TraitMech

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GmrSD system

traitmech:000506 · CLASS · PROPOSED

A type IV modification-dependent restriction system in which an organism possesses a GmrSD locus encoding either separate GmrS and GmrD proteins or a fused double-domain GmrSD-family protein, that targets glucosylated hydroxymethylcytosine-containing DNA.

Trait evidence (7)

  • DOI:10.1016/j.jmb.2006.11.051
    The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.

    Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA.

  • DOI:10.1016/j.jmb.2006.11.051
    Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins.

    Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity.

  • DOI:10.1186/s12859-015-0773-z
    GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA.

    Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease.

  • DOI:10.1186/s12859-015-0773-z
    It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains.

    Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family.

  • DOI:10.1186/s12859-015-0773-z
    Moreover, we found that GmrSD systems exist predominantly as a fused, double-domain form rather than as a heterodimer and that their homologs are often encoded in regions enriched in defense and gene mobility-related elements.

    Machnicka et al. report that fused double-domain GmrSD systems are common and are often found near defense- and mobility-linked features.

  • 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
    | GmrSD_RM_Type_IV | 10\.1016/j\.jmb\.2006\.11\.051 | A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs |

    The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black.

GmrSD restricts glucosylated HMC DNA

Conservative system-level sketch linking a GmrSD locus to modification-dependent restriction of glucosylated hydroxymethylcytosine DNA and to the Type IV restriction parent trait.

NONMECHANISTIC · The graph captures GmrSD as a named Type IV modification-dependent restriction system while leaving GmrS/GmrD domain activities, complete sugar-HMC substrate breadth, split-versus-fused host breadth, IPI inhibition, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.

GmrSD restricts glucosylated HMC DNA Interactive directed graph showing evidence-backed causal relationships for GmrSD system.

Edge evidence

  • GmrSD locus enables GmrSD-dependent Type IV restriction RO:0002327

    The GmrSD locus encodes the proteins that cleave glucosylated hydroxymethylcytosine DNA.

    • DOI:10.1016/j.jmb.2006.11.051 Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins. Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity.
    • DOI:10.1186/s12859-015-0773-z It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family.
  • GmrSD-dependent Type IV restriction mitigates glucosylated HMC DNA METPO:2007407

    GmrSD-dependent Type IV restriction targets glucosylated hydroxymethylcytosine DNA.

    • DOI:10.1016/j.jmb.2006.11.051 The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs. Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA.
    • DOI:10.1186/s12859-015-0773-z GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease.
  • GmrSD-dependent Type IV restriction confers GmrSD system METPO:2007700

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

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

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

    • DOI:10.1016/j.jmb.2006.11.051 The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs. Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine 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:10.1016/j.jmb.2006.11.051

Parent traits (1)

Synonyms (2)

  • GmrSD EXACT_SYNONYM · DOI:10.1016/j.jmb.2006.11.051
  • GmrSD_RM_Type_IV 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 exact GmrS/GmrD domain activities, complete sugar-modified HMC substrate breadth, split-versus-fused host breadth, phage IPI inhibition, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower GmrSD mechanism or component traits.

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

Attached to causal_graphs#gmrsd_restricts_glucosylated_hmc_dna

Bair and Black support split GmrS/GmrD as a Type IV modification-dependent restriction nuclease that targets glucosylated hydroxymethylcytosine DNA, Machnicka et al. support GmrSD homologs as either split or fused double-domain systems, and the pinned DefenseFinder article registry maps GmrSD_RM_Type_IV to Bair and Black. The pinned HMM inventory and rules table have no exact GmrSD or GmrSD_RM_Type_IV rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact split-versus-fused prevalence across natural hosts, the complete set of sugar-modified HMC targets, the exact domain contributions of GmrS and GmrD, or the relationship between phage IPI inhibition and the organism-level GmrSD system trait.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted GmrSD 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_v383.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed GmrSD system during initial curation and left canonical_examples empty because the Bair and Black and Machnicka et al. sources support the split CT596 GmrSD enzyme and broader split-or-fused GmrSD family, but not a single stable NCBITaxon strain exemplar for the organism-level GmrSD system trait. No paid research was used.