identifier: METPO:1003023
label: brown pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear brown
  due to accumulation of brown pigments such as pyomelanin or other melanins.
definition_source: DOI:10.1128/AEM.67.8.3463-3468.2001
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_brown
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1128/AEM.67.8.3463-3468.2001
  snippet: Brown pigments are produced when homogentisic acid accumulates
  notes: Supports brown microbial pigmentation as a homogentisic-acid/pyomelanin pathway
    phenotype.
causal_graphs:
- graph_id: brown_pigmented_pyomelanin_pathway
  title: Brown pigmentation pyomelanin mechanism
  description: Evidence-backed causal sketch linking brown microbial pigmentation
    to tyrosine catabolism, homogentisic acid accumulation, oxidative polymerization
    into pyomelanin, and visible brown color.
  nodes:
  - node_id: brown_pigmented_trait
    label: brown pigmented
    node_type: TRAIT
    grounding: METPO:1003023
    description: Microbial pigmentation appearing brown.
  - node_id: tyrosine_catabolism
    label: tyrosine catabolism
    node_type: BIOLOGICAL_PROCESS
    description: Catabolic pathway generating homogentisic acid intermediates.
    grounding: GO:0006572
  - node_id: hppD
    label: 4-hydroxyphenylpyruvate dioxygenase
    node_type: GENE_OR_PROTEIN
    description: Enzyme that can form homogentisic acid from 4-hydroxyphenylpyruvate.
    grounding: UniProtKB:A0A009PXB6
  - node_id: homogentisic_acid
    label: homogentisic acid
    node_type: CHEMICAL
    description: HGA precursor that oxidizes and polymerizes to pyomelanin.
    grounding: CHEBI:44747
  - node_id: pyomelanin
    label: pyomelanin
    node_type: CHEMICAL
    description: Brown-to-black phenolic polymer pigment.
  - node_id: visible_brown_color
    label: visible brown color
    node_type: MOLECULAR_FUNCTION
    description: Observed brown colony or medium color.
  - node_id: four_hydroxyphenylpyruvate
    label: 4-hydroxyphenylpyruvate
    node_type: CHEMICAL
    description: Tyrosine catabolism intermediate converted to homogentisic acid by
      HppD.
    grounding: CHEBI:36242
  - node_id: hmgA
    label: homogentisate 1,2-dioxygenase
    node_type: GENE_OR_PROTEIN
    description: Enzyme (HmgA) that degrades homogentisic acid to maleylacetoacetate,
      diverting flux away from pyomelanin.
    grounding: UniProtKB:A0A010REZ7
  - node_id: maleylacetoacetate
    label: maleylacetoacetate
    node_type: CHEMICAL
    description: Product of homogentisic acid ring cleavage by HmgA in the tyrosine
      catabolism pathway.
  - node_id: benzoquinoneacetic_acid
    label: benzoquinoneacetic acid
    node_type: CHEMICAL
    description: Auto-oxidation product of homogentisic acid that self-polymerizes
      into pyomelanin.
    grounding: CHEBI:137246
  edges:
  - subject: tyrosine_catabolism
    predicate: produces
    object: homogentisic_acid
    description: Tyrosine catabolism can generate homogentisic acid.
    evidence:
    - reference: DOI:10.1128/AEM.67.8.3463-3468.2001
      snippet: homogentisic acid accumulates in the medium
      notes: Supports HGA accumulation as upstream of brown pigment formation.
    predicate_id: METPO:2000202
  - subject: hppD
    predicate: catalyzes formation of
    object: homogentisic_acid
    description: HppD catalyzes formation of homogentisic acid in pyomelanin pathways.
    evidence:
    - reference: DOI:10.1371/journal.pone.0120923
      snippet: catalyzes the reaction from 4-hydroxyphenylpyruvate to HGA
      notes: Supports HppD-mediated HGA formation in bacterial pyomelanin production.
    predicate_id: biolink:catalyzes
  - subject: homogentisic_acid
    predicate: polymerizes to
    object: pyomelanin
    description: HGA oxidizes and polymerizes into pyomelanin.
    evidence:
    - reference: DOI:10.1128/AEM.67.8.3463-3468.2001
      snippet: spontaneously oxidize and polymerize
      notes: Supports HGA polymerization as the source of pyomelanin.
  - subject: pyomelanin
    predicate: causes
    object: visible_brown_color
    description: Pyomelanin causes visible brown pigmentation.
    evidence:
    - reference: DOI:10.1128/AEM.67.8.3463-3468.2001
      snippet: Brown pigments are produced
      notes: Supports brown color as the output of pyomelanin formation.
    predicate_id: biolink:causes
  - subject: visible_brown_color
    predicate: manifests as
    object: brown_pigmented_trait
    description: Visible brown color manifests the brown-pigmented phenotype.
    evidence:
    - reference: DOI:10.1016/j.biotechadv.2021.107773
      snippet: black/brown color to the cells
      notes: Supports brown microbial cell color as a melanin-related pigmentation
        phenotype.
    predicate_id: METPO:2007400
  - subject: tyrosine_catabolism
    predicate: produces
    object: four_hydroxyphenylpyruvate
    description: Tyrosine catabolism produces 4-hydroxyphenylpyruvate as an intermediate.
    evidence:
    - reference: DOI:10.1038/s41564-023-01517-5
      notes: Tyrosine aminotransferases convert L-tyrosine into 4-hydroxyphenylpyruvate;
        biochemically generalizable precursor step.
    predicate_id: METPO:2000202
  - subject: four_hydroxyphenylpyruvate
    predicate: converted to
    object: homogentisic_acid
    description: HppD converts 4-hydroxyphenylpyruvate to homogentisic acid.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: hppD codes for a protein responsible for conversion of 4-hydroxyphenylpyruvate
        to HGA.
  - subject: hmgA
    predicate: converts
    object: maleylacetoacetate
    description: HmgA converts homogentisic acid to maleylacetoacetate, the degradative
      branch.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: Homogentisate 1,2-dioxygenase (hmgA) converts HGA to maleylacetoacetate;
        core negative branch away from pigment formation.
  - subject: homogentisic_acid
    predicate: auto-oxidizes to
    object: benzoquinoneacetic_acid
    description: Excreted homogentisic acid spontaneously auto-oxidizes to benzoquinoneacetic
      acid.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: HGA is excreted and spontaneously auto-oxidizes to form benzoquinoneacetic
        acid.
  - subject: benzoquinoneacetic_acid
    predicate: polymerizes to
    object: pyomelanin
    description: Benzoquinoneacetic acid self-polymerizes to produce pyomelanin.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: Auto-oxidation followed by self-polymerization to produce pyomelanin.
curation_history:
- timestamp: '2026-05-05T01:35:46.943677+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T19:10:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added DOI-backed definition and causal graph for tyrosine catabolism, HppD,
    homogentisic acid, pyomelanin, and visible brown 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: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A009PXB6×1).
  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
    (biolink:catalyzes×1).
  llm_assisted: true
- timestamp: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0006572×1, CHEBI:44747×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  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: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:36242×1, CHEBI:137246×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A010REZ7×1).
  llm_assisted: true