identifier: traitmech:000224 label: DndCDEA-PbeABCD system definition: A phosphorothioate defense system in which an organism possesses a DndCDEA-PbeABCD locus that pairs DndCDEA-mediated host-DNA phosphorothioation with PbeABCD-dependent targeting of non-phosphorothioated viral DNA to inhibit viral DNA replication. definition_source: DOI:10.1038/s41467-019-09390-9 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000213 synonyms: - synonym_text: PbeABCD-mediated PT defence system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-019-09390-9 evidence: - reference: DOI:10.1038/s41467-019-09390-9 snippet: a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication notes: Xiong et al. name the DndCDEA-PbeABCD architecture as an archaeal PT-based antiviral system. - reference: DOI:10.1038/s41467-019-09390-9 snippet: can defend against viral attack together with pbeABCD, a conserved 4-gene cassette sharing no sequence homology with DndFGH notes: Xiong et al. support separating PbeABCD systems from canonical Dnd systems whose restriction module is DndFGH. - reference: DOI:10.1038/s41467-019-09390-9 snippet: DndCDEA-PbeABCD confers protection against the haloarchaeal virus SNJ1 notes: Xiong et al. experimentally support the antiviral output of the Haloterrigena jeotgali A29 DndCDEA-PbeABCD locus after heterologous expression in CJ7-F cells. - reference: DOI:10.1038/s41467-019-09390-9 snippet: PbeABCD exerted antiviral activity depending on the presence of PT modifications notes: Xiong et al. connect PbeABCD antiviral restriction to phosphorothioation-dependent self/non-self discrimination. - reference: DOI:10.1038/s41467-019-09390-9 snippet: the subsequent viral genome replication process is significantly inhibited by the DndCDEA-PbeABCD system notes: Xiong et al. directly connect DndCDEA-PbeABCD to inhibition of SNJ1 viral DNA replication after viral DNA injection. - reference: DOI:10.1038/s41467-019-09390-9 snippet: does not involve viral DNA degradation or cleavage, ruling out the involvement of currently known defence mechanisms notes: Xiong et al. bound the PbeABCD mechanism away from the DNA-cleavage mechanisms of canonical restriction systems. - reference: DOI:10.1134/S0006297921030081 snippet: instead of the dndFGH, the restriction function is performed by the pbeABCD gene cluster notes: Isaev et al. summarize pbeABCD as the restriction branch paired with archaeal DndCDEA phosphorothioation. - reference: DOI:10.1134/S0006297921030081 snippet: The dndCDEA-pbeABCD from Haloterrigena jeotgali was shown to provide antiviral defense notes: Isaev et al. independently summarize the Haloterrigena jeotgali DndCDEA-PbeABCD locus as an antiviral defense system. canonical_examples: - taxon_id: NCBITaxon:1455609 taxon_label: Natrinema thermotolerans A29 note: Xiong et al. identified the dndCDEA-pbeABCD locus in Haloterrigena jeotgali A29 and showed that the cloned locus confers DndCDEA- and PbeABCD-dependent resistance to the haloarchaeal virus SNJ1. reference: DOI:10.1038/s41467-019-09390-9 causal_graphs: - graph_id: dndcdea_pbeabcd_pt_viral_replication_inhibition title: DndCDEA-PbeABCD systems halt archaeal viral DNA replication description: Evidence-backed process sketch linking a DndCDEA-PbeABCD locus to host DNA phosphorothioation, PT-dependent PbeABCD antiviral activity, and inhibited replication of non-phosphorothioated viral DNA. scope_status: NONMECHANISTIC scope_notes: The graph captures DndCDEA-PbeABCD restriction at the system level without asserting one universal host taxon, PT motif outside characterized haloarchaeal systems, PbeABCD subunit cycle, direct viral DNA cleavage, or relationship to bacterial DndFGH and Ssp-family systems. nodes: - node_id: dndcdea_pbeabcd_locus label: DndCDEA-PbeABCD locus node_type: GENETIC_ELEMENT description: An archaeal phosphorothioation-dependent antiviral locus pairing DndCDEA host-DNA phosphorothioation with PbeABCD restriction activity. - node_id: dndcdea_dna_phosphorothioation label: DndCDEA DNA phosphorothioation node_type: BIOLOGICAL_PROCESS description: DndCDEA-mediated installation of sequence-specific phosphorothioate marks on host DNA. - node_id: pbeabcd_pt_dependent_virus_targeting label: PbeABCD PT-dependent virus targeting node_type: BIOLOGICAL_PROCESS description: Phosphorothioate-dependent PbeABCD antiviral activity against invading DNA that lacks host PT marks. - node_id: viral_dna_replication label: viral DNA replication node_type: BIOLOGICAL_PROCESS description: Replication of invading archaeal viral DNA after host cell entry. - node_id: dndcdea_pbeabcd_system_trait label: DndCDEA-PbeABCD system node_type: TRAIT grounding: traitmech:000224 description: Possession of a genome-encoded DndCDEA-PbeABCD phosphorothioation-dependent antiviral 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 antiviral defense system. edges: - subject: dndcdea_pbeabcd_locus predicate: contributes to predicate_id: RO:0002326 object: dndcdea_dna_phosphorothioation description: The DndCDEA modification module installs phosphorothioate marks on archaeal host DNA. evidence: - reference: DOI:10.1038/s41467-019-09390-9 snippet: involves DndCDEA-specific DNA phosphorothioate (PT) modification notes: Xiong et al. support DndCDEA-dependent host DNA phosphorothioation in the PbeABCD-coupled system. - subject: dndcdea_pbeabcd_locus predicate: contributes to predicate_id: RO:0002326 object: pbeabcd_pt_dependent_virus_targeting description: DndCDEA-PbeABCD loci pair host-DNA phosphorothioation with PbeABCD antiviral activity. evidence: - reference: DOI:10.1038/s41467-019-09390-9 snippet: can defend against viral attack together with pbeABCD notes: Xiong et al. support the paired DndCDEA modification and PbeABCD effector architecture. - subject: dndcdea_dna_phosphorothioation predicate: contributes to predicate_id: RO:0002326 object: pbeabcd_pt_dependent_virus_targeting description: PbeABCD antiviral activity depends on the presence of PT marks rather than direct PbeABCD-DndCDEA protein interactions. evidence: - reference: DOI:10.1038/s41467-019-09390-9 snippet: depending on the presence of PT modifications notes: Xiong et al. distinguish PT-dependent PbeABCD restriction from direct modification-effector protein coupling. - subject: pbeabcd_pt_dependent_virus_targeting predicate: mitigates predicate_id: METPO:2007407 object: viral_dna_replication description: PbeABCD-dependent targeting inhibits replication of non-phosphorothioated viral DNA. evidence: - reference: DOI:10.1038/s41467-019-09390-9 snippet: the subsequent viral genome replication process is significantly inhibited notes: Xiong et al. observed impaired SNJ1 genome replication in cells expressing DndCDEA-PbeABCD. - subject: pbeabcd_pt_dependent_virus_targeting predicate: confers predicate_id: METPO:2007700 object: dndcdea_pbeabcd_system_trait description: PT-dependent PbeABCD antiviral activity realizes the DndCDEA-PbeABCD defense trait. evidence: - reference: DOI:10.1038/s41467-019-09390-9 snippet: DndCDEA-PbeABCD confers resistance against invading viruses notes: Xiong et al. support PbeABCD-mediated restriction as the system's antiviral output. - subject: dndcdea_pbeabcd_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phosphorothioate_defense_system_trait description: DndCDEA-PbeABCD possession is a phosphorothioate-defense-system trait. evidence: - reference: DOI:10.1134/S0006297921030081 snippet: instead of the dndFGH, the restriction function is performed by the pbeABCD gene cluster notes: Isaev et al. place PbeABCD in the family of PT defense systems while distinguishing it from DndFGH. curation_history: - timestamp: '2026-09-15T17:36:16Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DndCDEA-PbeABCD 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_v101. llm_assisted: true