Metabolism of glucose and xylose as single and mixed feed in Debaryomyces nepalensis NCYC 3413: production of industrially important metabolites

Two-stage seeding strategy and its multi-response optimization for enhanced xylitol production by Debaryomyces nepalensis NCYC 3413

The aim was to develop a two-stage seeding strategy and its optimization to enhance the conversion of xylose to xylitol by Debaryomyces nepalensis NCYC 3413. To develop efficient seed, multi-response optimization was employed to obtain optimal inoculum age and volume where xylitol concentration, yield and productivity were maximized. The optimal conditions of inoculation age and volume were 5.86 h and 11.66 % (v/v), respectively. Maximized results were observed at 48 h as compared to 72 h pre-optimization. Xylitol concentration slightly improved from 56 g/L to 59.71 g/L (p-value = 0.043). Yield improved from 0.56 g/g to 0.66 g/g (p-value = 0.044), whereas, productivity showed a significant increase from 0.76 g/L.h to 1.24 g/L.h (p-value = 0.008). Xylose Reductase activity improved by 1.67-folds and Xylitol Dehydrogenase activity decreased by 1.3 folds. This work suggests a simple inoculum strategy that could expedite the enzyme system required for xylitol production, enabling a 1.7-fold increase in productivity.

Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates

Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log₂ fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.

Efficient production of (S)-1-phenyl-1,2-ethanediol using xylan as co-substrate by a coupled multi-enzyme Escherichia coli system

Background

(S)-1-phenyl-1,2-ethanediol is an important chiral intermediate in the synthesis of liquid crystals and chiral biphosphines. (S)-carbonyl reductase II from Candida parapsilosis catalyzes the conversion of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol with NADPH as a cofactor. Glucose dehydrogenase with a Ala258Phe mutation is able to catalyze the oxidation of xylose with concomitant reduction of NADP⁺ to NADPH, while endo-β-1,4-xylanase 2 catalyzes the conversion of xylan to xylose. In the present work, the Ala258Phe glucose dehydrogenase mutant and endo-β-1,4-xylanase 2 were introduced into the (S)-carbonyl reductase II-mediated chiral pathway to strengthen cofactor regeneration by using xylan as a naturally abundant co-substrate.

Results

We constructed several coupled multi-enzyme systems by introducing (S)-carbonyl reductase II, the A258F glucose dehydrogenase mutant and endo-β-1,4-xylanase 2 into Escherichia coli. Different strains were produced by altering the location of the encoding genes on the plasmid. Only recombinant E. coli/pET-G-S-2 expressed all three enzymes, and this strain produced (S)-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone as a substrate and xylan as a co-substrate. The optical purity was 100% and the yield was 98.3% (6 g/L 2-HAP) under optimal conditions of 35 °C, pH 6.5 and a 2:1 substrate-co-substrate ratio. The introduction of A258F glucose dehydrogenase and endo-β-1,4-xylanase 2 into the (S)-carbonyl reductase II-mediated chiral pathway caused a 54.6% increase in yield, and simultaneously reduced the reaction time from 48 to 28 h.

Conclusions

This study demonstrates efficient chiral synthesis using a pentose as a co-substrate to enhance cofactor regeneration. This provides a new approach for enantiomeric catalysis through the inclusion of naturally abundant materials.

Screening of new yeast Pichia manchurica for arabitol production

Arabitol has several applications in food and pharmaceutical industries as a natural sweetener, dental caries inhibitor, and texturing agent. Newly isolated yeast strains from seawater, sugarcane plantation soil samples, and Zygosaccharomyces rouxii 2635 from MTCC were tested for arabitol production. The yield of arabitol was found to be higher in seawater isolate (24.6 g L^-1 ) compared to two soil isolates (22.5 g L^-1 ) and Z. rouxii (19.4 g L^-1 ). Based on ITS 26S rDNA sequence analysis, the seawater isolate was identified as Pichia manchurica. In the present study, the effect of different substrates, trace elements, nitrogen sources, pH, and temperature on arabitol production was examined. Three different carbon sources viz. glucose, arabinose, and galactose were studied. Glucose was determined to be the best substrate for arabitol production (27.6 g L^-1 ) followed by arabinose (13.7 g L^-1 ) and galactose (7.7 g L^-1 ). Maximum production of arabitol was observed at pH 6.0 (34.7 g L^-1 ). In addition, arabitol production was high (35.7 g L^-1 ) at temperature of 30 °C. Among the different concentrations of ammonium sulfate tested (3, 4.5, 6, 7.5, and 9 g L^-1 ) concentration of 6 g L^-1 resulted in higher arabitol Individual metal ions had no effect on arabitol production by this strain as compared to control. Results obtained in this study identify ways for improved arabitol production with natural isolates using microbial processes.

Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis

Aldose reductases (ARs) belonging to the aldo-keto reductase (AKR) superfamily catalyze the conversion of carbonyl substrates into their respective alcohols. Here we report the crystal structures of the yeast Debaryomyces nepalensis xylose reductase (DnXR, AKR2B10) in the apo form and as a ternary complex with a novel NADP-DTT adduct. Xylose reductase, a key enzyme in the conversion of xylose to xylitol, has several industrial applications. The enzyme displayed the highest catalytic efficiency for l-threose (138 ± 7 mm^-1 ·s^-1 ) followed by d-erythrose (30 ± 3 mm^-1 ·s^-1 ). The crystal structure of the complex reveals a covalent linkage between the C4N atom of the nicotinamide ring of the cosubstrate and the S1 sulfur atom of DTT and provides the first structural evidence for a protein mediated NADP-low-molecular-mass thiol adduct. We hypothesize that the formation of the adduct is facilitated by an in-crystallo Michael addition of the DTT thiolate to the specific conformation of bound NADPH in the active site of DnXR. The interactions between DTT, a four-carbon sugar alcohol analog, and the enzyme are representative of a near-cognate product ternary complex and provide significant insights into the structural basis of aldose binding and specificity and the catalytic mechanism of ARs. DATABASE: Structural data are available in the PDB under the accession numbers 5ZCI and 5ZCM.

Gummadi S. A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization

Aldose reductase (AR) catalyzes the conversion of aldoses to polyols, the natural sugar substitutes. Here we provide gene sequence and characteristics of the first-ever halotolerant AR which could be exploited as a potential biocatalyst.

Multi response optimization for enhanced xylitol production by Debaryomyces nepalensis in bioreactor

In this study, the optimization of different process variables—pH (4–6), aeration rate (200–550 rpm) and agitation rate (0.6–1.8 vvm) were investigated using rotating simplex method and uniform design method to enhance xylitol production from xylose by D. nepalensis in a batch stirred tank bioreactor. Maximum xylitol productivity (0.576 g L⁻¹ h⁻¹) was obtained at pH 4.0, agitation 300 rpm and aeration 1.5 vvm by rotating simplex method. Individual optimum values of pH, agitation and aeration are 4.2, 370 rpm and 1.2 vvm, respectively, for productivity, 4.3, 350 rpm and 1.0 vvm, respectively for xylitol concentration and 4.4, 360 rpm and 0.8 vvm, respectively for yield. Using generalized distance approach, the simultaneous optimal values were found to be—pH 4.3, 370 rpm and 0.9 vvm. After multi-response analysis, batch fermentation at optimal operating conditions resulted in enhanced productivity (0.76 g L⁻¹ h⁻¹), xylitol concentration (59.4 g L⁻¹) and yield (0.58 g g⁻¹) with an increase of 76.74 % of xylitol productivity.

Modeling and simulation of xylitol production in bioreactor by Debaryomyces nepalensis NCYC 3413 using unstructured and artificial neural network models

This study examines the use of unstructured kinetic model and artificial neural networks as predictive tools for xylitol production by Debaryomyces nepalensis NCYC 3413 in bioreactor. An unstructured kinetic model was proposed in order to assess the influence of pH (4, 5 and 6), temperature (25°C, 30°C and 35°C) and volumetric oxygen transfer coefficient kLa (0.14h(-1), 0.28h(-1) and 0.56h(-1)) on growth and xylitol production. A feed-forward back-propagation artificial neural network (ANN) has been developed to investigate the effect of process condition on xylitol production. ANN configuration of 6-10-3 layers was selected and trained with 339 experimental data points from bioreactor studies. Results showed that simulation and prediction accuracy of ANN was apparently higher when compared to unstructured mechanistic model under varying operational conditions. ANN was found to be an efficient data-driven tool to predict the optimal harvest time in xylitol production.

Sugarcane bagasse as support for immobilization of Bacillus pumilus HZ-2 and its use in bioremediation of mesotrione-contaminated soils

The degrading microorganisms isolated from environment usually fail to degrade pollutants when used for bioremediation of contaminated soils; thus, additional treatments are needed to enhance biodegradation. In the present study, the potential of sugarcane bagasse as bacteria-immobilizing support was investigated in mesotrione biodegradation. A novel isolate Bacillus pumilus HZ-2 was applied in bacterial immobilization, which was capable of degrading over 95 % of mesotrione at initial concentrations ranging from 25 to 200 mg L(-1) within 4 days in flask-shaking tests. Scanning electron microscope (SEM) images showed that the bacterial cells were strongly absorbed and fully dispersed on bagasse surface after immobilization. Specially, 86.5 and 82.9 % of mesotrione was eliminated by bacteria immobilized on bagasse of 100 and 60 mesh, respectively, which indicated that this immobilization was able to maintain a high degrading activity of the bacteria. Analysis of the degradation products determined 2-amino-4-methylsulfonylbenzoic acid (AMBA) and 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) as the main metabolites in the biodegradation pathway of mesotrione. In the sterile soil, approximately 90 % of mesotrione was degraded after supplementing 5.0 % of molasses in bacteria-bagasse composite, which greatly enhanced microbial adaptability and growth in the soil environment. In the field tests, over 75 % of mesotrione in soil was degraded within 14 days. The immobilized preparation demonstrated that mesotrione could be degraded at a wide range of pH values (5.0-8.0) and temperatures (25-35 °C), especially at low concentrations of mesotrione (5 to 20 mg kg(-1)). These results showed that sugarcane bagasse might be a good candidate as bacteria-immobilizing support to enhance mesotrione degradation by Bacillus p. HZ-2 in contaminated soils.

Kinetics and Mechanism of Fenpropathrin Biodegradation by a Newly Isolated Pseudomonas aeruginosa sp. Strain JQ-41

A soil bacterium designated strain JQ-41, capable of growth on fenpropathrin as the sole carbon source and energy source, was isolated from a long-term pyrethroid insecticide-treated orchard. Based on the morphology, physio-biochemical characteristics, and 16S rDNA gene analysis, as well as the G+C content of the genomic DNA, the strain JQ-41 was identified as Pseudomonas aeruginosa. Up to 92.3% of 50 mg l(-1) fenpropathrin was degraded by P. aeruginosa strain at 30°C and pH 7 within 7 days. The kinetic parameters q max, K s, and K i were established to be 1.14 day(-1), 38.41 mg l(-1), and 137.67 mg l(-1), respectively, and the critical inhibitor concentration was determined to be 72.72 mg l(-1). Cell surface hydrophobicity of P. aeruginosa strain was enhanced during growth on fenpropathrin. Three metabolites from fenpropathrin degradation were identified by gas chromatography mass spectrometry, and then a possible degradation pathway was proposed. In addition, this isolate was also able to degrade a wide range of synthetic pyrethroid insecticides including cypermethrin, deltamethrin, bifenthrin, and cyhalothrin with the degradation process following the first-order kinetic model. Taken together, our results provide insights into the kinetics and mechanism of fenpropathrin degradation by P. aeruginosa strain and also highlight its promising potential in bioremediation of pyrethroid-contaminated environment.

Production of arabitol by yeasts: current status and future prospects

Arabitol belongs to the pentitol family and is used in the food industry as a sweetener and in the production of human therapeutics as an anticariogenic agent and an adipose tissue reducer. It can also be utilized as a substrate for chemical products such as arabinoic and xylonic acids, propylene, ethylene glycol, xylitol and others. It is included on the list of 12 building block C3-C6 compounds, designated for further biotechnological research. This polyol can be produced by yeasts in the processes of bioconversion or biotransformation of waste materials from agriculture, the forest industry (l-arabinose, glucose) and the biodiesel industry (glycerol). The present review discusses research on native yeasts from the genera Candida, Pichia, Debaryomyces and Zygosaccharomyces as well as genetically modified strains of Saccharomyces cerevisiae which are able to utilize biomass hydrolysates to effectively produce L- or D-arabitol. The metabolic pathways of these yeasts leading from sugars and glycerol to arabitol are presented. Although the number of reports concerning microbial production of arabitol is rather limited, the research on this topic has been growing for the last several years, with researchers looking for new micro-organisms, substrates and technologies.

Study of the potential of the air lift bioreactor for xylitol production in fed-batch cultures by Debaryomyces hansenii immobilized in alginate beads

Cell immobilization has shown to be especially adequate for xylitol production. This work studies the suitability of the air lift bioreactor for xylitol production by Debaryomyces hansenii immobilized in Ca-alginate operating in fed-batch cultures to avoid substrate inhibition. The results showed that the air lift bioreactor is an adequate system since the minimum air flow required for fluidization was even lower than that leading to the microaerobic conditions that trigger xylitol accumulation by this yeast, also maintaining the integrity of the alginate beads and the viability of the immobilized cells until 3 months of reuses. Maximum productivities and yields of 0.43 g/l/h and 0.71 g/g were achieved with a xylose concentration of 60 g/l after each feeding. The xylose feeding rate, the air flow, and the biomass concentration at the beginning of the fed-batch operation have shown to be critical parameters for achieving high productivities and yields. Although a maximum xylitol production of 139 g/l was obtained, product inhibition was evidenced in batch experiments, which allowed estimating at 200 and 275 g/l the IC50 for xylitol productivity and yield, respectively. The remarkable production of glycerol in the absence of glucose was noticeable, which could not only be attributed to the osmoregulatory function of this polyol in conditions of high osmotic pressure caused by high xylitol concentrations but also to the role of the glycerol synthesis pathway in the regeneration of NAD(+) in conditions of suboptimal microaeration caused by insufficient aeration or high oxygen demand when high biomass concentrations were achieved.

Production of ethanol and arabitol by Debaryomyces nepalensis: influence of process parameters

Debaryomyces nepalensis, osmotolerant yeast isolated from rotten apple, is known to utilize both hexoses and pentoses and produce industrially important metabolites like ethanol, xylitol and arabitol. In the present study, the effect of different growth substrates, trace elements, nitrogen concentration and initial pH on growth and formation of ethanol and arabitol were examined. Optimum conditions for maximizing the product yields were established: glucose as carbon source, an initial pH of 6.0, 6 g/L of ammonium sulphate and addition of micronutrients. Under these best suited conditions, a concentration of 11g/L of arabitol and 19 g/L of ethanol was obtained in shake flask fermentations. The fermentation was scaled up to 2.5 L bioreactor and the influence of aeration, agitation and initial substrate concentration was also determined. Under optimal conditions (150 g/L glucose, 400 rpm and 0.5 vvm) ethanol concentration reached 52 g/L, which corresponds to a yield of 0.34 g/g and volumetric productivity of 0.28 g/L/h, whereas arabitol production reached a maximum of 14 g/L with a yield and volumetric productivity of 0.1 g/g and 0.07 g/L/h respectively.

Multilocus phylogenetic study of the Scheffersomyces yeast clade and characterization of the N-terminal region of xylose reductase gene

Many of the known xylose-fermenting (X-F) yeasts are placed in the Scheffersomyces clade, a group of ascomycete yeasts that have been isolated from plant tissues and in association with lignicolous insects. We formally recognize fourteen species in this clade based on a maximum likelihood (ML) phylogenetic analysis using a multilocus dataset. This clade is divided into three subclades, each of which exhibits the biochemical ability to ferment cellobiose or xylose. New combinations are made for seven species of Candida in the clade, and three X-F taxa associated with rotted hardwood are described: Scheffersomyces illinoinensis (type strain NRRL Y-48827(T) = CBS 12624), Scheffersomyces quercinus (type strain NRRL Y-48825(T) = CBS 12625), and Scheffersomyces virginianus (type strain NRRL Y-48822(T) = CBS 12626). The new X-F species are distinctive based on their position in the multilocus phylogenetic analysis and biochemical and morphological characters. The molecular characterization of xylose reductase (XR) indicates that the regions surrounding the conserved domain contain mutations that may enhance the performance of the enzyme in X-F yeasts. The phylogenetic reconstruction using XYL1 or RPB1 was identical to the multilocus analysis, and these loci have potential for rapid identification of cryptic species in this clade.

Purification and biochemical characterization of a moderately halotolerant NADPH dependent xylose reductase from Debaryomyces nepalensis NCYC 3413

A Xylose reductase (XR) from the halotolerant yeast, Debaryomyces nepalensis NCYC 3413 was purified to apparent homogeneity. The enzyme has a molecular mass of 74 kDa with monomeric subunit of 36.4 kDa (MALDI-TOF/MS) and pI of 6.0. The enzyme exhibited its maximum activity at pH 7.0 and 45 °C (21.2U/mg). In situ gel digestion and peptide mass fingerprinting analysis showed 12-22% sequence homology with XR from other yeasts. Inhibition of the enzyme by DEPC (diethylpyrocarbonate) confirmed the presence of histidine residue in its active site. The enzyme exhibited high preference for pentoses over hexoses with greater catalytic efficiency for arabinose than xylose. The enzyme also showed absolute specificity with NADPH over NADH. The enzyme retained 90% activity with 100 mM of NaCl or KCl and 40% activity with 1 M KCl which suggest that the enzyme is moderately halotolerant and can be utilized for commercial production of xylitol under conditions where salts are present.