identifier: traitmech:000307 label: Brig1 system definition: A phage defense system in which an organism possesses a brig1-family locus whose encoded DNA glycosylase can excise alpha-glucosyl-hydroxymethylcytosine nucleobases from T-even bacteriophage DNA, generate abasic sites, and inhibit viral DNA replication. definition_source: DOI:10.1038/s41586-024-07329-9 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Brig1 synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-024-07329-9 - synonym_text: bacteriophage replication inhibition DNA glycosylase 1 synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-024-07329-9 evidence: - reference: DOI:10.1038/s41586-024-07329-9 snippet: Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication notes: Hallinan et al. identify Brig1 as a phage DNA-targeting DNA glycosylase. - reference: DOI:10.1038/s41586-024-07329-9 snippet: Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria notes: Hallinan et al. support modelling Brig1 as a bacterial phage-defence locus family rather than as one cloned environmental DNA insert. - reference: DOI:10.1038/s41586-024-07329-9 snippet: This result demonstrates that gene c not only inhibits T4 DNA replication but also causes a slight and gradual depletion of the phage DNA within the infected population notes: Hallinan et al. connect the gene later named brig1 to inhibited T4 DNA replication in infected cells. - reference: DOI:10.1038/s41586-024-07329-9 snippet: We named this gene bacteriophage replication inhibition DNA glycosylase 1 (brig1) notes: Hallinan et al. explicitly expand brig1 as bacteriophage replication inhibition DNA glycosylase 1. - reference: DOI:10.1038/s41586-024-07329-9 snippet: Together, these data demonstrate that Brig1 targets α-glucosylated hmC nucleobases in the viral DNA to provide defence against T4 notes: Hallinan et al. show that Brig1 defense is specific to alpha-glucosylated hydroxymethylcytosine in phage DNA. - reference: DOI:10.1038/s41586-024-07329-9 snippet: Together, these results demonstrate that Brig1 is a DNA glycosylase that excises α-glucosyl-hmC nucleobases from ssDNA to generate abasic sites notes: Hallinan et al. directly verify that Brig1 DNA glycosylase activity creates abasic sites on alpha-glucosyl-hmC-containing substrates. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Brig1 | 10\.1038/s41586-024-07329-9 | DNA glycosylases provide antiviral defence in prokaryotes notes: The DefenseFinder article registry maps the named Brig1 model namespace to the Hallinan et al. Brig1 DNA-glycosylase paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Brig1__Brig1 | | Brig1 | Custom | 20 |' notes: The DefenseFinder HMM inventory records Brig1__Brig1 under the Brig1 model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Brig1__ADP_ribosyl | | Brig1 | Custom | 20 |' notes: The DefenseFinder HMM inventory records Brig1__ADP_ribosyl under the Brig1 model namespace. causal_graphs: - graph_id: brig1_locus_restricts_t_even_phages title: Brig1 loci restrict T-even phage propagation description: Conservative locus-level sketch linking a brig1-family DefenseFinder locus to halted T4-like phage replication, restricted T-even phage propagation, and the Brig1 phage-defense-system trait. scope_status: NONMECHANISTIC scope_notes: The graph captures Brig1 as a named DefenseFinder DNA-glycosylase phage-defense system at locus level and deliberately defers a protein-resolved glycosylase mechanism. Hallinan et al. characterized the prototype Brig1 DNA glycosylase, alpha-glucosyl-hmC base excision, and abasic-site generation, but the natural host, accession-level Brig1-family proteins, broader substrate specificity, and the relationship of the DefenseFinder Brig1__ADP_ribosyl profile to characterized Brig1 activity remain unresolved. nodes: - node_id: brig1_locus label: brig1 locus node_type: GENETIC_ELEMENT description: A brig1-family phage-defense locus represented by the DefenseFinder Brig1 model namespace. - node_id: halted_phage_replication label: halted phage replication node_type: BIOLOGICAL_PROCESS description: Arrest of T-even bacteriophage DNA replication downstream of Brig1 locus expression. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced completion of phage propagation in a Brig1-containing infected host cell. - node_id: brig1_system_trait label: Brig1 system node_type: TRAIT grounding: traitmech:000307 description: Possession of a genome-encoded Brig1 DNA-glycosylase phage-defense system. - node_id: phage_defense_system_trait 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: brig1_locus predicate: contributes to predicate_id: RO:0002326 object: halted_phage_replication description: Expression of the gene later named brig1 inhibits T4 phage DNA replication, and DefenseFinder catalogs Brig1 profiles for Brig1-family loci. evidence: - reference: DOI:10.1038/s41586-024-07329-9 snippet: gene c not only inhibits T4 DNA replication but also causes a slight and gradual depletion of the phage DNA within the infected population notes: Hallinan et al. connect brig1 expression to inhibited T4 DNA replication in infected cells. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Brig1__Brig1 | | Brig1 | Custom | 20 |' notes: The DefenseFinder HMM inventory records Brig1__Brig1 under the Brig1 model namespace. - subject: halted_phage_replication predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: Brig1-associated inhibition of T4-like phage replication restricts T-even phage propagation after infection. evidence: - reference: DOI:10.1038/s41586-024-07329-9 snippet: Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria notes: Hallinan et al. connect Brig1-associated T4 replication inhibition to the broader Brig1-family T-even immunity phenotype. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: brig1_system_trait description: Restriction of T-even phage propagation realizes the Brig1 system trait. evidence: - reference: DOI:10.1038/s41586-024-07329-9 snippet: Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria notes: Hallinan et al. frame Brig1 homologues as a bacterial phage-defense locus family. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Brig1 | 10\.1038/s41586-024-07329-9 | DNA glycosylases provide antiviral defence in prokaryotes notes: The DefenseFinder article registry maps the named Brig1 model namespace to the Hallinan et al. Brig1 DNA-glycosylase paper. - subject: brig1_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system_trait description: Brig1 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41586-024-07329-9 snippet: Brig1, a previously unknown anti-phage defence system with homologues across distinct clades of bacteria notes: The Hallinan et al. editor summary places Brig1 in the anti-phage defense system class. discussions: - discussion_id: brig1-natural-host-and-profile-gap prompt: Resolve natural Brig1 host taxa, broader Brig1-family specificity, and the Brig1__ADP_ribosyl DefenseFinder profile before minting narrower Brig1 children, adding canonical examples, or curating the protein-resolved glycosylase mechanism. kind: KNOWLEDGE_GAP status: OPEN rationale: Hallinan et al. functionally isolated the first brig1 gene from a soil metagenomic fragment rather than a sequenced natural isolate, and they showed that experimentally tested Brig1 homologues can protect against T-even phages. The first TraitRecord therefore covers Brig1-family antiphage DNA-glycosylase-system possession at locus level while leaving natural host exemplars, accession-level Brig1-family proteins, the protein-grounded glycosylase mechanism, the full sequence-level system architecture, and the relationship between the DefenseFinder Brig1__Brig1 and Brig1__ADP_ribosyl profiles to separate subtype review. evidence: - reference: DOI:10.1038/s41586-024-07329-9 snippet: To uncover novel anti-phage defence systems present in unsequenced bacterial genomes, we screened an eDNA library generated in an earlier study notes: Hallinan et al. functionally isolated the first Brig1 source fragment from an environmental DNA library rather than a named natural organism. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Brig1__ADP_ribosyl | | Brig1 | Custom | 20 |' notes: The DefenseFinder HMM inventory records Brig1__ADP_ribosyl under the Brig1 model namespace. attaches_to: - causal_graphs#brig1_locus_restricts_t_even_phages posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T10:37:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Brig1 system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v184. llm_assisted: true - timestamp: '2026-09-20T11:12:00Z' curator: codex action: ADDRESSED_PR_REVIEW changes: 'Resolved PR #1130 review issues #1131, #1132, #1133, and #1134 by narrowing the Brig1 graph to a locus-level DefenseFinder sketch, quoting the brig1 naming sentence, removing weak edge evidence, and reusing halted phage replication instead of adding a singleton replication node.' llm_assisted: true