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Yeast Biotechnology Doctoral Training Programme

Periodic Reporting for period 1 - YEASTDOC (Yeast Biotechnology Doctoral Training Programme)

Reporting period: 2017-09-01 to 2019-08-31

Yeasts have been used in the production of fermented foods and beverages for thousands of years, and have many traits that make them very attractive and useful for modern biotechnology. Modern yeast biotechnology products include fermented foods and beverages, feeds, biofuels, industrial chemicals, flavours, enzymes, and pharmaceuticals. There is a demand for new and improved biotechnology products driven by consumer desire for novelty, pressure to reduce the environmental impact of production processes, and the effects of climate change (e.g. high sugar in grapes).
Yeast biotechnology has the potential to increase the suite of flavours available to the producers of fermented beverages, and to increase efficiencies in brewing and oenological processes. YEASTDOC Early Stage Researchers (ESRs) will carry out research in both of these areas and take advantage of the genetic diversity of food and beverage yeasts. Within the biotech industry, yeast cell factories can contribute to environmental protection by replacing petroleum as a source of chemical building blocks, among other applications. Developing more robust cell factory strains can improve the efficiency of existing industrial processes, increasing the range of applications and products for which yeast cell factories can be utilised. YEASTDOC research will also allow the use of waste products from other industries as the growth substrate for yeast cell factories, which will feed into the European vision of a circular economy and reduce production costs across industries.
There is an increasing need for highly-trained, interdisciplinary scientists to support this growing biotechnology industry, and to ensure that the fermented food and beverage sectors remain competitive and innovative. YEASTDOC will not only train talented researchers to drive innovation in the future; the research undertaken within the project will create new yeast strains, unlock the genetic potential of a range of yeast species and create research outcomes that have the potential for commercialisation.
In the first 24 months of the project, a joint doctoral programme between the six academic institutions in the YEASTDOC network was established and 12 ESRs were recruited. Each ESR is jointly registered for a PhD at two of these academic Institutions. The ESRs have developed their research plans and career development plans, and are settled into their research projects.

All of the scheduled training events have taken place, including two scientific summer schools and three complimentary skills workshops on the topics of 'Responsible Research & Innovation', 'Science Writing' and 'Knowledge Transfer'. Three of these training events were open to students from outside the network, expanding the impact of the training.

The first research objective of YEASTDOC is to apply modern genetics and develop methodology for improvement of yeast strains for novel applications in the fermented beverage industry. New lager yeast hybrids are being generated using methodology developed by one of the partners that overcomes the problem of hybrid sterility. This new methodology results in a huge increase in gene assortment increasing the diversity of the hybrid population. As an alternative to using hybrids, omics data from the non-traditional yeast, S. uvarum, are being used to understand the links between temperature, nitrogen regulation and aroma production. Two projects are addressing nutrient limitations that are common in industrial yeasts. One project has identified 15 yeast strains with high pectinolytic activity, which will be evaluated in wine fermentations. In the other project, strains containing a single fungal oligopeptide transporter (Fot) have been constructed and fermentation assays will assess the impact of the different Fot proteins. Two more projects are working on understanding the genetic basis of thermotolerance, acid resistance and osmotic tolerance. In both projects, significant method development has taken place. Phenotyping in solid media was optimized for Z. bailii and Z. parabailii strains and some extreme phenotypes have been identified. In K. marxianus, a classical genetics toolset has been established which will enable genetic mapping of biotechnologically interesting traits.

The second research objective is to enhance the robustness and performance of yeasts for industrial fermentation. Two projects are addressing the combinatorial stress of production conditions and process–induced stress. Results from one project show that modifying the expression of certain transcription factors involved in membrane lipid synthesis improves growth of S. cerevisiae in the presence of formic acid. The other project used Adaptive Laboratory Evolution (ALE) to generate and select K. marxianus variants that are better adapted to tolerate organic acids released from lignocellulosic biomass during pretreatment. The final three projects aim to improve the performance of yeast cell factory strains by focusing on uptake and utilisation of carbon on inexpensive commercial substrates and on product export from the cell. One project, tackling glycerol utilization has achieved large improvements by expressing certain glycerol catabolic pathways in an S. cerevisiae strain. Improving uptake and consumption of hexose and pentose from lignocellulosic biomass is important for development of yeast cell factory strains. Several new native transporters involved in pentose transport were identified in K. marxianus. The final project also studies transporters, but concentrates on those that can export organic acids from the cell. Several novel engineered transporter variants that show improved transport properties have been constructed and evaluated in S. cerevisiae.

In terms of dissemination, an inter-ITN symposium with two other projects (Aromagenesis and PaCMEN) active in the Microbial Biotechnologies for Food and Biochemicals area was organized. The symposium was part of the PYFF7 conference programme and was open to all attendees. It provided a showcase for the research being carried out within the cluster and highlighted synergies between the projects. Invited speakers contributed to sessions on policy, careers, doctoral training and MSCA. Three YEASTDOC ESRs gave oral presentations at the symposium while the rest of the ESRs presented posters as part of the main conference programme.

YEASTDOC ESRs have participated in a variety of outreach events, including European Researcher's Night in Cork, Braga and Kiel. They have met with high school students to discuss careers in biotechnology and used hands-on activities to engage with junior school students. Each of the ESRs has prepared a Communication Activity Plan which is linked to their career development and to the project goals.
YEASTDOC research will lead to:
New non-GM genetically characterised hybrid yeasts for application in the beverage industry
Identification of new nutrient-acquisition genes to enhance fermentation
Advanced genetics tools for improving food-related yeasts
Elucidation of the genetic basis of robustness in cell factory yeasts
Identification and validation of new functional sugar and acid membrane transporters
Strains with improved growth on sustainable substrates
Cell factory strains that have been validated at an industrial scale
12 highly qualified PhD graduates with knowledge, work experience, and transferrable skills that make them highly employable