identifier: traitmech:000095 label: restriction-modification system definition: A genomics trait describing possession of a restriction-modification system that distinguishes self from non-self DNA through sequence-specific methylation and cleavage of unmethylated DNA by a restriction endonuclease. definition_source: DOI:10.1128/MMBR.00044-12 trait_category: GENOMICS term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000188 synonyms: - synonym_text: R-M system synonym_type: RELATED_SYNONYM source: DOI:10.1128/MMBR.00044-12 evidence: - reference: DOI:10.1128/MMBR.00044-12 notes: Vasu & Nagaraja review restriction-modification systems and their defense and additional cellular functions. - reference: DOI:10.3389/fmicb.2015.00528 notes: Review of restriction-modification systems as engines of genomic diversity. canonical_examples: - taxon_id: NCBITaxon:727 taxon_label: Haemophilus influenzae note: "Source of HindII, the first type II restriction endonuclease characterized; classic restriction-modification model." reference: PMID:5312500 causal_graphs: - graph_id: rm_self_nonself_defense title: Restriction-modification distinguishes self from non-self DNA description: Evidence-backed causal sketch linking R-M system possession to sequence-specific cleavage of unmethylated foreign DNA. nodes: - node_id: rm_trait label: restriction-modification system node_type: TRAIT grounding: traitmech:000095 description: Possession of a paired methyltransferase / restriction endonuclease defense system. - node_id: dna_restriction_modification label: DNA restriction-modification system node_type: BIOLOGICAL_PROCESS grounding: GO:0009307 description: Sequence-specific methylation marking self DNA and cleavage of unmethylated foreign DNA. - node_id: foreign_dna label: foreign DNA node_type: ENVIRONMENTAL_FACTOR description: Invading phage or plasmid DNA challenging the cell. - node_id: cognate_mtase label: cognate DNA methyltransferase node_type: GENE_OR_PROTEIN description: Methyltransferase that methylates the host recognition sites of an R-M system. - node_id: host_site_methylation label: host recognition site methylation node_type: BIOLOGICAL_PROCESS description: Methylation marking self DNA at R-M recognition sites. - node_id: restriction_endonuclease label: restriction endonuclease node_type: GENE_OR_PROTEIN description: Endonuclease that cleaves unmethylated double-stranded DNA at recognition sites. grounding: UniProtKB:A0A015ZKG4 - node_id: endonuclease_cleavage label: restriction endonuclease cleavage node_type: MOLECULAR_FUNCTION description: Sequence-specific cleavage activity of the restriction endonuclease. - node_id: type_iv_restriction_enzyme label: type IV restriction enzyme node_type: GENE_OR_PROTEIN description: Modification-dependent restriction enzyme that cleaves methylated DNA motifs. - node_id: methylated_dna_motif label: methylated DNA motif node_type: CHEMICAL description: DNA motif carrying a methyl or other base modification, targeted by type IV enzymes. - node_id: plasmid_methylase label: plasmid-encoded methylase node_type: GENE_OR_PROTEIN description: Methyltransferase encoded by a mobile element that pre-methylates its DNA to evade host restriction. - node_id: phage_mtase label: phage-encoded DNA methyltransferase node_type: GENE_OR_PROTEIN description: Phage methyltransferase that methylates the phage genome to counter host restriction. edges: - subject: rm_trait predicate: enables object: dna_restriction_modification description: R-M systems realize self-vs-non-self discrimination by paired methylation and restriction. evidence: - reference: DOI:10.1128/MMBR.00044-12 notes: Vasu & Nagaraja review R-M systems and their defense functions. predicate_id: RO:0002327 - subject: dna_restriction_modification predicate: mitigates object: foreign_dna description: Restriction endonuclease cleavage destroys unmethylated foreign DNA before it can establish. evidence: - reference: DOI:10.3389/fmicb.2015.00528 notes: R-M systems as engines of genomic diversity through differential cleavage of foreign DNA. predicate_id: METPO:2007407 - subject: cognate_mtase predicate: methylates object: host_site_methylation description: The cognate methyltransferase methylates host recognition sites, marking self DNA. evidence: - reference: DOI:10.1093/nar/gkad452 notes: A methyltransferase methylates those sites to protect host DNA (shaw2023). - subject: host_site_methylation predicate: protects against object: endonuclease_cleavage description: Methylation of host recognition sites protects self DNA from cognate restriction endonuclease cleavage. evidence: - reference: DOI:10.1093/nar/gkad452 notes: Host DNA is protected while incoming foreign DNA lacking the same methylation is cleaved (shaw2023). - subject: restriction_endonuclease predicate: has function object: endonuclease_cleavage description: The restriction endonuclease cleaves unmethylated foreign double-stranded DNA. evidence: - reference: DOI:10.1093/nar/gkad452 notes: A restriction endonuclease cuts double-stranded DNA; unmethylated foreign DNA is cleaved (shaw2023). predicate_id: RO:0000085 - subject: endonuclease_cleavage predicate: mitigates object: foreign_dna description: Restriction endonuclease cleavage destroys unmethylated foreign DNA. evidence: - reference: DOI:10.1093/nar/gkad452 notes: Incoming foreign DNA lacking host methylation is cleaved (shaw2023). predicate_id: METPO:2007407 - subject: type_iv_restriction_enzyme predicate: cleaves object: methylated_dna_motif description: Type IV restriction enzymes cleave methylated DNA motifs, complementing Types I-III that cleave unmethylated DNA. evidence: - reference: DOI:10.3390/microorganisms11122962 notes: Type IV enzymes cut methylated motifs (kottenhahn2023). - subject: plasmid_methylase predicate: protects against object: endonuclease_cleavage description: Plasmid-encoded methylases pre-methylate plasmid DNA, protecting it from host restriction activity. evidence: - reference: DOI:10.1093/nar/gkae896 notes: Some plasmids encode methylases that protect against restriction activity (dimitriu2024). - subject: phage_mtase predicate: protects against object: endonuclease_cleavage description: Phage-encoded DNA methyltransferases methylate the phage genome to reduce host RM restriction. evidence: - reference: DOI:10.1128/MMBR.00044-12 notes: Phages encode DNA methyltransferases to protect their genomes from restriction (vasu2013). curation_history: - timestamp: '2026-06-05T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate GENOMICS trait (restriction-modification system) from literature research to fill the genome-defense-system gap. llm_assisted: true - timestamp: '2026-06-08T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (R-M self / non-self defense) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:11Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0000085×1, METPO:2007407×1). llm_assisted: true - timestamp: '2026-06-26T07:15:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A015ZKG4×1). llm_assisted: true