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Lamassu system

traitmech:000232 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Lamassu locus built around a conserved SMC-like LmuB sensor paired with a modular LmuA effector and subfamily-specific partner architecture, enabling viral-DNA sensing and effector-mediated antiviral activity.

Trait evidence (6)

  • DOI:10.1126/science.aar4120
    Lamassu LmuAB pfam14130, pfam02463 SMC ATPase N-terminal domain 697 682 (1.3%)

    Doron et al. reported Lamassu/LmuAB as an SMC-ATPase-linked system in their pangenome-scale antiphage-system discovery screen.

  • DOI:10.1073/pnas.2519643122
    Lamassu is a widespread antiviral system in bacteria that uses structural maintenance of chromosomes-like proteins

    Haudiquet et al. support defining Lamassu as a recurring bacterial antiviral system with an SMC-like component.

  • DOI:10.1073/pnas.2519643122
    a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor

    Haudiquet et al. support placing Lamassu at the family level rather than defining a single effector subtype.

  • DOI:10.1073/pnas.2519643122
    It comprises LmuB, an SMC-like protein, LmuC, a small protein with a domain of unknown function, and LmuA

    Haudiquet et al. support the LmuA/LmuB/LmuC composition of the structurally characterized Lamassu Vc-Cap4 branch.

  • DOI:10.1073/pnas.2519643122
    Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo

    Haudiquet et al. connect Lamassu to direct DNA-end and phage replication origin sensing.

  • DOI:10.1073/pnas.2519643122
    triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain

    Haudiquet et al. connect viral-DNA sensing to LmuA tetramer formation and Cap4 nuclease-domain activation in Lamassu Vc-Cap4.

Lamassu SMC-like complexes activate LmuA antiviral effectors

Evidence-backed process sketch linking a Lamassu locus to LmuABC complex formation, viral DNA sensing, LmuA effector activation, and inhibition of bacteriophage infection.

NONMECHANISTIC · The graph captures the structurally characterized Lamassu Vc-Cap4 system without asserting one exact effector domain, LmuC requirement, LmuB clade, zinc-hook architecture, viral DNA cue, cell-death output, or phage breadth across all Lamassu loci.

Lamassu SMC-like complexes activate LmuA antiviral effectors Interactive directed graph showing evidence-backed causal relationships for Lamassu system.

Edge evidence

  • Lamassu locus contributes to LmuABC complex assembly RO:0002326

    The characterized Lamassu Vc-Cap4 locus encodes LmuA, SMC-like LmuB, and LmuC components.

    • DOI:10.1073/pnas.2519643122 It comprises LmuB, an SMC-like protein, LmuC, a small protein with a domain of unknown function, and LmuA Haudiquet et al. support the LmuABC composition of the Lamassu Vc-Cap4 branch.
  • LmuABC complex assembly enables Lamassu viral DNA sensing RO:0002327

    Lamassu complexes bind double-stranded DNA and sense DNA ends or phage replication origins.

    • DOI:10.1073/pnas.2519643122 Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo Haudiquet et al. connect Lamassu to direct viral-DNA-associated sensing.
  • Lamassu viral DNA sensing activates LmuA effector activation RO:0002213

    Lamassu viral-DNA sensing triggers LmuA tetramer formation and Cap4 nuclease-domain activation.

    • DOI:10.1073/pnas.2519643122 triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain Haudiquet et al. connect Lamassu DNA sensing to LmuA Cap4 nuclease-domain activation.
  • LmuA effector activation mitigates phage infection METPO:2007407

    Lamassu effector activation helps halt phage infection in the bacterial host.

    • DOI:10.1073/pnas.2519643122 Lamassu is a widespread antiviral system in bacteria that uses structural maintenance of chromosomes-like proteins, typically associated with chromosome maintenance, to detect and halt phage infection Haudiquet et al. support coupling Lamassu SMC-like detection to inhibition of phage infection.
  • LmuA effector activation confers Lamassu system METPO:2007700

    Viral-DNA-triggered LmuA effector activation realizes the Lamassu system trait.

    • DOI:10.1073/pnas.2519643122 a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor Haudiquet et al. support the shared SMC-like sensor and diverse effector logic of Lamassu immunity.
  • Lamassu system is a phage defense system rdfs:subClassOf

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

    • DOI:10.1126/science.aar4120 Lamassu LmuAB pfam14130, pfam02463 SMC ATPase N-terminal domain 697 682 (1.3%) Doron et al. reported Lamassu in a table of candidate antiphage defense systems.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1073/pnas.2519643122

Parent traits (1)

Children (14)

Synonyms (1)

  • Lamassu EXACT_SYNONYM · DOI:10.1073/pnas.2519643122

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.

  • Vibrio cholerae NCBITaxon:666 DOI:10.1073/pnas.2519643122 Haudiquet et al. structurally characterized the Vibrio cholerae Lamassu Vc-Cap4 system and connected its LmuABC complex to dsDNA-end sensing and LmuA Cap4 nuclease-domain activation.

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 Lamassu subtype architecture, effector diversity, and viral-DNA trigger specificity before minting narrower Lamassu mechanism children.

KNOWLEDGE GAP OPEN lamassu-subtype-and-effector-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.

Haudiquet et al. support a structurally characterized Vibrio cholerae Lamassu Vc-Cap4 system with LmuABC DNA-end sensing and LmuA Cap4 nuclease activation, and the pinned DefenseFinder tables model Lamassu-Amidase, Lamassu-Cap4_nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, Lamassu-Sir2, and other Lamassu-Fam subtypes as rule-row variants. Lamassu-Amidase, Lamassu-Cap4 nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, and Lamassu-Sir2 now capture nine DefenseFinder rule-row subtypes, but long-versus-short LmuB clades, LmuC-independent subfamilies, the Lamassu-Fam base, Lamassu-Hydrolase_Protease, and Lamassu-Hypothetical rule rows, viral-DNA triggers, exact LmuA effector substrates, FMO acronym expansion, the Lamassu-FMO rule row's relationship to FMO-scoped LmuB/LmuC HMM rows, the Lamassu-Lipase rule row's relationship to its Lipase-scoped LmuB HMM row, the Lamassu-Mrr rule row's relationship to Mrr-scoped LmuB/LmuC HMM rows, the Lamassu-PDDEXK rule row's relationship to PDDEXK-scoped LmuB/LmuC HMM rows, the Lamassu-Sir2 rule row's relationship to Sir2-scoped LmuB/LmuC HMM rows, and cell-death outputs across Lamassu loci remain unresolved. Lamassu Hydrolase-Protease system (traitmech:000567) now captures the literature-supported paired architecture with LmuB and LmuC. Its pinned executable XML requires four components, whereas the summary TSV requires three matches and calls LmuC accessory. The existing table-defined Lamassu-Hydrolase and Lamassu-Protease siblings each forbid the other's effector profile and are not exact matches to this paired architecture. Reconciling the legacy table-based sibling definitions with executable models remains open; do not interpret the summary's profile labels as current executable model requirements. Lamassu-HNH system (traitmech:000568) now captures the literature-supported short-LmuB architecture with HNH-domain LmuA and LmuC. The published dataset supplies complete computational genome calls, not HNH-specific functional validation. The pinned executable HNH model accepts either long or short LmuB, whereas all HNH calls in that dataset use short LmuB; its software key is therefore not an exact synonym for this biological scope. HNH-specific activity, substrates, and activation remain unresolved. Lamassu-SMEK system (traitmech:000569) now captures a locus with SMEK-domain LmuA, LmuB, and LmuC. The paper describes SMEK as short-specific, but its dataset contains 124 short-profile system calls and one long-profile call; the latter requires reconciliation before asserting a biological long-LmuB subtype. The definition therefore does not impose a LmuB-length restriction. The three-component architecture is not equivalent to the single-gene DS-27 system that also uses SMEK as a working label. SMEK-specific functional validation and chemistry remain unresolved. Short Lamassu system (traitmech:000570) now captures the short-LmuB phylogenetic and structural family, not a fixed protein-length bin or an effector-specific detector. Lamassu-HNH is placed below it because its existing definition explicitly requires short-form LmuB. SMEK remains directly under the broader Lamassu parent because of its unresolved long-profile exception. The short family permits the reported LmuC-loss and effector-domain-loss architectures; type I is not an exact synonym for the whole short family. The Lamassu-Hypothetical registry label is not accepted as a separate biological trait here: unknown annotation does not establish effector-domain loss, and its relationship to the paper's clade O still needs explicit mapping. The long family and component-number subtypes remain separate discovery leads. Long Lamassu system (traitmech:000571) now captures the complementary long-LmuB phylogenetic and structural family, not an 800-residue cutoff or a particular effector model. The paper assigns the B. cereus B4077 Hydrolase-Protease system to this family, but that effector architecture also occurs in short Lamassu, so the whole Hydrolase-Protease trait is not reparented. The legacy table-defined FMO trait still needs model and biological-scope reconciliation before assigning the entire record to the long family. SMEK's exception remains unresolved. Raw detection gene_name hits must not be confused with exchangeable hit_gene_ref model slots, and ambiguous loci need phylogenetic classification. Component-number type I/II traits remain separate discovery leads. Lamassu type II system (traitmech:000572) now captures the LmuC-containing component architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and independently used by Li et al. (DOI:10.1038/s41589-025-02102-z). HNH, SMEK and Hydrolase-Protease already require LmuC in their definitions and now have this parent; HNH retains its short-family parent too. This does not assert a three-gene count, universal LmuC essentiality, or new antiviral validation of those children. Long/short families and legacy detector rows are not equivalent to this component class. Type I and family-wide mechanisms remain open discovery and curation questions. Lamassu type I system (traitmech:000573) now resolves the component-class discovery lead: Haudiquet et al. explicitly identify the LmuC-loss architecture as type I, and Li et al. independently study a type-I LmuA/LmuB complex. This is not equivalent to all short Lamassu or proof that every failed LmuC hit is biological absence. No existing effector-defined child is reparented. Family-wide mechanisms, legacy model reconciliation and native-host activity remain open.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted Lamassu 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_v109.

  2. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Amidase as split out in the open Lamassu subtype-effector discussion after minting traitmech:000556 for the DefenseFinder-backed Lamassu-Amidase child; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  3. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Cap4 nuclease as split out in the open Lamassu subtype-effector discussion after minting traitmech:000557 for the DefenseFinder-backed Lamassu-Cap4_nuclease child; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  4. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-FMO as split out in the open Lamassu subtype-effector discussion after minting traitmech:000558 for the DefenseFinder-backed Lamassu-FMO child; the first-pass record follows the pinned rule row while tracking its non-FMO-specific LmuB/LmuC profile names as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  5. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Hydrolase as split out in the open Lamassu subtype-effector discussion after minting traitmech:000561 for the DefenseFinder-backed Lamassu-Hydrolase child; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  6. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Lipase as split out in the open Lamassu subtype-effector discussion after minting traitmech:000562 for the DefenseFinder-backed Lamassu-Lipase child; the first-pass record follows the pinned rule row while tracking its non-Lipase-specific LmuB profile name as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  7. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Mrr as split out in the open Lamassu subtype-effector discussion after minting traitmech:000563 for the DefenseFinder-backed Lamassu-Mrr child; the first-pass record follows the pinned rule row while tracking its non-Mrr-specific LmuB/LmuC profile names as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  8. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-PDDEXK as split out in the open Lamassu subtype-effector discussion after minting traitmech:000564 for the DefenseFinder-backed Lamassu-PDDEXK child; the first-pass record follows the pinned rule row while tracking its non-PDDEXK-specific LmuB/LmuC profile names as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.

  9. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Protease as split out in the open Lamassu subtype-effector discussion after minting traitmech:000565 for the DefenseFinder-backed Lamassu-Protease child; remaining Lamassu-Fam rule rows and finer Lamassu activation mechanisms remain open.

  10. · TRACK_NARROWER_RECORD · codex

    Documented Lamassu-Sir2 as split out in the open Lamassu subtype-effector discussion after minting traitmech:000566 for the DefenseFinder-backed Lamassu-Sir2 child; remaining Lamassu-Fam rule rows and finer Lamassu activation mechanisms remain open.

  11. · TRACK_NARROWER_RECORD · codex

    Linked traitmech:000567 Lamassu Hydrolase-Protease system and documented disagreement between executable models and legacy tables; retained remaining subtype and mechanism gaps.

  12. · TRACK_NARROWER_RECORD · codex

    Linked traitmech:000568 Lamassu-HNH system and distinguished its short-LmuB genomic architecture from the broader executable detector. Retained HNH-specific functional-validation gaps.

  13. · TRACK_NARROWER_RECORD · codex

    Linked traitmech:000569 Lamassu-SMEK system; documented the long-profile dataset exception and distinction from the single-gene DS-27 SMEK working label. Retained function gaps.

  14. · TRACK_NARROWER_RECORD · codex

    Linked traitmech:000570 short Lamassu system and the HNH parent refinement; retained the SMEK length exception and rejected unproven equivalence of a Hypothetical label to effector-domain loss.

  15. · TRACK_NARROWER_RECORD · codex

    Linked traitmech:000571 long Lamassu system and recorded why Hydrolase-Protease, FMO and SMEK are not automatically reparented. Retained component-classification and family-mechanism gaps.

  16. · TRACK_TYPE_II_CLASS · codex

    Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.

  17. · TRACK_TYPE_I_CLASS · codex

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.