Effects of polyploidization during adaptive evolution in yeasts (PloidYeast)

Imagine a world where your favorite foods - from bread to beer, cheese to wine - are not just delicious, but also better for the planet. This might sound like science fiction, but we are working on a tiny hero that could make it a reality: yeast. We love food, and we are producing more of it than ever. But the way we make food is putting a big strain on the Earth. Climate change, destroyed habitats, and other human activities threaten our ability to keep feeding everyone sustainably. The United Nations has set ambitious goals to change this, and yeast could be a surprising solution. Yeast is more than just the magic that makes dough rise. It is a tiny factory that can transform plants into all sorts of tasty products. But the yeast we use now has limitations. That is where "Frankenyeast" comes in - a new breed of yeast designed to make food production more sustainable. Scientists have discovered that some yeast can increase their entire genome, a trick called polyploidization. It is like a built-in superpower that helps them adapt to tough conditions. By harnessing this power, scientists can create yeast that thrives in the demanding world of industrial food production. Our team will mix and match eight different yeast species to create new, super-powered hybrids. Then, we will challenge these yeasts to survive and thrive under four industrially-relevant conditions. Using cutting-edge genetic engineering and data analysis, we will select the strongest yeast population and we will explore their new traits. Yeasts that can turn food-waste into high-quality food, reducing waste. Yeasts that can work efficiently with minimal resources, shrinking the environmental footprint of food production. This could be a game-changer for achieving the UN’s sustainability goals. Creating the “Frankenyeasts” was not easy. Our team faced challenges like yeasts stress responses that slowed down progress. But with our multidisciplinary approach, we overcame some of these hurdles and generated a new collection of 32 unique strains, 168 autotetraploids and 14 autotetraploids from 8 species. There are still a few challenges in the “Frankenyeast” pipeline that need to be solved, but that is a chapter for another story. Yeasts might seem insignificant, but they have the potential to be a mighty ally in the fight for food sustainability. By tapping into yeasts’ natural powers and giving them a genetic boost, we can help create a food future that is better for both people and the planet.

Polyploidization is a recurrent evolutionary phenomenon that generates diversity and facilitates adaptation. The food production chain requires new industrial strains, more efficient or with innovative solutions to particular problems. Synthetic biology tools can introduce biological parts for improving industrial strains. However, some of those parts are still unknown. Industrially relevant yeasts are polyploids suggesting polyploidization as a mechanism to generate new industrial strains. Allopolyploids can combine multiple parental traits. But, the effects of polyploidization are not well understood. In PloidYeast, we will apply a multidisciplinary approach combining microbiology, molecular and genetic engineering methods, bioinformatics and mathematical modelling to generate a new generation of industrial strains with application in the food production chain and advance in our understanding of adaptation by polyploidization. First, we will ask whether polyploidization mechanism is a suitable mechanism to improve bioprocesses (Q1). We selected wild yeast species (WP1) to generate auto- and allopolyploids (WP2). We will test whether multi-species allopolyploids show multiple traits (Hypothesis: H1). Then, we will evolve the new polyploids on environments mimicking three industrial conditions (WP3) expecting adaptation to them (H2). After 500 generations of evolution, we will ask whether the effects of polyploidization are repeated (Q2) by sequencing the genomes, transcriptomes and quantifying their proteome, metabolome and other phenotypic traits (WP4). If Q2 is true, we will isolate genomic regions relevant to solve a biotechnological challenge (H3). We envision to use this new multiomic dataset to build the bases of a new generation of mathematical models applied to yeast polyploids to select wild strains (H4) and isolate biological parts contributing to solutions for sustainability of food systems and promotion of circular bioeconomy.