AbiA system

traitmech:000344 · CLASS · PROPOSED

An abortive infection system in which an organism possesses an AbiA-family locus whose copy number or expression modulates Lactococcus lactis resistance to multiple phages and that DefenseFinder represents with AbiA_large or AbiA_small model subrules.

Trait evidence (12)

PMID:16349225
The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication.

Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication.
PMID:16349225
Three abiA-containing plasmids of various copy numbers were introduced into both strains, and the recombinants were evaluated for resistance to phages c2, p2, sk1, and phi31.

Dinsmore and Klaenhammer tested AbiA across two Lactococcus lactis strains and four lactococcal phages.
PMID:16349225
Altering the gene dosage or expression level of abiA significantly affects the phage resistance levels.

Dinsmore and Klaenhammer show that AbiA dosage or expression modulates the strength of lactococcal phage resistance.
PMID:9661658
The abiA gene encodes an abortive bacteriophage infection mechanism that can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species.

Dinsmore and Klaenhammer support AbiA as a broad lactococcal abortive-infection mechanism.
PMID:9661658
the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.

Dinsmore and Klaenhammer connect residues in AbiA's leucine-repeat region to resistance against c2, sk1, and phi31.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiA | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

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

The DefenseFinder rules table models one AbiA subrule as the single-profile AbiA_large subsystem.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiA AbiA_small 2 2 AbiA_small__AbiA_SLATT, AbiA_small__AbiA_small

The DefenseFinder rules table models one AbiA subrule as a two-profile AbiA_small subsystem.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiA_large__AbiA_large | AbiA_large__AbiA_large | AbiA_large | Custom | 250 |

The DefenseFinder HMM inventory records AbiA_large__AbiA_large under the AbiA_large model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiA_small__AbiA_SLATT | AbiA_small__AbiA_SLATT | AbiA_small | Custom | 20 |

The DefenseFinder HMM inventory records AbiA_small__AbiA_SLATT under the AbiA_small model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiA_small__AbiA_small | AbiA_small__AbiA_small | AbiA_small | Custom | 300 |

The DefenseFinder HMM inventory records AbiA_small__AbiA_small under the AbiA_small model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiA_small__SLATT | | AbiA_small | Custom | 40 |

The DefenseFinder HMM inventory also records AbiA_small__SLATT under the AbiA_small model namespace.

AbiA activity inhibits lactococcal phage DNA replication

Conservative system-level sketch linking an AbiA-family locus to phage-DNA-replication inhibition, reduced lactococcal phage propagation, and AbiA-system possession without asserting the unresolved direct phage trigger or molecular target.

NONMECHANISTIC · The graph captures AbiA as a named DefenseFinder abortive-infection system with AbiA_large and AbiA_small subrules. It leaves the direct phage trigger, the natural boundaries of the DefenseFinder subrules, the molecular effector activity, the DNA-replication target, and phage escape routes unresolved.

Edge evidence

AbiA locus contributes to phage DNA replication inhibition RO:0002326
AbiA activity inhibits phage DNA replication, and DefenseFinder represents AbiA with AbiA_large and AbiA_small model subrules.
- PMID:16349225 The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication. Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiA AbiA_large 1 1 AbiA_large__AbiA_large The DefenseFinder rules table models one AbiA subrule as the single-profile AbiA_large subsystem.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiA AbiA_small 2 2 AbiA_small__AbiA_SLATT, AbiA_small__AbiA_small The DefenseFinder rules table models one AbiA subrule as a two-profile AbiA_small subsystem.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiA_large__AbiA_large | AbiA_large__AbiA_large | AbiA_large | Custom | 250 | The DefenseFinder HMM inventory records AbiA_large__AbiA_large under the AbiA_large model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiA_small__AbiA_small | AbiA_small__AbiA_small | AbiA_small | Custom | 300 | The DefenseFinder HMM inventory records AbiA_small__AbiA_small under the AbiA_small model namespace.
AbiA locus contributes to reduced lactococcal phage propagation RO:0002326
Changing abiA dosage or expression changes Lactococcus lactis resistance to c2, p2, sk1, and phi31.
- PMID:16349225 Altering the gene dosage or expression level of abiA significantly affects the phage resistance levels. Dinsmore and Klaenhammer connected abiA dosage and expression to lactococcal phage resistance level.
reduced lactococcal phage propagation confers AbiA system METPO:2007700
AbiA-mediated reduction of lactococcal phage propagation realizes the AbiA system trait.
- PMID:9661658 can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species Dinsmore and Klaenhammer describe the AbiA system as protecting Lactococcus from multiple phage species.
AbiA system is a abortive infection system rdfs:subClassOf
AbiA system possession is an abortive-infection-system trait.
- PMID:16349225 The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication. Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiA | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiA model namespace to a lactococcal abortive-infection review.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1128/aem.60.4.1129-1136.1994

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (4)

AbiA RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiA_large RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
AbiA_small RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
hsp RELATED_SYNONYM · DOI:10.1128/aem.60.4.1129-1136.1994

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.60.4.1129-1136.1994 Dinsmore and Klaenhammer varied abiA copy number in Lactococcus lactis MG1363 and NCK203 and assayed resistance to phages c2, p2, sk1, and phi31.

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 AbiA_large and AbiA_small system boundaries, phage trigger, direct DNA-replication target, and molecular effector output before minting narrower AbiA mechanism children.

KNOWLEDGE GAP OPEN abia-defensefinder-subrule-gap · raised by codex · 2026-09-21

Attached to causal_graphs#abia_locus_inhibits_phage_dna_replication

Dinsmore and Klaenhammer support AbiA as a lactococcal abortive-infection determinant whose copy number or expression changes phage resistance and whose leucine-repeat region is required for activity against multiple phage species. DefenseFinder models AbiA through AbiA_large and AbiA_small subrules, but this first system-level record leaves those subrules' natural locus boundaries, the direct phage trigger, the molecular effector output, the exact phage-DNA-replication target, and phage escape routes unresolved.

Evidence

PMID:16349225
The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication.
PMID:9661658
the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiA AbiA_large 1 1 AbiA_large__AbiA_large
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiA AbiA_small 2 2 AbiA_small__AbiA_SLATT, AbiA_small__AbiA_small
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiA_large__AbiA_large | AbiA_large__AbiA_large | AbiA_large | Custom | 250 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiA_small__AbiA_small | AbiA_small__AbiA_small | AbiA_small | Custom | 300 |

Curation history

2026-09-21T20:16:02Z · MINTED_TRAITMECH_ID · codex
Minted AbiA 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_v221.
2026-09-21T20:44:00Z · ADDRESS_PR_REVIEW · codex
Addressed PR #1218 review issues #1219 and #1220 by aligning the v221 METPO ROBOT TSV definition with this TraitRecord and moving the AbiA dosage and expression evidence onto a direct AbiA locus edge.