identifier: METPO:1003029
label: white pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear white
  or nonpigmented because visible chromophore accumulation is absent or low.
definition_source: DOI:10.2147/IDR.S49039
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_white
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.2147/IDR.S49039
  snippet: white phenotypic variant of Staphylococcus aureus
  notes: Supports white colony appearance as a microbial pigmentation phenotype tied
    to absent or inducible staphyloxanthin production in a representative bacterium.
causal_graphs:
- graph_id: white_pigmented_low_chromophore
  title: White pigmentation low-chromophore mechanism
  description: Evidence-backed causal sketch linking white colony pigmentation to
    reduced visible pigment accumulation, staphyloxanthin biosynthesis machinery,
    and absence or silencing of carotenoid production in representative bacteria.
  nodes:
  - node_id: white_pigmented_trait
    label: white pigmented
    node_type: TRAIT
    grounding: METPO:1003029
    description: White or nonpigmented microbial colony or cell appearance.
  - node_id: crtOPQMN_operon
    label: crtOPQMN operon
    node_type: GENE_OR_PROTEIN
    description: S. aureus carotenoid biosynthesis gene cluster for staphyloxanthin
      production.
  - node_id: staphyloxanthin_biosynthesis
    label: staphyloxanthin biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Biosynthesis of the golden carotenoid pigment staphyloxanthin.
  - node_id: staphyloxanthin
    label: staphyloxanthin
    node_type: CHEMICAL
    description: Golden carotenoid pigment of Staphylococcus aureus.
    grounding: CHEBI:71690
  - node_id: low_visible_chromophore
    label: low visible chromophore accumulation
    node_type: CHEMICAL
    description: Absence or low accumulation of colored pigment molecules.
  - node_id: visible_white_color
    label: visible white color
    node_type: MOLECULAR_FUNCTION
    description: Observed white or nonpigmented colony color.
  - node_id: melanin_biosynthesis
    label: melanin biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: PKS-type biosynthesis of melanin pigments (e.g. DHN melanin) in fungi
      and bacteria.
    grounding: GO:0042438
  - node_id: melanin
    label: melanin
    node_type: CHEMICAL
    description: Dark brown/black chromophore pigment class; a major visible microbial
      pigment.
    grounding: CHEBI:89634
  - node_id: reduced_melanin
    label: reduced melanin accumulation
    node_type: CHEMICAL
    description: Absent or lowered accumulation of melanin chromophore.
  - node_id: sigB
    label: SigB (sigma factor B)
    node_type: GENE_OR_PROTEIN
    description: Alternative sigma factor B; positive regulator of staphyloxanthin
      biosynthesis genes.
  - node_id: glmS
    label: GlmS
    node_type: GENE_OR_PROTEIN
    description: Glucosamine-6-phosphate synthase; transcriptional upregulator of
      sigB.
    grounding: UniProtKB:I6LB50
  edges:
  - subject: crtOPQMN_operon
    predicate: encodes
    object: staphyloxanthin_biosynthesis
    description: The crtOPQMN operon encodes machinery for staphyloxanthin biosynthesis.
    evidence:
    - reference: DOI:10.1038/s41426-018-0078-1
      snippet: controlled by the crtOPQMN operon
      notes: Supports the operon as staphyloxanthin biosynthetic machinery.
    predicate_id: biolink:encodes
  - subject: staphyloxanthin_biosynthesis
    predicate: produces
    object: staphyloxanthin
    description: Staphyloxanthin biosynthesis produces the golden carotenoid pigment.
    evidence:
    - reference: DOI:10.1084/jem.20050846
      snippet: Golden color imparted by carotenoid pigments
      notes: Supports the link from carotenoid biosynthesis to visible golden pigment
        in S. aureus.
    predicate_id: METPO:2000202
  - subject: low_visible_chromophore
    predicate: results from reduced
    object: staphyloxanthin_biosynthesis
    description: Reduced or absent staphyloxanthin biosynthesis lowers visible pigment
      accumulation.
    evidence:
    - reference: DOI:10.2147/IDR.S49039
      snippet: white-colony phenotype actually lacked the crtOPQMN operon
      notes: Supports white colony phenotype when staphyloxanthin synthesis machinery
        is absent in a representative case.
  - subject: low_visible_chromophore
    predicate: causes
    object: visible_white_color
    description: Lack of accumulated chromophore yields a white or nonpigmented colony
      appearance.
    evidence:
    - reference: DOI:10.2147/IDR.S49039
      snippet: white phenotypic variant
      notes: Supports white appearance as a phenotype of low or absent visible pigment.
    predicate_id: biolink:causes
  - subject: visible_white_color
    predicate: manifests as
    object: white_pigmented_trait
    description: Visible white colony color manifests the white-pigmented trait.
    evidence:
    - reference: DOI:10.2147/IDR.S49039
      snippet: white phenotypic variant of Staphylococcus aureus
      notes: Supports trait-level white pigmentation in a representative microbial
        context.
    predicate_id: METPO:2007400
  - subject: melanin_biosynthesis
    predicate: produces
    object: melanin
    description: PKS-mediated melanin biosynthesis produces the melanin chromophore.
    evidence:
    - reference: DOI:10.1007/s00792-024-01354-2
      notes: pks1 mutation abolishes melanization / decreased DHN melanin accumulation,
        establishing the PKS biosynthetic route to melanin.
    predicate_id: METPO:2000202
  - subject: reduced_melanin
    predicate: results from reduced
    object: melanin_biosynthesis
    description: Reduced melanin biosynthesis lowers melanin chromophore accumulation.
    evidence:
    - reference: DOI:10.1080/21501203.2023.2249010
      notes: Knockout of PKS gene (pksA) reduced melanin production, yielding melanin-deficient
        cells.
  - subject: reduced_melanin
    predicate: causes
    object: visible_white_color
    description: Loss of melanin chromophore yields a white colony surface / white
      cells.
    evidence:
    - reference: DOI:10.1080/21501203.2023.2249010
      notes: Mel- colonies are uneven with a white surface and white conidia; generic
        melanin-loss to white-pigment link.
    predicate_id: biolink:causes
  - subject: sigB
    predicate: positively regulates
    object: staphyloxanthin_biosynthesis
    description: Sigma factor B positively regulates staphyloxanthin biosynthesis
      genes; its loss reduces pigment.
    evidence:
    - reference: DOI:10.1128/mbio.00346-24
      notes: SigB positively regulates genes involved in staphyloxanthin synthesis;
        disruptive sigB mutations give white colonies.
  - subject: glmS
    predicate: positively regulates
    object: sigB
    description: GlmS directly upregulates sigB transcription, feeding the carotenoid-pigment
      regulatory cascade.
    evidence:
    - reference: DOI:10.1080/21505594.2024.2352476
      notes: GlmS directly upregulates sigB transcription (dual-luciferase and EMSA
        promoter binding); glmS knockout reduces sigB and golden pigment.
curation_history:
- timestamp: '2026-05-05T01:35:46.946745+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 staphyloxanthin biosynthesis
    machinery, low visible chromophore accumulation, and white colony appearance.
  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 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:encodes×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
    (CHEBI:71690×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1, biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  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: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:89634×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:I6LB50×1).
  llm_assisted: true