identifier: traitmech:000240 label: SPARTA system definition: A genomics trait describing possession of a short prokaryotic Argonaute TIR-APAZ (SPARTA) locus whose short pAgo and TIR-APAZ proteins form heterodimeric complexes that oligomerize after guide RNA-mediated target DNA binding and unleash TIR domain-mediated NAD(P)ase activity that depletes NAD(P)+ to remove plasmid-invaded cells. definition_source: DOI:10.1016/j.cell.2022.03.012 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000419 synonyms: - synonym_text: short prokaryotic Argonaute TIR-APAZ system synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.cell.2022.03.012 evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes notes: Koopal et al. define SPARTA as a short pAgo plus TIR-APAZ system rather than an individual gene or single protein. - reference: DOI:10.1016/j.cell.2022.03.012 snippet: Upon guide RNA-mediated target DNA binding, four SPARTA heterodimers form oligomers in which TIR domain-mediated NAD(P)ase activity is unleashed notes: Koopal et al. support the guide RNA and target DNA-triggered oligomerization mechanism that activates SPARTA NAD(P)ase activity. - reference: DOI:10.1016/j.cell.2022.03.012 snippet: SPARTA is activated in the presence of highly transcribed multicopy plasmid DNA, which causes cell death through NAD(P)+ depletion notes: Koopal et al. support plasmid-challenge activation and NAD(P)+ depletion as experimentally demonstrated SPARTA outcomes. - reference: DOI:10.1038/s41467-024-49271-4 snippet: cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA notes: Kottur et al. independently support the RNA/target-DNA activated oligomeric state of a SPARTA complex. causal_graphs: - graph_id: sparta_pago_tir_apaz_nadase_cell_death title: SPARTA complexes couple guide RNA target binding to NAD(P)ase-triggered cell death description: Evidence-backed process sketch linking a SPARTA locus to short-pAgo/TIR-APAZ heterodimer assembly, guide RNA-target DNA activation, oligomerization, TIR-domain NAD(P)ase activity, NAD(P)+ depletion, and removal of plasmid-invaded cells. scope_status: NONMECHANISTIC scope_notes: The graph stays at the SPARTA-family level and models the high-copy plasmid activation route from Koopal et al. without asserting that phage defense, SIR2-APAZ systems, nuclease-APAZ systems, or every other short-pAgo family uses the same enzymatic output. nodes: - node_id: sparta_locus label: SPARTA locus node_type: GENETIC_ELEMENT description: A short prokaryotic Argonaute TIR-APAZ locus encoding short pAgo and TIR-APAZ proteins. - node_id: sparta_heterodimer_assembly label: SPARTA heterodimer assembly node_type: BIOLOGICAL_PROCESS description: Assembly of short pAgo and TIR-APAZ proteins into SPARTA heterodimeric complexes. - node_id: guide_target_binding label: guide RNA-mediated target DNA binding node_type: BIOLOGICAL_PROCESS description: Recognition of target DNA by a SPARTA complex through a bound guide RNA. - node_id: sparta_oligomerization label: SPARTA oligomerization node_type: BIOLOGICAL_PROCESS description: Formation of a target-DNA-bound SPARTA oligomer from four guide-loaded heterodimers. - node_id: tir_nadpase_activity label: SPARTA TIR-domain NAD(P)ase activity node_type: MOLECULAR_FUNCTION description: NAD(P)+ hydrolysis by TIR domains assembled in an active SPARTA oligomer. - node_id: nadp_depletion label: NAD(P)+ depletion node_type: BIOLOGICAL_PROCESS description: Loss of cellular NAD(P)+ downstream of activated SPARTA TIR-domain NAD(P)ase activity. - node_id: invaded_cell_death label: plasmid-invaded cell death node_type: BIOLOGICAL_PROCESS description: Cell death triggered in host cells carrying highly transcribed multicopy plasmid DNA detected by SPARTA. - node_id: sparta_system_trait label: SPARTA system node_type: TRAIT grounding: traitmech:000240 description: Possession of a genome-encoded short prokaryotic Argonaute TIR-APAZ defense system. edges: - subject: sparta_locus predicate: contributes to predicate_id: RO:0002326 object: sparta_heterodimer_assembly description: SPARTA loci encode short pAgo and TIR-APAZ proteins that assemble into heterodimeric complexes. evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: SPARTA proteins form heterodimeric complexes notes: Koopal et al. support the paired-protein complex architecture of SPARTA. - subject: sparta_heterodimer_assembly predicate: contributes to predicate_id: RO:0002326 object: sparta_oligomerization description: SPARTA heterodimers are the building blocks of the target-DNA-bound SPARTA oligomer. evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: four SPARTA heterodimers form oligomers notes: Koopal et al. support oligomer formation from SPARTA heterodimers. - subject: guide_target_binding predicate: activates predicate_id: RO:0002213 object: sparta_oligomerization description: Guide RNA-mediated target DNA binding triggers SPARTA tetramer-of-heterodimers oligomerization. evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: Upon guide RNA-mediated target DNA binding, four SPARTA heterodimers form oligomers notes: Koopal et al. connect target recognition to SPARTA oligomer formation. - subject: sparta_oligomerization predicate: activates predicate_id: RO:0002213 object: tir_nadpase_activity description: SPARTA oligomerization aligns TIR domains and activates NAD(P)+ hydrolysis. evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: oligomers in which TIR domain-mediated NAD(P)ase activity is unleashed notes: Koopal et al. link oligomer formation to activation of TIR-domain NAD(P)ase activity. - reference: DOI:10.1038/s41467-024-49271-4 snippet: The TIR domains amass in a parallel-strands arrangement for catalysis notes: Kottur et al. structurally support TIR-domain arrangement in the active SPARTA assembly. - subject: tir_nadpase_activity predicate: contributes to predicate_id: RO:0002326 object: nadp_depletion description: Activated SPARTA TIR domains hydrolyze NAD(P)+, depleting the cellular NAD(P)+ pool. evidence: - reference: DOI:10.1038/s41467-024-49271-4 snippet: activated by invading DNA to unleash its TIR domain for NAD(P)+ hydrolysis notes: Kottur et al. describe DNA-triggered release of SPARTA TIR-domain NAD(P)+ hydrolysis. - subject: nadp_depletion predicate: contributes to predicate_id: RO:0002326 object: invaded_cell_death description: SPARTA-associated NAD(P)+ depletion contributes to death of plasmid-invaded host cells. evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: causes cell death through NAD(P)+ depletion notes: Koopal et al. connect SPARTA-driven NAD(P)+ depletion to cell death. - subject: invaded_cell_death predicate: confers predicate_id: METPO:2007700 object: sparta_system_trait description: Removal of plasmid-invaded cells is the cellular outcome of the SPARTA possession trait. evidence: - reference: DOI:10.1016/j.cell.2022.03.012 snippet: This results in the removal of plasmid-invaded cells from bacterial cultures notes: Koopal et al. support SPARTA-mediated removal of plasmid-invaded cells. discussions: - discussion_id: sparta-native-host-and-substrate-gap prompt: Resolve SPARTA natural-host substrates before adding canonical examples or narrower short-pAgo defense children. kind: KNOWLEDGE_GAP status: OPEN rationale: Koopal et al. support strong high-copy plasmid activation and only limited, NADase-independent phage effects; Kottur et al. support C. thermophila SPARTA structural activation. This first record therefore stays broad until natural-host activity, phage scope, and whether SIR2-APAZ or nuclease-APAZ relatives should be separate children are resolved. posed_by: codex posed_date: '2026-09-18' curation_history: - timestamp: '2026-09-18T11:59:02Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted SPARTA system as a DOI-backed GENOMICS TraitRecord under the quality root 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_v117. llm_assisted: true - timestamp: '2026-09-27T22:11:00Z' curator: codex action: REPAIRED_PARENT_TRAIT changes: Reparented SPARTA system from the generic quality root to the newly minted prokaryotic Argonaute defense system parent without changing SPARTA-specific evidence or mechanism claims. llm_assisted: true