Proteome analysis of the xylose‐fermenting mutant yeast strain TMB 3400

Abstract

Xylose fermentation in yeast has been a target of research for years, yet not all the factors that may affect xylose fermentation perfomance of yeast strains are known. In this study, the mutant S. cerevisiae strain TMB 3400, which has good xylose fermentation properties, was compared with its parental strain to examine the factors behind the improved xylose utilization at protein level. The proteome of the parental and the mutant strains were characterized by difference in gel electrophoresis (DiGE) to quantitatively identify proteins that are expressed at altered levels in the mutant. The most significant changes detected by proteome analysis were the 6-10-fold increased levels of xylose reductase, xylitol dehydrogenase and transketolase (Tkl1) in the mutant, which is in accordance with previous knowledge about xylose metabolism in yeast. The level of acetaldehyde dehydrogenase (Ald6) was also significantly increased. In addition, several proteins homologous to proteins from yeast species other than S. cerevisiae were identified in both strains, demonstrating the genetic heterogeneity of industrial yeast strains. The results were also compared with a previously reported transcription analysis performed with identical experimental set-up; however, very little correlation between the two datasets was observed. The results of the proteome analysis were in good agreement with a parallel study in which rationally designed overexpression of XR, XDH and the non-oxidative pentose phosphate pathway resulted in similar improvement in xylose utilization, which demonstrates the usefulness of proteome analysis for the identification of target genes for further metabolic engineering strategies in industrial yeast strains.

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

“…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). GPM2 encodes a phosphoglycerate mutase which, however, is not the major isoform in glycolysis (Heinisch et al 1998).…”

Rewiring yeast sugar transporter preference through modifying a conserved protein motif

“…However, S. cerevisiae lacks an endogenous xylose catabolic pathway and thus is unable to natively use the second most abundant sugar in lignocellulosic biomass. Decades of research have been focused on improving xylose catabolic pathways in recombinant S. cerevisiae (17)(18)(19)(20)(21)(22), but less work has been focused on the first committed step of the process-xylose transport, an outstanding limitation in the efficient conversion of lignocellulosic sugars (23,24).…”

Limitations in Xylose-FermentingSaccharomyces cerevisiae, Made Evident through Comprehensive Metabolite Profiling and Thermodynamic Analysis

“…Therefore, this implies a catabolic function for the PP pathway during pentose utilization. Evidence from different studies in which the yeast transcriptome and proteome were analyzed under different substrate (glucose, xylose) conditions suggests that S. cerevisiae is not well adapted for fueling lower glycolysis via the PP pathway (24,28,(51)(52)(53)(54). It also appeared from the "omics" data that xylose was poorly "sensed" as a substrate for alcoholic fermentation.…”