DdmDE system

traitmech:000275 · CLASS · PROPOSED

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.

Trait evidence (7)

DOI:10.1038/s41586-022-04546-y
two plasmid defence systems conserved in the Vibrio cholerae El Tor strains

Jaskolska et al. support discovery of plasmid-defense systems in V. cholerae El Tor strains.
DOI:10.1038/s41586-022-04546-y
These systems, termed DdmABC and DdmDE

Jaskolska et al. identify DdmDE as one of those plasmid-defense systems.
DOI:10.1038/s41586-024-07515-9
DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids

Bravo et al. support DdmDE as a plasmid-elimination DNA defense module.
DOI:10.1038/s41586-024-07515-9
DNA recognition triggers processive plasmid destruction

Bravo et al. connect target DNA recognition in DdmDE to processive plasmid destruction.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
DdmDE | 10\.1038/s41586-022-04546-y | Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae

The DefenseFinder article registry maps the named DdmDE system to the Jaskolska et al. Nature paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DdmDE__DdmD | DdmDE__DdmD | DdmDE | Custom | 20

The DefenseFinder HMM inventory records the custom DdmD profile for DdmDE.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DdmDE__DdmE | DdmDE__DdmE | DdmDE | Custom | 20

The DefenseFinder HMM inventory records the custom DdmE profile for DdmDE.

DdmDE couples DNA recognition to plasmid destruction

Process sketch linking a DdmDE locus to target DNA recognition, processive plasmid destruction, plasmid clearance, and the DdmDE system trait.

NONMECHANISTIC · 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.

Edge evidence

DdmDE locus contributes to DdmDE target DNA recognition RO:0002326
The DdmDE locus encodes DdmE and DdmD components that support DdmDE target DNA recognition.
- DOI:10.1038/s41586-024-07515-9 DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo Bravo et al. define DdmE as the DNA-guided DdmDE pAgo component.
- DOI:10.1038/s41586-024-07515-9 helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets Bravo et al. connect DdmD to target-DNA loading and the monomeric active state.
DdmDE target DNA recognition triggers processive plasmid destruction
DdmDE DNA recognition triggers processive plasmid destruction.
- DOI:10.1038/s41586-024-07515-9 DNA recognition triggers processive plasmid destruction Bravo et al. place plasmid destruction downstream of DNA recognition by DdmDE.
processive plasmid destruction contributes to plasmid clearance RO:0002326
Processive DdmDE-mediated plasmid DNA destruction clears invasive plasmids.
- DOI:10.1038/s41586-024-07515-9 pAgos utilize ancillary factors to achieve plasmid clearance Bravo et al. frame DdmD as the ancillary factor that helps a pAgo clear plasmids.
plasmid clearance confers DdmDE system METPO:2007700
DdmDE-mediated clearance of small multicopy plasmids realizes the DdmDE system trait.
- DOI:10.1038/s41586-024-07515-9 DdmDE system, which rapidly eliminates small, multicopy plasmids Bravo et al. support plasmid elimination as the DdmDE defense output.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41586-024-07515-9

Parent traits (1)

prokaryotic Argonaute defense system traitmech:000419

Synonyms (1)

DdmDE EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md

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.

Vibrio cholerae NCBITaxon:666 DOI:10.1038/s41586-022-04546-y The DdmDE system was characterized from V. cholerae seventh pandemic strains.

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 DdmDE natural guide sources, plasmid-substrate breadth, and DdmABC cooperation before minting narrower DdmDE mechanism or subtype traits.

KNOWLEDGE GAP OPEN ddmde-substrate-and-guide-source-gap · raised by codex · 2026-09-19

Attached to causal_graphs#ddmde_pago_helicase_plasmid_destruction

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.

Curation history

2026-09-19T10:17:05Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-19T10:30:00Z · ADVERSARIAL_REVIEW_REPAIR · codex
Resolved #1055 by simplifying the DdmDE causal graph to a source-supported target-DNA-recognition sketch and removing unsupported guide-target handover input edges.
2026-09-27T22:11:00Z · REPAIRED_PARENT_TRAIT · codex
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.