identifier: traitmech:000237 label: PARIS system definition: An abortive infection system in which an organism possesses a phage anti-restriction-induced system locus encoding an AriA ABC ATPase sensor and an AriB TOPRIM-family nuclease whose activation by phage anti-restriction or other foreign proteins releases AriB to inhibit translation through lysine tRNA cleavage and block bacteriophage propagation. definition_source: DOI:10.1016/j.chom.2022.02.018 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: phage anti-restriction-induced system synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.chom.2022.02.018 - synonym_text: phage antirestriction induced system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41586-024-07874-3 evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein notes: Rousset et al. support PARIS as a named abortive infection system activated by a phage anti-restriction protein. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: phage anti-restriction-induced system (PARIS), an abortive infection system that triggers growth arrest upon sensing an anti-restriction protein notes: Rousset et al. support the PARIS long-form name and the growth-arrest output of the system. - reference: DOI:10.1038/s41586-024-07772-8 snippet: operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr notes: Deep et al. support defining the Ocr-triggered PARIS mechanism around the AriA antitoxin and AriB toxin. - reference: DOI:10.1038/s41586-024-07772-8 snippet: AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA notes: Deep et al. support the AriB nuclease, lysine-tRNA cleavage, translational-inhibition, growth-arrest, and phage-propagation outputs. - reference: DOI:10.1038/s41586-024-07874-3 snippet: The phage antirestriction induced system (PARIS) is a defence system, often encoded in viral genomes, that is composed of a 55 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB) notes: Burman et al. independently support the AriA ABC ATPase and AriB TOPRIM nuclease components. - reference: DOI:10.1038/s41586-024-07874-3 snippet: ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA notes: Burman et al. support an activation model in which foreign-protein detection releases AriB to cleave host lysine tRNA. - reference: DOI:10.1038/s41586-024-07874-3 snippet: Phage T5 subverts PARIS immunity through expression of a lysine transfer RNA variant that is not cleaved by PARIS, thereby restoring viral infection notes: Burman et al. support recording T5 lysine tRNA anti-defense as a reviewed counter-defense gap before minting narrower PARIS subtype children. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: While the system from E. coli B185 provided robust defense when expressed from its natural promoter notes: Rousset et al. support E. coli as a canonical organism by cloning the E. coli B185 PARIS system with its native promoter and observing robust antiphage defense. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: Rousset et al. cloned the native-promoter PARIS locus from E. coli B185 and showed that it provided robust defense. reference: DOI:10.1016/j.chom.2022.02.018 causal_graphs: - graph_id: paris_ariab_trna_cleavage_abortive_defense title: PARIS loci couple phage anti-restriction sensing to AriB tRNA cleavage description: Evidence-backed process sketch linking a complete PARIS locus to AriA/AriB immune-complex assembly, foreign-protein sensing, AriB activation, host lysine tRNA cleavage, translational inhibition, and inhibition of phage propagation. scope_status: NONMECHANISTIC scope_notes: The graph stays at the PARIS-family level and uses characterized E. coli B185 AriA/AriB examples without asserting one universal phage trigger, Ocr response, Ptr1/Ptr2 response, T5 lysine tRNA suppressor, exact AriA/AriB stoichiometry, or anti-anti-restriction context across all PARIS loci. nodes: - node_id: paris_locus label: PARIS locus node_type: GENETIC_ELEMENT description: A complete phage anti-restriction-induced system locus encoding the AriA ABC ATPase sensor and AriB TOPRIM-family nuclease effector. - node_id: aria_arib_complex_assembly label: AriA/AriB immune complex assembly node_type: BIOLOGICAL_PROCESS description: Assembly of an AriA scaffold that sequesters and inactivates AriB nuclease subunits before PARIS activation. - node_id: foreign_protein_sensing label: foreign protein sensing node_type: BIOLOGICAL_PROCESS description: AriA-dependent detection of activating phage proteins such as the T7 Ocr anti-restriction protein. - node_id: arib_nuclease_activation label: AriB nuclease activation node_type: BIOLOGICAL_PROCESS description: Release and dimerization of the AriB TOPRIM-family nuclease effector from the AriA scaffold. - node_id: lysine_trna_cleavage label: lysine tRNA cleavage node_type: BIOLOGICAL_PROCESS description: AriB-dependent cleavage of host lysine transfer RNA after PARIS activation. - node_id: translation_inhibition label: translation inhibition node_type: BIOLOGICAL_PROCESS description: Global protein-translation inhibition and growth arrest following host lysine tRNA cleavage. - node_id: phage_propagation label: phage propagation node_type: BIOLOGICAL_PROCESS description: Completion of bacteriophage replication and spread in a susceptible bacterial population. - node_id: paris_system_trait label: PARIS system node_type: TRAIT grounding: traitmech:000237 description: Possession of a genome-encoded PARIS abortive-infection defense system. - node_id: abortive_infection_system_trait label: abortive infection system node_type: TRAIT grounding: traitmech:000214 description: Possession of a genome-encoded abortive-infection phage defense system. edges: - subject: paris_locus predicate: contributes to predicate_id: RO:0002326 object: aria_arib_complex_assembly description: PARIS loci encode AriA and AriB components that assemble into an immune complex. evidence: - reference: DOI:10.1038/s41586-024-07874-3 snippet: Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex notes: Burman et al. support AriA/AriB complex assembly as a direct PARIS system activity. - subject: aria_arib_complex_assembly predicate: enables predicate_id: RO:0002327 object: foreign_protein_sensing description: The AriA/AriB immune complex detects foreign proteins in an ATP-dependent way. evidence: - reference: DOI:10.1038/s41586-024-07874-3 snippet: ATP-dependent detection of foreign proteins triggers the release of AriB notes: Burman et al. support AriA-dependent foreign protein detection as the triggering event for PARIS activation. - subject: foreign_protein_sensing predicate: activates predicate_id: RO:0002213 object: arib_nuclease_activation description: T7 Ocr or other foreign-protein detection releases AriB from AriA and activates the AriB nuclease. evidence: - reference: DOI:10.1038/s41586-024-07772-8 snippet: After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate notes: Deep et al. support Ocr-triggered AriB release and dimerization in the E. coli B185 PARIS system. - subject: arib_nuclease_activation predicate: contributes to predicate_id: RO:0002326 object: lysine_trna_cleavage description: Activated AriB cleaves host lysine transfer RNA. evidence: - reference: DOI:10.1038/s41586-024-07874-3 snippet: AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA notes: Burman et al. support host lysine-tRNA cleavage by activated AriB. - subject: lysine_trna_cleavage predicate: contributes to predicate_id: RO:0002326 object: translation_inhibition description: AriB-mediated lysine tRNA cleavage inhibits host-cell translation. evidence: - reference: DOI:10.1038/s41586-024-07772-8 snippet: globally inhibiting protein translation through specific cleavage of a lysine tRNA notes: Deep et al. connect AriB lysine-tRNA cleavage to global inhibition of protein translation. - subject: translation_inhibition predicate: mitigates predicate_id: METPO:2007407 object: phage_propagation description: PARIS-associated translational arrest blocks phage infection. evidence: - reference: DOI:10.1038/s41586-024-07772-8 snippet: arrests cell growth and inhibits phage propagation by globally inhibiting protein translation notes: Deep et al. support the growth-arrest and phage-inhibition output of AriB activation. - subject: translation_inhibition predicate: confers predicate_id: METPO:2007700 object: paris_system_trait description: AriB-dependent translational inhibition realizes the PARIS abortive-infection phenotype. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: Therefore, ariAB seem to halt growth in infected cells, preventing the completion of the phage cycle, a typical feature of abortive infection systems notes: Rousset et al. connect AriA/AriB to growth arrest, phage-cycle inhibition, and abortive infection. - subject: paris_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: PARIS system possession is an abortive-infection system trait. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein notes: Rousset et al. explicitly describe PARIS as an abortive infection system. discussions: - discussion_id: paris-trigger-and-counterdefense-gap prompt: Resolve PARIS trigger specificity, AriA/AriB stoichiometry, phage T5 lysine-tRNA suppression, and non-Ocr phage triggers before minting narrower PARIS subtype children. kind: KNOWLEDGE_GAP status: OPEN rationale: Rousset et al. discovered PARIS as an abortive infection system triggered by T7 Ocr; Deep et al. resolved Ocr-dependent AriA release of AriB for the E. coli B185 system; and Burman et al. showed that T5 Ptr1 and Ptr2 can activate PARIS while a phage T5 lysine tRNA variant can evade AriB cleavage. The first TraitRecord therefore stays at the broad PARIS-system level until separate subtype review resolves which foreign-protein triggers, AriB activities, and anti-defense suppressors apply across each PARIS family. posed_by: codex posed_date: '2026-09-18' curation_history: - timestamp: '2026-09-18T08:27:56Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted PARIS system as a DOI-backed GENOMICS TraitRecord under the abortive infection 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_v114. llm_assisted: true - timestamp: '2026-09-18T09:16:05Z' curator: codex action: ADVERSARIAL_REVIEW_REPAIR changes: 'Resolved PR #976 review issue #977 by scoping the PARIS canonical example note to the Rousset et al. E. coli B185 evidence cited by that example.' llm_assisted: true