identifier: traitmech:000513 label: TagI system definition: A type IV modification-dependent restriction system in which an organism possesses a TagI-family locus encoding an SRA-HNH restriction endonuclease that recognizes 5-methylcytosine- or 5-hydroxymethylcytosine-modified DNA. definition_source: DOI:10.1093/nar/gky781 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000496 synonyms: - synonym_text: TagI synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: PMID:30202937 snippet: TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). notes: Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family. - reference: PMID:30202937 snippet: Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers. notes: Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites. - reference: PMID:30202937 snippet: Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). notes: Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases. - reference: PMID:30202937 snippet: Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays. notes: Kisiala et al. support TagI modification dependence and phage restriction activity. - reference: PMID:30202937 snippet: The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base. notes: Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts. - 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: '| TagI | 10\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI | ' notes: The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural paper. causal_graphs: - graph_id: tagi_restricts_modified_cytosine_dna title: TagI restricts modified-cytosine DNA description: Conservative system-level sketch linking a TagI-family locus to 5mC/5hmC-dependent DNA restriction and to the Type IV restriction parent trait. scope_status: NONMECHANISTIC scope_notes: The graph captures TagI as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact modified-DNA sequence-context specificity across SRA-HNH homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved. nodes: - node_id: tagi_family_locus label: TagI-family locus node_type: GENETIC_ELEMENT description: A locus encoding a TagI-family SRA-HNH modification-dependent restriction endonuclease. - node_id: tagi_modified_cytosine_dna label: TagI-targeted modified-cytosine DNA node_type: ENVIRONMENTAL_FACTOR description: DNA containing 5-methylcytosine or 5-hydroxymethylcytosine in a TagI-family recognition context. - node_id: tagi_modified_cytosine_restriction label: TagI modified-cytosine DNA restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of 5mC/5hmC-modified DNA by a TagI-family endonuclease. - node_id: tagi_system_trait label: TagI system node_type: TRAIT grounding: traitmech:000513 description: Possession of a genome-encoded TagI-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: tagi_family_locus predicate: enables predicate_id: RO:0002327 object: tagi_modified_cytosine_restriction description: TagI-family loci encode SRA-HNH endonucleases that restrict 5mC/5hmC-modified DNA. evidence: - reference: PMID:30202937 snippet: Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers. notes: Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites. - reference: PMID:30202937 snippet: Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). notes: Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases. - subject: tagi_modified_cytosine_restriction predicate: mitigates predicate_id: METPO:2007407 object: tagi_modified_cytosine_dna description: TagI-family restriction targets 5mC- or 5hmC-modified DNA. evidence: - reference: PMID:30202937 snippet: Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). notes: Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases. - reference: PMID:30202937 snippet: Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays. notes: Kisiala et al. support TagI modification dependence and phage restriction activity. - reference: PMID:30202937 snippet: The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base. notes: Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts. - subject: tagi_modified_cytosine_restriction predicate: confers predicate_id: METPO:2007700 object: tagi_system_trait description: TagI-family modified-cytosine DNA restriction realizes the organism-level TagI system possession trait. evidence: - reference: PMID:30202937 snippet: TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). notes: Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TagI | 10\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI | ' notes: The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural paper. - subject: tagi_system_trait predicate: is a predicate_id: rdfs:subClassOf object: type_iv_modification_dependent_restriction description: TagI system possession is a Type IV modification-dependent restriction system trait. evidence: - reference: PMID:30202937 snippet: TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). notes: Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family. - 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: tagi-defensefinder-model-gap prompt: Resolve TagI-family breadth, modified-cytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower TagI mechanism or component traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Kisiala et al. support TagI as an SRA-HNH modification-dependent restriction endonuclease that recognizes 5mC/5hmC bases and restricts phage in assays. The pinned DefenseFinder article registry maps TagI to that paper, but the pinned HMM inventory and rules table have no exact TagI rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of TagI-like systems across natural hosts, or the complete set of natural modified-cytosine sequence contexts. evidence: - reference: PMID:30202937 snippet: TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). notes: Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family. - reference: PMID:30202937 snippet: Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers. notes: Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites. - reference: PMID:30202937 snippet: Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). notes: Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases. - reference: PMID:30202937 snippet: Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays. notes: Kisiala et al. support TagI modification dependence and phage restriction activity. - reference: PMID:30202937 snippet: The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base. notes: Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TagI | 10\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI | ' notes: The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural 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 TagI 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 TagI system row. attaches_to: - causal_graphs#tagi_restricts_modified_cytosine_dna posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T11:10:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted TagI system as a DOI/PMID- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v390. llm_assisted: true - timestamp: '2026-10-01T11:10:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed TagI system during initial curation and left canonical_examples empty because Kisiala et al. support the purified TagI enzyme, structure, and phage restriction assays, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level TagI system trait. No paid research was used. llm_assisted: true