How scientists are engineering Yarrowia lipolytica to produce β-carotene through metabolic engineering
Imagine if the vibrant orange color of carrots could be brewed like beer—grown in giant vats rather than harvested from fields.
This isn't science fiction; it's the cutting edge of biotechnology, where scientists are turning microscopic yeast into tiny factories for producing β-carotene, the compound that gives carrots their characteristic color and nutritional value. This golden pigment is much more than just natural food coloring; it's a powerful antioxidant and the precursor to vitamin A, an essential nutrient that prevents blindness and supports immune function 2 .
Scientists are harnessing the efficiency of microorganisms to produce this valuable compound sustainably using Yarrowia lipolytica, genetically supercharged to become a remarkable β-carotene producer.
Yarrowia lipolytica isn't your typical baker's yeast. This microbial specialist has some extraordinary natural abilities that make it ideal for industrial biotechnology.
Classified as "Generally Recognized as Safe" (GRAS) by regulatory agencies, this yeast has a long history of use in food and pharmaceutical applications 1 6 .
As an "oleaginous" yeast, it can accumulate massive amounts of oils within its cells, sometimes making up more than 20% of its dry weight 6 .
The yeast is remarkably versatile in its diet, capable of growing on various inexpensive carbon sources, including agricultural waste and industrial by-products 6 .
Transforming Yarrowia lipolytica from a lipid specialist into a β-carotene factory requires sophisticated genetic engineering. Scientists have developed a multi-pronged strategy to redirect the yeast's metabolism toward producing this valuable compound.
Since Y. lipolytica doesn't naturally produce β-carotene, the first step involves introducing the necessary genetic blueprints. Researchers insert optimized genes from other organisms:
A particularly innovative approach involves engineering subcellular compartmentalization and promoting the multivesicular body (MVB) pathway to enhance β-carotene production 1 9 .
The MVB pathway, typically involved in cellular transport and waste processing, may facilitate the packaging and storage of hydrophobic β-carotene molecules.
| Tool Category | Specific Examples | Function in Engineering |
|---|---|---|
| Gene Editing | CRISPR-Cas9 systems 8 | Precise genetic modifications |
| Selection Markers | Hygromycin resistance (hph), auxotrophic markers (leu2, ura3) 8 | Identification of successfully engineered strains |
| Expression Systems | Strong promoters (TEF, GPD), codon-optimized genes 2 8 | Enhanced production of pathway enzymes |
| Compartmentalization | Peroxisomal targeting signals (PTS), lipid droplet tags 1 | Creating specialized production environments |
A groundbreaking 2025 study exemplifies how systematic engineering can dramatically improve β-carotene production in Y. lipolytica by optimizing central carbon metabolism and redox balance 4 5 .
Introduction of optimized β-carotene biosynthesis pathway with removal of regulatory inhibition points.
Overexpression of key native enzymes in the mevalonate pathway and engineering redox cofactor regeneration systems.
Testing two approaches to enhance NADPH supply: pentose phosphate pathway vs. phosphoketolase-phosphotransacetylase (PK-PTA) pathway.
| Engineering Strategy | Effectiveness | Key Advantage | Challenge |
|---|---|---|---|
| MVA Pathway Strengthening |
|
Directly increases precursor supply | Potential enzyme inhibition |
| Pentose Phosphate Pathway Enhancement |
|
Native pathway, efficient NADPH generation | Requires balanced carbon flux |
| PK-PTA Pathway Introduction |
|
Alternative NADPH route | Lower efficiency in Y. lipolytica context |
| Peroxisomal Compartmentalization |
|
Concentrates substrates and enzymes | Requires precise protein targeting |
| Lipid Pathway Modulation |
|
Enhances storage capacity | Over-expression can hinder growth 4 5 |
Engineering microbial cell factories requires specialized molecular tools and reagents. The following toolkit highlights essential components used in developing advanced Y. lipolytica strains for β-carotene production.
| Reagent/Resource | Function in Research | Example in β-carotene Studies |
|---|---|---|
| Codon-Optimized Genes | Enhances heterologous gene expression | Synthetic crtE, crtI, crtYB genes optimized for Y. lipolytica codon usage 2 |
| Strong Promoters | Drives high-level gene transcription | TEF and GPD promoters for constitutive expression 2 |
| Selection Markers | Identifies successfully transformed strains | Hygromycin B resistance (hph), ura3 and leu2 auxotrophic markers 8 |
| Genome Editing Systems | Enables precise genetic modifications | CRISPR-Cas9 platforms for targeted integration and gene knockout 8 |
| Fluorescent Reporters | Visualizes gene expression and protein localization | Superfolder GFP for tracking organelle dynamics and pathway activity 8 |
The engineering of Yarrowia lipolytica for β-carotene production represents just the beginning of a broader revolution in microbial biotechnology. As our understanding of yeast metabolism deepens, researchers are developing increasingly sophisticated tools to optimize these microbial factories.
| Strain/Study | Achievement | Engineering Strategy |
|---|---|---|
| Larroude et al. (2017) | 6.5 g/L in fed-batch fermentation | Lipid overproducer base strain + multiple car-cassette integrations |
| Yli-C2AH2 | 2.7 g/L in 5-L fermenter 2 7 | Multi-copy gene expression + tHMGR + fatty acid pathway enhancement |
| Carbon & Redox Study (2025) | 809.2 mg/L 4 5 | Central carbon pathway rebalancing + redox optimization |
The progression from laboratory curiosity to industrial reality is already underway. Recent achievements demonstrating production of 2.7 g/L and even up to 6.5 g/L of β-carotene in scaled-up fermenters signal that microbial production is nearing commercial viability 2 . As engineering strategies become more refined, we move closer to a future where vibrant orange β-carotene is produced sustainably through fermentation—brewed by microscopic yeast working as efficient, environmentally-friendly cellular factories.