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Ambrosia system

traitmech:000329 · CLASS · PROPOSED

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.

Trait evidence (6)

  • DOI:10.1101/2025.09.30.679545
    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.

    Keesman et al. named Ambrosia among three modular phage-defense candidates validated experimentally from an initial pool of more than 500 candidates.

  • DOI:10.1101/2025.09.30.679545
    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

    Keesman et al. support Ambrosia as a five-gene system that limits propagation of Mesyanzhinovviridae siphophages and Pbunavirus myophages.

  • DOI:10.1101/2025.09.30.679545
    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)

    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.

  • DOI:10.1101/2025.09.30.679545
    Each protein is required for anti-phage activity, since mutating conserved residues in any of the predicted functional domains completely abolishes Ambrosia defense activity

    Keesman et al. support each predicted functional domain as required for the tested Ambrosia anti-phage activity.

  • DOI:10.1101/2025.09.30.679545
    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

    Keesman et al. argue that Ambrosia is distinct from a conventional type II restriction-modification system and is regulated in response to phage infection.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    Ambrosia | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks

    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.

Ambrosia loci confer bacterial phage defense

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.

NONMECHANISTIC · 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.

Ambrosia loci confer bacterial phage defense Interactive directed graph showing evidence-backed causal relationships for Ambrosia system.

Edge evidence

  • Ambrosia locus contributes to restricted phage propagation RO:0002326

    The five-gene Ambrosia locus provides protection against siphophages and myophages.

    • DOI:10.1101/2025.09.30.679545 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 Keesman et al. connect the named Ambrosia locus to phage-propagation restriction in solid and liquid cultures.
    • DOI:10.1101/2025.09.30.679545 Each protein is required for anti-phage activity, since mutating conserved residues in any of the predicted functional domains completely abolishes Ambrosia defense activity Keesman et al. report that conserved-residue mutations in any predicted functional domain abolished Ambrosia defense.
  • restricted phage propagation confers Ambrosia system METPO:2007700

    Ambrosia-mediated phage restriction realizes the Ambrosia system trait.

    • DOI:10.1101/2025.09.30.679545 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 Keesman et al. report Ambrosia-mediated limitation of propagation for tested siphophages and myophages.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ambrosia | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks 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.
  • Ambrosia system is a phage defense system rdfs:subClassOf

    Ambrosia system possession is a phage-defense-system trait.

    • DOI:10.1101/2025.09.30.679545 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. Keesman et al. list Ambrosia among experimentally validated phage-defense systems.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ambrosia | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks 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.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1101/2025.09.30.679545

Parent traits (1)

Synonyms (1)

  • Ambrosia EXACT_SYNONYM · DOI:10.1101/2025.09.30.679545

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve Ambrosia phage triggers, DNA targets, and model coverage before minting narrower Ambrosia mechanism children.

KNOWLEDGE GAP OPEN ambrosia-regulatory-mechanism-gap · raised by codex · 2026-09-21

Attached to causal_graphs#ambrosia_locus_restricts_phage

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.