identifier: traitmech:000399
label: Old exonuclease system
definition: A phage defense system in which an organism possesses an Old exonuclease
  locus represented by DefenseFinder as a single-profile model, Old_exonuclease__Old_exonuclease,
  and experimentally linked to interference with phage lambda by the bacteriophage
  P2 Old protein.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: Old_exonuclease
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
- synonym_text: Old_exonuclease__Old_exonuclease
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1128/jb.177.3.497-501.1995
  snippet: The Old protein of bacteriophage P2 is responsible for interference with
    the growth of phage lambda and for killing of recBC mutant Escherichia coli.
  notes: The 1995 Old nuclease study identifies the P2 Old protein as responsible
    for phage-lambda interference.
- reference: DOI:10.1128/jb.177.3.497-501.1995
  snippet: The Old protein fused to maltose-binding protein has exonuclease activity
    on double-stranded DNA as well as nuclease activity on single-stranded DNA and
    RNA.
  notes: The 1995 biochemical study shows Old has nuclease activity on double-stranded
    DNA, single-stranded DNA, and RNA.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
  snippet: It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995},
    and when cloned with the P2 Tin accessory gene, it was shown to protect against
    other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}.
  notes: The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection
    and to broader P2 Old plus Tin protection.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
  snippet: The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction
    :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the
    molecular mechanisms remain unknown.
  notes: The pinned DefenseFinder wiki page supports Old dsDNA exonuclease activity
    while leaving the remaining molecular mechanism unresolved.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
  snippet: 'The Old_exonuclease is composed of 1 protein: Old_exonuclease.'
  notes: The pinned DefenseFinder wiki page describes Old_exonuclease as a one-protein
    system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
  snippet: 'The Old_exonuclease system in *Shewanella xiamenensis* (GCF_022453805.1,
    NZ_CP092630) is composed of 1 protein: Old_exonuclease (WP_240293412.1)'
  notes: The pinned DefenseFinder wiki page illustrates a predicted Old_exonuclease
    locus in RefSeq assembly GCF_022453805.1 on NZ_CP092630.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.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[Enterobacteria phage P2 \n<a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>]\
    \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> Lambda\
    \ & T4 & LF82_P8 & Al505_P2"
  notes: The DefenseFinder experimental-validation diagram links Rousset et al. to
    Enterobacteria phage P2 Old expressed in Escherichia coli against lambda, T4,
    LF82_P8, and Al505_P2.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
  snippet: "subgraph Title4[Protects against]\n        Lambda\n        T4\n      \
    \  LF82_P8\n        Al505_P2"
  notes: The DefenseFinder experimental-validation diagram lists lambda, T4, LF82_P8,
    and Al505_P2 in the Old_exonuclease protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: Old_exonuclease | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots
    of bacterial immune systems
  notes: The DefenseFinder article registry maps the named Old_exonuclease system
    to the Rousset et al. preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\
    \t\t"
  notes: The DefenseFinder rules table models Old_exonuclease as a single-profile
    system requiring Old_exonuclease__Old_exonuclease.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| Old_exonuclease__Old_exonuclease                 | Old_exonuclease__Old_exonuclease                 |
    Old_exonuclease        | Custom                  | 200    |'
  notes: The DefenseFinder HMM inventory records Old_exonuclease__Old_exonuclease
    under the Old_exonuclease system namespace.
causal_graphs:
- graph_id: old_exonuclease_locus_interferes_with_lambda
  title: Old exonuclease loci interfere with phage lambda
  description: Conservative system-level sketch linking a named Old_exonuclease one-profile
    model to phage-lambda interference.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures Old_exonuclease as a named DefenseFinder single-profile
    phage-defense system while leaving natural host breadth, Tin accessory dependence,
    RecBCD-triggered activation, profile-to-protein mapping, and the lambda interference
    mechanism unresolved.
  nodes:
  - node_id: old_exonuclease_locus
    label: Old exonuclease locus
    node_type: GENETIC_ELEMENT
    description: A single-profile Old-exonuclease phage-defense locus represented
      by the custom DefenseFinder Old_exonuclease profile.
  - node_id: lambda_phage_interference
    label: lambda phage interference
    node_type: BIOLOGICAL_PROCESS
    description: Interference with growth of phage lambda in a host expressing bacteriophage
      P2 Old.
  - node_id: old_exonuclease_system_trait
    label: Old exonuclease system
    node_type: TRAIT
    grounding: traitmech:000399
    description: Possession of a genome-encoded Old exonuclease 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: old_exonuclease_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: lambda_phage_interference
    description: The P2 Old protein is linked to phage-lambda interference, and DefenseFinder
      models Old_exonuclease as a single-profile system.
    evidence:
    - reference: DOI:10.1128/jb.177.3.497-501.1995
      snippet: The Old protein of bacteriophage P2 is responsible for interference
        with the growth of phage lambda and for killing of recBC mutant Escherichia
        coli.
      notes: The 1995 Old nuclease study identifies the P2 Old protein as responsible
        for phage-lambda interference.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\
        \t\t"
      notes: The DefenseFinder rules table models Old_exonuclease as a single-profile
        system requiring Old_exonuclease__Old_exonuclease.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| Old_exonuclease__Old_exonuclease                 | Old_exonuclease__Old_exonuclease                 |
        Old_exonuclease        | Custom                  | 200    |'
      notes: The DefenseFinder HMM inventory records Old_exonuclease__Old_exonuclease
        under the Old_exonuclease system namespace.
  - subject: lambda_phage_interference
    predicate: confers
    predicate_id: METPO:2007700
    object: old_exonuclease_system_trait
    description: Old-mediated phage-lambda interference realizes the Old exonuclease
      system trait.
    evidence:
    - reference: DOI:10.1128/jb.177.3.497-501.1995
      snippet: The Old protein of bacteriophage P2 is responsible for interference
        with the growth of phage lambda and for killing of recBC mutant Escherichia
        coli.
      notes: The 1995 Old nuclease study identifies the P2 Old protein as responsible
        for phage-lambda interference.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.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[Enterobacteria phage P2 \n\
        <a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> Lambda\
        \ & T4 & LF82_P8 & Al505_P2"
      notes: The DefenseFinder experimental-validation diagram links Rousset et al.
        to Enterobacteria phage P2 Old expressed in Escherichia coli against lambda,
        T4, LF82_P8, and Al505_P2.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
      snippet: "subgraph Title4[Protects against]\n        Lambda\n        T4\n  \
        \      LF82_P8\n        Al505_P2"
      notes: The DefenseFinder experimental-validation diagram lists lambda, T4, LF82_P8,
        and Al505_P2 in the Old_exonuclease protects-against subgraph.
  - subject: old_exonuclease_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Old exonuclease system possession is a phage-defense-system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
      snippet: It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995},
        and when cloned with the P2 Tin accessory gene, it was shown to protect against
        other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}.
      notes: The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection
        and to broader P2 Old plus Tin protection.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Old_exonuclease | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded
        hotspots of bacterial immune systems
      notes: The DefenseFinder article registry maps the named Old_exonuclease system
        to the Rousset et al. preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\
        \t\t"
      notes: The DefenseFinder rules table models Old_exonuclease as a single-profile
        system requiring Old_exonuclease__Old_exonuclease.
discussions:
- discussion_id: old-exonuclease-tin-trigger-mechanism-gap
  prompt: Resolve Old_exonuclease natural host breadth, Tin accessory dependence,
    RecBCD-triggered activation, profile-to-protein mapping, and lambda interference
    mechanism before minting narrower Old nuclease mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The 1995 P2 Old paper supports Old nuclease activity and phage-lambda
    interference, and DefenseFinder represents Old_exonuclease as a required single-profile
    model. This first system-level record leaves Tin dependence in the Rousset et
    al. assay, natural host breadth, RecBCD-linked activation, profile-to-protein
    mapping, and the exact phage-interference mechanism unresolved.
  evidence:
  - reference: DOI:10.1128/jb.177.3.497-501.1995
    snippet: The Old protein of bacteriophage P2 is responsible for interference with
      the growth of phage lambda and for killing of recBC mutant Escherichia coli.
    notes: The 1995 Old nuclease study identifies the P2 Old protein as responsible
      for phage-lambda interference.
  - reference: DOI:10.1128/jb.177.3.497-501.1995
    snippet: The Old protein fused to maltose-binding protein has exonuclease activity
      on double-stranded DNA as well as nuclease activity on single-stranded DNA and
      RNA.
    notes: The 1995 biochemical study shows Old has nuclease activity on double-stranded
      DNA, single-stranded DNA, and RNA.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
    snippet: The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3'
      direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects
      of the molecular mechanisms remain unknown.
    notes: The pinned DefenseFinder wiki page supports Old dsDNA exonuclease activity
      while leaving the remaining molecular mechanism unresolved.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
    snippet: 'The Old_exonuclease is composed of 1 protein: Old_exonuclease.'
    notes: The pinned DefenseFinder wiki page describes Old_exonuclease as a one-protein
      system.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\
      \t\t"
    notes: The DefenseFinder rules table models Old_exonuclease as a single-profile
      system requiring Old_exonuclease__Old_exonuclease.
  attaches_to:
  - causal_graphs#old_exonuclease_locus_interferes_with_lambda
  posed_by: codex
  posed_date: '2026-09-27'
curation_history:
- timestamp: '2026-09-27T01:44:29Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted Old exonuclease system as a DOI- and DefenseFinder-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_v276.
  llm_assisted: true
- timestamp: '2026-09-27T01:44:30Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed Old exonuclease system during canonical-example issue 444 enforcement
    and left canonical_examples empty because the sources support a bacteriophage
    P2 Old protein, a heterologous Old plus Tin protection assay in Escherichia coli,
    and a DefenseFinder RefSeq model example, but not a direct native microbial isolate
    exemplar with experimentally verified Old_exonuclease activity. No paid research
    was used.
  llm_assisted: true