identifier: traitmech:000219 label: Hachiman system definition: A phage defense system in which an organism possesses a Hachiman antiphage locus encoding a HamA/HamB core. definition_source: DOI:10.1016/j.cell.2024.09.020 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Hachiman antiphage defense system synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.cell.2024.09.020 - synonym_text: Hachiman defense system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-025-57851-1 evidence: - reference: DOI:10.1016/j.cell.2024.09.020 snippet: Hachiman is a broad-spectrum antiphage defense system of unknown function notes: Tuck et al. support Hachiman as a named broad-spectrum antiphage system. - reference: DOI:10.1016/j.cell.2024.09.020 snippet: Hachiman is a heterodimeric nuclease-helicase complex, HamAB notes: Tuck et al. support the HamA/HamB nuclease-helicase core of characterized Hachiman systems. - reference: DOI:10.1016/j.cell.2024.09.020 snippet: When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity notes: Tuck et al. connect HamB helicase activity with HamA nuclease activation after DNA-damage detection. - reference: DOI:10.1016/j.cell.2024.09.020 snippet: Hachiman activation degrades all DNA in the cell, creating "phantom" cells devoid of both phage and host DNA notes: Tuck et al. support nonspecific DNA degradation as the type I-A Hachiman antiviral output. - reference: DOI:10.1038/s41467-025-57851-1 snippet: The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins notes: Cui et al. support the recurring Hachiman system name and its HamA/HamB composition. - reference: DOI:10.1038/s41467-025-57851-1 snippet: HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage, thus implementing antiphage defense notes: Cui et al. support a type I-B HamAB heterodimer that couples ATP hydrolysis to antiphage DNA cleavage. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: Tuck et al. identified Hachiman loci in E. coli ECOR04, ECOR28, and ECOR31, and showed that ECOR31 HamAB reduced plaquing by diverse double-stranded DNA phages. reference: DOI:10.1016/j.cell.2024.09.020 causal_graphs: - graph_id: hachiman_hamab_dna_cleavage title: Hachiman HamAB complexes cleave DNA during antiphage defense description: Evidence-backed process sketch linking a Hachiman locus to HamAB nuclease-helicase activity, cellular DNA degradation, and inhibition of bacteriophage progeny production. scope_status: NONMECHANISTIC scope_notes: The graph captures characterized type I-A and type I-B Hachiman nuclease-helicase outputs without asserting one universal DNA-damage trigger, DNA substrate, active nuclease domain, HamC accessory role, Cap4 architecture, phage breadth, or abortive-infection pathway across all Hachiman loci. nodes: - node_id: hachiman_locus label: Hachiman locus node_type: GENETIC_ELEMENT description: A Hachiman antiphage locus encoding a HamA/HamB core. This graph describes characterized type-I systems, not the HamC-containing type-II architecture represented by traitmech:000574. - node_id: hamab_complex_assembly label: HamAB complex assembly node_type: BIOLOGICAL_PROCESS description: Formation of a Hachiman HamA/HamB nuclease-helicase complex capable of ATP-dependent DNA processing. - node_id: hachiman_dna_cleavage label: Hachiman DNA cleavage node_type: BIOLOGICAL_PROCESS description: HamAB-mediated cleavage or degradation of DNA during Hachiman activation. - node_id: phage_particle_production label: phage particle production node_type: BIOLOGICAL_PROCESS description: Production of new infectious bacteriophage particles inside an infected bacterial host. - node_id: hachiman_system_trait label: Hachiman system node_type: TRAIT grounding: traitmech:000219 description: Possession of a genome-encoded Hachiman antiphage defense locus. - 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: hachiman_locus predicate: contributes to predicate_id: RO:0002326 object: hamab_complex_assembly description: Hachiman loci encode HamA and HamB components that assemble into HamAB nuclease-helicase complexes. evidence: - reference: DOI:10.1016/j.cell.2024.09.020 snippet: One such system is Hachiman, a two-gene locus encoding HamA notes: Tuck et al. support HamA/HamB as the two-gene Hachiman locus core. - reference: DOI:10.1038/s41467-025-57851-1 snippet: The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins notes: Cui et al. also support HamA/HamB as the core Hachiman components. - subject: hamab_complex_assembly predicate: enables predicate_id: RO:0002327 object: hachiman_dna_cleavage description: HamA/HamB complexation enables ATP-dependent DNA cleavage by Hachiman systems. evidence: - reference: DOI:10.1016/j.cell.2024.09.020 snippet: When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity notes: Tuck et al. connect HamAB activation with HamA nuclease activity. - reference: DOI:10.1038/s41467-025-57851-1 snippet: HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage notes: Cui et al. support ATP-hydrolysis-coupled DNA cleavage by a type I-B HamAB heterodimer. - subject: hachiman_dna_cleavage predicate: mitigates predicate_id: METPO:2007407 object: phage_particle_production description: Hachiman-mediated DNA degradation inhibits the generation of new phage particles. evidence: - reference: DOI:10.1016/j.cell.2024.09.020 snippet: Hachiman activation degrades all DNA in the cell notes: Tuck et al. support DNA degradation as the activated Hachiman output. - reference: DOI:10.1016/j.cell.2024.09.020 snippet: We confirmed that Hachiman limits the production of new phage particles notes: Tuck et al. connect Hachiman activity to restriction of phage progeny production. - subject: hachiman_dna_cleavage predicate: confers predicate_id: METPO:2007700 object: hachiman_system_trait description: HamAB-mediated DNA cleavage is the antiviral output that realizes the Hachiman system trait. evidence: - reference: DOI:10.1038/s41467-025-57851-1 snippet: execute DNA cleavage, thus implementing antiphage defense notes: Cui et al. support DNA cleavage as an antiphage output of the Hachiman complex. - subject: hachiman_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Hachiman system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41467-025-57851-1 snippet: The Hachiman system is a novel prokaryotic antiphage defense system notes: Cui et al. place Hachiman in the antiphage-defense-system family. discussions: - discussion_id: hachiman-subtype-and-trigger-gap prompt: Resolve Hachiman subtype effectors, DNA substrates, and activation triggers before minting narrower Hachiman mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Tuck et al. support DNA-damage-triggered type I-A HamAB activation and Cui et al. support type I-B HamAB ATPase and DNA-cleavage activity, but Hachiman variants need separate review before TraitMech asserts one universal triggering DNA substrate, HamA catalytic domain, HamC accessory role, Cap4 fusion architecture, phage range, or abortive-infection output. Hachiman type II system (traitmech:000574) now resolves the HamABC architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and retained by Cui et al. The DSM 14551 locus has heterologous antiphage evidence, but HamC function and type-II mechanism remain open. The family definition no longer requires universal DNA cleavage; this graph and its evidence remain restricted to characterized type-I systems. Proposal v451 replaces v96's overgeneralized family definition while preserving the stable local family identifier. Type I remains a separate architecture-class discovery lead. That architecture-class lead is now represented by traitmech:000575 Hachiman type I system for HamAB loci without HamC. The component definition follows Payne and Cui, not a failed detector hit or a type-II knockout. The existing graph still describes characterized I-A/I-B mechanisms, not all type-I subtypes. Subtype-specific mechanisms and native-locus activity remain open; no graph, example or hierarchy is changed. posed_by: codex posed_date: '2026-09-15' curation_history: - timestamp: '2026-09-15T14:47:54Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Hachiman 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_v96. llm_assisted: true - timestamp: '2026-10-03T18:08:00Z' curator: codex action: SCOPE_HACHIMAN_FAMILY_AND_TYPE_II changes: 'Addressed #1630: removed the unsupported universal DNA-cleavage condition from the family definition while retaining the type-I mechanism evidence and graph scope. Linked the new HamABC child traitmech:000574; HamC chemistry remains an open question. Proposal v451 supersedes v96 without editing the old TSV.' llm_assisted: true - timestamp: '2026-10-03T18:37:00Z' curator: codex action: TRACK_HACHIMAN_TYPE_I_CLASS changes: Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output. llm_assisted: true