identifier: traitmech:000500
label: Crouga system
definition: A phage defense system in which an organism possesses a Crouga antiviral
  locus that is encoded by P4-like phage satellites and can protect bacteria from
  bacteriophage infection.
definition_source: DOI:10.1093/nar/gkag898
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: Crouga
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1093/nar/gkag898
evidence:
- reference: DOI:10.1093/nar/gkag898
  snippet: The Crouga system has some evidence of being an RM-like system, with one
    of its proteins containing PFAM domains (ResIII, DEAD, and Helicase C) associated
    with other RM systems
  notes: de Sousa et al. identify Crouga as a named novel P4-associated system with
    restriction-modification-like domain evidence.
- reference: DOI:10.1093/nar/gkag898
  snippet: We named the novel functional systems according to deities from Lusitanian
    mythology
  notes: de Sousa et al. introduce Crouga among the named novel functional P4 antiviral
    systems.
- reference: DOI:10.1093/nar/gkag898
  snippet: Our experimental validation of anti-phage activity for 13 novel systems
    encoded by P4 confirms that the contribution of defence functions to the pangenomes
    of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts,
    will keep surprising us
  notes: de Sousa et al. summarize the validated P4-encoded novel-system cohort in
    their discussion.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| Crouga | 10\.64898/2026\.02\.27\.708500 | Shuttling, swapping and mixing:
    the rapid modular evolution of antiviral repertoires in temperate phages and their
    satellites | '
  notes: The pinned DefenseFinder article registry maps the Crouga source key to the
    de Sousa et al. P4/P2 antiviral-repertoire paper preprint.
causal_graphs:
- graph_id: crouga_locus_restricts_phage
  title: Crouga loci confer bacterial phage defense
  description: Conservative system-level sketch linking possession of a Crouga locus
    to restricted bacteriophage propagation without asserting the unresolved trigger
    or molecular output.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures Crouga as a named P4 anti-phage system while leaving
    its source locus, phage trigger, restriction-modification-like molecular roles,
    antiviral effector output, source-system table rows, and DefenseFinder HMM/rule
    model coverage unresolved.
  nodes:
  - node_id: crouga_locus
    label: Crouga locus
    node_type: GENETIC_ELEMENT
    description: A P4-associated Crouga anti-phage defense locus.
  - node_id: restricted_phage_propagation
    label: restricted phage propagation
    node_type: BIOLOGICAL_PROCESS
    description: Reduced propagation of bacteriophage in cells carrying the Crouga
      system.
  - node_id: crouga_system_trait
    label: Crouga system
    node_type: TRAIT
    grounding: traitmech:000500
    description: Possession of a genome-encoded Crouga 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: crouga_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: restricted_phage_propagation
    description: Crouga loci are among the novel P4-encoded systems that can reduce
      bacteriophage infection.
    evidence:
    - reference: DOI:10.1093/nar/gkag898
      snippet: The Crouga system has some evidence of being an RM-like system, with
        one of its proteins containing PFAM domains (ResIII, DEAD, and Helicase C)
        associated with other RM systems
      notes: de Sousa et al. place Crouga in the newly named functional-system set
        and describe its RM-like domain evidence.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: '| Crouga | 10\.64898/2026\.02\.27\.708500 | Shuttling, swapping and
        mixing: the rapid modular evolution of antiviral repertoires in temperate
        phages and their satellites | '
      notes: The pinned DefenseFinder article registry maps the Crouga source key
        to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint.
  - subject: restricted_phage_propagation
    predicate: confers
    predicate_id: METPO:2007700
    object: crouga_system_trait
    description: Crouga-mediated phage protection realizes the Crouga system trait.
    evidence:
    - reference: DOI:10.1093/nar/gkag898
      snippet: Our experimental validation of anti-phage activity for 13 novel systems
        encoded by P4 confirms that the contribution of defence functions to the pangenomes
        of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts,
        will keep surprising us
      notes: de Sousa et al. connect the named novel P4-system cohort to anti-phage
        activity.
  - subject: crouga_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Crouga system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1093/nar/gkag898
      snippet: Our experimental validation of anti-phage activity for 13 novel systems
        encoded by P4 confirms that the contribution of defence functions to the pangenomes
        of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts,
        will keep surprising us
      notes: de Sousa et al. frame the named Crouga cohort as newly validated P4-encoded
        anti-phage defense functions.
discussions:
- discussion_id: crouga-mechanism-and-modelling-gap
  prompt: Resolve Crouga locus breadth, exact phage triggers, restriction-modification-like
    molecular roles, direct antiviral output, source-system table rows, and DefenseFinder
    HMM/rule coverage before minting narrower Crouga mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: de Sousa et al. support Crouga as one of the novel P4-encoded systems
    with experimental phage-protection activity, and the pinned DefenseFinder article
    registry maps the Crouga source key to the corresponding preprint. The pinned
    HMM inventory and rules table have no exact Crouga rows, and this first-pass record
    does not resolve the tested source locus, complete phage breadth, exact trigger,
    molecular output, or detection rule.
  evidence:
  - reference: DOI:10.1093/nar/gkag898
    snippet: The Crouga system has some evidence of being an RM-like system, with
      one of its proteins containing PFAM domains (ResIII, DEAD, and Helicase C) associated
      with other RM systems
    notes: de Sousa et al. support Crouga as a named RM-like defense system while
      leaving exact mechanism for separate review.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| Crouga | 10\.64898/2026\.02\.27\.708500 | Shuttling, swapping and
      mixing: the rapid modular evolution of antiviral repertoires in temperate phages
      and their satellites | '
    notes: The pinned DefenseFinder article registry maps the Crouga source key to
      the de Sousa et al. P4/P2 antiviral-repertoire paper preprint.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    notes: A structured first-pass search of the pinned DefenseFinder HMM inventory
      found no exact Crouga row.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: A structured first-pass search of the pinned DefenseFinder rules table
      found no exact Crouga system row.
  attaches_to:
  - causal_graphs#crouga_locus_restricts_phage
  posed_by: codex
  posed_date: '2026-09-30'
curation_history:
- timestamp: '2026-09-30T20:55:13Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted Crouga 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_v377.
  llm_assisted: true
- timestamp: '2026-09-30T20:55:14Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed Crouga system canonical_examples and left them empty because de
    Sousa et al. support P4-encoded Crouga phage protection and a DefenseFinder article-registry
    row, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous Crouga activity. No paid research was used.
  llm_assisted: true