Transcription analysis of recombinant industrial and laboratory Saccharomyces cerevisiae strains reveals the molecular basis for fermentation of glucose and xylose

Abstract

BackgroundThere has been much research on the bioconversion of xylose found in lignocellulosic biomass to ethanol by genetically engineered Saccharomyces cerevisiae. However, the rate of ethanol production from xylose in these xylose-utilizing yeast strains is quite low compared to their glucose fermentation. In this study, two diploid xylose-utilizing S. cerevisiae strains, the industrial strain MA-R4 and the laboratory strain MA-B4, were employed to investigate the differences between anaerobic fermentation of xylose and glucose, and general differences between recombinant yeast strains, through genome-wide transcription analysis.ResultsIn MA-R4, many genes related to ergosterol biosynthesis were expressed more highly with glucose than with xylose. Additionally, these ergosterol-related genes had higher transcript levels in MA-R4 than in MA-B4 during glucose fermentation. During xylose fermentation, several genes related to central metabolic pathways that typically increase during growth on non-fermentable carbon sources were expressed at higher levels in both strains. Xylose did not fully repress the genes encoding enzymes of the tricarboxylic acid and respiratory pathways, even under anaerobic conditions. In addition, several genes involved in spore wall metabolism and the uptake of ammonium, which are closely related to the starvation response, and many stress-responsive genes mediated by Msn2/4p, as well as trehalose synthase genes, increased in expression when fermenting with xylose, irrespective of the yeast strain. We further observed that transcript levels of genes involved in xylose metabolism, membrane transport functions, and ATP synthesis were higher in MA-R4 than in MA-B4 when strains were fermented with glucose or xylose.ConclusionsOur transcriptomic approach revealed the molecular events underlying the response to xylose or glucose and differences between MA-R4 and MA-B4. Xylose-utilizing S. cerevisiae strains may recognize xylose as a non-fermentable carbon source, which induces a starvation response and adaptation to oxidative stress, resulting in the increased expression of stress-response genes.

Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures

“…This is in accordance with the previous observation of partial CCR in xylose-grown S. cerevisiae under anaerobiosis by Runquist et al (2009). The observed higher expression levels of gluconeogenetic FBP1 and PCK1 in S. cerevisiae during anaerobic growth on xylose compared to growth on glucose are consistent with a number of previous observations (Wahlbom et al 2003;Jin et al 2004;Salusjärvi et al 2008;Matsushika et al 2014). Accordingly, TDH1 and GPM2 have been found more highly expressed during xylose dissimilation (i.e.…”

“…at 24.5 h in mixed glucose-xylose cultures) compared to catabolism of glucose (i.e. at 6.5 h in the glucose cultures), as previously reported (Runquist et al 2009;Matsushika et al 2014). TDH1 encodes a glyceraldehyde 3-phosphate dehydrogenase isoform, which is responsive to NADH stress (Valadi et al 2004), and downregulated in evolved strains as a consequence of improved xylose utilisation (Karhumaa et al 2009;Linck et al 2014).…”

Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast

“…Cat8 and Hap4 are respiratory factors active in the general cellular response to xylose, and deletion of HAP4 was recently shown to improve cellobiose consumption rates (28,30). MSN2 and MSN4, encoding stress-associated factors, were observed to be highly up-regulated in xylose and their transcriptional targets misregulated (31). ADR1 is an activator of ADH2, a glucoserepressed gene that encodes an alcohol dehydrogenase that catalyzes a key step in ethanol consumption (32,33).…”

Increased ethanol production by deletion of HAP4 in recombinant xylose-assimilating Saccharomyces cerevisiae

“…Another study found that xylose also acts as a weakly repressive carbon source, less strongly than glucose [7,8]. In addition, transcript levels of HAP4, which encode a transcriptional activator and global regulator of respiratory gene expression [9], were induced manyfold in the presence of xylose compared to induction in the presence of glucose [5,6]. Thus, S. cerevisiae engineered for xylose metabolism does not exhibit a fermentative response to xylose even under anaerobic conditions, and the regulation of xylose metabolism in recombinant S. cerevisiae is similar to glucose metabolism in Crabtree-negative yeast [10].…”

“…Investigations using genome-wide transcription analysis have suggested that xylose-utilizing S. cerevisiae strains recognize xylose as a non-fermentable carbon source [5,6]. Another study found that xylose also acts as a weakly repressive carbon source, less strongly than glucose [7,8].…”