identifier: traitmech:000410 label: integrative conjugative element definition: A genomic island trait in which an organism possesses an integrative and conjugative element, a self-transmissible mobile genetic element that integrates into host DNA, excises under induced expression, and encodes type IV secretion machinery for conjugative transfer to recipient cells. definition_source: DOI:10.1146/annurev-genet-112414-055018 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000093 synonyms: - synonym_text: ICE synonym_type: RELATED_SYNONYM source: DOI:10.1146/annurev-genet-112414-055018 evidence: - reference: DOI:10.1146/annurev-genet-112414-055018 snippet: 'There are two defining features of ICEs: (a) They are found integrated in a host genome; and (b) they encode a functional conjugation system, a type IV secretion system' notes: Johnson and Grossman define integrative and conjugative elements as host-integrated mobile genetic elements that encode a functional type IV secretion conjugation system. - reference: DOI:10.1093/nar/gkad644 snippet: The term ‘genomic island’ encompasses diverse types of mobile genetic elements that exhibit various structures and gene contents, including prophages, transposons, integrated plasmids, integrative and mobilizable elements (IMEs), and integrative and conjugative elements (ICEs) notes: Bioteau et al. place integrative and conjugative elements among the mobile-genetic-element subclasses encompassed by genomic islands. canonical_examples: - taxon_id: NCBITaxon:1423 taxon_label: Bacillus subtilis note: ICEBs1 reference: DOI:10.1146/annurev-genet-112414-055018 - taxon_id: NCBITaxon:1351 taxon_label: Enterococcus faecalis note: Tn916 reference: DOI:10.1146/annurev-genet-112414-055018 causal_graphs: - graph_id: ice_excision_conjugation_integration title: ICEs excise, transfer by conjugation, and reintegrate description: Conservative ICE life-cycle sketch linking an integrated ICE locus to circularization, oriT processing, T4SS-mediated conjugative transfer, recipient integration, and the genomic-island possession trait. scope_status: NONMECHANISTIC scope_notes: This genomics graph summarizes the shared ICE life cycle at the mobile-element level. It does not assert exact protein-family groundings for heterogeneous ICE integrases, relaxases, type IV coupling proteins, or T4SS subunits. nodes: - node_id: integrated_ice_locus label: integrated ICE locus node_type: GENETIC_ELEMENT description: An integrative and conjugative element integrated into a host replicon. - node_id: ice_excision_circularization label: ICE excision and circularization node_type: BIOLOGICAL_PROCESS description: Induction-associated excision of an integrated ICE to a circular double-stranded DNA intermediate. - node_id: orit_processing label: oriT processing node_type: BIOLOGICAL_PROCESS description: Processing at the ICE origin of transfer to generate the linear transfer-DNA complex. - node_id: conjugation label: conjugation node_type: BIOLOGICAL_PROCESS grounding: GO:0009291 description: Contact-dependent transfer of ICE DNA into a recipient cell through the conjugation machinery. - node_id: ice_integration label: ICE integration node_type: BIOLOGICAL_PROCESS description: Recombination of circular ICE DNA into the recipient host chromosome. - node_id: integrative_conjugative_element label: integrative conjugative element node_type: TRAIT grounding: traitmech:000410 description: Possession of a genome-encoded integrative and conjugative element. - node_id: genomic_island label: genomic island node_type: TRAIT grounding: traitmech:000093 description: Possession of a horizontally acquired chromosomal island. edges: - subject: integrated_ice_locus predicate: enables predicate_id: RO:0002327 object: ice_excision_circularization description: Upon induction, an integrated ICE excises from the chromosome and forms a circular dsDNA intermediate. evidence: - reference: DOI:10.1146/annurev-genet-112414-055018 snippet: When ICE gene expression is induced, by specific cellular conditions or perhaps stochastically, the ICE excises from the chromosome and forms a circular dsDNA molecule notes: Johnson and Grossman summarize induction-linked ICE excision and circular double-stranded DNA intermediate formation. - subject: ice_excision_circularization predicate: enables predicate_id: RO:0002327 object: orit_processing description: The circular ICE is processed at oriT to generate the linear ssDNA-protein transfer complex. evidence: - reference: DOI:10.1146/annurev-genet-112414-055018 snippet: Other host and ICE-encoded proteins recognize the origin of transfer (oriT) and process the ICE DNA to generate a linear ssDNA-protein complex notes: Johnson and Grossman describe oriT recognition and ICE DNA processing that produces the linear transfer-DNA complex. - subject: orit_processing predicate: enables predicate_id: RO:0002327 object: conjugation description: The mating machinery transports the processed transfer DNA into a recipient cell. evidence: - reference: DOI:10.1146/annurev-genet-112414-055018 snippet: The mating machinery pumps the T-DNA into the recipient notes: The Johnson and Grossman life-cycle summary places mating-machinery transport after transfer-DNA generation. - subject: conjugation predicate: enables predicate_id: RO:0002327 object: ice_integration description: Transferred ICE DNA recircularizes and becomes a double-stranded integration substrate in the recipient. evidence: - reference: DOI:10.1146/annurev-genet-112414-055018 snippet: In both the donor and recipient, the circular dsDNA ICE integrates into the host chromosome. notes: Johnson and Grossman's ICE life-cycle figure caption states that the circular double-stranded ICE reintegrates in donor and recipient cells. - subject: ice_integration predicate: confers predicate_id: METPO:2007700 object: integrative_conjugative_element description: Recipient-chromosome integration completes possession of an integrated conjugative element. evidence: - reference: DOI:10.1146/annurev-genet-112414-055018 snippet: 'There are two defining features of ICEs: (a) They are found integrated in a host genome; and (b) they encode a functional conjugation system, a type IV secretion system' notes: Johnson and Grossman define integrative and conjugative elements as host-integrated mobile genetic elements that encode a functional type IV secretion conjugation system. - subject: integrative_conjugative_element predicate: is a predicate_id: rdfs:subClassOf object: genomic_island description: Integrative-conjugative-element possession is a genomic-island possession trait. evidence: - reference: DOI:10.1093/nar/gkad644 snippet: The term ‘genomic island’ encompasses diverse types of mobile genetic elements that exhibit various structures and gene contents, including prophages, transposons, integrated plasmids, integrative and mobilizable elements (IMEs), and integrative and conjugative elements (ICEs) notes: Bioteau et al. place integrative and conjugative elements among the mobile-genetic-element subclasses encompassed by genomic islands. discussions: - discussion_id: ice-family-resolution-gap prompt: Resolve bacterial ICE subfamilies, Actinomycete ICE boundaries, integrase/relaxase/T4SS signatures, and cargo-phenotype scope before minting narrower ICE mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Johnson and Grossman define ICEs by host-genome integration and a functional type IV secretion conjugation system, while Bioteau et al. classify ICEs as self-transmissible genomic islands. This first record captures the genome-level possession trait without claiming exact molecular groundings for heterogeneous integrases, relaxases, T4SS variants, Actinomycete ICE machinery, or adaptive cargo phenotypes. attaches_to: - causal_graphs#ice_excision_conjugation_integration posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T14:42:32Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted integrative conjugative element as a DOI-backed GENOMICS TraitRecord under genomic island with ICEBs1 and Tn916 canonical examples after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v287. llm_assisted: true