identifier: traitmech:000220 label: Shedu system definition: 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. definition_source: DOI:10.1016/j.cell.2024.11.030 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Shedu anti-phage defense system synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.cell.2024.11.030 evidence: - reference: DOI:10.1016/j.cell.2024.11.030 snippet: Shedu is a single-component defense system comprising a putative nuclease SduA notes: Loeff et al. support Shedu as a named, single-component antiphage defense system centered on SduA. - reference: DOI:10.1016/j.cell.2024.11.030 snippet: 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 notes: Loeff et al. connect Shedu DNA-end recognition to positioned double-stranded DNA nicking. - reference: DOI:10.1016/j.cell.2024.11.030 snippet: The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA notes: Loeff et al. support DNA-end-directed nicking as an antiviral Shedu output that blocks linear DNA propagation. - reference: DOI:10.1016/j.molcel.2024.12.004 snippet: Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease notes: Gu et al. also place Shedu among prokaryotic antiphage immune systems and support its single-protein nuclease architecture. - reference: DOI:10.1016/j.molcel.2024.12.004 snippet: we reveal the structural basis for activation of Bacillus cereus Shedu notes: Gu et al. support Bacillus cereus Shedu as a structurally characterized representative. - reference: DOI:10.1016/j.molcel.2024.12.004 snippet: these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs notes: Gu et al. support defining Shedu at the immune-nuclease family level while leaving N-terminal domain diversity for narrower subtype review. canonical_examples: - taxon_id: NCBITaxon:1396 taxon_label: Bacillus cereus note: Gu et al. structurally characterized Bacillus cereus Shedu and reported that this nuclease cleaves near DNA ends with a 3' single-stranded overhang. reference: DOI:10.1016/j.molcel.2024.12.004 causal_graphs: - graph_id: shedu_dna_end_nicking title: Shedu immune nucleases nick DNA ends during antiphage defense description: Evidence-backed process sketch linking a Shedu locus to SduA-like sensor-dependent nuclease activation, DNA-end nicking, and inhibition of bacteriophage DNA propagation. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: shedu_locus label: Shedu locus node_type: GENETIC_ELEMENT description: A Shedu antiphage defense locus encoding a single-protein SduA-like immune nuclease. - node_id: shedu_nuclease_activation label: Shedu nuclease activation node_type: BIOLOGICAL_PROCESS description: Sensor-dependent activation of the Shedu nuclease core. - node_id: shedu_dna_end_nicking label: Shedu DNA end nicking node_type: BIOLOGICAL_PROCESS description: Shedu-mediated recognition and nicking of DNA near free or structured ends. - node_id: phage_dna_propagation label: phage DNA propagation node_type: BIOLOGICAL_PROCESS description: Propagation of bacteriophage DNA inside an infected bacterial host. - node_id: shedu_system_trait label: Shedu system node_type: TRAIT grounding: traitmech:000220 description: Possession of a genome-encoded Shedu antiphage defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: shedu_locus predicate: contributes to predicate_id: RO:0002326 object: shedu_nuclease_activation description: Shedu loci encode SduA-like single-protein immune nucleases whose sensor domains regulate a common nuclease core. evidence: - reference: DOI:10.1016/j.cell.2024.11.030 snippet: Shedu is a single-component defense system comprising a putative nuclease SduA notes: Loeff et al. support the single-component SduA-centered Shedu architecture. - reference: DOI:10.1016/j.molcel.2024.12.004 snippet: these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs notes: Gu et al. support Shedu as a broader family of sensor-regulated immune nucleases. - subject: shedu_nuclease_activation predicate: enables predicate_id: RO:0002327 object: shedu_dna_end_nicking description: Shedu sensor-domain activation enables PD-(D/E)XK nuclease-domain nicking of DNA near DNA ends. evidence: - reference: DOI:10.1016/j.cell.2024.11.030 snippet: the N-terminal domains of SduA form a clamp that recognizes free DNA ends notes: Loeff et al. support free DNA-end recognition by the N-terminal SduA clamp. - reference: DOI:10.1016/j.cell.2024.11.030 snippet: 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 notes: Loeff et al. connect DNA-end binding to SduA nuclease-domain positioning and double-stranded DNA nicking. - subject: shedu_dna_end_nicking predicate: mitigates predicate_id: METPO:2007407 object: phage_dna_propagation description: Shedu-mediated nicking or degradation of phage DNA ends inhibits bacteriophage DNA propagation. evidence: - reference: DOI:10.1016/j.cell.2024.11.030 snippet: The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA notes: Loeff et al. support Shedu DNA nicking as a barrier to linear DNA propagation. - reference: DOI:10.1016/j.molcel.2024.12.004 snippet: Shedu cleaves near DNA ends with a 3' single-stranded overhang, likely enabling it to specifically degrade the DNA injected by certain bacteriophages notes: Gu et al. connect B. cereus Shedu DNA-end cleavage to likely degradation of injected phage DNA. - subject: shedu_dna_end_nicking predicate: confers predicate_id: METPO:2007700 object: shedu_system_trait description: DNA-end nicking is a characterized antiviral output that realizes the Shedu system trait. evidence: - reference: DOI:10.1016/j.cell.2024.11.030 snippet: Taken together, these results define the antiviral mechanism of Shedu systems notes: Loeff et al. connect DNA-end sensing and cleavage to the Shedu antiviral mechanism. - subject: shedu_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Shedu system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.molcel.2024.12.004 snippet: Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease notes: Gu et al. place Shedu in the family of prokaryotic antiphage immune systems. discussions: - discussion_id: shedu-sensor-and-substrate-gap prompt: Resolve Shedu sensor classes and DNA substrate preferences before minting narrower Shedu subtype or mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: 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. posed_by: codex posed_date: '2026-09-15' curation_history: - timestamp: '2026-09-15T15:25:04Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true