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Gabija system

traitmech:000215 · CLASS · PROPOSED

A genomics trait describing possession of a Gabija antiphage defense locus whose GajA and GajB proteins assemble into a complex that inhibits bacteriophage replication.

Trait evidence (4)

  • DOI:10.1093/nar/gkad951
    Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB

    Oh et al. support defining Gabija at the two-component antiviral-system level.

  • DOI:10.1093/nar/gkad951
    The Gabija anti-phage defense system was first identified in Bacillus cereus and is present in >4000 prokaryotic genomes

    Oh et al. support B. cereus as the source organism for the Gabija system and support broad prokaryotic distribution.

  • DOI:10.1016/j.chom.2023.06.014
    synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense against virulent bacteriophages

    Cheng et al. support the combined DNA-cleavage and nucleotide-depletion output of the Gabija complex.

  • DOI:10.1038/s41586-023-06855-2
    Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo

    Antine et al. support the GajAB complex as essential for Gabija-mediated phage resistance.

Gabija GajAB complexes deplete nucleotides and cleave DNA

Evidence-backed process sketch linking a Gabija gajA-gajB operon to GajAB complex assembly, nucleotide depletion, DNA cleavage, and inhibition of bacteriophage replication.

NONMECHANISTIC · The graph captures the characterized Gabija GajA/GajB outputs without asserting one universal phage sensor, DNA substrate, GajA:GajB stoichiometry, host death trigger, or anti-Gabija evasion mechanism across all Gabija loci.

Gabija GajAB complexes deplete nucleotides and cleave DNA Interactive directed graph showing evidence-backed causal relationships for Gabija system.

Edge evidence

  • Gabija gajA-gajB operon contributes to GajAB complex assembly RO:0002326

    The gajA and gajB genes encode proteins that assemble into the Gabija GajAB antiphage complex.

    • DOI:10.1093/nar/gkad951 GajB interacts with GajA to form a heterooctameric Gabija complex Oh et al. support assembly of B. cereus VD045 GajA and GajB into a stable complex.
    • DOI:10.1038/s41586-023-06855-2 create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo Antine et al. support the GajAB assembly as required for phage resistance.
  • GajAB complex assembly contributes to Gabija nucleotide depletion RO:0002326

    The Gabija complex enables GajB-mediated nucleotide hydrolysis and nucleotide-pool depletion.

    • DOI:10.1016/j.chom.2023.06.014 GajA requires GajB, which senses DNA termini produced by GajA to hydrolyze (d)A/(d)GTP, depleting essential nucleotides Cheng et al. connect the GajA/GajB complex with depletion of adenine and guanine nucleotide pools.
  • GajAB complex assembly contributes to Gabija DNA cleavage RO:0002326

    The Gabija GajAB complex catalyzes GajA-mediated DNA cleavage during antiviral defense.

    • DOI:10.1016/j.chom.2023.06.014 synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense Cheng et al. support DNA cleavage as a GajA-dependent component of Gabija defense.
  • Gabija nucleotide depletion mitigates phage replication METPO:2007407

    Gabija nucleotide depletion helps inhibit bacteriophage replication.

    • DOI:10.1016/j.chom.2023.06.014 depleting essential nucleotides. This ATPase activity of Gabija complex is only activated upon DNA binding Cheng et al. connect GajB ATPase activity to depletion of nucleotide pools required for phage replication.
  • Gabija DNA cleavage mitigates phage replication METPO:2007407

    Gabija DNA cleavage helps inhibit bacteriophage replication.

    • DOI:10.1038/s41586-023-06855-2 Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA Antine et al. support phage-DNA degradation as an output of the GajAB complex.
  • Gabija DNA cleavage confers Gabija system METPO:2007700

    GajAB DNA cleavage is part of the antiviral output that realizes the Gabija system defense phenotype.

    • DOI:10.1016/j.chom.2023.06.014 synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense Cheng et al. support GajA-mediated DNA cleavage as part of the Gabija defense phenotype.
  • Gabija system is a phage defense system rdfs:subClassOf

    Gabija system possession is a phage-defense-system trait.

    • DOI:10.1093/nar/gkad951 Gabija is one of the most abundant prokaryotic antiviral systems Oh et al. place Gabija among prokaryotic antiviral systems.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1093/nar/gkad951

Parent traits (1)

Synonyms (2)

  • Gabija anti-phage defense system EXACT_SYNONYM · DOI:10.1093/nar/gkad951
  • Gabija anti-phage defence system EXACT_SYNONYM · DOI:10.1038/s41586-023-06855-2

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 cereus NCBITaxon:1396 DOI:10.1093/nar/gkad951 Oh et al. report that the Gabija anti-phage defense system was first identified in Bacillus cereus and characterize GajB from the B. cereus VD045 Gabija system.

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 Gabija activation, stoichiometry, cell-outcome, and phage anti-defense breadth before minting narrower Gabija mechanistic children.

KNOWLEDGE GAP OPEN gabija-activation-and-antidefense-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.

Cheng et al. support nucleotide depletion and DNA cleavage as Gabija outputs, and Antine et al. support GajAB complex assembly plus Gad1-mediated inhibition, but Gabija family members need separate review before TraitMech asserts one universal trigger, exact GajA:GajB stoichiometry, host death program, DNA substrate, or anti-Gabija phage inhibitor.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted Gabija 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_v92.