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Scalable toolkit streamlines genetic engineering of yeast for industrial biotechnology

Researchers at DTU Biosustain (The Novo Nordisk Foundation Center for Biosustainability at DTU) have developed a new tool that significantly accelerates and simplifies the genetic engineering of yeast strains used in industrial biotechnology. The work is in the journal Proceedings of the National Academy of Sciences.

The approach with the name TUNE^YALI allows scientists to fine-tune gene expression in microbial cell factories, reducing both time and cost associated with strain optimization.

The breakthrough, developed by researchers Wei Jiang, Shengbao Wang and Professor Irina Borodina, is expected to benefit a wide range of biotechnological applications, from pharmaceuticals and food ingredients to sustainable chemicals and agricultural inputs.

"Our goal was to make strain engineering more efficient without sacrificing precision," says Wei Jiang, researcher at DTU Biosustain and co-author of the study. "With TUNE^YALI, we can now rapidly test and select the best-performing strains, making it easier to develop yeast-based production systems at an industrial scale."

A scalable toolkit for modern industrial biotech

In industrial biotechnology, microbes such as Saccharomyces cerevisiae and Yarrowia lipolytica are genetically engineered to produce valuable compounds through fermentation. These include insulin, omega-3 fatty acids, stevia sweeteners, and pheromones used in pest control. However, the process of strain engineering -optimizing microbial performance at scale -is typically slow and resource-intensive.

TUNE^YALI addresses this challenge by introducing a modular and iterative method for controlling gene expression. The system is based on creating promoter libraries that swap the native promoters in front of the target genes, allowing researchers to screen and identify the most effective genome modification for the desired phenotype.

In this study, the researchers constructed a promoter library targeting 56 transcription factors, each with seven expression levels. Applied to Y. lipolytica, the toolkit enabled rapid selection of strains with:

• Improved thermotolerance
• Altered cell morphology
• Increased production of betanin, a red food color from red beets

"What makes TUNE^YALI powerful is its adaptability," explains researcher Shengbao Wang, co-author of the study. "It's not limited to transcription factors. One can expand it to explore entire metabolic pathways or regulatory networks and use it for different strain development programs."

New toolkit publicly available

In support of open science, the team has made the toolkit and libraries publicly available via , a non-profit repository.

TUNE^YALI is especially relevant for:

• Metabolic engineering researchers working on non-conventional yeasts or emerging microbial platforms
• Biotech companies developing yeast-based production of chemicals, food, feed, and pharmaceuticals
• Biofoundries seeking scalable, high-throughput strain optimization systems

Professor at DTU Biosustain and co-author of the study Irina Borodina highlights the broader implications:

"Strain engineering is central to creating novel bio-based processes and it is also the most time- and effort-consuming part of the R&D. Changing to library-based high-throughput strain engineering methods will accelerate the development tremendously. We hope that TUNE^YALI approach will be useful for developing new Yarrowia cell factories and that this library-based promoter-swapping approach will be extended to other microorganisms"