identifier: traitmech:000087
label: natural competence
definition: A physiological state in which a cell takes up free extracellular DNA
  from the environment and integrates it into its genome (natural genetic transformation).
definition_source: DOI:10.1038/nrmicro3199
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: natural transformation
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1038/nrmicro3199
evidence:
- reference: DOI:10.1038/nrmicro3199
  notes: Johnston et al. review the distribution, shared mechanisms, and control of
    natural bacterial transformation (competence for DNA uptake).
- reference: DOI:10.1038/s41579-021-00650-4
  notes: Review of horizontal gene transfer supports natural transformation as a major
    route of bacterial DNA acquisition.
canonical_examples:
- taxon_id: NCBITaxon:1313
  taxon_label: Streptococcus pneumoniae
  note: "Where natural genetic transformation was discovered (Griffith 1928; Avery 1944). Bacillus subtilis is the competence-regulation (ComK) model."
  reference: PMID:25445643
causal_graphs:
- graph_id: natural_competence_dna_uptake
  title: Competence-driven DNA uptake and transformation
  description: Evidence-backed causal sketch linking the competence program to uptake
    of extracellular DNA and genomic integration.
  nodes:
  - node_id: natural_competence_trait
    label: natural competence
    node_type: TRAIT
    grounding: traitmech:000087
    description: Capacity to take up and integrate environmental DNA.
  - node_id: competence_process
    label: establishment of competence for transformation
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0030420
    description: Development of the DNA-uptake state.
  - node_id: extracellular_dna
    label: extracellular DNA
    node_type: CHEMICAL
    description: Free environmental DNA taken up by competent cells.
  - node_id: competence_pilus
    label: type IV competence pilus
    node_type: GENE_OR_PROTEIN
    description: Retractile DNA-binding pilus filament of the competence apparatus.
  - node_id: pilus_retraction
    label: competence pilus retraction
    node_type: BIOLOGICAL_PROCESS
    description: Disassembly of the competence pilus that pulls bound DNA toward the
      cell.
  - node_id: dna_uptake
    label: extracellular DNA uptake
    node_type: BIOLOGICAL_PROCESS
    description: Import of bound extracellular DNA across the cell envelope.
  - node_id: comec
    label: ComEC
    node_type: GENE_OR_PROTEIN
    description: Inner-membrane channel required for DNA uptake into the cytoplasm.
    grounding: UniProtKB:A0A087CUH4
  - node_id: comea
    label: ComEA
    node_type: GENE_OR_PROTEIN
    description: DNA receptor that binds incoming DNA and mediates transfer toward
      the periplasm.
    grounding: UniProtKB:A0A0H2VI18
  - node_id: periplasm
    label: periplasm
    node_type: CELLULAR_LOCALIZATION
    description: Compartment to which bound DNA is transferred during uptake.
    grounding: GO:0042597
  - node_id: dpra
    label: DprA
    node_type: GENE_OR_PROTEIN
    description: Competence ssDNA-binding protein that protects incoming DNA and recruits
      RecA.
    grounding: UniProtKB:A0A1J0LTK6
  - node_id: reca
    label: RecA
    node_type: GENE_OR_PROTEIN
    description: Recombinase that mediates homologous recombination of transforming
      DNA.
    grounding: UniProtKB:A0A023H996
  - node_id: homologous_recombination
    label: homologous recombination of transforming DNA
    node_type: BIOLOGICAL_PROCESS
    description: Integration of incoming ssDNA into the genome via homologous recombination.
  edges:
  - subject: competence_process
    predicate: consumes
    object: extracellular_dna
    description: Competence drives uptake of extracellular DNA.
    evidence:
    - reference: DOI:10.1038/nrmicro3199
      notes: Johnston et al. review DNA-uptake mechanisms of competence.
    predicate_id: biolink:consumes
  - subject: competence_process
    predicate: enables
    object: natural_competence_trait
    description: The competence program realizes the natural-competence trait.
    evidence:
    - reference: DOI:10.1038/s41579-021-00650-4
      notes: Transformation is a major route of bacterial DNA acquisition.
    predicate_id: RO:0002327
  - subject: competence_pilus
    predicate: binds
    object: extracellular_dna
    description: Competence pili are retractile, DNA-binding filaments that capture
      extracellular DNA.
    evidence:
    - reference: DOI:10.1128/mmbr.00125-23
      notes: Competence pili "produce retractile, DNA-binding pili" and co-localize
        DNA at their tips (Zuke & Burton 2024).
  - subject: pilus_retraction
    predicate: promotes
    object: dna_uptake
    description: Pilus retraction is mechanistically coupled to DNA delivery into
      the uptake apparatus.
    evidence:
    - reference: DOI:10.1128/mmbr.00125-23
      notes: Physical obstruction of T4P retraction decreased transformation rate
        (Zuke & Burton 2024).
    predicate_id: RO:0002213
  - subject: comec
    predicate: required for
    object: dna_uptake
    description: ComEC forms a membrane channel required for DNA uptake.
    evidence:
    - reference: DOI:10.1101/2024.02.06.579203
      notes: '"ComEC is a membrane channel required for DNA uptake" (Hardy et al.
        2024).'
  - subject: comea
    predicate: mediates transfer to
    object: periplasm
    description: ComEA acts as an external DNA receptor and mediates transfer of DNA
      into the periplasm.
    evidence:
    - reference: DOI:10.1101/2024.02.06.579203
      notes: '"ComEA functions as an external DNA receptor and mediates transfer into
        the periplasm" (Hardy et al. 2024).'
  - subject: dpra
    predicate: recruits
    object: reca
    description: DprA protects incoming ssDNA and recruits RecA for recombination.
    evidence:
    - reference: DOI:10.1371/journal.pbio.3002814
      notes: '"DprA hands incoming ssDNA to RecA" / "protection of incoming ssDNA
        by DprA and recruitment of RecA" (Mazzamurro et al. 2024).'
  - subject: reca
    predicate: mediates
    object: homologous_recombination
    description: RecA mediates homologous recombination of incoming transforming DNA
      into the genome.
    evidence:
    - reference: DOI:10.1371/journal.pbio.3002814
      notes: Transformation is followed by RecA-dependent homologous recombination
        (Mazzamurro et al. 2024).
curation_history:
- timestamp: '2026-06-04T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate PHYSIOLOGY trait (natural competence) from literature
    research to fill the genetic-plasticity gap.
  llm_assisted: true
- timestamp: '2026-06-08T13:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (competence DNA uptake) with GO node
    grounding and biolink/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 (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:35Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0042597×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A087CUH4×1, UniProtKB:A0A0H2VI18×1, UniProtKB:A0A1J0LTK6×1, UniProtKB:A0A023H996×1).
  llm_assisted: true