TraitMech

TraitMech › GENOMICS

EcoKMcrA system

traitmech:000509 · CLASS · PROPOSED

A type IV modification-dependent restriction system in which an organism possesses an EcoKMcrA mcrA locus encoding a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease whose nuclease active site is required for efficient restriction of DNA modified in the correct sequence context.

Trait evidence (5)

  • DOI:10.1093/nar/gky731
    Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease.

    Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA.

  • DOI:10.1093/nar/gky731
    We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity

    Czapinska et al. experimentally demonstrated EcoKMcrA endonuclease activity in vitro.

  • DOI:10.1093/nar/gky731
    In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.

    Czapinska et al. support cellular modified-DNA restriction by EcoKMcrA and tie efficient restriction to the nuclease active site.

  • 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
    | EcoKMcrA | 10\.1093/nar/gky731 | Activity and structure of EcoKMcrA |

    The pinned DefenseFinder article registry maps the EcoKMcrA source key to the Czapinska et al. Activity and structure of EcoKMcrA paper.

EcoKMcrA restricts modified-cytosine DNA

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

NONMECHANISTIC · The graph captures EcoKMcrA as a named E. coli K-strain McrA Type IV modification-dependent restriction system while leaving EcoKMcrA-family breadth, sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.

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

Edge evidence

  • EcoKMcrA mcrA locus enables EcoKMcrA modified-DNA restriction RO:0002327

    The EcoKMcrA mcrA locus encodes a modified-cytosine-dependent restriction endonuclease.

    • DOI:10.1093/nar/gky731 Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease. Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA.
    • DOI:10.1093/nar/gky731 We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity Czapinska et al. experimentally demonstrated EcoKMcrA endonuclease activity in vitro.
  • EcoKMcrA modified-DNA restriction mitigates modified-cytosine DNA METPO:2007407

    EcoKMcrA-dependent Type IV restriction targets DNA modified in the correct sequence context.

    • DOI:10.1093/nar/gky731 Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest that the N-terminal domains can sense the presence and sequence context of modified cytosines. Czapinska et al. support EcoKMcrA sensing of the presence and sequence context of modified cytosines.
    • DOI:10.1093/nar/gky731 In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed. Czapinska et al. support cellular modified-DNA restriction by EcoKMcrA and tie efficient restriction to the nuclease active site.
  • EcoKMcrA modified-DNA restriction confers EcoKMcrA system METPO:2007700

    EcoKMcrA-dependent Type IV restriction realizes the organism-level EcoKMcrA system possession trait.

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

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

    • DOI:10.1093/nar/gky731 Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease. Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA.
    • 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/gky731

Parent traits (1)

Synonyms (1)

  • EcoKMcrA RELATED_SYNONYM · DOI:10.1093/nar/gky731

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 EcoKMcrA-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 EcoKMcrA mechanism or component traits.

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

Attached to causal_graphs#ecokmcra_restricts_modified_cytosine_dna

Czapinska et al. support E. coli EcoKMcrA as a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease with cellular modified-DNA restriction activity tied to the nuclease active site, and the pinned DefenseFinder article registry maps EcoKMcrA to that paper. The pinned HMM inventory and rules table have no exact EcoKMcrA rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of EcoKMcrA-like systems beyond E. coli K strains, or the complete set of natural methylcytosine and hydroxymethylcytosine sequence contexts.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted EcoKMcrA 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_v386.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed EcoKMcrA system during initial curation and left canonical_examples empty because Czapinska et al. support the E. coli K-strain EcoKMcrA enzyme and the DefenseFinder EcoKMcrA source key, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level EcoKMcrA system trait. No paid research was used.