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natural competence

traitmech:000087 · CLASS · REVIEWED

A physiological state in which a cell takes up free extracellular DNA from the environment and integrates it into its genome (natural genetic transformation).

Competence-driven DNA uptake and transformation

Evidence-backed causal sketch linking the competence program to uptake of extracellular DNA and genomic integration.

Competence-driven DNA uptake and transformation Interactive directed graph showing evidence-backed causal relationships for natural competence.

Edge evidence

  • establishment of competence for transformation consumes extracellular DNA biolink:consumes

    Competence drives uptake of extracellular DNA.

    • DOI:10.1038/nrmicro3199 Johnston et al. review DNA-uptake mechanisms of competence.
  • establishment of competence for transformation enables natural competence RO:0002327

    The competence program realizes the natural-competence trait.

    • DOI:10.1038/s41579-021-00650-4 Transformation is a major route of bacterial DNA acquisition.
  • type IV competence pilus binds extracellular DNA

    Competence pili are retractile, DNA-binding filaments that capture extracellular DNA.

    • DOI:10.1128/mmbr.00125-23 Competence pili "produce retractile, DNA-binding pili" and co-localize DNA at their tips (Zuke & Burton 2024).
  • competence pilus retraction promotes extracellular DNA uptake RO:0002213

    Pilus retraction is mechanistically coupled to DNA delivery into the uptake apparatus.

    • DOI:10.1128/mmbr.00125-23 Physical obstruction of T4P retraction decreased transformation rate (Zuke & Burton 2024).
  • ComEC required for extracellular DNA uptake

    ComEC forms a membrane channel required for DNA uptake.

    • DOI:10.1101/2024.02.06.579203 "ComEC is a membrane channel required for DNA uptake" (Hardy et al. 2024).
  • ComEA mediates transfer to periplasm

    ComEA acts as an external DNA receptor and mediates transfer of DNA into the periplasm.

    • DOI:10.1101/2024.02.06.579203 "ComEA functions as an external DNA receptor and mediates transfer into the periplasm" (Hardy et al. 2024).
  • DprA recruits RecA

    DprA protects incoming ssDNA and recruits RecA for recombination.

    • DOI:10.1371/journal.pbio.3002814 "DprA hands incoming ssDNA to RecA" / "protection of incoming ssDNA by DprA and recruitment of RecA" (Mazzamurro et al. 2024).
  • RecA mediates homologous recombination of transforming DNA

    RecA mediates homologous recombination of incoming transforming DNA into the genome.

    • DOI:10.1371/journal.pbio.3002814 Transformation is followed by RecA-dependent homologous recombination (Mazzamurro et al. 2024).

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1038/nrmicro3199

Parent traits (1)

Synonyms (1)

  • natural transformation RELATED_SYNONYM · DOI:10.1038/nrmicro3199

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Curation history

  1. · PROPOSED_FROM_RESEARCH · claude

    Proposed candidate PHYSIOLOGY trait (natural competence) from literature research to fill the genetic-plasticity gap.

  2. · CURATED_CAUSAL_GRAPH · claude

    Added evidence-backed causal graph (competence DNA uptake) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.

  3. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1).

  5. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042597×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A087CUH4×1, UniProtKB:A0A0H2VI18×1, UniProtKB:A0A1J0LTK6×1, UniProtKB:A0A023H996×1).