identifier: METPO:1003022
label: black pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear black
  or very dark due to accumulation of dark pigments such as melanins.
definition_source: DOI:10.1016/j.biotechadv.2021.107773
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_black
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1016/j.biotechadv.2021.107773
  snippet: dark-colored pigment
  notes: Supports black/dark microbial pigmentation as a melanin-associated color
    phenotype.
canonical_examples:
- taxon_id: NCBITaxon:837
  taxon_label: Porphyromonas gingivalis
  note: "black-pigmented anaerobe on blood agar"
  reference: PMID:26903954
- taxon_id: NCBITaxon:28132
  taxon_label: Prevotella melaninogenica
  note: "black-pigmented anaerobe"
  reference: DOI:10.1099/00207713-32-4-399
causal_graphs:
- graph_id: black_pigmented_melanin_polymer
  title: Black pigmentation melanin polymer mechanism
  description: Evidence-backed causal sketch linking black microbial pigmentation
    to phenolic precursors, oxidase-catalyzed melanin biosynthesis, dark melanin polymers,
    and visible black color.
  nodes:
  - node_id: black_pigmented_trait
    label: black pigmented
    node_type: TRAIT
    grounding: METPO:1003022
    description: Microbial pigmentation appearing black or very dark.
  - node_id: phenolic_precursors
    label: phenolic precursors
    node_type: CHEMICAL
    description: Tyrosine-derived, DOPA-like, DHN-like, or HGA-like precursors for
      melanin formation.
  - node_id: tyrosinase_laccase_oxidases
    label: tyrosinase/laccase oxidases
    node_type: GENE_OR_PROTEIN
    description: Oxidative enzymes that can catalyze melanin precursor oxidation.
  - node_id: melanin_biosynthesis
    label: melanin biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Oxidative polymerization process producing microbial melanins.
    grounding: GO:0042438
  - node_id: black_brown_melanin
    label: black-brown melanin
    node_type: CHEMICAL
    description: Dark melanin polymer causing black or brown pigmentation.
  - node_id: visible_black_color
    label: visible black color
    node_type: MOLECULAR_FUNCTION
    description: Observed black or very dark colony or cell color.
  - node_id: dopaquinone
    label: dopaquinone/dihydroxyindole intermediates
    node_type: CHEMICAL
    description: Reactive quinone and dihydroxyindole intermediates that polymerize
      into eumelanin.
  - node_id: dhn_precursor
    label: DHN (1,8-dihydroxynaphthalene)
    node_type: CHEMICAL
    description: Naphthalene-derived precursor polymerized into DHN-melanin.
  - node_id: polyketide_synthase
    label: polyketide synthase (PKS)
    node_type: GENE_OR_PROTEIN
    description: Enzyme synthesizing tetrahydroxynaphthalene precursor of the DHN-melanin
      pathway.
    grounding: UniProtKB:Q5Y9G5
  - node_id: dhn_melanin
    label: DHN-melanin (allomelanin)
    node_type: CHEMICAL
    description: Dark melanin polymer formed from DHN via laccase-catalyzed polymerization.
  - node_id: tyrosinase
    label: tyrosinase
    node_type: GENE_OR_PROTEIN
    description: Copper-dependent oxidase catalyzing hydroxylation and oxidation steps
      of the DOPA-melanin pathway.
    grounding: UniProtKB:A0A023Y3L4
  - node_id: hydroxyphenylpyruvate
    label: 4-hydroxyphenylpyruvate
    node_type: CHEMICAL
    description: Tyrosine-catabolism intermediate, substrate of HppD.
    grounding: CHEBI:36242
  - node_id: copper_ion
    label: copper ion
    node_type: CHEMICAL
    description: Copper cofactor required for catalytic activity of tyrosinase.
  - node_id: l_tyrosine
    label: L-tyrosine
    node_type: CHEMICAL
    description: Aromatic amino acid precursor for DOPA-melanin biosynthesis.
  - node_id: dopa_melanin
    label: DOPA-melanin (eumelanin)
    node_type: CHEMICAL
    description: Black-to-brown eumelanin polymer formed from DOPA-derived intermediates.
  - node_id: hppd
    label: HppD (4-hydroxyphenylpyruvate dioxygenase)
    node_type: GENE_OR_PROTEIN
    description: Enzyme converting 4-hydroxyphenylpyruvate to homogentisic acid in
      the pyomelanin route.
  - node_id: homogentisic_acid
    label: homogentisic acid (HGA)
    node_type: CHEMICAL
    description: Pyomelanin precursor that auto-oxidizes and polymerizes into pyomelanin.
  - node_id: hmga
    label: HmgA (homogentisate 1,2-dioxygenase)
    node_type: GENE_OR_PROTEIN
    description: Enzyme converting HGA to maleylacetoacetate; loss leads to HGA accumulation
      and pyomelanin.
  edges:
  - subject: phenolic_precursors
    predicate: feed into
    object: melanin_biosynthesis
    description: Phenolic precursors feed oxidative melanin-forming pathways.
    evidence:
    - reference: DOI:10.1007/s11274-020-02941-z
      snippet: oxidative polymerization of tyrosine derivatives
      notes: Supports phenolic or tyrosine-derived precursors as melanin biosynthetic
        substrates.
  - subject: tyrosinase_laccase_oxidases
    predicate: catalyzes
    object: melanin_biosynthesis
    description: Oxidases catalyze precursor oxidation in melanin formation.
    evidence:
    - reference: DOI:10.1016/j.biotechadv.2021.107773
      snippet: biosynthesis ... oxidative polymerization
      notes: Supports oxidative enzymatic routes for microbial melanin formation.
    predicate_id: biolink:catalyzes
  - subject: melanin_biosynthesis
    predicate: produces
    object: black_brown_melanin
    description: Melanin biosynthesis produces dark melanin polymers.
    evidence:
    - reference: DOI:10.1016/j.biotechadv.2021.107773
      snippet: Eumelanin and allomelanin impart black/brown color
      notes: Supports black-brown melanins as microbial colorants.
    predicate_id: METPO:2000202
  - subject: black_brown_melanin
    predicate: causes
    object: visible_black_color
    description: Dark melanin polymers cause visible black pigmentation when sufficiently
      accumulated.
    evidence:
    - reference: DOI:10.1016/j.biotechadv.2021.107773
      snippet: black/brown color
      notes: Supports black color as an outcome of dark melanin accumulation.
    predicate_id: biolink:causes
  - subject: visible_black_color
    predicate: manifests as
    object: black_pigmented_trait
    description: Visible black color manifests the black-pigmented phenotype.
    evidence:
    - reference: DOI:10.1016/j.biotechadv.2021.107773
      snippet: black/brown color to the cells
      notes: Supports the trait-level assignment.
    predicate_id: METPO:2007400
  - subject: tyrosinase
    predicate: catalyzes conversion of
    object: l_tyrosine
    description: Tyrosinase hydroxylates L-tyrosine to L-DOPA, initiating the DOPA-melanin
      pathway.
    evidence:
    - reference: DOI:10.3390/ijms25053013
      notes: Tyrosinase first catalyzes the hydroxylation of L-tyrosine to L-DOPA.
  - subject: dopaquinone
    predicate: polymerizes into
    object: dopa_melanin
    description: Dopaquinone/dihydroxyindole intermediates polymerize into DOPA-melanin
      (eumelanin).
    evidence:
    - reference: DOI:10.3390/jof9090891
      notes: Dopaquinone oxidized to dopachrome then dihydroxy-indoles which polymerize
        to form DOPA-melanins.
  - subject: copper_ion
    predicate: required cofactor for
    object: tyrosinase
    description: Copper ions are required cofactors for tyrosinase catalytic activity.
    evidence:
    - reference: DOI:10.3390/microorganisms12071352
      notes: Tyrosinases are copper-dependent enzymes.
  - subject: polyketide_synthase
    predicate: synthesizes precursor for
    object: dhn_precursor
    description: Polyketide synthase forms tetrahydroxynaphthalene leading to DHN,
      precursor of DHN-melanin.
    evidence:
    - reference: DOI:10.3390/microorganisms12071352
      notes: Polyketide synthase forms 1,3,6,8-tetrahydroxynaphthalene; polymerization
        of DHN leads to melanin.
  - subject: dhn_precursor
    predicate: polymerizes into
    object: dhn_melanin
    description: DHN polymerizes into DHN-melanin (allomelanin), a dark pigment.
    evidence:
    - reference: DOI:10.3390/microorganisms12071352
      notes: Polymerization of DHN leads to the formation of melanin.
  - subject: hppd
    predicate: converts
    object: hydroxyphenylpyruvate
    description: HppD converts 4-hydroxyphenylpyruvate to homogentisic acid in the
      pyomelanin pathway.
    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: homogentisic_acid
    description: HmgA (homogentisate 1,2-dioxygenase) converts HGA to maleylacetoacetate.
    evidence:
    - reference: DOI:10.1128/spectrum.00410-24
      notes: Homogentisate 1,2-dioxygenase encoded by hmgA converts HGA to maleylacetoacetate.
curation_history:
- timestamp: '2026-05-05T01:35:46.942877+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 phenolic precursors, oxidative
    melanin biosynthesis, black-brown melanin polymers, and visible black 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 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:catalyzes×1, 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: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0042438×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (12 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:36242×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:Q5Y9G5×1, UniProtKB:A0A023Y3L4×1).
  llm_assisted: true