identifier: traitmech:000091 label: prophage definition: A genomics trait describing possession of an integrated (or extrachromosomal) temperate bacteriophage genome (a prophage) maintained in the host during lysogeny, often contributing genes that alter host phenotype. definition_source: DOI:10.1128/MMBR.67.2.238-276.2003 trait_category: GENOMICS term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000089 synonyms: - synonym_text: lysogen synonym_type: RELATED_SYNONYM source: DOI:10.1038/ismej.2017.16 evidence: - reference: DOI:10.1128/MMBR.67.2.238-276.2003 notes: Canchaya et al. review prophage genomics, showing most sequenced bacterial genomes carry prophage sequences. - reference: DOI:10.1038/ismej.2017.16 notes: Howard-Varona et al. review lysogeny in nature, the maintenance of temperate phage genomes within hosts. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: "lambda and other integrated prophages" reference: PMID:21266997 - taxon_id: NCBITaxon:28901 taxon_label: Salmonella enterica note: "Gifsy/Fels prophages" reference: PMID:29780368 causal_graphs: - graph_id: prophage_lysogeny title: Prophage maintenance during lysogeny alters host phenotype description: Evidence-backed causal sketch linking prophage carriage to lysogenic maintenance and lysogenic conversion of the host. nodes: - node_id: prophage_trait label: prophage node_type: TRAIT grounding: traitmech:000091 description: Possession of an integrated or maintained temperate phage genome. - node_id: lysogeny label: lysogeny node_type: BIOLOGICAL_PROCESS description: Maintenance of a temperate phage genome within the host without lysis. - node_id: host_phenotype label: host phenotype node_type: QUALITY description: Phage-encoded gene functions expressed in the lysogen. - node_id: host_chromosome label: bacterial chromosome node_type: CELLULAR_LOCALIZATION description: Host genomic DNA into which a temperate prophage integrates. - node_id: ci_repressor label: CI master repressor node_type: GENE_OR_PROTEIN description: Phage-encoded cI-family repressor that maintains lysogeny by blocking lytic gene expression. - node_id: lytic_gene_expression label: lytic gene expression node_type: BIOLOGICAL_PROCESS description: Expression of phage lytic genes (from promoter PR) leading to the lytic cycle. - node_id: dna_damage label: DNA damage / replication stress node_type: ENVIRONMENTAL_FACTOR description: Genotoxic stress or replication inhibition that generates ssDNA and triggers the SOS response. - node_id: sos_response label: RecA-LexA SOS response node_type: BIOLOGICAL_PROCESS description: Bacterial DNA-damage-inducible SOS response mediated by RecA and LexA. - node_id: reca_filament label: RecA* nucleoprotein filament node_type: GENE_OR_PROTEIN description: Activated RecA nucleoprotein filament that promotes autocleavage of LexA and phage repressors. - node_id: lexa_repressor label: LexA repressor node_type: GENE_OR_PROTEIN description: Host SOS master repressor inactivated by RecA*-stimulated autoproteolysis. grounding: UniProtKB:A0A016XIE2 - node_id: prophage_induction label: prophage induction node_type: BIOLOGICAL_PROCESS description: Switch from lysogeny to the lytic cycle following derepression of phage lytic genes. grounding: GO:0098689 - node_id: phage_plasmid label: phage-plasmid node_type: GENE_OR_PROTEIN description: Hybrid mobile genetic element; a temperate phage maintained extrachromosomally as a plasmid. - node_id: extrachromosomal_maintenance label: extrachromosomal prophage maintenance node_type: BIOLOGICAL_PROCESS description: Maintenance of a temperate phage genome episomally rather than integrated in the chromosome. edges: - subject: prophage_trait predicate: enables object: lysogeny description: Prophage carriage is the genomic state realized during lysogeny. evidence: - reference: DOI:10.1128/MMBR.67.2.238-276.2003 notes: Canchaya et al. document widespread prophage maintenance in sequenced bacterial genomes. predicate_id: RO:0002327 - subject: prophage_trait predicate: contributes to object: host_phenotype description: Prophage-encoded genes can alter host virulence or fitness (lysogenic conversion). evidence: - reference: DOI:10.1038/ismej.2017.16 notes: Howard-Varona et al. review host-phenotype effects of lysogeny in nature. predicate_id: RO:0002326 - subject: prophage_trait predicate: integrates into object: host_chromosome description: Temperate prophages canonically integrate into the host chromosome (though some persist extrachromosomally). evidence: - reference: DOI:10.1038/s41586-023-06376-y notes: Temperate phages remain dormant as prophages integrated into the host genome and passed to host progeny. - subject: ci_repressor predicate: represses object: lytic_gene_expression description: Lysogeny is maintained by a phage-encoded CI repressor that binds the lysis promoter PR to block lytic gene expression. evidence: - reference: DOI:10.1038/s41586-023-06376-y notes: cI repressor binds the lysis promoter (PR) to block lytic gene expression. - subject: dna_damage predicate: activates object: sos_response description: DNA damage / replication stress generates ssDNA that triggers the RecA-LexA SOS response. evidence: - reference: DOI:10.1073/pnas.2407832121 notes: Replication inhibition creates ssDNA gaps that trigger the classical SOS response. predicate_id: RO:0002213 - subject: reca_filament predicate: promotes autocleavage of object: lexa_repressor description: Activated RecA* promotes LexA autoproteolysis, de-repressing the SOS regulon. evidence: - reference: DOI:10.1128/aem.01716-22 notes: RecA* activation induces LexA autoproteolysis; SOS response is mediated by RecA and LexA. - subject: reca_filament predicate: promotes autocleavage of object: ci_repressor description: RecA* stimulates self-cleavage/inactivation of the phage CI repressor, de-repressing lysis and triggering induction. evidence: - reference: DOI:10.1038/s41586-023-06376-y notes: Host RecA activation leads to autoproteolysis and inactivation of cI, de-repressing lysis. - subject: ci_repressor predicate: prevents object: prophage_induction description: While intact, the CI repressor maintains lysogeny and prevents prophage induction; its inactivation triggers induction. evidence: - reference: DOI:10.1038/s41586-023-06376-y notes: CI repression must be relieved (cI inactivation) to de-repress lysis and drive prophage induction. predicate_id: RO:0002212 - subject: phage_plasmid predicate: enables object: extrachromosomal_maintenance description: Phage-plasmids are temperate phages maintained extrachromosomally, so prophages need not be integrated. evidence: - reference: DOI:10.1038/s41467-024-45757-3 notes: Phage-plasmids are temperate phages maintained extrachromosomally as low-copy-number episomal forms. predicate_id: RO:0002327 curation_history: - timestamp: '2026-06-05T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate GENOMICS trait (prophage / lysogeny); 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 (prophage lysogeny) with RO predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:11Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1, RO:0002212×1, RO:0002327×1). 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:0098689×1). 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:A0A016XIE2×1). llm_assisted: true