TraitMech

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AbiI system

traitmech:000316 · CLASS · PROPOSED

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.

Trait evidence (11)

  • PMID:9195753
    Plasmid pND852 (56 kb) encodes nisin resistance and was isolated from Lactococcus lactis ssp lactis (L. lactis) M138 by conjugation to L. lactis LM0230

    Su et al. identified plasmid pND852 from Lactococcus lactis M138 as the source of the abiI-associated phage resistance locus.

  • PMID:9195753
    It conferred strong resistance to the isometric-headed phage phi 712 and partial resistance to the prolate-headed phage phi c2

    Su et al. show that pND852 confers resistance to tested lactococcal phages.

  • PMID:9195753
    A 2.6 kb HpaII fragment encoding phage resistance was cloned into the streptococcal/Bacillus hybrid vector pGB301 to generate pND817

    Su et al. localized phage resistance from pND852 to the 2.6 kb fragment in pND817.

  • PMID:9195753
    The mechanism of phage resistance encoded by pND817 involved abortive infection

    Su et al. classified the pND817 phage-resistance mechanism as abortive infection.

  • PMID:9195753
    reduction in burst size from 166 to 6 at 30 degrees C and from 160 to 90 at 37 degrees C

    Su et al. measured reduced phage burst size from the cloned pND817 abortive-infection locus.

  • PMID:9195753
    DNA sequencing revealed that the abortive infection was encoded by a single open reading frame (ORF), designated abiI, encoding a 332 amino acid protein

    Su et al. support a single abiI open reading frame as the coding sequence for the pND817 abortive-infection locus.

  • PMID:9195753
    Frame shift mutation at the unique EcoRI site within the ORF resulted in loss of the Abi+ phenotype

    Su et al. verified that the abiI open reading frame is required for the phage-resistance phenotype.

  • PMID:9195753
    Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database

    Su et al. did not resolve AbiI molecular activity or homology during the original characterization.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    AbiI | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

    The DefenseFinder article registry maps the named AbiI model namespace to a lactococcal abortive-infection review.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    AbiI AbiI 1 1 AbiI__AbiI

    The DefenseFinder rules table models AbiI as a one-component system requiring the AbiI__AbiI profile.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    | AbiI__AbiI | AbiI__AbiI | AbiI | Custom | 20 |

    The DefenseFinder HMM inventory records AbiI__AbiI under the AbiI model namespace.

AbiI activity restricts lactococcal phage burst size

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.

NONMECHANISTIC · 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.

AbiI activity restricts lactococcal phage burst size Interactive directed graph showing evidence-backed causal relationships for AbiI system.

Edge evidence

  • abiI locus contributes to AbiI antiphage activity RO:0002326

    The abiI-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiI as a one-profile system.

  • AbiI antiphage activity contributes to restricted phage propagation RO:0002326

    AbiI activity strongly restricts phi 712 and partially restricts phi c2 propagation in Lactococcus lactis.

    • PMID:9195753 It conferred strong resistance to the isometric-headed phage phi 712 and partial resistance to the prolate-headed phage phi c2 Su et al. measured strong or partial resistance from the AbiI-containing pND852 plasmid for two tested lactococcal phages.
    • PMID:9195753 reduction in burst size from 166 to 6 at 30 degrees C and from 160 to 90 at 37 degrees C Su et al. connect pND817 to sharply reduced phi 712 burst size.
  • restricted phage propagation confers AbiI system METPO:2007700

    Restriction of lactococcal phage propagation realizes the AbiI abortive-infection trait.

  • AbiI system is a abortive infection system rdfs:subClassOf

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

    • PMID:9195753 The mechanism of phage resistance encoded by pND817 involved abortive infection Su et al. place AbiI in the abortive infection class of phage defense.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1016/S0168-1656(97)01692-1

Parent traits (1)

Synonyms (1)

  • AbiI RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md

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:10.1016/S0168-1656(97)01692-1 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.

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 AbiI phage trigger, molecular activity, and direct arrest target before minting narrower AbiI mechanism children.

KNOWLEDGE GAP OPEN abii-trigger-and-effector-gap · raised by codex · 2026-09-20

Attached to causal_graphs#abii_locus_reduces_lactococcal_phage_burst

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

  • PMID:9195753
    Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.