RNA-seq based transcriptomic analysis of the non-conventional yeast Spathaspora passalidarum during Melle-boinot cell recycle in xylose-glucose mixtures

Abstract

The Melle-Boinot is a promising process for second-generation ethanol production by xylose-fermenting yeasts. However, the impact of this process on the physiology of the non-conventional yeast Spathaspora passalidarum during second-generation ethanol production remains unclear. Therefore, we performed a transcriptomic analysis of S. passalidarum to determine the differences and global responses of differentially expressed genes (DEGs) during five fed-batch fermentations with cell recycle. A cycle-to-cycle metabolic reprogramming was observed resulting in an increase in ethanol yield (32%), volumetric productivity (33%), and titer (33%); and an expressive decrease of 94% of xylitol production. A broad set of pathways operated synergically such as fatty acid metabolism, N-glycan biosynthesis, glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, glutathione metabolism and sulfur metabolism, indicating those as important mechanisms for cell recycling adaptations due to increased ethanol concentration, long-term ethanol exposure and osmotic stress. Together these results suggest that cellular energy was redirected towards the production of cell wall components enabling S. passalidarum cells to thrive on consecutive recycles. Furthermore, these results are instrumental to guide genetic-engineering efforts of xylose-fermenting yeasts to improve the productiveness and feasibility of renewable energy production from lignocellulosic biomass and hemicellulosic hydrolysates.