They develop yeast for sustainable bioproduction

Microbial cell factories, in the form of yeast, fungi or bacteria, can be used for industrial production of food, various types of biochemicals and biomaterials. During a fermentation process, the cell factories convert sugars in biomass into a desired product. Development of such processes contributes to creating a bio-based economy where the products are made from renewable organic material, biomass, instead of fossil-based raw materials.

Breakdown of xylan important for future production

Plants consist largely of the polysaccharide xylan, and the breakdown of xylan from residual raw materials from agriculture and forestry can play a significant role in the future bio-based production. For example, xylan can be used in so-called consolidated bioprocesses, where the yeast breaks down the polysaccharides to more simple sugars and then further converts them into products. However, microorganisms that are to be used industrially for this purpose need to be developed using genetic engineering to perform optimally during fermentation.

“In this study, we have looked at what happens in nature, which is a fantastic source of inspiration for how to attack the xylan structures in the biomass,” says Jonas Ravn, postdoc in the Division of Industrial Biotechnology and first author of the study.

Use enzymatic strategies to engineer industrial strains 

Over a 100 different yeast species can grow on xylan, which requires the yeasts to express several different enzymes. Through analysis of the yeast species, the research group has established that many of them lack known enzymes, xylanases, which are needed for the breakdown.

“We realized that there was a large knowledge gap, which we wanted to fill. Which xylananses do these yeasts use, what are their enzymatic strategies? This knowledge can then be used to metabolically engineer industrial yeast strains, into efficient xylan degraders,” says Cecilia Geijer, Associate Professor in Industrial Biotechnology.

Different strategies for xylan degradation

In the current study, three yeast species isolated from different environments and that grow on xylan were selected for further analysis: Blastobotrys mokoenaii from soil, Scheffersomyces lignosus found in insect guts and Wickerhamomyces canadensis from trees. The species are far apart on the phylogenic tree, but all effectively degrade xylan and use different sets of enzymes for the breakdown.

Where the yeasts grow can play a role in their strategies to break down xylan. For example, some spit out the degrading enzymes in their immediate environment, while others attach them on their own cell surface. In their studies, the research group has discovered a new xylanase from an enzyme family that is enriched in yeast and which they believe may be a specialized way for certain yeast species to break down xylan. They also show that different yeasts can cooperate or benefit from each other for different parts of the degradation process − strategies that can be copied when optimizing industrial fermentation.

“Mapping xylan-degrading yeast strains can also lead to finding new cell factory candidates,” says Cecilia Geijer.

In other words, the findings from the study can play a major role in the design and development of microbial cell factories and biorefineries that use renewable plant biomass. And the work to develop yeast strains that can grow on xylan continues.

“I have received a grant from the Novo Nordisk Foundation to take the project to the next level, and we will now transfer several of the xylan-degrading enzymes to strains of Saccharomyces cerevisiae, baker's yeast, which is already used in industry,” says Jonas Ravn.

Aim to create an efficient yeast platform

To genetically modify the yeast cells, the researchers are using the Nobel Prize-winning CRISPR-Cas9 technology. It allows for precise insertion of genes for xylan-degrading enzymes into robust industrial strains, such as Saccharomyces cerevisiae.

“We aim to create a so-called yeast platform with an enzyme profile that provides the best possible xylan fermentation. Once the platform is established, we can choose what it should produce, e.g., biochemicals, lipids or be used in the food industry. The important thing for us at the moment is not what the final product in the bioprocesses will be, but that we first build a stable and efficient platform for sustainable production,” says Jonas Ravn.

Strenght to involve researchers from different fields

The study is part of a longer project where researchers have collaborated across group and division levels at the Department of Life Sciences, and with international partners, to gather the right expertise.

“We have relied on three pillars - microbiology, enzymology, and bioinformatics − to tackle this project in a new and, for us, very successful way. Engaging researchers from different fields has been a strength. While we have obtained excellent results, we have also learned to navigate new research fields and have had many exciting discussions,” says Cecilia Geijer.

More about the study

• Read the full study: Yeasts Have Evolved Divergent Enzyme Strategies To Deconstruct and Metabolize Xylan
• The authors of the study are Jonas Ravn, Amanda Sörensen Ristinmaa, Tom Coleman, Johan Larsbrink, and Cecilia Geijer from the Division of Industrial Biotechnology, Department of Life Sciences.
• The project is funded by H2020 Research and Innovation Programme (grant agreement No 964430), Formas (2017-01417) and Carl Tryggers stiftelse (18:118).
• Learn about previous results from the researchers: CAZyme prediction in ascomycetous yeast genomes guides discovery of novel xylanolytic species with diverse capacities for hemicellulose hydrolysis (2021) and Cellulose- and xylan-degrading yeasts: Enzymes, applications and biotechnological potential (2022).