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MspJI system

traitmech:000510 · CLASS · PROPOSED

A type IV modification-dependent restriction system in which an organism possesses an MspJI-family Mrr-like locus encoding a restriction endonuclease that recognizes methylcytosine- or hydroxymethylcytosine-modified DNA and cleaves both strands at a fixed distance from the modified cytosine.

Trait evidence (5)

  • DOI:10.1073/pnas.1018448108
    MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site.

    Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target.

  • DOI:10.1073/pnas.1018448108
    All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine.

    Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases.

  • DOI:10.1093/nar/gkq327
    Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine.

    Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved.

  • 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
    | MspJI | 10\.1073/pnas\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies |

    The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper.

MspJI restricts modified-cytosine DNA

Conservative system-level sketch linking an MspJI-family locus to modified-cytosine DNA restriction and to the Type IV restriction parent trait.

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

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

Edge evidence

  • MspJI-family locus enables MspJI modified-cytosine restriction RO:0002327

    MspJI-family loci encode Mrr-like modification-dependent restriction endonucleases.

    • DOI:10.1073/pnas.1018448108 MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target.
    • DOI:10.1073/pnas.1018448108 All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases.
  • MspJI modified-cytosine restriction mitigates MspJI-targeted modified-cytosine DNA METPO:2007407

    MspJI-family restriction targets methylcytosine- or hydroxymethylcytosine-containing DNA.

    • DOI:10.1073/pnas.1018448108 All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases.
    • DOI:10.1093/nar/gkq327 Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved.
  • MspJI modified-cytosine restriction confers MspJI system METPO:2007700

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

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

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

    • DOI:10.1073/pnas.1018448108 MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target.
    • 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:10.1073/pnas.1018448108

Parent traits (1)

Synonyms (1)

  • MspJI 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 MspJI-family breadth, methylcytosine and hydroxymethylcytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower MspJI mechanism or component traits.

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

Attached to causal_graphs#mspji_restricts_modified_cytosine_dna

Zheng et al. support MspJI as a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease, Cohen-Karni et al. support MspJI homologs as a family of C5-modified-cytosine-dependent restriction endonucleases, and the pinned DefenseFinder article registry maps MspJI to the Cohen-Karni et al. paper. The pinned HMM inventory and rules table have no exact MspJI rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of MspJI-like systems across natural hosts, or the complete set of natural methylcytosine and hydroxymethylcytosine sequence contexts.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted MspJI 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_v387.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

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