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Hachiman system

traitmech:000219 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Hachiman antiphage locus encoding a HamA/HamB core.

Trait evidence (6)

  • DOI:10.1016/j.cell.2024.09.020
    Hachiman is a broad-spectrum antiphage defense system of unknown function

    Tuck et al. support Hachiman as a named broad-spectrum antiphage system.

  • DOI:10.1016/j.cell.2024.09.020
    Hachiman is a heterodimeric nuclease-helicase complex, HamAB

    Tuck et al. support the HamA/HamB nuclease-helicase core of characterized Hachiman systems.

  • DOI:10.1016/j.cell.2024.09.020
    When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity

    Tuck et al. connect HamB helicase activity with HamA nuclease activation after DNA-damage detection.

  • DOI:10.1016/j.cell.2024.09.020
    Hachiman activation degrades all DNA in the cell, creating "phantom" cells devoid of both phage and host DNA

    Tuck et al. support nonspecific DNA degradation as the type I-A Hachiman antiviral output.

  • DOI:10.1038/s41467-025-57851-1
    The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins

    Cui et al. support the recurring Hachiman system name and its HamA/HamB composition.

  • DOI:10.1038/s41467-025-57851-1
    HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage, thus implementing antiphage defense

    Cui et al. support a type I-B HamAB heterodimer that couples ATP hydrolysis to antiphage DNA cleavage.

Hachiman HamAB complexes cleave DNA during antiphage defense

Evidence-backed process sketch linking a Hachiman locus to HamAB nuclease-helicase activity, cellular DNA degradation, and inhibition of bacteriophage progeny production.

NONMECHANISTIC · 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.

Hachiman HamAB complexes cleave DNA during antiphage defense Interactive directed graph showing evidence-backed causal relationships for Hachiman system.

Edge evidence

  • Hachiman locus contributes to HamAB complex assembly RO:0002326

    Hachiman loci encode HamA and HamB components that assemble into HamAB nuclease-helicase complexes.

    • DOI:10.1016/j.cell.2024.09.020 One such system is Hachiman, a two-gene locus encoding HamA Tuck et al. support HamA/HamB as the two-gene Hachiman locus core.
    • DOI:10.1038/s41467-025-57851-1 The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins Cui et al. also support HamA/HamB as the core Hachiman components.
  • HamAB complex assembly enables Hachiman DNA cleavage RO:0002327

    HamA/HamB complexation enables ATP-dependent DNA cleavage by Hachiman systems.

    • DOI:10.1016/j.cell.2024.09.020 When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity Tuck et al. connect HamAB activation with HamA nuclease activity.
    • DOI:10.1038/s41467-025-57851-1 HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage Cui et al. support ATP-hydrolysis-coupled DNA cleavage by a type I-B HamAB heterodimer.
  • Hachiman DNA cleavage mitigates phage particle production METPO:2007407

    Hachiman-mediated DNA degradation inhibits the generation of new phage particles.

    • DOI:10.1016/j.cell.2024.09.020 Hachiman activation degrades all DNA in the cell Tuck et al. support DNA degradation as the activated Hachiman output.
    • DOI:10.1016/j.cell.2024.09.020 We confirmed that Hachiman limits the production of new phage particles Tuck et al. connect Hachiman activity to restriction of phage progeny production.
  • Hachiman DNA cleavage confers Hachiman system METPO:2007700

    HamAB-mediated DNA cleavage is the antiviral output that realizes the Hachiman system trait.

    • DOI:10.1038/s41467-025-57851-1 execute DNA cleavage, thus implementing antiphage defense Cui et al. support DNA cleavage as an antiphage output of the Hachiman complex.
  • Hachiman system is a phage defense system rdfs:subClassOf

    Hachiman system possession is a phage-defense-system trait.

    • DOI:10.1038/s41467-025-57851-1 The Hachiman system is a novel prokaryotic antiphage defense system Cui et al. place Hachiman in the antiphage-defense-system family.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1016/j.cell.2024.09.020

Parent traits (1)

Children (2)

Synonyms (2)

  • Hachiman antiphage defense system EXACT_SYNONYM · DOI:10.1016/j.cell.2024.09.020
  • Hachiman defense system EXACT_SYNONYM · DOI:10.1038/s41467-025-57851-1

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Escherichia coli NCBITaxon:562 DOI:10.1016/j.cell.2024.09.020 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.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve Hachiman subtype effectors, DNA substrates, and activation triggers before minting narrower Hachiman mechanism children.

KNOWLEDGE GAP OPEN hachiman-subtype-and-trigger-gap · raised by codex · 2026-09-15

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · SCOPE_HACHIMAN_FAMILY_AND_TYPE_II · codex

    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.

  3. · TRACK_HACHIMAN_TYPE_I_CLASS · codex

    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.