identifier: traitmech:000090 label: plasmid carriage definition: A genomics trait describing possession of one or more plasmids — extrachromosomal, typically circular DNA replicons that carry accessory genes such as resistance, virulence, or metabolic functions and can transfer by conjugation. definition_source: DOI:10.1128/MMBR.00020-10 trait_category: GENOMICS term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000089 synonyms: - synonym_text: plasmid-bearing synonym_type: RELATED_SYNONYM source: DOI:10.1128/MMBR.00020-10 evidence: - reference: DOI:10.1128/MMBR.00020-10 notes: Smillie et al. review plasmid mobility, classifying conjugative and mobilizable plasmids as key vectors of horizontal gene transfer. - reference: DOI:10.1038/nrmicro1235 notes: Frost et al. include plasmids among the principal mobile genetic elements. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: "F/R plasmid carriage" reference: PMID:36409140 - taxon_id: NCBITaxon:139 taxon_label: Borreliella burgdorferi note: "numerous linear/circular plasmids" reference: PMID:9403685 causal_graphs: - graph_id: plasmid_conjugation_hgt title: Plasmid carriage drives conjugative horizontal gene transfer description: Evidence-backed causal sketch linking plasmid possession to conjugation and accessory-function delivery. nodes: - node_id: plasmid_carriage_trait label: plasmid carriage node_type: TRAIT grounding: traitmech:000090 description: Possession of extrachromosomal plasmid replicons. - node_id: conjugation label: conjugation node_type: BIOLOGICAL_PROCESS grounding: GO:0000746 description: Cell-to-cell transfer of genetic material via direct contact. - node_id: accessory_function label: accessory function node_type: QUALITY description: Plasmid-encoded resistance, virulence, or metabolic capability. - node_id: ta_system label: toxin-antitoxin system node_type: GENE_OR_PROTEIN description: Selfish genetic module mediating plasmid addiction / post-segregational killing. - node_id: plasmid_vertical_inheritance label: plasmid vertical inheritance node_type: BIOLOGICAL_PROCESS description: Stable transmission of a plasmid to daughter cells across generations. - node_id: plasmid_methylase label: plasmid-encoded methylase node_type: MOLECULAR_FUNCTION description: Plasmid-borne methyltransferase shielding plasmid DNA from restriction. - node_id: restriction_of_plasmid_dna label: restriction of incoming plasmid DNA node_type: BIOLOGICAL_PROCESS description: Cleavage of unmethylated incoming plasmid DNA by restriction-modification systems. - node_id: anti_restriction_genes label: plasmid-encoded anti-restriction genes node_type: GENE_OR_PROTEIN description: Plasmid genes inhibiting host restriction-modification defence. - node_id: antibiotic_selective_pressure label: antibiotic selective pressure node_type: ENVIRONMENTAL_FACTOR description: Antibiotic exposure selecting for retention of resistance plasmids. - node_id: fitness_cost label: plasmid fitness cost node_type: QUALITY description: Reduced host fitness from additional material and energy consumption of plasmid carriage. - node_id: compensatory_mutation label: compensatory mutation node_type: BIOLOGICAL_PROCESS description: Chromosomal or plasmid mutation that ameliorates plasmid-imposed fitness cost. edges: - subject: plasmid_carriage_trait predicate: enables object: conjugation description: Conjugative plasmids encode the machinery for cell-to-cell transfer. evidence: - reference: DOI:10.1128/MMBR.00020-10 notes: Smillie et al. classify conjugative and mobilizable plasmids. predicate_id: RO:0002327 - subject: plasmid_carriage_trait predicate: contributes to object: accessory_function description: Plasmids carry accessory genes that extend host phenotype. evidence: - reference: DOI:10.1038/nrmicro1235 notes: Frost et al. include plasmids among the principal MGEs delivering accessory functions. predicate_id: RO:0002326 - subject: ta_system predicate: stabilizes object: plasmid_vertical_inheritance description: Toxin-antitoxin systems increase vertical stability of their replicons. evidence: - reference: DOI:10.1093/nar/gkae018 notes: TA systems are small selfish genetic modules that increase vertical stability of their replicons. - subject: plasmid_methylase predicate: protects against object: restriction_of_plasmid_dna description: Plasmid-encoded methylases protect plasmid DNA from host restriction. evidence: - reference: DOI:10.1093/nar/gkae896 notes: plasmid-encoded methylases that protect plasmids from restriction. - subject: anti_restriction_genes predicate: protects against object: restriction_of_plasmid_dna description: Plasmid-encoded anti-restriction genes counter multiple RM system types. evidence: - reference: DOI:10.1093/nar/gkae896 notes: plasmid-encoded anti-restriction genes that protect against multiple RM types. - subject: antibiotic_selective_pressure predicate: promotes retention of object: plasmid_carriage_trait description: Without selection plasmids tend to be lost; antibiotic pressure promotes retention. evidence: - reference: DOI:10.1080/22221751.2024.2352432 notes: without selection plasmids tend to be lost, whereas antibiotic (or metal) selective pressure promotes retention. - subject: plasmid_carriage_trait predicate: imposes object: fitness_cost description: Plasmid carriage imposes a fitness cost from additional material and energy consumption. evidence: - reference: DOI:10.1080/22221751.2024.2352432 notes: Plasmid carriage imposes fitness costs (additional material and energy consumption). - subject: compensatory_mutation predicate: reduces object: fitness_cost description: Compensatory evolution of chromosomes and plasmids counteracts plasmid fitness cost. evidence: - reference: DOI:10.1002/ece3.70121 notes: Compensatory evolution of chromosomes and plasmids counteracts the plasmid fitness cost. predicate_id: METPO:2000017 curation_history: - timestamp: '2026-06-05T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate GENOMICS trait (plasmid carriage); sub-variant of mobile genetic element. llm_assisted: true - timestamp: '2026-06-08T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (plasmid conjugation / HGT) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:11Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017×1). llm_assisted: true