identifier: traitmech:000275 label: DdmDE system definition: A genomics trait describing possession of a DdmDE anti-plasmid defense locus encoding the DNA-guided prokaryotic Argonaute DdmE and the helicase-nuclease DdmD, whose DNA recognition and handoff trigger processive plasmid destruction. definition_source: DOI:10.1038/s41586-024-07515-9 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000419 synonyms: - synonym_text: DdmDE synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1038/s41586-022-04546-y snippet: two plasmid defence systems conserved in the Vibrio cholerae El Tor strains notes: Jaskolska et al. support discovery of plasmid-defense systems in V. cholerae El Tor strains. - reference: DOI:10.1038/s41586-022-04546-y snippet: These systems, termed DdmABC and DdmDE notes: Jaskolska et al. identify DdmDE as one of those plasmid-defense systems. - reference: DOI:10.1038/s41586-024-07515-9 snippet: DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids notes: Bravo et al. support DdmDE as a plasmid-elimination DNA defense module. - reference: DOI:10.1038/s41586-024-07515-9 snippet: DNA recognition triggers processive plasmid destruction notes: Bravo et al. connect target DNA recognition in DdmDE to processive plasmid destruction. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: DdmDE | 10\.1038/s41586-022-04546-y | Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae notes: The DefenseFinder article registry maps the named DdmDE system to the Jaskolska et al. Nature paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: DdmDE__DdmD | DdmDE__DdmD | DdmDE | Custom | 20 notes: The DefenseFinder HMM inventory records the custom DdmD profile for DdmDE. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: DdmDE__DdmE | DdmDE__DdmE | DdmDE | Custom | 20 notes: The DefenseFinder HMM inventory records the custom DdmE profile for DdmDE. canonical_examples: - taxon_id: NCBITaxon:666 taxon_label: Vibrio cholerae note: The DdmDE system was characterized from V. cholerae seventh pandemic strains. reference: DOI:10.1038/s41586-022-04546-y causal_graphs: - graph_id: ddmde_pago_helicase_plasmid_destruction title: DdmDE couples DNA recognition to plasmid destruction description: Process sketch linking a DdmDE locus to target DNA recognition, processive plasmid destruction, plasmid clearance, and the DdmDE system trait. scope_status: NONMECHANISTIC scope_notes: The graph captures the DdmDE activation pathway resolved by Bravo et al. without asserting every guide-maturation route, native plasmid substrate, DdmABC cooperation mode, or Vibrio-specific locus boundary as universal for all DdmDE systems. nodes: - node_id: ddmde_locus label: DdmDE locus node_type: GENETIC_ELEMENT description: An anti-plasmid defense locus encoding DdmD and DdmE components. - node_id: ddmde_dna_recognition label: DdmDE target DNA recognition node_type: BIOLOGICAL_PROCESS description: DdmDE DNA recognition coordinated by the DNA-targeting pAgo DdmE and helicase-nuclease DdmD. - node_id: processive_plasmid_destruction label: processive plasmid destruction node_type: BIOLOGICAL_PROCESS description: Processive destruction of plasmid DNA after DdmDE target recognition. - node_id: plasmid_clearance label: plasmid clearance node_type: BIOLOGICAL_PROCESS description: Elimination of invasive small multicopy plasmids. - node_id: ddmde_system_trait label: DdmDE system node_type: TRAIT grounding: traitmech:000275 description: Possession of a genome-encoded DdmDE anti-plasmid defense system. edges: - subject: ddmde_locus predicate: contributes to predicate_id: RO:0002326 object: ddmde_dna_recognition description: The DdmDE locus encodes DdmE and DdmD components that support DdmDE target DNA recognition. evidence: - reference: DOI:10.1038/s41586-024-07515-9 snippet: DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo notes: Bravo et al. define DdmE as the DNA-guided DdmDE pAgo component. - reference: DOI:10.1038/s41586-024-07515-9 snippet: helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets notes: Bravo et al. connect DdmD to target-DNA loading and the monomeric active state. - subject: ddmde_dna_recognition predicate: triggers object: processive_plasmid_destruction description: DdmDE DNA recognition triggers processive plasmid destruction. evidence: - reference: DOI:10.1038/s41586-024-07515-9 snippet: DNA recognition triggers processive plasmid destruction notes: Bravo et al. place plasmid destruction downstream of DNA recognition by DdmDE. - subject: processive_plasmid_destruction predicate: contributes to predicate_id: RO:0002326 object: plasmid_clearance description: Processive DdmDE-mediated plasmid DNA destruction clears invasive plasmids. evidence: - reference: DOI:10.1038/s41586-024-07515-9 snippet: pAgos utilize ancillary factors to achieve plasmid clearance notes: Bravo et al. frame DdmD as the ancillary factor that helps a pAgo clear plasmids. - subject: plasmid_clearance predicate: confers predicate_id: METPO:2007700 object: ddmde_system_trait description: DdmDE-mediated clearance of small multicopy plasmids realizes the DdmDE system trait. evidence: - reference: DOI:10.1038/s41586-024-07515-9 snippet: DdmDE system, which rapidly eliminates small, multicopy plasmids notes: Bravo et al. support plasmid elimination as the DdmDE defense output. discussions: - discussion_id: ddmde-substrate-and-guide-source-gap prompt: Resolve DdmDE natural guide sources, plasmid-substrate breadth, and DdmABC cooperation before minting narrower DdmDE mechanism or subtype traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Jaskolska et al. support DdmDE as a V. cholerae plasmid-defense system and Bravo et al. resolve how DdmE and DdmD cooperate for plasmid destruction, but this first system-level record does not assert a universal guide-maturation route, full natural plasmid substrate range, or whether cooperation with DdmABC is required in some hosts. attaches_to: - causal_graphs#ddmde_pago_helicase_plasmid_destruction posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T10:17:05Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DdmDE 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_v152. llm_assisted: true - timestamp: '2026-09-19T10:30:00Z' curator: codex action: ADVERSARIAL_REVIEW_REPAIR changes: 'Resolved #1055 by simplifying the DdmDE causal graph to a source-supported target-DNA-recognition sketch and removing unsupported guide-target handover input edges.' llm_assisted: true - timestamp: '2026-09-27T22:11:00Z' curator: codex action: REPAIRED_PARENT_TRAIT changes: Reparented DdmDE system from the generic quality root to the newly minted prokaryotic Argonaute defense system parent without changing DdmDE-specific evidence or mechanism claims. llm_assisted: true