identifier: traitmech:000295
label: Charlie gp32 system
definition: A phage defense system in which an organism possesses a Charlie gp32 locus
  that can protect bacteria from bacteriophage infection.
definition_source: DOI:10.1038/nmicrobiol.2016.251
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: Charlie gp32 defense system
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1038/nmicrobiol.2016.251
- synonym_text: Charlie_gp32
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
evidence:
- reference: DOI:10.1038/nmicrobiol.2016.251
  snippet: at least five distinct prophage-expressed viral defense systems that interfere
    with infection
  notes: Dedrick et al. place the Cluster N Charlie gp32 system in a cohort of prophage-expressed
    defenses against lytic and temperate mycobacteriophages.
- reference: DOI:10.1038/nmicrobiol.2016.251
  snippet: The gene responsible is Charlie 32 (and presumably the analogous genes
    in Xeno and SkinnyPete), and a Charlie lysogen in which 32 is deleted loses defense
    against Che9c
  notes: Dedrick et al. localize a Cluster N prophage-mediated heterotypic defense
    to Charlie gene 32.
- reference: DOI:10.1038/nmicrobiol.2016.251
  snippet: The Charlie gp32 defense system is notable in that although it has the
    characteristics of superinfection exclusion systems – being membrane located and
    preventing DNA injection – it has remarkable specificity for a single phage among
    those tested
  notes: Dedrick et al. explicitly name the Charlie gp32 defense system as an exclusion-like
    viral-defense system.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: Charlie_gp32 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence
    against viral attack and viral counter-defence
  notes: The DefenseFinder model registry maps the named Charlie_gp32 system to the
    Dedrick et al. prophage-mediated viral-defense paper.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: Charlie_gp32__gp32                               | Charlie_gp32__gp32                               |
    Charlie_gp32
  notes: The DefenseFinder HMM inventory records gp32 in the Charlie_gp32 model namespace.
causal_graphs:
- graph_id: charlie_gp32_locus_blocks_phage_entry
  title: Charlie gp32 loci confer heterotypic phage exclusion
  description: Conservative system-level sketch linking possession of a Charlie gp32
    locus to blocked Che9c DNA injection and restricted bacteriophage propagation.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures Charlie gp32 as a named anti-phage system with a
    DefenseFinder gp32 profile and a proposed Che9c-exclusion output while leaving
    the direct gp32 target, the membrane-blocking mechanism, and homolog breadth unresolved.
  nodes:
  - node_id: charlie_gp32_locus
    label: Charlie gp32 locus
    node_type: GENETIC_ELEMENT
    description: A Charlie gp32 anti-phage defense locus cataloged in DefenseFinder
      with a gp32 HMM profile.
  - node_id: blocked_che9c_dna_injection
    label: blocked Che9c DNA injection
    node_type: BIOLOGICAL_PROCESS
    description: Reduced Che9c bacteriophage DNA injection across the cell envelope
      in cells carrying Charlie gp32.
  - node_id: restricted_phage_propagation
    label: restricted phage propagation
    node_type: BIOLOGICAL_PROCESS
    description: Reduced propagation of bacteriophage in cells carrying the Charlie
      gp32 system.
  - node_id: charlie_gp32_system_trait
    label: Charlie gp32 system
    node_type: TRAIT
    grounding: traitmech:000295
    description: Possession of a genome-encoded Charlie gp32 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: charlie_gp32_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: blocked_che9c_dna_injection
    description: Dedrick et al. identify Charlie 32 as the gene responsible for Che9c
      defense, and DefenseFinder catalogs a gp32 profile in the Charlie_gp32 model
      namespace.
    evidence:
    - reference: DOI:10.1038/nmicrobiol.2016.251
      snippet: The gene responsible is Charlie 32 (and presumably the analogous genes
        in Xeno and SkinnyPete), and a Charlie lysogen in which 32 is deleted loses
        defense against Che9c
      notes: Dedrick et al. support Charlie gp32 as the genetic determinant of the
        Che9c-exclusion phenotype.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: Charlie_gp32__gp32                               | Charlie_gp32__gp32                               |
        Charlie_gp32
      notes: The DefenseFinder HMM inventory records gp32 in the Charlie_gp32 model
        namespace.
  - subject: blocked_che9c_dna_injection
    predicate: contributes to
    predicate_id: RO:0002326
    object: restricted_phage_propagation
    description: Charlie-gp32-mediated blockade of Che9c DNA injection reduces productive
      phage infection.
    evidence:
    - reference: DOI:10.1038/nmicrobiol.2016.251
      snippet: We propose that Charlie gp32 confers heterotypic exclusion, blocking
        Che9c DNA injection across the membrane
      notes: Dedrick et al. interpret Charlie gp32 defense as an exclusion-like block
        to Che9c DNA injection.
  - subject: restricted_phage_propagation
    predicate: confers
    predicate_id: METPO:2007700
    object: charlie_gp32_system_trait
    description: Charlie-gp32-mediated Che9c exclusion realizes the Charlie gp32 system
      trait.
    evidence:
    - reference: DOI:10.1038/nmicrobiol.2016.251
      snippet: Charlie gp32 confers survival to Che9c infection, which also is a temperate
        phage
      notes: Dedrick et al. show a cellular survival outcome for Charlie-gp32-mediated
        Che9c defense.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Charlie_gp32 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence
        against viral attack and viral counter-defence
      notes: DefenseFinder records Charlie_gp32 as a named system from the Dedrick
        et al. prophage-defense paper.
  - subject: charlie_gp32_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Charlie gp32 system possession is a phage-defense-system trait.
    evidence:
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: '| Charlie_gp32 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated
        defence against viral attack and viral counter-defence |'
      notes: DefenseFinder associates Charlie_gp32 with the Dedrick et al. prophage-mediated
        viral-defense paper.
discussions:
- discussion_id: charlie_gp32-mechanism-gap
  prompt: Resolve the Charlie gp32 membrane target, Che9c specificity, and homolog
    breadth before minting narrower Charlie gp32 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Dedrick et al. and DefenseFinder support Charlie gp32 as a named anti-phage
    system with a gp32 profile, but the direct membrane target, determinants of its
    Che9c specificity, and breadth of homologous loci are not resolved enough here
    to assert a narrower mechanistic child trait.
  attaches_to:
  - causal_graphs#charlie_gp32_locus_blocks_phage_entry
  posed_by: codex
  posed_date: '2026-09-19'
curation_history:
- timestamp: '2026-09-19T22:40:37Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted Charlie gp32 system as a DOI-backed GENOMICS TraitRecord under phage
    defense system after an ignored-and-hidden duplicate review found no exact live
    TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved
    in proposals/metpo_traitmech_v172.
  llm_assisted: true
- timestamp: '2026-09-19T23:02:19Z'
  curator: codex
  action: CURATION_REVIEW_REVISION
  changes: 'Resolved PR #1089 review issues #1090 and #1091 by dropping the proposed
    heterotypic-exclusion mechanism from the definition and tightening the Charlie
    gp32 exact-synonym evidence snippet after rechecking the Dedrick et al. full text
    and pinned DefenseFinder rows.'
  llm_assisted: true
- timestamp: '2026-09-19T23:11:07Z'
  curator: codex
  action: CURATION_REVIEW_REVISION
  changes: 'Resolved the follow-up PR #1089 review issue #1091 by restoring a complete
    Dedrick et al. P25 source clause, including American defense spelling as verified
    in the local PMC full text.'
  llm_assisted: true