Comparative transcriptomes reveal novel evolutionary strategies adopted by Saccharomyces cerevisiae with improved xylose utilization capability

Abstract

Production of ethanol from xylose by recombinant Saccharomyces cerevisiae is suboptimal with slow fermentation rate, compared with that from glucose. In this study, a strain-expressing Scheffersomyces stipitis xylose reductase-xylitol dehydrogenase (XR-XDH) pathway was subjected to adaptive evolution on xylose; this approach generated populations with the significantly improved cell growth and ethanol production rate. Mutants were isolated, and the best one was used for sporulation to generate eight stable mutant strains with improved xylose fermentation ability. They were used in a microarray assay to study the molecular basis of the enhanced phenotype. The enriched transcriptional differences among the eight mutant strains and the native strain revealed novel responses to xylose, which likely contributes to the improved xylose utilization. The upregulated vitamin B1 and B6 biosynthesis indicated that thiamine served as an important cofactor in xylose metabolism and may alleviate the redox stress. The increased expression of genes involved in sulfur amino acid biosynthesis and the decreased expression of genes related to Fe(II) transport may alleviate redox stress as well. Meanwhile, it was remarkable that several glucose-repressible genes, including genes of the galactose metabolism, gluconeogenesis, and ethanol catabolism, had a lower expression level after adaptive evolution. Concomitantly, the expression levels of two regulators of the glucose signaling pathway, Rgs2 and Sip4, decreased, indicating a reshaped signaling pathway to xylose after adaptive evolution. Our findings provide new targets for construction of a superior bioethanol producing strain through inverse metabolic engineering.

Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae

“…In other words, the yeasts recycle xylose back to the production of glucose-6-phosphate through the non-oxidative pentose-phosphate pathway to realize xylose metabolism [ 46 ]. However, downregulation of key genes in the gluconeogenesis pathway was also revealed in an evolved yeast with improved xylose-utilization ability [ 11 ], suggesting that differential strategies were adopted by the natural strain and lab-evolved yeast. Taken together, higher flux rate of gluconeogenesis is one of the distinguishing features of YB-2625 from the laboratory strain S288C.…”

“…It is very important to explore the innate regulatory mechanisms in the host strains, which are responsible for the optimized metabolic flux for xylose utilization. However, related studies have been only performed using the recombinant strains or the evolved recombinants [ 4 , 9 – 11 ].…”

Biochemical routes for uptake and conversion of xylose by microorganisms

“…The evolved strain YNBX26-21 showed significantly improved cell growth and ethanol production rate. Comparative transcriptome analysis revealed novel responses to xylose, including the biosynthesis of vitamins B1 and B6 and sulfur amino acid and decreased expression of Fe(II) transport-related genes and several glucose-repressible genes, which probably contributed to the improved xylose utilization [72]. All these results from adaptive evolution provided new insights into the construction of a superior xylose-utilizing strain through inverse metabolic engineering.…”

The effect of glutathione and mannitol on androgenesis in anther and isolated microspore cultures of rye (Secale cereale L.)

“…Although the protective role of antioxidative enzymes cannot be replaced even by high activity of non-enzymatic antioxidants, the use of substances which reduce oxidative stress (e.g. low molecular weight (LMW) antioxidants) could stimulate androgenesis induction and improve regeneration of green plants (Stasolla et al 2008;Cistué et al 2009;Asif et al 2013;Zeng et al 2017;Żur et al 2019). Among LMW antioxidants, the reduced form of glutathione (GSH) is one of the most important ROS scavengers and plays a significant role in maintaining the cellular redox potential, which determines proper cell growth and differentiation, and in the control over programmed cell death (PCD) initiation.…”