Cloning and expression of a xylitol-4-dehydrogenase gene from Pantoea ananatis

Cloning, expression, and characterization of an arabitol dehydrogenase and coupled with NADH oxidase for effective production of L-xylulose

A novel arabitol dehydrogenase (ArDH) gene was cloned from a bacterium named Aspergillus nidulans and expressed heterologously in Escherichia coli. The purified ArDH exhibited the maximal activity in pH 9.5 Tris-HCl buffer at 40 °C, showed K_m and V_max of 1.2 mg/mL and 9.1 U/mg, respectively. The ArDH was used to produce the L-xylulose and coupled with the NADH oxidase (Nox) for the regeneration of NAD⁺. In further optimization, a high conversion of 84.6% in 8 hours was achieved under the optimal conditions: 20 mM of xylitol, 100 µM NAD⁺ in pH 9.0 Tris-HCl buffer at 30 °C. The results indicated the coupling system with cofactor regeneration provides a promising approach for L-xylulose production from xylitol.

Construction of recombinant Escherichia coli expressing xylitol-4-dehydrogenase and optimization for enhanced L-xylulose biotransformation from xylitol

L-Xylulose is a rare ketopentose which inhibits α-glucosidase and is an indicator of hepatitis or liver cirrhosis. This pentose is also a precursor of other rare sugars such as L-xylose, L-ribose or L-lyxose. Recombinant E. coli expressing xylitol-4-dehydrogenase gene of Pantoea ananatis was constructed. A cost-effective culture media were used for L-xylulose production using the recombinant E. coli strain constructed. Response surface methodology was used to optimize these media components for L-xylulose production. A high conversion rate of 96.5% was achieved under an optimized pH and temperature using 20 g/L xylitol, which is the highest among the reports. The recombinant E. coli cells expressing the xdh gene were immobilized in calcium alginate to improve recycling of cells. Effective immobilization was achieved with 2% (w/v) sodium alginate and 3% (w/v) calcium chloride. The immobilized E. coli cells retained good stability and enzyme activity for 9 batches with conversion between 53 and 92% which would be beneficial for economical production of L-xylulose.

Enhancement of NAD(H) pool for formation of oxidized biochemicals in Escherichia coli

The NAD⁺/NADH ratio and the total NAD(H) play important roles for whole-cell biochemical redox transformations. After the carbon source is exhausted, the degradation of NAD(H) could contribute to a decline in the rate of a desired conversion. In this study, methods to slow the native rate of NAD(H) degradation were examined using whole-cell Escherichia coli with two model oxidative NAD⁺-dependent biotransformations. A high phosphate concentration (50 mM) was observed to slow NAD(H) degradation. We also constructed E. coli strains with deletions in genes coding several enzymes involved in NAD⁺ degradation. In shake-flask experiments, the total NAD(H) concentration positively correlated with conversion of xylitol to L-xylulose by xylitol 4-dehydrogenase, and the greatest conversion (80%) was observed using MG1655 nadR nudC mazG/pZE12-xdh/pCS27-nox. Controlled 1-L batch processes comparing E. coli nadR nudC mazG with a wild-type background strain demonstrated a 30% increase in final L-xylulose concentration (5.6 vs. 7.9 g/L) and a 25% increase in conversion (0.53 vs. 0.66 g/g). MG1655 nadR nudC mazG was also examined for the conversion of galactitol to L-tagatose by galactitol 2-dehydrogenase. A batch process using 15 g/L glycerol and 10 g/L galactitol generated over 9.4 g/L L-tagatose, corresponding to 90% conversion and a yield of 0.95 g L-tagatose/g galactitol consumed. The results demonstrate the value of minimizing NAD(H) degradation as a means to improve NAD⁺-dependent biotransformations.

Coupling xylitol dehydrogenase with NADH oxidase improves l-xylulose production in Escherichia coli culture

Escherichia coli expressing NAD-dependent xylitol-4-dehydrogenase (XDH) from Pantoea ananatis and growing on glucose or glycerol converts xylitol to the rare sugar l-xylulose. Although blocking potential l-xylulose consumption (l-xylulosekinase, lyxK) or co-expression of the glycerol facilitator (glpF) did not significantly affect l-xylulose formation, co-expressing XDH with water-forming NADH oxidase (NOX) from Streptococcus pneumoniae increased l-xylulose formation in shake flasks when glycerol was the carbon source. Controlled batch processes at the 1L scale demonstrated that the final equilibrium l-xylulose/xylitol ratio was correlated to the intracellular NAD⁺/NADH ratio, with 69% conversion of xylitol to l-xylulose and a yield of 0.88g l-xylulose/g xylitol consumed attained for MG1655/pZE12-xdh/pCS27-nox growing on glycerol. NADH oxidase was less effective at improving l-xylulose formation in the bioreactor than in shake flasks, likely as a result of an intrinsic maximum NAD⁺/NADH and l-xylulose/xylitol equilibrium ratio being attained. Intermittently feeding carbon source was ineffective at increasing the final l-xylulose concentration because introduction of carbon source was accompanied by a reduction in NAD⁺/NADH ratio. A batch process using 12g/L glycerol and 22g/L xylitol generated over 14g/L l-xylulose after 80h, corresponding to 65% conversion and a yield of 0.89g l-xylulose/g xylitol consumed.

Immobilization of Multi-biocatalysts in Alginate Beads for Cofactor Regeneration and Improved Reusability

We have recently developed a simple, reusable and coupled whole-cell biocatalytic system with the capability of cofactor regeneration and biocatalyst immobilization for improved production yield and sustained synthesis. Described herewith is the experimental procedure for the development of such a system consisting of two E. coli strains that express functionally complementary enzymes. Together, these two enzymes can function co-operatively to mediate the regeneration of expensive cofactors for improving the product yield of the bioreaction. In addition, the method of synthesizing an immobilized form of the coupled biocatalytic system by encapsulation of whole cells in calcium alginate beads is reported. As an example, we present the improved biosynthesis of L-xylulose from L-arabinitol by coupling E. coli cells expressing the enzymes L-arabinitol dehydrogenase or NADH oxidase. Under optimal conditions and using an initial concentration of 150 mM L-arabinitol, the maximal L-xylulose yield reached 96%, which is higher than those reported in the literature. The immobilized form of the coupled whole-cell biocatalysts demonstrated good operational stability, maintaining 65% of the yield obtained in the first cycle after 7 cycles of successive re-use, while the free cell system almost completely lost the catalytic activity. Therefore, the methods reported here provides two strategies that could help improve the industrial production of L-xylulose, as well as other value-added compounds requiring the use of cofactors in general.

Rare sugar production by coupling of NADH oxidase and l-arabinitol dehydrogenase

An efficient biocatalytic cell-free system containing l-arabinitol dehydrogenase (LAD) for l-arabinitol oxidation and NADH oxidase (Nox) for cofactor regeneration was successfully constructed and used for l-rare sugar production.

Role of surface residue 184 in the catalytic activity of NADH oxidase from Streptococcus pyogenes

Nicotinamide adenine dinucleotide (NADH) oxidase from Streptococcus pyogenes (SpNox) is a flavoprotein harboring one molecule of noncovalently bound flavin adenine dinucleotide. It catalyzes the oxidation of NADH by reducing molecular O2 to H2O directly through a four-electron reduction. In this study, we selected the lysine residues on the surface of SpNox and mutated them into arginine residues to study the effect on the enzyme activity. A single-point mutation (K184R) at the surface of SpNox enhanced NADH oxidase activity by approximately 50 % and improved thermostability with 46.6 % longer half life at 30 °C. Further insights into the function of residue K184 were obtained by substituting it with other nonpolar, polar, positively charged, and negatively charged residues. To elucidate the role of this residue, computer-assisted molecular modeling and substrate docking were performed. The results demonstrate that even a single mutation at the surface of the enzyme induces changes in the interaction at the active site and affects the activity and stability. Additionally, the data also suggest that the K184R mutant can be used as an effective biocatalyst for NAD(+) regeneration in L-rare sugar production.

Identification of a xylitol dehydrogenase gene from Kluyveromyces marxianus NBRC1777

Xylitol dehydrogenase (XDH) (EC 1.1.1.9) is one of the key enzymes in the xylose fermentation pathway in yeast and fungi. A xylitol dehydrogenase gene (XYL2) encoding a XDH was cloned from Kluyveromyces marxianus NBRC 1777, and the in vivo function was validated by disruption and complementation analysis. The highest activity of KmXDH could be observed at pH 9.5 during 55°C. The values of k(cat)/K(m) indicate that KmXDH prefers NAD(+) to NADP(+) (k(cat)/K(m NAD)(+) 3681/min mM and k(cat)/K(m NADP)(+) 1361/min mM). The different coenzyme preference between KmXR and KmXDH caused an accumulation of NADH in the xylose utilization pathway. The redox imbalance may be one of the reasons to cause the poor xylose fermentation under oxygen-limited conditions in K. marxianus NBRC1777.

Molecular cloning of gluconobacter oxydans DSM 2003 xylitol dehydrogenase gene

Due to the widespread applications of xylitol dehydrogenase, an enzyme used for the production of xylitol, the present study was designed for the cloning of xylitol dehydrogenase gene from Glcunobacter oxydans DSM 2003. After extraction of genomic DNA from this bacterium, xylitol dehydrogenase gene was replicated using polymerase chain reaction (PCR). The amplified product was entered into pTZ57R cloning vector by T/A cloning method and transformation was performed by heat shocking of the E. coli XL1-blue competent cells. Following plasmid preparation, the cloned gene was digested out and ligated into the expression vector pET-22b(+). Electrophoresis of PCR product showed a 789 bp band. Recombinant plasmid (rpTZ57R) was then constructed. This plasmid was double digested with XhoI and EcoRI resulting in 800 bp and 2900 bp bands. The obtained insert was ligated into pET-22b(+) vector and its orientation was confirmed with XhoI and BamHI restriction enzymes. In conclusion, in the present study the recombinant expression vector containing xylitol dehydrogenase gene has been constructed and can be used for the production of this enzyme in high quantities.

The 'true' L-xylulose reductase of filamentous fungi identified in Aspergillus niger

L-Xylulose reductase is part of the eukaryotic pathway for l-arabinose catabolism. A previously identified L-xylulose reductase in Hypocrea jecorina turned out to be not the 'true' one since it was not upregulated during growth on L-arabinose and the deletion strain showed no reduced L-xylulose reductase activity but instead lost the D-mannitol dehydrogenase activity. In this communication we identified the 'TRUE'L-xylulose reductase in Aspergillus niger. The gene, lxrA (JGI177736), is upregulated on L-arabinose and the deletion results in a strain lacking the NADPH-specific L-xylulose reductase activity and having reduced growth on l-arabinose. The purified enzyme had a K(m) for L-xylulose of 25 mM and a nu(max) of 650 U/mg.

Cloning and characterization of a thermostable xylitol dehydrogenase from Rhizobium etli CFN42

An NAD(+)-dependent xylitol dehydrogenase from Rhizobium etli CFN42 (ReXDH) was cloned and overexpressed in Escherichia coli. The DNA sequence analysis revealed an open reading frame of 1,044 bp, capable of encoding a polypeptide of 347 amino acid residues with a calculated molecular mass of 35,858 Da. The ReXDH protein was purified as an active soluble form using GST affinity chromatography. The molecular mass of the purified enzyme was estimated to be approximately 34 kDa by sodium dodecyl sulfate-polyacrylamide gel and approximately 135 kDa with gel filtration chromatography, suggesting that the enzyme is a homotetramer. Among various polyols, xylitol was the preferred substrate of ReXDH with a K (m) = 17.9 mM and k(cat) /K (m) = 0.5 mM(-1) s(-1) for xylitol. The enzyme had an optimal pH and temperature of 9.5 and 70 degrees C, respectively. Heat inactivation studies revealed a half life of the ReXDH at 40 degrees C of 120 min and a half denaturation temperature (T (1/2)) of 53.1 degrees C. ReXDH showed the highest optimum temperature and thermal stability among the known XDHs. Homology modeling and sequence analysis of ReXDH shed light on the factors contributing to the high thermostability of ReXDH. Although XDHs have been characterized from several other sources, ReXDH is distinguished from other XDHs by its high thermostability.

Isolation of an operon involved in xylitol metabolism from a xylitol-utilizing Pantoea ananatis mutant

An operon involved in cryptic xylitol metabolism of Pantoea ananatis was cloned by transposon tagging. A xylitol negative mutant with a transposon insertion in the xylitol 4-dehydrogenase gene (xdh) was isolated and genomic DNA around the transposon was sequenced. Consequently, six consecutive genes, xytB-G are located downstream of xdh in the same strand. These seven genes are cotranscribed as a single transcript in a P. ananatis xylitol-utilizing mutant, suggesting that they comprise an operon. In addition to xdh, xytF also encodes oxidoreductase that is a member of the short-chain dehydrogenase/reductase family. Recombinant Escherichia coli that heterologously expresses the Xdh protein converts xylitol to xylulose as expected. On the other hand, the recombinant XytF protein has activity with l-arabitol but not with xylitol. XytB, xytD and xytE have significant sequence similarities to genes encoding the substrate-binding, ATP-binding and permease subunits, respectively, of ATP-binding cassette transporters. Although the physiological role of the operon remains unknown, the operon appears to be involved in uptake and metabolism of a various sugar alcohols. A gene encoding a DeoR-type transcriptional regulator, xytR, is located upstream of the operon in the opposite strand and a single nucleotide substitution that could cause a nonsense mutation is present in the xytR gene of the xylitol-utilizing mutant. This result suggests that the product of xytR negatively controls expression of the operon like other DeoR regulators.

Efficient conversion of allitol to d-psicose by Bacillus pallidus Y25

An efficient method for conversion of allitol to D-psicose was achieved by a resting cell reaction of Bacillus pallidus Y25 for the first time. Notably, it was possible to produce D-allose and D-altrose from allitol directly via D-psicose by prolonging the reaction time. This method was applied for the preparation of D-psicose using the extract of Itea virginica as a starting material in this study. D-Psicose which is the absolutely key precursor for the production of other six carbon sugars could be obtained as the sole product at high yield.

Metabolic engineering for pentose utilization in Saccharomyces cerevisiae

The introduction of pentose utilization pathways in baker's yeast Saccharomyces cerevisiae is summarized together with metabolic engineering strategies to improve ethanolic pentose fermentation. Bacterial and fungal xylose and arabinose pathways have been expressed in S. cerevisiae but do not generally convey significant ethanolic fermentation traits to this yeast. A large number of rational metabolic engineering strategies directed among others toward sugar transport, initial pentose conversion, the pentose phosphate pathway, and the cellular redox metabolism have been exploited. The directed metabolic engineering approach has often been combined with random approaches including adaptation, mutagenesis, and hybridization. The knowledge gained about pentose fermentation in S. cerevisiae is primarily limited to genetically and physiologically well-characterized laboratory strains. The translation of this knowledge to strains performing in an industrial context is discussed.