_locus predicate: contributes to predicate_id: RO:0002326 object: abiv_antiphage_activity description: The abiV locus encodes the protein required for the cloned phage-resistance phenotype. evidence: - reference: DOI:10.1128/AEM.00780-08 snippet: A subsequent frameshift mutation in the ORF completely eliminated the phage resistance phenotype notes: Haaber et al. abolish the phenotype with a frameshift in the AbiV open reading frame. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiV__AbiV | AbiV__AbiV | AbiV | Custom | 20 |' notes: The DefenseFinder HMM inventory records the custom AbiV profile in the AbiV model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiV\tAbiV\t1\t1\tAbiV__AbiV" notes: The DefenseFinder rules table models AbiV as a single-profile system requiring the AbiV profile. - subject: sav_phage_gene predicate: contributes to predicate_id: RO:0002326 object: abiv_sav_complex_formation description: The early phage sav gene encodes SaV, the phage protein needed for AbiV sensitivity. evidence: - reference: DOI:10.1128/AEM.02093-08 snippet: we concluded that orf26 of phage p2 is involved in sensitivity to AbiV, and the gene was renamed sav notes: Haaber et al. identify phage p2 orf26 as the AbiV sensitivity determinant. - reference: DOI:10.1128/AEM.02093-08 snippet: Analyses of the sav regions in other AbiV-insensitive phage mutants from both the 936 and c2 groups revealed amino acid changes in the central region of the SaV protein notes: Haaber et al. show that AbiV escape in multiple 936- and c2-like phages maps to sav homologues. - subject: abiv_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: abiv_sav_complex_formation description: AbiV directly and specifically interacts with SaV to form a stable AbiV-SaV complex. evidence: - reference: DOI:10.1128/AEM.00093-10 snippet: they strongly and specifically interact with each other to form a stable protein complex notes: Haaber et al. use SEC-MALS/UV/RI and fluorescence quenching to show direct AbiV-SaV complex formation. - subject: abiv_sav_complex_formation predicate: contributes to predicate_id: RO:0002326 object: inhibited_host_translation description: The AbiV-SaV complex inhibits host translational machinery after early sav expression. evidence: - reference: DOI:10.1128/AEM.00093-10 snippet: A small amount of SaV is produced early and rapidly interacts with the host AbiV protein to form an active complex that inhibits the translational machinery of the cell notes: Haaber et al. conclude that early SaV interacts with AbiV to form the active translation-inhibiting complex. - subject: inhibited_host_translation predicate: contributes to predicate_id: RO:0002326 object: blocked_phage_protein_synthesis description: AbiV-SaV-mediated translation inhibition blocks early and late phage protein production. evidence: - reference: DOI:10.1128/AEM.00093-10 snippet: Western blotting showed that translation of both early and late phage proteins was severely inhibited in the presence of AbiV notes: Haaber et al. show that AbiV blocks translation of phage protein products including SaV, ORF11, and ORF16. - subject: blocked_phage_protein_synthesis predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: Blocked phage translation prevents completion of the AbiV-sensitive phage lytic program. evidence: - reference: DOI:10.1128/AEM.00093-10 snippet: AbiV is an abortive infection protein that inhibits the lytic cycle of several virulent phages infecting Lactococcus lactis, while a mutation in the phage gene sav confers insensitivity to AbiV. In this study, we have further characterized the effects of the bacterial AbiV and its interaction with the phage p2 protein SaV. First, we showed that during phage infection of lactococcal AbiV⁺ cells, AbiV rapidly inhibited protein synthesis notes: Haaber et al. frame the AbiV protein-synthesis block as part of AbiV inhibition of the phage lytic cycle. - subject: abiv_antiphage_activity predicate: contributes to predicate_id: RO:0002326 object: stalled_phage_dna_maturation description: AbiV activity prevents cleavage of replicated 936-like phage DNA into mature resolved DNA as a downstream infection-cycle defect. evidence: - reference: DOI:10.1128/AEM.00780-08 snippet: The results described above showed that AbiV prevented cleavage of the replicated phage DNA notes: Haaber et al. connect AbiV to failed cleavage of replicated phage DNA. - subject: stalled_phage_dna_maturation predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: Accumulation of nonmature concatemeric phage DNA limits completion of AbiV-sensitive phage infection. evidence: - reference: DOI:10.1128/AEM.00780-08 snippet: indicated that phage DNA accumulated in its concatemeric (nonmature) form in the resistant L. lactis cells notes: Haaber et al. observed uncleaved concatemeric phage DNA in AbiV-containing resistant cells. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abiv_system_trait description: Restriction of 936-like or c2-like phage propagation realizes the AbiV abortive-infection defense trait. evidence: - reference: DOI:10.1128/AEM.00780-08 snippet: This ORF provided resistance against virulent lactococcal phages belonging to the 936 and c2 species with an efficiency of plaquing of 10−4 notes: Haaber et al. support AbiV-mediated resistance to multiple 936- and c2-group lactococcal phages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: AbiV | 10\.1128/AEM\.00780-08 | AbiV, a novel antiphage abortive infection mechanism on the chromosome of Lactococcus lactis subsp\. cremoris MG1363 notes: DefenseFinder records AbiV as a named antiphage abortive-infection system from the Haaber et al. paper. - subject: abiv_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiV system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1128/AEM.00780-08 snippet: the gene was designated abiV and the Abi mechanism was designated AbiV notes: Haaber et al. name the abiV-encoded phage resistance determinant as an Abi mechanism. discussions: - discussion_id: abiv-mechanism-gap prompt: Resolve the host translational target of the AbiV-SaV complex before minting narrower AbiV mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Haaber et al. identify phage sav as the determinant of AbiV sensitivity and support direct AbiV-SaV complex formation followed by inhibition of phage protein translation, but the precise host translational target and complete route from the AbiV-SaV complex to abortive infection remain unresolved. attaches_to: - causal_graphs#abiv_sav_translation_block posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T03:07:25Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiV 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_v177. llm_assisted: true - timestamp: '2026-09-20T03:38:10Z' curator: codex action: ADD_FOLLOWUP_MECHANISM_EVIDENCE changes: Added the Haaber et al. 2009 and 2010 AbiV follow-up papers after adversarial review; revised the definition, causal graph, and knowledge gap to include phage sav, direct AbiV-SaV complex formation, and AbiV-SaV-linked inhibition of phage protein translation. llm_assisted: true - timestamp: '2026-09-20T04:10:00Z' curator: codex action: REFINE_FOLLOWUP_MECHANISM_EVIDENCE changes: Refined the AbiV follow-up graph after adversarial review by using lytic-cycle and protein-synthesis evidence for the translation-block propagation edge. llm_assisted: true