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AbiAlpha system

traitmech:000322 · CLASS · PROPOSED

An abortive infection system in which an organism possesses an abi-alpha-family locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile and exemplified by the Enterococcus faecalis V583 prophage 6 abi-alpha determinant, whose encoded DUF4393/PF14337-family activity perturbs the Idefix lytic cycle and causes premature lysis of infected Enterococcus faecalis.

Trait evidence (8)

  • PMID:30634666
    We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abiα.

    Lossouarn et al. named a new Abi mechanism from Enterococcus faecalis V583 prophage 6.

  • PMID:30634666
    It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis

    Lossouarn et al. connected AbiAlpha to DUF4393 and an infected-cell premature-lysis phenotype.

  • PMID:30634666
    The abiα gene is widespread among prophages of enterococci and other Gram-positive bacteria.

    Lossouarn et al. describe AbiAlpha homologs as prophage features rather than a single V583-only gene.

  • DOI:10.3390/v11010048
    These results confirmed that ef2833 is responsible for the abortive mechanism.

    Lossouarn et al. experimentally connected ef2833 to the V583 prophage 6 Abi phenotype.

  • DOI:10.3390/v11010048
    We concluded that Abiα provokes a lysis asynchrony.

    Lossouarn et al. linked the AbiAlpha mechanism to altered Idefix lysis timing.

  • DOI:10.3390/v11010048
    Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed

    Lossouarn et al. summarized the system as infected-cell death with perturbed Idefix lytic-cycle progression.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    AbiAlpha | 10\.3390/v11010048 | Enterococcus faecalis countermeasures defeat a virulent Picovirinae bacteriophage

    The DefenseFinder article registry maps the named AbiAlpha model namespace to the enterococcal AbiAlpha discovery paper.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    | AbiAlpha__AbiAlpha | | AbiAlpha | PF14337.11 | 27.1 |

    The DefenseFinder HMM inventory records AbiAlpha__AbiAlpha under the AbiAlpha model namespace with Pfam PF14337.11.

AbiAlpha perturbs Idefix lysis in Enterococcus faecalis

Conservative system-level sketch linking an abi-alpha-family locus to AbiAlpha antiphage activity, Idefix lytic-cycle perturbation, premature lysis of infected Enterococcus faecalis, and AbiAlpha-system possession without asserting the direct DUF4393-family molecular target.

NONMECHANISTIC · The graph captures AbiAlpha as a named DefenseFinder single-profile abortive-infection system whose V583 prophage 6 prototype restricts Idefix by perturbing lysis timing. It leaves the direct phage trigger, DUF4393-family molecular function, direct Idefix target, natural host range, and phage escape routes unresolved.

AbiAlpha perturbs Idefix lysis in Enterococcus faecalis Interactive directed graph showing evidence-backed causal relationships for AbiAlpha system.

Edge evidence

  • abi-alpha locus contributes to AbiAlpha antiphage activity RO:0002326

    The abi-alpha-family locus encoded by V583 prophage 6 is responsible for AbiAlpha antiphage activity, and DefenseFinder models AbiAlpha as a single PF14337-family HMM profile.

  • AbiAlpha antiphage activity contributes to Idefix lytic-cycle perturbation RO:0002326

    AbiAlpha activity perturbs the Idefix lytic cycle in infected Enterococcus faecalis cells.

    • DOI:10.3390/v11010048 Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed Lossouarn et al. summarized the AbiAlpha output as death of infected cells while the Idefix lytic cycle is perturbed.
  • AbiAlpha antiphage activity contributes to infected-cell premature lysis RO:0002326

    AbiAlpha activity causes premature lysis of Idefix-infected Enterococcus faecalis.

    • PMID:30634666 conferred a typical Abi phenotype by causing a premature lysis Lossouarn et al. reported premature lysis as the AbiAlpha-infected-cell output.
    • DOI:10.3390/v11010048 Based on our results, we can only speculate that Abiα interferes with lysis Lossouarn et al. framed the direct AbiAlpha lysis target as unresolved.
  • Idefix lytic-cycle perturbation contributes to AbiAlpha system RO:0002326

    Perturbation of Idefix lytic-cycle progression contributes to the AbiAlpha system trait.

    • DOI:10.3390/v11010048 Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed Lossouarn et al. connected AbiAlpha with Idefix lytic-cycle perturbation.
  • infected-cell premature lysis confers AbiAlpha system METPO:2007700

    Premature lysis of Idefix-infected Enterococcus faecalis realizes the AbiAlpha abortive-infection trait.

  • AbiAlpha system is a abortive infection system rdfs:subClassOf

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

    • PMID:30634666 a new abortive infection (Abi) mechanism, which we designated Abiα Lossouarn et al. place AbiAlpha in the abortive-infection class of phage defense.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.3390/v11010048

Parent traits (1)

Synonyms (1)

  • AbiAlpha 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.

  • Enterococcus faecalis NCBITaxon:1351 DOI:10.3390/v11010048 Lossouarn et al. characterized AbiAlpha from Enterococcus faecalis V583 prophage 6 and showed that it causes premature lysis during Idefix infection.

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 AbiAlpha direct molecular target, Idefix trigger, lysis route, natural host range, and phage escape routes before minting narrower AbiAlpha mechanism children.

KNOWLEDGE GAP OPEN abialpha-lysis-route-gap · raised by codex · 2026-09-20

Attached to causal_graphs#abialpha_locus_causes_enterococcal_premature_lysis

Lossouarn et al. support AbiAlpha as a prophage-encoded Enterococcus faecalis abortive-infection system that maps to DUF4393/PF14337 and perturbs Idefix lysis timing. DefenseFinder represents AbiAlpha with a one-profile HMM inventory row but does not resolve the direct phage trigger, DUF4393-family molecular function, Idefix lysis target, natural host range, or escape routes.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted AbiAlpha 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_v199.

  2. · EDIT · codex

    Addressed PR 1163 review issue 1165 by broadening the AbiAlpha class boundary from a prophage locus to an abi-alpha-family locus while keeping Enterococcus faecalis V583 prophage 6 as the characterized example.

  3. · EDIT · codex

    Re-copied the DefenseFinder AbiAlpha HMM registry row byte-exactly from the pinned Liste_hmm_system.md source while confirming the article-registry title casing against List_system_article.md for PR 1163 review issue 1168.