identifier: traitmech:000329 label: Ambrosia system definition: A phage defense system in which an organism possesses a five-gene Ambrosia locus encoding AbrR, AbrA, AbrB, AbrC, and AbrD components that can limit siphophage and myophage propagation. definition_source: DOI:10.1101/2025.09.30.679545 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Ambrosia synonym_type: EXACT_SYNONYM source: DOI:10.1101/2025.09.30.679545 evidence: - reference: DOI:10.1101/2025.09.30.679545 snippet: 'From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.' notes: Keesman et al. named Ambrosia among three modular phage-defense candidates validated experimentally from an initial pool of more than 500 candidates. - reference: DOI:10.1101/2025.09.30.679545 snippet: Ambrosia, named after the food and drinks that provide immortality to the Greek gods, consists of five genes and provides protection against siphophages from the Mesyanzhinovviridae family and myophages from the Pbunavirus genus, limiting phage propagation in both solid and liquid cultures notes: Keesman et al. support Ambrosia as a five-gene system that limits propagation of Mesyanzhinovviridae siphophages and Pbunavirus myophages. - reference: DOI:10.1101/2025.09.30.679545 snippet: The five genes of Ambrosia encode a HipB-like XRE transcriptional regulator (AbrR), a RM type II-associated N6 adenine-specific DNA methylase (MTase, AbrA), a sensor histidine kinase/heat-shock-protein(HSP)90-like ATPase (HATPase, AbrB), a response regulator (REC, AbrC), and an RM type IV HNH endonuclease (AbrD) notes: Keesman et al. describe the Ambrosia locus as encoding AbrR, AbrA, AbrB, AbrC, and AbrD components with RM-like and two-component regulatory-system features. - reference: DOI:10.1101/2025.09.30.679545 snippet: Each protein is required for anti-phage activity, since mutating conserved residues in any of the predicted functional domains completely abolishes Ambrosia defense activity notes: Keesman et al. support each predicted functional domain as required for the tested Ambrosia anti-phage activity. - reference: DOI:10.1101/2025.09.30.679545 snippet: Overall, our results indicate that the RM-like components of Ambrosia do not operate as a conventional type II RM system. Instead, Ambrosia appears to represent a distinct, tightly regulated phage defense system in which a HipB-like XRE protein and a two-component regulatory module control the expression of RM-like enzymes in response to infection notes: Keesman et al. argue that Ambrosia is distinct from a conventional type II restriction-modification system and is regulated in response to phage infection. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Ambrosia | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks notes: The DefenseFinder article registry maps the named Ambrosia system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ambrosia, so this row is name-to-paper evidence rather than model-component evidence. causal_graphs: - graph_id: ambrosia_locus_restricts_phage title: Ambrosia loci confer bacterial phage defense description: Conservative system-level sketch linking possession of an Ambrosia locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, transcriptional wiring, or nuclease substrate. scope_status: NONMECHANISTIC scope_notes: The graph captures Ambrosia as a named five-gene anti-phage system while leaving its direct phage trigger, the AbrB/AbrC regulatory chain, the exact AbrA/AbrD substrate and DNA modification, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved. nodes: - node_id: ambrosia_locus label: Ambrosia locus node_type: GENETIC_ELEMENT description: A five-gene Ambrosia anti-phage defense locus encoding AbrR, AbrA, AbrB, AbrC, and AbrD components. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Ambrosia system. - node_id: ambrosia_system_trait label: Ambrosia system node_type: TRAIT grounding: traitmech:000329 description: Possession of a genome-encoded Ambrosia 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: ambrosia_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The five-gene Ambrosia locus provides protection against siphophages and myophages. evidence: - reference: DOI:10.1101/2025.09.30.679545 snippet: Ambrosia, named after the food and drinks that provide immortality to the Greek gods, consists of five genes and provides protection against siphophages from the Mesyanzhinovviridae family and myophages from the Pbunavirus genus, limiting phage propagation in both solid and liquid cultures notes: Keesman et al. connect the named Ambrosia locus to phage-propagation restriction in solid and liquid cultures. - reference: DOI:10.1101/2025.09.30.679545 snippet: Each protein is required for anti-phage activity, since mutating conserved residues in any of the predicted functional domains completely abolishes Ambrosia defense activity notes: Keesman et al. report that conserved-residue mutations in any predicted functional domain abolished Ambrosia defense. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: ambrosia_system_trait description: Ambrosia-mediated phage restriction realizes the Ambrosia system trait. evidence: - reference: DOI:10.1101/2025.09.30.679545 snippet: Ambrosia, named after the food and drinks that provide immortality to the Greek gods, consists of five genes and provides protection against siphophages from the Mesyanzhinovviridae family and myophages from the Pbunavirus genus, limiting phage propagation in both solid and liquid cultures notes: Keesman et al. report Ambrosia-mediated limitation of propagation for tested siphophages and myophages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Ambrosia | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks notes: The DefenseFinder article registry maps the named Ambrosia system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ambrosia, so this row is name-to-paper evidence rather than model-component evidence. - subject: ambrosia_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Ambrosia system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1101/2025.09.30.679545 snippet: 'From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.' notes: Keesman et al. list Ambrosia among experimentally validated phage-defense systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Ambrosia | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks notes: The DefenseFinder article registry maps the named Ambrosia system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ambrosia, so this row is name-to-paper evidence rather than model-component evidence. discussions: - discussion_id: ambrosia-regulatory-mechanism-gap prompt: Resolve Ambrosia phage triggers, DNA targets, and model coverage before minting narrower Ambrosia mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Keesman et al. support Ambrosia as a five-gene anti-phage system with tightly regulated RM-like components, but the direct phage trigger, the AbrB/AbrC regulatory chain, the exact AbrA/AbrD substrate and DNA modification, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait. attaches_to: - causal_graphs#ambrosia_locus_restricts_phage posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T06:37:06Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Ambrosia 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_v206. llm_assisted: true