Understanding gene cluster interactions enables cell factory application of non-conventional yeast Candida intermedia

Conference poster, 2023

Lactose-rich cheese whey is an abundant industrial side stream that can be converted into value-added products using lactose-assimilating yeasts. Whereas the dairy yeasts Kluyveromyces lactis and marxianus have been well studied in terms of their lactose-metabolising traits, most other lactose-assimilating yeast species have not yet been characterized at a genomic and molecular level. The aim of this project was to elucidate the genetic determinants behind the lactose metabolism in one such yeast, Candida intermedia, and thereafter demonstrate the yeast’s potential as a cell factory for production of metabolites from cheese whey. 

Through comparative growth assays, we found that C. intermedia is one of the top ten among 36 tested lactose-growing ascomycetous yeast, ranked on growth rates in lactose containing media. Transcriptomic analysis revealed that in addition to the well conserved LAC and GAL metabolic gene clusters for (ga)lactose metabolism, C. intermedia also contains a third gene cluster that we refer to as the GALLAC cluster, which is unique to this yeast and essential for its (ga)lactose metabolism. Through targeted genome editing we have confirmed and assigned physiological functions to individual genes in the three clusters and revealed close cluster interdependence. Using the acquired knowledge, we have managed to engineer a C. intermedia that overproduces the sugar alcohol galactitol from lactose. Subsequent strain improvement led to an increased productivity and a >95% galactitol yield from the galactose moiety of lactose. 

Our work sheds light on gene clusters dynamics and lactose metabolism in C. intermedia. We envision that C. intermedia can be used as a new model organism for deciphering evolutionary aspects of lactose metabolism in ascomycetous yeast as well as a cell factory for production of added-value chemicals using lactose-rich industrial side streams as raw material.