TraitMech

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AbiF system

traitmech:000504 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a pNP40-derived abiF locus whose single complete open reading frame encodes a phage-insensitivity determinant that inhibits bacteriophage phi 712 DNA replication.

Trait evidence (5)

  • DOI:10.1128/AEM.61.12.4321-4328.1995
    Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity

    Garvey et al. localized the pNP40 AbiF determinant to the EcoRV-XbaI fragment carried by recombinant plasmid pCG1.

  • DOI:10.1128/AEM.61.12.4321-4328.1995
    The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity

    Garvey et al. showed that the single complete ORF in the pNP40-derived EcoRV-XbaI fragment is required for AbiF-associated phage resistance.

  • DOI:10.1128/AEM.61.12.4321-4328.1995
    The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively

    Garvey et al. designated the pNP40 phage-insensitivity determinant cloned on pCG1 as AbiF.

  • DOI:10.1128/AEM.61.12.4321-4328.1995
    Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication

    Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF.

  • DOI:10.1093/femsre/fuag009
    13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu

    The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems.

AbiF inhibits lactococcal phage DNA replication

Conservative system-level sketch linking a pNP40-derived abiF locus to inhibited phage phi 712 DNA replication, restricted phage propagation, and AbiF abortive-infection system possession.

NONMECHANISTIC · The graph captures the original AbiF determinant as a pNP40-derived abortive-infection locus cloned on pCG1 that inhibits the rate of phage phi 712 DNA replication while leaving the exact AbiF protein function, phage trigger, host target, possible AbiD/AbiD1 homology-derived family boundary, natural locus breadth, and phage escape routes unresolved.

AbiF inhibits lactococcal phage DNA replication Interactive directed graph showing evidence-backed causal relationships for AbiF system.

Edge evidence

  • abiF locus contributes to restricted phage DNA replication RO:0002326

    The pNP40 AbiF open reading frame is responsible for the phage-insensitivity phenotype and inhibits the rate of phage phi 712 DNA replication.

    • DOI:10.1128/AEM.61.12.4321-4328.1995 The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity Garvey et al. showed that the single complete ORF in the pNP40-derived EcoRV-XbaI fragment is required for AbiF-associated phage resistance.
    • DOI:10.1128/AEM.61.12.4321-4328.1995 Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF.
  • restricted phage DNA replication contributes to restricted phage propagation RO:0002326

    Inhibition of phage phi 712 DNA replication contributes to AbiF phage insensitivity.

    • DOI:10.1128/AEM.61.12.4321-4328.1995 Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity Garvey et al. localized the pNP40 AbiF determinant to the EcoRV-XbaI fragment carried by recombinant plasmid pCG1.
    • DOI:10.1128/AEM.61.12.4321-4328.1995 Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF.
  • restricted phage propagation confers AbiF system METPO:2007700

    Restricted phage propagation realizes the AbiF abortive-infection system possession trait.

    • DOI:10.1128/AEM.61.12.4321-4328.1995 The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively Garvey et al. designated the pNP40 phage-insensitivity determinant cloned on pCG1 as AbiF.
    • DOI:10.1093/femsre/fuag009 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems.
  • AbiF system is a abortive infection system rdfs:subClassOf

    AbiF system possession is an abortive-infection-system trait.

    • DOI:10.1128/AEM.61.12.4321-4328.1995 The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively Garvey et al. designated the pNP40 phage-insensitivity determinant cloned on pCG1 as AbiF.
    • DOI:10.1093/femsre/fuag009 13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/AEM.61.12.4321-4328.1995

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Lactococcus lactis NCBITaxon:1358 DOI:10.1128/AEM.61.12.4321-4328.1995 Garvey et al. cloned the pNP40 AbiF determinant into pCG1 and showed that the cloned pNP40 region conferred abortive-infection phage insensitivity in Lactococcus lactis subsp. lactis MG1614.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve the exact AbiF protein function, phage trigger, host target, AbiD/AbiD1 homology-derived family boundary, and natural locus breadth before minting narrower AbiF mechanism children.

KNOWLEDGE GAP OPEN abif-function-and-host-breadth-gap · raised by codex · 2026-10-01

Attached to causal_graphs#abif_locus_inhibits_lactococcal_phage_dna_replication

Garvey et al. support AbiF as a pNP40 determinant cloned on pCG1 that conforms to abortive-infection criteria, depends on a single complete open reading frame, and inhibits the rate of phage phi 712 DNA replication; the FEMS review retains AbiF among confirmed two-component lactococcal Abi-like systems. This first system-level record therefore leaves the direct phage trigger, exact AbiF molecular activity, relevant host target, AbiD/AbiD1-related family boundary, natural locus breadth, cell-death or growth-arrest route, and phage escape routes unresolved.

Evidence

  • DOI:10.1128/AEM.61.12.4321-4328.1995
    The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity
  • DOI:10.1128/AEM.61.12.4321-4328.1995
    Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication
  • DOI:10.1093/femsre/fuag009
    13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted AbiF 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_v381.

  2. · ADDRESS_ABIF_REVIEW_FINDING · codex

    Addressed adversarial review issue #1505 by clarifying that pNP40 is the AbiF determinant source context and that pCG1 is the recombinant plasmid clone used in the Garvey et al. subcloning experiment.