AbiB system

traitmech:000319 · CLASS · PROPOSED

An abortive infection system in which an organism possesses an abiB-family locus represented by the DefenseFinder AbiB__AbiB profile and exemplified by the Lactococcus lactis IL1403 determinant whose AbiB activity blocks sensitive bIL170 phage growth and promotes rapid degradation of sensitive phage transcripts after infection.

Trait evidence (8)

PMID:8825768
The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170, but not of the resistant phage bIL41, on Lactococcus lactis strain IL1403

Parreira et al. place AbiB in the abortive-infection class and show that it blocks the sensitive lactococcal phage bIL170 on Lactococcus lactis IL1403.
PMID:8825768
AbiB promotes a dramatic degradation of sensitive phage transcripts, starting 10-15 min after infection

Parreira et al. connect AbiB activity to rapid decay of transcripts from sensitive phages after infection.
PMID:8825768
The decay of the transcripts is the probable cause of the arrest of the sensitive phage development

Parreira et al. infer that phage transcript decay causes arrest of AbiB-sensitive phage development.
PMID:8825768
Mapping of the 5' end of degradation products established that they result from endonucleolytic cleavage preferentially at U/U, A/U and U/A sites

Parreira et al. map AbiB-associated phage transcript decay products to preferential endonucleolytic cleavage sites.
PMID:8825768
an early product of the sensitive phage either induces the synthesis or stimulates the activity of an RNase in an AbiB+ cell

Parreira et al. leave the AbiB trigger and nuclease identity unresolved, favoring an open knowledge gap for narrower mechanism children.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiB | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named AbiB model namespace to a lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiB AbiB 1 1 AbiB__AbiB

The DefenseFinder rules table models AbiB as a one-component system requiring the AbiB__AbiB profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiB__AbiB | AbiB__AbiB | AbiB | Custom | 20 |

The DefenseFinder HMM inventory records AbiB__AbiB under the AbiB model namespace.

AbiB activity degrades sensitive lactococcal phage transcripts

Conservative system-level sketch linking an abiB-family locus to AbiB antiphage activity, sensitive-phage transcript degradation, sensitive-phage arrest, and abortive-infection system possession without asserting the unresolved phage trigger or nuclease effector.

NONMECHANISTIC · The graph captures AbiB as a named DefenseFinder single-profile abortive-infection system whose IL1403 prototype restricts bIL170 phage by promoting rapid sensitive-phage transcript degradation. It leaves the direct phage trigger, AbiB molecular function, RNase effector identity, natural locus breadth, and phage escape routes unresolved.

Edge evidence

abiB locus contributes to AbiB antiphage activity RO:0002326
The abiB-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiB as a one-profile system.
- PMID:8825768 The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170 Parreira et al. identify AbiB as an abortive-infection determinant that blocks sensitive phage growth.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiB AbiB 1 1 AbiB__AbiB The DefenseFinder rules table models AbiB as a one-component system requiring the AbiB__AbiB profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiB__AbiB | AbiB__AbiB | AbiB | Custom | 20 | The DefenseFinder HMM inventory records AbiB__AbiB under the AbiB model namespace.
AbiB antiphage activity contributes to sensitive phage transcript degradation RO:0002326
AbiB activity promotes rapid degradation of sensitive phage transcripts after infection.
- PMID:8825768 AbiB promotes a dramatic degradation of sensitive phage transcripts, starting 10-15 min after infection Parreira et al. connect AbiB to rapid decay of sensitive phage transcripts.
sensitive phage transcript degradation contributes to sensitive phage development arrest RO:0002326
Transcript decay probably arrests development of AbiB-sensitive phages.
- PMID:8825768 The decay of the transcripts is the probable cause of the arrest of the sensitive phage development Parreira et al. interpret phage transcript decay as the likely cause of sensitive phage developmental arrest.
sensitive phage development arrest confers AbiB system METPO:2007700
Arrest of sensitive lactococcal phage development realizes the AbiB abortive-infection trait.
- PMID:8825768 The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170 Parreira et al. show that AbiB prevents sensitive lactococcal phage growth.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiB | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiB model namespace to a lactococcal abortive-infection review.
AbiB system is a abortive infection system rdfs:subClassOf
AbiB system possession is an abortive-infection-system trait.
- PMID:8825768 The abortive infection determinant AbiB Parreira et al. place AbiB in the abortive-infection class of phage defense.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1046/j.1365-2958.1996.371896.x

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (1)

AbiB RELATED_SYNONYM · DOI:10.1046/j.1365-2958.1996.371896.x

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:10.1046/j.1365-2958.1996.371896.x Parreira et al. studied AbiB in Lactococcus lactis IL1403 and showed that it prevented sensitive bIL170 phage growth while promoting sensitive phage transcript decay.

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 AbiB phage trigger, AbiB molecular function, and RNase effector before minting narrower AbiB mechanism children.

KNOWLEDGE GAP OPEN abib-trigger-and-rnase-gap · raised by codex · 2026-09-20

Attached to causal_graphs#abib_locus_degrades_sensitive_phage_transcripts

Parreira et al. support AbiB as a named lactococcal abortive-infection determinant that prevents bIL170 growth and promotes sensitive phage transcript degradation. DefenseFinder represents AbiB with a one-profile rule, but this first system-level record leaves the phage trigger, AbiB molecular function, RNase effector identity, natural locus breadth, and phage escape routes unresolved.

Curation history

2026-09-20T21:21:12Z · MINTED_TRAITMECH_ID · codex
Minted AbiB 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_v196.