identifier: traitmech:000215 label: Gabija system definition: A genomics trait describing possession of a Gabija antiphage defense locus whose GajA and GajB proteins assemble into a complex that inhibits bacteriophage replication. definition_source: DOI:10.1093/nar/gkad951 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Gabija anti-phage defense system synonym_type: EXACT_SYNONYM source: DOI:10.1093/nar/gkad951 - synonym_text: Gabija anti-phage defence system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41586-023-06855-2 evidence: - reference: DOI:10.1093/nar/gkad951 snippet: Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB notes: Oh et al. support defining Gabija at the two-component antiviral-system level. - reference: DOI:10.1093/nar/gkad951 snippet: The Gabija anti-phage defense system was first identified in Bacillus cereus and is present in >4000 prokaryotic genomes notes: Oh et al. support B. cereus as the source organism for the Gabija system and support broad prokaryotic distribution. - reference: DOI:10.1016/j.chom.2023.06.014 snippet: synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense against virulent bacteriophages notes: Cheng et al. support the combined DNA-cleavage and nucleotide-depletion output of the Gabija complex. - reference: DOI:10.1038/s41586-023-06855-2 snippet: 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 notes: Antine et al. support the GajAB complex as essential for Gabija-mediated phage resistance. canonical_examples: - taxon_id: NCBITaxon:1396 taxon_label: Bacillus cereus note: 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. reference: DOI:10.1093/nar/gkad951 causal_graphs: - graph_id: gabija_gajab_complex_antiphage_defense title: Gabija GajAB complexes deplete nucleotides and cleave DNA description: Evidence-backed process sketch linking a Gabija gajA-gajB operon to GajAB complex assembly, nucleotide depletion, DNA cleavage, and inhibition of bacteriophage replication. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: gabija_operon label: Gabija gajA-gajB operon node_type: GENETIC_ELEMENT description: A Gabija defense locus encoding GajA and GajB proteins. - node_id: gajab_complex_assembly label: GajAB complex assembly node_type: BIOLOGICAL_PROCESS description: Assembly of GajA and GajB proteins into the antiphage Gabija complex. - node_id: gabija_nucleotide_depletion label: Gabija nucleotide depletion node_type: BIOLOGICAL_PROCESS description: GajB-dependent hydrolysis of host dATP, dGTP, ATP, or GTP nucleotide pools. - node_id: gabija_dna_cleavage label: Gabija DNA cleavage node_type: BIOLOGICAL_PROCESS description: GajA-dependent cleavage of DNA during Gabija antiviral defense. - node_id: phage_replication label: phage replication node_type: BIOLOGICAL_PROCESS description: Replication of invading bacteriophage DNA after host-cell entry. - node_id: gabija_system_trait label: Gabija system node_type: TRAIT grounding: traitmech:000215 description: Possession of a genome-encoded Gabija antiphage defense locus. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: gabija_operon predicate: contributes to predicate_id: RO:0002326 object: gajab_complex_assembly description: The gajA and gajB genes encode proteins that assemble into the Gabija GajAB antiphage complex. evidence: - reference: DOI:10.1093/nar/gkad951 snippet: GajB interacts with GajA to form a heterooctameric Gabija complex notes: Oh et al. support assembly of B. cereus VD045 GajA and GajB into a stable complex. - reference: DOI:10.1038/s41586-023-06855-2 snippet: create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo notes: Antine et al. support the GajAB assembly as required for phage resistance. - subject: gajab_complex_assembly predicate: contributes to predicate_id: RO:0002326 object: gabija_nucleotide_depletion description: The Gabija complex enables GajB-mediated nucleotide hydrolysis and nucleotide-pool depletion. evidence: - reference: DOI:10.1016/j.chom.2023.06.014 snippet: GajA requires GajB, which senses DNA termini produced by GajA to hydrolyze (d)A/(d)GTP, depleting essential nucleotides notes: Cheng et al. connect the GajA/GajB complex with depletion of adenine and guanine nucleotide pools. - subject: gajab_complex_assembly predicate: contributes to predicate_id: RO:0002326 object: gabija_dna_cleavage description: The Gabija GajAB complex catalyzes GajA-mediated DNA cleavage during antiviral defense. evidence: - reference: DOI:10.1016/j.chom.2023.06.014 snippet: synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense notes: Cheng et al. support DNA cleavage as a GajA-dependent component of Gabija defense. - subject: gabija_nucleotide_depletion predicate: mitigates predicate_id: METPO:2007407 object: phage_replication description: Gabija nucleotide depletion helps inhibit bacteriophage replication. evidence: - reference: DOI:10.1016/j.chom.2023.06.014 snippet: depleting essential nucleotides. This ATPase activity of Gabija complex is only activated upon DNA binding notes: Cheng et al. connect GajB ATPase activity to depletion of nucleotide pools required for phage replication. - subject: gabija_dna_cleavage predicate: mitigates predicate_id: METPO:2007407 object: phage_replication description: Gabija DNA cleavage helps inhibit bacteriophage replication. evidence: - reference: DOI:10.1038/s41586-023-06855-2 snippet: Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA notes: Antine et al. support phage-DNA degradation as an output of the GajAB complex. - subject: gabija_dna_cleavage predicate: confers predicate_id: METPO:2007700 object: gabija_system_trait description: GajAB DNA cleavage is part of the antiviral output that realizes the Gabija system defense phenotype. evidence: - reference: DOI:10.1016/j.chom.2023.06.014 snippet: synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense notes: Cheng et al. support GajA-mediated DNA cleavage as part of the Gabija defense phenotype. - subject: gabija_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Gabija system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1093/nar/gkad951 snippet: Gabija is one of the most abundant prokaryotic antiviral systems notes: Oh et al. place Gabija among prokaryotic antiviral systems. discussions: - discussion_id: gabija-activation-and-antidefense-gap prompt: Resolve Gabija activation, stoichiometry, cell-outcome, and phage anti-defense breadth before minting narrower Gabija mechanistic children. kind: KNOWLEDGE_GAP status: OPEN rationale: 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. posed_by: codex posed_date: '2026-09-15' curation_history: - timestamp: '2026-09-15T12:36:55Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true