Hidden Reaction: Mesophilic Cellobiose 2-Epimerases Produce Lactulose

High-efficiency secretion expression of cellobiose 2-epimerase in Escherichia coli and its applications

Cellobiose 2-epimerase (CE) plays a crucial role in catalyzing the conversion of lactose. In this study, the N-terminal 20 amino acids of Lactobacillus amylovorus feruloyl esterase (N20) were employed as a signal peptide and fused with the CE gene from Caldicellulosiruptor bescii for recombinant expression. Following ligation with the pET-22b(+) vector, Escherichia coli BL21 (DE3) was transformed. SDS-PAGE analysis confirmed the extracellular secretion of the CE following fusion with the signal peptide. Following fermentation optimization to maximize extracellular protein secretion, the optimal conditions were identified as a 2 × YT medium, supplemented with 0.8 mM IPTG, 0.1 mM ferrous ion (Fe2+), and 25 mM glycine after a 2.5 h induction, with incubation at 37 °C and 200 rpm for 36 h. The CE was purified using ammonium sulfate precipitation at 60 % saturation, yielding 1529.61 mg of enzyme protein per liter of fermentation broth, with a specific activity of 19.25 U/mg. A lactose substrate at 40 % concentration was employed, with varying enzyme concentrations (0.3825 g/L, 0.765 g/L, 1.1475 g/L, and 1.53 g/L) and reaction times (3 h, 6 h, 9 h, 12 h, and 24 h). After reaction, high-performance liquid chromatography (HPLC) was used for analysis, determining that an enzyme concentration of 1.53 g/L reacting with the lactose substrate for 24 h achieved the highest lactulose conversion rate at 56 %. This constitutes the first study on the direct extracellular secretion of CE, laying the groundwork for its production and application.

Advances and prospects on production of lactulose and epilactose by cellobiose 2-epimerases: A review

Lactulose and epilactose are nondigestible disaccharides with a wide range of applications in clinical medicine, nutrition, and the food industry due to their health-benefiting properties. Their chemical synthesis typically involves stringent catalytic conditions and intricate reaction procedures, resulting in elevated production costs and challenges in product separation. Cellobiose 2-epimerases (CEs) facilitate the isomerization and epimerization of lactose to produce lactulose and epilactose directly, without the need for co-substrates. This enzymatic process offers advantages such as mild reaction conditions, straightforward operation, high conversion efficiency, and reduced by-product formation. Recently, numerous CE genes have been identified and characterized, with their enzymatic properties undergoing extensive analysis. This review consolidates information on the properties of CEs from various sources and examines their catalytic mechanisms based on crystal structure data. Additionally, the current research progress in the enzymatic synthesis of lactulose and epilactose is comprehensively reviewed. The future direction of CE research is discussed, highlighting the potential for large-scale production of lactulose and epilactose through environmentally sustainable enzymatic methods.

Loop engineering of cellobiose 2-epimerase from Dictyoglomus thermophilum for efficient synthesis of lactulose

Lactulose holds broad application due to its unique pharmaceutical and prebiotic properties. Cellobiose 2-epimerase (CE) efficiently catalyzes the production of lactulose, offering an eco-friendly biosynthetic alternative. However, its relatively low isomerization activity hampers widespread application in the manufacture of lactulose. In this study, we selected DtCE sourced from Dictyoglomus thermophilum and successfully generated mutants M4 and M5 through an innovative loop engineering process that integrates computer-aided design with directed evolution. Remarkably, the isomerization activities of the mutants M4 and M5 increased by 46.5 % and 81.8 %, respectively, marking a significant improvement compared to the wild-type. Conversely, their epimerization activities underwent a dramatic decline, dropping by 80.0 % and 50.0 %, respectively. Therefore, these mutants demonstrated considerable superiority in the synthesis of lactulose. Moreover, molecular dynamics simulations showed that modifications of the flexible loop affected protonation, enhancing isomerization selectivity. This study underscores the precision and efficacy of our engineering approach in customizing DtCE's properties to meet specific needs, while concurrently establishing a technical foundation for industrial-scale biosynthetic production of lactulose.

Computer-aided mining of a psychrophilic cellobiose 2-epimerase from the Qinghai-Tibet Plateau gene catalogue

Cellobiose 2-epimerase (CE) catalyzes the conversion of the lactose into its high-value derivatives, epilactose and lactulose, which has great prospects in food applications. In this study, CE sequences from the Qinghai-Tibet Plateau gene catalogue, we screened these for structural flexibility through molecular dynamics simulation to identify potential psychrophilic CE candidates. One such psychrophilic CE we termed psyCE demonstrated exceptional epimerization activity, achieving an optimum activity of 122.2 ± 1.6 U/mg. Its kinetic parameters (Kcat and Km) for epimerization activity were 219.9 ± 5.6 s-1 and 261.9 ± 18.1 mM, respectively, representing the highest Kcat recorded among known cold-active CEs. Notably, this is the first report of a psychrophilic CE. The psyCE can effectively produce epilactose at 8 °C, converting 20.3 % of 200 mM lactose into epilactose within four hours. These findings suggest that psyCE is highly suitable for cryogenic food processing, and glaciers may serve as a valuable repository of psychrophilic enzymes.

Engineering Bacillus subtilis for highly efficient production of functional disaccharide lactulose from lactose

Bioconversion of lactose to functional lactose derivatives attracts increasing attention. Lactulose is an important high-value lactose derivative, which has been widely used in pharmaceutical, nutraceutical, and food industries. Lactulose can be enzymatically produced from lactose by cellobiose 2-epimerase (CEase). Several studies have already focused on the food-grade expression of CEase, but they are all aimed at the biosynthesis of epilactose. Herein, we reported for the first time the biosynthesis of lactulose using the recombinant food-grade Bacillus subtilis. Lactulose biosynthesis was optimized by varying lactulose-producing CEases and expression vectors. Caldicellulosiruptor saccharolyticus CEase and pP43NMK were determined to be the optimal CEase and expression vector. Fine-tuning of CEase expression was investigated by screening a beneficial N-terminal coding sequence. After fed-batch cultivation, the highest fermentation isomerization activity reached 11.6 U/mL. Lactulose was successfully produced by the broth of the engineered B. subtilis with a yield of 52.1 %.

A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction

Promiscuous enzymes play a crucial role in organism survival and new reaction mining. However, comprehensive mapping of the catalytic and regulatory mechanisms hasn't been well studied due to the characteristic complexity. The cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) with complex epimerization and isomerization was chosen to comprehensively investigate the promiscuous mechanisms. Here, the catalytic frame of ring-opening, cis-enediol mediated catalysis and ring-closing was firstly determined. To map the full view of promiscuous CE, the structure of CsCE complex with the isomerized product glucopyranosyl-β1,4-fructose was determined. Combined with computational calculation, the promiscuity was proved a precise cooperation of the double subsites, loop rearrangement, and intermediate swaying. The flexible loop was like a gear, whose structural reshaping regulates the sway of the intermediates between the two subsites of H377-H188 and H377-H247, and thus regulates the catalytic directions. The different protonated states of cis-enediol intermediate catalyzed by H188 were the key point for the catalysis. The promiscuous enzyme tends to utilize all elements at hand to carry out the promiscuous functions.

Isomerase and epimerase: overview and practical application in production of functional sugars

The biosynthesis of functional sugars has gained significant attention due to their potential health benefits and increasing demand in the food industry. Enzymatic synthesis has emerged as a promising approach, offering high catalytic efficiency, chemoselectivity, and stereoselectivity. However, challenges such as poor thermostability, low catalytic efficiency, and food safety concerns have limited the commercial production of functional sugars. Protein engineering, including directed evolution and rational design, has shown promise in overcoming these barriers and improving biocatalysts for large-scale production. Furthermore, enzyme immobilization has proven effective in reducing costs and facilitating the production of functional sugars. To ensure food safety, the use of food-grade expression systems has been explored. However, downstream technologies, including separation, purification, and crystallization, still pose challenges in terms of efficiency and cost-effectiveness. Addressing these challenges is crucial to optimize the overall production process. Despite the obstacles, the future outlook for functional sugars is promising, driven by increasing awareness of their health benefits and continuous technological advancements. With further research and technological breakthroughs, industrial-scale production of functional sugars through biosynthesis will become a reality, leading to their widespread incorporation in various industries and products.

Integrated Whole-Cell Biocatalysis for Trehalose Production from Maltose Using Permeabilized Pseudomonas monteilii Cells and Bioremoval of Byproduct

Trehalose is a non-conventional sugar with potent applications in the food, healthcare and biopharma industries. In this study, trehalose was synthesized from maltose using whole-cell Pseudomonas monteilii TBRC 1196 producing trehalose synthase (TreS) as the biocatalyst. The reaction condition was optimized using 1% Triton X-100 permeabilized cells. According to our central composite design (CCD) experiment, the optimal process was achieved at 35°C and pH 8.0 for 24 h, resulting in the maximum trehalose yield of 51.60 g/g after 12 h using an initial cell loading of 94 g/l. Scale-up production in a lab-scale bioreactor led to the final trehalose concentration of 51.91 g/l with a yield of 51.60 g/g and productivity of 4.37 g/l/h together with 8.24 g/l glucose as a byproduct. A one-pot process integrating trehalose production and byproduct bioremoval showed 53.35% trehalose yield from 107.4 g/l after 15 h by permeabilized P. moteilii cells. The residual maltose and glucose were subsequently removed by Saccharomyces cerevisiae TBRC 12153, resulting in trehalose recovery of 99.23% with 24.85 g/l ethanol obtained as a co-product. The present work provides an integrated alternative process for trehalose production from maltose syrup in bio-industry.

Identification of a thermostable cellobiose 2-epimerase from Caldicellulosiruptor sp. Rt8.B8 and production of epilactose using Bacillus subtilis

BACKGROUND

Epilactose, a potential prebiotics, was derived from lactose through enzymatic catalysis. However, production and purification of epilactose are currently difficult due to powerless enzymes and inefficient downstream processing steps.

RESULTS

The encoding gene of cellobiose 2-epimerase (CE) from Caldicellulosiruptor sp. Rt8.B8 was cloned and expressed in Escherichia coli BL21(DE3). The enzyme was purified and it was suitable for industrial production of epilactose from lactose without by-products, because of high k_cat (197.6 s^-1 ) and preferable thermostability. The Rt8-CE gene was further expressed in the Bacillus subtilis strain. We successfully produced epilactose from 700 g L^-1 lactose in 30.4% yield by using the recombinant Bacillus subtilis whole cells. By screening of a β-galactosidase from Bacillus stearothermophilus (BsGal), a process for separating epilactose and lactose was established, which showed a purity of over 95% in a total yield of 69.2%. In addition, a mixed rare sugar syrup composed of epilactose and d-tagatose was successfully produced from lactose through the co-expression of l-arabinose isomerase and β-galactosidase.

CONCLUSION

Our study shed light on the efficient production of epilactose using a food-grade host expressing a novel CE enzyme. Moreover, an efficient and low-cost process was attempted to obtain high purity epilactose. In order to improve the utilization of raw materials, the production process of mixed syrup containing epilactose and d-tagatose with prebiotic properties produced from lactose was also established for the first time. © 2021 Society of Chemical Industry.

Screening, Cloning, Expression and Characterization of New Alkaline Trehalose Synthase from Pseudomonas monteilii and Its Application for Trehalose Production

Trehalose is a non-reducing disaccharide in increasing demand for applications in food, nutraceutical, and pharmaceutical industries. Single-step trehalose production by trehalose synthase (TreS) using maltose as a starting material is a promising alternative process for industrial application due to its simplicity and cost advantage. Pseudomonas monteilii TBRC 1196 was identified using the developed screening method as a potent strain for TreS production. The TreS gene from P. monteilii TBRC 1196 was first cloned and expressed in Escherichia coli. Purified recombinant trehalose synthase (PmTreS) had a molecular weight of 76 kDa and showed optimal pH and temperature at 9.0 and 40°C, respectively. The enzyme exhibited >90% residual activity under mesophilic condition under a broad pH range of 7-10 for 6 h. Maximum trehalose yield by PmTreS was 68.1% with low yield of glucose (4%) as a byproduct under optimal conditions, equivalent to productivity of 4.5 g/l/h using enzyme loading of 2 mg/g substrate and high concentration maltose solution (100 g/l) in a lab-scale bioreactor. The enzyme represents a potent biocatalyst for energy-saving trehalose production with potential for inhibiting microbial contamination by alkaline condition.

Molecular Characterization of a Mesophilic Cellobiose 2-Epimerase That Maintains a High Catalytic Efficiency at Low Temperatures

Cellobiose 2-epimerase (CE) can catalyze bioconversion of lactose to its prebiotic derivative epilactose. The catalytic property of a novel CE from Treponema brennaborense (Trbr-CE) was investigated. Trbr-CE showed the highest catalytic efficiency of epimerization toward lactose among all of the previously reported CEs. This enzyme's specific activity could reach as high as 208.5 ± 5.3 U/mg at its optimum temperature, which is 45 °C. More importantly, this enzyme demonstrated a considerably high activity at low temperatures, suggesting Trbr-CE as a promising enzyme for industrial low-temperature production of epilactose. This structurally flexible enzyme exhibited a comparatively high binding affinity toward substrates, which was confirmed by both experimental verification and computational analysis. Molecular dynamics (MD) simulations and binding free energy calculations were applied to provide insights into molecular recognition upon temperature changes. Compared with thermophilic CEs, Trbr-CE presents a more negative enthalpy change and a higher entropy change when the temperature drops.

Enhancement of the Isomerization Activity and Thermostability of Cellobiose 2-Epimerase from Caldicellulosiruptor saccharolyticus by Exchange of a Flexible Loop

Cellobiose 2-epimerase (CE) offers a promising enzymatic approach to produce lactulose. However, its application is limited by the unsatisfactory isomerization activity and thermostability. Our study attempted to optimize the catalytic performances of CEs by flexible loop exchange, for which four mutants were constructed using CsCE (CE from Caldicellulosiruptor saccharolyticus) as a template. As a result, all mutants maintained the same catalytic directions as the templates. Mutant RmC displayed a 2.2- and 1.34-fold increase in the isomerization activity and catalytic efficiency, respectively. According to the results of molecular dynamics (MD) simulations, it was revealed that the loop exchange in RmC enlarged the entrance of the active site for substrate binding and benefited proton transfer involved in the isomerization process. Besides, the t_1/2 of mutant StC at 70 °C was increased from 29.07 to 38.29 h, owing to the abundance of rigid residues (proline) within the flexible loop of StC. Our work demonstrated that the isomerization activity and thermostability of CEs were closely related to the flexible loop surrounding the active site, which provides a new perspective to engineer CEs for higher lactulose production.

Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis

Cellobiose 2-epimerase (CE) is commonly recognized as an epimerase as most CEs mainly exhibit an epimerization activity towards disaccharides. In recent years, several CEs have been found to possess bifunctional epimerization and isomerization activities. They can convert lactose into lactulose, a high-value disaccharide that is widely used in the food and pharmaceutical industries. However, the factors that determine the catalytic direction in CEs are still not clear. In this study, the crystal structures of three newly discovered CEs, CsCE (a bifunctional CE from Caldicellulosiruptor saccharolyticus), StCE (a bifunctional CE from Spirochaeta thermophila DSM 6578) and BtCE (a monofunctional CE from Bacillus thermoamylovorans B4166), were determined at 1.54, 2.05 and 1.80 Å resolution, respectively, in order to search for structural clues to their monofunctional/bifunctional properties. A comparative analysis of the hydrogen-bond networks in the active pockets of diverse CEs, YihS and mannose isomerase suggested that the histidine corresponding to His188 in CsCE is uniquely required to catalyse isomerization. By alignment of the apo and ligand-bound structures of diverse CEs, it was found that bifunctional CEs tend to have more flexible loops and a larger entrance around the active site, and that the flexible loop 148-181 in CsCE displays obvious conformational changes during ligand binding. It was speculated that the reconstructed molecular interactions of the flexible loop during ligand binding helped to motivate the ligands to stretch in a manner beneficial for isomerization. Further site-directed mutagenesis analysis of the flexible loop in CsCE indicated that the residue composition of the flexible loop did not greatly impact epimerization but affects isomerization. In particular, V177D and I178D mutants showed a 50% and 80% increase in isomerization activity over the wild type. This study provides new information about the structural characteristics involved in the catalytic properties of CEs, which can be used to guide future molecular modifications.

Computer-aided search for a cold-active cellobiose 2-epimerase

Cellobiose 2-epimerase (CE) is a promising industrial enzyme that can catalyze bioconversion of lactose to its high-value derivatives, namely epilactose and lactulose. A need exists in the dairy industry to catalyze lactose bioconversions at low temperatures to avoid microbial growth. We focused on the discovery of cold-active CE in this study. A genome mining method based on computational prediction was used to screen the potential genes encoding cold-active enzymes. The CE-encoding gene from Roseburia intestinalis, with a predicted high structural flexibility, was expressed heterologously in Escherichia coli. The catalytic property of the recombinant enzyme was extensively studied. The optimum temperature and pH of the enzyme were 45°C and 7.0, respectively. The specific activity of this enzyme to catalyze conversion of lactose to epilactose was measured to be 77.3 ± 1.6 U/mg. The kinetic parameters, including turnover number (k_cat), Michaelis constant (K_m), and catalytic efficiency (k_cat/K_m) using lactose as a substrate were 117.0 ± 7.7 s^-1, 429.9 ± 57.3 mM, and 0.27 mM^-1s^-1, respectively. In situ production of epilactose was carried out at 8°C: 20.9% of 68.4 g/L lactose was converted into epilactose in 4 h using 0.02 mg/mL (1.5 U/mL, measured at 45°C) of recombinant enzyme. The enzyme discovered by this in silico method is suitable for low-temperature applications.

Simulation-guided enzyme discovery: A new microbial source of cellobiose 2-epimerase

Cellobiose 2-epimerase (CE) is a promising industrial enzyme that can be utilized in the dairy industry. More thermostable CEs from different microorganisms are still needed for a higher lactulose productivity. This study demonstrated the feasibility to use molecular dynamics (MD) simulation as the preliminary computational filter for thermostable enzymes screening. Sequence information of eleven uncharacterized CEs were chosen to be analyzed by MD simulations. The CE from Dictyoglomus thermophilum (Dith-CE) was determined experimentally to be one of the most thermostable CEs with the highest epimerization (160 ± 6.5 U mg^-1) and isomerization activities (3.52 ± 0.23 U mg^-1) among all the reported CEs. This enzyme shows the highest isomerization activity at 85 °C and pH 7.0. The kinetic parameters (k_cat and K_m) of isomerization activity of this CE are 3.98 ± 0.3 s^-1 and 235.2 ± 11.2 mM, respectively. These results suggest that the CE from Dith-CE is a promising lactulose-producing enzyme.

Preparation and Characterization of Sugar-Assisted Cross-Linked Enzyme Aggregates (CLEAs) of Recombinant Cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus ( CsCE)

High-efficiency lactulose-producing enzyme of Caldicellulosiruptor saccharolyticus cellobiose 2-epimerase (WT- CsCE) was immobilized in the form of cross-linked enzyme aggregates (CLEAs). Conditions for enzyme aggregation and cross-linking were optimized, and a sugar-assisted strategy with less damage to enzyme secondary structures was developed to improve the activity yield of CLEAs up to approximately 65%. The resulting CLEAs with multiple-layer network structures exhibited an enlarged optimal temperature range (70-80 °C) and maintained higher activity at 50-90 °C. Besides, CLEAs retained more than 95% of their initial activity after 10 successive batches at 60 °C, demonstrating superior reusability. Moreover, CLEAs displayed an equivalent or higher catalytic ability to free WT- CsCE in lactulose biosynthesis, and the final sugar ratios were similar, lactulose 58.8-61.7%, epilactose 9.3-10.2%, and lactose 27.8-30%, with a constant isomerization selectivity of 0.84-0.87 regardless of enzymes used and temperature applied. The proposed strategy is the first trial for enzymatic synthesis of lactulose catalyzed by CLEAs of WT- CsCE.

Rational modification of substrate binding site by structure-based engineering of a cellobiose 2-epimerase in Caldicellulosiruptor saccharolyticus

BACKGROUND

Lactulose, a synthetic disaccharide, has received increasing interest due to its role as a prebiotic, specifically proliferating Bifidobacilli and Lactobacilli and enhancing absorption of calcium and magnesium. The use of cellobiose 2-epimerase (CE) is considered an interesting alternative for industrial production of lactulose. CE reversibly converts D-glucose residues into D-mannose residues at the reducing end of unmodified β-1,4-linked oligosaccharides, including β-1,4-mannobiose, cellobiose, and lactose. Recently, a few CE 3D structure were reported, revealing mechanistic details. Using this information, we redesigned the substrate binding site of CE to extend its activity from epimerization to isomerization.

RESULTS

Using superimposition with 3 known CE structure models, we identified 2 residues (Tyr114, Asn184) that appeared to play an important role in binding epilactose. We modified these residues, which interact with C2 of the mannose moiety, to prevent epimerization to epilactose. We found a Y114E mutation led to increased release of a by-product, lactulose, at 65 °C, while its activity was low at 37 °C. Notably, this phenomenon was observed only at high temperature and more reliably when the substrate was increased. Using Y114E, isomerization of lactose to lactulose was investigated under optimized conditions, resulting in 86.9 g/l of lactulose and 4.6 g/l of epilactose for 2 h when 200 g/l of lactose was used.

CONCLUSION

These results showed that the Y114E mutation increased isomerization of lactose, while decreasing the epimerization of lactose. Thus, a subtle modification of the active site pocket could extend its native activity from epimerization to isomerization without significantly impairing substrate binding. While additional studies are required to scale this to an industrial process, we demonstrated the potential of engineering this enzyme based on structural analysis.