prokaryotic Argonaute defense system

traitmech:000419 · CLASS · PROPOSED

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.

Trait evidence (8)

DOI:10.1186/1745-6150-4-29
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

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.
DOI:10.1016/j.cell.2022.03.012
short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes

Koopal et al. support SPARTA as one experimentally resolved short pAgo and TIR-APAZ defense system.
DOI:10.1038/s41586-022-04546-y
These systems, termed DdmABC and DdmDE

Jaskolska et al. support DdmDE as another prokaryotic Argonaute defense system in Vibrio cholerae.
DOI:10.1038/s41586-024-07515-9
DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo

Bravo et al. directly identify DdmE as the DNA-targeting prokaryotic Argonaute component of DdmDE.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| 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 |

The pinned DefenseFinder article registry maps the pAgo model namespace to the Makarova et al. prokaryotic Argonaute mobile genetic element defense paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
pAgo pAgo 1 3 pAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A, pAgo__pAgo_S2B, pAgo__pAgo_SPARTA pAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS, pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ

The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| pAgo__pAgo_SPARTA | pAgo__pAgo_SPARTA | pAgo | Custom | 20 |

The pinned DefenseFinder HMM inventory records pAgo__pAgo_SPARTA under the pAgo model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| pAgo__TIRAPAZ | pAgo__TIRAPAZ | pAgo | Custom | 20 |

The pinned DefenseFinder HMM inventory records pAgo__TIRAPAZ under the pAgo model namespace.

Prokaryotic Argonaute systems include SPARTA and DdmDE defense loci

Nonmechanistic family sketch linking the pAgo possession trait to experimentally curated SPARTA and DdmDE child systems.

NONMECHANISTIC · 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.

Edge evidence

SPARTA system is a prokaryotic Argonaute defense system rdfs:subClassOf
SPARTA is a short-pAgo TIR-APAZ system within the broader prokaryotic Argonaute defense family.
- DOI:10.1016/j.cell.2022.03.012 short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes Koopal et al. define SPARTA around a short pAgo and TIR-APAZ protein pair.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv pAgo pAgo 1 3 pAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A, pAgo__pAgo_S2B, pAgo__pAgo_SPARTA pAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS, pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups.
DdmDE system is a prokaryotic Argonaute defense system rdfs:subClassOf
DdmDE is an anti-plasmid defense system with a DNA-guided pAgo component.
- DOI:10.1038/s41586-024-07515-9 DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo Bravo et al. identify DdmE as the pAgo component of DdmDE.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1186/1745-6150-4-29

Parent traits (1)

quality METPO:1000188

Children (2)

Synonyms (1)

pAgo RELATED_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 V. cholerae seventh pandemic strains carry the prokaryotic-Argonaute DdmDE plasmid defense system.

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 pAgo subfamily boundaries, accessory-protein requirements, and substrate breadth before minting narrower long-pAgo or APAZ-associated defense children.

KNOWLEDGE GAP OPEN pago-subfamily-boundary-gap · raised by codex · 2026-09-27

Attached to causal_graphs#pago_system_family_hierarchy

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

DOI:10.1016/j.cell.2022.03.012
short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes
DOI:10.1038/s41586-024-07515-9
DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
pAgo pAgo 1 3 pAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A, pAgo__pAgo_S2B, pAgo__pAgo_SPARTA pAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS, pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ

Curation history

2026-09-27T22:11:00Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-27T22:20:00Z · LOCAL_VALIDATION_REPAIR · codex
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.