identifier: METPO:1003028
label: red pigmented
definition: A pigmentation phenotype in which microbial colonies or cells appear red
  due to production of red pigments such as prodiginines or carotenoids.
definition_source: DOI:10.1038/nrmicro1531
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_red
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1038/nrmicro1531
  snippet: red-pigmented prodiginines
  notes: Supports red microbial pigmentation as a prodiginine-associated color phenotype
    in representative bacteria.
canonical_examples:
- taxon_id: NCBITaxon:615
  taxon_label: Serratia marcescens
  note: "Classic red-pigmented bacterium (prodigiosin); historical model for bacterial pigmentation."
  reference: PMID:18805986
causal_graphs:
- graph_id: red_pigmented_prodiginine_pathway
  title: Red pigmentation prodiginine mechanism
  description: Evidence-backed causal sketch linking red microbial pigmentation to
    prodiginine biosynthesis, PigC/RedH condensation, prodigiosin accumulation, and
    visible red color.
  nodes:
  - node_id: red_pigmented_trait
    label: red pigmented
    node_type: TRAIT
    grounding: METPO:1003028
    description: Microbial pigmentation appearing red.
  - node_id: prodiginine_biosynthesis
    label: prodiginine biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Bifurcated biosynthetic pathway yielding prodiginine pigments.
  - node_id: pigC_redH_condensation
    label: PigC/RedH condensation
    node_type: MOLECULAR_FUNCTION
    description: Condensation reaction forming prodigiosin or related prodiginines.
  - node_id: prodigiosin
    label: prodigiosin
    node_type: CHEMICAL
    description: Red tripyrrole pigment produced by some bacteria.
    grounding: CHEBI:82758
  - node_id: visible_red_color
    label: visible red color
    node_type: MOLECULAR_FUNCTION
    description: Observed red color produced by pigment absorption spectra.
  - node_id: pig_red_gene_cluster
    label: prodiginine biosynthetic gene cluster (Pig/Red)
    node_type: GENE_OR_PROTEIN
    description: Variable gene cluster (Pig in Serratia, Red in Streptomyces) encoding
      prodiginine biosynthesis.
  - node_id: pigC_ligase
    label: PigC ligase
    node_type: GENE_OR_PROTEIN
    description: Key condensing enzyme/ligase encoded by pigC that links MAP and MBC
      to form prodigiosin.
  - node_id: cpxA_cpxR_system
    label: CpxA/CpxR two-component system
    node_type: GENE_OR_PROTEIN
    description: Sensor histidine kinase/response regulator system whose activation
      represses pig gene cluster transcription.
  - node_id: carotenoid_biosynthesis
    label: carotenoid biosynthesis (phytoene synthase pathway)
    node_type: BIOLOGICAL_PROCESS
    description: Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization
      yields lycopene.
  - node_id: lycopene
    label: lycopene
    node_type: CHEMICAL
    description: Red-colored carotenoid pigment produced via the phytoene synthase
      pathway.
    grounding: CHEBI:15948
  edges:
  - subject: prodiginine_biosynthesis
    predicate: includes
    object: pigC_redH_condensation
    description: Prodiginine biosynthesis culminates in PigC/RedH-catalyzed condensation.
    evidence:
    - reference: DOI:10.1038/nrmicro1531
      snippet: culminating in the PigC/RedH catalysed condensation
      notes: Supports PigC/RedH condensation as a key step in prodiginine biosynthesis.
    predicate_id: biolink:has_part
  - subject: pigC_redH_condensation
    predicate: produces
    object: prodigiosin
    description: PigC/RedH condensation produces prodigiosin or related prodiginines.
    evidence:
    - reference: DOI:10.1038/nrmicro1531
      snippet: to form prodigiosin
      notes: Supports prodigiosin as a pathway product.
    predicate_id: METPO:2000202
  - subject: prodigiosin
    predicate: causes
    object: visible_red_color
    description: Prodigiosin causes red colony pigmentation in representative bacteria.
    evidence:
    - reference: DOI:10.1021/acs.chemrev.6b00024
      snippet: bright red pigment prodigiosin
      notes: Supports prodigiosin as a red pigment.
    predicate_id: biolink:causes
  - subject: visible_red_color
    predicate: manifests as
    object: red_pigmented_trait
    description: Visible red color manifests the red-pigmented phenotype.
    evidence:
    - reference: DOI:10.1038/nrmicro1531
      snippet: red-pigmented prodiginines
      notes: Supports trait-level red pigmentation from prodiginines.
    predicate_id: METPO:2007400
  - subject: pig_red_gene_cluster
    predicate: enables
    object: red_pigmented_trait
    description: Prodiginine biosynthetic gene clusters (Pig/Red) encode the pathway
      producing red tripyrrole pigments, enabling the red-pigmented phenotype across
      taxa.
    evidence:
    - reference: DOI:10.3390/microorganisms11122920
      notes: Prodiginines are red tripyrrole pigments genetically encoded by variable
        gene clusters (Pig in Serratia, Red in Streptomyces); broad cross-taxon mechanism.
    predicate_id: RO:0002327
  - subject: pig_red_gene_cluster
    predicate: has part
    object: pigC_ligase
    description: The pig gene cluster encodes the PigC ligase that catalyzes the final
      condensation step.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1412776
      notes: The ligase encoded by pigC is the key enzyme that links MAP and MBC.
  - subject: pigC_ligase
    predicate: catalyzes
    object: pigC_redH_condensation
    description: PigC ligase catalyzes the condensation of MAP and MBC that forms
      prodigiosin.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1412776
      notes: The ligase encoded by pigC is the key enzyme that links MAP and MBC to
        form prodigiosin.
    predicate_id: biolink:catalyzes
  - subject: cpxA_cpxR_system
    predicate: represses transcription of
    object: pig_red_gene_cluster
    description: Activation of the CpxA/CpxR system triggers a phosphorylation cascade
      that inhibits transcription of pig gene clusters, reducing prodigiosin and red
      pigmentation.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1412776
      notes: Activated CpxA triggers a phosphorylation cascade that inhibits transcription
        of pig gene clusters and reduces PG production.
  - subject: carotenoid_biosynthesis
    predicate: produces
    object: lycopene
    description: Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization
      yields the red pigment lycopene.
    evidence:
    - reference: DOI:10.3390/microorganisms11122920
      notes: Two GGPP molecules condensed by phytoene synthase form phytoene, ultimately
        yielding lycopene, a red-colored pigment.
    predicate_id: METPO:2000202
  - subject: lycopene
    predicate: causes
    object: visible_red_color
    description: Lycopene is a red-colored carotenoid pigment that confers red color,
      providing a carotenoid route to red pigmentation.
    evidence:
    - reference: DOI:10.3390/microorganisms11122920
      notes: Lycopene described explicitly as 'a red-colored pigment'.
    predicate_id: biolink:causes
curation_history:
- timestamp: '2026-05-05T01:35:46.946258+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 prodiginine biosynthesis,
    PigC/RedH condensation, prodigiosin, and visible red 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 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (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: '2026-06-13T21:03:26Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:has_part×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:82758×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, biolink:catalyzes×1, METPO:2000202×1, biolink:causes×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:15948×1).
  llm_assisted: true