identifier: METPO:1003026
label: orange pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear orange
  due to production and accumulation of orange pigments such as carotenoids.
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_orange
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1080/1040841X.2025.2526423
  snippet: orange ... pigmentation in bacteria
  notes: Supports orange microbial pigmentation as a bacterial carotenoid-associated
    color phenotype.
canonical_examples:
- taxon_id: NCBITaxon:1299
  taxon_label: Deinococcus radiodurans
  note: "orange carotenoid colonies"
  reference: PMID:39119139
- taxon_id: NCBITaxon:1830
  taxon_label: Rhodococcus ruber
  note: "orange-red carotenoid-pigmented actinobacterium"
  reference: DOI:10.1016/j.cej.2025.160950
causal_graphs:
- graph_id: orange_pigmented_carotenoid_accumulation
  title: Orange pigmentation carotenoid mechanism
  description: Evidence-backed causal sketch linking orange microbial pigmentation
    to Crt enzymes, carotenoid biosynthesis, orange carotenoid accumulation, and visible
    orange color.
  nodes:
  - node_id: orange_pigmented_trait
    label: orange pigmented
    node_type: TRAIT
    grounding: METPO:1003026
    description: Microbial pigmentation appearing orange.
  - 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: orange_carotenoids
    label: orange carotenoids
    node_type: CHEMICAL
    description: Carotenoid pigments with orange visible coloration.
  - node_id: staphyloxanthin
    label: staphyloxanthin
    node_type: CHEMICAL
    description: Golden-orange C30 carotenoid pigment from Staphylococcus aureus.
    grounding: CHEBI:71690
  - node_id: visible_orange_color
    label: visible orange color
    node_type: MOLECULAR_FUNCTION
    description: Observed orange colony or cell color.
  - node_id: crt_y_lycopene_cyclase
    label: lycopene beta-cyclase (CrtY)
    node_type: GENE_OR_PROTEIN
    description: Lycopene cyclase converting lycopene toward beta-carotene in bacteria.
  - node_id: lycopene
    label: lycopene
    node_type: CHEMICAL
    description: Red carotenoid intermediate upstream of cyclization.
    grounding: CHEBI:15948
  - node_id: beta_carotene
    label: beta-carotene
    node_type: CHEMICAL
    description: Common orange carotenoid end product or branch intermediate in many
      microbes.
    grounding: CHEBI:17579
  - node_id: crt_z_hydroxylase
    label: beta-carotene hydroxylase (CrtZ)
    node_type: GENE_OR_PROTEIN
    description: Enzyme converting beta-carotene to zeaxanthin.
  - node_id: zeaxanthin
    label: zeaxanthin
    node_type: CHEMICAL
    description: Oxygenated carotenoid contributing yellow-orange coloration.
    grounding: CHEBI:27547
  - node_id: crt_w_ketolase
    label: carotenoid ketolase (CrtW)
    node_type: GENE_OR_PROTEIN
    description: Ketolase producing orange/red ketocarotenoids such as canthaxanthin
      and astaxanthin.
  - node_id: ketocarotenoid_biosynthesis
    label: ketocarotenoid biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Pathway branch producing orange-to-red ketocarotenoids.
  - node_id: carotenoid_accumulation
    label: carotenoid accumulation
    node_type: BIOLOGICAL_PROCESS
    description: High-level mechanistic basis for many orange microbial phenotypes
      across bacteria, archaea, and yeasts.
  - node_id: oxidative_stress
    label: oxidative stress / reactive oxygen species
    node_type: ENVIRONMENTAL_FACTOR
    description: Oxidative stressor (ROS) against which carotenoids confer protection.
  edges:
  - subject: crt_enzymes
    predicate: catalyzes
    object: carotenoid_biosynthesis
    description: Crt enzymes catalyze bacterial carotenoid biosynthetic reactions.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: crt genes ... reactions they catalyze
      notes: Supports Crt enzymes as catalysts in bacterial carotenoid pathways.
    predicate_id: biolink:catalyzes
  - subject: carotenoid_biosynthesis
    predicate: produces
    object: orange_carotenoids
    description: Carotenoid biosynthesis produces orange pigments in representative
      bacteria.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: orange ... pigmentation in bacteria
      notes: Supports carotenoid biosynthesis as a route to orange bacterial pigmentation.
    predicate_id: METPO:2000202
  - subject: carotenoid_biosynthesis
    predicate: produces
    object: staphyloxanthin
    description: The S. aureus carotenoid pathway produces staphyloxanthin.
    evidence:
    - reference: DOI:10.1128/JB.147.3.900-913.1981
      snippet: triterpenoid carotenoids possessing a C30 chain
      notes: Supports staphyloxanthin-related C30 carotenoid pigments in S. aureus.
    predicate_id: METPO:2000202
  - subject: orange_carotenoids
    predicate: causes
    object: visible_orange_color
    description: Orange carotenoids cause visible orange pigmentation.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: responsible for ... orange ... pigmentation
      notes: Supports carotenoid pigments as determinants of orange color.
    predicate_id: biolink:causes
  - subject: visible_orange_color
    predicate: manifests as
    object: orange_pigmented_trait
    description: Visible orange color manifests the orange-pigmented phenotype.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: orange ... pigmentation in bacteria
      notes: Supports the trait-level color assignment.
    predicate_id: METPO:2007400
  - subject: crt_y_lycopene_cyclase
    predicate: converts
    object: lycopene
    description: CrtY lycopene beta-cyclase acts on lycopene as substrate.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: lycopene is converted to beta-carotene by ring-forming lycopene cyclases;
        in bacteria the enzyme is crtY. Broad microbial applicability.
  - subject: lycopene
    predicate: is converted to
    object: beta_carotene
    description: Lycopene cyclization yields orange beta-carotene.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: lycopene is converted to beta-carotene by ring-forming lycopene cyclases
        (crtY). Broad microbial applicability.
  - subject: crt_z_hydroxylase
    predicate: converts
    object: beta_carotene
    description: CrtZ beta-carotene hydroxylase acts on beta-carotene.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: conversion of beta-carotene to zeaxanthin by crtZ. Strong general edge
        supporting orange/yellow branches.
  - subject: beta_carotene
    predicate: is converted to
    object: zeaxanthin
    description: Hydroxylation of beta-carotene yields zeaxanthin.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: crtZ encodes a beta-carotene hydroxylase converting beta-carotene to
        zeaxanthin. Strong general edge.
  - subject: crt_w_ketolase
    predicate: contributes to
    object: ketocarotenoid_biosynthesis
    description: CrtW ketolase drives ketocarotenoid (e.g., canthaxanthin/astaxanthin)
      formation.
    evidence:
    - reference: DOI:10.3390/microorganisms11030614
      notes: ketolation by ketolases such as crtW yields ketocarotenoids (canthaxanthin/astaxanthin).
        Strong for the ketocarotenoid branch; orange-to-red hue.
    predicate_id: RO:0002326
  - subject: carotenoid_accumulation
    predicate: protects against
    object: oxidative_stress
    description: Accumulated carotenoids act as antioxidants neutralizing reactive
      oxygen species.
    evidence:
    - reference: DOI:10.7759/cureus.59892
      notes: acts as an antioxidant protecting against hydrogen peroxide and hydroxyl
        radicals. Strong, broad functional edge across taxa.
  - subject: orange_pigmented_trait
    predicate: has material basis in
    object: carotenoid_accumulation
    description: The orange-pigmented phenotype is materially based on carotenoid
      accumulation.
    evidence:
    - reference: DOI:10.7759/cureus.59892
      notes: orange carotenoid; golden yellow-orange pigment. High-level edge suitable
        for TraitMech root graph across diverse taxa.
curation_history:
- timestamp: '2026-05-05T01:35:46.945311+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 Crt enzymes, carotenoid
    biosynthesis, orange carotenoids, staphyloxanthin, and visible orange color.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×2).
  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: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:71690×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (9 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
    (RO:0002326×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15948×1, CHEBI:17579×1, CHEBI:27547×1).
  llm_assisted: true