SpbK system

traitmech:000325 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a SpbK-family locus represented by the DefenseFinder SpbK__SpbK profile and exemplified by the ICEBs1 spbK gene whose SPβ-YonE-dependent activity inhibits SPβ production and kills infected cells.

Trait evidence (6)

DOI:10.1371/journal.pgen.1010065
The ICEBs1 gene spbK, although dispensable for conjugation, was necessary and sufficient for the inhibition of SPß.

Johnson et al. support spbK as the ICEBs1 locus sufficient for SPβ inhibition.
DOI:10.1371/journal.pgen.1010065
The anti-SPß phenotype (abortive infection) caused by spbK was dependent on the SPß gene yonE.

Johnson et al. support yonE-dependent abortive infection as the phage-specific SpbK output.
DOI:10.1371/journal.pgen.1010065
Co-expression of spbK and yonE inhibited host cell growth and caused a drop in cell viability, even in the absence of any other ICEBs1 or SPß genes.

Johnson et al. support SpbK/YonE-associated host growth inhibition and cell death.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
SpbK | 10\.1371/journal\.pgen\.1010065 | Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage

The DefenseFinder article registry maps the named SpbK model namespace to the ICEBs1 SpbK anti-phage paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
SpbK SpbK 1 1 SpbK__SpbK

The DefenseFinder rules table models SpbK as a single-profile system requiring the SpbK__SpbK profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| SpbK__SpbK | SpbK__SpbK | SpbK | Custom | 80 |

The DefenseFinder HMM inventory records SpbK__SpbK under SpbK.

SpbK loci mediate SPβ abortive defense

Conservative system-level sketch linking SpbK-family locus possession to SPβ YonE-dependent abortive infection and the SpbK system trait without asserting the direct SpbK-YonE coupling event or TIR-domain effector chemistry.

NONMECHANISTIC · The graph captures SpbK as a named DefenseFinder single-profile abortive-infection system whose Bacillus ICEBs1 prototype requires the SPβ YonE trigger. It leaves the direct SpbK-YonE coupling, TIR-domain output, essential host target, and homolog breadth unresolved.

Edge evidence

SpbK locus contributes to SpbK/YonE-dependent abortive infection RO:0002326
The ICEBs1 spbK locus is necessary and sufficient for YonE-dependent SPβ abortive infection, and DefenseFinder represents SpbK with a required SpbK profile.
- DOI:10.1371/journal.pgen.1010065 The ICEBs1 gene spbK, although dispensable for conjugation, was necessary and sufficient for the inhibition of SPß. Johnson et al. connect the ICEBs1 spbK gene to SPβ inhibition.
- DOI:10.1371/journal.pgen.1010065 The anti-SPß phenotype (abortive infection) caused by spbK was dependent on the SPß gene yonE. Johnson et al. support YonE dependence of SpbK-mediated abortive infection.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv SpbK SpbK 1 1 SpbK__SpbK The DefenseFinder rules table models SpbK as a single-profile system requiring the SpbK__SpbK profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | SpbK__SpbK | SpbK__SpbK | SpbK | Custom | 80 | The DefenseFinder HMM inventory records SpbK__SpbK under SpbK.
SpbK/YonE-dependent abortive infection confers SpbK system METPO:2007700
SpbK/YonE-dependent abortive infection realizes the SpbK system trait.
- DOI:10.1371/journal.pgen.1010065 Whatever the mechanism, we conclude that ICEBs1 encodes an abortive infection system that protects its host from predation by SPß. Johnson et al. classify ICEBs1 spbK activity as an abortive infection system that protects its host from SPβ predation.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md SpbK | 10\.1371/journal\.pgen\.1010065 | Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage The DefenseFinder article registry maps the named SpbK model namespace to the ICEBs1 SpbK anti-phage paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1371/journal.pgen.1010065

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (1)

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

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.

Bacillus subtilis NCBITaxon:1423 DOI:10.1371/journal.pgen.1010065 Johnson et al. showed that ICEBs1 encodes an SpbK-dependent abortive infection system that protects B. subtilis host populations from SPβ.

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 direct SPβ YonE trigger, SpbK TIR-domain output, essential host target, and broader SpbK homolog scope before minting narrower SpbK mechanism children.

KNOWLEDGE GAP OPEN spbk-mechanism-gap · raised by codex · 2026-09-21

Attached to causal_graphs#spbk_locus_mediates_spb_defense

Johnson et al. support ICEBs1 spbK as a YonE-dependent abortive infection gene that inhibits SPβ and causes cell death, and DefenseFinder maps SpbK to the SpbK__SpbK profile. The direct SpbK-YonE coupling event, TIR-domain output, essential host target, and homolog breadth remain unresolved.

Curation history

2026-09-21T03:22:00Z · MINTED_TRAITMECH_ID · codex
Minted SpbK 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_v202.
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.