identifier: traitmech:000232 label: Lamassu system definition: 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. definition_source: DOI:10.1073/pnas.2519643122 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Lamassu synonym_type: EXACT_SYNONYM source: DOI:10.1073/pnas.2519643122 evidence: - reference: DOI:10.1126/science.aar4120 snippet: Lamassu LmuAB pfam14130, pfam02463 SMC ATPase N-terminal domain 697 682 (1.3%) notes: Doron et al. reported Lamassu/LmuAB as an SMC-ATPase-linked system in their pangenome-scale antiphage-system discovery screen. - reference: DOI:10.1073/pnas.2519643122 snippet: Lamassu is a widespread antiviral system in bacteria that uses structural maintenance of chromosomes-like proteins notes: Haudiquet et al. support defining Lamassu as a recurring bacterial antiviral system with an SMC-like component. - reference: DOI:10.1073/pnas.2519643122 snippet: a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor notes: Haudiquet et al. support placing Lamassu at the family level rather than defining a single effector subtype. - reference: DOI:10.1073/pnas.2519643122 snippet: It comprises LmuB, an SMC-like protein, LmuC, a small protein with a domain of unknown function, and LmuA notes: Haudiquet et al. support the LmuA/LmuB/LmuC composition of the structurally characterized Lamassu Vc-Cap4 branch. - reference: DOI:10.1073/pnas.2519643122 snippet: Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo notes: Haudiquet et al. connect Lamassu to direct DNA-end and phage replication origin sensing. - reference: DOI:10.1073/pnas.2519643122 snippet: triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain notes: Haudiquet et al. connect viral-DNA sensing to LmuA tetramer formation and Cap4 nuclease-domain activation in Lamassu Vc-Cap4. canonical_examples: - taxon_id: NCBITaxon:666 taxon_label: Vibrio cholerae note: 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. reference: DOI:10.1073/pnas.2519643122 causal_graphs: - graph_id: lamassu_smc_dna_sensing_nuclease_activation title: Lamassu SMC-like complexes activate LmuA antiviral effectors description: Evidence-backed process sketch linking a Lamassu locus to LmuABC complex formation, viral DNA sensing, LmuA effector activation, and inhibition of bacteriophage infection. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: lamassu_locus label: Lamassu locus node_type: GENETIC_ELEMENT description: A Lamassu antiviral locus built around an SMC-like LmuB core and a cognate LmuA effector. - node_id: lmuabc_complex_assembly label: LmuABC complex assembly node_type: BIOLOGICAL_PROCESS description: Assembly of LmuA, SMC-like LmuB, and LmuC into a Lamassu Vc-Cap4 complex. - node_id: lamassu_viral_dna_sensing label: Lamassu viral DNA sensing node_type: BIOLOGICAL_PROCESS description: Lamassu-mediated sensing of viral double-stranded DNA ends or phage replication origins. - node_id: lmuA_effector_activation label: LmuA effector activation node_type: BIOLOGICAL_PROCESS description: Oligomerization-dependent activation of a LmuA effector nuclease domain. - node_id: phage_infection label: phage infection node_type: BIOLOGICAL_PROCESS description: Bacteriophage infection and propagation inside a bacterial host cell. - node_id: lamassu_system_trait label: Lamassu system node_type: TRAIT grounding: traitmech:000232 description: Possession of a genome-encoded Lamassu 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: lamassu_locus predicate: contributes to predicate_id: RO:0002326 object: lmuabc_complex_assembly description: The characterized Lamassu Vc-Cap4 locus encodes LmuA, SMC-like LmuB, and LmuC components. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: It comprises LmuB, an SMC-like protein, LmuC, a small protein with a domain of unknown function, and LmuA notes: Haudiquet et al. support the LmuABC composition of the Lamassu Vc-Cap4 branch. - subject: lmuabc_complex_assembly predicate: enables predicate_id: RO:0002327 object: lamassu_viral_dna_sensing description: Lamassu complexes bind double-stranded DNA and sense DNA ends or phage replication origins. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo notes: Haudiquet et al. connect Lamassu to direct viral-DNA-associated sensing. - subject: lamassu_viral_dna_sensing predicate: activates predicate_id: RO:0002213 object: lmuA_effector_activation description: Lamassu viral-DNA sensing triggers LmuA tetramer formation and Cap4 nuclease-domain activation. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain notes: Haudiquet et al. connect Lamassu DNA sensing to LmuA Cap4 nuclease-domain activation. - subject: lmuA_effector_activation predicate: mitigates predicate_id: METPO:2007407 object: phage_infection description: Lamassu effector activation helps halt phage infection in the bacterial host. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: 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 notes: Haudiquet et al. support coupling Lamassu SMC-like detection to inhibition of phage infection. - subject: lmuA_effector_activation predicate: confers predicate_id: METPO:2007700 object: lamassu_system_trait description: Viral-DNA-triggered LmuA effector activation realizes the Lamassu system trait. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor notes: Haudiquet et al. support the shared SMC-like sensor and diverse effector logic of Lamassu immunity. - subject: lamassu_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Lamassu system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1126/science.aar4120 snippet: Lamassu LmuAB pfam14130, pfam02463 SMC ATPase N-terminal domain 697 682 (1.3%) notes: Doron et al. reported Lamassu in a table of candidate antiphage defense systems. discussions: - discussion_id: lamassu-subtype-and-effector-gap prompt: Resolve Lamassu subtype architecture, effector diversity, and viral-DNA trigger specificity before minting narrower Lamassu mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: '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.' posed_by: codex posed_date: '2026-09-15' curation_history: - timestamp: '2026-09-15T23:14:40Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-10-02T21:43:25Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-02T22:16:25Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-02T23:11:38Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T03:10:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T03:48:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T04:26:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T05:05:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T05:46:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T06:34:01Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T09:29:00Z' curator: codex action: TRACK_NARROWER_RECORD changes: Linked traitmech:000567 Lamassu Hydrolase-Protease system and documented disagreement between executable models and legacy tables; retained remaining subtype and mechanism gaps. llm_assisted: true - timestamp: '2026-10-03T10:35:00Z' curator: codex action: TRACK_NARROWER_RECORD changes: Linked traitmech:000568 Lamassu-HNH system and distinguished its short-LmuB genomic architecture from the broader executable detector. Retained HNH-specific functional-validation gaps. llm_assisted: true - timestamp: '2026-10-03T11:15:00Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T12:33:00Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T14:29:24Z' curator: codex action: TRACK_NARROWER_RECORD changes: 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. llm_assisted: true - timestamp: '2026-10-03T15:14:27Z' curator: codex action: TRACK_TYPE_II_CLASS changes: 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. llm_assisted: true - timestamp: '2026-10-03T15:57:07Z' curator: codex action: TRACK_TYPE_I_CLASS changes: 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. llm_assisted: true