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Shedu system

traitmech:000220 · CLASS · PROPOSED

A genomics trait describing possession of a Shedu antiphage defense system encoding a single-protein immune nuclease with a conserved nuclease core and regulated sensor domain architecture.

Trait evidence (6)

  • DOI:10.1016/j.cell.2024.11.030
    Shedu is a single-component defense system comprising a putative nuclease SduA

    Loeff et al. support Shedu as a named, single-component antiphage defense system centered on SduA.

  • DOI:10.1016/j.cell.2024.11.030
    End binding positions the DNA over the PD-(D/E)XK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5' end

    Loeff et al. connect Shedu DNA-end recognition to positioned double-stranded DNA nicking.

  • DOI:10.1016/j.cell.2024.11.030
    The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA

    Loeff et al. support DNA-end-directed nicking as an antiviral Shedu output that blocks linear DNA propagation.

  • DOI:10.1016/j.molcel.2024.12.004
    Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease

    Gu et al. also place Shedu among prokaryotic antiphage immune systems and support its single-protein nuclease architecture.

  • DOI:10.1016/j.molcel.2024.12.004
    we reveal the structural basis for activation of Bacillus cereus Shedu

    Gu et al. support Bacillus cereus Shedu as a structurally characterized representative.

  • DOI:10.1016/j.molcel.2024.12.004
    these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs

    Gu et al. support defining Shedu at the immune-nuclease family level while leaving N-terminal domain diversity for narrower subtype review.

Shedu immune nucleases nick DNA ends during antiphage defense

Evidence-backed process sketch linking a Shedu locus to SduA-like sensor-dependent nuclease activation, DNA-end nicking, and inhibition of bacteriophage DNA propagation.

NONMECHANISTIC · The graph captures SduA/Shedu immune-nuclease outputs without asserting one universal N-terminal sensor class, DNA-end substrate, overhang preference, phage target, activation signal, escape strategy, or Bacillus-specific mechanism across all Shedu homologs.

Shedu immune nucleases nick DNA ends during antiphage defense Interactive directed graph showing evidence-backed causal relationships for Shedu system.

Edge evidence

  • Shedu locus contributes to Shedu nuclease activation RO:0002326

    Shedu loci encode SduA-like single-protein immune nucleases whose sensor domains regulate a common nuclease core.

    • DOI:10.1016/j.cell.2024.11.030 Shedu is a single-component defense system comprising a putative nuclease SduA Loeff et al. support the single-component SduA-centered Shedu architecture.
    • DOI:10.1016/j.molcel.2024.12.004 these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs Gu et al. support Shedu as a broader family of sensor-regulated immune nucleases.
  • Shedu nuclease activation enables Shedu DNA end nicking RO:0002327

    Shedu sensor-domain activation enables PD-(D/E)XK nuclease-domain nicking of DNA near DNA ends.

    • DOI:10.1016/j.cell.2024.11.030 the N-terminal domains of SduA form a clamp that recognizes free DNA ends Loeff et al. support free DNA-end recognition by the N-terminal SduA clamp.
    • DOI:10.1016/j.cell.2024.11.030 End binding positions the DNA over the PD-(D/E)XK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5' end Loeff et al. connect DNA-end binding to SduA nuclease-domain positioning and double-stranded DNA nicking.
  • Shedu DNA end nicking mitigates phage DNA propagation METPO:2007407

    Shedu-mediated nicking or degradation of phage DNA ends inhibits bacteriophage DNA propagation.

    • DOI:10.1016/j.cell.2024.11.030 The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA Loeff et al. support Shedu DNA nicking as a barrier to linear DNA propagation.
    • DOI:10.1016/j.molcel.2024.12.004 Shedu cleaves near DNA ends with a 3' single-stranded overhang, likely enabling it to specifically degrade the DNA injected by certain bacteriophages Gu et al. connect B. cereus Shedu DNA-end cleavage to likely degradation of injected phage DNA.
  • Shedu DNA end nicking confers Shedu system METPO:2007700

    DNA-end nicking is a characterized antiviral output that realizes the Shedu system trait.

    • DOI:10.1016/j.cell.2024.11.030 Taken together, these results define the antiviral mechanism of Shedu systems Loeff et al. connect DNA-end sensing and cleavage to the Shedu antiviral mechanism.
  • Shedu system is a phage defense system rdfs:subClassOf

    Shedu system possession is a phage-defense-system trait.

    • DOI:10.1016/j.molcel.2024.12.004 Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease Gu et al. place Shedu in the family of prokaryotic antiphage immune systems.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1016/j.cell.2024.11.030

Parent traits (1)

Synonyms (1)

  • Shedu anti-phage defense system EXACT_SYNONYM · DOI:10.1016/j.cell.2024.11.030

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.

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 Shedu sensor classes and DNA substrate preferences before minting narrower Shedu subtype or mechanism children.

KNOWLEDGE GAP OPEN shedu-sensor-and-substrate-gap · raised by codex · 2026-09-15

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Loeff et al. support free-DNA-end recognition and end-directed DNA nicking by SduA, and Gu et al. support a common Shedu nuclease core regulated by diverse N-terminal domains, but Shedu homologs need separate review before TraitMech asserts one universal N-terminal sensor class, activating DNA substrate, overhang preference, phage target, or escape strategy.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted Shedu system as a DOI-backed GENOMICS TraitRecord under the phage 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_v97.