identifier: traitmech:000506 label: GmrSD system definition: 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. definition_source: DOI:10.1016/j.jmb.2006.11.051 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000496 synonyms: - synonym_text: GmrSD synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.jmb.2006.11.051 - synonym_text: GmrSD_RM_Type_IV synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: 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. notes: Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA. - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins. notes: Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity. - reference: DOI:10.1186/s12859-015-0773-z snippet: GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. notes: Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease. - reference: DOI:10.1186/s12859-015-0773-z snippet: It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. notes: Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family. - reference: DOI:10.1186/s12859-015-0773-z snippet: 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. notes: Machnicka et al. report that fused double-domain GmrSD systems are common and are often found near defense- and mobility-linked features. - 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: '| 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 | ' notes: The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black. causal_graphs: - graph_id: gmrsd_restricts_glucosylated_hmc_dna title: GmrSD restricts glucosylated HMC DNA description: Conservative system-level sketch linking a GmrSD locus to modification-dependent restriction of glucosylated hydroxymethylcytosine DNA and to the Type IV restriction parent trait. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: gmrsd_locus label: GmrSD locus node_type: GENETIC_ELEMENT description: A locus encoding split GmrS and GmrD proteins or a fused double-domain GmrSD-family protein. - node_id: glucosylated_hmc_dna label: glucosylated HMC DNA node_type: ENVIRONMENTAL_FACTOR description: DNA containing glucosylated hydroxymethylcytosine base modifications. - node_id: gmrsd_dependent_type_iv_restriction label: GmrSD-dependent Type IV restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of glucosylated-hydroxymethylcytosine DNA by GmrSD. - node_id: gmrsd_system_trait label: GmrSD system node_type: TRAIT grounding: traitmech:000506 description: Possession of a genome-encoded GmrSD 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: gmrsd_locus predicate: enables predicate_id: RO:0002327 object: gmrsd_dependent_type_iv_restriction description: The GmrSD locus encodes the proteins that cleave glucosylated hydroxymethylcytosine DNA. evidence: - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins. notes: Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity. - reference: DOI:10.1186/s12859-015-0773-z snippet: It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. notes: Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family. - subject: gmrsd_dependent_type_iv_restriction predicate: mitigates predicate_id: METPO:2007407 object: glucosylated_hmc_dna description: GmrSD-dependent Type IV restriction targets glucosylated hydroxymethylcytosine DNA. evidence: - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: 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. notes: Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA. - reference: DOI:10.1186/s12859-015-0773-z snippet: GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. notes: Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease. - subject: gmrsd_dependent_type_iv_restriction predicate: confers predicate_id: METPO:2007700 object: gmrsd_system_trait description: GmrSD-dependent Type IV restriction realizes the organism-level GmrSD system possession trait. evidence: - reference: DOI:10.1186/s12859-015-0773-z snippet: GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. notes: Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| 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 | ' notes: The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black. - subject: gmrsd_system_trait predicate: is a predicate_id: rdfs:subClassOf object: type_iv_modification_dependent_restriction description: GmrSD system possession is a Type IV modification-dependent restriction system trait. evidence: - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: 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. notes: Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA. - 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: gmrsd-defensefinder-model-gap prompt: 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. kind: KNOWLEDGE_GAP status: OPEN rationale: 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: - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: 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. notes: Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA. - reference: DOI:10.1016/j.jmb.2006.11.051 snippet: Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins. notes: Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity. - reference: DOI:10.1186/s12859-015-0773-z snippet: GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. notes: Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease. - reference: DOI:10.1186/s12859-015-0773-z snippet: It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. notes: Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family. - reference: DOI:10.1186/s12859-015-0773-z snippet: 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. notes: Machnicka et al. report that fused double-domain GmrSD systems are common and are often found near defense- and mobility-linked features. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| 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 | ' notes: The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black. - 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 GmrSD or GmrSD_RM_Type_IV 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 GmrSD or GmrSD_RM_Type_IV system row. attaches_to: - causal_graphs#gmrsd_restricts_glucosylated_hmc_dna posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T04:21:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-10-01T04:21:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 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. llm_assisted: true