AbiJ system

traitmech:000339 · CLASS · PROPOSED

An abortive infection system in which an organism possesses an AbiJ-family locus represented by the DefenseFinder AbiJ model namespace and mandatory AbiJ__AbiJ profile.

Trait evidence (9)

DOI:10.1111/j.1574-6968.1997.tb10185.x
A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis

Europe PMC metadata verifies the Deng et al. 1997 AbiJ primary paper title and PMID:8997719; the DOI landing page was Cloudflare-blocked and Europe PMC exposed no abstract or full text, so this record cites Deng et al. for the primary AbiJ identity and uses later accessible sources for snippet-backed system details.
DOI:10.1093/femsre/fuag009
Experimentally confirmed lactococcal Abi-like systems, as well as information on their antiphage activity range

The FEMS review frames Table 1 as a curated set of experimentally confirmed lactococcal Abi-like systems.
DOI:10.1093/femsre/fuag009
AbiJ (Also abi-859)

The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems.
DOI:10.1073/pnas.2426508122
we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)

Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation.
DOI:10.1093/femsre/fuag009
AbiA escape mutants also circumvent AbiJ, which was not observed for other combinations

The FEMS review summarizes Mosterd et al.'s escape-mutant evidence linking AbiA escape mutations to AbiJ bypass while not yet identifying AbiJ's direct molecular trigger.
DOI:10.1093/femsre/fuag009
Although no particular mechanistic information is currently available for AbiJ

The FEMS review explicitly keeps AbiJ mechanism unresolved; this record therefore avoids protein-level chemistry and TA-system mechanism claims.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiJ | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named AbiJ model namespace to the Chopin et al. lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiJ AbiJ 1 1 AbiJ__AbiJ

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

The DefenseFinder HMM inventory records AbiJ__AbiJ under the AbiJ model namespace.

AbiJ loci confer abortive-infection phage defense

Conservative system-level sketch linking possession of a DefenseFinder AbiJ locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, molecular activity, or arrest route.

NONMECHANISTIC · The graph captures AbiJ as a named single-profile lactococcal abortive-infection system with a DefenseFinder AbiJ__AbiJ HMM profile while leaving its direct phage trigger, AbiJ molecular function, exact relationship to AbiA escape routes, natural locus breadth, and cell-arrest or death route unresolved.

Edge evidence

AbiJ locus contributes to restricted phage propagation RO:0002326
The DefenseFinder AbiJ namespace is modeled as a one-profile AbiJ__AbiJ system, and AbiJ is a plasmid-encoded lactococcal phage-resistance system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiJ AbiJ 1 1 AbiJ__AbiJ The DefenseFinder rules table models AbiJ as a one-component system requiring the AbiJ__AbiJ profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiJ__AbiJ | AbiJ__AbiJ | AbiJ | Custom | 20 | The DefenseFinder HMM inventory records AbiJ__AbiJ under the AbiJ model namespace.
- DOI:10.1073/pnas.2426508122 we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP) Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation.
restricted phage propagation confers AbiJ system METPO:2007700
Restriction of phage propagation realizes the AbiJ abortive-infection system possession trait.
- DOI:10.1093/femsre/fuag009 AbiJ (Also abi-859) The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems.
- DOI:10.1073/pnas.2426508122 we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP) Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation.
AbiJ system is a abortive infection system rdfs:subClassOf
AbiJ system possession is an abortive-infection-system trait.
- DOI:10.1093/femsre/fuag009 AbiJ (Also abi-859) The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiJ | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiJ model namespace to the Chopin et al. lactococcal abortive-infection review.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1111/j.1574-6968.1997.tb10185.x

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (3)

AbiJ RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiJ__AbiJ RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
abi-859 RELATED_SYNONYM · DOI:10.1093/femsre/fuag009

kg-microbe context

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

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 AbiJ phage trigger, molecular activity, and exact AbiA escape-mutant overlap before minting narrower AbiJ mechanism children.

KNOWLEDGE GAP OPEN abij-trigger-and-effector-gap · raised by codex · 2026-09-21

Attached to causal_graphs#abij_locus_restricts_lactococcal_phage

Deng et al. support AbiJ as a lactococcal plasmid-encoded abortive-infection system, and DefenseFinder represents AbiJ with a one-profile rule. Mosterd et al. show that AbiJ escape behavior overlaps with AbiA escape mutants, but the FEMS review notes that AbiJ still lacks a resolved mechanism. This first system-level record therefore leaves AbiJ's direct phage trigger, molecular effector activity, natural locus breadth, exact HEPN-domain interpretation, growth-arrest or cell-death route, and phage escape routes unresolved.

Evidence

DOI:10.1093/femsre/fuag009
While AbiB and AbiJ show only weak predictions (HHpred hits for HEPN domain containing-proteins with E-values > 0.1) or lack identifiable functional domains based on InterPro and HHpred
DOI:10.1093/femsre/fuag009
Although no particular mechanistic information is currently available for AbiJ

Curation history

2026-09-21T16:24:09Z · MINTED_TRAITMECH_ID · codex
Minted AbiJ 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_v216.
2026-09-21T16:48:47Z · FIX_EVIDENCE_SNIPPET · codex
Replaced the AbiJ subclass-edge FEMS table-heading evidence with the AbiJ-specific table row after PR 1208 review issue 1209 found that the original snippet did not itself mention AbiJ.