Characterization of a Recombinant D-Allulose 3-epimerase from Thermoclostridium caenicola with Potential Application in D-Allulose Production

Advances in the biosynthesis of D-allulose

D-allulose is a rare monosaccharide and a C-3 epimer of D-fructose. It has physiological functions, such as antihyperglycemic, obesity-preventing, neuroprotective, and reactive oxygen species (ROS) scavenging effects, making it an ideal sugar substitute. The synthesis methods for D-allulose include chemical synthesis and biosynthesis. Chemical synthesis requires strict reaction conditions and tends to produce byproducts. Biosynthesis is mainly an enzymatic process. Enzymatic catalysis for the conversion of starch or glycerol to D-allulose is performed mainly by enzymes such as isoamylase (IA), glucose isomerase (GI), D-allulose 3-epimerase (DPE), D-allulose-6-phosphate 3-epimerase (A6PE), D-allulose 6-phosphate phosphatase (A6PP), ribitol 2-dehydrogenase (RDH), glycerophosphate kinase (GK), glycerophosphate oxidase (GPO), and dihydroxyacetone phosphate (DHAP)-dependent aldolase. Biosynthesis is a more energy-efficient process, producing fewer harmful by-products and pollutants, and significantly reducing negative environmental impacts. Furthermore, the specific catalytic activity of enzymes facilitates the production of compounds of higher purity, thereby facilitating the isolation and purification of the products. It has thus become the main method for producing D-allulose. This article reviews the progress in research on the biosynthetic production of D-allulose, focusing on the enzymes involved and their enzymatic properties, and discusses the production prospects for D-allulose.

Comprehensive Analysis of Allulose Production: A Review and Update

Advancements in D-allulose production have seen significant strides in recent years, focusing on enzymatic conversion methods. Key developments include traditional immobilization techniques, the discovery of novel enzymes, directed evolution studies, and biosynthesis through metabolic pathway modification. Enzymatic conversion, particularly utilizing D-allulose 3-epimerase, remains fundamental for industrial-scale production. Innovative immobilization strategies, such as functionalized nano-beads and magnetic MOF nanoparticles, have significantly enhanced enzyme stability and reusability. Directed evolution has led to improved enzyme thermostability and catalytic efficiency, while synthetic biology methods, including phosphorylation-driven and thermodynamics-driven pathways, have optimized production processes. High-throughput screening methods have been crucial in identifying and refining enzyme variants for industrial applications. Collectively, these advancements not only enhance production efficiency and cost-effectiveness but also adhere to sustainable and economically viable manufacturing practices. The past five years have witnessed critical developments with significant potential impact on the commercial viability and global demand for allulose.

Rational design improves both thermostability and activity of a new D-tagatose 3-epimerase from Kroppenstedtia eburnean to produce D-allulose

D-allulose is a naturally occurring rare sugar and beneficial to human health. However, the efficient biosynthesis of D-allulose remains a challenge. Here, we mined a new D-tagatose 3-epimerase from Kroppenstedtia eburnean (KeDt3e) with high catalytic efficiency. Initially, crucial factors contributing to the low conversion of KeDt3e were identified through crystal structure analysis, density functional theory calculations (DFT), and molecular dynamics (MD) simulations. Subsequently, based on the mechanism, combining restructuring the flexible region, proline substitution based onconsensus sequence analysis, introducing disulfide bonds, and grafting properties, and reshaping the active center, the optimal mutant M5 of KeDt3e was obtained with enhanced thermostability and activity. The optimal mutant M5 exhibited an enzyme activity of 130.8 U/mg, representing a 1.2-fold increase; Tm value increased from 52.7 °C to 71.2 °C; and half-life at 55 °C extended to 273.7 min, representing a 58.2-fold improvement, and the detailed mechanism of performance improvement was analyzed. Finally, by screening the ribosome-binding site (RBS) of the optimal mutant M5 recombinant bacterium (G01), the engineered strain G08 with higher expression levels was obtained. The engineered strain G08 catalyzed 500 g/L D-fructose to produce 172.4 g/L D-allulose, with a conversion of 34.4% in 0.5 h and productivity of 344.8 g/L/h on a 1 L scale. This study presents a promising approach for industrial-scale production of D-allulose.

D-allulose 3-epimerase for low-calorie D-allulose synthesis: microbial production, characterization, and applications

D-allulose, an epimer of D-fructose at C-3 position, is a low-calorie rare sugar with favorable physiochemical properties and special physiological functions, which displays promising perspectives in the food and pharmaceutical industries. Currently, D-allulose is extremely sparse in nature and is predominantly biosynthesized through the isomerization of D-fructose by D-allulose 3-epimerase (DAEase). In recent years, D-allulose 3-epimerase as the key biocatalyst for D-allulose production has received increasing interest. The current review begins by providing a summary of D-allulose regarding its characteristics and applications, as well as different synthesis pathways dominated by biotransformation. Then, the research advances of D-allulose 3-epimerase are systematically reviewed, focusing on heterologous expression and biochemical characterization, crystal structure and molecular modification, and application in D-allulose production. Concerning the constraint of low yield of DAEase for industrial application, this review addresses the various attempts made to promote the production of DAEase in different expression systems. Also, various strategies have been adopted to improve its thermotolerance and catalytic activity, which is mainly based on the structure-function relationship of DAEase. The application of DAEase in D-allulose biosynthesis from D-fructose or low-cost feedstocks through single- or multi-enzymatic cascade reaction has been discussed. Finally, the prospects for related research of D-allulose 3-epimerase are also proposed, facilitating the industrialization of DAEase and more efficient and economical bioproduction of D-allulose.

Enhancement of the d-Allulose 3-Epimerase Expression in Bacillus subtilis through Both Transcriptional and Translational Regulations

d-Allulose, a functional bulk sweetener, has recently attracted increasing attention because of its low-caloric-ness properties and diverse health effects. d-Allulose is industrially produced by the enzymatic epimerization of d-fructose, which is catalyzed by ketose 3-epimerase (KEase). In this study, the food-grade expression of KEase was studied using Bacillus subtills as the host. Clostridium sp. d-allulose 3-epimerase (Clsp-DAEase) was screened from nine d-allulose-producing KEases, showing better potential for expression in B. subtills WB600. Promoter-based transcriptional regulation and N-terminal coding sequence (NCS)-based translational regulation were studied to enhance the DAEase expression level. In addition, the synergistic effect of promoter and NCS on the Clsp-DAEase expression was studied. Finally, the strain with the combination of a PHapII promoter and gln A-Up NCS was selected as the best Clsp-DAEase-producing strain. It efficiently produced Clsp-DAEase with a total activity of 333.2 and 1860.6 U/mL by shake-flask and fed-batch cultivations, respectively.

Biochemical characterization, structure-guided mutagenesis, and application of a recombinant D-allulose 3-epimerase from Christensenellaceae bacterium for the biocatalytic production of D-allulose

D-Allulose has become a promising alternative sweetener due to its unique properties of low caloric content, moderate sweetness, and physiological effects. D-Allulose 3-epimerase (DAEase) is a promising enzyme for D-Allulose production. However, the low catalytic efficiency limited its large-scale industrial applications. To obtain a more effective biocatalyst, a putative DAEase from Christensenellaceae bacterium (CbDAE) was identified and characterized. The recombinant CbDAE exhibited optimum activity at pH 7.5°C and 55°C, retaining more than 60% relative activity from 40°C to 70°C, and the catalytic activity could be significantly increased by Co2+ supplementation. These enzymatic properties of purified CbDAE were compared with other DAEases. CbDAE was also found to possess desirable thermal stability at 55°C with a half-life of 12.4 h. CbDAE performed the highest relative activity towards D-allulose and strong affinity for D-fructose but relatively low catalytic efficiency towards D-fructose. Based on the structure-guided design, the best double-mutation variant G36N/W112E was obtained which reached up to 4.21-fold enhancement of catalytic activity compared with wild-type (WT) CbDAE. The catalytic production of G36N/W112E with 500 g/L D-fructose was at a medium to a higher level among the DAEases in 3.5 h, reducing 40% catalytic reaction time compared to the WT CbDAE. In addition, the G36N/W112E variant was also applied in honey and apple juice for D-allulose conversion. Our research offers an extra biocatalyst for D-allulose production, and the comprehensive report of this enzyme makes it potentially interesting for industrial applications and will aid the development of industrial biocatalysts for D-allulose.

Crystal structure of a novel homodimeric D-allulose 3-epimerase from a Clostridia bacterium

D-Allulose, a low-calorie rare sugar with various physiological functions, is mainly produced through the isomerization of D-fructose by ketose 3-epimerases (KEases), which exhibit various substrate specificities. A novel KEase from a Clostridia bacterium (CDAE) was identified to be a D-allulose 3-epimerase and was further characterized as thermostable and metal-dependent. In order to explore its structure–function relationship, the crystal structure of CDAE was determined using X-ray diffraction at 2.10 Å resolution, revealing a homodimeric D-allulose 3-epimerase structure with extensive interactions formed at the dimeric interface that contribute to structure stability. Structural analysis identified the structural features of CDAE, which displays a common (β/α)8-TIM barrel and an ordered Mn2+-binding architecture at the active center, which may explain the positive effects of Mn2+ on the activity and stability of CDAE. Furthermore, comparison of CDAE and other KEase structures revealed several structural differences, highlighting the remarkable differences in enzyme–substrate binding at the O4, O5 and O6 sites of the bound substrate, which are mainly induced by distinct hydrophobic pockets in the active center. The shape and hydrophobicity of this pocket appear to produce the differences in specificity and affinity for substrates among KEase family enzymes. Exploration of the crystal structure of CDAE provides a better understanding of its structure–function relationship, which might provide a basis for molecular modification of CDAE and further provides a reference for other KEases.

Expression and characterization of thermostable D-allulose 3-epimerase from Arthrobacter psychrolactophilus (Ap DAEase) with potential catalytic activity for bioconversion of D-allulose from d-fructose

A novel D-allulose 3-epimerase (DAEase) from Arthrobacter psychrolactophilus (Ap DAEase) was first characterized in this study. The enzyme catalyzes the epimerization of d-fructose into a functional rare sugar, D-allulose. Ap DAEase was the first record of DAEase identified as a homotrimer with the molecular weight of its subunit at approximately 34 kDa. It had an optimum activity at pH 8.5 and 70 °C in the presence of 1 mM Mg²⁺. Ap DAEase was found to be an excellent thermostable enzyme. The half-life value at 70 °C was 128.4 min. The k_cat and catalytic efficiency of the enzyme toward d-fructose were 2920.00 s^-1 and 3.953 mM^-1 s^-1, respectively. To the best of our knowledge, Ap DAEase possesses the highest k_cat among the previously reported DAEases. The conversion ratio of 500 and 100 mg L^-1d-fructose to D-allulose was approximately 27 % in 15 and 90 min, respectively. These research findings suggest that Ap DAEase is a promising candidate for the industrial production of D-allulose.

Computer-Aided Targeted Mutagenesis of Thermoclostridium caenicola d-Allulose 3-Epimerase for Improved Thermostability

d-Allulose 3-epimerase (DAEase) is a key enzyme in d-allulose bioproduction. DAEase from Thermoclostridium caenicola suffers from poor thermostability, hampering its large-scale applications in industry. In this study, mutants A70P, G107P, F155Y, and D162T with increased melting point temperature (T_m) were obtained by targeted mutagenesis based on the calculation of the free energy of folding. The optimal single-point mutant G107P showed 11.08 h, 5, and 5.70 °C increases in the values of half-life (t_1/2) at 60 °C, the optimum temperature (T_opt), and T_m, respectively. Beneficial mutations were combined by ordered recombination mutagenesis, and the combinational mutant Var3 (G107P/F155Y/D162T/A70P) was generated with ΔT_opt of 10 °C and ΔT_m of 12.25 °C. Its t_1/2 value at 65 °C was more than 140 times higher than that of the wild-type enzyme. Molecular dynamics simulations and homology modeling analysis indicated that the enhanced overall rigidity, increased hydrogen bonds between subunits, and redistributed surface electrostatic charges might be responsible for the improved thermostability of the mutant Var3.

D-allulose, a versatile rare sugar: recent biotechnological advances and challenges

D-Allulose is the C-3 epimer of D-fructose, and widely regarded as a promising substitute for sucrose. It's an excellent low-calorie sweetener, with 70% sweetness of sucrose, 0.4 kcal/g dietary energy, and special physiological functions. It has been approved as GRAS by the U.S. Food and Drug Administration, and is allowed to be excluded from total and added sugar counts on the food labels. Therefore, D-allulose gradually attracts more public attention. Owing to scarcity in nature, the bioproduction of D-allulose by using ketose 3-epimerase (KEase) has become the research hotspot. Herein, we give a summary of the physicochemical properties, physiological function, applications, and the chemical and biochemical synthesis methods of D-allulose. In addition, the recent progress in the D-allulose bioproduction using KEases, and the possible solutions for existing challenges in the D-allulose industrial production are comprehensively discussed, focusing on the molecular modification, immobilization, food-grade expression, utilizing low-cost biomass as feedstock, overcoming thermodynamic limitation, as well as the downstream separation and purification. Finally, Prospects for further development are also proposed.

Biochemical identification of a hyperthermostable l-ribulose 3-epimerase from Labedella endophytica and its application for d-allulose bioconversion

Currently, low sugar and low energy have become an important trend in the food industries. Therefore, the bioconversion of the functional low-calorie rare sugars attracts more and more attention. l-Ribulose 3-epimerase (LREase) belongs to the ketose 3-epimerase (KEase) family, which could not only efficiently catalyze the reversible C-3 epimerization between l-ribulose and l-xylulose but also between d-fructose and d-allulose. In this paper, a hyperthermostable LREase from Labedella endophytica was identified and characterized. It exhibited maximum catalytic activity at pH 6.0 and 80 °C with 1 mM Ni²⁺. In the presence of Co²⁺, the t_1/2 values at 60, 65, and 70 °C were 37.7, 9.0, and 4.6 h, respectively, and T_m value was 80.9 °C. From 500 g/L d-fructose, it could produce 154.2 g/L d-allulose with a conversion rate of 30.8% in 10 h. In view of its strong thermostability and high catalytic efficiency, L. endophytica LREase might be a good potential alternative for d-allulose industrial production.

Research Advances of d-allulose: An Overview of Physiological Functions, Enzymatic Biotransformation Technologies, and Production Processes

d-allulose has a significant application value as a sugar substitute, not only as a food ingredient and dietary supplement, but also with various physiological functions, such as improving insulin resistance, anti-obesity, and regulating glucolipid metabolism. Over the decades, the physiological functions of d-allulose and the corresponding mechanisms have been studied deeply, and this product has been applied to various foods to enhance food quality and prolong shelf life. In recent years, biotransformation technologies for the production of d-allulose using enzymatic approaches have gained more attention. However, there are few comprehensive reviews on this topic. This review focuses on the recent research advances of d-allulose, including (1) the physiological functions of d-allulose; (2) the major enzyme families used for the biotransformation of d-allulose and their microbial origins; (3) phylogenetic and structural characterization of d-allulose 3-epimerases, and the directed evolution methods for the enzymes; (4) heterologous expression of d-allulose ketose 3-epimerases and biotransformation techniques for d-allulose; and (5) production processes for biotransformation of d-allulose based on the characterized enzymes. Furthermore, the future trends on biosynthesis and applications of d-allulose in food and health industries are discussed and evaluated in this review.