identifier: METPO:1003030
label: yellow pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear yellow
  due to production of yellow 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_yellow
  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 yellow microbial pigmentation as a carotenoid-associated bacterial
    color phenotype.
canonical_examples:
- taxon_id: NCBITaxon:339
  taxon_label: Xanthomonas campestris
  note: "Yellow-pigmented (xanthomonadin) phytopathogen; the namesake xanthous bacterium."
  reference: PMID:12024217
causal_graphs:
- graph_id: yellow_pigmented_carotenoid_color
  title: Yellow pigmentation carotenoid mechanism
  description: Evidence-backed causal sketch linking yellow microbial pigmentation
    to crt-catalyzed carotenoid biosynthesis, yellow carotenoid accumulation, and
    visible yellow colony color.
  nodes:
  - node_id: yellow_pigmented_trait
    label: yellow pigmented
    node_type: TRAIT
    grounding: METPO:1003030
    description: Microbial pigmentation appearing yellow.
  - 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: yellow_carotenoids
    label: yellow carotenoids
    node_type: CHEMICAL
    description: Carotenoid pigments that contribute yellow coloration.
  - node_id: visible_yellow_color
    label: visible yellow color
    node_type: MOLECULAR_FUNCTION
    description: Observed yellow color produced by pigment absorption spectra.
  - node_id: ipp_dmapp
    label: IPP/DMAPP
    node_type: CHEMICAL
    description: C5 isoprenoid precursors isopentenyl diphosphate and dimethylallyl
      diphosphate.
  - node_id: ggpp
    label: geranylgeranyl diphosphate (GGPP)
    node_type: CHEMICAL
    description: C20 isoprenoid precursor of carotenoid backbones.
  - node_id: idsa_crte
    label: IdsA/CrtE (GGPP synthase)
    node_type: GENE_OR_PROTEIN
    description: Geranylgeranyl diphosphate synthase converting IPP and DMAPP to GGPP.
  - node_id: lycopene
    label: lycopene
    node_type: CHEMICAL
    description: C40 carotenoid backbone intermediate.
    grounding: CHEBI:15948
  - node_id: crti
    label: CrtI (phytoene desaturase)
    node_type: GENE_OR_PROTEIN
    description: Phytoene desaturase that produces lycopene in carotenoid biosynthesis.
  - node_id: lycopene_biosynthesis
    label: lycopene biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Pathway steps producing lycopene from phytoene.
    grounding: GO:1901177
  - node_id: crty
    label: CrtY (lycopene beta-cyclase)
    node_type: GENE_OR_PROTEIN
    description: Lycopene beta-cyclase converting lycopene to beta-carotene.
  - node_id: beta_carotene
    label: beta-carotene
    node_type: CHEMICAL
    description: Canonical yellow/orange carotenoid pigment.
    grounding: CHEBI:17579
  - node_id: flexirubin_pigment
    label: flexirubin-type pigment
    node_type: CHEMICAL
    description: Aryl polyene yellow pigment class distinct from carotenoids.
  - node_id: ros_damage
    label: reactive oxygen species damage
    node_type: BIOLOGICAL_PROCESS
    description: Oxidative damage caused by reactive oxygen species.
  edges:
  - subject: crt_enzymes
    predicate: catalyzes
    object: carotenoid_biosynthesis
    description: Crt enzymes catalyze 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: yellow_carotenoids
    description: Carotenoid biosynthesis produces yellow-pigment carotenoids in representative
      bacteria.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: yellow pigmentation in bacteria
      notes: Supports carotenoids as one source of yellow pigmentation.
    predicate_id: METPO:2000202
  - subject: yellow_carotenoids
    predicate: causes
    object: visible_yellow_color
    description: Yellow carotenoids cause visible yellow colony or cell color.
    evidence:
    - reference: DOI:10.1016/j.tim.2010.07.007
      snippet: Carotenoids are natural pigments
      notes: Supports carotenoids as visible pigments in bacteria.
    predicate_id: biolink:causes
  - subject: visible_yellow_color
    predicate: manifests as
    object: yellow_pigmented_trait
    description: Visible yellow color manifests the yellow-pigmented phenotype.
    evidence:
    - reference: DOI:10.1080/1040841X.2025.2526423
      snippet: yellow pigmentation in bacteria
      notes: Supports trait-level yellow pigmentation.
    predicate_id: METPO:2007400
  - subject: ipp_dmapp
    predicate: precursor of
    object: ggpp
    description: C5 precursors IPP/DMAPP are elongated to the C20 carotenoid precursor
      GGPP.
    evidence:
    - reference: DOI:10.1038/s41598-024-58700-9
      notes: Carotenoid synthesis begins from the C5 isoprenoid precursors IPP and
        DMAPP, which are converted via chain elongation to the C20 precursor GGPP.
  - subject: idsa_crte
    predicate: catalyzes
    object: ggpp
    description: IdsA/CrtE (GGPP synthase) catalyzes formation of GGPP from IPP and
      DMAPP.
    evidence:
    - reference: DOI:10.1038/s41598-024-58700-9
      notes: IdsA, the major geranylgeranyl diphosphate synthase converting IPP and
        DMAPP to GGPP; GGPPS annotated CrtE/IdsA.
    predicate_id: biolink:catalyzes
  - subject: ggpp
    predicate: precursor of
    object: lycopene
    description: Two GGPP molecules condense to form the C40 backbone lycopene.
    evidence:
    - reference: DOI:10.1038/s41598-024-58700-9
      notes: Two GGPP molecules condense to form the C40 backbone lycopene.
  - subject: crti
    predicate: enables
    object: lycopene_biosynthesis
    description: CrtI (phytoene desaturase) enables lycopene biosynthesis.
    evidence:
    - reference: DOI:10.3390/microorganisms12040803
      notes: Phytoene desaturase (CrtI) to produce lycopene.
    predicate_id: RO:0002327
  - subject: lycopene_biosynthesis
    predicate: produces
    object: lycopene
    description: Lycopene biosynthesis produces lycopene.
    evidence:
    - reference: DOI:10.3390/microorganisms12040803
      notes: Pathway proceeds through phytoene synthase (CrtB) and phytoene desaturase
        (CrtI) to produce lycopene.
    predicate_id: METPO:2000202
  - subject: crty
    predicate: catalyzes conversion to
    object: beta_carotene
    description: CrtY (lycopene beta-cyclase) cyclizes lycopene to beta-carotene.
    evidence:
    - reference: DOI:10.1038/s41598-024-58700-9
      notes: Lycopene is cyclized to beta-carotene by lycopene beta-cyclase (crtY).
  - subject: beta_carotene
    predicate: causes or contributes to
    object: yellow_pigmented_trait
    description: beta-carotene is a canonical yellow/orange carotenoid that contributes
      to the yellow phenotype.
    evidence:
    - reference: DOI:10.4014/jmb.2404.04018
      notes: beta-carotene serves as a colorant and is the classic yellow/orange carotenoid
        pigment.
  - subject: flexirubin_pigment
    predicate: contributes to
    object: yellow_pigmented_trait
    description: Flexirubin-type pigments produce yellow colony coloration, a carotenoid-independent
      yellow pigment route.
    evidence:
    - reference: DOI:10.1038/s41467-024-54112-5
      notes: Flexirubin-type pigment-producing bacterium is yellow (or orange) in
        color; flexirubin is a known yellow pigment.
    predicate_id: RO:0002326
  - subject: flexirubin_pigment
    predicate: protects against
    object: ros_damage
    description: Flexirubin protects against reactive oxygen species damage.
    evidence:
    - reference: DOI:10.1038/s41467-024-54112-5
      notes: Flexirubin is known as a yellow pigment that effectively protects against
        reactive oxygen species damage.
curation_history:
- timestamp: '2026-05-05T01:35:46.947204+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 Crt enzymes, carotenoid
    biosynthesis, yellow carotenoids, and visible yellow 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: '2026-05-20T05:49:25Z'
  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 9 evidence-backed generic edges (10 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:catalyzes×1, RO:0002327×1, METPO:2000202×1, RO:0002326×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15948×1, GO:1901177×1, CHEBI:17579×1).
  llm_assisted: true