AbiR system

traitmech:000317 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a multicomponent AbiR determinant represented by the DefenseFinder AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles and capable of restricting lactococcal phage propagation by an early abortive-infection mechanism that impedes phage DNA replication, as exemplified by the two pKR223 loci from Lactococcus lactis subsp. lactis KR2 separated by the LlaKR2I restriction-modification genes.

Trait evidence (10)

PMID:10831451
The native lactococcal plasmid pKR223 encodes two distinct phage resistance mechanisms, a restriction and modification (R/M) system designated LlaKR2I and an abortive infection mechanism (Abi) which affects prolate-headed-phage proliferation

Twomey et al. identify native Lactococcus lactis plasmid pKR223 as the source of a restriction-modification system and a separate abortive-infection determinant.
PMID:10831451
sequence analysis has validated the novelty of the Abi system, which has now been designated AbiR

Twomey et al. name AbiR as the novel abortive-infection system from pKR223.
PMID:10831451
Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes

Twomey et al. show that the AbiR phenotype requires two pKR223 loci separated by the LlaKR2I restriction-modification genes.
PMID:10831451
Mechanistic studies on the AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication

Twomey et al. connect AbiR activity to a heat-sensitive abortive-infection phenotype that impedes phage DNA replication.
PMID:10831451
These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning Abi system

Twomey et al. classify AbiR as a multicomponent early abortive-infection system.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiR | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named AbiR model namespace to a lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiR AbiR 3 3 AbiR__AbiRa, AbiR__AbiRb, AbiR__AbiRc

The DefenseFinder rules table models AbiR as a three-component system requiring the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiR__AbiRa | AbiR__AbiRa | AbiR | Custom | 20 |

The DefenseFinder HMM inventory records AbiR__AbiRa under the AbiR model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiR__AbiRb | AbiR__AbiRb | AbiR | Custom | 20 |

The DefenseFinder HMM inventory records AbiR__AbiRb under the AbiR model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiR__AbiRc | AbiR__AbiRc | AbiR | Custom | 20 |

The DefenseFinder HMM inventory records AbiR__AbiRc under the AbiR model namespace.

AbiR activity impedes lactococcal phage DNA replication

Conservative system-level sketch linking the separated pKR223 AbiR loci to AbiR antiphage activity, impeded phage DNA replication, restricted lactococcal phage propagation, and abortive-infection system possession without resolving the phage trigger or individual component activities.

NONMECHANISTIC · The graph captures AbiR as a named DefenseFinder three-profile abortive-infection system whose pKR223 prototype is encoded by two genetic loci and impedes phage DNA replication. It leaves the direct phage trigger, the profile-to-locus mapping, AbiRa, AbiRb, and AbiRc molecular functions, the reason the R/M genes interrupt the two AbiR loci, and phage escape routes unresolved.

Edge evidence

AbiR loci contributes to AbiR antiphage activity RO:0002326
The pKR223 AbiR determinant is encoded by two genetic loci separated by LlaKR2I genes, and DefenseFinder models AbiR as a three-profile system requiring AbiRa, AbiRb, and AbiRc components.
- PMID:10831451 Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes Twomey et al. show that the AbiR phenotype requires two separated pKR223 genetic loci.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiR AbiR 3 3 AbiR__AbiRa, AbiR__AbiRb, AbiR__AbiRc The DefenseFinder rules table models AbiR as a three-component system requiring the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiR__AbiRa | AbiR__AbiRa | AbiR | Custom | 20 | The DefenseFinder HMM inventory records AbiR__AbiRa under the AbiR model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiR__AbiRb | AbiR__AbiRb | AbiR | Custom | 20 | The DefenseFinder HMM inventory records AbiR__AbiRb under the AbiR model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiR__AbiRc | AbiR__AbiRc | AbiR | Custom | 20 | The DefenseFinder HMM inventory records AbiR__AbiRc under the AbiR model namespace.
AbiR antiphage activity mitigates phage DNA replication METPO:2007407
AbiR antiphage activity impedes sensitive phage DNA replication as an early abortive-infection output.
- PMID:10831451 Mechanistic studies on the AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication Twomey et al. classify the AbiR phenotype as heat-sensitive and DNA-replication impeding.
AbiR antiphage activity contributes to restricted phage propagation RO:0002326
AbiR antiphage activity affects prolate-headed-phage proliferation through a multicomponent early Abi mechanism.
- PMID:10831451 These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning Abi system Twomey et al. summarize the AbiR phenotype as multicomponent, heat-sensitive, and early functioning.
restricted phage propagation confers AbiR system METPO:2007700
Restriction of lactococcal phage propagation realizes the AbiR abortive-infection trait.
- PMID:10831451 sequence analysis has validated the novelty of the Abi system, which has now been designated AbiR Twomey et al. name AbiR as the novel pKR223 abortive-infection system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiR | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiR model namespace to a lactococcal abortive-infection review.
AbiR system is a abortive infection system rdfs:subClassOf
AbiR system possession is an abortive-infection-system trait.
- PMID:10831451 These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning Abi system Twomey et al. classify AbiR in the abortive-infection class of phage defense.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1128/AEM.66.6.2647-2651.2000

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (1)

AbiR RELATED_SYNONYM · DOI:10.1128/AEM.66.6.2647-2651.2000

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:10.1128/AEM.66.6.2647-2651.2000 Twomey et al. characterized AbiR from native plasmid pKR223 of Lactococcus lactis subsp. lactis KR2 and showed a multicomponent, two-locus Abi phenotype that impeded phage DNA replication.

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 AbiR phage trigger, profile-to-locus mapping, and AbiRa, AbiRb, and AbiRc molecular functions before minting narrower AbiR mechanism children.

KNOWLEDGE GAP OPEN abir-component-activity-gap · raised by codex · 2026-09-20

Attached to causal_graphs#abir_loci_impede_phage_dna_replication

Twomey et al. support AbiR as a multicomponent abortive-infection system encoded by two separated pKR223 loci, and DefenseFinder represents AbiR with a three-profile rule. This first system-level record leaves the phage trigger, the mapping from the two original genetic loci to AbiRa, AbiRb, and AbiRc profiles, the component molecular activities, and the direct reason that AbiR impedes phage DNA replication unresolved.

Evidence

PMID:10831451
Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes

Curation history

2026-09-20T19:30:10Z · MINTED_TRAITMECH_ID · codex
Minted AbiR 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_v194.
2026-09-20T20:02:22Z · REVISED_SCOPE · codex
Addressed PR 1154 review issue 1155 by narrowing the AbiR definition to the DefenseFinder AbiR determinant and treating the two separated pKR223 loci from Lactococcus lactis subsp. lactis KR2 as exemplar evidence rather than a constitutive class restriction.