Anaerobic xylose fermentation through modification of kinase signaling pathways and iron-sulfur cluster biogenesis in yeast

A major bottleneck in the generation of lignocellulosic biofuels is the inability of native Saccharomyces cerevisiae yeast strains to convert xylose to ethanol efficiently in the absence of oxygen.  To understand the genes and pathways regulating this metabolic limitation, we combined Illumina and PacBio sequencing to assemble the complete genomes of wild yeast strains that were experimentally evolved to metabolize xylose under various oxygen conditions.  Genome sequence comparisons identified mutations in genes regulating the high osmolarity glycerol (HOG) MAP Kinase (MAPK) and Protein Kinase A (PKA) signaling pathways, as well as iron-sulfur (Fe-S) cluster biogenesis, which contribute to the xylose metabolism phenotypes.  Analysis of intracellular metabolite and gene expression levels by metabolomic and RNA-seq profiling suggested that these mutations cause losses of function in HOG MAPK signaling and Fe-S cluster protein assembly, and constitutively active PKA signaling.  Importantly, targeted deletion of these genes conferred ability to ferment xylose anaerobically from both lab media and Ammonia Fiber Expansion-pretreated corn stover hydrolysate in the unevolved parent and an unrelated laboratory yeast strain.  Furthermore, by phenotyping various mutant combinations, we were able to reconstruct the probable evolutionary path for the xylose metabolism phenotype.  Interestingly, these genetic modifications did not appear to have the identical effect on galactose metabolism.  Together, these results establish that the ability to ferment xylose into ethanol efficiently can be rapidly engineered into different native S. cerevisiae strains, which should allow researchers to develop customized yeast strains for cellulosic ethanol production.