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PvuRts1I system

traitmech:000511 · CLASS · PROPOSED

A type IV modification-dependent restriction system in which an organism possesses a PvuRts1I-family locus encoding a restriction endonuclease that recognizes 5-hydroxymethylcytosine or 5-glucosylhydroxymethylcytosine in double-stranded DNA and cleaves both strands on the 3'-side away from the recognized modified cytosine.

Trait evidence (5)

  • DOI:10.1093/nar/gkr607
    Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties.

    Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes.

  • DOI:10.1093/nar/gkr607
    PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA.

    Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA.

  • DOI:10.1093/nar/gkr607
    We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine.

    Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine.

  • DOI:10.1093/nar/gkt747
    The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.

    Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | PvuRts1I | 10\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine |

    The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper.

PvuRts1I restricts modified-HMC DNA

Conservative system-level sketch linking a PvuRts1I-family locus to modified-hydroxymethylcytosine DNA restriction and to the Type IV restriction parent trait.

NONMECHANISTIC · The graph captures PvuRts1I as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact target selectivity across characterized homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.

PvuRts1I restricts modified-HMC DNA Interactive directed graph showing evidence-backed causal relationships for PvuRts1I system.

Edge evidence

  • PvuRts1I-family locus enables PvuRts1I modified-HMC restriction RO:0002327

    PvuRts1I-family loci encode modification-dependent restriction endonucleases.

    • DOI:10.1093/nar/gkr607 Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes.
    • DOI:10.1093/nar/gkr607 We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine.
  • PvuRts1I modified-HMC restriction mitigates PvuRts1I-targeted modified-HMC DNA METPO:2007407

    PvuRts1I-family restriction targets DNA with 5hmC or 5ghmC modifications.

    • DOI:10.1093/nar/gkr607 PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA.
    • DOI:10.1093/nar/gkr607 We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine.
  • PvuRts1I modified-HMC restriction confers PvuRts1I system METPO:2007700

    PvuRts1I-family modified-HMC restriction realizes the organism-level PvuRts1I system possession trait.

  • PvuRts1I system is a type IV modification-dependent restriction system rdfs:subClassOf

    PvuRts1I system possession is a Type IV modification-dependent restriction system trait.

    • DOI:10.1093/nar/gkr607 Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes.
    • DOI:10.1093/nar/gkt747 The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1093/nar/gkr607

Parent traits (1)

Synonyms (1)

  • PvuRts1I RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.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 PvuRts1I-family breadth, 5hmC and 5ghmC target selectivity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower PvuRts1I mechanism or component traits.

KNOWLEDGE GAP OPEN pvurts1i-defensefinder-model-gap · raised by codex · 2026-10-01

Attached to causal_graphs#pvurts1i_restricts_modified_hmc_dna

Wang et al. support PvuRts1I as the founding member of a family of 5hmC- and 5ghmC-recognizing modification-dependent restriction endonucleases, and the pinned DefenseFinder article registry maps PvuRts1I to the Wang et al. paper. The pinned HMM inventory and rules table have no exact PvuRts1I rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of PvuRts1I-like systems across natural hosts, or the complete set of natural 5hmC and 5ghmC target contexts.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted PvuRts1I system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent 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_v388.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed PvuRts1I system during initial curation and left canonical_examples empty because Wang et al. support PvuRts1I and PvuRts1I-family enzymes, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level PvuRts1I system trait. No paid research was used.

  3. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #1514 adversarial review issue #1515 by tightening the PvuRts1I system definition to match the Wang et al. 3'-side cleavage evidence without claiming a fixed cleavage distance.