identifier: traitmech:000089 label: mobile genetic element definition: A genomics trait describing possession of DNA segments that can move within or between genomes and mediate horizontal gene transfer, including plasmids, prophages, transposable elements, and genomic islands. definition_source: DOI:10.1038/nrmicro1235 trait_category: GENOMICS term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000188 synonyms: - synonym_text: MGE synonym_type: RELATED_SYNONYM source: DOI:10.1038/nrmicro1235 evidence: - reference: DOI:10.1038/nrmicro1235 notes: Frost et al. review mobile genetic elements as the agents of horizontal gene transfer and genome plasticity; parent of the plasmid, prophage, transposable- element, and genomic-island sub-variants. - reference: DOI:10.1111/1574-6976.12067 notes: Siguier, Gourbeyre & Chandler review insertion sequences as a major class of mobile genetic elements shaping bacterial genomes. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: "plasmids, IS elements, integrons" reference: PMID:32807088 causal_graphs: - graph_id: mge_horizontal_gene_transfer title: Mobile genetic elements mediate horizontal gene transfer description: Evidence-backed causal sketch linking MGE possession to horizontal gene transfer and resulting genome plasticity. nodes: - node_id: mge_trait label: mobile genetic element node_type: TRAIT grounding: traitmech:000089 description: Possession of DNA segments that move within or between genomes. - node_id: horizontal_gene_transfer label: horizontal gene transfer node_type: BIOLOGICAL_PROCESS description: Transfer of genetic material between organisms outside vertical descent. grounding: GO:0009292 - node_id: genome_plasticity label: genome plasticity node_type: QUALITY description: Capacity of a genome for rearrangement and gene gain/loss. - node_id: relaxase label: relaxase node_type: GENE_OR_PROTEIN description: Conjugation enzyme that nicks and unwinds DNA at oriT and covalently attaches to the 5-prime end. grounding: UniProtKB:A0A015YCT3 - node_id: orit label: origin of transfer (oriT) node_type: CELLULAR_LOCALIZATION description: DNA site where the relaxase nicks to initiate rolling-circle conjugative transfer. - node_id: coupling_protein label: type IV coupling protein node_type: GENE_OR_PROTEIN description: VirD4/TraD-like ATPase that recruits the relaxase-DNA substrate to the T4SS. - node_id: t4ss label: type IV secretion system node_type: GENE_OR_PROTEIN description: VirB4/VirD4-containing macromolecular machine that mediates conjugative DNA transfer. - node_id: conjugative_dna_transfer label: conjugative DNA transfer node_type: BIOLOGICAL_PROCESS description: Cell-to-cell transfer of single-stranded DNA through the mating apparatus. - node_id: integrase_excisionase label: integrase and excisionase node_type: GENE_OR_PROTEIN description: Recombinase plus recombination directionality factor that mediate ICE/IME excision. - node_id: ice_excision label: ICE excision and circularization node_type: BIOLOGICAL_PROCESS description: Excision of an integrated conjugative element to form a circular dsDNA transfer intermediate. - node_id: integron_integrase label: integron integrase (IntI) node_type: GENE_OR_PROTEIN description: Site-specific recombinase that captures and excises gene cassettes at attI/attC sites. - node_id: cassette_recombination label: attI/attC cassette recombination node_type: BIOLOGICAL_PROCESS description: Site-specific recombination inserting or excising integron gene cassettes. - node_id: transposition label: transposition node_type: BIOLOGICAL_PROCESS description: Movement of insertion sequences and transposons within or between replicons. grounding: GO:0032196 - node_id: transduction label: transduction of host DNA node_type: BIOLOGICAL_PROCESS description: Phage-mediated packaging and transfer of host DNA during prophage induction or lytic infection. - node_id: antibiotic_selection label: antibiotic selective pressure node_type: ENVIRONMENTAL_FACTOR description: Selective pressure from antibiotics that enriches resistance gene cargo on mobile elements. - node_id: amr_cargo label: antimicrobial resistance gene cargo node_type: QUALITY description: Accumulation of antimicrobial resistance genes carried on self-transmissible ICEs and genomic islands. edges: - subject: mge_trait predicate: enables object: horizontal_gene_transfer description: MGEs serve as the vehicles of horizontal gene transfer. evidence: - reference: DOI:10.1038/nrmicro1235 notes: Frost et al. frame MGEs as the agents of horizontal gene transfer. predicate_id: RO:0002327 - subject: horizontal_gene_transfer predicate: contributes to object: genome_plasticity description: HGT mediated by MGEs drives gene gain/loss and rearrangement. evidence: - reference: DOI:10.1111/1574-6976.12067 notes: Siguier et al. review insertion-sequence-driven genome plasticity. predicate_id: RO:0002326 - subject: relaxase predicate: nicks/unwinds at object: orit description: Relaxase nicks and unwinds DNA at oriT, covalently attaching to the 5-prime end to initiate transfer. evidence: - reference: DOI:10.1128/AEM.01360-24 notes: nicking/unwinding by a relaxase at oriT, covalent attachment of relaxase to the 5-prime end. - subject: coupling_protein predicate: recruits substrate to object: t4ss description: The cognate coupling protein recruits the relaxase-DNA substrate to the secretion apparatus. evidence: - reference: DOI:10.1093/nar/gkac1079 notes: the secretion apparatus by the cognate coupling protein TraD; type IV coupling proteins (T4CPs). - subject: t4ss predicate: mediates object: conjugative_dna_transfer description: VirB4/VirD4-containing T4SS mediates conjugative DNA transfer between donor and recipient. evidence: - reference: DOI:10.1093/nar/gkad024 notes: VirB4 and VirD4 ATPases of the Type IV secretion system (T4SS) mediate conjugative transfer. - subject: conjugative_dna_transfer predicate: enables object: horizontal_gene_transfer description: Conjugative DNA transfer is a major route of MGE-mediated horizontal gene transfer. evidence: - reference: DOI:10.1111/1751-7915.14408 notes: transfer of a single-stranded DNA molecule, followed by integration into the recipient chromosome. predicate_id: RO:0002327 - subject: integrase_excisionase predicate: enables object: ice_excision description: Integrase and excisionase mediate ICE excision and circular dsDNA intermediate formation. evidence: - reference: DOI:10.1128/AEM.01360-24 notes: excision mediated by an integrase (recombinase) and an excisionase, formation of a circular dsDNA intermediate. predicate_id: RO:0002327 - subject: ice_excision predicate: enables object: conjugative_dna_transfer description: Excision and circularization produce the transferable form required for conjugative transfer. evidence: - reference: DOI:10.1128/AEM.01360-24 notes: Circular dsDNA intermediate is the transferable form prior to conjugation. predicate_id: RO:0002327 - subject: integron_integrase predicate: catalyzes object: cassette_recombination description: Integron integrase catalyzes site-specific recombination at attI/attC to capture or excise cassettes. evidence: - reference: DOI:10.1111/1751-7915.14408 notes: IntI recognises attI/attC and catalyses site-specific recombination inserting cassettes. predicate_id: biolink:catalyzes - subject: mge_trait predicate: enables object: transposition description: Insertion sequences and transposons excise and move within or between regions of the genome. evidence: - reference: DOI:10.1146/annurev-micro-032521-022006 notes: transposons and insertion sequences excise and move or transpose between regions of the genome. predicate_id: RO:0002327 - subject: transposition predicate: contributes to object: genome_plasticity description: Transposition drives genome rearrangement and gene gain/loss. evidence: - reference: DOI:10.1146/annurev-micro-032521-022006 notes: IS/transposon mobility reshapes replicons, contributing to genome plasticity. predicate_id: RO:0002326 - subject: transduction predicate: contributes to object: horizontal_gene_transfer description: Prophage induction and lytic infection package and transduce host DNA, a route of HGT. evidence: - reference: DOI:10.1093/nar/gkae489 notes: host DNA packaged and transduced during both prophage induction and lytic infection. predicate_id: RO:0002326 - subject: antibiotic_selection predicate: enriches object: amr_cargo description: Antibiotic selective pressure enriches AMR genes on self-transmissible ICEs and genomic islands. evidence: - reference: DOI:10.1093/nar/gkad644 notes: antibiotic selective pressure tied to the accumulation and spread of resistance on self-transmissible ICEs. curation_history: - timestamp: '2026-06-05T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate GENOMICS axis class (mobile genetic element) to parent plasmid carriage, prophage, transposable element, and genomic island. llm_assisted: true - timestamp: '2026-06-08T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (MGE-mediated horizontal gene transfer) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-14T06:55:38Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 11 evidence-backed generic edges (13 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:11Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×4, RO:0002326×2, biolink:catalyzes×1). llm_assisted: true - timestamp: '2026-06-24T17:23:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0032196×1). llm_assisted: true - timestamp: '2026-06-26T07:15:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A015YCT3×1). llm_assisted: true