identifier: traitmech:000331
label: Ophion system
definition: 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.
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: Ophion
  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 Ophion 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: 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)
  notes: Keesman et al. support Ophion as a three-gene system encoding OpnA, OpnB,
    and OpnC components with Radical SAM, PHP, and phosphoribosyl-transferase domains.
- reference: DOI:10.1101/2025.09.30.679545
  snippet: Ophion shows strong protection against jumbo phages
  notes: Keesman et al. support Ophion as a system that strongly protects against
    jumbo phages.
- reference: DOI:10.1101/2025.09.30.679545
  snippet: Mutating conserved residues of the rSAM and PRTase domains revealed these
    to be essential for protection, with partial dependence on the PHP domain
  notes: 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.
- reference: DOI:10.1101/2025.09.30.679545
  snippet: 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
  notes: 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.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: Ophion | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense systems
    through component modularity networks
  notes: 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.
causal_graphs:
- graph_id: ophion_locus_restricts_phage
  title: Ophion loci confer bacterial phage defense
  description: 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.
  scope_status: NONMECHANISTIC
  scope_notes: 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.
  nodes:
  - node_id: ophion_locus
    label: Ophion locus
    node_type: GENETIC_ELEMENT
    description: A three-gene Ophion anti-jumbo-phage defense locus encoding OpnA,
      OpnB, and OpnC components.
  - node_id: restricted_phage_propagation
    label: restricted phage propagation
    node_type: BIOLOGICAL_PROCESS
    description: Reduced propagation of jumbo bacteriophages in cells carrying the
      Ophion system.
  - node_id: ophion_system_trait
    label: Ophion system
    node_type: TRAIT
    grounding: traitmech:000331
    description: Possession of a genome-encoded Ophion 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: ophion_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: restricted_phage_propagation
    description: The three-gene Ophion locus restricts infection by jumbo phages.
    evidence:
    - reference: DOI:10.1101/2025.09.30.679545
      snippet: Ophion shows strong protection against jumbo phages
      notes: Keesman et al. report that Ophion protects against jumbo phages.
    - reference: DOI:10.1101/2025.09.30.679545
      snippet: Mutating conserved residues of the rSAM and PRTase domains revealed
        these to be essential for protection, with partial dependence on the PHP domain
      notes: 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.
  - subject: restricted_phage_propagation
    predicate: confers
    predicate_id: METPO:2007700
    object: ophion_system_trait
    description: Ophion-mediated phage restriction realizes the Ophion system trait.
    evidence:
    - reference: DOI:10.1101/2025.09.30.679545
      snippet: 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
      notes: Keesman et al. connect Ophion activity to blocking progression from the
        jumbo-phage early phage infection vesicle stage to the nucleus stage.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Ophion | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense
        systems through component modularity networks
      notes: 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.
  - subject: ophion_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Ophion 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 Ophion among experimentally validated phage-defense
        systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Ophion | 10\.1101/2025\.09\.30\.679545 | Discovery of phage defense
        systems through component modularity networks
      notes: 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.
discussions:
- discussion_id: ophion-jumbo-phage-mechanism-gap
  prompt: Resolve Ophion phage triggers, nucleotide-modification products, and model
    coverage before minting narrower Ophion mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: 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.
  attaches_to:
  - causal_graphs#ophion_locus_restricts_phage
  posed_by: codex
  posed_date: '2026-09-21'
curation_history:
- timestamp: '2026-09-21T08:20:12Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: 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.
  llm_assisted: true
- timestamp: '2026-09-21T08:47:47Z'
  curator: codex
  action: ADDRESS_PR_REVIEW
  changes: 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.
  llm_assisted: true