Transcriptome profiling and phenotypic stability of evolved Saccharomyces cerevisiae strains capable of ethanol production in high solids pine fermentations

A strain of S. cerevisiae used commercially for corn ethanol production was subjected to directed evolution and adaptation in pretreated pine biomass and derived strains displayed improved growth and fermentative ability on pretreated pine in the presence of related inhibitory compounds. These evolved strains displayed different phenotypes.  Some strains were able to grow and produce ethanol independent of fermentation inoculum culturing conditions while other strains failed to grow and/or produce ethanol unless cultured with the selective pressure of a synthetic cocktail of inhibitory compounds. Analysis of the inhibitory environment at the initial and final stages of fermentations identified 13 compounds that exhibited significant changes in concentrations between the performing strains and nonperforming strains. Differential expression analysis conducted on an isolate from each performance profile (with and without inhibitors) revealed 52 genes that potentially account for the ability to perform in high solids pine fermentations.  Improved robustness and changes in stress response, metabolic pathways, fatty acid synthesis and degradation, transport, and membrane and organelle stability were all observed. Florescence microscopy revealed tubular intact mitochondria networks for the evolved strains in comparison to damaged structures of the parental strain in the presence of inhibitors. These data combined with transcriptome data of mitochondria-associated genes suggested improved resistance of mitochondria to inhibitors.