identifier: traitmech:000212 label: CBASS system definition: A genomics trait describing possession of a cyclic-oligonucleotide-based antiphage signaling locus in which an oligonucleotide cyclase produces cyclic oligonucleotide signals during phage infection that activate an effector to inhibit bacteriophage replication. definition_source: DOI:10.1038/s41586-019-1605-5 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: cyclic-oligonucleotide-based anti-phage signalling system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41564-020-0777-y - synonym_text: cyclic-oligonucleotide-based anti-phage signaling system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41564-020-0777-y evidence: - reference: DOI:10.1038/s41586-019-1605-5 snippet: cGAMP signalling is part of an antiphage defence system that is common in bacteria notes: Cohen et al. experimentally established a bacterial cGAS-phospholipase system as a common antiphage defense system. - reference: DOI:10.1038/s41586-019-1605-5 snippet: Phage infection triggers the production of cGAMP notes: Cohen et al. support phage-triggered cyclic oligonucleotide production in an experimentally characterized cGAMP-phospholipase CBASS. - reference: DOI:10.1038/s41564-020-0777-y snippet: CBASS systems are composed of an oligonucleotide cyclase, which generates signalling cyclic oligonucleotides in response to phage infection notes: Millman et al. generalized CBASS systems as oligonucleotide-cyclase-centered antiphage signaling loci. - reference: DOI:10.1038/s41564-020-0777-y snippet: identified more than 5,000 CBASS systems, which have diverse architectures notes: Millman et al. support CBASS as a diverse recurring family across bacterial and archaeal genomes rather than a single four-gene operon. canonical_examples: - taxon_id: NCBITaxon:913088 taxon_label: Escherichia coli TW11681 note: Cohen et al. cloned the native E. coli TW11681 four-gene CBASS operon into E. coli MG1655 and measured P1 and coliphage resistance. reference: DOI:10.1038/s41586-019-1605-5 causal_graphs: - graph_id: cbass_cyclic_oligonucleotide_antiphage_defense title: CBASS cyclic oligonucleotides activate abortive cell death description: Evidence-backed process sketch linking CBASS oligonucleotide-cyclase activation to effector activation, abortive cell death, and blocked phage replication. scope_status: NONMECHANISTIC scope_notes: The graph captures the shared system-level CBASS logic of phage-triggered cyclic oligonucleotide synthesis and effector activation across multiple effector subtypes. The subtype-specific protein families carry the exact mechanistic edges and remain shifted from this first organism-level trait. nodes: - node_id: cbass_oligonucleotide_cyclase_activation label: CBASS oligonucleotide cyclase activation node_type: BIOLOGICAL_PROCESS description: Phage-infection-associated activation of a CBASS oligonucleotide cyclase. - node_id: cyclic_oligonucleotide_synthesis label: CBASS cyclic oligonucleotide synthesis node_type: BIOLOGICAL_PROCESS description: Production of cyclic oligonucleotide second messengers by an activated CBASS oligonucleotide cyclase. - node_id: cbass_effector_activation label: CBASS effector activation node_type: BIOLOGICAL_PROCESS description: Activation of a CBASS effector by a cyclic oligonucleotide signal. - node_id: abortive_cell_death label: abortive cell death node_type: BIOLOGICAL_PROCESS description: Programmed death of an infected host cell before phage replication is completed. - node_id: phage_replication label: phage replication node_type: BIOLOGICAL_PROCESS description: Replication and completion of a bacteriophage infection cycle inside a host cell. - node_id: cbass_system_trait label: CBASS system node_type: TRAIT grounding: traitmech:000212 description: Possession of a genome-encoded CBASS 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: cbass_oligonucleotide_cyclase_activation predicate: activates predicate_id: RO:0002213 object: cyclic_oligonucleotide_synthesis description: Phage sensing activates a CBASS oligonucleotide cyclase to synthesize cyclic oligonucleotide signals. evidence: - reference: DOI:10.1038/s41564-020-0777-y snippet: oligonucleotide cyclase, which generates signalling cyclic oligonucleotides in response to phage infection notes: Millman et al. summarize phage-triggered oligonucleotide cyclase activation in their general CBASS model. - subject: cyclic_oligonucleotide_synthesis predicate: activates predicate_id: RO:0002213 object: cbass_effector_activation description: CBASS cyclic oligonucleotide second messengers activate cognate effector proteins. evidence: - reference: DOI:10.1038/s41564-020-0777-y snippet: an effector that is activated by the cyclic oligonucleotides and promotes cell death notes: Millman et al. support effector activation as the central output of CBASS cyclic oligonucleotide signaling. - subject: cbass_effector_activation predicate: activates predicate_id: RO:0002213 object: abortive_cell_death description: CBASS effector activation induces host cell death through subtype-specific nuclease, phospholipase, or other toxic activities. evidence: - reference: DOI:10.1038/s41564-020-0777-y snippet: six effector subtypes that promote cell death by membrane impairment, DNA degradation or other means notes: Millman et al. classified multiple CBASS effector subtypes that converge on host cell death. - subject: abortive_cell_death predicate: mitigates predicate_id: METPO:2007407 object: phage_replication description: CBASS-induced death of the infected host cell aborts infection before phage replication is completed. evidence: - reference: DOI:10.1038/s41586-019-1605-5 snippet: to cell death before completion of phage reproduction notes: Cohen et al. experimentally tied CBASS cGAMP-phospholipase signaling to abortive cell death before the phage cycle completed. - subject: abortive_cell_death predicate: confers predicate_id: METPO:2007700 object: cbass_system_trait description: CBASS effector-induced abortive cell death realizes CBASS-mediated antiphage defense. evidence: - reference: DOI:10.1038/s41564-020-0777-y snippet: therefore preventing the spread of phages to nearby cells notes: Millman et al. link cell death before phage replication completion to the protective output of CBASS loci. - subject: cbass_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: CBASS possession is a cyclic-oligonucleotide-mediated phage-defense-system trait. evidence: - reference: DOI:10.1038/s41564-020-0777-y snippet: a family of defence systems against bacteriophages notes: Millman et al. place CBASS in the phage defense system family. discussions: - discussion_id: cbass-subtype-mechanism-gap prompt: Resolve CBASS subtype-specific sensing and effector mechanisms before splitting cGAMP-phospholipase, cAAA-nuclease, ancillary-gene, or individual CD-NTase protein-family edges into reviewed graph groundings. kind: KNOWLEDGE_GAP status: OPEN rationale: Cohen et al. resolved a phage-triggered cGAMP-phospholipase CBASS system and Millman et al. classified CBASS loci into four major types with multiple signaling molecules, effectors, and ancillary genes; exact phage sensors and subtype-specific effector families remain shifted from this first organism-level trait. posed_by: codex posed_date: '2026-09-15' curation_history: - timestamp: '2026-09-15T10:20:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted CBASS 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_v89. llm_assisted: true