Quantitative metabolomics of a xylose-utilizing Saccharomyces cerevisiae strain expressing the Bacteroides thetaiotaomicron xylose isomerase on glucose and xylose

Comparative metabolome analysis of sake yeast with enhanced fermentation performance in sake fermentation conditions

Japanese sake is fermented with specific strains of budding yeast Saccharomyces cerevisiae. Sake yeasts can allow the ethanol concentration of sake to exceed 20 % without distillation. While the genetic mutations responsible for these exceptional properties have been investigated, the underlying metabolism has not been fully explored. It is because yeast cells cultured in sake mash are difficult to collect for metabolome analysis. This study aimed to clarify the metabolic differences of K701 sake yeast and the X2180 diploid laboratory strain when cultured under sake fermentation conditions. To find an alternative medium that mimics sake fermentation and is applicable to measurements of intracellular metabolome, we compared three liquid media, including SD2 medium (synthetic dextrose medium containing 2 % glucose), SD20 medium (synthetic dextrose medium containing 20 % glucose and 1.8 % lactic acid) and pseudo-sake medium (a supernatant of saccharified rice supplemented with 1.8 % lactic acid). Culture profile data demonstrated that the pseudo-sake medium successfully reproduced the metabolic traits of K701 observed in sake mash. Targeted metabolome analysis of yeast cells cultured in the pseudo-sake medium revealed that levels of glycolytic metabolites, such as glucose-6-phosphate (G6P), fructose-6-phosphate (F6P), and fructose-1,6-bisphosphate (FBP), were significantly higher with K701. Based on metabolite concentration data, we inferred that K701 cells had a higher ATP regeneration rate. Calculation of differential Gibbs free energy changes revealed that the glucokinase reaction was upregulated in K701. The present study has, for the first time, revealed the metabolism of K701 sake yeast responsible for its exceptional fermentation ability under sake fermentation conditions.

Carbon starvation drives biosynthesis of high mannose-composition polysaccharides in Ganoderma lucidum

Polysaccharides with high mannose composition exhibit favorable antitumor activity, but there is currently a lack of well-defined and practical approaches to efficiently manufacture this type of polysaccharide. This study explores the impact of carbon utilization on exopolysaccharide (EPS) production and monosaccharide composition in Ganoderma lucidum, aiming to promote the biosynthesis of polysaccharides with high mannose composition. Sucrose supply significantly increased the mannose proportion to 35.52 % in EPS via carbon starvation. To enhance polysaccharide production with high mannose composition, a joint control by carbon starvation and glucose feeding strategy was developed, achieving 0.42 g/L EPS and 18.67 % mannose with 5 g/L glucose supplementation on day 6 in an initial 10 g/L glucose medium. Using this approach, G. lucidum mycelia exhibited normal growth patterns similar to those in sucrose culture. Essentially, carbon starvation upregulated key genes in the GDP-mannose synthesis pathway, including phosphomannose isomerase (PMI), phosphomannose mutase (PMM), and GDP-mannose pyrophosphorylase (GMP), by over 2-fold, facilitating high mannose-composition polysaccharide synthesis in both sucrose and carbon starvation conditions. This work provides insights into the biosynthesis of structurally specific polysaccharides in G. lucidum and offers a foundation for developing polysaccharides with diverse applications in food, medicine, and other fields.

Engineering of Saccharomyces cerevisiae for co-fermentation of glucose and xylose: Current state and perspectives

The use of non-food lignocellulosic biomass to produce ethanol fits into the strategy of a global circular economy with low dependence on fossil energy resources. Xylose is the second most abundant sugar in lignocellulosic hydrolysate, and its utilization in fermentation is a key issue in making the full use of raw plant materials for ethanol production and reduce production costs. Saccharomyces cerevisiae is the best ethanol producer but the organism is not a native xylose user. In recent years, great efforts have been made in the construction of xylose utilizing S. cerevisiae strains by metabolic and evolutionary engineering approaches. In addition, managing global transcriptional regulation works provides an effective means to increase the xylose utilization capacity of recombinant strains. Here we review the common strategies and research advances in the research field in order to facilitate the researches in xylose metabolism and xylose-based fermentation.

Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications

Isomerases are enzymes that induce physical changes in a molecule without affecting the original molecular formula. Among this class of enzymes, xylose isomerases (XIs) are the most studied to date, partly due to their extensive application in industrial processes to produce high-fructose corn sirups. In recent years, the need for sustainable initiatives has triggered efforts to improve the biobased economy through the use of renewable raw materials. In this context, D-xylose usage is crucial as it is the second-most abundant sugar in nature. The application of XIs in biotransforming xylose, enabling downstream metabolism in several microorganisms, is a smart strategy for ensuring a low-carbon footprint and producing several value-added biochemicals with broad industrial applications such as in the food, cosmetics, pharmaceutical, and polymer industries. Considering recent advancements that have expanded the range of applications of XIs, this review provides a comprehensive and concise overview of XIs, from their primary sources to the biochemical and structural features that influence their mechanisms of action. This comprehensive review may help address the challenges involved in XI applications in different industries and facilitate the exploitation of xylose bioprocesses.

Yeast-Based Biosynthesis of Natural Products From Xylose

Xylose is the second most abundant sugar in lignocellulosic hydrolysates. Transformation of xylose into valuable chemicals, such as plant natural products, is a feasible and sustainable route to industrializing biorefinery of biomass materials. Yeast strains, including Saccharomyces cerevisiae, Scheffersomyces stipitis, and Yarrowia lipolytica, display some paramount advantages in expressing heterologous enzymes and pathways from various sources and have been engineered extensively to produce natural products. In this review, we summarize the advances in the development of metabolically engineered yeasts to produce natural products from xylose, including aromatics, terpenoids, and flavonoids. The state-of-the-art metabolic engineering strategies and representative examples are reviewed. Future challenges and perspectives are also discussed on yeast engineering for commercial production of natural products using xylose as feedstocks.

Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae

Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.

Production of biofuels and chemicals from xylose using native and engineered yeast strains

Numerous metabolic engineering strategies have allowed yeasts to efficiently assimilate xylose, the second most abundant sugar component of lignocellulosic biomass. During the investigation of xylose utilization by yeasts, a global rewiring of metabolic networks upon xylose cultivation has been captured, as opposed to a pattern of glucose repression. A clear understanding of the xylose-induced metabolic reprogramming in yeast would shed light on the optimization of yeast-based bioprocesses to produce biofuels and chemicals using xylose. In this review, we delved into the characteristics of yeast xylose metabolism, and potential benefits of using xylose as a carbon source to produce various biochemicals with examples. Transcriptomic and metabolomic patterns of xylose-grown yeast cells were distinct from those on glucose-a conventional sugar of industrial biotechnology-and the gap might lead to opportunities to produce biochemicals efficiently. Indeed, limited glycolytic metabolic fluxes during xylose utilization could result in enhanced production of metabolites whose biosynthetic pathways compete for precursors with ethanol fermentation. Also, alleviation of glucose repression on cytosolic acetyl coenzyme A (acetyl-CoA) synthesis, and respiratory energy metabolism during xylose utilization enhanced production of acetyl-CoA derivatives. Consideration of singular properties of xylose metabolism, such as redox cofactor imbalance between xylose reductase and xylitol dehydrogenase, is necessary to maximize these positive xylose effects. This review argues the importance and benefits of xylose utilization as not only a way of expanding a substrate range, but also an effective environmental perturbation for the efficient production of advanced biofuels and chemicals in yeasts.

Widespread effect of N-acetyl-D-glucosamine assimilation on the metabolisms of amino acids, purines, and pyrimidines in Scheffersomyces stipitis

BACKGROUND

Following cellulose, chitin is the most abundant renewable resource and is composed of the monomeric amino sugar N-acetyl-D-glucosamine (GlcNAc). Although many yeasts, including Saccharomyces cerevisiae, have lost their ability to utilize GlcNAc, some yeasts are able to use GlcNAc as a carbon source. However, our understanding of the effects of GlcNAc on the intracellular metabolism of nitrogen-containing compounds in these yeast species is limited.

RESULTS

In the present study, we quantitatively investigated the metabolic responses to GlcNAc in the GlcNAc-assimilating yeast Scheffersomyces stipitis (formerly known as Pichia stipitis) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The comprehensive analysis of the metabolites extracted from S. stipitis cells grown in glucose, xylose, or GlcNAc revealed increased intracellular accumulation of a wide range of nitrogen-containing compounds during GlcNAc assimilation in this yeast. The levels of aromatic, branched-chain, and sulfur-containing amino acids and adenine, guanine, and cytosine nucleotides were the highest in GlcNAc-grown cells.

CONCLUSIONS

The CE-TOFMS analysis revealed a positive effect for GlcNAc on the intracellular concentration of a wide range of nitrogen-containing compounds. The metabolomic data gathered in this study will be useful for designing effective genetic engineering strategies to develop novel S. stipitis strains for the production of valuable nitrogen-containing compounds from GlcNAc.