identifier: METPO:1003025
label: green pigmented
definition: A pigmentation phenotype in which microbial colonies or cultures appear
  green or blue-green due to pigments such as pyocyanin and pyoverdine.
definition_source: DOI:10.1186/s12934-023-02122-1
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_green
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1186/s12934-023-02122-1
  snippet: green colorization of the culture plate
  notes: Supports green/blue-green pigmentation from pyocyanin and fluorescein or
    pyoverdine-like pigments in representative bacteria.
canonical_examples:
- taxon_id: NCBITaxon:1097
  taxon_label: Chlorobaculum tepidum
  note: "green sulfur bacterium (bacteriochlorophyll/chlorosome)"
  reference: PMID:12093901
- taxon_id: NCBITaxon:1108
  taxon_label: Chloroflexus aurantiacus
  note: "green non-sulfur bacterium"
  reference: PMID:21714912
causal_graphs:
- graph_id: green_pigmented_pyocyanin_phenazine
  title: Green pigmentation pyocyanin phenazine mechanism
  description: Evidence-backed causal sketch linking green or blue-green microbial
    pigmentation to phenazine biosynthesis, phz genes, pyocyanin production, and visible
    green culture color.
  nodes:
  - node_id: green_pigmented_trait
    label: green pigmented
    node_type: TRAIT
    grounding: METPO:1003025
    description: Microbial pigmentation appearing green or blue-green.
  - node_id: phz_operons
    label: phz operons
    node_type: GENE_OR_PROTEIN
    description: Phenazine biosynthesis gene clusters in representative bacteria.
  - node_id: phenazine_biosynthesis
    label: phenazine biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Biosynthetic pathway producing phenazine pigments.
    grounding: GO:0002047
  - node_id: pyocyanin
    label: pyocyanin
    node_type: CHEMICAL
    description: Blue-green phenazine pigment produced by Pseudomonas aeruginosa.
  - node_id: visible_green_color
    label: visible green color
    node_type: MOLECULAR_FUNCTION
    description: Observed green or blue-green culture color.
  - node_id: chorismate
    label: chorismate
    node_type: CHEMICAL
    description: Shikimate-pathway intermediate; precursor of phenazines.
    grounding: CHEBI:29748
  - node_id: phenazine_1_carboxylic_acid
    label: phenazine-1-carboxylic acid (PCA)
    node_type: CHEMICAL
    description: Core phenazine intermediate converted toward pyocyanin.
  - node_id: quorum_sensing
    label: quorum sensing
    node_type: BIOLOGICAL_PROCESS
    description: Cell-density-dependent regulatory signaling controlling phenazine
      production.
    grounding: GO:0009372
  - node_id: pyocyanin_redox_ph
    label: pyocyanin redox state and pH
    node_type: ENVIRONMENTAL_FACTOR
    description: Environmental redox/pH conditions altering apparent pyocyanin color.
  - node_id: pyoverdine_biosynthesis
    label: pyoverdine biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: NRPS-driven biosynthesis of the fluorescent siderophore pyoverdine.
  - node_id: pvd_nrps
    label: pyoverdine NRPS enzymes (PvdL/PvdI/PvdJ/PvdD)
    node_type: GENE_OR_PROTEIN
    description: Nonribosomal peptide synthetases assembling the pyoverdine peptide
      backbone.
  - node_id: iron_limitation
    label: iron-deficient conditions
    node_type: ENVIRONMENTAL_FACTOR
    description: Low-iron growth conditions that induce pyoverdine biosynthesis.
  edges:
  - subject: phz_operons
    predicate: encodes
    object: phenazine_biosynthesis
    description: phz operons encode enzymes required for phenazine biosynthesis.
    evidence:
    - reference: DOI:10.1186/s12934-023-02122-1
      snippet: phenazine synthesis operons including phzA1, phzA2, phzS, and phzM
      notes: Supports phz genes as pyocyanin/phenazine biosynthesis machinery.
    predicate_id: biolink:encodes
  - subject: phenazine_biosynthesis
    predicate: produces
    object: pyocyanin
    description: Phenazine biosynthesis produces pyocyanin.
    evidence:
    - reference: DOI:10.1128/jb.138.3.846-852.1979
      snippet: pyocyanine biosynthesis
      notes: Supports pyocyanin production as a phenazine biosynthetic process.
    predicate_id: METPO:2000202
  - subject: pyocyanin
    predicate: causes
    object: visible_green_color
    description: Pyocyanin contributes blue-green visible pigmentation.
    evidence:
    - reference: DOI:10.1186/s12934-023-02122-1
      snippet: Pyocyanin is a blue phenazine pigment
      notes: Supports pyocyanin as a visible blue/green pigment.
    predicate_id: biolink:causes
  - subject: visible_green_color
    predicate: manifests as
    object: green_pigmented_trait
    description: Visible green or blue-green culture color manifests the green-pigmented
      phenotype.
    evidence:
    - reference: DOI:10.1186/s12934-023-02122-1
      snippet: lead to the green colorization of the culture plate
      notes: Supports trait-level green pigmentation from pyocyanin and related pigments
        in representative cultures.
    predicate_id: METPO:2007400
  - subject: chorismate
    predicate: precursor of
    object: phenazine_1_carboxylic_acid
    description: Chorismate is the shikimate-pathway precursor of phenazine-1-carboxylic
      acid.
    evidence:
    - reference: DOI:10.1007/s11274-023-03548-w
      notes: Biosynthesis of PYO and other phenazines proceeds from chorismate via
        the shikimate pathway.
  - subject: phenazine_1_carboxylic_acid
    predicate: precursor of
    object: pyocyanin
    description: Phenazine-1-carboxylic acid is the core intermediate converted toward
      pyocyanin.
    evidence:
    - reference: DOI:10.1007/s11274-023-03548-w
      notes: PCA is the central phenazine from which pyocyanin is derived via the
        shikimate/phenazine pathway.
  - subject: quorum_sensing
    predicate: positively regulates
    object: pyocyanin
    description: Quorum sensing positively regulates pyocyanin production.
    evidence:
    - reference: DOI:10.1186/s12934-023-02122-1
      notes: Quorum sensing controls pyocyanin synthesis; AHL and PQS autoinducers
        and LasR-LasI/RhlR-RhlI systems activate pyocyanin expression.
  - subject: pyocyanin_redox_ph
    predicate: modifies
    object: visible_green_color
    description: Redox state and pH alter the apparent color of pyocyanin pigment.
    evidence:
    - reference: DOI:10.1007/s11274-023-03548-w
      notes: PYO exhibits blue-green color at neutral/alkaline pH, shifting to pink-red
        in acidic conditions; oxidized PYO is blue while reduced form is transparent.
  - subject: pvd_nrps
    predicate: participates in
    object: pyoverdine_biosynthesis
    description: PvdL/PvdI/PvdJ/PvdD NRPS enzymes synthesize the pyoverdine peptide
      backbone.
    evidence:
    - reference: DOI:10.3390/ijms25116013
      notes: The pyoverdine peptide backbone is synthesized by four NRPSs (PvdL, PvdI,
        PvdJ, PvdD).
    predicate_id: biolink:participates_in
  - subject: iron_limitation
    predicate: induces
    object: pyoverdine_biosynthesis
    description: Iron-deficient conditions induce expression of pyoverdine biosynthetic
      enzymes.
    evidence:
    - reference: DOI:10.3390/ijms25116013
      notes: Expression of the fluorescent (pyoverdine) enzymes was induced by iron-deficient
        growing conditions.
  - subject: pyoverdine_biosynthesis
    predicate: contributes to
    object: visible_green_color
    description: Pyoverdine, a yellow-green fluorescent pigment, contributes to green
      coloration alongside pyocyanin.
    evidence:
    - reference: DOI:10.1186/s12934-023-02122-1
      notes: Blue (pyocyanin) and yellow (fluorescein/pyoverdine-like) pigments combine
        to produce green colorization of the culture.
    predicate_id: RO:0002326
curation_history:
- timestamp: '2026-05-05T01:35:46.944814+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 phz operons, phenazine
    biosynthesis, pyocyanin, and visible green/blue-green 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: '2026-05-23T08:21:50Z'
  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: '2026-06-14T06:55:38Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0002047×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (7 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
    (biolink:participates_in×1, RO:0002326×1).
  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:29748×1, GO:0009372×1).
  llm_assisted: true