Effects of polyploidization during adaptive evolution in yeasts (PloidYeast)

Climate change, habitat destruction and other human activities are threating the sustainability of food security. UN has launched four aims within the sustainable development plan to maintain and ensure food security. In PloidYeast, we aim to apply a new collection of yeasts to offer new biotechnological approaches that will address the UN challenges and bring the food chain in a more sustainable direction, including more circular processes. To accomplish this objective, we will make use of a recurrent evolutionary phenomenon observed in several industrial yeasts and other organisms. This phenomenon is called polyploidization, which leads to an increase in the number of copies of the genome. Polyploidization facilitates the adaptation of the organism to new environmental conditions, such as the harsh conditions found in the food industry. Through several evolutionary steps, we aim to generate yeasts with desired industrial traits, accommodated to reach the sustainability of the food security. We will apply a multidisciplinary approach combining microbiology, molecular and genetic engineering methods, bioinformatics and mathematical modelling to select and generate a new yeast collection. At the end of the project, we expect to learn how polyploidization improves adaptation to industrial conditions, which will help to solve some of the UN challenges. Not so far, but we already know that by increasing the number of copies in the yeast genome through hybridization will combine traits from the parental yeasts and in this way introduce desired industrial traits.

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.