Direct evidence for a xylose metabolic pathway inSaccharomyces cerevisiae

An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae

Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae-a microbial cell widely used industrially for ethanol production-is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.

The novel properties of Kluyveromyces marxianus glucose sensor/receptor repressor pathway and the construction of glucose repression-released strains

BACKGROUND

Glucose repression in yeast leads to the sequential or diauxic utilization of mixed sugars and reduces the co-utilization of glucose and xylose from lignocellulosic biomasses. Study of the glucose sensing pathway helps to construct glucose repression-released yeast strains and enhance the utilization of lignocellulosic biomasses.

RESULTS

Herein, the glucose sensor/receptor repressor (SRR) pathway of Kluyveromyces marxianus which mainly consisted of KmSnf3, KmGrr1, KmMth1, and KmRgt1 was studied. The disruption of KmSNF3 led to a release of glucose repression, enhanced xylose consumption and did not result in deficient glucose utilization. Over-expression of glucose transporter gene restored the mild decrease of glucose utilization ability of Kmsnf3 strain to a similar level of the wildtype strain but did not restore glucose repression. Therefore, the repression on glucose transporter is parallel to glucose repression to xylose and other alternative carbon utilization. KmGRR1 disruption also released glucose repression and kept glucose utilization ability, although its xylose utilization ability was very weak with xylose as sole carbon source. The stable mutant of KmMth1-ΔT enabled the release of glucose repression irrespective that the genetic background was Kmsnf3, Kmmth1, or wildtype. Disruption of KmSNF1 in the Kmsnf3 strain or KmMTH1-ΔT overexpression in Kmsnf1 strain kept constitutive glucose repression, indicating that KmSNF1 was necessary to release the glucose repression in both SRR and Mig1-Hxk2 pathway. Finally, overexpression of KmMTH1-ΔT released the glucose repression to xylose utilization in S. cerevisiae.

CONCLUSION

The glucose repression-released K. marxianus strains constructed via a modified glucose SRR pathway did not lead to a deficiency in the utilization ability of sugar. The obtained thermotolerant, glucose repression-released, and xylose utilization-enhanced strains are good platforms for the construction of efficient lignocellulosic biomass utilization yeast strains.

Xylose Metabolization by a Saccharomyces cerevisiae Strain Isolated in Colombia

Saccharomyces cerevisiae (S. cerevisiae) is the most widely used yeast in biotechnology in the world because its well-known metabolism and physiology as well as its recognized ability to ferment sugars such as hexoses. However, it does not metabolize pentoses such as arabinose and xylose, which are present in lignocellulosic biomass. Lignocellulose is a widely available raw material, with xylose content of approximately 35% of total sugars. This xylose fraction could be used to obtain high added-value chemical products such as xylitol. One of these yeasts isolated from a Colombian locality, designated as 202-3, showed interesting properties. 202-3 was identified through different approaches as a strain of S. cerevisiae, with an interesting consumption of xylose metabolizing into xylitol, in addition with excellent ability as a hexose fermenter with high ethanol yields and shows resistance to inhibitors present in lignocellulosic hydrolysates. The xylose metabolization by the 202-3 strain and their kinetics parameters had not been previously reported for any other natural strain of S. cerevisiae. These results suggest the great potential of natural strains for obtaining high value-added chemical products using sugars available in lignocellulosic biomass.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01054-z.

Effect of Laccase Detoxification on Bioethanol Production from Liquid Fraction of Steam-Pretreated Olive Tree Pruning

During lignocellulosic bioethanol production, the whole slurry obtained by steam explosion is filtered, generating a water-insoluble fraction rich in cellulose which is used for saccharification and ethanol fermentation, as well as a liquid fraction containing solubilised glucose and xylose but also some inhibitory by-products (furan derivatives, weak acids and phenols), which limits its use for this purpose. Since utilization of this liquid fraction to ethanol is essential for an economically feasible cellulosic ethanol process, this work studied a laccase from Myceliophthora thermophila to detoxify the liquid fraction obtained from steam-pretreated olive tree pruning (OTP) and to overcome the effects of these inhibitors. Then, the fermentation of laccase-treated liquid fraction was evaluated on ethanol production by different Saccharomyces cerevisiae strains, including the Ethanol Red, with the capacity to ferment glucose but not xylose, and the xylose-fermenting recombinant strain F12. Laccase treatment reduced total phenols content by 87% from OTP liquid fraction, not affecting furan derivatives and weak acids concentration. Consequently, the fermentative behavior of both Ethanol Red and F12 strains was improved, and ethanol production and yields were increased. Moreover, F12 strain was capable of utilizing some xylose, which increased ethanol production (10.1 g/L) compared to Ethanol Red strain (8.6 g/L).

Sugarcane Bagasse-Based Ethanol Production and Utilization of Its Vinasse for Xylitol Production as an Approach in Integrated Biorefinery

Biorefinery of sugarcane bagasse into ethanol and xylitol was investigated in this study. Ethanol fermentation of sugarcane bagasse hydrolysate was carried out by Saccharomyces cerevisiae. After ethanol distillation, the vinasse containing xylose was used to produce xylitol through fermentation by Candida guilliermondii TISTR 5068. During the ethanol fermentation, it was not necessary to supplement a nitrogen source to the hydrolysate. Approximately 50 g/L of bioethanol was produced after 36 h of fermentation. The vinasse was successfully used to produce xylitol. Supplementing the vinasse with 1 g/L of yeast extract improved xylitol production 1.4-fold. Cultivating the yeast with 10% controlled dissolved oxygen resulted in the best xylitol production and yields of 10.2 ± 1.12 g/L and 0.74 ± 0.04 g/g after 60 h fermentation. Supplementing the vinasse with low fraction of molasses to improve xylitol production did not yield a positive result. The supplementation caused decreases of up to 34% in xylitol production rate, 24% in concentration, and 24% in yield.

Evaluation of Napier Grass for Bioethanol Production through a Fermentation Process

Ethanol is one of the widely used liquid biofuels in the world. The move from sugar-based production into the second-generation, lignocellulosic-based production has been of interest due to an abundance of these non-edible raw materials. This study interested in the use of Napier grass (Pennisetum purpureum Schumach), a common fodder in tropical regions and is considered an energy crop, for ethanol production. In this study, we aim to evaluate the ethanol production potential from the grass and to suggest a production process based on the results obtained from the study. Pretreatments of the grass by alkali, dilute acid, and their combination prepared the grass for further hydrolysis by commercial cellulase (Cellic® CTec2). Separate hydrolysis and fermentation (SHF), and simultaneous saccharification and fermentation (SSF) techniques were investigated in ethanol production using Saccharomyces cerevisiae and Scheffersomyces shehatae, a xylose-fermenting yeast. Pretreating 15% w/v Napier grass with 1.99 M NaOH at 95.7 °C for 116 min was the best condition to prepare the grass for further enzymatic hydrolysis using the enzyme dosage of 40 Filter Paper Unit (FPU)/g for 117 h. Fermentation of enzymatic hydrolysate by S. cerevisiae via SHF resulted in the best ethanol production of 187.4 g/kg of Napier grass at 44.7 g/L ethanol concentration. The results indicated that Napier grass is a promising lignocellulosic raw material that could serve a fermentation with high ethanol concentration.

d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review

Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.

Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis

Xylose fermentation is a rare trait that is immensely important to the cellulosic biofuel industry, and Candida tenuis is one of the few yeasts that has been reported with this trait. Here we report the isolation of two strains representing a candidate sister species to C. tenuis. Integrated analysis of genome sequence and physiology suggested the genetic basis of a number of traits, including variation between the novel species and C. tenuis in lactose metabolism due to the loss of genes encoding lactose permease and β-galactosidase in the former. Surprisingly, physiological characterization revealed that neither the type strain of C. tenuis nor this novel species fermented xylose in traditional assays. We reexamined three xylose-fermenting strains previously identified as C. tenuis and found that these strains belong to the genus Scheffersomyces and are not C. tenuis. We propose Yamadazyma laniorum f.a. sp. nov. to accommodate our new strains and designate its type strain as yHMH7 (=CBS 14780 = NRRL Y-63967T). Furthermore, we propose the transfer of Candida tenuis to the genus Yamadazyma as Yamadazyma tenuis comb. nov. This approach provides a roadmap for how integrated genome sequence and physiological analysis can yield insight into the mechanisms that generate yeast biodiversity.

Xylose transport in yeast for lignocellulosic ethanol production: Current status

Lignocellulosic ethanol has been considered as an alternative transportation fuel. Utilization of hemicellulosic fraction in lignocelluloses is crucial in economical production of lignocellulosic ethanol. However, this fraction has not efficiently been utilized by traditional yeast Saccharomyces cerevisiae. Genetically modified S. cerevisiae, which can utilize xylose, has several limitations including low ethanol yield, redox imbalance, and undesired metabolite formation similar to native xylose utilizing yeasts. Besides, xylose uptake is a major issue, where sugar transport system plays an important role. These genetically modified and wild-type yeast strains have further been engineered for improved xylose uptake. Various techniques have been employed to facilitate the xylose transportation in these strains. The present review is focused on the sugar transport machineries, mechanisms of xylose transport, limitations and how to deal with xylose transport for xylose assimilation in yeast cells. The recent advances in different techniques to facilitate the xylose transportation have also been discussed.

Analysis of metabolisms and transports of xylitol using xylose- and xylitol-assimilating Saccharomyces cerevisiae

To clarify the relationship between NAD(P)⁺/NAD(P)H redox balances and the metabolisms of xylose or xylitol as carbon sources, we analyzed aerobic and anaerobic batch cultures of recombinant Saccharomyces cerevisiae in a complex medium containing 20 g/L xylose or 20 g/L xylitol at pH 5.0 and 30°C. The TDH3p-GAL2 or gal80Δ strain completely consumed the xylose within 24 h and aerobically consumed 92-100% of the xylitol within 96 h, but anaerobically consumed only 20% of the xylitol within 96 h. Cells of both strains grew well in aerobic culture. The addition of acetaldehyde (an effective oxidizer of NADH) increased the xylitol consumption by the anaerobically cultured strain. These results indicate that in anaerobic culture, NAD⁺ generated in the NAD(P)H-dependent xylose reductase reaction was likely needed in the NAD⁺-dependent xylitol dehydrogenase reaction, whereas in aerobic culture, the NAD⁺ generated by oxidation of NADH in the mitochondria is required in the xylitol dehydrogenase reaction. The role of Gal2 and Fps1 in importing xylitol into the cytosol and exporting it from the cells was analyzed by examining the xylitol consumption in aerobic culture and the export of xylitol metabolized from xylose in anaerobic culture, respectively. The xylitol consumptions of gal80Δ gal2Δ and gal80Δ gal2Δ fps1Δ strains were reduced by 81% and 88% respectively, relative to the gal80Δ strain. The maximum xylitol concentration accumulated by the gal80Δ, gal80Δ gal2Δ, and gal80Δ gal2Δ fps1Δ strains was 7.25 g/L, 5.30 g/L, and 4.27 g/L respectively, indicating that Gal2 and Fps1 transport xylitol both inward and outward.

Transcriptomes of a xylose-utilizing industrial flocculating Saccharomyces cerevisiae strain cultured in media containing different sugar sources

Lignocellulosic hydrolysates used for bioethanol production contain a mixture of sugars, with xylose being the second most abundant after glucose. Since xylose is not a natural substrate for Saccharomyces cerevisiae, recombinant S. cerevisiae strongly prefers glucose over xylose, and the fermentation rate and ethanol yield with xylose are both lower than those with glucose. To determine the molecular basis for glucose and xylose fermentation, we used microarrays to investigate the transcriptional difference of a xylose-utilizing industrial strain cultured in both single sugar media and a mixed sugar medium of glucose and xylose. The transcriptomes were nearly identical between glucose metabolizing cells in the glucose alone medium and those in the glucose fermentation phase in the mixed-sugar medium. Whereas the transcriptomes highly differed between the xylose metabolizing cells in the xylose alone medium and those in the xylose fermentation phase in the mixed sugar medium, and the differences mainly involved sulfur metabolism. When the transcriptional profiles were compared between glucose fermentation state and xylose fermentation state, we found the expression patterns of hexose transporters and glucose signaling pathway differed in response to different sugar sources, and the expression levels of the genes involved in gluconeogenesis, the glyoxylate and tricarboxylic acid cycles and respiration increased with xylose, indicating that the xylose-metabolizing cells had high requirements for maintenance energy and lacked the carbon catabolite repression capability. The effect of carbon catabolite repression by glucose lasted after glucose depletion for specific genes to different extents.

Simultaneous Saccharification and Fermentation of Sugar Beet Pulp for Efficient Bioethanol Production

Sugar beet pulp, a byproduct of sugar beet processing, can be used as a feedstock in second-generation ethanol production. The objective of this study was to investigate the effects of pretreatment, of the dosage of cellulase and hemicellulase enzyme preparations used, and of aeration on the release of fermentable sugars and ethanol yield during simultaneous saccharification and fermentation (SSF) of sugar beet pulp-based worts. Pressure-thermal pretreatment was applied to sugar beet pulp suspended in 2% w/w sulphuric acid solution at a ratio providing 12% dry matter. Enzymatic hydrolysis was conducted using Viscozyme and Ultraflo Max (Novozymes) enzyme preparations (0.015-0.02 mL/g dry matter). Two yeast strains were used for fermentation: Ethanol Red (S. cerevisiae) (1 g/L) and Pichia stipitis (0.5 g/L), applied sequentially. The results show that efficient simultaneous saccharification and fermentation of sugar beet pulp was achieved. A 6 h interval for enzymatic activation between the application of enzyme preparations and inoculation with Ethanol Red further improved the fermentation performance, with the highest ethanol concentration reaching 26.9 ± 1.2 g/L and 86.5 ± 2.1% fermentation efficiency relative to the theoretical yield.

Feasibility of xylose fermentation by engineered Saccharomyces cerevisiae overexpressing endogenous aldose reductase (GRE3), xylitol dehydrogenase (XYL2), and xylulokinase (XYL3) from Scheffersomyces stipitis

Saccharomyces cerevisiae has been engineered for producing ethanol from xylose, the second most abundant sugar in cellulosic biomass hydrolyzates. Heterologous expressions of xylose reductase (XYL1) and xylitol dehydrogenase (XYL2), or of xylose isomerase (xylA), either case of which being accompanied by overexpression of xylulokinase (XKS1 or XYL3), are known as the prevalent strategies for metabolic engineering of S. cerevisiae to ferment xylose. In this study, we propose an alternative strategy that employs overexpression of GRE3 coding for endogenous aldose reductase instead of XYL1 to construct efficient xylose-fermenting S. cerevisiae. Replacement of XYL1 with GRE3 has been regarded as an undesirable approach because NADPH-specific aldose reductase (GRE3) would aggravate redox balance with xylitol dehydrogenase (XYL2) using NAD(+) exclusively. Here, we demonstrate that engineered S. cerevisiae overexpressing GRE3, XYL2, and XYL3 can ferment xylose as well as a mixture of glucose and xylose with higher ethanol yields (0.29-0.41 g g(-1) sugars) and productivities (0.13-0.85 g L(-1) h(-1)) than those (0.23-0.39 g g(-1) sugars, 0.10-0.74 g L(-1) h(-1)) of an isogenic strain overexpressing XYL1, XYL2, and XYL3 under oxygen-limited conditions. We found that xylose fermentation efficiency of a strain overexpressing GRE3 was dramatically increased by high expression levels of XYL2. Our results suggest that optimized expression levels of GRE3, XYL2, and XYL3 could overcome redox imbalance during xylose fermentation by engineered S. cerevisiae under oxygen-limited conditions.

Hyperexpression of Escherichia coli Xylose Isomerase

The xylose isomerase (xylA) structural gene was cloned under the control of the tac promoter and expressed in a xyl(+) E. coli strain. Xylose isomerase accounted for approximately 28% of the total cell protein when this tac-xylA fusion was induced with isopropylthio beta-D-galactopyranoside. Hyperexpression of the xylA gene inhibited xylose utilization. E. coli carrying this tac-xylA fusion was encapsulated in calcium-alginate beads and used to isomerase xylose in a column reactor. Conversion of xylose to xylulose was 3-4% with a residence time in the column of 2 minutes and a maximum of 12% upon recycling.

Chemical and Synthetic Genetic Array Analysis Identifies Genes that Suppress Xylose Utilization and Fermentation in Saccharomyces cerevisiae

Though highly efficient at fermenting hexose sugars, Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomass is the five-carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars, commonly by the addition of exogenous genes from xylose fermenting fungi. However, these recombinant strains grow poorly on xylose and require further improvement through rational engineering or evolutionary adaptation. To identify unknown genes that contribute to improved xylose fermentation in these recombinant S. cerevisiae, we performed genome-wide synthetic interaction screens to identify deletion mutants that impact xylose utilization of strains expressing the xylose isomerase gene XYLA from Piromyces sp. E2 alone or with an additional copy of the endogenous xylulokinase gene XKS1. We also screened the deletion mutant array to identify mutants whose growth is affected by xylose. Our genetic network reveals that more than 80 nonessential genes from a diverse range of cellular processes impact xylose utilization. Surprisingly, we identified four genes, ALP1, ISC1, RPL20B, and BUD21, that when individually deleted improved xylose utilization of both S. cerevisiae S288C and CEN.PK strains. We further characterized BUD21 deletion mutant cells in batch fermentations and found that they produce ethanol even the absence of exogenous XYLA. We have demonstrated that the ability of laboratory strains of S. cerevisiae to utilize xylose as a sole carbon source is suppressed, which implies that S. cerevisiae may not require the addition of exogenous genes for efficient xylose fermentation.

Genetic improvement of Saccharomyces cerevisiae for xylose fermentation

There is considerable interest in recent years in the bioconversion of forestry and agricultural residues into ethanol and value-added chemicals. High ethanol yields from lignocellulosic residues are dependent on efficient use of all the available sugars including glucose and xylose. The well-known fermentative yeast Saccharomyces cerevisiae is the preferred microorganism for ethanol production, but unfortunately, this yeast is unable to ferment xylose. Over the last 15 years, this yeast has been the subject of various research efforts aimed at improving its ability to utilize xylose and ferment it to ethanol. This review examines the research on S. cerevisiae strains that have been genetically modified or adapted to ferment xylose to ethanol. The current state of these efforts and areas where further research is required are identified and discussed.

Development of efficient xylose fermentation in Saccharomyces cerevisiae: xylose isomerase as a key component

Metabolic engineering of Saccharomyces cerevisiae for ethanol production from D-xylose, an abundant sugar in plant biomass hydrolysates, has been pursued vigorously for the past 15 years. Whereas wild-type S. cerevisiae cannot ferment D-xylose, the keto-isomer D-xylulose can be metabolised slowly. Conversion of D-xylose into D-xylulose is therefore crucial in metabolic engineering of xylose fermentation by S. cerevisiae. Expression of heterologous xylose reductase and xylitol dehydrogenase does enable D-xylose utilisation, but intrinsic redox constraints of this pathway result in undesirable byproduct formation in the absence of oxygen. In contrast, expression of xylose isomerase (XI, EC 5.3.1.5), which directly interconverts D-xylose and D-xylulose, does not have these constraints. However, several problems with the functional expression of various bacterial and Archaeal XI genes have precluded successful use of XI in yeast metabolic engineering. This changed with the discovery of a fungal XI gene in Piromyces sp. E2, expression of which led to high XI activities in S. cerevisiae. When combined with over-expression of the genes of the non-oxidative pentose phosphate pathway of S. cerevisiae, the resulting strain grew anaerobically on D-xylose with a doubling time of ca. 8 h, with the same ethanol yield as on glucose. Additional evolutionary engineering was used to improve the fermentation kinetics of mixed-substrate utilisation, resulting in efficient D-xylose utilisation in synthetic media. Although industrial pilot experiments have already demonstrated high ethanol yields from the D-xylose present in plant biomass hydrolysates, strain robustness, especially with respect to tolerance to inhibitors present in hydrolysates, can still be further improved.

Investigation of the role of a conserved glycine motif in the Saccharomyces cerevisiae xylose reductase

All yeast xylose reductases, with the exception of that from Schizosaccharomyces pombe, possess the catalytic and coenzyme-binding elements from both the aldo-keto reductase and short-chain dehydrogenase-reductase (SDR) enzyme families in their primary sequences. In the Saccharomyces cerevisiae xylose reductase (XR), the SDR-like coenzyme-binding GXXXGXG motif (Gly motif) is located between residues 128 and 134, with the third Gly residue being replaced by an Asp. We used site-directed mutagenesis to study the role of this SDR-like Gly motif in the S. cerevisiae xylose reductase. Site-directed mutagenesis of the individual conserved Gly residue positions (G128A, G132A, D134G, and D134A) did not significantly affect the specific activity, kinetic constants (K(m), K(cat), and K(cat)/K(m)), or dissociation constants (K(d)) in any of the variants compared with the wild type. Deletion of the entire Gly motif produced an unstable protein that could not be purified. These results indicate that the SDR-like Gly motif likely provides support to the overall structure of the enzyme, but it does not contribute directly to coenzyme binding in this XR.

Endogenous xylose pathway in Saccharomyces cerevisiae

The baker's yeast Saccharomyces cerevisiae is generally classified as a non-xylose-utilizing organism. We found that S. cerevisiae can grow on D-xylose when only the endogenous genes GRE3 (YHR104w), coding for a nonspecific aldose reductase, and XYL2 (YLR070c, ScXYL2), coding for a xylitol dehydrogenase (XDH), are overexpressed under endogenous promoters. In nontransformed S. cerevisiae strains, XDH activity was significantly higher in the presence of xylose, but xylose reductase (XR) activity was not affected by the choice of carbon source. The expression of SOR1, encoding a sorbitol dehydrogenase, was elevated in the presence of xylose as were the genes encoding transketolase and transaldolase. An S. cerevisiae strain carrying the XR and XDH enzymes from the xylose-utilizing yeast Pichia stipitis grew more quickly and accumulated less xylitol than did the strain overexpressing the endogenous enzymes. Overexpression of the GRE3 and ScXYL2 genes in the S. cerevisiae CEN.PK2 strain resulted in a growth rate of 0.01 g of cell dry mass liter(-1) h(-1) and a xylitol yield of 55% when xylose was the main carbon source.

Xylose fermentation by genetically modified Saccharomyces cerevisiae 259ST in spent sulfite liquor

Spent sulfite pulping liquor (SSL) is a high-organic content byproduct of acid bisulfite pulp manufacture which is fermented to make industrial ethanol. SSL is typically concentrated to 240 g/l (22% w/w) total solids prior to fermentation, and contains up to 24 g/l xylose and 30 g/l hexose sugars, depending upon the wood species used. The xylose present in SSL is difficult to ferment using natural xylose-fermenting yeast strains due to the presence of inhibitory compounds, such as organic acids. Using sequential batch shake flask experiments, Saccharomyces cerevisiae 259ST, which had been genetically modified to ferment xylose, was compared with the parent strain, 259A, and an SSL adapted strain, T2, for ethanol production during SSL fermentation. With an initial SSL pH of 6, without nutrient addition or SSL pretreatment, the ethanol yield ranged from 0.32 to 0.42 g ethanol/g total sugar for 259ST, compared to 0.15-0.32 g ethanol/g total sugar for non-xylose fermenting strains. For most fermentations, minimal amounts of xylitol (<1 g/l) were produced, and glycerol yields were approximately 0.12 g glycerol/g sugar consumed. By using 259ST for SSL fermentation up to 130% more ethanol can be produced compared to fermentations using non-xylose fermenting yeast.

Generation of the improved recombinant xylose-utilizing Saccharomyces cerevisiae TMB 3400 by random mutagenesis and physiological comparison with Pichia stipitis CBS 6054

The recombinant xylose-utilizing Saccharomyces cerevisiae TMB 3399 was constructed by chromosomal integration of the genes encoding D-xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulokinase (XK). S. cerevisiae TMB 3399 was subjected to chemical mutagenesis with ethyl methanesulfonate and, after enrichment, 33 mutants were selected for improved growth on D-xylose and carbon dioxide formation in Durham tubes. The best-performing mutant was called S. cerevisiae TMB 3400. The novel, recombinant S. cerevisiae strains were compared with Pichia stipitis CBS 6054 through cultivation under aerobic, oxygen-limited, and anaerobic conditions in a defined mineral medium using only D-xylose as carbon and energy source. The mutation led to a more than five-fold increase in maximum specific growth rate, from 0.0255 h(-1) for S. cerevisiae TMB 3399 to 0.14 h(-1) for S. cerevisiae TMB 3400, whereas P. stipitis grew at a maximum specific growth rate of 0.44 h(-1). All yeast strains formed ethanol only under oxygen-limited and anaerobic conditions. The ethanol yields and maximum specific ethanol productivities during oxygen limitation were 0.21, 0.25, and 0.30 g ethanol g xylose(-1) and 0.001, 0.10, and 0.16 g ethanol g biomass(-1) h(-1) for S. cerevisiae TMB 3399, TMB 3400, and P. stipitis CBS 6054, respectively. The xylitol yield under oxygen-limited and anaerobic conditions was two-fold higher for S. cerevisiae TMB 3399 than for TMB 3400, but the glycerol yield was higher for TMB 3400. The specific activity, in U mg protein(-1), was higher for XDH than for XR in both S. cerevisiae TMB 3399 and TMB 3400, while P. stipitis CBS 6054 showed the opposite relation. S. cerevisiae TMB 3400 displayed higher specific XR, XDH and XK activities than TMB 3399. Hence, we have demonstrated that a combination of metabolic engineering and random mutagenesis was successful to generate a superior, xylose-utilizing S. cerevisiae, and uncovered distinctive physiological properties of the mutant.

Proteome analysis of recombinant xylose-fermenting Saccharomyces cerevisiae

Introduction of an active xylose utilization pathway into Saccharomyces cerevisiae, which does not naturally ferment pentose sugars, is likely to have a major impact on the overall cellular metabolism as the carbon introduced to the cells will now flow through the pentose phosphate pathway. The metabolic responses in the recombinant xylose-fermenting S. cerevisiae were studied at the proteome level by comparative two-dimensional gel electrophoresis of cellular proteins within a pH range of 3-10. Glucose-limited chemostat cultivations and corresponding chemostat cultivations performed in media containing xylose as the major carbon source were compared. The cultivations were studied in aerobic and anaerobic metabolic steady states and in addition at time points 5, 30 and 60 min after the switch-off of oxygen supply. We identified 22 proteins having a significant abundance difference on xylose compared to glucose, and 12 proteins that responded to change from aerobic to anaerobic conditions on both carbon sources. On xylose in all conditions studied, major changes were seen in the abundance of alcohol dehydrogenase 2 (Adh2p), acetaldehyde dehydrogenases 4 and 6 (Ald4p and Ald6p), and DL-glycerol 3-phosphatase (Gpp1p). Our results give indications of altered metabolic fluxes especially in the acetate and glycerol pathways in cells growing on xylose compared to glucose.

Identification of lysine-78 as an essential residue in the Saccharomyces cerevisiae xylose reductase

Yeast xylose reductases are hypothesized as hybrid enzymes as their primary sequences contain elements of both the aldo-keto reductases (AKR) and short chain dehydrogenase/reductase (SDR) enzyme families. During catalysis by members of both enzyme families, an essential Lys residue H-bonds to a Tyr residue that donates proton to the aldehyde substrate. In the Saccharomyces cerevisiae xylose reductase, Tyr49 has been identified as the proton donor. However, the primary sequence of the enzyme contains two Lys residues, Lys53 and Lys78, corresponding to the conserved motifs for SDR and AKR enzyme families, respectively, that may H-bond to Tyr49. We used site-directed mutagenesis to substitute each of these Lys residues with Met. The activity of the K53M variant was slightly decreased as compared to the wild-type, while that of the K78M variant was negligible. The results suggest that Lys78 is the essential residue that H-bonds to Tyr49 during catalysis and indicate that the active site residues of yeast xylose reductases match those of the AKR, rather than SDR, enzymes. Intrinsic enzyme fluorescence spectroscopic analysis suggests that Lys78 may also contribute to the efficient binding of NADPH to the enzyme.

Evidence that the gene YLR070c of Saccharomyces cerevisiae encodes a xylitol dehydrogenase

The open reading frame YLR070c of Saccharomyces cerevisiae has high sequence similarity to S. cerevisiae sorbitol dehydrogenase and to xylitol dehydrogenase of Pichia stipitis. Overexpression of this open reading frame in S. cerevisiae resulted in xylitol dehydrogenase activity. The enzyme is specific for NADH. The following Michaelis constants were estimated: D-xylulose, 1.1 mM; NADH, 240 microM (at pH 7.0); xylitol, 25 mM; NAD, 100 microM (at pH 9.0). Xylitol dehydrogenase activity with the same kinetic properties can also be induced by xylose in wild type S. cerevisiae cells.

Simultaneous bioconversion of cellulose and hemicellulose to ethanol

Lignocellulosic materials containing cellulose, hemicellulose, and lignin as their main constituents are the most abundant renewable organic resource present on Earth. The conversion of both cellulose and hemicellulose for production of fuel ethanol is being studied intensively with a view to develop a technically and economically viable bioprocess. The fermentation of glucose, the main constituent of cellulose hydrolyzate, to ethanol can be carried out efficiently. On the other hand, although bioconversion of xylose, the main pentose sugar obtained on hydrolysis of hemicellulose, to ethanol presents a biochemical challenge, especially if it is present along with glucose, it needs to be fermented to make the biomass-to-ethanol process economical. A lot of attention therefore has been focussed on the utilization of both glucose and xylose to ethanol. Accordingly, while describing the advancements that have taken place to get xylose converted efficiently to ethanol by xylose-fermenting organisms, the review deals mainly with the strategies that have been put forward for bioconversion of both the sugars to achieve high ethanol concentration, yield, and productivity. The approaches, which include the use of (1) xylose-fermenting yeasts alone, (2) xylose isomerase enzyme as well as yeast, (3) immobilized enzymes and cells, and (4) sequential fermentation and co-culture process are described with respect to their underlying concepts and major limitations. Genetic improvements in the cultures have been made either to enlarge the range of substrate utilization or to channel metabolic intermediates specifically toward ethanol. These contributions represent real significant advancements in the field and have also been adequately dealt with from the point of view of their impact on utilization of both cellulose and hemicellulose sugars to ethanol.

Regulation of phosphotransferases in glucose- and xylose-fermenting yeasts

This research examined the titers of hexokinase (HK), phosphofructokinase (PFK), and xylulokinase (XUK) in Saccharomyces cerevisiae and two xylose fermenting yeasts, Pachysolen tannophilus and Candida shehatae, following shifts in carbon source and aeration. Xylose-grown C. shehatae, glucose-grown P. tannophilus, and glucose-grown S. cerevisiae, had the highest specific activities of XUK, HK, and PFK, respectively. XUK was induced by xylose to moderate levels in both P. tannophilus and C. shehatae, but was present only in trace levels in S. cerevisiae. HK activities in P. tannophilus were two to three fold higher when cells were grown on glucose than when grown on xylose, but HK levels were less inducible in C. shehatae. The PFK activities in S. cerevisiae were 1.5 to 2 times higher than in the two xylose-fermenting yeasts. Transfer from glucose to xylose rapidly inactivated HK in P. tannophilus, and transfer from xylose to glucose inactivated XUK in C. shehatae. The patterns of induction and inactivation indicate that the basic regulatory mechanisms differ in the two xylose fermenting yeasts.

Purification and partial characterization of an aldo-keto reductase from Saccharomyces cerevisiae

A cytosolic aldo-keto reductase was purified from Saccharomyces cerevisiae ATCC 26602 to homogeneity by affinity chromatography, chromatofocusing, and hydroxylapatite chromatography. The relative molecular weights of the aldo-keto reductase as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and size exclusion chromatography were 36,800 and 35,000, respectively, indicating that the enzyme is monomeric. Amino acid composition and N-terminal sequence analysis revealed that the enzyme is closely related to the aldose reductases of xylose-fermenting yeasts and mammalian tissues. The enzyme was apparently immunologically unrelated to the aldose reductases of other xylose-fermenting yeasts. The aldo-keto reductase is NADPH specific and catalyzes the reduction of a variety of aldehydes. The best substrate for the enzyme is the aromatic aldehyde p-nitrobenzaldehyde (Km = 46 microM; kcat/Km = 52,100 s-1 M-1), whereas among the aldoses, DL-glyceraldehyde was the preferred substrate (Km = 1.44 mM; kcat/Km = 1,790 s-1 M-1). The enzyme failed to catalyze the reduction of menadione and p-benzoquinone, substrates for carbonyl reductase. The enzyme was inhibited only slightly by 2 mM sodium valproate and was activated by pyridoxal 5'-phosphate. The optimum pH of the enzyme is 5. These data indicate that the S. cerevisiae aldo-keto reductase is a monomeric NADPH-specific reductase with strong similarities to the aldose reductases.

Role of D-ribose as a cometabolite in D-xylose metabolism by Saccharomyces cerevisiae

The influence of D-ribose as a cosubstrate on the uptake and metabolism of the non-growth substrate D-xylose by Saccharomyces cerevisiae ATCC 26602 was investigated. Xylose was taken up by means of low- and high-affinity glucose transport systems. In cells exposed for 2 days to a mixture of xylose and ribose, only the high-affinity system could be detected. Glucose strongly inhibited the transport of xylose by both systems. Starvation or exposure to either xylose or ribose resulted in inactivation of xylose transport, which did not occur in the presence of a mixture of ribose and xylose. A constitutive non-glucose-repressible NADPH2-dependent xylose reductase with a specific activity of ca. 5 mU/mg of protein that converted xylose to xylitol was present in a glucose-grown culture. No activity converting xylitol to xylulose or vice versa was found in crude extracts. Both xylose and ribose were converted to their corresponding polyols, xylitol and ribitol, as indicated by 13C nuclear magnetic resonance spectroscopy. Furthermore, ethanol was detected, and this implied that pathways for the complete catabolism of xylose and ribose exist. However, the NADPH2 required for the conversion of xylose to xylitol is apparently not supplied by the pentose phosphate pathway since the ethanol produced from D-[1-13C]xylose was labelled only in the C-2 position. Acetic acid was produced from ribose and may assist in the conversion of xylose to xylitol by cycling NADPH2.

Isolation and characterization of acetic acid-tolerant galactose-fermenting strains of Saccharomyces cerevisiae from a spent sulfite liquor fermentation plant

From a continuous spent sulfite liquor fermentation plant, two species of yeast were isolated, Saccharomyces cerevisiae and Pichia membranaefaciens. One of the isolates of S. cerevisiae, no. 3, was heavily flocculating and produced a higher ethanol yield from spent sulfite liquor than did commercial baker's yeast. The greatest difference between isolate 3 and baker's yeast was that of galactose fermentation, even when galactose utilization was induced, i.e., when they were grown in the presence of galactose, prior to fermentation. Without acetic acid present, both baker's yeast and isolate 3 fermented glucose and galactose sequentially. Galactose fermentation with baker's yeast was strongly inhibited by acetic acid at pH values below 6. Isolate 3 fermented galactose, glucose, and mannose without catabolite repression in the presence of acetic acid, even at pH 4.5. The xylose reductase (EC 1.1.1.21) and xylitol dehydrogenase (EC 1.1.1.9) activities were determined in some of the isolates as well as in two strains of S. cerevisiae (ATCC 24860 and baker's yeast) and Pichia stipitis CBS 6054. The S. cerevisiae strains manifested xylose reductase activity that was 2 orders of magnitude less than the corresponding P. stipitis value of 890 nmol/min/mg of protein. The xylose dehydrogenase activity was 1 order of magnitude less than the corresponding activity of P. stipitis (330 nmol/min/mg of protein).

Effects of increased transaldolase activity on D-xylulose and D-glucose metabolism in Saccharomyces cerevisiae cell extracts

In vitro metabolism of D-xylulose and D-glucose in extracts obtained from D-glucose- and D-xylulose-fermenting Saccharomyces cerevisiae cells was investigated with 10- and 100-fold-increased activity of the enzyme transaldolase (EC 2.2.1.2). The rate of sugar consumption was the same in most cases, whereas the rate of ethanol formation decreased with increased levels of transaldolase. The formation of glycerol, pentitols, and acetic acid was not dependent on added transaldolase but was dependent on the sugar used as the growth substrate and on the sugar used in the in vitro metabolism experiments. The carbon balance showed that the dissimilated carbon could not be accounted for in products when transaldolase was added. The concentration of D-fructose-1,6.-diphosphate in the extracts was not influenced by added transaldolase but was higher with D-xylulose than with D-glucose. Levels of pyruvate, comparable with the two substrates, decreased with increasing levels of transaldolase. Exogenously added transaldolase decreased D-sedoheptulose-7-phosphate levels when D-xylulose was the substrate. The results are discussed in relation to the dissimilation of carbon through the upper part of glycolysis and the pentose phosphate pathway.

Isolation of xylose reductase gene of Pichia stipitis and its expression in Saccharomyces cerevisiae

A NADPH/NADH-dependent xylose reductase gene was isolated from the xylose-assimilating yeast, Pichia stipitis. DNA sequence analysis showed that the gene consists of 951 bp. The gene introduced in Saccharomyces cerevisiae was transcribed to mRNA, and a considerable amount of enzyme activity was observed constitutively, whereas transcription and translation in P stipitis were inducible. S. cerevisiae carrying the xylose reductase gene could not, however, grow on xylose medium, and could not produce ethanol from xylose. Since xylose uptake and accumulation of xylitol by S. cerevisiae were observed, the conversion of xylitol to xylulose seemed to be limited.