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carotenoid pigmentation

METPO:1003031 · CLASS · REVIEWED

A pigmentation phenotype caused by microbial production and accumulation of carotenoid pigments.

Carotenoid pigmentation crt-pathway mechanism

Evidence-backed causal sketch linking bacterial carotenoid pigmentation to isoprenoid precursors, crt enzymes, conjugated carotenoids, and yellow-orange-red visible color.

Carotenoid pigmentation crt-pathway mechanism Interactive directed graph showing evidence-backed causal relationships for carotenoid pigmentation.

Edge evidence

  • isoprenoid precursors feed into carotenoid biosynthesis

    Isoprenoid precursors provide substrate for carotenoid production.

    • DOI:10.1016/j.gene.2004.11.038 isoprenoid precursor biosynthesis Supports isoprenoid precursor biosynthesis as a major step in eubacterial carotenoid pathways.
  • Crt enzymes catalyzes carotenoid biosynthesis biolink:catalyzes

    Crt gene products catalyze bacterial carotenoid biosynthetic reactions.

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

    Carotenoid biosynthesis produces conjugated carotenoid pigments.

    • DOI:10.1080/1040841X.2025.2526423 biosynthesis pathways of bacterial carotenoids Supports bacterial carotenoid biosynthesis as the source of carotenoid pigments.
  • conjugated carotenoids causes yellow-orange-red color biolink:causes

    Conjugated carotenoids absorb visible light and produce yellow-orange-red pigmentation.

    • DOI:10.1080/1040841X.2025.2526423 red, pink, orange, and yellow pigmentation in bacteria Supports carotenoids as color determinants for this pigment class.
  • yellow-orange-red color manifests as carotenoid pigmentation METPO:2007400

    Yellow-orange-red visible color manifests carotenoid pigmentation.

    • DOI:10.1080/1040841X.2025.2526423 responsible for the red, pink, orange, and yellow pigmentation Supports the trait-level mapping from carotenoid chemistry to pigmentation.
  • phytoene synthase converts phytoene

    Phytoene synthase condenses prenyl diphosphate (GFDP) to form phytoene.

    • DOI:10.3390/molecules29174235 Through the catalytic action of phytoene synthase, GFDP undergoes condensation to form phytoene.
  • phytoene is substrate for phytoene desaturase

    Phytoene is dehydrogenated by phytoene desaturase en route to lycopene.

    • DOI:10.3390/molecules29174235 Phytoene is further dehydrogenated by dehydrogenase to generate phytofluene, which is subsequently converted into lycopene.
  • phytoene desaturase produces lycopene METPO:2007800

    Phytoene desaturase converts phytoene (via phytofluene) to lycopene.

    • DOI:10.3390/molecules29174235 Phytoene is further dehydrogenated... which is subsequently converted into lycopene.
  • lycopene cyclases converts cyclic carotenes

    Lycopene cyclases cyclize lycopene into alpha-, epsilon-, and beta-carotene.

    • DOI:10.3390/molecules29174235 The cyclization of lycopene... lead[s] to the formation of alpha-carotene, epsilon-carotene, and beta-carotene under the catalysis of various lycopene cyclases.
  • lycopene is substrate for lycopene cyclases

    Lycopene is the substrate cyclized by lycopene cyclases.

    • DOI:10.3390/molecules29174235 The cyclization of lycopene... under the catalysis of various lycopene cyclases.
  • cyclic carotenes is a conjugated carotenoids rdfs:subClassOf

    Cyclic carotenes are conjugated carotenoid pigments contributing to coloration.

    • DOI:10.3390/molecules29174235 Cyclic carotenes (alpha-/epsilon-/beta-carotene) are conjugated carotenoid pigment products of the pathway.

Provenance

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

Parent traits (1)

Synonyms (1)

  • Pigment_carotenoid RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1003031 [-2.345, -1.877, -1.987, -1.228, …]

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/carotenoid_pigmentation-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 carotenoid pigmentation

## Executive scope

**Target trait:** carotenoid pigmentation  
**Identifier:** **METPO:1003031**  
**Category/kind:** MORPHOLOGY / CLASS  
**Parent:** METPO:1003021  
**Synonym:** *Pigment_carotenoid*

The trait should represent an **observable microbial pigmentation phenotype caused by endogenous production and cellular accumulation of one or more carotenoids**. The pigments are conjugated isoprenoids whose visible absorption can produce yellow, orange, red, pink, or golden colonies/cells. The core causal chain is therefore:

**isoprenoid precursors → carotenoid biosynthesis → carotenoid accumulation/localization → visible pigmentation.**

Pigmentation is not equivalent to the mere presence of a *crt* gene. Strong trait evidence combines color or spectroscopy with chemical identification, pathway perturbation, or genetic complementation. For example, a 2023 *Mycobacterium kansasii* screen recovered 204 pigmentation mutants—0.14% of approximately 150,000 transposon mutants—and mapped most characterized insertions to carotenoid synthesis, cleavage, or fatty-acid-associated loci. Loss of *crtI* or *crtB* yielded off-white colonies after illumination, whereas restoration of the complete CRT locus restored the wild-type phenotype. (janisch2023geneticunderpinningsof pages 14-15, janisch2023geneticunderpinningsof pages 4-5)

### Boundaries

**Include:**

- Constitutive or environmentally induced carotenoid coloration.
- C40 carotenes and xanthophylls, including lycopene, β-carotene, astaxanthin, deinoxanthin, spheroidene, and spirilloxanthin.
- C30 carotenoid pigmentation such as staphyloxanthin, but as a separate taxon-specific branch.
- Color changes caused by altered carotenoid composition or accumulation, if chemically or genetically supported.

**Exclude or keep separate:**

- Non-carotenoid pigments such as melanin, prodigiosin, violacein, chlorophyll, flavins, and hemes.
- Uptake of exogenous carotenoids without microbial biosynthesis, unless the intended ontology scope explicitly includes acquired pigmentation.
- Carotenoid-pathway capacity inferred only from sequence, without demonstrated production or phenotype.
- Antioxidant, photoprotective, virulence, or membrane phenotypes as definitions of pigmentation. These are possible consequences of carotenoid accumulation, not the pigmentation trait itself.
- Color assignments based only on colony appearance where mixtures of lycopene, γ-carotene, β-carotene, or unrelated pigments were not resolved.

## Current mechanistic model

The most portable bacterial module is **IPP/DMAPP → GGPP → phytoene → an unsaturated carotene → downstream colored carotenoids**. CrtE supplies GGPP; CrtB condenses two GGPP molecules into 15-cis-phytoene; and CrtI performs sequential desaturation. CrtI product specificity varies: some enzymes terminate at neurosporene, whereas four-step enzymes produce lycopene. Cyclases and modifying enzymes then determine the final pigment. (sandmann2023genesandpathway pages 5-6, sandmann2023genesandpathway pages 3-5)

This model must not be treated as universal. In the green alga *Dunaliella salina*, phytoene-to-lycopene conversion follows a plant-like PDS–ZISO–ZDS–CRTISO sequence rather than relying mainly on one bacterial-type CrtI. Heterologous reconstruction also showed that DsZISO and DsCRTISO were essential for isomerization in the tested system. (chen2023engineeringtheβcarotene pages 1-3)

## Candidate nodes

### Trait and process nodes

- carotenoid pigmentation — **METPO:1003031**
- carotenoid biosynthetic process — **GO:0016117**
- isoprenoid biosynthetic process — GO grounding recommended after record verification
- carotenoid accumulation — label-only candidate
- photochromogenicity — label-only phenotype; condition-dependent subtype
- carotenoid degradation / cleavage — label-only process or verified GO term
- visible-light absorption — molecular/physical consequence, not itself the trait
- reactive oxygen species detoxification — downstream function; do not make obligatory

### Pathways and modules

- MEP/DOXP pathway for IPP and DMAPP
- mevalonate pathway, especially in fungi and engineered hosts
- conserved bacterial C40 carotenoid core: *crtE–crtB–crtI*
- lycopene cyclization module: *crtY* or lineage-specific cyclases
- *Dunaliella* plant-like module: GGPS–PSY–PDS–ZISO–ZDS–CRTISO–LYCB
- *Deinococcus* deinoxanthin branch: CrtLm–CruF–CrtD–CrtO–DR2473/CYP287A1

Showing the first 60 of 297 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 isoprenoid precursors, Crt enzymes, carotenoid biosynthesis, conjugated carotenoids, and visible pigmentation.

  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 6 evidence-backed generic edges (6 new nodes) from the deep-research report.

  8. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948×1, CHEBI:35163×1).

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A023WN98×1, UniProtKB:A0A060JDC8×1).

  11. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  12. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 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.

  13. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. 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. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.

  14. · 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.