identifier: traitmech:000419 label: prokaryotic Argonaute defense system definition: A genomics trait describing possession of a prokaryotic Argonaute-centered defense locus that uses a pAgo protein, alone or with cognate accessory proteins, to defend against plasmids, bacteriophages, or other mobile genetic elements. definition_source: DOI:10.1186/1745-6150-4-29 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000188 synonyms: - synonym_text: pAgo synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1186/1745-6150-4-29 snippet: The hypothesis that pAgos are key components of a novel prokaryotic immune system that employs guide RNA or DNA molecules to degrade nucleic acids of invading mobile elements notes: Makarova et al. link prokaryotic Argonaute homologs to a predicted defense system against mobile genetic elements; later SPARTA and DdmDE experiments support two branches of this family. - 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. support SPARTA as one experimentally resolved short pAgo and TIR-APAZ defense system. - reference: DOI:10.1038/s41586-022-04546-y snippet: These systems, termed DdmABC and DdmDE notes: Jaskolska et al. support DdmDE as another prokaryotic Argonaute defense system in Vibrio cholerae. - reference: DOI:10.1038/s41586-024-07515-9 snippet: DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo notes: Bravo et al. directly identify DdmE as the DNA-targeting prokaryotic Argonaute component of DdmDE. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| pAgo | 10\.1186/1745-6150-4-29 | Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements |' notes: The pinned DefenseFinder article registry maps the pAgo model namespace to the Makarova et al. prokaryotic Argonaute mobile genetic element defense paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "pAgo\tpAgo\t1\t3\tpAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A,\ \ pAgo__pAgo_S2B, pAgo__pAgo_SPARTA\tpAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS,\ \ pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ\t\t" notes: The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| pAgo__pAgo_SPARTA | pAgo__pAgo_SPARTA | pAgo | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records pAgo__pAgo_SPARTA under the pAgo model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| pAgo__TIRAPAZ | pAgo__TIRAPAZ | pAgo | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records pAgo__TIRAPAZ under the pAgo model namespace. canonical_examples: - taxon_id: NCBITaxon:666 taxon_label: Vibrio cholerae note: V. cholerae seventh pandemic strains carry the prokaryotic-Argonaute DdmDE plasmid defense system. reference: DOI:10.1038/s41586-022-04546-y causal_graphs: - graph_id: pago_system_family_hierarchy title: Prokaryotic Argonaute systems include SPARTA and DdmDE defense loci description: Nonmechanistic family sketch linking the pAgo possession trait to experimentally curated SPARTA and DdmDE child systems. scope_status: NONMECHANISTIC scope_notes: The graph is deliberately limited to family hierarchy because long pAgo, SPARTA, DdmDE, SIR2-APAZ, TIR-APAZ, and other APAZ-associated pAgo systems can differ in effector chemistry, guide origin, accessory proteins, and plasmid or phage target breadth. nodes: - node_id: sparta_system label: SPARTA system node_type: TRAIT grounding: traitmech:000240 description: Possession of a short prokaryotic Argonaute TIR-APAZ defense system. - node_id: ddmde_system label: DdmDE system node_type: TRAIT grounding: traitmech:000275 description: Possession of a DNA-guided prokaryotic Argonaute DdmDE defense system. - node_id: pago_system_trait label: prokaryotic Argonaute defense system node_type: TRAIT grounding: traitmech:000419 description: Possession of a genome-encoded prokaryotic Argonaute-centered defense system. edges: - subject: sparta_system predicate: is a predicate_id: rdfs:subClassOf object: pago_system_trait description: SPARTA is a short-pAgo TIR-APAZ system within the broader prokaryotic Argonaute defense family. 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 around a short pAgo and TIR-APAZ protein pair. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "pAgo\tpAgo\t1\t3\tpAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A,\ \ pAgo__pAgo_S2B, pAgo__pAgo_SPARTA\tpAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS,\ \ pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ\t\t" notes: The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups. - subject: ddmde_system predicate: is a predicate_id: rdfs:subClassOf object: pago_system_trait description: DdmDE is an anti-plasmid defense system with a DNA-guided pAgo component. evidence: - reference: DOI:10.1038/s41586-024-07515-9 snippet: DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo notes: Bravo et al. identify DdmE as the pAgo component of DdmDE. discussions: - discussion_id: pago-subfamily-boundary-gap prompt: Resolve pAgo subfamily boundaries, accessory-protein requirements, and substrate breadth before minting narrower long-pAgo or APAZ-associated defense children. kind: KNOWLEDGE_GAP status: OPEN rationale: SPARTA and DdmDE support prokaryotic Argonaute defense systems as a reusable genomics family, and DefenseFinder models a pAgo namespace with long pAgo, SPARTA, and optional APAZ-associated profiles. This parent does not yet resolve whether every DefenseFinder pAgo submodel has the same plasmid or phage substrate range, whether standalone APAZ-associated profiles are exact children, or which native-host examples support each subfamily. 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. support one short-pAgo branch as a paired SPARTA system. - reference: DOI:10.1038/s41586-024-07515-9 snippet: DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo notes: Bravo et al. support one DdmDE branch with DdmE as a DNA-guided pAgo. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "pAgo\tpAgo\t1\t3\tpAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A,\ \ pAgo__pAgo_S2B, pAgo__pAgo_SPARTA\tpAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS,\ \ pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ\t\t" notes: The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups. attaches_to: - causal_graphs#pago_system_family_hierarchy posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T22:11:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted prokaryotic Argonaute defense system as a DOI-backed GENOMICS TraitRecord under the quality root after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; scoped the graph to SPARTA and DdmDE family hierarchy and reserved the replacement placeholder in proposals/metpo_traitmech_v296. llm_assisted: true - timestamp: '2026-09-27T22:20:00Z' curator: codex action: LOCAL_VALIDATION_REPAIR changes: Added a contiguous Makarova et al. abstract snippet after the evidence snippet audit flagged the prokaryotic Argonaute defense system record as a new MISSING_SNIPPET finding. llm_assisted: true