identifier: traitmech:000221 label: Dnd system definition: A phosphorothioate defense system in which an organism possesses a Dnd restriction-modification locus that pairs a Dnd-family DNA phosphorothioation module with a DndFGH restriction module to nick invading DNA that lacks phosphorothioate modification. definition_source: DOI:10.1038/s41564-020-0700-6 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000213 synonyms: - synonym_text: Dnd R-M system synonym_type: EXACT_SYNONYM source: DOI:10.1128/mbio.00933-23 - synonym_text: Dnd-related R-M system synonym_type: EXACT_SYNONYM source: DOI:10.1128/mbio.00933-23 - synonym_text: Dnd-related restriction and modification system synonym_type: EXACT_SYNONYM source: DOI:10.1128/mbio.00933-23 evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component notes: Xiong et al. summarize Dnd as a named PT-dependent restriction system with DNA-modification and restriction modules. - reference: DOI:10.1128/mbio.00933-23 snippet: Usually, this modification gene cluster is paired with a restriction module consisting of DndF, DndG, and DndH notes: Jiang et al. support DndFGH as the restriction module paired with Dnd DNA phosphorothioation. - reference: DOI:10.1128/mbio.00933-23 snippet: In general, some dnd or ssp clusters lack dndA or sspA; DndA or SspA is instead functionally replaced by other cysteine desulfurases, such as IscS, in bacteria notes: Jiang et al. support defining the Dnd system by a Dnd-family modification module without requiring a contiguous dndA gene in every locus. - reference: DOI:10.1128/mbio.00933-23 snippet: In the presence of exogenous DNA that lacks PT, the macromolecular machine consisting of DndF, DndG, and DndH undergoes conformational changes to perform DNA binding, translocation, and DNA nicking activities and scavenge the foreign DNA notes: Jiang et al. connect DndFGH to detection and nicking of foreign DNA lacking PT modification. - reference: DOI:10.1128/mbio.00933-23 snippet: we discussed the action of Dnd-related R-M systems against phages and demonstrated that the host could benefit from the protection provided by Dnd-related R-M systems against infection by various lytic phages as well as temperate phages notes: Jiang et al. support the phage-resistance output of Dnd restriction-modification systems. - reference: DOI:10.1128/mbio.00933-23 snippet: the 8,286-bp and 8,321-bp fragments containing the whole dndBCDEFGH gene cluster were amplified from the genomic DNA of E. coli B7A notes: Jiang et al. support Escherichia coli B7A as a direct source of the cloned dndBCDEFGH Dnd system. canonical_examples: - taxon_id: NCBITaxon:340184 taxon_label: Escherichia coli B7A note: Jiang et al. amplified the whole dndBCDEFGH gene cluster from E. coli B7A and assayed the cloned DndB7A R-M system for resistance against lytic and temperate phages. reference: DOI:10.1128/mbio.00933-23 causal_graphs: - graph_id: dnd_dna_phosphorothioation_foreign_dna_nicking title: Dnd systems use DNA phosphorothioation to restrict foreign DNA description: Evidence-backed process sketch linking a Dnd restriction-modification locus to host DNA phosphorothioation, PT-guided DndFGH foreign-DNA nicking, and Dnd-mediated phage defense. scope_status: NONMECHANISTIC scope_notes: The graph captures Dnd-family modification and DndFGH restriction outputs without asserting one universal DndA cysteine-desulfurase source, PT motif, DndFGH conformational pathway, exogenous substrate class, phage spectrum, methylation interaction, or relationship to Ssp systems across all Dnd loci. nodes: - node_id: dnd_restriction_modification_locus label: Dnd restriction-modification locus node_type: GENETIC_ELEMENT description: A Dnd phosphorothioation-dependent restriction locus pairing a Dnd-family DNA modification module with a DndFGH restriction module. - node_id: dna_phosphorothioation label: DNA phosphorothioation node_type: BIOLOGICAL_PROCESS description: Replacement of a nonbridging oxygen in the DNA phosphate backbone with sulfur. - node_id: dndfgh_foreign_dna_targeting label: DndFGH foreign DNA targeting node_type: BIOLOGICAL_PROCESS description: DndFGH-mediated binding and translocation on unmodified exogenous DNA before restriction. - node_id: foreign_dna_nicking label: foreign DNA nicking node_type: BIOLOGICAL_PROCESS description: Introduction of nicks into unmodified invading DNA by a PT-associated restriction module. - node_id: phage_infection label: phage infection node_type: BIOLOGICAL_PROCESS description: Entry and intracellular replication attempt by a bacteriophage infecting a host bacterium. - node_id: dnd_system_trait label: Dnd system node_type: TRAIT grounding: traitmech:000221 description: Possession of a genome-encoded Dnd restriction-modification defense system. - node_id: phosphorothioate_defense_system_trait label: phosphorothioate defense system node_type: TRAIT grounding: traitmech:000213 description: Possession of a genome-encoded phosphorothioate-based phage defense system. edges: - subject: dnd_restriction_modification_locus predicate: contributes to predicate_id: RO:0002326 object: dna_phosphorothioation description: Dnd-family modification modules install sequence-specific phosphorothioate marks on host DNA. evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification notes: Xiong et al. support Dnd-mediated host DNA phosphorothioation. - subject: dnd_restriction_modification_locus predicate: contributes to predicate_id: RO:0002326 object: dndfgh_foreign_dna_targeting description: Dnd restriction-modification loci pair host DNA phosphorothioation genes with the DndFGH restriction module. evidence: - reference: DOI:10.1128/mbio.00933-23 snippet: To build up a line of defense, the dndABCDE gene cluster is usually paired with dndFGH, which acts as a restriction module notes: Jiang et al. support the paired modification-plus-restriction architecture of Dnd systems. - subject: dna_phosphorothioation predicate: contributes to predicate_id: RO:0002326 object: dndfgh_foreign_dna_targeting description: DNA phosphorothioation marks host DNA as self and leaves unmodified exogenous DNA susceptible to DndFGH targeting. evidence: - reference: DOI:10.1128/mbio.00933-23 snippet: In the presence of exogenous DNA that lacks PT, the macromolecular machine consisting of DndF, DndG, and DndH undergoes conformational changes notes: Jiang et al. connect absence of PT on exogenous DNA to DndFGH restriction-complex activation. - subject: dndfgh_foreign_dna_targeting predicate: activates predicate_id: RO:0002213 object: foreign_dna_nicking description: DndFGH targeting leads to DNA binding, translocation, and nicking of invading DNA. evidence: - reference: DOI:10.1128/mbio.00933-23 snippet: DndFGH exerts DNA binding, translocation, and nicking activities to initiate the destructive DNA-shredding program to eliminate genetic parasites notes: Jiang et al. summarize the nicking output of DndFGH foreign-DNA targeting. - subject: foreign_dna_nicking predicate: mitigates predicate_id: METPO:2007407 object: phage_infection description: DndFGH-mediated nicking restricts lytic phages and blocks lysogenization by temperate phages. evidence: - reference: DOI:10.1128/mbio.00933-23 snippet: Dnd R-M systems protect the host from various lytic phages as well as the lysogenization of temperate phages notes: Jiang et al. summarize Dnd-mediated protection against lytic phages and temperate phage lysogenization. - subject: foreign_dna_nicking predicate: confers predicate_id: METPO:2007700 object: dnd_system_trait description: PT-guided foreign-DNA nicking realizes the Dnd restriction-modification system trait. evidence: - reference: DOI:10.1128/mbio.00933-23 snippet: the host could benefit from Dnd-related R-M systems for a broad range of antiphage activities notes: Jiang et al. support DndFGH restriction as the Dnd antiphage defense output. - subject: dnd_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phosphorothioate_defense_system_trait description: Dnd system possession is a phosphorothioate-defense-system trait. evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component notes: Xiong et al. place Dnd within phosphorothioation-dependent restriction systems. curation_history: - timestamp: '2026-09-15T16:03:58Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Dnd system as a DOI-backed GENOMICS TraitRecord under the phosphorothioate defense system parent 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_v98. llm_assisted: true