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Genomic and phenotypic characterization of a refactored xylose utilizing Saccharomyces cerevisiae for lignocellulosic biofuels/biochemicals production

ABSTRACT: To understand the mechanisms of enhanced xylose metabolism of XUSE, we reported transcriptome analysis of XUS (rationally engineered strain) and XUSE (evolved XUS strain) grown on xylose by performing RNA-sequencing. Compared with XUS, XUSE showed significantly different gene expression landscape with 463 up-regulated and 675 down-regulated genes (>2-fold, p-value<0.05). While the genes involved in non-oxidative pentose phosphate pathway, such as TKL1, TKL2 and TAL1, were down-regulated in XUSE, it shows the decreased transcriptional patterns of a number of genes encoding TCA cycle and respiratory enzymes. Also, the genes involved in the cellular metal ion regulation and sugar transporters showed significantly changed expression levels in XUSE. This study shows the gene expression landscape of XUSE revealing engineering strategies for the enhanced xylose metabolism in S. cerevisiae.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE116076 | GEO | 2018/12/26

REPOSITORIES: GEO

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Project description:Xylose induced effects on metabolism and gene expression during anaerobic growth of an engineered Saccharomyces cerevisiae on mixed glucose-xylose medium were quantified. Gene expression of S. cerevisiae harbouring an XR-XDH pathway for xylose utilisation was analysed from early cultivation when mainly glucose was metabolised, to times when xylose was co-consumed in the presence of low glucose concentrations, and finally, to glucose depletion and solely xylose being consumed. Cultivations on glucose as a sole carbon source were used as a control. Genome-scale dynamic flux balance analysis models were developed and simulated to analyse the metabolic dynamics of S. cerevisiae in the cultivations. Model simulations quantitatively estimated xylose dependent dynamics of fluxes and challenges to the metabolic network utilisation. Increased relative xylose utilisation was predicted to induce two-directionality of glycolytic flux and a redox challenge already at low glucose concentrations. Xylose effects on gene expression were observed also when glucose was still abundant. Remarkably, xylose was observed to specifically delay the glucose-dependent repression of particular genes in mixed glucose-xylose cultures compared to glucose cultures. The delay occurred during similar metabolic flux activities in the both cultures. Xylose is abundantly present together with glucose in lignocellulosic streams that would be available for the valorisation to biochemicals or biofuels. Yeast S. cerevisiae has superior characteristics for a host of the bioconversion except that it strongly prefers glucose and the co-consumption of xylose is yet a challenge. Further, since xylose is not a natural substrate of S. cerevisiae, the regulatory response it induces in an engineered yeast strain cannot be expected to have evolved for its utilisation. Dynamic cultivation experiments on mixed glucose-xylose medium having glucose cultures as control integrated with mathematical modelling allowed to resolve specific effects of xylose on the gene expression and metabolism of engineered S. cerevisiae in the presence of varying amounts of glucose.