A unique metabolic gene cluster regulates lactose and galactose metabolism in the yeast Candida intermedia

Other conference contribution, 2024

Lactose assimilation is a relatively rare trait in yeasts, and Kluyveromyces yeast species have long served as model organisms for studying lactose metabolism. Meanwhile, the metabolic strategies of most other lactose-assimilating yeasts remain unknown. In this work, we have elucidated the genetic determinants of the superior lactose-growing yeast Candida intermedia. Through genomic and transcriptomic analyses, we identified three interdependent gene clusters responsible for the metabolism of lactose and its hydrolysis product galactose: the conserved LAC cluster (LAC12, LAC4) for lactose uptake and hydrolysis, the conserved GAL cluster (GAL1, GAL7, GAL10) for galactose catabolism through the Leloir pathway, and a “GALLAC” cluster containing the transcriptional activator gene LAC9, second copies of GAL1 and GAL10 and a XYL1 gene encoding an aldose reductase. Bioinformatic analysis suggests that the GALLAC cluster is unique to C. intermedia and has evolved through gene duplication and divergence, and deletion mutant phenotyping proved that the cluster is indispensable for C. intermedia’s growth on lactose and galactose. Moreover, analysing the network topology using a genome scale metabolic model of C. intermedia revealed the presence of an additional galactose catabolic pathway called the oxidoreductive pathway. Our results point to that C. intermedia uses the upper part of this pathway to produce the sugar alcohol galactitol as a key overflow metabolite, enabling efficient co-factor regeneration and balancing during both lactose and galactose growth. With the Leloir pathway of budding yeasts acting like a model system for understanding the function, evolution and regulation of eukaryotic metabolism, this work provides new evolutionary insights into yeast metabolic pathways and regulatory networks. In extension, the results will facilitate future development and use of C. intermedia as a cell-factory for conversion of lactose-rich whey into value-added products.