AbiO system

traitmech:000342 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a single-component AbiO-family locus represented by DefenseFinder as a mandatory AbiO__AbiO profile.

Trait evidence (8)

DOI:10.3168/jds.S0022-0302(98)75713-3
Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO

Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI.
DOI:10.1093/femsre/fuag009
the majority (18 systems) are each represented by single protein-coding genes

The FEMS review lists AbiO among the confirmed lactococcal Abi-like systems in Table 1 and omits AbiO from the named two- and three-component exception lists.
DOI:10.1093/femsre/fuag009
the AbiO N-terminal domain resembles a restriction endonuclease type II-like domain-containing protein

The FEMS review summarizes a predicted nuclease-like AbiO N-terminal domain but does not establish the exact AbiO trigger or effector activity.
DOI:10.1093/femsre/fuag009
Its C-terminal domain is predicted to encompass a superfamily 1B (SF1B) helicase

The FEMS review summarizes a predicted SF1B helicase-like AbiO C-terminal domain without resolving how AbiO arrests infected cells.
DOI:10.1093/femsre/fuag009
AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector

The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiO | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

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

The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiO__AbiO | AbiO__AbiO | AbiO | Custom | 50 |

The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace.

AbiO loci confer abortive-infection phage defense

Conservative system-level sketch linking possession of a DefenseFinder AbiO locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, predicted nuclease activity, or predicted helicase activity.

NONMECHANISTIC · The graph captures AbiO as a named single-profile lactococcal Abi-like system with the DefenseFinder AbiO__AbiO HMM while leaving its direct phage trigger, restriction-endonuclease interpretation, helicase interpretation, exact molecular activity, phage escape routes, and growth-arrest or cell-death route unresolved.

Edge evidence

AbiO locus contributes to restricted phage propagation RO:0002326
The DefenseFinder AbiO namespace is modeled as a one-profile AbiO__AbiO system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv AbiO AbiO 1 1 AbiO__AbiO The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | AbiO__AbiO | AbiO__AbiO | AbiO | Custom | 50 | The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace.
restricted phage propagation confers AbiO system METPO:2007700
Restriction of phage propagation realizes the AbiO abortive-infection system possession trait.
- DOI:10.3168/jds.S0022-0302(98)75713-3 Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI.
- DOI:10.1093/femsre/fuag009 AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype.
AbiO system is a abortive infection system rdfs:subClassOf
AbiO system possession is an abortive-infection-system trait.
- DOI:10.3168/jds.S0022-0302(98)75713-3 Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md AbiO | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named AbiO model namespace to the Chopin et al. lactococcal abortive-infection review.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.3168/jds.S0022-0302(98)75713-3

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (2)

AbiO RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
AbiO__AbiO RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

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 AbiO phage trigger, restriction-endonuclease and helicase activity, and growth-arrest or cell-death route before minting narrower AbiO mechanism children.

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

Attached to causal_graphs#abio_locus_restricts_lactococcal_phage

Prevots and Ritzenthaler support AbiO as a lactococcal abortive phage resistance gene, the FEMS review retains AbiO among confirmed lactococcal Abi-like systems, and DefenseFinder represents AbiO with a mandatory AbiO__AbiO profile. The FEMS table leaves the AbiO effect on the cell and phage escape proteins unknown for the tested phages, and the FEMS structural discussion predicts restriction-endonuclease-like and SF1B-helicase-like domains while not resolving the molecular trigger or effector activity. This first system-level record therefore leaves the direct phage trigger, exact molecular activity, growth-arrest or cell-death route, and phage escape routes unresolved.

Evidence

DOI:10.1093/femsre/fuag009
the AbiO N-terminal domain resembles a restriction endonuclease type II-like domain-containing protein
DOI:10.1093/femsre/fuag009
Its C-terminal domain is predicted to encompass a superfamily 1B (SF1B) helicase
DOI:10.1093/femsre/fuag009
AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
AbiO AbiO 1 1 AbiO__AbiO
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| AbiO__AbiO | AbiO__AbiO | AbiO | Custom | 50 |

Curation history

2026-09-21T18:34:41Z · MINTED_TRAITMECH_ID · codex
Minted AbiO 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_v219.