identifier: METPO:1003021
label: pigmentation
definition: A phenotype characterized by the color of pigments produced by a microorganism.
definition_source: DOI:10.1016/j.procbio.2013.06.006
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
evidence:
- reference: DOI:10.1016/j.procbio.2013.06.006
  snippet: bacterial pigments in food, pharmaceuticals, dyeing and other aspects
  notes: Supports bacterial pigments as chemically produced microbial color phenotypes.
causal_graphs:
- graph_id: pigmentation_biosynthetic_colorants
  title: Microbial pigmentation biosynthetic mechanism
  description: Evidence-backed causal sketch linking microbial pigmentation to pigment
    biosynthesis pathways, chromophore-containing metabolites, environmental regulation,
    and visible colony color.
  nodes:
  - node_id: pigmentation_trait
    label: pigmentation
    node_type: TRAIT
    grounding: METPO:1003021
    description: Microbial phenotype defined by pigment-derived color.
  - node_id: pigment_biosynthesis
    label: pigment biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Enzymatic production of colored microbial metabolites.
    grounding: GO:0046148
  - node_id: chromophore_metabolites
    label: chromophore-containing metabolites
    node_type: CHEMICAL
    description: Colored molecules such as carotenoids, prodiginines, melanins, and
      phenazines.
  - node_id: environmental_regulation
    label: environmental regulation
    node_type: ENVIRONMENTAL_FACTOR
    description: Culture and environmental conditions that alter pigment production.
  - node_id: visible_colony_color
    label: visible colony color
    node_type: MOLECULAR_FUNCTION
    description: Absorption and reflection phenotype observed as microbial color.
  - node_id: mva_pathway
    label: mevalonate pathway
    node_type: PATHWAY
    description: Pathway producing C5 isoprenoid precursors (IPP and DMAPP) for terpenoid
      biosynthesis.
  - node_id: mep_pathway
    label: MEP pathway
    node_type: PATHWAY
    description: 2-C-methyl-D-erythritol 4-phosphate pathway producing C5 isoprenoid
      precursors IPP and DMAPP.
  - node_id: carotenoid_biosynthesis
    label: carotenoid biosynthesis
    node_type: PATHWAY
    description: Biosynthetic pathway producing carotenoid pigments from isoprenoid
      precursors.
    grounding: GO:0016117
  - node_id: shikimate_pathway
    label: shikimate pathway
    node_type: PATHWAY
    description: Pathway providing aromatic precursors used in phenazine biosynthesis.
    grounding: GO:0009423
  - node_id: phenazine_biosynthesis
    label: phenazine biosynthesis
    node_type: PATHWAY
    description: Biosynthetic pathway producing phenazine pigments such as pyocyanin.
  - node_id: crt_carotenoid_genes
    label: crtE/crtB/crtI/crtY gene set
    node_type: GENE_OR_PROTEIN
    description: Core carotenogenic genes encoding enzymes for beta-carotene biosynthesis.
  - node_id: beta_carotene_biosynthesis
    label: beta-carotene biosynthesis
    node_type: PATHWAY
    description: Biosynthetic route producing the carotenoid pigment beta-carotene.
    grounding: GO:1901812
  - node_id: hppd_gene
    label: hppD 4-hydroxyphenylpyruvate dioxygenase
    node_type: GENE_OR_PROTEIN
    description: Enzyme converting 4-hydroxyphenylpyruvate to homogentisate.
  - node_id: homogentisate
    label: homogentisate
    node_type: CHEMICAL
    description: Aromatic metabolite that auto-oxidizes and polymerizes to pyomelanin.
    grounding: CHEBI:16169
  - node_id: pyomelanin
    label: pyomelanin
    node_type: CHEMICAL
    description: Brown-black pigment formed by polymerization of homogentisate.
  - node_id: hmga_gene
    label: hmgA homogentisate 1,2-dioxygenase
    node_type: GENE_OR_PROTEIN
    description: Enzyme converting homogentisate to maleylacetoacetate, preventing
      pyomelanin accumulation.
  edges:
  - subject: pigment_biosynthesis
    predicate: produces
    object: chromophore_metabolites
    description: Pigment biosynthetic pathways produce colored metabolites.
    evidence:
    - reference: DOI:10.1016/j.procbio.2013.06.006
      snippet: bacterial pigments and their applications
      notes: Review supports bacterial pigment production as biosynthesis of colored
        compounds.
    predicate_id: METPO:2000202
  - subject: chromophore_metabolites
    predicate: causes
    object: visible_colony_color
    description: Chromophore-containing metabolites cause visible microbial color.
    evidence:
    - reference: DOI:10.1177/1934578X1801301240
      snippet: such as melanin, carotenoids, pyocyanin, bacteriochlorophylls, violacein,
        prodigiosin
      notes: Supports multiple chemically distinct bacterial pigments as colorants.
    predicate_id: biolink:causes
  - subject: environmental_regulation
    predicate: modulates
    object: pigment_biosynthesis
    description: Growth and environmental conditions can modulate pigment biosynthesis.
    evidence:
    - reference: DOI:10.3389/fsufs.2020.00100
      snippet: bacterial pigments ... production ... genetic engineering
      notes: Supports pigment production as condition- and regulation-sensitive; retained
        as a broad regulatory edge.
    predicate_id: RO:0002211
  - subject: visible_colony_color
    predicate: manifests as
    object: pigmentation_trait
    description: Visible colony color manifests the pigmentation phenotype.
    evidence:
    - reference: DOI:10.1016/j.procbio.2013.06.006
      snippet: focus on applications of bacterial pigments
      notes: Supports pigmentation as a visible output of bacterial pigment chemistry.
    predicate_id: METPO:2007400
  - subject: mva_pathway
    predicate: provides precursor for
    object: carotenoid_biosynthesis
    description: The mevalonate pathway supplies C5 isoprenoid precursors (IPP/DMAPP)
      for carotenoid biosynthesis.
    evidence:
    - reference: DOI:10.3390/microorganisms11122920
      notes: GGPP originates from C5 precursors (IPP and DMAPP) via either the MVA
        or MEP pathways.
  - subject: mep_pathway
    predicate: provides precursor for
    object: carotenoid_biosynthesis
    description: The MEP pathway supplies C5 isoprenoid precursors (IPP/DMAPP) for
      carotenoid biosynthesis.
    evidence:
    - reference: DOI:10.3390/microorganisms11122920
      notes: GGPP originates from C5 precursors (IPP and DMAPP) via either the MVA
        or MEP pathways.
  - subject: crt_carotenoid_genes
    predicate: enables
    object: beta_carotene_biosynthesis
    description: The crtE/crtB/crtI/crtY gene set encodes enzymes enabling beta-carotene
      biosynthesis.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: 'beta-carotene: crtE, crtY, crtI, crtB; curate as generic carotenoid
        module.'
    predicate_id: RO:0002327
  - subject: beta_carotene_biosynthesis
    predicate: is a
    object: carotenoid_biosynthesis
    description: Beta-carotene biosynthesis is a specific carotenoid biosynthetic
      route.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: Beta-carotene is a carotenoid pigment produced by carotenogenic crt genes.
    predicate_id: rdfs:subClassOf
  - subject: shikimate_pathway
    predicate: precursor of
    object: phenazine_biosynthesis
    description: The shikimate pathway provides aromatic precursors for phenazine
      biosynthesis.
    evidence:
    - reference: DOI:10.3390/microorganisms11122920
      notes: Phenazine pigments (including pyocyanin) derive from the shikimate pathway.
  - subject: hppd_gene
    predicate: produces
    object: homogentisate
    description: HppD converts 4-hydroxyphenylpyruvate to homogentisate in the pyomelanin
      pathway.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: Conversion of 4-hydroxyphenylpyruvate to HGA by HppD.
    predicate_id: METPO:2000202
  - subject: homogentisate
    predicate: polymerizes to form
    object: pyomelanin
    description: Homogentisate auto-oxidizes and polymerizes to form the pigment pyomelanin.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: HGA, excretion of HGA, spontaneous auto-oxidation and polymerization
        to pyomelanin.
  - subject: hmga_gene
    predicate: prevents accumulation of
    object: pyomelanin
    description: HmgA converts homogentisate to maleylacetoacetate, preventing pyomelanin
      accumulation.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: HmgA normally converts HGA to maleylacetoacetate, preventing pigment
        accumulation.
curation_history:
- timestamp: '2026-05-05T01:35:46.942456+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T18:45:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Reviewed pigmentation and added DOI-backed causal graph for pigment biosynthesis,
    chromophore metabolites, environmental regulation, and visible colony color.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-20T05:49:24Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007400×1).
  llm_assisted: true
- timestamp: '2026-06-13T21:03:26Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0046148×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (11 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, rdfs:subClassOf×1, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0016117×1, GO:0009423×1, GO:1901812×1, CHEBI:16169×1).
  llm_assisted: true