identifier: METPO:1003027
label: pink pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear pink
  due to accumulation of pink or rose carotenoid pigments.
definition_source: DOI:10.1080/1040841X.2025.2526423
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_pink
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1080/1040841X.2025.2526423
  snippet: red, pink, orange, and yellow pigmentation in bacteria
  notes: Supports pink bacterial pigmentation as a carotenoid-associated color phenotype.
canonical_examples:
- taxon_id: NCBITaxon:408
  taxon_label: Methylorubrum extorquens
  note: "pink-pigmented facultative methylotroph"
  reference: PMID:29472323
- taxon_id: NCBITaxon:125216
  taxon_label: Roseomonas
  note: "pink-pigmented"
  reference: PMID:8308122
causal_graphs:
- graph_id: pink_pigmented_carotenoid_color
  title: Pink pigmentation carotenoid mechanism
  description: Evidence-backed causal sketch linking pink microbial pigmentation to
    carotenoid biosynthesis, conjugated carotenoid pigments, and visible pink color.
  nodes:
  - node_id: pink_pigmented_trait
    label: pink pigmented
    node_type: TRAIT
    grounding: METPO:1003027
    description: Microbial pigmentation appearing pink.
  - node_id: isoprenoid_precursors
    label: isoprenoid precursors
    node_type: CHEMICAL
    description: Prenyl building blocks used in carotenoid biosynthesis.
  - node_id: crt_enzymes
    label: Crt enzymes
    node_type: GENE_OR_PROTEIN
    description: Bacterial carotenoid biosynthetic enzymes.
  - node_id: carotenoid_biosynthesis
    label: carotenoid biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Enzymatic pathway producing carotenoid pigments.
    grounding: GO:0016117
  - node_id: pink_carotenoids
    label: pink carotenoids
    node_type: CHEMICAL
    description: Carotenoid pigments that produce pink or rose coloration.
  - node_id: visible_pink_color
    label: visible pink color
    node_type: MOLECULAR_FUNCTION
    description: Observed pink colony or cell color.
  - node_id: lycopene
    label: lycopene
    node_type: CHEMICAL
    description: Central acyclic carotenoid precursor of colored downstream carotenoids.
    grounding: CHEBI:15948
  - node_id: photosynthesis_gene_cluster
    label: photosynthesis gene cluster
    node_type: GENE_OR_PROTEIN
    description: Genomic module that co-localizes crt carotenoid genes with photosynthesis
      genes in phototrophs.
  - node_id: oxygen
    label: oxygen
    node_type: ENVIRONMENTAL_FACTOR
    description: Environmental oxygen level regulating carotenoid biosynthetic gene
      expression.
    grounding: ENVO:01001495
  - node_id: crt_operon
    label: crtI-crtB operon
    node_type: GENE_OR_PROTEIN
    description: Carotenoid biosynthetic operon encoding phytoene synthase and desaturase.
  edges:
  - subject: isoprenoid_precursors
    predicate: feed into
    object: carotenoid_biosynthesis
    description: Isoprenoid precursors provide substrate for carotenoid production.
    evidence:
    - reference: DOI:10.1016/j.gene.2004.11.038
      snippet: isoprenoid precursor biosynthesis
      notes: Supports isoprenoid precursor biosynthesis as an upstream step in eubacterial
        carotenoid pathways.
  - subject: crt_enzymes
    predicate: catalyzes
    object: carotenoid_biosynthesis
    description: Crt enzymes catalyze reactions in carotenoid biosynthesis.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: crt genes ... reactions they catalyze
      notes: Supports Crt enzymes as pathway catalysts.
    predicate_id: biolink:catalyzes
  - subject: carotenoid_biosynthesis
    predicate: produces
    object: pink_carotenoids
    description: Carotenoid biosynthesis can produce pink bacterial pigments.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: pink ... pigmentation in bacteria
      notes: Supports carotenoids as one source of pink bacterial pigmentation.
    predicate_id: METPO:2000202
  - subject: pink_carotenoids
    predicate: causes
    object: visible_pink_color
    description: Pink carotenoids cause visible pink pigmentation.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: responsible for the red, pink, orange, and yellow pigmentation
      notes: Supports the color-producing role of carotenoid pigments.
    predicate_id: biolink:causes
  - subject: visible_pink_color
    predicate: manifests as
    object: pink_pigmented_trait
    description: Visible pink color manifests the pink-pigmented phenotype.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: pink ... pigmentation in bacteria
      notes: Supports trait-level pink pigmentation from bacterial carotenoids.
    predicate_id: METPO:2007400
  - subject: lycopene
    predicate: precursor of
    object: pink_carotenoids
    description: Lycopene is the central precursor converted into colored downstream
      carotenoid pigments.
    evidence:
    - reference: DOI:10.3390/biology12101346
      notes: 'Sandmann review: lycopene is the central carotenoid intermediate from
        which colored carotenoid pigments are formed via crt pathway reactions.'
  - subject: carotenoid_biosynthesis
    predicate: feeds from
    object: lycopene
    description: Carotenoid biosynthesis proceeds through lycopene toward colored
      carotenoid products.
    evidence:
    - reference: DOI:10.3390/biology12101346
      notes: crtI/phytoene desaturase generates lycopene as a committed colored-carotenoid
        intermediate in the biosynthetic pathway.
  - subject: crt_enzymes
    predicate: part of
    object: photosynthesis_gene_cluster
    description: crt carotenoid genes are part of photosynthesis gene clusters in
      phototrophic bacteria.
    evidence:
    - reference: DOI:10.3390/biology12101346
      notes: '"the genes of the carotenoid pathways are part of photosynthesis gene
        clusters" (Sandmann 2023).'
    predicate_id: biolink:part_of
  - subject: photosynthesis_gene_cluster
    predicate: contributes to
    object: visible_pink_color
    description: Carotenoid genes embedded in photosynthesis gene clusters contribute
      to visible pigmentation.
    evidence:
    - reference: DOI:10.3390/biology12101346
      notes: '"The pigmentation of purple bacteria is caused by a combination of bacteriochlorophylls
        and carotenoids" with crt genes in PGCs.'
    predicate_id: RO:0002326
  - subject: oxygen
    predicate: upregulates
    object: crt_operon
    description: Oxygen availability upregulates the carotenoid biosynthetic operon,
      an environmental regulator of pigment output.
    evidence:
    - reference: DOI:10.3390/biology12101346
      notes: '"oxygen up-regulates the crtI-crtB operon" (Sandmann 2023), making oxygen
        a causal environmental regulator of pigmentation.'
  - subject: crt_operon
    predicate: catalyzes
    object: carotenoid_biosynthesis
    description: The crtI-crtB operon encodes enzymes carrying out carotenoid biosynthetic
      reactions.
    evidence:
    - reference: DOI:10.3390/biology12101346
      notes: crtB (phytoene synthase) and crtI (phytoene desaturase) catalyze committed
        steps producing colored carotenoids.
    predicate_id: biolink:catalyzes
curation_history:
- timestamp: '2026-05-05T01:35:46.945783+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 isoprenoid precursors,
    Crt enzymes, carotenoid biosynthesis, pink carotenoids, and visible pink 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: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0016117×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 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 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:part_of×1, RO:0002326×1, biolink:catalyzes×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15948×1, ENVO:01001495×1).
  llm_assisted: true