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Dnd system

traitmech:000221 · CLASS · PROPOSED

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.

Trait evidence (6)

  • DOI:10.1038/s41564-020-0700-6
    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

    Xiong et al. summarize Dnd as a named PT-dependent restriction system with DNA-modification and restriction modules.

  • DOI:10.1128/mbio.00933-23
    Usually, this modification gene cluster is paired with a restriction module consisting of DndF, DndG, and DndH

    Jiang et al. support DndFGH as the restriction module paired with Dnd DNA phosphorothioation.

  • DOI:10.1128/mbio.00933-23
    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

    Jiang et al. support defining the Dnd system by a Dnd-family modification module without requiring a contiguous dndA gene in every locus.

  • DOI:10.1128/mbio.00933-23
    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

    Jiang et al. connect DndFGH to detection and nicking of foreign DNA lacking PT modification.

  • DOI:10.1128/mbio.00933-23
    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

    Jiang et al. support the phage-resistance output of Dnd restriction-modification systems.

  • DOI:10.1128/mbio.00933-23
    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

    Jiang et al. support Escherichia coli B7A as a direct source of the cloned dndBCDEFGH Dnd system.

Dnd systems use DNA phosphorothioation to restrict foreign DNA

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.

NONMECHANISTIC · 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.

Dnd systems use DNA phosphorothioation to restrict foreign DNA Interactive directed graph showing evidence-backed causal relationships for Dnd system.

Edge evidence

  • Dnd restriction-modification locus contributes to DNA phosphorothioation RO:0002326

    Dnd-family modification modules install sequence-specific phosphorothioate marks on host DNA.

    • DOI:10.1038/s41564-020-0700-6 uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification Xiong et al. support Dnd-mediated host DNA phosphorothioation.
  • Dnd restriction-modification locus contributes to DndFGH foreign DNA targeting RO:0002326

    Dnd restriction-modification loci pair host DNA phosphorothioation genes with the DndFGH restriction module.

    • DOI:10.1128/mbio.00933-23 To build up a line of defense, the dndABCDE gene cluster is usually paired with dndFGH, which acts as a restriction module Jiang et al. support the paired modification-plus-restriction architecture of Dnd systems.
  • DNA phosphorothioation contributes to DndFGH foreign DNA targeting RO:0002326

    DNA phosphorothioation marks host DNA as self and leaves unmodified exogenous DNA susceptible to DndFGH targeting.

    • DOI:10.1128/mbio.00933-23 In the presence of exogenous DNA that lacks PT, the macromolecular machine consisting of DndF, DndG, and DndH undergoes conformational changes Jiang et al. connect absence of PT on exogenous DNA to DndFGH restriction-complex activation.
  • DndFGH foreign DNA targeting activates foreign DNA nicking RO:0002213

    DndFGH targeting leads to DNA binding, translocation, and nicking of invading DNA.

    • DOI:10.1128/mbio.00933-23 DndFGH exerts DNA binding, translocation, and nicking activities to initiate the destructive DNA-shredding program to eliminate genetic parasites Jiang et al. summarize the nicking output of DndFGH foreign-DNA targeting.
  • foreign DNA nicking mitigates phage infection METPO:2007407

    DndFGH-mediated nicking restricts lytic phages and blocks lysogenization by temperate phages.

    • DOI:10.1128/mbio.00933-23 Dnd R-M systems protect the host from various lytic phages as well as the lysogenization of temperate phages Jiang et al. summarize Dnd-mediated protection against lytic phages and temperate phage lysogenization.
  • foreign DNA nicking confers Dnd system METPO:2007700

    PT-guided foreign-DNA nicking realizes the Dnd restriction-modification system trait.

    • DOI:10.1128/mbio.00933-23 the host could benefit from Dnd-related R-M systems for a broad range of antiphage activities Jiang et al. support DndFGH restriction as the Dnd antiphage defense output.
  • Dnd system is a phosphorothioate defense system rdfs:subClassOf

    Dnd system possession is a phosphorothioate-defense-system trait.

    • DOI:10.1038/s41564-020-0700-6 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 Xiong et al. place Dnd within phosphorothioation-dependent restriction systems.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41564-020-0700-6

Parent traits (1)

Synonyms (3)

  • Dnd R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
  • Dnd-related R-M system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23
  • Dnd-related restriction and modification system EXACT_SYNONYM · DOI:10.1128/mbio.00933-23

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.

  • Escherichia coli B7A NCBITaxon:340184 DOI:10.1128/mbio.00933-23 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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.