identifier: traitmech:000511 label: PvuRts1I system definition: 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. definition_source: DOI:10.1093/nar/gkr607 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000496 synonyms: - synonym_text: PvuRts1I synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1093/nar/gkr607 snippet: Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. notes: Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes. - reference: DOI:10.1093/nar/gkr607 snippet: PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. notes: Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA. - reference: DOI:10.1093/nar/gkr607 snippet: We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. notes: 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. - reference: DOI:10.1093/nar/gkt747 snippet: The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. notes: Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| PvuRts1I | 10\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine | ' notes: The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper. causal_graphs: - graph_id: pvurts1i_restricts_modified_hmc_dna title: PvuRts1I restricts modified-HMC DNA description: Conservative system-level sketch linking a PvuRts1I-family locus to modified-hydroxymethylcytosine DNA restriction and to the Type IV restriction parent trait. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: pvurts1i_family_locus label: PvuRts1I-family locus node_type: GENETIC_ELEMENT description: A locus encoding a PvuRts1I-family modification-dependent restriction endonuclease. - node_id: pvurts1i_modified_hmc_dna label: PvuRts1I-targeted modified-HMC DNA node_type: ENVIRONMENTAL_FACTOR description: Double-stranded DNA containing 5hmC or 5ghmC in a PvuRts1I-family recognition context. - node_id: pvurts1i_modified_hmc_restriction label: PvuRts1I modified-HMC restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of 5hmC- or 5ghmC-containing DNA by a PvuRts1I-family endonuclease. - node_id: pvurts1i_system_trait label: PvuRts1I system node_type: TRAIT grounding: traitmech:000511 description: Possession of a genome-encoded PvuRts1I-family modification-dependent restriction system. - node_id: type_iv_modification_dependent_restriction label: type IV modification-dependent restriction system node_type: TRAIT grounding: traitmech:000496 description: Possession of a genome-encoded Type IV modification-dependent restriction system. edges: - subject: pvurts1i_family_locus predicate: enables predicate_id: RO:0002327 object: pvurts1i_modified_hmc_restriction description: PvuRts1I-family loci encode modification-dependent restriction endonucleases. evidence: - reference: DOI:10.1093/nar/gkr607 snippet: Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. notes: Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes. - reference: DOI:10.1093/nar/gkr607 snippet: We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. notes: 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. - subject: pvurts1i_modified_hmc_restriction predicate: mitigates predicate_id: METPO:2007407 object: pvurts1i_modified_hmc_dna description: PvuRts1I-family restriction targets DNA with 5hmC or 5ghmC modifications. evidence: - reference: DOI:10.1093/nar/gkr607 snippet: PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. notes: Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA. - reference: DOI:10.1093/nar/gkr607 snippet: We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. notes: 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. - subject: pvurts1i_modified_hmc_restriction predicate: confers predicate_id: METPO:2007700 object: pvurts1i_system_trait description: PvuRts1I-family modified-HMC restriction realizes the organism-level PvuRts1I system possession trait. evidence: - reference: DOI:10.1093/nar/gkr607 snippet: PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. notes: Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| PvuRts1I | 10\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine | ' notes: The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper. - subject: pvurts1i_system_trait predicate: is a predicate_id: rdfs:subClassOf object: type_iv_modification_dependent_restriction description: PvuRts1I system possession is a Type IV modification-dependent restriction system trait. evidence: - reference: DOI:10.1093/nar/gkr607 snippet: Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. notes: Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes. - reference: DOI:10.1093/nar/gkt747 snippet: The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. notes: Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes. discussions: - discussion_id: pvurts1i-defensefinder-model-gap prompt: 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. kind: KNOWLEDGE_GAP status: OPEN rationale: 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: - reference: DOI:10.1093/nar/gkr607 snippet: Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. notes: Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes. - reference: DOI:10.1093/nar/gkr607 snippet: PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. notes: Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA. - reference: DOI:10.1093/nar/gkr607 snippet: We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. notes: 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. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| PvuRts1I | 10\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine | ' notes: The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact PvuRts1I row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: A structured first-pass search of the pinned DefenseFinder rules table found no exact PvuRts1I system row. attaches_to: - causal_graphs#pvurts1i_restricts_modified_hmc_dna posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T09:01:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-10-01T09:01:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 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. llm_assisted: true - timestamp: '2026-10-01T09:28:12Z' curator: codex action: ADVERSARIAL_REVIEW_REPAIR changes: '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.' llm_assisted: true