Sequential Co-Immobilization of Enzymes on Magnetic Nanoparticles for Efficient l-Xylulose Production.

Multi-enzymatic strategies have shown improvement in bioconversion during cofactor regeneration. In this study, purified l-arabinitol 4-dehydrogenase (LAD) and nicotinamide adenine dinucleotide oxidase (Nox) were immobilized via individual, mixed, and sequential co-immobilization approaches on magnetic nanoparticles, and were evaluated to enhance the conversion of l-arabinitol to l-xylulose. Initially, the immobilization of LAD or Nox on the nanoparticles resulted in a maximum immobilization yield and relative activity of 91.4% and 98.8%, respectively. The immobilized enzymes showed better pH and temperature profiles than the corresponding free enzymes. Furthermore, co-immobilization of these enzymes via mixed and sequential methods resulted in high loadings of 114 and 122 mg/g of support, respectively. Sequential co-immobilization of these enzymes proved more beneficial for higher conversion than mixed co-immobilization because of better retaining Nox residual activity. Sequentially co-immobilized enzymes showed a high relative conversion yield with broader pH, temperature, and storage stability profiles than the controls, along with high reusability. To the best of our knowledge, this is the first report on the mixed or sequential co-immobilization of LAD and Nox on magnetic nanoparticles for l-xylulose production. This finding suggests that selecting a sequential co-immobilization strategy is more beneficial than using individual or mixed co-immobilized enzymes on magnetic nanoparticles for enhancing conversion applications.

Investigation of the effect of oligo-xylulose on the intestinal flora under pressure overload in mice based on 16S rRNA gene sequencing.

The relationship between gut microbiota dysbiosis and heart failure has been drawing increasing attention. This study aimed to investigate the effects of oligo-xylulose (XOS) on the gut microbiota of mice with heart failure induced by pressure overload. A chronic heart failure mouse model was constructed by pressure overload, and XOS were administered in their diet. The gut microbiota was analyzed using 16S rRNA gene sequencing, and the effects of XOS on the microbiota composition were evaluated. . XOS supplementation improved the balance of intestinal microbiota in mice under pressure overload, increasing the abundance of beneficial bacteria, such as Bifidobacterium and Lactobacillus, while decreasing the abundance of harmful bacteria, such as Desulfovibrio and Enterococcus. XOS has potential as a dietary supplement to improve the balance of intestinal microbiota and benefit individuals with heart failure. The findings of this study suggest that modulating the gut microbiota could be a novel strategy for treating heart failure.

Sustainable bio-manufacturing of D-arabitol through combinatorial engineering of Zygosaccharomyces rouxii, bioprocess optimization and downstream separation.

Biosynthesis of D-arabitol, a high value-added platform chemical, from renewable carbon sources provides a sustainable and eco-friendly alternative to the chemical industry. Here, a robust brewing yeast, Zygosaccharomyces rouxii, capable of naturally producing D-arabitol was rewired through genome sequencing-based metabolic engineering. The recombinant Z. rouxii obtained by reinforcing the native D-xylulose pathway, improving reductive power of the rate-limiting step, and inhibiting the shunt pathway, produced 73.61% higher D-arabitol than the parent strain. Subsequently, optimization of the fermentation medium composition for the engineered strain provided 137.36 g/L D-arabitol, with a productivity of 0.64 g/L/h in a fed-batch experiment. Finally, the downstream separation of D-arabitol from the complex fermentation broth using an ethanol precipitation method provided a purity of 96.53%. This study highlights the importance of D-xylulose pathway modification in D-arabitol biosynthesis, and pave a complete and efficient way for the sustainable manufacturing of this value-added compound from biosynthesis to preparation.

Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography.

Phosphoketolase and transketolase are thiamine diphosphate-dependent enzymes and play a central role in the primary metabolism of bifidobacteria: the bifid shunt. The enzymes both catalyze phosphorolytic cleavage of xylulose 5-phosphate or fructose 6-phosphate in the first reaction step, but possess different substrate specificity in the second reaction step, where phosphoketolase and transketolase utilize inorganic phosphate (Pi) and D-ribose 5-phosphate, respectively, as the acceptor substrate. Structures of Bifidobacterium longum phosphoketolase holoenzyme and its complex with a putative inhibitor, phosphoenolpyruvate, were determined at 2.5 Šresolution by serial femtosecond crystallography using an X-ray free-electron laser. In the complex structure, phosphoenolpyruvate was present at the entrance to the active-site pocket and plugged the channel to thiamine diphosphate. The phosphate-group position of phosphoenolpyruvate coincided well with those of xylulose 5-phosphate and fructose 6-phosphate in the structures of their complexes with transketolase. The most striking structural change was observed in a loop consisting of Gln546-Asp547-His548-Asn549 (the QN-loop) at the entrance to the active-site pocket. Contrary to the conformation of the QN-loop that partially covers the entrance to the active-site pocket (`closed form') in the known crystal structures, including the phosphoketolase holoenzyme and its complexes with reaction intermediates, the QN-loop in the current ambient structures showed a more compact conformation with a widened entrance to the active-site pocket (`open form'). In the phosphoketolase reaction, the `open form' QN-loop may play a role in providing the binding site for xylulose 5-phosphate or fructose 6-phosphate in the first step, and the `closed form' QN-loop may help confer specificity for Pi in the second step.

Development of an enzymatic cascade to systematically utilize lignocellulosic monosaccharide.

BACKGROUND: The fermentation valorization of two main lignocellulosic monosaccharides, glucose and xylose, is extensively developed; however, it is restricted by limited yield and process complexity. An in vitro enzymatic cascade reaction can be an alternative approach. RESULTS: In this study, a three-stage, five-enzyme cascade was developed to convert pretreated biomass to valuable chemicals. First, a ribose-5-phosphate isomerase B mutant isomerized xylose to d-xylulose with high substrate specificity, and a d-arabinose dehydrogenase continued to reduce d-xylulose to d-arabitol. Simultaneously, glucose was utilized for the coenzyme regeneration catalyzed by a glucose dehydrogenase, generating useful gluconic acid and achieving 73% of total conversion rate after 36 h. Then, six kinds of pretreated biomass lignocellulose were hydrolyzed by cellulase and hemicellulase, and corn cob was identified as the initial substrate for providing the highest monosaccharide content. A 65% conversion rate of the lignocellulosic xylose was obtained after 24 h. CONCLUSIONS: This study presents a proof of concept to convert main lignocellulosic monosaccharides systematically by an enzymatic cascade at stoichiometric ratio. © 2022 Society of Chemical Industry.

Antibacterial Target DXP Synthase Catalyzes the Cleavage of d-Xylulose 5-Phosphate: a Study of Ketose Phosphate Binding and Ketol Transfer Reaction.

The bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) in a thiamin diphosphate (ThDP)-dependent manner. In addition to its role in isoprenoid biosynthesis, DXP is required for ThDP and pyridoxal phosphate biosynthesis. Due to its function as a branch-point enzyme and its demonstrated substrate and catalytic promiscuity, we hypothesize that DXPS could be key for bacterial adaptation in the dynamic metabolic landscape during infection. Prior work in the Freel Meyers laboratory has illustrated that DXPS displays relaxed specificity toward donor and acceptor substrates and varies acceptor specificity according to the donor used. We have reported that DXPS forms dihydroxyethyl (DHE)ThDP from ketoacid or aldehyde donor substrates via decarboxylation and deprotonation, respectively. Here, we tested other DHE donors and found that DXPS cleaves d-xylulose 5-phosphate (X5P) at C2-C3, producing DHEThDP through a third mechanism involving d-GAP elimination. We interrogated DXPS-catalyzed reactions using X5P as a donor substrate and illustrated (1) production of a semi-stable enzyme-bound intermediate and (2) O2, H+, and d-erythrose 4-phosphate act as acceptor substrates, highlighting a new transketolase-like activity of DXPS. Furthermore, we examined X5P binding to DXPS and suggest that the d-GAP binding pocket plays a crucial role in X5P binding and turnover. Overall, this study reveals a ketose-cleavage reaction catalyzed by DXPS, highlighting the remarkable flexibility for donor substrate usage by DXPS compared to other C-C bond-forming enzymes.

Effects of herbivory on carotenoid biosynthesis and breakdown.

The carotenoid content of plants may be impacted by stress with major consequences for photosynthesis and photoprotection. Most carotenoid stress research, however, has concentrated on abiotic stresses, and we know little about how biological stresses, such as herbivory, alter profiles of plant carotenoids and their degradation products. For example, carotenoid derivatives such as ß-cyclocitral and ß-ionone have been recently shown to act as signals in plant growth and protection against oxidative stress and herbivory. To understand how carotenoid composition is influenced by herbivory, changes in biosynthesis and degradation should be investigated. This chapter describes methods to simulate herbivory in a simple reproducible fashion and to assess carotenoid biosynthesis and degradation. Carotenoid biosynthesis depends on precursors provided by the methylerythritol 4-phosphate (MEP) pathway, which converts pyruvate and glyceraldehyde-3-phosphate to the five-carbon units used for construction of larger isoprenoids. We present protocols to quantify the activity of the first enzyme of the MEP pathway, deoxy-xylulose 5-phosphate synthase (DXS), usually assumed to be rate-controlling, and to estimate the concentration of the first intermediate of the pathway, deoxy-xylulose 5-phosphate (DXP). We also discuss procedures to measure the formation of volatile carotenoid breakdown products after herbivory. To monitor the activity of carotenoid-specific biosynthetic enzymes, such as phytoene synthase, protocols are available elsewhere in this volume (Wurtzel, 2022b).

Characterization of D-xylose isomerase from Shinella zoogloeoides NN6 and its application for producing D-allulose and two D-ketopentoses in a one-pot multi-step transformation.

Researchers continue to search for efficient processes to reduce the production costs of rare sugars. In this paper, we report a novel D-xylose isomerase from Shinella zoogloeoides NN6 (SzXI) and its application for efficient rare sugar production. Purified SzXI did not show remarkable properties when compared with those of a previously reported D-xylose isomerase. However, NN6 was found to express inducible SzXI and constitutive D-allulose 3-epimerase (SzAE) when cultivated with D-xylose as the sole carbon source. These two enzymes were partially purified and immobilized onto HPA25L, an anion exchange resin. The co-immobilized SzXI and SzAE (i-XA) showed optimal activity at 65°C in sodium phosphate buffer (pH 7.5) and 90°C in sodium phosphate buffer (pH 6.5), respectively. i-XA produced D-ribulose via D-xylulose from D-xylose at a conversion ratio of D-xylose:D-xylulose:D-ribulose of 72:18:10. Furthermore, D-allulose was also produced via D-fructose using D-glucose as the substrate, with a D-allulose yield of 11.2%. This is the first report describing a bacterium expressing D-xylose isomerase and D-allulose 3-epimerase that converts readily available sugars such as D-glucose and D-xylose to rare sugars.

Density functional theory study on the initial reactions of d-Xylose and d-Xylulose dehydration to furfural.

The mechanism of the initial reactions in the acid-catalytic conversion of d-xylose/d-xylulose to furfural was studied with density functional theory. The reactions included mutual transformations among d-xylose, d-xylulose and the intermediate of 1,2-enediol. The catalytic performances of several acids including H2SO4, HNO3, HCl, HBr and HI, and the solvent effects of water and THF (tetrahydrofuran) were studied. A simplified kinetic model of the d-xylose/d-xylulose-to-furfural conversion in water solvent was built, with the assumption that the conversion from 1,2-enediol to furfural was the rate-limiting step and could be treated as one-step reaction. The simulation can well fit the experimental regulation, which verifies the rationality of the model simplification. The dominant reaction pathways from d-xylose/d-xylulose to furfural were deduced based on the calculated energy barriers and corresponding reaction rate constants, with different acid catalysis and reaction mediums.

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 Km and Vmax 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.

Milestones in treatments for inborn errors of metabolism: Reflections on Where chemistry and medicine meet.

From Sir Archibald Garrod's initial description of the tetrad of albinism, alkaptonuria, cystinuria, and pentosuria to today, the field of medicine dedicated to inborn errors of metabolism has evolved from disease identification and mechanistic discovery to the development of therapies designed to subvert biochemical defects. In this review, we highlight major milestones in the treatment and diagnosis of inborn errors of metabolism, starting with dietary therapy for phenylketonuria in the 1950s and 1960s, and ending with current approaches in genetic manipulation.

Effect of D-allulose feeding on the hepatic metabolomics profile in male Wistar rats.

The rare sugar d-allulose is a C-3 epimer of d-fructose and is known to have several health benefits such as anti-obesity and anti-diabetic effects through the alteration of enzymatic and genetic expressions in each organ. Most of the ingested d-allulose is absorbed in the small intestine and then rapidly excreted in the urine. As d-allulose was reported to be present in the liver before it is excreted, d-allulose may modulate some hepatic metabolites including glucose and lipid metabolism. Therefore, we investigated the hepatic metabolomics profile in rats after feeding d-allulose to study the overall alteration of hepatic metabolism. Wistar rats were fed an AIN-93G diet with/without 3% d-allulose for 4 weeks. Their liver samples were then collected and subjected to metabolomics analysis using CE-TOFMS and LC-TOFMS. The results showed that d-allulose induced significant increases in 42 metabolites and significant decreases in 21 metabolites. In particular, we found at the substance levels that d-allulose regulated metabolites involved in the metabolic pathways of fatty acid ß-oxidation, cholesterol, and bile acid. In addition, this study newly showed the possibility that d-allulose alters glucuronic acid/xylulose pathways. In the future, we need more detailed research on the metabolomics profile of other organs related to these pathways for a comprehensive understanding of d-allulose functions.

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.

Recent advances in properties, production, and applications of L-ribulose.

Currently, due to the special functions and potential application values, rare sugars become the hot topic in carbohydrate fields. L-Ribulose, an isomer of L-ribose, is an expensive rare ketopentose. As an important precursor for other rare sugars and L-nucleoside analogue synthesis, L-ribulose attracts more and more attention in recent days. Compared with complicated chemical synthesis, the bioconversion method becomes a good alternative approach to L-ribulose production. Generally, the bioconversion of L-ribulose was linked with ribitol, L-arabinose, L-ribose, L-xylulose, and L-arabitol. Herein, an overview of recent advances in the metabolic pathway, chemical synthesis, bioproduction of L-ribulose, and the potential application of L-ribulose is reviewed in detail in this paper. KEY POINTS: 1. L-Ribulose is a rare sugar and the key precursor for L-ribose production. 2. L-Ribulose is the starting material for L-nucleoside derivative synthesis. 3. Chemical synthesis, bioproduction, and applications of L-ribulose are reviewed.

Interaction of (-)-Epigallocatechin Gallate and Deoxyosones Blocking the Subsequent Maillard Reaction and Improving the Yield of N-(1-Deoxy-d-xylulos-1-yl)alanine.

(-)-Epigallocatechin gallate (EGCG) had a significant effect on Maillard reaction intermediate formation in the xylose/alanine model system. A trapping effect of EGCG on the reactive deoxyosones was observed to change the reaction pathways. The rate constant of Amadori rearrangement product (ARP) conversion to deoxyosones was decreased with EGCG addition, indicating an inhibition of ARP degradation. Dehydration improved the ARP formation during the thermal reaction and synergistically improved the yield of ARP with the EGCG trapping effect on the deoxyosones. Additionally, EGCG decreased the activation energy for the conversion of xylose/alanine to ARP (from 77.8 to 62.8 kJ/mol) and in turn accelerated the ARP formation. The effect of EGCG was further facilitated at the optimal conditions of 90 °C, at pH 7.5, and a molar ratio of xylose to alanine of 2:1, which improved the yield of ARP (N-(1-deoxy-d-xylulos-1-yl)alanine) from 2 to 95%.

The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2.

The methylotrophic yeast Pichia pastoris is widely used in the manufacture of industrial enzymes and pharmaceuticals. Like most biotechnological production hosts, P. pastoris is heterotrophic and grows on organic feedstocks that have competing uses in the production of food and animal feed. In a step toward more sustainable industrial processes, we describe the conversion of P. pastoris into an autotroph that grows on CO2. By addition of eight heterologous genes and deletion of three native genes, we engineer the peroxisomal methanol-assimilation pathway of P. pastoris into a CO2-fixation pathway resembling the Calvin-Benson-Bassham cycle, the predominant natural CO2-fixation pathway. The resulting strain can grow continuously with CO2 as a sole carbon source at a µmax of 0.008 h-1. The specific growth rate was further improved to 0.018 h-1 by adaptive laboratory evolution. This engineered P. pastoris strain may promote sustainability by sequestering the greenhouse gas CO2, and by avoiding consumption of an organic feedstock with alternative uses in food production.

Biosynthesis of Isoprene Units in Euphorbia lathyris Laticifers vs. Other Tissues: MVA and MEP Pathways, Compartmentation and Putative Endophytic Fungi Contribution.

Euphorbia species are characterized by a net of laticifers producing large amounts of triterpenes. These hydrocarbon-like metabolites can be converted into fuel by the methods of the oil industry. Euphorbia lathyris is easily grown at an industrial scale. In an attempt to increase its triterpene production, the metabolic pathways leading to isoprenoid were investigated by incorporation of 13C labeled glucose and mevalonate and 2H labeled deoxyxylulose as well as by natural abundance isotope ratio GC-MS. Latex triterpenes are exclusively synthesized via the mevalonate (MVA) pathway: this may orient future search for improving the triterpene production in E. lathyris. Phytosterols and their precursors are mainly derived from MVA pathway with a slight contribution of the methylerythritol phosphate (MEP) pathway, whereas phytol is issued from MEP pathway with a minor contribution of the MVA pathway: this is in accordance with the metabolic cross-talk between cytosolic and plastidial compartments in plants. In addition, hopenol B behaved differently from the other latex triterpenes. Its 13C isotope abundance after incorporation of 13C labeled glucose and its natural abundance δ2H signature clearly differed from those of the other latex triterpenes indicating another metabolic origin and suggesting that it may be synthesized by an endophytic fungus.

Comparative global metabolite profiling of xylose-fermenting Saccharomyces cerevisiae SR8 and Scheffersomyces stipitis.

Bioconversion of lignocellulosic biomass into ethanol requires efficient xylose fermentation. Previously, we developed an engineered Saccharomyces cerevisiae strain, named SR8, through rational and inverse metabolic engineering strategies, thereby improving its xylose fermentation and ethanol production. However, its fermentation characteristics have not yet been fully evaluated. In this study, we investigated the xylose fermentation and metabolic profiles for ethanol production in the SR8 strain compared with native Scheffersomyces stipitis. The SR8 strain showed a higher maximum ethanol titer and xylose consumption rate when cultured with a high concentration of xylose, mixed sugars, and under anaerobic conditions than Sch. stipitis. However, its ethanol productivity was less on 40 g/L xylose as the sole carbon source, mainly due to the formation of xylitol and glycerol. Global metabolite profiling indicated different intracellular production rates of xylulose and glycerol-3-phosphate in the two strains. In addition, compared with Sch. stipitis, SR8 had increased abundances of metabolites from sugar metabolism and decreased abundances of metabolites from energy metabolism and free fatty acids. These results provide insights into how to control and balance redox cofactors for the production of fuels and chemicals from xylose by the engineered S. cerevisiae.

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.

[Enzymatic synthesis of xylulose from formaldehyde].

Xylulose as a metabolic intermediate is the precursor of rare sugars, and its unique pattern of biological activity plays an important role in the fields of food, health, medicine and so on. The aim of this study was to design a new pathway for xylulose synthesis from formaldehyde, which is one of the most simple and basic organic substrate. The pathway was comprised of 3 steps: (1) formaldehyde was converted to glycolaldehyde by benzoylformate decarboxylase mutant BFD-M3 (from Pseudomonas putida); (2) formaldehyde and glycolaldehyde were converted to dihydroxyacetone by BFD-M3 as well; (3) glycolaldehyde and dihydroxyacetone were converted to xylulose by transaldolase mutant TalB-F178Y (from Escherichia coli). By adding formaldehyde (5 g/L), BFD-M3 and TalB-F178Y in one pot, xylulose was produced at a conversion rate of 0.4%. Through optimizing the concentration of formaldehyde, the conversion rate of xylulose was increased to 4.6% (20 g/L formaldehyde), which is 11.5 folds higher than the initial value. In order to further improve the xylulose conversion rate, we employed Scaffold Self-Assembly technique to co-immobilize BFD-M3 and TalB-F178Y. Finally, the xylulose conversion rate reached 14.02%. This study provides a new scheme for the biosynthesis of rare sugars.