identifier: traitmech:000402
label: Rst_Hydrolase-3Tm system
definition: A phage defense system in which an organism possesses a two-protein Rst_Hydrolase-3Tm
  locus represented by DefenseFinder as a two-profile Rst_Hydrolase-Tm model requiring
  Rst_Hydrolase-Tm__Hydrolase and Rst_Hydrolase-Tm__Hydrolase-Tm and experimentally
  linked to T7 protection when expressed in Escherichia coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: Rst_Hydrolase-3Tm
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
- synonym_text: Rst_Hydrolase-Tm
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
- synonym_text: Rst_Hydrolase-Tm__Hydrolase
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: Rst_Hydrolase-Tm__Hydrolase-Tm
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: Hydrolase-Tm
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
evidence:
- reference: DOI:10.1016/j.chom.2022.02.018
  snippet: 'two systems that specifically inhibit the growth of phage T7: an ATP-dependent
    helicase associated with a DUF2290 protein and a HAD-like hydrolase associated
    with a transmembrane protein'
  notes: Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein
    pair to specific inhibition of phage T7 growth.
- reference: DOI:10.1016/j.chom.2022.02.018
  snippet: Phage resistance heatmap of the validated defense systems shows the mean
    fold resistance of three independent replicates against a panel of eight phages
  notes: The Figure 2 legend frames the cloned P4-hotspot hits, including the hydrolase
    plus transmembrane-protein system, as validated defense systems in a replicated
    phage-resistance heatmap.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
  snippet: 'The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.'
  notes: The pinned DefenseFinder wiki page names Rst_Hydrolase-3Tm as a two-component
    Hydrolase/Hydrolase-Tm system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
  snippet: The Rst_Hydrolase-Tm system in *Pectobacterium versatile* (GCF_003031305.1,
    NZ_CP024842) is composed of 2 proteins Hydrolase (WP_107333258.1) Hydrolase-Tm
    (WP_107333259.1)
  notes: The DefenseFinder wiki illustrates a predicted two-protein Rst_Hydrolase-Tm
    locus in RefSeq assembly GCF_003031305.1 on NZ_CP024842.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
  snippet: "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset\
    \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli P4 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>]\
    \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7"
  notes: The DefenseFinder experimental-validation diagram links Rousset et al. to
    an Escherichia coli P4-locus source expressed in Escherichia coli against T7.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
  snippet: "subgraph Title4[Protects against]\n        T7"
  notes: The DefenseFinder experimental-validation diagram lists T7 in the Rst_Hydrolase-3Tm
    protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: Rst_Hydrolase-3Tm | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots
    of bacterial immune systems
  notes: The DefenseFinder article registry maps the named Rst_Hydrolase-3Tm system
    to the Rousset et al. preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "Rst_Hydrolase-3Tm\tRst_Hydrolase-Tm\t2\t2\tRst_Hydrolase-Tm__Hydrolase,\
    \ Rst_Hydrolase-Tm__Hydrolase-Tm\t\t\t"
  notes: The DefenseFinder rules table maps Rst_Hydrolase-3Tm to a two-profile Rst_Hydrolase-Tm
    model requiring Hydrolase and Hydrolase-Tm profiles.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm__Hydrolase                      |
    Rst_Hydrolase-Tm       | Custom                  | 20     |

    | Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm__Hydrolase-Tm                   |
    Rst_Hydrolase-Tm       | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records Hydrolase and Hydrolase-Tm profiles
    under the normalized Rst_Hydrolase-Tm system namespace.
causal_graphs:
- graph_id: rst_hydrolase_3tm_locus_restricts_t7
  title: Rst_Hydrolase-3Tm loci restrict T7
  description: Conservative system-level sketch linking a named Rst_Hydrolase-3Tm
    two-gene locus model to T7 phage resistance.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures Rst_Hydrolase-3Tm as a named DefenseFinder two-profile
    phage-defense system while leaving native host breadth, the exact Rst_Hydrolase-3Tm-to-Rst_Hydrolase-Tm
    naming relationship, Hydrolase and Hydrolase-Tm molecular roles, and the mechanism
    of T7 restriction unresolved.
  nodes:
  - node_id: rst_hydrolase_3tm_locus
    label: Rst_Hydrolase-3Tm locus
    node_type: GENETIC_ELEMENT
    description: A two-gene hydrolase/transmembrane phage-defense locus represented
      by the DefenseFinder Rst_Hydrolase-Tm profiles.
  - node_id: t7_phage_resistance
    label: T7 phage resistance
    node_type: BIOLOGICAL_PROCESS
    description: Resistance against phage T7 in a host expressing an Rst_Hydrolase-3Tm
      locus.
  - node_id: rst_hydrolase_3tm_system_trait
    label: Rst_Hydrolase-3Tm system
    node_type: TRAIT
    grounding: traitmech:000402
    description: Possession of a genome-encoded Rst_Hydrolase-3Tm 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: rst_hydrolase_3tm_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: t7_phage_resistance
    description: Rousset et al. linked a HAD-like hydrolase plus transmembrane-protein
      locus to T7 restriction, and DefenseFinder models Rst_Hydrolase-3Tm as a two-profile
      Rst_Hydrolase-Tm system.
    evidence:
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: 'two systems that specifically inhibit the growth of phage T7: an ATP-dependent
        helicase associated with a DUF2290 protein and a HAD-like hydrolase associated
        with a transmembrane protein'
      notes: Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein
        pair to specific inhibition of phage T7 growth.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
      snippet: 'The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.'
      notes: The pinned DefenseFinder wiki page names Rst_Hydrolase-3Tm as a two-component
        Hydrolase/Hydrolase-Tm system.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "Rst_Hydrolase-3Tm\tRst_Hydrolase-Tm\t2\t2\tRst_Hydrolase-Tm__Hydrolase,\
        \ Rst_Hydrolase-Tm__Hydrolase-Tm\t\t\t"
      notes: The DefenseFinder rules table maps Rst_Hydrolase-3Tm to a two-profile
        Rst_Hydrolase-Tm model requiring Hydrolase and Hydrolase-Tm profiles.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm__Hydrolase                      |
        Rst_Hydrolase-Tm       | Custom                  | 20     |

        | Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm__Hydrolase-Tm                   |
        Rst_Hydrolase-Tm       | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records Hydrolase and Hydrolase-Tm profiles
        under the normalized Rst_Hydrolase-Tm system namespace.
  - subject: t7_phage_resistance
    predicate: confers
    predicate_id: METPO:2007700
    object: rst_hydrolase_3tm_system_trait
    description: Rst_Hydrolase-3Tm-linked T7 resistance realizes the Rst_Hydrolase-3Tm
      system trait.
    evidence:
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: 'two systems that specifically inhibit the growth of phage T7: an ATP-dependent
        helicase associated with a DUF2290 protein and a HAD-like hydrolase associated
        with a transmembrane protein'
      notes: Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein
        pair to specific inhibition of phage T7 growth.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
      snippet: "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli P4 loci \n\
        <a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ T7"
      notes: The DefenseFinder experimental-validation diagram links Rousset et al.
        to an Escherichia coli P4-locus source expressed in Escherichia coli against
        T7.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
      snippet: "subgraph Title4[Protects against]\n        T7"
      notes: The DefenseFinder experimental-validation diagram lists T7 in the Rst_Hydrolase-3Tm
        protects-against subgraph.
  - subject: rst_hydrolase_3tm_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Rst_Hydrolase-3Tm system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1016/j.chom.2022.02.018
      snippet: Phage resistance heatmap of the validated defense systems shows the
        mean fold resistance of three independent replicates against a panel of eight
        phages
      notes: The Figure 2 legend frames the cloned P4-hotspot hits, including the
        hydrolase plus transmembrane-protein system, as validated defense systems
        in a replicated phage-resistance heatmap.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Rst_Hydrolase-3Tm | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded
        hotspots of bacterial immune systems
      notes: The DefenseFinder article registry maps the named Rst_Hydrolase-3Tm system
        to the Rousset et al. preprint.
discussions:
- discussion_id: rst-hydrolase-3tm-host-mechanism-gap
  prompt: Resolve Rst_Hydrolase-3Tm native host breadth, the Rst_Hydrolase-3Tm and
    Rst_Hydrolase-Tm namespace relationship, accession-level Hydrolase/Hydrolase-Tm
    roles, and the mechanism of T7 restriction before minting narrower Rst_Hydrolase-3Tm
    mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Rousset et al. support a two-gene HAD-like hydrolase plus transmembrane-protein
    P4-hotspot system that inhibits T7 growth, and DefenseFinder maps Rst_Hydrolase-3Tm
    to a required two-profile Rst_Hydrolase-Tm model. This first system-level record
    leaves native host breadth, profile-to-gene mapping, the model-namespace mismatch,
    the molecular activities of the Hydrolase and Hydrolase-Tm components, and the
    T7 restriction mechanism unresolved.
  evidence:
  - reference: DOI:10.1016/j.chom.2022.02.018
    snippet: 'two systems that specifically inhibit the growth of phage T7: an ATP-dependent
      helicase associated with a DUF2290 protein and a HAD-like hydrolase associated
      with a transmembrane protein'
    notes: Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein
      pair to specific inhibition of phage T7 growth.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md
    snippet: 'The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.'
    notes: The pinned DefenseFinder wiki page names Rst_Hydrolase-3Tm as a two-component
      Hydrolase/Hydrolase-Tm system.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "Rst_Hydrolase-3Tm\tRst_Hydrolase-Tm\t2\t2\tRst_Hydrolase-Tm__Hydrolase,\
      \ Rst_Hydrolase-Tm__Hydrolase-Tm\t\t\t"
    notes: The DefenseFinder rules table maps Rst_Hydrolase-3Tm to a two-profile Rst_Hydrolase-Tm
      model requiring Hydrolase and Hydrolase-Tm profiles.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm__Hydrolase                      |
      Rst_Hydrolase-Tm       | Custom                  | 20     |

      | Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm__Hydrolase-Tm                   |
      Rst_Hydrolase-Tm       | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records Hydrolase and Hydrolase-Tm profiles
      under the normalized Rst_Hydrolase-Tm system namespace.
  attaches_to:
  - causal_graphs#rst_hydrolase_3tm_locus_restricts_t7
  posed_by: codex
  posed_date: '2026-09-27'
curation_history:
- timestamp: '2026-09-27T05:04:25Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted Rst_Hydrolase-3Tm system as a DOI/stable-URL-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_v279.
  llm_assisted: true
- timestamp: '2026-09-27T05:04:26Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed Rst_Hydrolase-3Tm during canonical-example issue 444 enforcement
    and left canonical_examples empty because the sources support a cloned P4-hotspot
    Hydrolase/Hydrolase-Tm locus assayed in Escherichia coli and a DefenseFinder RefSeq
    model example, but not a direct native microbial host exemplar with experimentally
    verified Rst_Hydrolase-3Tm activity. No paid research was used.
  llm_assisted: true