identifier: traitmech:000217 label: Zorya system definition: A genomics trait describing possession of a Zorya antiphage defense locus in which conserved ZorA/ZorB membrane-motor core proteins and subtype-specific effector proteins inhibit bacteriophage propagation. definition_source: DOI:10.1038/s41586-024-08493-8 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Zorya anti-phage defence system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41586-024-08493-8 - synonym_text: Zorya phage defense system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-025-57397-2 evidence: - reference: DOI:10.1038/s41586-024-08493-8 snippet: Zorya is a recently identified and widely distributed bacterial immune system that protects bacteria from viral (phage) infections notes: Hu et al. support Zorya as a bacterial antiviral immune system. - reference: DOI:10.1038/s41467-025-57397-2 snippet: The Zorya phage defense system was first discovered in 2018 notes: Mariano et al. support the standard US-English family name for the Zorya system. - reference: DOI:10.1038/s41467-025-57397-2 snippet: all Zorya systems share two components, ZorA and ZorB, containing domains distantly related, respectively, to the MotA and MotB subunits of the bacterial flagellar motor notes: Mariano et al. support the conserved ZorA/ZorB motor-core architecture shared by Zorya systems. - reference: DOI:10.1038/s41586-024-08493-8 snippet: ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors notes: Hu et al. support the Type I ZorAB-dependent effector recruitment and activation step. - reference: DOI:10.1038/s41467-025-57397-2 snippet: For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB notes: Mariano et al. support Type II ZorE as a ZorAB-recruited effector. - reference: DOI:10.1038/s41467-025-57397-2 snippet: We observed that homologs of Zorya I from Serratia marcescens ATCC 274 and Zorya II from E. coli ATCC 8739 provide protection against several phages from the Durham collection notes: Mariano et al. support experimentally validated Zorya phage protection from native Serratia marcescens and E. coli loci. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: Mariano et al. report that a Zorya II locus from E. coli ATCC 8739 protected E. coli MT56 against several tested coliphages. reference: DOI:10.1038/s41467-025-57397-2 causal_graphs: - graph_id: zorya_zorab_effector_antiphage_defense title: Zorya ZorAB motors recruit antiphage effectors description: Evidence-backed process sketch linking a Zorya locus to phage-triggered ZorAB ion-motor activation, effector recruitment, and inhibition of bacteriophage replication. scope_status: NONMECHANISTIC scope_notes: The graph captures characterized Type I ZorC/ZorD and Type II ZorE outputs without asserting one universal ZorAB-coupled effector, ion substrate, DNA target, cell-death pathway, Type III mechanism, or anti-Zorya-evasion mechanism across all Zorya loci. nodes: - node_id: phage_invasion label: phage invasion node_type: BIOLOGICAL_PROCESS description: Entry of a bacteriophage and its nucleic acid into a bacterial host cell. - node_id: zorya_locus label: Zorya locus node_type: GENETIC_ELEMENT description: A Zorya antiphage defense locus encoding conserved ZorA/ZorB membrane core proteins and subtype-specific effector proteins. - node_id: zorab_ion_motor_activation label: ZorAB ion-motor activation node_type: BIOLOGICAL_PROCESS description: Activation of a membrane-anchored ZorA/ZorB ion-driven motor after detection of phage invasion. - node_id: zorya_effector_activity label: Zorya effector activity node_type: BIOLOGICAL_PROCESS description: Activity of ZorAB-coupled Zorya effector proteins such as Type I ZorC/ZorD or Type II ZorE. - node_id: phage_replication label: phage replication node_type: BIOLOGICAL_PROCESS description: Replication of invading bacteriophage DNA after host-cell entry. - node_id: zorya_system_trait label: Zorya system node_type: TRAIT grounding: traitmech:000217 description: Possession of a genome-encoded Zorya antiphage defense locus. - 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: zorya_locus predicate: contributes to predicate_id: RO:0002326 object: zorab_ion_motor_activation description: Zorya loci encode the conserved ZorA and ZorB membrane core proteins that form the ZorAB motor. evidence: - reference: DOI:10.1038/s41467-025-57397-2 snippet: all Zorya systems share two components, ZorA and ZorB, containing domains distantly related, respectively, to the MotA and MotB subunits of the bacterial flagellar motor notes: Mariano et al. support ZorA/ZorB as the conserved Zorya core proteins. - subject: phage_invasion predicate: activates predicate_id: RO:0002213 object: zorab_ion_motor_activation description: Phage invasion activates the ZorAB ion motor after Zorya senses bacteriophage challenge. evidence: - reference: DOI:10.1038/s41586-024-08493-8 snippet: ZorAB operates as a proton-driven motor that becomes activated after sensing of phage invasion notes: Hu et al. support phage-invasion-dependent ZorAB activation. - subject: zorab_ion_motor_activation predicate: activates predicate_id: RO:0002213 object: zorya_effector_activity description: ZorAB motor activation recruits and activates subtype-specific Zorya effector proteins. evidence: - reference: DOI:10.1038/s41586-024-08493-8 snippet: ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors notes: Hu et al. support ZorAB-mediated Type I ZorC/ZorD activation. - reference: DOI:10.1038/s41467-025-57397-2 snippet: For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB notes: Mariano et al. support ZorAB-mediated recruitment of the Type II ZorE effector. - subject: zorya_effector_activity predicate: mitigates predicate_id: METPO:2007407 object: phage_replication description: Zorya effector activity helps inhibit invading bacteriophages. evidence: - reference: DOI:10.1038/s41586-024-08493-8 snippet: soluble ZorC and ZorD effectors, which facilitate the degradation of the phage DNA notes: Hu et al. support Type I ZorC/ZorD effectors as phage-DNA-degradation outputs. - subject: zorya_effector_activity predicate: confers predicate_id: METPO:2007700 object: zorya_system_trait description: Zorya effector activity is the antiviral output that realizes the Zorya system defense phenotype. evidence: - reference: DOI:10.1038/s41467-025-57397-2 snippet: Our work reveals the molecular basis of the activity of Zorya systems and highlights the ZorE nickase as crucial for population-wide immunity in the type II system notes: Mariano et al. support ZorE nickase activity as a Type II Zorya effector output. - subject: zorya_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Zorya system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41467-025-57397-2 snippet: The Zorya phage defense system was first discovered in 2018 notes: Mariano et al. place Zorya in the phage-defense-system family. discussions: - discussion_id: zorya-subtype-effector-and-trigger-gap prompt: Resolve Zorya subtype effectors, ion usage, and phage triggers before minting narrower Zorya mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Hu et al. support Type I ZorAB activation and ZorC/ZorD-mediated phage-DNA degradation, Mariano et al. support Type I/II ZorAB architecture plus a recruited Type II ZorE nickase, and the pinned DefenseFinder rules table supports distinct Zorya_TypeI and Zorya_TypeII subtype rows. Zorya type I and type II TraitRecords now capture those DefenseFinder subtypes, but Zorya variants still need separate review before TraitMech asserts one universal ion substrate, effector composition, nuclease target, cell-death pathway, Type III mechanism, or anti-defense breadth. The type-III architecture is now represented by traitmech:000576 Zorya type III system for ZorA/ZorB/ZorF/ZorG loci. Payne Figure 2C and Discussion plus Mariano's Introduction support that composition despite the conflicting zorBC wording in Payne's Results. DefenseFinder's three-match threshold is not a complete four-component biological definition. Type-III component roles and native-host mechanisms remain open; the family definition, graph and type-I/II records are unchanged. posed_by: codex posed_date: '2026-09-15' curation_history: - timestamp: '2026-09-15T13:45:12Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Zorya 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_v94. llm_assisted: true - timestamp: '2026-10-02T18:08:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: Documented Zorya type II as split out in the open Zorya subtype-effector discussion after minting traitmech:000552 for the DefenseFinder-backed Zorya_TypeII child; Type I, Type III, and finer Zorya subtype mechanisms remain open. llm_assisted: true - timestamp: '2026-10-02T20:10:34Z' curator: codex action: TRACK_NARROWER_RECORD changes: Documented Zorya type I as split out in the open Zorya subtype-effector discussion after minting traitmech:000554 for the DefenseFinder-backed Zorya_TypeI child; Type III and finer Zorya subtype mechanisms remain open. llm_assisted: true - timestamp: '2026-10-03T19:16:00Z' curator: codex action: TRACK_ZORYA_TYPE_III_CLASS changes: Linked traitmech:000576 using DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2. Kept the family definition, hierarchy, graph, evidence and example unchanged; type-III component functions remain open rather than inheriting type-I/II chemistry. llm_assisted: true