identifier: traitmech:000407 label: Panoptes system definition: A phage defense system in which an organism possesses a two-gene optSE locus encoding an OptS protein that constitutively produces cyclic dinucleotides and an OptE transmembrane effector that is released from cyclic-dinucleotide repression when phage Acb2-like proteins sequester those signals, leading to inner-membrane disruption. definition_source: DOI:10.1038/s41586-025-09557-z trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Panoptes antiphage system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41586-025-09557-z - synonym_text: optSE synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-025-09557-z - synonym_text: OptSE synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-025-09557-z evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. notes: Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE. - reference: DOI:10.1038/s41586-025-09557-z snippet: We named OptSE the Panoptes antiphage system for Argus Panoptes, the all-seeing, many-eyed giant in Greek mythology who was a faithful watchman to Hera. notes: Sullivan et al. name OptSE as the Panoptes antiphage system. - reference: DOI:10.1038/s41586-025-09557-z snippet: OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2′,3′-cyclic diadenosine monophosphate (2′,3′-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. notes: OptS orthologues produce cyclic dinucleotides, including 2′,3′-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector. - reference: DOI:10.1038/s41586-025-09557-z snippet: Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence. notes: Phage replication was restricted by Panoptes, while Acb2 loss-of-function mutations escaped defense. - reference: DOI:10.1038/s41586-025-09557-z snippet: Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. notes: Acb2 cyclic-nucleotide sequestration releases OptE toxicity and leads to inner-membrane disruption. - reference: DOI:10.1038/s41586-025-09557-z snippet: We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis. notes: Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays. - reference: DOI:10.1038/s41586-025-09557-z snippet: We expressed the operon from its endogenous promoter in Escherichia coli MG1655 and challenged these bacteria with a panel of diverse phages. The VnOptSE operon specifically defended against phages from the Straboviridae family notes: The V. navarrensis operon was expressed from its endogenous promoter in E. coli MG1655 and protected the heterologous host against Straboviridae phages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Panoptes | 10\.1038/s41586-025-09557-z | The Panoptes system uses decoy cyclic nucleotides to defend against phage |' notes: The pinned DefenseFinder article registry maps the Panoptes key to Sullivan et al.; the same pinned rules and HMM inventory omit a Panoptes model. canonical_examples: - taxon_id: NCBITaxon:29495 taxon_label: Vibrio navarrensis note: Species carrying the assayed VnOptSE Panoptes system; defense activity was tested heterologously from the endogenous V. navarrensis promoter in E. coli MG1655. reference: DOI:10.1038/s41586-025-09557-z causal_graphs: - graph_id: panoptes_decoy_cyclic_nucleotide_defense title: Panoptes loci couple cyclic-nucleotide sequestration to OptE membrane disruption description: Evidence-backed process sketch linking an optSE locus to OptS cyclic-dinucleotide synthesis, OptE repression, Acb2-like sequestration of the OptS-derived signal, inner-membrane disruption, and phage restriction. scope_status: MECHANISTIC scope_notes: The graph captures OptS/OptE/Acb2 coupling from Sullivan et al. while leaving cyclic-dinucleotide identity, anti-defense breadth, phage breadth, and OptE oligomerization unspecified for untested optSE homologs. nodes: - node_id: optse_locus label: optSE locus node_type: GENETIC_ELEMENT description: A two-gene Panoptes locus encoding OptS and OptE. - node_id: opts_cyclic_dinucleotide_synthase label: OptS cyclic-dinucleotide synthase node_type: GENE_OR_PROTEIN grounding: InterPro:IPR040942 grounding_notes: InterPro:IPR040942 is a Minimal_Cpol polymerase domain present in VnOptS; it is broader than Panoptes-specific OptS and is retained as a domain-level grounding because no narrower taxon-agnostic OptS family identifier is available. description: Minimal CRISPR polymerase domain protein that synthesizes cyclic dinucleotides in Panoptes operons. protein_examples: - uniprot_id: UniProtKB:A0A099LXT1 protein_label: Minimal CRISPR polymerase domain-containing protein gene_symbol: optS taxon_id: NCBITaxon:29495 taxon_label: Vibrio navarrensis proteome_id: UP000029994 entry_status: UNREVIEWED retrieved_on: '2026-09-27' entry_version: 30 sequence_version: 1 role: VnOptS is the OptS synthase encoded by the V. navarrensis optSE Panoptes operon. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis. notes: Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays. - reference: DOI:10.1038/s41586-025-09557-z snippet: OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2′,3′-cyclic diadenosine monophosphate (2′,3′-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. notes: OptS orthologues produce cyclic dinucleotides, including 2′,3′-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector. - node_id: opte_transmembrane_effector label: OptE transmembrane effector node_type: GENE_OR_PROTEIN grounding: InterPro:IPR041208 grounding_notes: InterPro:IPR041208 is the Cap15 family carried by VnOptE and retained as the closest taxon-agnostic grounding for the OptE transmembrane effector pending a narrower Panoptes-specific profile. description: OptE-family transmembrane effector encoded by Panoptes operons. protein_examples: - uniprot_id: UniProtKB:A0A099LW44 protein_label: CD-NTase-associated protein 15 domain-containing protein gene_symbol: optE taxon_id: NCBITaxon:29495 taxon_label: Vibrio navarrensis proteome_id: UP000029994 entry_status: UNREVIEWED retrieved_on: '2026-09-27' entry_version: 37 sequence_version: 1 role: VnOptE is the OptE transmembrane effector encoded by the V. navarrensis optSE Panoptes operon. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. notes: Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE. - reference: DOI:10.1038/s41586-025-09557-z snippet: OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2′,3′-cyclic diadenosine monophosphate (2′,3′-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. notes: OptS orthologues produce cyclic dinucleotides, including 2′,3′-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector. - reference: DOI:10.1038/s41586-025-09557-z snippet: We expressed the operon from its endogenous promoter in Escherichia coli MG1655 and challenged these bacteria with a panel of diverse phages. The VnOptSE operon specifically defended against phages from the Straboviridae family notes: The V. navarrensis operon was expressed from its endogenous promoter in E. coli MG1655 and protected the heterologous host against Straboviridae phages. - node_id: opts_cyclic_dinucleotide_synthesis label: OptS cyclic dinucleotide synthesis node_type: BIOLOGICAL_PROCESS description: Constitutive OptS-dependent production of 2′,3′-c-di-AMP and other cyclic dinucleotides. - node_id: opte_cyclic_dinucleotide_repression label: OptE cyclic dinucleotide repression node_type: STATE description: Inactive-state repression of OptE by OptS-derived cyclic dinucleotides. - node_id: acb2_like_signal_sequestration label: Acb2-like signal sequestration node_type: BIOLOGICAL_PROCESS description: Sequestration or depletion of OptS-derived cyclic nucleotides by phage Acb2 or similar immune-evasion proteins. - node_id: phage_infection label: phage infection node_type: BIOLOGICAL_PROCESS description: Infection by a bacteriophage that expresses Acb2 or similar cyclic-nucleotide sequestration proteins. - node_id: opte_inner_membrane_disruption label: OptE inner membrane disruption node_type: BIOLOGICAL_PROCESS description: OptE effector toxicity that disrupts the bacterial inner membrane during Panoptes defense. - node_id: phage_replication label: phage replication node_type: BIOLOGICAL_PROCESS description: Replication of bacteriophages that would proceed in a susceptible host. - node_id: panoptes_system_trait label: Panoptes system node_type: TRAIT grounding: traitmech:000407 description: Possession of a genome-encoded Panoptes phage-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: optse_locus predicate: encodes object: opts_cyclic_dinucleotide_synthase description: Panoptes optSE loci encode OptS cyclic-dinucleotide synthases. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. notes: Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE. - reference: DOI:10.1038/s41586-025-09557-z snippet: We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis. notes: Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays. - subject: optse_locus predicate: encodes object: opte_transmembrane_effector description: Panoptes optSE loci encode OptE transmembrane effectors. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. notes: Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE. - reference: DOI:10.1038/s41586-025-09557-z snippet: We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis. notes: Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays. - subject: opts_cyclic_dinucleotide_synthase predicate: contributes to predicate_id: RO:0002326 object: opts_cyclic_dinucleotide_synthesis description: OptS is the Panoptes synthase that generates OptE-binding cyclic dinucleotides. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2′,3′-cyclic diadenosine monophosphate (2′,3′-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. notes: OptS orthologues produce cyclic dinucleotides, including 2′,3′-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector. - subject: opts_cyclic_dinucleotide_synthesis predicate: contributes to predicate_id: RO:0002326 object: opte_cyclic_dinucleotide_repression description: OptS-derived cyclic dinucleotides bind OptE and hold the effector in an inactive state before phage counter-defense challenge. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2′,3′-cyclic diadenosine monophosphate (2′,3′-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. notes: OptS orthologues produce cyclic dinucleotides, including 2′,3′-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector. - reference: DOI:10.1038/s41586-025-09557-z snippet: we found that OptS constitutively produced signalling nucleotides to repress OptE-mediated growth inhibition. notes: OptS constitutive signalling nucleotide production represses OptE-mediated growth inhibition. - subject: opte_cyclic_dinucleotide_repression predicate: negatively regulates predicate_id: RO:0002212 object: opte_inner_membrane_disruption description: Cyclic-dinucleotide binding restrains OptE-mediated toxicity and inner-membrane disruption. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: we found that OptS constitutively produced signalling nucleotides to repress OptE-mediated growth inhibition. notes: OptS constitutive signalling nucleotide production represses OptE-mediated growth inhibition. - subject: opte_transmembrane_effector predicate: contributes to predicate_id: RO:0002326 object: opte_inner_membrane_disruption description: OptE is the Panoptes effector whose released toxicity disrupts the inner membrane. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. notes: Acb2 cyclic-nucleotide sequestration releases OptE toxicity and leads to inner-membrane disruption. - subject: phage_infection predicate: activates predicate_id: RO:0002213 object: acb2_like_signal_sequestration description: Phage infection produces Acb2 or similar immune-evasion proteins that sequester OptS-derived cyclic nucleotide signals. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: During phage infection, Acb2 or similar immune evasion proteins are produced that sequester the OptS-derived signalling molecule, leading to a population of OptE that is no longer bound to cyclic dinucleotide and is free to become activated, in turn disrupting the bacterial membrane and resulting in phage defence notes: The Panoptes model links Acb2-like signal sequestration to OptE activation, bacterial membrane disruption, and phage defense. - subject: acb2_like_signal_sequestration predicate: activates predicate_id: RO:0002213 object: opte_inner_membrane_disruption description: Acb2 or similar immune-evasion proteins sequester the OptS-derived signal and release OptE-mediated membrane disruption. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. notes: Acb2 cyclic-nucleotide sequestration releases OptE toxicity and leads to inner-membrane disruption. - subject: opte_inner_membrane_disruption predicate: mitigates predicate_id: METPO:2007407 object: phage_replication description: Panoptes-associated OptE membrane disruption restricts bacteriophage replication. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence. notes: Phage replication was restricted by Panoptes, while Acb2 loss-of-function mutations escaped defense. - subject: opte_inner_membrane_disruption predicate: confers predicate_id: METPO:2007700 object: panoptes_system_trait description: OptE-mediated inner-membrane disruption is the phage-defense output that realizes the Panoptes system trait. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: During phage infection, Acb2 or similar immune evasion proteins are produced that sequester the OptS-derived signalling molecule, leading to a population of OptE that is no longer bound to cyclic dinucleotide and is free to become activated, in turn disrupting the bacterial membrane and resulting in phage defence notes: The Panoptes model links Acb2-like signal sequestration to OptE activation, bacterial membrane disruption, and phage defense. - subject: panoptes_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Panoptes system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: We named OptSE the Panoptes antiphage system for Argus Panoptes, the all-seeing, many-eyed giant in Greek mythology who was a faithful watchman to Hera. notes: Sullivan et al. name OptSE as the Panoptes antiphage system. discussions: - discussion_id: panoptes-defensefinder-model-gap prompt: Recheck DefenseFinder Panoptes rules and HMM profiles before using DefenseFinder model rows as optSE profile evidence. kind: CURATION_TODO status: OPEN rationale: The pinned DefenseFinder article registry maps Panoptes to Sullivan et al. and the Nature article title, but the pinned DefenseFinder rules and HMM inventories do not include Panoptes rows. This record therefore cites the DOI-backed article and treats the article registry as name-to-paper evidence rather than as profile support. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Panoptes | 10\.1038/s41586-025-09557-z | The Panoptes system uses decoy cyclic nucleotides to defend against phage |' notes: The pinned DefenseFinder article registry maps the Panoptes key to Sullivan et al.; the same pinned rules and HMM inventory omit a Panoptes model. posed_by: codex posed_date: '2026-09-27' - discussion_id: panoptes-natural-host-gap prompt: Find a native endogenous microbial isolate with direct chromosomal Panoptes antiphage validation beyond the heterologous VnOptSE source-species exemplar. kind: KNOWLEDGE_GAP status: OPEN rationale: Sullivan et al. investigated a candidate Vibrio navarrensis optSE operon and showed that VnOptSE defended against Straboviridae phages when expressed in E. coli MG1655 from its endogenous promoter. V. navarrensis is retained as the operon source for mechanistic protein examples, but that heterologous challenge assay does not establish a direct endogenous V. navarrensis chromosomal Panoptes assay. evidence: - reference: DOI:10.1038/s41586-025-09557-z snippet: We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis. notes: Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays. - reference: DOI:10.1038/s41586-025-09557-z snippet: We expressed the operon from its endogenous promoter in Escherichia coli MG1655 and challenged these bacteria with a panel of diverse phages. The VnOptSE operon specifically defended against phages from the Straboviridae family notes: The V. navarrensis operon was expressed from its endogenous promoter in E. coli MG1655 and protected the heterologous host against Straboviridae phages. attaches_to: - causal_graphs#panoptes_decoy_cyclic_nucleotide_defense posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T09:24:21Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Panoptes system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v284. llm_assisted: true - timestamp: '2026-09-27T09:24:22Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Panoptes system canonical_examples and added V. navarrensis as the VnOptSE operon source for the mechanistic protein examples; direct native chromosomal Panoptes activity remains open because the current challenge assay used heterologous E. coli MG1655. No paid research was used. llm_assisted: true - timestamp: '2026-09-27T11:38:27Z' curator: codex action: VERIFY_PANOPTES_PROTEIN_GROUNDINGS changes: 'Verified the Panoptes UniProt protein examples with audit_uniprot_grounding.py: UniProtKB:A0A099LXT1 is a current unreviewed V. navarrensis UP000029994 primary accession at entry version 30 / sequence version 1, UniProtKB:A0A099LW44 is a current unreviewed V. navarrensis UP000029994 primary accession at entry version 37 / sequence version 1, and UniProt cross-references link them to InterPro:IPR040942 (Minimal_Cpol) and InterPro:IPR041208 (Cap15).' llm_assisted: true - timestamp: '2026-09-27T11:59:19Z' curator: codex action: DOCUMENT_PANOPTES_INTERPRO_SCOPE changes: 'Added grounding notes for the new Panoptes InterPro CURIEs: InterPro:IPR040942 is a broader Minimal_Cpol domain present in VnOptS rather than an OptS-only family, and InterPro:IPR041208 is the Cap15 family carried by VnOptE.' llm_assisted: true