Old exonuclease system

traitmech:000399 · CLASS · PROPOSED

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.

Trait evidence (11)

DOI:10.1128/jb.177.3.497-501.1995
The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli.

The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference.
DOI:10.1128/jb.177.3.497-501.1995
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.

The 1995 biochemical study shows Old has nuclease activity on double-stranded DNA, single-stranded DNA, and RNA.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
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}.

The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection and to broader P2 Old plus Tin protection.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
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.

The pinned DefenseFinder wiki page supports Old dsDNA exonuclease activity while leaving the remaining molecular mechanism unresolved.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
The Old_exonuclease is composed of 1 protein: Old_exonuclease.

The pinned DefenseFinder wiki page describes Old_exonuclease as a one-protein system.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
The Old_exonuclease system in *Shewanella xiamenensis* (GCF_022453805.1, NZ_CP092630) is composed of 1 protein: Old_exonuclease (WP_240293412.1)

The pinned DefenseFinder wiki page illustrates a predicted Old_exonuclease locus in RefSeq assembly GCF_022453805.1 on NZ_CP092630.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Enterobacteria phage P2 <a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2

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.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
subgraph Title4[Protects against] Lambda T4 LF82_P8 Al505_P2

The DefenseFinder experimental-validation diagram lists lambda, T4, LF82_P8, and Al505_P2 in the Old_exonuclease protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Old_exonuclease | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems

The DefenseFinder article registry maps the named Old_exonuclease system to the Rousset et al. preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Old_exonuclease Old_exonuclease 1 1 Old_exonuclease__Old_exonuclease

The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Old_exonuclease__Old_exonuclease | Old_exonuclease__Old_exonuclease | Old_exonuclease | Custom | 200 |

The DefenseFinder HMM inventory records Old_exonuclease__Old_exonuclease under the Old_exonuclease system namespace.

Old exonuclease loci interfere with phage lambda

Conservative system-level sketch linking a named Old_exonuclease one-profile model to phage-lambda interference.

NONMECHANISTIC · 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.

Edge evidence

Old exonuclease locus contributes to lambda phage interference RO:0002326
The P2 Old protein is linked to phage-lambda interference, and DefenseFinder models Old_exonuclease as a single-profile system.
- DOI:10.1128/jb.177.3.497-501.1995 The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli. The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Old_exonuclease Old_exonuclease 1 1 Old_exonuclease__Old_exonuclease The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Old_exonuclease__Old_exonuclease | Old_exonuclease__Old_exonuclease | Old_exonuclease | Custom | 200 | The DefenseFinder HMM inventory records Old_exonuclease__Old_exonuclease under the Old_exonuclease system namespace.
lambda phage interference confers Old exonuclease system METPO:2007700
Old-mediated phage-lambda interference realizes the Old exonuclease system trait.
- DOI:10.1128/jb.177.3.497-501.1995 The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli. The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0 Origin_0[Enterobacteria phage P2 <a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2 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.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md subgraph Title4[Protects against] Lambda T4 LF82_P8 Al505_P2 The DefenseFinder experimental-validation diagram lists lambda, T4, LF82_P8, and Al505_P2 in the Old_exonuclease protects-against subgraph.
Old exonuclease system is a phage defense system rdfs:subClassOf
Old exonuclease system possession is a phage-defense-system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md 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}. The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection and to broader P2 Old plus Tin protection.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Old_exonuclease | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems The DefenseFinder article registry maps the named Old_exonuclease system to the Rousset et al. preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Old_exonuclease Old_exonuclease 1 1 Old_exonuclease__Old_exonuclease The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

Old_exonuclease RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Old_exonuclease__Old_exonuclease RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN old-exonuclease-tin-trigger-mechanism-gap · raised by codex · 2026-09-27

Attached to causal_graphs#old_exonuclease_locus_interferes_with_lambda

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

DOI:10.1128/jb.177.3.497-501.1995
The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli.
DOI:10.1128/jb.177.3.497-501.1995
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.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
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.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md
The Old_exonuclease is composed of 1 protein: Old_exonuclease.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Old_exonuclease Old_exonuclease 1 1 Old_exonuclease__Old_exonuclease

Curation history

2026-09-27T01:44:29Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-27T01:44:30Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.