Production of L-xylose from L-xylulose using Escherichia coli L-fucose isomerase

l-Xylulose was used as a raw material for the production of l-xylose with a recombinantly produced Escherichia colil-fucose isomerase as the catalyst. The enzyme had a very alkaline pH optimum (over 10.5) and displayed Michaelis-Menten kinetics for l-xylulose with a K_m of 41 mM and a V_max of 0.23 μmol/(mg min). The half-lives determined for the enzyme at 35 °C and at 45 °C were 6 h 50 min and 1 h 31 min, respectively. The reaction equilibrium between l-xylulose and l-xylose was 15:85 at 35 °C and thus favored the formation of l-xylose. Contrary to the l-rhamnose isomerase catalyzed reaction described previously [14]l-lyxose was not detected in the reaction mixture with l-fucose isomerase. Although xylitol acted as an inhibitor of the reaction, even at a high ratio of xylitol to l-xylulose the inhibition did not reach 50%.     

Hydroxylation of l-proline to cis-3-hydroxy-l-proline by recombinant Escherichia coli expressing a synthetic l-proline-3-hydroxylase gene

A synthetic gene encoding a Streptomyces l-proline-3-hydroxylase was constructed and used to produce the hydroxylase protein in recombinant Escherichia coli. A fermentation process for growth of this recombinant E. coli for enzyme production was scaled-up to 250 L. A biotransformation process was developed using cell suspensions of the recombinant E. coli and subsequently scaled-up to 10 L for conversion of l-proline to cis-3-hydroxy-l-proline. A reaction yield of 85 M% and d.e. of 99.9% was obtained for cis-3-hydroxy-l-proline.     

l-Malic acid formation by immobilized Saccharomyces cerevisiae amplified for fumarase

The yeast Saccharomyces cerevisiae was amplified for the enzyme fumarase by cloning the single nuclear gene downstream of a strong promoter. The overproducing strain converted fumaric acid to l-malic acid at a rate of 65 mM g⁻¹ h⁻¹ in free cell experiments, and approximately 87% of the fumaric acid was converted to l-malic acid within 45 min. Activity was dependent on the addition of surfactant to the medium, and minimal activity was seen with the wild-type yeast strain. The constructed strain was immobilized in agarose beads (2.4 mm mean diameter) and within agarose microspheres (193 and 871 μm mean diameter). The rate of bioconversion increased with decreasing bead diameter, with similar rates observed with the 193-μm diameter microspheres to that achieved with the free cells. The presence of surfactant was essential for initial activity of the immobilized cells; however, high activity was observed in subsequent experiments in the absence of surfactant. Stable activities over a 48-h period were maintained within the large-diameter agarose beads, while decreasing activities were observed within the agarose microspheres.     

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 [17]. 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 ν_max of 650 U/mg.     

The Hypocrea jecorina (syn. Trichoderma reesei) lxr1 gene encodes a d-mannitol dehydrogenase and is not involved in l-arabinose catabolism

The Hypocrea jecorina LXR1 was described as the first fungal l-xylulose reductase responsible for NADPH dependent reduction of l-xylulose to xylitol in l-arabinose catabolism. Phylogenetic analysis now reveals that LXR1 forms a clade with fungal d-mannitol 2-dehydrogenases. Lxr1 and the orthologous Aspergillus nigermtdA are not induced by l-arabinose but expressed at low levels during growth on different carbon sources. Deletion of lxr1 does not affect growth on l-arabinose and l-xylulose reductase activity remains unaltered whereas d-mannitol 2-dehydrogenase activities are reduced. We conclude that LXR1 is a d-mannitol 2-dehydrogenase and that a true LXR1 is still awaiting discovery.     

Acetonation of l-pentoses and 6-deoxy-l-hexoses under kinetic control using heterogeneous acid catalysts

The fibrous polymer-supported sulfonic acid catalyst Smopex-101 H⁺ proved to be an efficient catalyst for the preparation of O-isopropylidene derivatives from a series of rare sugars. Acetonation of the reducing sugars l-arabinose, l-ribose, l-xylose, l-fucose, and l-rhamnose in N,N-dimethylformamide by 2,2-dimethoxypropane or 2-methoxypropene led to the formation of the kinetically favored di-O- and/or mono-O-isopropylidene derivatives in 46-88% yields. The method consists of a simple experimental procedure which does not require predried solvents or reagents. The catalyst is easily recovered and can be regenerated making the procedure economically viable even for large-scale synthesis.     

l-Dopa synthesis using tyrosinase immobilized on magnetic beads

Magnetic beads were prepared via suspension polymerization of glycidyl methacrylate (GMA) and methyl methacrylate (MMA) in the presence of ferric ions. Following polymerization, thermal co-precipitation of the Fe(III) ions in the beads with Fe(II) ions under alkaline condition resulted in encapsulation of Fe₃O₄ nano-crystals within the polymer matrix. The magnetic beads were activated with glutaraldehyde, and tyrosinase enzyme was covalently immobilized on the support via reaction of amino groups under mild conditions. The immobilized enzyme was used for the synthesis of l-Dopa (1-3,4-dihydroxy phenylalanine) which is a precursor of dopamine. The immobilized enzyme was characterized by temperature, pH, operational and storage stability experiments. Kinetic parameters, maximum velocity of the enzyme (V_max) and Michaelis–Menten constant (K_m) values were determined as 1.05 U/mg protein and 1.0 mM for 50–75 μm and 2.00 U/mg protein and 4.0 mM for 75–150 μm beads fractions, respectively. Efficiency factor and catalytic efficiency were found to be 1.39 and 0.91 for 75–150 μm beads and 0.73 and 0.75 for 50–75 μm beads fractions, respectively. The catalytic efficiency of the soluble tyrosinase was 0.37. The amounts of immobilized protein were on the 50–75 μm and 75–150 μm fractions were 2.7 and 2.8 mg protein/g magnetic beads, respectively.     

Enzymatic epimerization of d-erythro-dihydroneopterin triphosphate to l-threo-dihydroneopterin triphosphate

An enzyme has been discovered in Escherichia coli that catalyzes the conversion of the triphosphate ester of 2-amino-4-hydroxy-6-(d-erythro-1′,2′,3′-trihydroxypropyl)-7,8-dihydropteridine, (i.e. d-erythro-dihydroneopterin triphosphate) to an epimer of this compound, l-threo-dihydroneopterin triphophate. The enzyme, which is here named “d-erythro-dihydroneopterin triphosphate 2′-epimerase,” needs a divalent cation (Mg²⁺ or Mn²⁺ is most effective) for maximal activity. Its molecular weight is estimated at 87 000–89 000. Little or no activity can be detected if either the monophosphate or the phosphate-free form of the substrate is incubated with the enzyme. Evidence is presented to establish that all three phosphate residues of the substrate are retained in the product and that the product is of the l-threo configuration.     

Construction and co-expression of polycistronic plasmid encoding d-hydantoinase and d-carbamoylase for the production of d-amino acids

d-Hydantoinase and d-carbamoylase genes from Agrobacterium radiobacter TH572 were cloned by polymerase chain reaction (PCR). The plasmid pUCCH3 with a polycistronic structure that is controlled by the native hydantoinase promoter was constructed to co-express the two genes and transformed into Escherichia coli strain JM105. To obtain the highest level of expression of the d-carbamoylase and avoid intermediate accumulation, the d-carbamoylase gene was cloned closer to the promoter and the RBS region in the upstream of it was optimized. This resulted in high active expression of soluble d-hydantoinase and d-carbamoylase that is obtained without any inducer. Thus, by the constitutive recombinant JM105/pUCCH3, d-p-hydroxyphenylglycine (d-HPG) was obtained directly with 95.2% production yield and 96.3% conversion yield.     

Microbial production of d-amino acids

The production of d-aminoacylase by Alcaligenes denitrificans and Alcaligenes faecalis has been studied. The enzyme was inducibly produced and N-acetyl-d-leucine and N-acetyl-d-valine were the most effective inducers. d-methionine, d-valine, d-phenylalamine and d-leucine were produced by the enzymic hydrolysis of the appropriate N-acetyl-d-amino-acids with whole cell biomass. The hydrolysis of N-acetyl-d-methionine by A. denitrificans and N-acetyl-d-valine by A. faecalis was preferential. Maximum yields of d-methionine and d-valine were 94.3 and 84.7% at a specific product formation rate of 20.10 and 19.19 μmol min⁻¹ mg⁻¹ of wet cells at 20 mM substrate concentration and 5 mg ml⁻¹ of cell density.     

Ensemble modeling for strain development of l-lysine-producing Escherichia coli

One of the main strategies to improve the production of relevant metabolites has been the manipulation of single or multiple key genes in the metabolic pathways. This kind of strategy requires several rounds of experiments to identify enzymes that impact either yield or productivity. The use of mathematical tools to facilitate this process is desirable. In this work, we apply the Ensemble Modeling (EM) framework, which uses phenotypic data (effects of enzyme overexpression or genetic knockouts on the steady-state production rate) to screen for potential models capable of describe existing data and thus gaining insight to improve strains for l-lysine production. Described herein is a strategy to generate a set of kinetic models that describe a set of enzyme overexpression phenotypes previously determined in an Escherichia coli strain that produces increased levels of l-lysine in an industrial laboratory. This final ensemble of models captures the kinetic characteristics of the cell through screening of phenotypes after sequential overexpression of enzymes. Furthermore, these models demonstrate some predictive capability, as starting from the reference producing strain (overexpressing desensitized dihydrodipicolinate synthetase (dapA*)) this set of models is able to predict that the desensitization of aspartate kinase (lysC*) is the next rate-controlling step in the l-lysine pathway. Moreover, this set of models allows for the generation of further targets for testing, for example, phosphoenolpyruvate (Ppc), aspartate aminotransferase (AspC), and glutamate dehydrogenase (GdhA). This work demonstrates the usefulness, applicability, and scope that the Ensemble Modeling framework offers to build production strains.     

Overproduction of d-xylose isomerase in Escherichia coli by cloning the d-xylose isomerase gene

The Escherichia coli d-xylose isomerase (d-xylose ketol-isomerase, EC 5.3.1.5) gene, xylA, has been cloned on various E. coli plasmids. However, it has been found that high levels of overproduction of the d-xylose isomerase, the protein product of the xylA gene, cannot be accomplished by cloning the intact gene on high copy-number plasmids alone. This is believed to be due to the fact that the expression of the gene through its natural promoter is highly regulated in E. coli. In order to overcome this, the xylA structural gene has been fused with other strong promoters such as tac and lac, resulting in the construction of a number of fused genes. Analysis of the E. coli transformants containing the fused genes, cloned on high copy-number plasmids, indicated that a 20-fold overproduction of the enzyme can now be obtained. It is expected that overproduction of the enzyme in E. coli can still be substantially improved through additional manipulation with recombinant DNA techniques.     

Structure and Engineering of l-Arabinitol 4-Dehydrogenase from Neurospora crassa

l-Arabinitol 4-dehydrogenase (LAD) catalyzes the conversion of l-arabinitol into l-xylulose with concomitant NAD⁺ reduction. It is an essential enzyme in the development of recombinant organisms that convert l-arabinose into fuels and chemicals using the fungal l-arabinose catabolic pathway. Here we report the crystal structure of LAD from the filamentous fungus Neurospora crassa at 2.6 Å resolution. In addition, we created a number of site-directed variants of N. crassa LAD that are capable of utilizing NADP⁺ as cofactor, yielding the first example of LAD with an almost completely switched cofactor specificity. This work represents the first structural data on any LAD and provides a molecular basis for understanding the existing literature on the substrate specificity and cofactor specificity of this enzyme. The engineered LAD mutants with altered cofactor specificity should be useful for applications in industrial biotechnology.     

Growth of Rhodopseudomonas capsulata on l- and d-malic acid

d-malate replaced l-malate in supporting both photosynthetic (anaerobic, light) and heterotrophic (aerobic, dark) growth of Rhodopseudomonas capsulata. Growth rates and cell yields were nearly equivalent with both enantiomorphs. Addition of glucose to malate culture media increased the growth rate and doubled the cell yield of heterotrophic cultures, but had little effect on photosynthetic cultures. Aerobically-grown cells showed a higher level of substrate-dependent oxygen uptake with l-malate than with d-malate. This preference for l-malate occured even in cells grown on d-malate. No malic racemase activity was detected in extracts of heterotrophically- or photosynthetically-grown cells.     

Modification of optimal pH in l-arabinose isomerase from Geobacillus stearothermophilus for d-galactose isomerization

l-Arabinose isomerase from Geobacillus stearothermophilus (GSAI; EC 5.3.1.4) has been genetically evolved to increase the reaction rate toward d-galactose, which is not a natural substrate. To change the optimal pH of GSAI for d-galactose isomerization (pH optimum at 8.5), we investigated the single point mutations influencing the activity based on the sequences of the previously evolved enzymes. Among the seven point mutations found in the evolved enzymes, mutations at Val⁴⁰⁸ and Asn⁴⁷⁵ were determined to be highly influential mutation points for d-galactose isomerization activity. A random mutation was introduced into sites Val⁴⁰⁸ and Asn⁴⁷⁵ (X408V and X475N), and candidates were screened based on non-optimal pH conditions. Among the mutations of X408V and X475N, mutations of Q408V and R408V were selected. The optimal pH of the both mutations Q408V and R408V was shifted to pH 7.5. At the shifted optimal pH, the d-galactose isomerization activities of Q408V and R408V were 60 and 30% higher than that of the wild type at pH 8.5, respectively.     

Alternate pathways of l-rhamnose transport in Arthrobacter pyridinolis

Phosphoenolpyruvate: hexose phosphotransferase-negative mutants of Arthrobacterpyridinolis fail to grow on l-rhamnose. Although phosphoenolpyruvate: l-rhamnose phosphotransferase activity could not be consistently demonstrated in extracts of rhamnose-grown cells, low levels of phosphoenolpyruvate-dependent uptake of rhamnose were found using isolated membrane vesicles from rhamnose-grown cells. This uptake was not inhibited by uncoupling agents or an inhibitor of the respiratory chain. Phosphotransferase-negative mutants could grow on l-rhamnose if l-malate was also present in the medium. l-Malate- and succinate-dependent uptake of rhamnose was found in membrane vesicles. Either of the two oxidizable substrates caused a 5-fold stimulation of the rate of l-rhamnose uptake over that observed in the absence of additions. Malate-dependent l-rhamnose uptake had a K_m for rhamnose of 2.9 × 10^?6m. It was inhibited by uncoupling agents, inhibitors of the respiratory chain, and sulfhydryl reagents.     

Enzymatic conversion of N carbamoyl-d-amino acids to d-amino acids

An enzyme isolated from Agrobacterium radiobacter was shown to catalyse the following reaction: H₂O + N-carbamoyl-d-amino acid→ d-amino acid + NH₃ + CO₂ Some properties of this new enzyme, N-carbamoyl-d-amino acid amidohydrolase, are presented in this paper. The potential application of this enzyme for the preparation of some d-amino acids used as pharmaceutical intermediates is discussed.     

Convenient,laboratory procedure for producing solid d-arabino-hexos-2-ulose (d-glucosone)

The production of solid d-arabino-hexos-2-ulose (d-glucosone) from d-glucose by use of an enzyme, pyranose-2-oxidase (EC 1.1.3.10), is described. The enzyme is extracted from the mycelia of Polyporus obtusus, partially purified, and then immobilized on activated CH-Sepharose 4B. The enzymic conversion of d-glucose into d-glucosone is simple and convenient, and provides a product free from residual d-glucose. Lyophilization of the filtered reaction-solution yields the product, solid d-glucosone. Assay methods have been developed for monitoring the enzymic reaction and evaluating the purity of the final product.     

Immobilization of d-hydantoinase in polyaniline

Polyaniline (PANI) is a water-insoluble polymer that has been used as support for enzyme immobilization due to its desirable characteristics, such as ease of preparation, high synthesis yield, high stability to temperature and pH, and resistance to microbial attack. In this work an investigation was carried out to determine the best conditions to immobilize d-hydantoinase (E.C. 3.5.2.2) in this support. As result, a simple and fast methodology for d-hydantoinase immobilization in PANI is described. 100% of proteins were immobilized on the support in concentrations up to 2 mg solid/ml. Higher concentrations led to a lower protein percentage immobilized. After five reaction cycles about a half of d-hydantoinase initial activity was conserved.     

d-Amino acid production by E. coli co-expressed three genes encoding hydantoin racemase, d-hydantoinase and N-carbamoyl-d-amino acid amidohydrolase

Three genes respectively encoding d-specific hydantoinase (DHHase), N-carbamoyl-d-amino acid amidohydrolase (DCHase) and hydantoin racemase (HRase) were co-expressed in E. coli in a system designed for the efficient enzymatic production of d-amino acids via a combination of hydantoin hydrolysis and hydantoin racemization. With the use of whole cells, the d-forms of eight amino acids – d-phenylalanine, d-tyrosine, d-tryptophan, O-benzyl-d-serine, d-valine, d-norvaline, d-leucine and d-norleucine – were efficiently converted from the corresponding dl-5-monosubtituted hydantoin compounds.