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Ophion system

traitmech:000331 · CLASS · PROPOSED

A phage defense system in which an organism possesses a three-gene Ophion locus encoding OpnA, OpnB, and OpnC components that can block jumbo-phage infection before phage-nucleus formation.

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 Ophion among three modular phage-defense candidates validated experimentally from an initial pool of more than 500 candidates.

  • DOI:10.1101/2025.09.30.679545
    Ophion, named after a primordial serpent from Greek mythology, is a three gene system encoding a radical S-adenosyl-L-methionine (rSAM) enzyme (OpnA), a polymerase-and histidinol-phosphatase (PHP, OpnB), and a phosphoribosyl transferase (PRTase, OpnC)

    Keesman et al. support Ophion as a three-gene system encoding OpnA, OpnB, and OpnC components with Radical SAM, PHP, and phosphoribosyl-transferase domains.

  • DOI:10.1101/2025.09.30.679545
    Ophion shows strong protection against jumbo phages

    Keesman et al. support Ophion as a system that strongly protects against jumbo phages.

  • DOI:10.1101/2025.09.30.679545
    Mutating conserved residues of the rSAM and PRTase domains revealed these to be essential for protection, with partial dependence on the PHP domain

    Keesman et al. support the OpnA Radical SAM and OpnC phosphoribosyl-transferase domains as essential in the tested Ophion system, with partial dependence on OpnB PHP.

  • DOI:10.1101/2025.09.30.679545
    Ophion provides potent and specific defense against jumbo phages by blocking progression from the EPI vesicle to the nucleus stage, possibly by halting the transcription of the nucleus forming genes

    Keesman et al. connect Ophion-mediated defense to arrest of jumbo phages as they progress from the early phage infection vesicle stage to nucleus formation.

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

    The DefenseFinder article registry maps the named Ophion system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ophion, so this row is name-to-paper evidence rather than model-component evidence.

Ophion loci confer bacterial phage defense

Conservative system-level sketch linking possession of an Ophion locus to restricted jumbo-phage propagation without asserting the direct phage trigger, modified nucleotide product, or early-transcription target.

NONMECHANISTIC · The graph captures Ophion as a named three-gene anti-jumbo-phage system while leaving its direct phage trigger, the OpnA/OpnB/OpnC interaction sequence, the nucleotide-modification product, the natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.

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

Edge evidence

  • Ophion locus contributes to restricted phage propagation RO:0002326

    The three-gene Ophion locus restricts infection by jumbo phages.

    • DOI:10.1101/2025.09.30.679545 Ophion shows strong protection against jumbo phages Keesman et al. report that Ophion protects against jumbo phages.
    • DOI:10.1101/2025.09.30.679545 Mutating conserved residues of the rSAM and PRTase domains revealed these to be essential for protection, with partial dependence on the PHP domain Keesman et al. report that conserved-residue mutations establish the OpnA Radical SAM and OpnC phosphoribosyl-transferase domains as essential, with partial dependence on OpnB PHP.
  • restricted phage propagation confers Ophion system METPO:2007700

    Ophion-mediated phage restriction realizes the Ophion system trait.

    • DOI:10.1101/2025.09.30.679545 Ophion provides potent and specific defense against jumbo phages by blocking progression from the EPI vesicle to the nucleus stage, possibly by halting the transcription of the nucleus forming genes Keesman et al. connect Ophion activity to blocking progression from the jumbo-phage early phage infection vesicle stage to the nucleus stage.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ophion | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks The DefenseFinder article registry maps the named Ophion system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ophion, so this row is name-to-paper evidence rather than model-component evidence.
  • Ophion system is a phage defense system rdfs:subClassOf

    Ophion 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 Ophion among experimentally validated phage-defense systems.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ophion | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems through component modularity networks The DefenseFinder article registry maps the named Ophion system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ophion, 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)

  • Ophion 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 Ophion phage triggers, nucleotide-modification products, and model coverage before minting narrower Ophion mechanism children.

KNOWLEDGE GAP OPEN ophion-jumbo-phage-mechanism-gap · raised by codex · 2026-09-21

Attached to causal_graphs#ophion_locus_restricts_phage

Keesman et al. support Ophion as a three-gene anti-jumbo-phage system that blocks progression from the early phage infection vesicle to the phage nucleus, but the direct phage trigger, exact OpnA/OpnB/OpnC interaction sequence, modified nucleotide product, 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 Ophion 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_v208.

  2. · ADDRESS_PR_REVIEW · codex

    Tightened the Ophion conserved-residue evidence note after the PR 1183 adversarial review filed issue 1184, narrowing the claim to essential OpnA Radical SAM and OpnC phosphoribosyl-transferase domains plus partial OpnB PHP dependence.