identifier: METPO:1003031
label: carotenoid pigmentation
definition: A pigmentation phenotype caused by microbial production and accumulation
  of 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_carotenoid
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1080/1040841X.2025.2526423
  snippet: Carotenoids are isoprenoid pigments
  notes: Supports carotenoid pigmentation as a bacterial isoprenoid-pigment phenotype.
canonical_examples:
- taxon_id: NCBITaxon:1280
  taxon_label: Staphylococcus aureus
  note: "Golden carotenoid pigmentation (staphyloxanthin); well-studied bacterial carotenoid and virulence factor."
  reference: PMID:16009720
causal_graphs:
- graph_id: carotenoid_pigmentation_crt_pathway
  title: Carotenoid pigmentation crt-pathway mechanism
  description: Evidence-backed causal sketch linking bacterial carotenoid pigmentation
    to isoprenoid precursors, crt enzymes, conjugated carotenoids, and yellow-orange-red
    visible color.
  nodes:
  - node_id: carotenoid_pigmentation_trait
    label: carotenoid pigmentation
    node_type: TRAIT
    grounding: METPO:1003031
    description: Microbial pigmentation caused by carotenoid compounds.
  - 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 encoded by crt genes.
  - node_id: carotenoid_biosynthesis
    label: carotenoid biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Enzymatic pathway producing carotenoid pigments.
    grounding: GO:0016117
  - node_id: conjugated_carotenoids
    label: conjugated carotenoids
    node_type: CHEMICAL
    description: Colored carotenoid molecules with conjugated double bonds.
  - node_id: yellow_orange_red_color
    label: yellow-orange-red color
    node_type: MOLECULAR_FUNCTION
    description: Visible colors associated with carotenoid absorption spectra.
  - node_id: phytoene_synthase
    label: phytoene synthase
    node_type: GENE_OR_PROTEIN
    description: CrtB-type enzyme condensing prenyl diphosphate to phytoene.
    grounding: UniProtKB:A0A023WN98
  - node_id: phytoene
    label: phytoene
    node_type: CHEMICAL
    description: Colorless C40 carotenoid precursor.
  - node_id: phytoene_desaturase
    label: phytoene desaturase
    node_type: GENE_OR_PROTEIN
    description: CrtI-type enzyme desaturating phytoene toward lycopene.
    grounding: UniProtKB:A0A060JDC8
  - node_id: lycopene
    label: lycopene
    node_type: CHEMICAL
    description: Red C40 carotenoid intermediate formed by desaturation.
    grounding: CHEBI:15948
  - node_id: lycopene_cyclases
    label: lycopene cyclases
    node_type: GENE_OR_PROTEIN
    description: CrtY-type enzymes cyclizing lycopene into cyclic carotenes.
  - node_id: cyclic_carotenes
    label: cyclic carotenes
    node_type: CHEMICAL
    description: alpha-, epsilon-, and beta-carotene formed by lycopene cyclization.
    grounding: CHEBI:35163
  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 a major step in eubacterial
        carotenoid pathways.
  - subject: crt_enzymes
    predicate: catalyzes
    object: carotenoid_biosynthesis
    description: Crt gene products catalyze bacterial carotenoid biosynthetic reactions.
    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: conjugated_carotenoids
    description: Carotenoid biosynthesis produces conjugated carotenoid pigments.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: biosynthesis pathways of bacterial carotenoids
      notes: Supports bacterial carotenoid biosynthesis as the source of carotenoid
        pigments.
    predicate_id: METPO:2000202
  - subject: conjugated_carotenoids
    predicate: causes
    object: yellow_orange_red_color
    description: Conjugated carotenoids absorb visible light and produce yellow-orange-red
      pigmentation.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: red, pink, orange, and yellow pigmentation in bacteria
      notes: Supports carotenoids as color determinants for this pigment class.
    predicate_id: biolink:causes
  - subject: yellow_orange_red_color
    predicate: manifests as
    object: carotenoid_pigmentation_trait
    description: Yellow-orange-red visible color manifests carotenoid pigmentation.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: responsible for the red, pink, orange, and yellow pigmentation
      notes: Supports the trait-level mapping from carotenoid chemistry to pigmentation.
    predicate_id: METPO:2007400
  - subject: phytoene_synthase
    predicate: converts
    object: phytoene
    description: Phytoene synthase condenses prenyl diphosphate (GFDP) to form phytoene.
    evidence:
    - reference: DOI:10.3390/molecules29174235
      notes: Through the catalytic action of phytoene synthase, GFDP undergoes condensation
        to form phytoene.
  - subject: phytoene
    predicate: is substrate for
    object: phytoene_desaturase
    description: Phytoene is dehydrogenated by phytoene desaturase en route to lycopene.
    evidence:
    - reference: DOI:10.3390/molecules29174235
      notes: Phytoene is further dehydrogenated by dehydrogenase to generate phytofluene,
        which is subsequently converted into lycopene.
  - subject: phytoene_desaturase
    predicate: produces
    object: lycopene
    description: Phytoene desaturase converts phytoene (via phytofluene) to lycopene.
    evidence:
    - reference: DOI:10.3390/molecules29174235
      notes: Phytoene is further dehydrogenated... which is subsequently converted
        into lycopene.
    predicate_id: METPO:2000202
  - subject: lycopene_cyclases
    predicate: converts
    object: cyclic_carotenes
    description: Lycopene cyclases cyclize lycopene into alpha-, epsilon-, and beta-carotene.
    evidence:
    - reference: DOI:10.3390/molecules29174235
      notes: The cyclization of lycopene... lead[s] to the formation of alpha-carotene,
        epsilon-carotene, and beta-carotene under the catalysis of various lycopene
        cyclases.
  - subject: lycopene
    predicate: is substrate for
    object: lycopene_cyclases
    description: Lycopene is the substrate cyclized by lycopene cyclases.
    evidence:
    - reference: DOI:10.3390/molecules29174235
      notes: The cyclization of lycopene... under the catalysis of various lycopene
        cyclases.
  - subject: cyclic_carotenes
    predicate: is a
    object: conjugated_carotenoids
    description: Cyclic carotenes are conjugated carotenoid pigments contributing
      to coloration.
    evidence:
    - reference: DOI:10.3390/molecules29174235
      notes: Cyclic carotenes (alpha-/epsilon-/beta-carotene) are conjugated carotenoid
        pigment products of the pathway.
    predicate_id: rdfs:subClassOf
curation_history:
- timestamp: '2026-05-05T01:35:46.947657+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: Added DOI-backed definition and causal graph for isoprenoid precursors,
    Crt enzymes, carotenoid biosynthesis, conjugated carotenoids, and visible pigmentation.
  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 (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1, rdfs:subClassOf×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:15948×1, CHEBI:35163×1).
  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:A0A023WN98×1, UniProtKB:A0A060JDC8×1).
  llm_assisted: true