TraitMech

TraitMech › GENOMICS

AbiU system

traitmech:000321 · CLASS · PROPOSED

An abortive infection system in which an organism possesses an abiU-family locus represented by the DefenseFinder AbiU__AbiU profile and exemplified by the Lactococcus lactis LL51-1 AbiU determinant, whose abiU1 open reading frame is responsible for phage resistance, whose abiU2 region may downregulate 936/P335 resistance, and whose activity reduces c2, 936, and P335 lactococcal phage plaquing while delaying transcription of phages 712 and c2.

Trait evidence (9)

  • PMID:11679349
    This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis.

    Dai et al. identify AbiU as a novel Lactococcus lactis abortive-infection system.

  • PMID:11679349
    AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335.

    Dai et al. measured the AbiU activity spectrum across representative c2, 936, and P335 lactococcal phages.

  • PMID:11679349
    The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 x 10(-1), 1.0 x 10(-2), and 1.0 x 10(-1), respectively.

    Dai et al. quantified phage-specific AbiU reductions in efficiency of plaquing against c2, 936, and P335 representatives.

  • PMID:11679349
    abiU involves two open reading frames, abiU1 (1,772 bp) and abiU2 (1,019 bp).

    Dai et al. reported a two-ORF abiU locus rather than resolving AbiU as a single isolated protein trait.

  • PMID:11679349
    Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage.

    Dai et al. connected AbiU1 to the phage-resistance phenotype and left AbiU2 as a likely regulator of a phage-species-specific resistance output.

  • PMID:11679349
    AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.

    Dai et al. linked AbiU to delayed phage transcription without resolving the direct phage trigger or AbiU1 target.

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

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

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

    The DefenseFinder rules table models AbiU as a one-component system requiring the AbiU__AbiU profile.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    | AbiU__AbiU | AbiU__AbiU | AbiU | Custom | 60 |

    The DefenseFinder HMM inventory records AbiU__AbiU under the AbiU model namespace.

AbiU activity delays lactococcal phage transcription

Conservative system-level sketch linking an abiU-family locus to AbiU antiphage activity, reduced c2/936/P335 phage plaquing, delayed phage 712 and c2 transcription, and AbiU-system possession without asserting the unresolved phage trigger or AbiU1 molecular target.

NONMECHANISTIC · The graph captures AbiU as a named DefenseFinder single-profile abortive-infection system whose LL51-1 prototype restricts c2, 936, and P335 lactococcal phages. It leaves the direct phage trigger, AbiU1 molecular function, AbiU2 downregulation route, natural locus breadth, and phage escape routes unresolved.

AbiU activity delays lactococcal phage transcription Interactive directed graph showing evidence-backed causal relationships for AbiU system.

Edge evidence

  • abiU locus contributes to AbiU antiphage activity RO:0002326

    The abiU-family locus encodes AbiU antiphage activity, and DefenseFinder models AbiU as a one-profile system.

  • AbiU antiphage activity contributes to lactococcal phage plaquing reduction RO:0002326

    AbiU activity reduces plaquing of c2, 936, and P335 lactococcal phages.

    • PMID:11679349 AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. Dai et al. measured AbiU activity against c2, 936, and P335 phages.
    • PMID:11679349 The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 x 10(-1), 1.0 x 10(-2), and 1.0 x 10(-1), respectively. Dai et al. quantified phage-specific AbiU EOP reductions.
  • AbiU antiphage activity contributes to phage transcription delay RO:0002326

    AbiU activity delays transcription of lactococcal phages 712 and c2.

    • PMID:11679349 AbiU appeared to delay transcription of both phage 712 and c2 Dai et al. detected delayed phage 712 and c2 transcription in the presence of AbiU.
  • lactococcal phage plaquing reduction confers AbiU system METPO:2007700

    Reduced c2/936/P335 lactococcal phage plaquing realizes the AbiU abortive-infection trait.

  • phage transcription delay contributes to AbiU system RO:0002326

    Delayed 712/c2 phage transcription contributes to the AbiU abortive-infection trait.

    • PMID:11679349 AbiU appeared to delay transcription of both phage 712 and c2 Dai et al. identified delayed phage transcription as an AbiU-associated output.
  • AbiU system is a abortive infection system rdfs:subClassOf

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

    • PMID:11679349 This study reports on the identification and characterization of a novel abortive infection system, AbiU Dai et al. place AbiU in the abortive-infection class of phage defense.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/AEM.67.11.5225-5232.2001

Parent traits (1)

Synonyms (1)

  • AbiU RELATED_SYNONYM · DOI:10.1128/AEM.67.11.5225-5232.2001

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.

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 AbiU phage trigger, direct AbiU1 and AbiU2 functions, and phage-transcription-delay route before minting narrower AbiU mechanism children.

KNOWLEDGE GAP OPEN abiu-orf-and-transcription-gap · raised by codex · 2026-09-20

Attached to causal_graphs#abiu_locus_delays_lactococcal_phage_transcription

Dai et al. support AbiU as a named lactococcal abortive-infection system that reduces plaquing of c2, 936, and P335 phages and delays 712 and c2 phage transcription. DefenseFinder represents AbiU with a one-profile rule, but this first system-level record leaves the phage trigger, AbiU1 molecular function, AbiU2 downregulation route, natural locus breadth, and phage escape routes unresolved.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted AbiU 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_v198.