TraitMech

TraitMech › GENOMICS

TagI system

traitmech:000513 · CLASS · PROPOSED

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.

Trait evidence (7)

  • PMID:30202937
    TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1).

    Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family.

  • PMID:30202937
    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.

    Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites.

  • PMID:30202937
    Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).

    Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases.

  • PMID:30202937
    Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays.

    Kisiala et al. support TagI modification dependence and phage restriction activity.

  • PMID:30202937
    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.

    Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts.

  • 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
    | TagI | 10\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI |

    The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural paper.

TagI restricts modified-cytosine DNA

Conservative system-level sketch linking a TagI-family locus to 5mC/5hmC-dependent DNA restriction and to the Type IV restriction parent trait.

NONMECHANISTIC · 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.

TagI restricts modified-cytosine DNA Interactive directed graph showing evidence-backed causal relationships for TagI system.

Edge evidence

  • TagI-family locus enables TagI modified-cytosine DNA restriction RO:0002327

    TagI-family loci encode SRA-HNH endonucleases that restrict 5mC/5hmC-modified DNA.

    • PMID:30202937 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. Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites.
    • PMID:30202937 Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases.
  • TagI modified-cytosine DNA restriction mitigates TagI-targeted modified-cytosine DNA METPO:2007407

    TagI-family restriction targets 5mC- or 5hmC-modified DNA.

    • PMID:30202937 Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases.
    • PMID:30202937 Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays. Kisiala et al. support TagI modification dependence and phage restriction activity.
    • PMID:30202937 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. Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts.
  • TagI modified-cytosine DNA restriction confers TagI system METPO:2007700

    TagI-family modified-cytosine DNA restriction realizes the organism-level TagI system possession trait.

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

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

    • PMID:30202937 TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family.
    • 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/gky781

Parent traits (1)

Synonyms (1)

  • TagI 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 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.

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

Attached to causal_graphs#tagi_restricts_modified_cytosine_dna

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    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.