Involvement of oxygen and mitochondrial function in the metabolism of D-xylulose by Saccharomyces cerevisiae

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.

Enhancement of xylose uptake in 2-deoxyglucose tolerant mutant of Saccharomyces cerevisiae

Chemical mutation of Saccharomyces cerevisiae using ethyl methane sulfonate was performed to enhance its ability of xylose uptake for ethanol production from lignocellulose under microaerobic condition. Among the appeared mutants, the mutant no. 2 (M2) strain screened using inhibitory effects of 2-deoxyglucose (DOG) showed more than 4-fold high ability in xylose uptake compared with the wild type strain, under the presence of glucose. The catabolite repression by glucose was sufficiently reduced in M2 strain due to its tolerance to the high concentration of DOG (0.5%, wt./vol.). Metabolomic analyses of various sugars in the cell revealed that some of xylose was reduced to xylitol in M2 cell, providing the concentration gradient of xylose and more uptake of xylose. Xylulose-5-phosphate was significantly detected in the crude cell extract from M2 strain, indicating higher metabolic activity in pentose phosphate pathway. This was also confirmed by in vitro analyses of key enzymes involved in glucose and xylose metabolism, such as hexokinase, glucose-6-phosphate dehydrogenase and xylose reductase. Glucose uptake was moderately suppressed in the presence of trehalose-6-phosphate inhibiting the activation of hexokinase, resulting in more uptake of xylose through hexose transport system. To our knowledge, this study is the first report verifying that the mutation technique successfully enhances the xylose uptake by S. cerevisiae, particularly under the presence of glucose.

Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response

Native strains of Saccharomyces cerevisiae do not assimilate xylose. S. cerevisiae engineered for d-xylose utilization through the heterologous expression of genes for aldose reductase (XYL1), xylitol dehydrogenase (XYL2), and d-xylulokinase (XYL3 or XKS1) produce only limited amounts of ethanol in xylose medium. In recombinant S. cerevisiae expressing XYL1, XYL2, and XYL3, mRNA transcript levels for glycolytic, fermentative, and pentose phosphate enzymes did not change significantly on glucose or xylose under aeration or oxygen limitation. However, expression of genes encoding the tricarboxylic acid cycle, respiration enzymes (HXK1, ADH2, COX13, NDI1, and NDE1), and regulatory proteins (HAP4 and MTH1) increased significantly when cells were cultivated on xylose, and the genes for respiration were even more elevated under oxygen limitation. These results suggest that recombinant S. cerevisiae does not recognize xylose as a fermentable carbon source and that respiratory proteins are induced in response to cytosolic redox imbalance; however, lower sugar uptake and growth rates on xylose might also induce transcripts for respiration. A petite respiration-deficient mutant (rho degrees ) of the engineered strain produced more ethanol and accumulated less xylitol from xylose. It formed characteristic colonies on glucose, but it did not grow on xylose. These results are consistent with the higher respiratory activity of recombinant S. cerevisiae when growing on xylose and with its inability to grow on xylose under anaerobic conditions.

Ethanol and thermotolerance in the bioconversion of xylose by yeasts

The mechanisms underlying ethanol and heat tolerance are complex. Many different genes are involved, and the exact basis is not fully understood. The integrity of cytoplasmic and mitochondrial membranes is critical to maintain proton gradients for metabolic energy and nutrient uptake. Heat and ethanol stress adversely affect membrane integrity. These factors are particularly detrimental to xylose-fermenting yeasts because they require oxygen for biosynthesis of essential cell membrane and nucleic acid constituents, and they depend on respiration for the generation of ATP. Physiological responses to ethanol and heat shock have been studied most extensively in S. cerevisiae. However, comparative biochemical studies with other organisms suggest that similar mechanisms will be important in xylose-fermenting yeasts. The composition of a cell's membrane lipids shifts with temperature, ethanol concentration, and stage of cultivation. Levels of unsaturated fatty acids and ergosterol increase in response to temperature and ethanol stress. Inositol is involved in phospholipid biosynthesis, and it can increase ethanol tolerance when provided as a supplement. Membrane integrity determines the cell's ability to maintain proton gradients for nutrient uptake. Plasma membrane ATPase generates the proton gradient, and the biochemical characteristics of this enzyme contribute to ethanol tolerance. Organisms with higher ethanol tolerance have ATPase activities with low pH optima and high affinity for ATP. Likewise, organisms with ATPase activities that resist ethanol inhibition also function better at high ethanol concentrations. ATPase consumes a significant fraction of the total cellular ATP, and under stress conditions when membrane gradients are compromised the activity of ATPase is regulated. In xylose-fermenting yeasts, the carbon source used for growth affects both ATPase activity and ethanol tolerance. Cells can adapt to heat and ethanol stress by synthesizing trehalose and heat-shock proteins, which stabilize and repair denatured proteins. The capacity of cells to produce trehalose and induce HSPs correlate with their thermotolerance. Both heat and ethanol increase the frequency of petite mutations and kill cells. This might be attributable to membrane effects, but it could also arise from oxidative damage. Cytoplasmic and mitochondrial superoxide dismutases can destroy oxidative radicals and thereby maintain cell viability. Improved knowledge of the mechanisms underlying ethanol and thermotolerance in S. cerevisiae should enable the genetic engineering of these traits in xylose-fermenting yeasts.

Genetic engineering for improved xylose fermentation by yeasts

Xylose utilization is essential for the efficient conversion of lignocellulosic materials to fuels and chemicals. A few yeasts are known to ferment xylose directly to ethanol. However, the rates and yields need to be improved for commercialization. Xylose utilization is repressed by glucose which is usually present in lignocellulosic hydrolysates, so glucose regulation should be altered in order to maximize xylose conversion. Xylose utilization also requires low amounts of oxygen for optimal production. Respiration can reduce ethanol yields, so the role of oxygen must be better understood and respiration must be reduced in order to improve ethanol production. This paper reviews the central pathways for glucose and xylose metabolism, the principal respiratory pathways, the factors determining partitioning of pyruvate between respiration and fermentation, the known genetic mechanisms for glucose and oxygen regulation, and progress to date in improving xylose fermentations by yeasts.

Ethanolic fermentation of pentoses in lignocellulose hydrolysates

In the fermentation of lignocellulose hydrolysates to ethanol, two major problems are encountered: the fermentation of the pentose sugar xylose, and the presence of microbial inhibitors. Xylose can be directly fermented with yeasts, such as Pachysolen tannophilus, Candida shehatae, and Pichia stipis, or by isomerization of xylose to xylulose with the enzyme glucose (xylose) isomerase (XI; EC 5.3.1.5), and subsequent fermentation with bakers' yeast, Saccharomyces cerevisiae. The direct fermentation requires low, carefully controlled oxygenation, as well as the removal of inhibitors. Also, the xylose-fermenting yeasts have a limited ethanol tolerance. The combined isomerization and fermentation with XI and S. cerevisiae gives yields and productivities comparable to those obtained in hexose fermentations without oxygenation and removal of inhibitors. However, the enzyme is not very stable in a lignocellulose hydrolysate, and S. cerevisiae has a poorly developed pentose phosphate shunt. Different strategies involving strain adaptation, and protein and genetic engineering adopted to overcome these different obstacles, are discussed.

Genetic and Biochemical Characterization of Mutations Affecting the Ability of the Yeast Pachysolen tannophilus To Metabolize d -Xylose

Induced mutants, selected for their defective growth on d -xylose while retaining the ability to grow normally on d -glucose, were studied in Pachysolen tannophilus , a yeast capable of converting d -xylose to ethanol. Fourteen of the mutations were found to occur at nine distinct loci, and data indicated that many more loci remain to be detected. Most of the mutations were pleiotropic in character, and the expression of some of them was much affected by nutritional conditions and by genetic background. Mutations at several loci resulted in poor growth on at least one compound that was either an intermediate of the tricarboxylic acid cycle, succinate or α-ketoglutarate, or on compounds metabolizable via this cycle, ethanol or glycerol. An initial biochemical characterization of the mutants was undertaken. Analysis for xylose reductase, xylitol dehydrogenase, and xylulose kinase activity showed that one or more of these activities was affected in 12 of 13 mutants. However, drastic reduction in activity of a single enzyme was confined to that of xylitol dehydrogenase by mutations at three different loci and to that of d -xylose reductase by mutation at another locus. Growth of these latter four mutants was normal on all carbon sources tested that were not five-carbon sugars.

Conversion of pentoses to ethanol by yeasts and fungi

Fermentation of D-xylose is of interest in enhancing the yield of ethanol obtainable from lignocellulosic hydrolysates. Such hydrolysates can contain both pentoses and hexoses, and while technology to convert hexoses to ethanol is well established, the fermentation of pentoses had been problematical. To overcome the difficulty, yeasts and fungi have been sought and identified in recent years that can convert D-xylose into ethanol. However, operation of their cultures in the presence of the pentose to obtain rapid and efficient ethanol production is somewhat more complex than in the archetype alcoholic fermentation, Saccharomyces cerevisiae on D-glucose. The complexity stems, in part, from the association of ethanol accumulation in cultures where D-xylose is the sole carbon source with conditions that limit growth, by oxygen in particular, although limitation by other nutrients might also be implicated. Aspects of screening for appropriate organisms and of the parameters that play a role in determining culture variables, especially those associated with ethanol productivity, are reviewed. Performance with D-xylose as sole carbon source, in sugar mixtures, and in lignocellulosic hydrolysates is discussed. A model that involves biochemical considerations of D-xylose metabolism is presented that rationalizes the effects of oxygen on cultures where D-xylose is the sole carbon source, notably effects of the specific rate of oxygen use on the rate and extent of ethanol accumulation. Alternate methods to direct fermentation of D-xylose have been developed that depend on its prior isomerization to D-xylose, followed by fermentation of the pentulose by certain yeasts and fungi. Factors involved in the biochemistry, use, and performance of these methods, which with some organisms involves sensitivity to oxygen, are reviewed.

The requirement of oxygen for incorporation of carbon from D-xylose and D-glucose by Pachysolen tannophilus

Oxygen was required for growth of Pachysolen tannophilus on D-xylose, as well as on D-glucose. The reason was not identical to that of other yeasts whose anaerobic growth is stimulated by supplementation of the medium with lipids or organic hydrogen acceptors, as such supplements were ineffective with P. tannophilus. The requirement of oxygen was found to be due to its involvement in the incorporation of carbon from D-xylose, and to a large extent D-glucose as well, into trichloracetic acid-insoluble material. The role it played was associated with the channeling of catabolic intermediates into biosynthetic routes, since ethanol was formed anaerobically, but aeration was required for induction of several enzymes associated with the catabolism of D-xylose. The requirement suggested that normally functioning mitochondria were necessary for incorporation and growth, but not ethanol formation. This view was supported by the inability to obtain stable petite mutants, and by the effects of inhibitors of mitochondrial function, which caused effects on incorporation and growth under aerobic conditions similar to those of anaerobiosis.