How synthetic biology is transforming yeast from sugar-consuming organisms to CO₂-utilizing factories
For centuries, bakers and brewers have relied on yeast's remarkable ability to transform sugar into bubbles and alcohol. This fungal workhorse has become biotechnology's favorite microscopic factory, producing everything from life-saving medicines to sustainable biofuels. Yet, yeast's sugar dependency presents both economic and environmental challenges, requiring vast agricultural resources that compete with food production.
But what if we could reprogram yeast to abandon its sweet tooth and instead feast on carbon dioxide—the very same waste gas that contributes to climate change?
Recent breakthroughs in synthetic biology have accomplished exactly that, engineering yeast strains that can grow autotrophically like plants, using CO₂ as their sole carbon source. This metabolic transformation represents more than just a scientific curiosity—it promises to revolutionize sustainable bioproduction by turning greenhouse gases into valuable chemicals, fuels, and materials.
The global bioethanol market, primarily produced by yeast fermentation, is projected to reach $117.4 billion by 2030, highlighting the economic significance of yeast-based bioprocessing.
To appreciate the engineering marvel of autotrophic yeast, we must first understand nature's own carbon capture system. The Calvin-Benson-Bassham cycle (named after its Nobel Prize-winning discoverer Melvin Calvin and his collaborators) is the biochemical pathway that enables plants, algae, and certain bacteria to convert atmospheric CO₂ into organic molecules 8 .
CO₂ molecules are attached to a five-carbon sugar named ribulose-1,5-bisphosphate (RuBP) by the enzyme RuBisCO—arguably the most abundant protein on Earth. This reaction produces an unstable six-carbon intermediate that immediately splits into two molecules of 3-phosphoglycerate (3-PGA).
The 3-PGA molecules are phosphorylated using ATP and then reduced by NADPH, producing glyceraldehyde-3-phosphate (G3P)—a three-carbon sugar that can be used to build glucose and other carbohydrates.
Most of the G3P is used to regenerate the initial RuBP acceptor molecule, completing the cycle and preparing it to fix another CO₂ molecule. This regeneration phase requires additional ATP, making the entire process energy-intensive.
Despite being nature's primary carbon fixation pathway, the Calvin cycle suffers from significant limitations. RuBisCO is notoriously inefficient and prone to confusing oxygen with CO₂, initiating a wasteful process called photorespiration that can reduce photosynthetic efficiency by up to 25% 8 . These limitations have motivated scientists to develop synthetic alternatives that might outperform nature's design.
The ambitious project to convert heterotrophic yeast into an autotrophic organism represents a triumph of synthetic biology—a field that combines engineering principles with biological systems to create new functions. Yeast (Saccharomyces cerevisiae) has long been biotechnology's model eukaryotic organism, with its fully mapped genome and well-established genetic tools making it ideal for metabolic engineering 6 .
Introducing genes for the entire Calvin cycle into yeast, primarily focusing on the two key enzymes: RuBisCO and phosphoribulokinase (PRK). However, this approach faces numerous hurdles including enzyme compatibility and energy demands 6 .
Creative hybrid approaches that combine biological and mechanical systems, such as engineering cyanobacteria to secrete glucose produced from their photosynthesis, which then feeds yeast cells in a co-culture system .
One of the most successful demonstrations of autotrophic yeast comes from the research of Gassler et al. (2020), who engineered the methylotrophic yeast Komagataella phaffii (formerly Pichia pastoris) to incorporate and utilize a functional Calvin cycle 6 .
The engineered K. phaffii strains demonstrated measurable autotrophic growth, though at rates significantly slower than natural photosynthetic organisms 6 .
| Yeast Species | Engineering Approach | Growth Rate (μ, h⁻¹) | Key Products | Reference |
|---|---|---|---|---|
| Komagataella phaffii | Calvin cycle + peroxisomal compartmentalization | 0.007-0.009 | Biomass, lactic acid, itaconic acid | 6 |
| Saccharomyces cerevisiae | Cyanobacterial endosymbiosis | 0.09 (on galactose) | Biomass, limonene | |
| Saccharomyces cerevisiae | Reductive glycine pathway | 0.006 | Glycine, serine | 6 |
| Yarrowia lipolytica | Native glycine synthesis pathway | 0.039 (evolved) | Biomass | 6 |
Engineering autotrophy into yeast requires a sophisticated array of biological tools and reagents. The following tools are essential for such metabolic engineering endeavors:
Precise genome editing for gene knockouts, pathway integration, and promoter swaps.
Visualizing gene expression and localization, tagging metabolic enzymes.
Tracing metabolic fluxes and confirming CO₂ incorporation.
Tunable control of gene expression and optimizing enzyme expression levels.
Assisting protein folding and assembly, enhancing RuBisCO assembly.
Selecting for improved phenotypes and enhancing growth rates.
While the Calvin cycle represents nature's predominant carbon fixation pathway, synthetic biology isn't limited to mimicking nature. Researchers have developed and implemented several alternative pathways that may offer advantages for engineered systems:
Recently, Dronsella et al. (2025) demonstrated remarkable success with the reductive glycine pathway in bacteria 1 3 . By replacing the native Calvin cycle in Cupriavidus necator with the synthetic rGlyP, they achieved a 17% higher biomass yield on formate and CO₂ compared to the wild-type strain using the natural pathway 3 .
The Crotonyl-CoA/Ethylmalonyl-CoA/Hydroxybutyryl-CoA (CETCH) cycle is a completely synthetic carbon fixation pathway developed by Tobias Erb's team that incorporates enzymes from nine different organisms 3 . While not yet fully implemented in living cells, the CETCH cycle has demonstrated superior efficiency in test tube experiments.
Some of the most innovative approaches combine biological carbon fixation with electrochemical systems. In these setups, electrochemical cells convert CO₂ to formate or other simple organic molecules, which are then fed to engineered yeast strains optimized to assimilate these compounds through pathways like the rGlyP 3 .
The engineering of autotrophic yeast represents more than just a technical achievement—it offers a vision of a fundamentally more sustainable biotechnology paradigm. By enabling yeast to grow on CO₂ rather than sugar, we could potentially decouple bioproduction from agricultural land use, reducing competition between food and chemical production while simultaneously sequestering greenhouse gases.
| Pathway | Organisms | Energy Efficiency | Advantages | Disadvantages |
|---|---|---|---|---|
| Calvin Cycle | Plants, cyanobacteria, algae | Moderate (3 ATP + 2 NADPH per CO₂) | Universal; compatible with photosynthesis | RuBisCO inefficiency; photorespiration |
| Reductive Glycine Pathway | Engineered bacteria and yeast | High (1.5 ATP + 1 NADPH per CO₂) | Energy efficient; linear structure | Formate toxicity; redox balancing challenges |
| CETCH Cycle | In vitro implementation | High (theoretically superior) | Custom-designed; avoids photorespiration | Not yet functional in living cells |
| Wood-Ljungdahl | Acetogenic bacteria | Very high (minimal ATP requirement) | Anaerobic operation; extremely efficient | Oxygen sensitivity; complex enzyme requirements |
| Engineered Yeast | Laboratory strains | Variable (depends on design) | Eukaryotic compatibility; biotech ready | Currently slow growth; energy challenges |