identifier: traitmech:000370 label: MADS system definition: A phage defense system in which an organism possesses a methylation-associated defense system locus whose canonical architecture has mad1 through mad8 genes and whose methylation-coupled self/non-self discrimination can restrict bacteriophage infection. definition_source: DOI:10.1016/j.chom.2024.07.005 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: MADS synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.chom.2024.07.005 - synonym_text: methylation-associated defense system synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.chom.2024.07.005 - synonym_text: MADS__mad1 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad3 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad4 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad5 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad6 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad7 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: MADS__mad8 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1016/j.chom.2024.07.005 snippet: coined methylation-associated defense system (MADS) notes: Maestri et al. coin methylation-associated defense system (MADS) for the newly discovered phage-defense locus. - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages notes: Maestri et al. show that native-host MADS and CRISPR-Cas cooperate to provide robust phage resistance. - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS encodes a defense system that is active against at least 4 different DNA phages notes: Maestri et al. support MADS activity against DMS3vir and three additional DNA phages. - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS uses a methylation-based self/non-self discrimination mechanism notes: Maestri et al. connect MADS to methylation-based self/non-self discrimination. - reference: DOI:10.1101/2023.03.30.534895 snippet: Bacterial defences interact synergistically by disrupting phage cooperation notes: The bioRxiv version of Maestri et al. is the DOI cited in DefenseFinder's MADS article-registry row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: MADS | 10\.1101/2023\.03\.30\.534895 | Bacterial defences interact synergistically by disrupting phage cooperation notes: The DefenseFinder article registry maps the named MADS system to the Maestri et al. preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "MADS\tMADS\t3\t3\tMADS__mad1, MADS__mad2, MADS__mad3, MADS__mad4, MADS__mad5,\ \ MADS__mad6, MADS__mad7, MADS__mad8\t\t\t" notes: The DefenseFinder rules table models MADS with MADS__mad1 through MADS__mad8 profiles and a minimum of three mandatory matches. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad1 | MADS__mad1 | MADS | Custom | 20 |' notes: The DefenseFinder HMM inventory records MADS__mad1 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad2 | MADS__mad2 | MADS | Custom | 150 |' notes: The DefenseFinder HMM inventory records MADS__mad2 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad3 | MADS__mad3 | MADS | Custom | 200 |' notes: The DefenseFinder HMM inventory records MADS__mad3 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad4 | MADS__mad4 | MADS | Custom | 50 |' notes: The DefenseFinder HMM inventory records MADS__mad4 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad5 | MADS__mad5 | MADS | Custom | 50 |' notes: The DefenseFinder HMM inventory records MADS__mad5 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad6 | MADS__mad6 | MADS | Custom | 150 |' notes: The DefenseFinder HMM inventory records MADS__mad6 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad7 | MADS__mad7 | MADS | Custom | 100 |' notes: The DefenseFinder HMM inventory records MADS__mad7 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad8 | MADS__mad8 | MADS | Custom | 100 |' notes: The DefenseFinder HMM inventory records MADS__mad8 under the MADS model namespace. canonical_examples: - taxon_id: NCBITaxon:287 taxon_label: Pseudomonas aeruginosa note: Maestri et al. discovered MADS in the native Pseudomonas aeruginosa SMC4386 locus and showed that deleting the locus reduced resistance to phage DMS3vir. reference: DOI:10.1016/j.chom.2024.07.005 causal_graphs: - graph_id: mads_methylation_restricts_phage title: MADS loci confer methylation-associated phage defense description: Conservative system-level sketch linking possession of a MADS locus to methylation-based self/non-self discrimination, restriction of DNA phages, and the MADS system trait. scope_status: NONMECHANISTIC scope_notes: The graph captures MADS as a named eight-gene DefenseFinder profile set whose activity is associated with methylation and DNA restriction while leaving the exact mapping from the MADS__mad profiles to nuclease, ATPase, kinase, specificity, and methyltransferase activities unresolved. nodes: - node_id: mads_locus label: MADS locus node_type: GENETIC_ELEMENT description: A methylation-associated phage-defense locus in the MADS family. - node_id: mads_self_nonself_discrimination label: MADS self/non-self discrimination node_type: BIOLOGICAL_PROCESS description: Methylation-based discrimination between host DNA and unmethylated mobile genetic element DNA by MADS. - node_id: dna_phage_restriction label: DNA phage restriction node_type: BIOLOGICAL_PROCESS description: Restriction of infecting DNA bacteriophages by the MADS locus. - node_id: mads_system_trait label: MADS system node_type: TRAIT grounding: traitmech:000370 description: Possession of a genome-encoded MADS phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: mads_locus predicate: contributes to predicate_id: RO:0002326 object: mads_self_nonself_discrimination description: MADS loci encode an eight-gene methylation-associated defense system, and DefenseFinder models MADS as an eight-profile rule with at least three mandatory matches. evidence: - reference: DOI:10.1016/j.chom.2024.07.005 snippet: coined methylation-associated defense system (MADS) notes: Maestri et al. coin methylation-associated defense system (MADS) for the newly discovered phage-defense locus. - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS uses a methylation-based self/non-self discrimination mechanism notes: Maestri et al. connect MADS to methylation-based self/non-self discrimination. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: MADS | 10\.1101/2023\.03\.30\.534895 | Bacterial defences interact synergistically by disrupting phage cooperation notes: The DefenseFinder article registry maps the named MADS system to the Maestri et al. preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "MADS\tMADS\t3\t3\tMADS__mad1, MADS__mad2, MADS__mad3, MADS__mad4,\ \ MADS__mad5, MADS__mad6, MADS__mad7, MADS__mad8\t\t\t" notes: The DefenseFinder rules table models MADS with MADS__mad1 through MADS__mad8 profiles and a minimum of three mandatory matches. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad1 | MADS__mad1 | MADS | Custom | 20 |' notes: The DefenseFinder HMM inventory records MADS__mad1 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad2 | MADS__mad2 | MADS | Custom | 150 |' notes: The DefenseFinder HMM inventory records MADS__mad2 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad3 | MADS__mad3 | MADS | Custom | 200 |' notes: The DefenseFinder HMM inventory records MADS__mad3 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad4 | MADS__mad4 | MADS | Custom | 50 |' notes: The DefenseFinder HMM inventory records MADS__mad4 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad5 | MADS__mad5 | MADS | Custom | 50 |' notes: The DefenseFinder HMM inventory records MADS__mad5 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad6 | MADS__mad6 | MADS | Custom | 150 |' notes: The DefenseFinder HMM inventory records MADS__mad6 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad7 | MADS__mad7 | MADS | Custom | 100 |' notes: The DefenseFinder HMM inventory records MADS__mad7 under the MADS model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| MADS__mad8 | MADS__mad8 | MADS | Custom | 100 |' notes: The DefenseFinder HMM inventory records MADS__mad8 under the MADS model namespace. - subject: mads_self_nonself_discrimination predicate: contributes to predicate_id: RO:0002326 object: dna_phage_restriction description: MADS-associated methylation-based self/non-self discrimination contributes to DNA-phage restriction. evidence: - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS uses a methylation-based self/non-self discrimination mechanism notes: Maestri et al. connect MADS to methylation-based self/non-self discrimination. - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS encodes a defense system that is active against at least 4 different DNA phages notes: Maestri et al. support MADS activity against DMS3vir and three additional DNA phages. - subject: dna_phage_restriction predicate: confers predicate_id: METPO:2007700 object: mads_system_trait description: MADS-mediated DNA-phage restriction realizes the MADS system trait. evidence: - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS encodes a defense system that is active against at least 4 different DNA phages notes: Maestri et al. support MADS activity against DMS3vir and three additional DNA phages. - subject: mads_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: MADS system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.chom.2024.07.005 snippet: coined methylation-associated defense system (MADS) notes: Maestri et al. coin methylation-associated defense system (MADS) for the newly discovered phage-defense locus. - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages notes: Maestri et al. show that native-host MADS and CRISPR-Cas cooperate to provide robust phage resistance. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: MADS | 10\.1101/2023\.03\.30\.534895 | Bacterial defences interact synergistically by disrupting phage cooperation notes: The DefenseFinder article registry maps the named MADS system to the Maestri et al. preprint. discussions: - discussion_id: mads-profile-activity-gap prompt: Resolve MADS subtype boundaries, MADS3-4 relationships, and Mad1-Mad8 profile-to-activity mappings before minting narrower MADS mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Maestri et al. support MADS as a methylation-associated defense system active against DNA phages, and DefenseFinder models MADS as an eight-profile rule. The pinned model does not resolve which combinations of MADS__mad profiles correspond to methylation, specificity, nuclease, ATPase, or kinase activities, so this first record stays at system level. evidence: - reference: DOI:10.1016/j.chom.2024.07.005 snippet: MADS encodes a defense system that is active against at least 4 different DNA phages notes: Maestri et al. support MADS activity against DMS3vir and three additional DNA phages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "MADS\tMADS\t3\t3\tMADS__mad1, MADS__mad2, MADS__mad3, MADS__mad4, MADS__mad5,\ \ MADS__mad6, MADS__mad7, MADS__mad8\t\t\t" notes: The DefenseFinder rules table models MADS with MADS__mad1 through MADS__mad8 profiles and a minimum of three mandatory matches. attaches_to: - causal_graphs#mads_methylation_restricts_phage posed_by: codex posed_date: '2026-09-24' curation_history: - timestamp: '2026-09-25T03:36:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted MADS system as a DOI-backed GENOMICS TraitRecord under phage defense system 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_v247. llm_assisted: true