abortive infection system

traitmech:000214 · CLASS · PROPOSED

A genomics trait describing possession of a bacteriophage abortive-infection defense system in which phage infection activates a host-encoded growth-arrest or cell-death program that prevents completion of phage replication and protects nearby bacterial cells.

Trait evidence (4)

DOI:10.1146/annurev-virology-011620-040628
A commonly used phage resistance strategy is abortive infection (Abi), in which the infected cell commits suicide before the phage can complete its replication cycle

Lopatina et al. support abortive infection as a phage resistance strategy that blocks completion of the phage replication cycle.
DOI:10.1146/annurev-virology-011620-040628
The Abi strategy is manifested by a plethora of mechanistically diverse defense systems that are abundant in bacterial genomes

Lopatina et al. support defining the trait at the broad Abi system level rather than as one toxin-antitoxin family.
DOI:10.1073/pnas.0808832106
Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population

Fineran et al. summarize the cell-death and phage-limitation outputs of abortive infection systems.
DOI:10.1093/nar/gkt1419
AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism

Dy et al. support AbiE as a bacteriostatic toxin-antitoxin Abi family, one reason the parent record should cover growth arrest as well as cell death.

Abortive infection halts infected cells to limit phage spread

Evidence-backed process sketch linking phage-triggered Abi activation to infected-host growth arrest or death, restricted phage replication, and protection of nearby bacterial cells.

NONMECHANISTIC · The graph captures the shared Abi strategy without claiming that other abortive-infection families use one exact sensor, effector, toxin-antitoxin architecture, or cell-death mechanism.

Edge evidence

phage infection activates abortive infection system activation RO:0002213
Phage infection triggers Abi defense-system activation.
- DOI:10.1093/nar/gkt1419 Bacterial abortive infection (Abi) systems are ‘altruistic’ cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population Dy et al. support phage-triggered activation as a defining Abi-system behavior.
abortive infection system activation activates host growth arrest or cell death RO:0002213
Abi activation produces growth-arrest or cell-death outputs through family-specific effectors.
- DOI:10.1073/pnas.0808832106 Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population Fineran et al. support cell death as an abortive-infection output.
- DOI:10.1093/nar/gkt1419 AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism Dy et al. support bacteriostasis as an AbiE output, distinct from obligate cell death.
host growth arrest or cell death mitigates phage replication METPO:2007407
Arrest or death of the infected host cell limits completion of phage replication.
- DOI:10.1146/annurev-virology-011620-040628 A commonly used phage resistance strategy is abortive infection (Abi), in which the infected cell commits suicide before the phage can complete its replication cycle Lopatina et al. connect infected-cell death to premature phage-cycle termination.
host growth arrest or cell death contributes to bacterial population protection RO:0002326
The local cost of infected-cell arrest or death protects neighboring bacteria by limiting onward phage spread.
- DOI:10.1146/annurev-virology-011620-040628 Abi prevents the phage epidemic from spreading to nearby cells, thus protecting the bacterial colony Lopatina et al. support the population-level benefit of abortive infection.
host growth arrest or cell death confers abortive infection system METPO:2007700
Phage-triggered infected-host arrest or death realizes the abortive-infection defense phenotype.
- DOI:10.1073/pnas.0808832106 abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population Fineran et al. support cell death coupled to limited phage replication as the Abi defense output.
abortive infection system is a phage defense system rdfs:subClassOf
Abortive-infection-system possession is a phage-defense-system trait.
- DOI:10.1146/annurev-virology-011620-040628 The Abi strategy is manifested by a plethora of mechanistically diverse defense systems that are abundant in bacterial genomes Lopatina et al. place abortive infection among bacterial antiviral defense systems.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1146/annurev-virology-011620-040628

Parent traits (1)

phage defense system traitmech:000209

Children (33)

Synonyms (1)

Abi system EXACT_SYNONYM · DOI:10.1093/nar/gkt1419

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.

Pectobacterium atrosepticum NCBITaxon:29471 DOI:10.1073/pnas.0808832106 Fineran et al. identified the native toxIN locus from Erwinia carotovora subspecies atroseptica 1039 and demonstrated ToxIN-mediated phage resistance.

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 other abortive-infection families before minting narrower children under the broad abortive infection system parent.

KNOWLEDGE GAP OPEN abortive-infection-subfamily-split-gap · raised by codex · 2026-09-15

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

ToxIN, AbiQ, AbiE, AbiF, AbiZ, AbiK, AbiT, AbiV, BstA, Stk2, AbiH, AbiG, AbiI, AbiR, AbiD, AbiB, AbiC, AbiU, AbiAlpha, Pif, RexAB, SpbK, CmdTAC, Abi2, AbiJ, AbiL, AbiN, AbiO, AbiP2, AbiA, and PD-T4-10 are split out as traitmech:000226, traitmech:000225, traitmech:000227, traitmech:000504, traitmech:000228, traitmech:000229, traitmech:000230, traitmech:000300, traitmech:000301, traitmech:000303, traitmech:000304, traitmech:000306, traitmech:000316, traitmech:000317, traitmech:000318, traitmech:000319, traitmech:000320, traitmech:000321, traitmech:000322, traitmech:000323, traitmech:000324, traitmech:000325, traitmech:000335, traitmech:000338, traitmech:000339, traitmech:000340, traitmech:000341, traitmech:000342, traitmech:000343, traitmech:000344, and traitmech:000394, respectively. Lopatina et al., Fineran et al., Dy et al., Garvey et al., Durmaz and Klaenhammer, Wang et al., Bouchard et al., Haaber et al., Owen et al., Depardieu et al., Prevots et al., O'Connor et al., Su et al., Twomey et al., McLandsborough et al., Parreira et al., Durmaz et al., Dai et al., Lossouarn et al., Cram et al., Parma et al., Johnson et al., Vassallo et al., Chopin et al., Anba et al., Deng et al., Prevots et al., Prevots and Ritzenthaler, Odegrip et al., Dinsmore and Klaenhammer, and Dinsmore et al. still support abortive infection as a genomically encoded phage defense strategy that spans mechanistically diverse toxin-antitoxin, pNP40-derived lactococcal AbiF DNA-replication-inhibition, premature-lysis, RT-related polymerase, two-component, translation-inhibition, prophage-encoded DNA-replication-inhibition, staphylococcal-kinase-triggered cell death, lactococcal AbiH phage resistance, two-gene lactococcal AbiG RNA-synthesis interference, single-ORF lactococcal AbiI burst-size reduction, two-separated-locus lactococcal AbiR DNA-replication impediment, pBF61-derived lactococcal AbiD burst-size reduction, lactococcal AbiB phage-transcript decay, lactococcal AbiC Prf infected-cell death, lactococcal AbiU phage-transcription delay, enterococcal AbiAlpha premature lysis, F-plasmid pif-region T7 abortive infection, lambda Rex two-component phage exclusion, ICEBs1 SpbK abortive SPβ defense, CmdTAC mRNA ADP-ribosyltransferase abortive infection, DefenseFinder Abi2/PF07751 Abi-like loci, single-profile lactococcal AbiJ loci, two-component lactococcal AbiL ATPase/TOPRIM-family loci, single-gene lactococcal AbiN loci, single-profile lactococcal AbiO loci, single-profile coliphage AbiP2 reverse-transcriptase-like loci, lactococcal AbiA loci represented by DefenseFinder AbiA-large and AbiA-small subrules, DefenseFinder PD-T4-10 two-profile loci, and other families. Additional narrower TraitRecords need separate review to ground each subfamily's trigger, effector, growth-arrest or cell-death mechanism, and phage escape routes.

Curation history

2026-09-15T11:47:52Z · MINTED_TRAITMECH_ID · codex
Minted abortive infection system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v91.
2026-09-15T18:45:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Removed AbiQ from the open abortive-infection subfamily split-gap discussion after minting traitmech:000225 for the AbiQ system; ToxIN, AbiE, and other abortive-infection families remain open.
2026-09-15T19:25:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Removed ToxIN from the open abortive-infection subfamily split-gap discussion after minting traitmech:000226 for the ToxIN system; AbiE and other abortive-infection families remain open.
2026-09-15T19:46:31Z · RESOLVE_DISCUSSION_SCOPE · codex
Removed AbiE from the open abortive-infection subfamily split-gap discussion after minting traitmech:000227 for the AbiE system; other abortive-infection families remain open.
2026-09-15T20:35:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiZ as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000228 for the AbiZ system; other abortive-infection families remain open.
2026-09-15T21:30:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiK as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000229 for the AbiK system; other abortive-infection families remain open.
2026-09-15T22:05:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiT as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000230 for the AbiT system; other abortive-infection families remain open.
2026-09-20T03:07:26Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiV as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000300 for the AbiV system; other abortive-infection families remain open.
2026-09-20T04:10:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Reframed AbiV in the open abortive-infection subfamily split-gap discussion as a translation-inhibition family after adding the Haaber et al. AbiV-SaV follow-up evidence.
2026-09-20T04:37:49Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented BstA as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000301 for the BstA system; other abortive-infection families remain open.
2026-09-20T07:41:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented Stk2 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000303 for the Stk2 system; other abortive-infection families remain open.
2026-09-20T08:12:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiH as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000304 for the AbiH system; other abortive-infection families remain open.
2026-09-20T09:16:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiG as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000306 for the AbiG system; other abortive-infection families remain open.
2026-09-20T18:33:35Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiI as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000316 for the AbiI system; other abortive-infection families remain open.
2026-09-20T19:30:11Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiR as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000317 for the AbiR system; other abortive-infection families remain open.
2026-09-20T20:30:21Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiD as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000318 for the AbiD system; other abortive-infection families remain open.
2026-09-20T21:21:13Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiB as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000319 for the AbiB system; other abortive-infection families remain open.
2026-09-20T22:01:25Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiC as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000320 for the AbiC system; other abortive-infection families remain open.
2026-09-20T22:48:13Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiU as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000321 for the AbiU system; other abortive-infection families remain open.
2026-09-20T23:47:18Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiAlpha as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000322 for the AbiAlpha system; other abortive-infection families remain open.
2026-09-21T01:30:13Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented Pif as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000323 for the Pif system; other abortive-infection families remain open.
2026-09-21T02:17:08Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented RexAB as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000324 for the RexAB system; other abortive-infection families remain open.
2026-09-21T03:22:01Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented SpbK as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000325 for the SpbK system; other abortive-infection families remain open.
2026-09-21T03:45:00Z · REVISED_TEXT · codex
Standardized curator-written SPβ phage mentions to the canonical Greek beta spelling while preserving Johnson et al. evidence snippets exactly as exposed by the PLOS XML.
2026-09-21T12:07:14Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented CmdTAC as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000335 for the CmdTAC system; other abortive-infection families remain open.
2026-09-21T12:26:31Z · ADDRESS_PR_REVIEW · codex
Corrected the CmdTAC split-gap source attribution from Goesswein et al. to Vassallo et al. after verifying DOI:10.1038/s41586-024-08102-8 against Crossref and Europe PMC metadata.
2026-09-21T14:52:54Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented Abi2 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000338 for the Abi2 system; other abortive-infection families remain open.
2026-09-21T16:24:10Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiJ as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000339 for the AbiJ system; other abortive-infection families remain open.
2026-09-21T17:17:23Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiL as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000340 for the AbiL system; other abortive-infection families remain open.
2026-09-21T17:52:23Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiN as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000341 for the AbiN system; other abortive-infection families remain open.
2026-09-21T18:34:42Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiO as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000342 for the AbiO system; other abortive-infection families remain open.
2026-09-21T19:10:27Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiP2 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000343 for the AbiP2 system; other abortive-infection families remain open.
2026-09-21T20:16:03Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiA as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000344 for the AbiA system; other abortive-infection families remain open.
2026-09-26T21:25:00Z · RESOLVE_DISCUSSION_SCOPE · codex
Addressed review issue #1298 by documenting PD-T4-10 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000394 for the PD-T4-10 system; other abortive-infection families remain open.
2026-10-01T01:32:45Z · RESOLVE_DISCUSSION_SCOPE · codex
Documented AbiF as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000504 for the AbiF system; other abortive-infection families remain open.
2026-10-01T03:14:00Z · ADDRESS_ABIF_REVIEW_FINDING · codex
Addressed adversarial review issue #1505 by clarifying that pNP40 is the AbiF determinant source context and that pCG1 is the recombinant plasmid clone used in the Garvey et al. subcloning experiment.