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yellow pigmented

METPO:1003030 · CLASS · REVIEWED

A pigmentation phenotype in which microbial colonies or cells appear yellow due to production of yellow pigments such as carotenoids.

Yellow pigmentation carotenoid mechanism

Evidence-backed causal sketch linking yellow microbial pigmentation to crt-catalyzed carotenoid biosynthesis, yellow carotenoid accumulation, and visible yellow colony color.

Yellow pigmentation carotenoid mechanism Interactive directed graph showing evidence-backed causal relationships for yellow pigmented.

Edge evidence

  • Crt enzymes catalyzes carotenoid biosynthesis biolink:catalyzes

    Crt enzymes catalyze carotenoid biosynthetic reactions.

    • DOI:10.1080/1040841X.2025.2526423 crt genes ... reactions they catalyze Supports Crt enzymes as catalysts in bacterial carotenoid pathways.
  • carotenoid biosynthesis has output yellow carotenoids RO:0002234

    Carotenoid biosynthesis produces yellow-pigment carotenoids in representative bacteria.

    • DOI:10.1080/1040841X.2025.2526423 yellow pigmentation in bacteria Supports carotenoids as one source of yellow pigmentation.
  • yellow carotenoids causes visible yellow color biolink:causes

    Yellow carotenoids cause visible yellow colony or cell color.

    • DOI:10.1016/j.tim.2010.07.007 Carotenoids are natural pigments Supports carotenoids as visible pigments in bacteria.
  • visible yellow color manifests as yellow pigmented METPO:2007400

    Visible yellow color manifests the yellow-pigmented phenotype.

    • DOI:10.1080/1040841X.2025.2526423 yellow pigmentation in bacteria Supports trait-level yellow pigmentation.
  • IPP/DMAPP precursor of geranylgeranyl diphosphate (GGPP)

    C5 precursors IPP/DMAPP are elongated to the C20 carotenoid precursor GGPP.

    • DOI:10.1038/s41598-024-58700-9 Carotenoid synthesis begins from the C5 isoprenoid precursors IPP and DMAPP, which are converted via chain elongation to the C20 precursor GGPP.
  • IdsA/CrtE (GGPP synthase) catalyzes geranylgeranyl diphosphate (GGPP) biolink:catalyzes

    IdsA/CrtE (GGPP synthase) catalyzes formation of GGPP from IPP and DMAPP.

    • DOI:10.1038/s41598-024-58700-9 IdsA, the major geranylgeranyl diphosphate synthase converting IPP and DMAPP to GGPP; GGPPS annotated CrtE/IdsA.
  • geranylgeranyl diphosphate (GGPP) precursor of lycopene

    Two GGPP molecules condense to form the C40 backbone lycopene.

    • DOI:10.1038/s41598-024-58700-9 Two GGPP molecules condense to form the C40 backbone lycopene.
  • CrtI (phytoene desaturase) enables lycopene biosynthesis RO:0002327

    CrtI (phytoene desaturase) enables lycopene biosynthesis.

    • DOI:10.3390/microorganisms12040803 Phytoene desaturase (CrtI) to produce lycopene.
  • lycopene biosynthesis has output lycopene RO:0002234

    Lycopene biosynthesis produces lycopene.

    • DOI:10.3390/microorganisms12040803 Pathway proceeds through phytoene synthase (CrtB) and phytoene desaturase (CrtI) to produce lycopene.
  • CrtY (lycopene beta-cyclase) catalyzes conversion to beta-carotene

    CrtY (lycopene beta-cyclase) cyclizes lycopene to beta-carotene.

    • DOI:10.1038/s41598-024-58700-9 Lycopene is cyclized to beta-carotene by lycopene beta-cyclase (crtY).
  • beta-carotene causes or contributes to yellow pigmented

    beta-carotene is a canonical yellow/orange carotenoid that contributes to the yellow phenotype.

    • DOI:10.4014/jmb.2404.04018 beta-carotene serves as a colorant and is the classic yellow/orange carotenoid pigment.
  • flexirubin-type pigment contributes to yellow pigmented RO:0002326

    Flexirubin-type pigments produce yellow colony coloration, a carotenoid-independent yellow pigment route.

    • DOI:10.1038/s41467-024-54112-5 Flexirubin-type pigment-producing bacterium is yellow (or orange) in color; flexirubin is a known yellow pigment.
  • flexirubin-type pigment protects against reactive oxygen species damage

    Flexirubin protects against reactive oxygen species damage.

    • DOI:10.1038/s41467-024-54112-5 Flexirubin is known as a yellow pigment that effectively protects against reactive oxygen species damage.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1080/1040841X.2025.2526423

Parent traits (1)

Synonyms (1)

  • Pigment_yellow RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1003030 [-3.392, -1.132, -2.360, -0.296, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/morphology/yellow_pigmented-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial “yellow pigmented”

**Target:** `METPO:1003030`  
**Category:** MORPHOLOGY | **Kind:** CLASS | **Mapping:** REVIEWED  
**Parent:** `METPO:1003021` | **Synonym:** *Pigment_yellow*

## 1. Scope and current interpretation

`METPO:1003030` should represent an **observed yellow appearance of microbial colonies or cells under stated assay conditions**, not merely possession of a pigment-biosynthesis gene or the ability to produce an extractable pigment. The proximate cause is accumulation of chromophores whose visible absorption produces a yellow phenotype. Carotenoids are especially important: they are lipid-soluble isoprenoids, generally absorb at 440–520 nm, and span yellow through deep-red colors depending on structure. Bacteria principally derive them through the MEP/DOXP or mevalonate precursor pathways. More than 700 carotenoid varieties have been described, emphasizing that color does not uniquely identify a compound (huang2024bacterialpigmentsas pages 3-4).

The strongest experimentally resolved examples are **β-carotene, zeaxanthin, and nostoxanthin**. In *Novosphingobium aromaticivorans*, both a zeaxanthin-accumulating `ΔcrtG` mutant and a β-carotene-accumulating `ΔcrtGΔcrtZ` mutant formed yellow colonies; the authors explicitly noted that colonies can look similar despite containing different carotenoids because their absorption spectra overlap (hall2023productionofcarotenoids pages 2-6). Thus, yellow appearance is a morphological endpoint downstream of several possible chemistries—not a synonym for “carotenoid producer.”

### Boundary cases

Include only when the cells or colonies themselves are documented as yellow:

- **Include:** yellow or deep-yellow colony/cell pigmentation supported by visual observation, colorimetry, or a linked pigment assay.
- **Do not automatically include:** an organism carrying `crt` genes without observed yellow color; genomic prediction is insufficient.
- **Distinguish from adjacent colors:** lycopene accumulation can produce red or light-pink colonies, whereas phytoene is colorless. Orange, golden, cream, tan, and pink phenotypes require explicit mapping policy rather than automatic inclusion (hall2023productionofcarotenoids pages 2-6, liu2021engineeringsphingobiumsp. pages 2-4).
- **Distinguish from medium pigmentation:** secreted yellow pigment that colors the supernatant is a pigment-production phenotype unless cell/colony color is also demonstrated.
- **Distinguish from fluorescence:** yellow fluorescence under excitation is not necessarily yellow pigmentation in visible reflected light.
- **Non-carotenoid boundary:** flexirubin-type pigments, xanthomonadins, aryl polyenes, and some melanins can appear yellow. They belong in this trait only where yellow colony/cell appearance is documented; their pathways should remain separate from the carotenoid branch.
- **Condition dependence:** temperature, pH, nutrients, light, oxygen, growth phase, and medium can alter pigment abundance. Record assay conditions rather than treating color as invariably expressed.

## 2. Recommended graph architecture

A useful graph should separate:

1. **precursor supply**—MEP/DOXP or MVA pathway → IPP/DMAPP → GGPP;
2. **carotenoid pathway**—GGPP → phytoene → lycopene → β-carotene → zeaxanthin → caloxanthin/nostoxanthin;
3. **regulation and environment**—for example, cAMP–CRP regulation and culture conditions;
4. **physical accumulation/localization**—cell-associated or membrane-associated carotenoid;
5. **assay endpoint**—yellow colony/cell appearance (`METPO:1003030`).

This avoids asserting that every upstream carotenoid step directly causes yellow color: phytoene is colorless and lycopene is generally red, while pathway blocks can change the final hue (liu2021engineeringsphingobiumsp. pages 4-5, liu2021engineeringsphingobiumsp. pages 2-4).

## 3. Candidate nodes grouped by type

### Trait and assay nodes

- Yellow pigmented — `METPO:1003030`
- Pigmentation phenotype — `METPO:1003021`
- Yellow colony appearance — label-only assay endpoint
- Yellow cell appearance — label-only assay endpoint
- Nonpigmented colony; light-pink colony; red colony; deep-yellow colony — label-only comparator states
- HPLC/UV–visible carotenoid detection; LC–MS pigment identification; visual colony-color screening — label-only experimental nodes

### Pathways and biological processes

- Carotenoid biosynthetic process — `GO:0016117`
- Isoprenoid biosynthetic process — `GO:0008299`
- MEP/DOXP pathway — label plus pathway-database mapping after curator verification
- Mevalonate pathway — label plus pathway-database mapping after curator verification
- β-carotene biosynthesis, zeaxanthin biosynthesis, nostoxanthin biosynthesis — label-only until exact pathway identifiers are verified
- Carotenoid accumulation; pigment accumulation; response to oxidative stress; photoprotection — GO grounding should be selected only after matching the precise experimental claim

### Genes, proteins, and enzymes

- `crtE` / geranylgeranyl-diphosphate synthase
- `crtB` / phytoene synthase

Showing the first 60 of 237 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_WITH_LITERATURE · codex

    Added DOI-backed definition and causal graph for Crt enzymes, carotenoid biosynthesis, yellow carotenoids, and visible yellow color.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes×1, biolink:causes×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016117×1).

  7. · ENRICH_CAUSAL_GRAPH · claude

    Added 9 evidence-backed generic edges (10 new nodes) from the deep-research report.

  8. · GROUND_CAUSAL_PREDICATES · claude

    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).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948×1, GO:1901177×1, CHEBI:17579×1).

  10. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  11. · NORMALISE_NODE_TYPE · claude

    Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche.