identifier: traitmech:000279
label: DRT system
definition: A phage defense system in which an organism possesses a defense-associated
  reverse transcriptase locus whose RT-domain component or components can confer bacteriophage
  defense and are modeled by DefenseFinder as DRT subtypes.
definition_source: DOI:10.1126/science.aba0372
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: DRT
  synonym_type: EXACT_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
- synonym_text: defense-associated RT
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1126/science.aba0372
- synonym_text: defense-associated reverse transcriptase
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1126/science.aba0372
evidence:
- reference: DOI:10.1126/science.aba0372
  snippet: We discovered that a family of uncharacterized reverse transcriptases (RTs)
    are active defense systems
  notes: Gao et al. experimentally support previously uncharacterized reverse transcriptases
    as active antiphage defense systems rather than mobile-element RT features alone.
- reference: DOI:10.1126/science.aba0372
  snippet: six of these candidates (UG1, UG2, UG3, UG8, UG15, and UG16) provided robust
    protection against dsDNA phages
  notes: Gao et al. support DRT defense activity across several reverse-transcriptase
    candidate groups.
- reference: DOI:10.1126/science.aba0372
  snippet: We named these genes defense-associated RTs (DRTs)
  notes: Gao et al. coined the defense-associated RT naming that underlies the DRT
    system label.
- reference: DOI:10.1126/science.aba0372
  snippet: In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where
    x is any amino acid] abolished activity
  notes: Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase
    active-site residues.
- reference: DOI:10.1126/science.aba0372
  snippet: the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense
    system (DRT type 3), with both RTs required for defense activity
  notes: Gao et al. support the multi-component DRT type 3 system while separating
    it from single-gene DRT subtypes.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: DRT | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate
    antiviral immunity in prokaryotes
  notes: The DefenseFinder article registry maps the named DRT system to the Gao et
    al. antiphage-system discovery paper.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b"
  notes: The DefenseFinder rules table models DRT_1 as a two-profile DRT subtype.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: DRT_1__drt1a                                     | DRT_1__drt1a                                     |
    DRT_1
  notes: The DefenseFinder HMM inventory records the drt1a profile in the DRT_1 model
    namespace.
causal_graphs:
- graph_id: drt_reverse_transcriptase_antiphage_defense
  title: DRT loci use reverse transcriptases for antiphage defense
  description: Conservative system-level sketch linking a DRT locus to reverse-transcriptase
    active-site dependence, subtype-specific bacteriophage resistance, and the DRT
    system trait.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DRT systems at the family level while leaving the
    direct RT products, phage triggers, subtype-specific partner proteins or non-coding
    RNAs, additional subtype mechanisms, and exact phage targets unresolved.
  nodes:
  - node_id: drt_locus
    label: DRT locus
    node_type: GENETIC_ELEMENT
    description: A defense-associated reverse transcriptase antiphage locus represented
      by DRT subtype profiles.
  - node_id: defense_associated_rt_activity
    label: defense-associated RT activity
    node_type: MOLECULAR_FUNCTION
    description: Reverse-transcriptase active-site-dependent activity of DRT antiphage
      proteins.
  - node_id: subtype_specific_phage_resistance
    label: subtype-specific phage resistance
    node_type: BIOLOGICAL_PROCESS
    description: Protection against particular bacteriophages by one of several DRT
      subtypes.
  - node_id: drt_system_trait
    label: DRT system
    node_type: TRAIT
    grounding: traitmech:000279
    description: Possession of a genome-encoded defense-associated reverse transcriptase
      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: drt_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: defense_associated_rt_activity
    description: DRT loci encode defense-associated RT-domain proteins.
    evidence:
    - reference: DOI:10.1126/science.aba0372
      snippet: We named these genes defense-associated RTs (DRTs)
      notes: Gao et al. connect the DRT name to reverse-transcriptase defense genes.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: DRT_1__drt1a                                     | DRT_1__drt1a                                     |
        DRT_1
      notes: DefenseFinder includes drt1a in the custom DRT_1 model profile inventory.
  - subject: defense_associated_rt_activity
    predicate: contributes to
    predicate_id: RO:0002326
    object: subtype_specific_phage_resistance
    description: Conserved reverse-transcriptase active-site residues are required
      for DRT-mediated defense activity.
    evidence:
    - reference: DOI:10.1126/science.aba0372
      snippet: In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA,
        where x is any amino acid] abolished activity
      notes: Gao et al. show DRT antiphage activity requires RT active-site residues.
  - subject: drt_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: subtype_specific_phage_resistance
    description: Experimentally reconstructed DRT candidate systems provide protection
      against dsDNA phages.
    evidence:
    - reference: DOI:10.1126/science.aba0372
      snippet: six of these candidates (UG1, UG2, UG3, UG8, UG15, and UG16) provided
        robust protection against dsDNA phages
      notes: Gao et al. support DRT loci as defensive against bacteriophages in heterologous
        reconstruction assays.
    - reference: DOI:10.1126/science.aba0372
      snippet: the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense
        system (DRT type 3), with both RTs required for defense activity
      notes: Gao et al. support multi-component DRT type 3 as one DRT-system subtype.
  - subject: subtype_specific_phage_resistance
    predicate: confers
    predicate_id: METPO:2007700
    object: drt_system_trait
    description: DefenseFinder models DRT as a phage-defense system with subtype models
      such as DRT_1.
    evidence:
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b"
      notes: The DefenseFinder rules table supports DRT_1 as a named defense-system
        subtype model with drt1a and drt1b profiles.
  - subject: drt_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DRT system possession is a phage-defense-system trait.
    evidence:
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: DRT | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate
        antiviral immunity in prokaryotes
      notes: DefenseFinder associates DRT with the Gao et al. prokaryotic antiviral-immunity
        paper.
discussions:
- discussion_id: drt-subtype-mechanism-gap
  prompt: Resolve DRT subtype products, partner RNAs or proteins, phage triggers,
    and antiphage substrates before minting narrower DRT subtype mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Gao et al. support several active reverse-transcriptase-containing antiphage
    systems, and DefenseFinder models DRT subtypes such as DRT_1. This first record
    stays at DRT-family level because the direct products of DRT RT activity, the
    exact phage triggers, the non-coding RNA role in DRT type 3, and the mechanisms
    for additional DRT subtypes are not resolved.
  attaches_to:
  - causal_graphs#drt_reverse_transcriptase_antiphage_defense
  posed_by: codex
  posed_date: '2026-09-19'
curation_history:
- timestamp: '2026-09-19T12:30:14Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DRT 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_v156.
  llm_assisted: true