Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae

Abstract

Haploid laboratory strains of Saccharomyces cerevisiae are commonly used for genetic engineering to enable their xylose utilization but little is known about the industrial yeast which is often recognized as diploid and as well as haploid and tetraploid. Here we report three unique signature pathway expression patterns and gene interactions in the centre metabolic pathways that signify xylose utilization of genetically engineered industrial yeast S. cerevisiae NRRL Y-50463, a diploid yeast. Quantitative expression analysis revealed outstanding high levels of constitutive expression of YXI, a synthesized yeast codon-optimized xylose isomerase gene integrated into chromosome XV of strain Y-50463. Comparative expression analysis indicated that the YXI was necessary to initiate the xylose metabolic pathway along with a set of heterologous xylose transporter and utilization facilitating genes including XUT4, XUT6, XKS1 and XYL2. The highly activated transketolase and transaldolase genes TKL1, TKL2, TAL1 and NQM1 as well as their complex interactions in the non-oxidative pentose phosphate pathway branch were critical for the serial of sugar transformation to drive the metabolic flow into glycolysis for increased ethanol production. The significantly increased expression of the entire PRS gene family facilitates functions of the life cycle and biosynthesis superpathway for the yeast. The outstanding higher levels of constitutive expression of YXI and the first insight into the signature pathway expression and the gene interactions in the closely related centre metabolic pathways from the industrial yeast aid continued efforts for development of the next-generation biocatalyst. Our results further suggest the industrial yeast is a desirable delivery vehicle for new strain development for efficient lignocellulose-to-advanced biofuels production.

Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain

“…Mut genes were expressed weakly in Y‐7556, YB‐378, YB‐4289, and Y‐17741 relative to the other strains (Figure S3). Strong relative expression of TKL1 in these strains may suggest an increased flux through the PPP to create intermediates for central metabolism (Feng, Liu, Weber, & Li, ; Krainer et al, ). Increased utilization of the PPP could explain in part how these strains still attain reasonable cell densities despite weak expression of Mut genes (Figure S1; Nocon et al, ).…”

Metabolic engineering considerations for the heterologous expression of xylose-catabolic pathways in Saccharomyces cerevisiae

“…However, the improved strain was still inferior to an isogenic strain expressing xylose oxidoreductase pathway: xylose reductase (XYL1) and xylitol dehydrogenase (XYL2). Because the above mentioned approaches for the xylose isomerase pathway were successfully demonstrated in other studies, we think that other unknown factors are required such as different source of the xylA gene [53,54], different strain backgrounds [55,56], and/or other metabolic engineering designs. Although recent studies successfully discovered several knockout targets (ISU1, HOG1, GRE3, IRA2, SSK2) to improve the xylose isomerase pathway, they still required a strain background with the overexpression of the genes in the pentose phosphate pathway and/or the expression of multiple copies of the xylA gene [22,24].…”

The NHR1-1 of Prs1 and the pentameric motif 284KKCPK288 of Prs3 permit multi-functionality of the PRPP synthetase in Saccharomyces cerevisiae

“…A recent publication has highlighted that increased expression of the five-membered PRS gene family of S. cerevisiae correlates with xylose utilisation in a genetically engineered industrial strain of S. cerevisiae, emphasising the central role of PRPP synthesis in the metabolic pathway for biofuel production from lignocellulose (Feng et al 2018).…”