Thermostability enhancement of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus by site-directed mutagenesis

Production of lactulose from lactose using a novel cellobiose 2-epimerase from Clostridium disporicum

Lactulose is a semisynthetic nondigestive sugar derived from lactose, with wide applications in the food and pharmaceutical industries. Its biological production routes which use cellobiose 2-epimerase (C2E) as the key enzyme have attracted widespread attention. In this study, a set of C2Es from different sources were overexpressed in Escherichia coli to produce lactulose. We obtained a novel and highly efficient C2E from Clostridium disporicum (CDC2E) to synthesize lactulose from lactose. The effects of different heat treatment conditions, reaction pH, reaction temperature, and substrate concentrations were investigated. Under the optimum biotransformation conditions, the final concentration of lactulose was up to 1.45 M (496.3 g/L), with a lactose conversion rate of 72.5 %. This study provides a novel C2E for the biosynthesis of lactulose from low-cost lactose.

Rational Design of Loop Dynamics for a Barrel-Shaped Enzyme by Introducing Disulfide Bonds

Loop dynamics redesign is an important strategy to manipulate protein function. Cellobiose 2-epimerase (CE) and other members of its superfamily are widely used for diverse industrial applications. The structural feature of the loops connecting barrel helices contributes greatly to the differences in their functional characteristics. Inspired by the in-silico mutation with molecular dynamics (MD) simulation analysis, we propose a strategy for identifying disulfide bond mutation candidates based on the prediction of protein flexibility and residue-residue interaction. The most beneficial mutant with the newly introduced disulfide bond would simultaneously improve both its thermostability and its reaction propensity to the targeting isomerization product. The ratio of the isomerization/epimerization catalytic rate was improved from 4:103 to 9:22. MD simulation and binding free energy calculations were applied to provide insights into molecular recognition upon mutations. The comparative analysis of enzyme/substrate binding modes indicates that the altered catalytic reaction pathway is due to less efficient binding of the native product. The key residue responsible for the observed phenotype was identified by energy decomposition and was further confirmed by the mutation experiment. The rational design of the key loop region might be a promising strategy to alter the catalytic behavior of all (α/α)6-barrel-like proteins.

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 %.

Computer-aided design of novel cellobiose 2-epimerase for efficient synthesis of lactulose using lactose

Cellobiose 2-epimerase (CE) is ideally suited to synthesize lactulose from lactose, but the poor thermostability and catalytic efficiency restrict enzymatic application. Herein, a non-characterized CE originating from Caldicellulosiruptor morganii (CmCE) was discovered in the NCBI database. Then, a smart mutation library was constructed based on FoldX ΔΔG calculation and modeling structure analysis, from which a positive mutant D226G located within the α₈/α₉ loop exhibited longer half-lives at 65-75 °C as well as lower K_m and higher k_cat/K_m values compared with CmCE. Molecular modeling demonstrated that the improvement of D226G was largely attributed to the rigidification of the flexible loop, the compactness of the catalysis pocket and the increment of substrate-binding capability. Finally, the yield of synthesizing lactulose catalyzed by D226G reached 45.5%, higher than the 35.9% achieved with CmCE. The disclosed effect of the flexible loop on enzymatic stability and catalysis provides insight to redesign efficient CEs to biosynthesize lactulose.

Biochemical characteristics of point mutated Capra hircus lysosome α-mannosidase

Locoweeds, a type of poisonous weedare, are widely distributed throughout the world and have a significant impact on the development of herbivore animal husbandry. Swainsonine (SW), the main toxin in locoweeds, can competitively inhibit lysosomes α-mannosidase (LAM) in animal cells, resulting in α-mannosidosis. However, the specifics of the interaction between SW and LAM are still unclear. Here, we used molecular docking to predicte the interaction points between SW and LAM, built mutated lysosomes α-mannosidase (LAM^M), and analyzed its biochemical properties changes in presumption points. The Trp at the 28th position and the Tyr at the 599th position of the LAM were interaction point candidates, and the above two amino acids in Capra hircus LAM (chLAM), were successfully mutated to glycine by constructing recombinant yeast GS115/PIC9K- LAM^M. The results showed that the sensitivity of Capra hircus LAM^M (chLAM^M), to SW decreased significantly compared with wild-type LAM, the enzyme activity of LAM decreased approximately threefold, the optimum temperature of LAM^M decreased from 55°C to 50°C, the optimum pH value increased from 4.5 to 5.0, and the effects of Mn²⁺, Fe³⁺, Al³⁺, Co²⁺, Cr³⁺, and ethylenediaminetetraacetic acid (EDTA) on LAM enzyme activity before and after point mutation changed significantly. These findings help us better understanding the molecular mechanism of the interaction mechanism between SW and chLAM, and provide new reference for solving locoweeds poisoning.

Reshaping the Binding Pocket of Cellobiose 2-Epimerase for Improved Substrate Affinity and Isomerization Activity for Enabling Green Synthesis of Lactulose

Enzymatic isomerization of lactose into lactulose via cellobiose 2-epimerase (CE) could provide an eco-friendly route for the industrial production of lactulose, a valuable food prebiotic. However, poor substrate affinity for lactose and preference for epimerization over isomerization hinder this application. Previous studies on CE improvement have focused on random mutagenesis or active site rational design; little is known about the relationship between substrate binding and enzyme efficacy, which was hence the subject of this study. First, residues 372W and 308W were identified as key for disaccharide recognition in CEs based on crystal structure alignment of the N-acetyl-glucosamine 2-epimerase superfamily and site-directed mutation. This binding domain was then reshaped through site saturation mutagenesis, resulting in seven mutants with enhanced isomerization activity. The optimal mutant CsCE/Q371E had significantly enhanced substrate affinity (K_m, 269.65 mM vs K_m, 417.5 mM), reduced epimerization activity, and 3.3-fold increased isomerization activity over the original CsCE. Molecular dynamics simulation further revealed that substituting Gln-371 with Glu strengthened the hydrogen-bonding network and altered the active site-substrate interactions, increasing the substrate stability and shifting the catalytic direction. This study uncovered new information about the substrate binding region and its mechanisms and impact on CE catalytic performance, paving the way for potential commercial applications.

Lactulose production from lactose isomerization by chemo-catalysts and enzymes: Current status and future perspectives

Lactulose, a semisynthetic nondigestive disaccharide with versatile applications in the food and pharmaceutical industries, has received increasing interest due to its significant health-promoting effects. Currently, industrial lactulose production is exclusively carried out by chemical isomerization of lactose via the Lobry de Bruyn-Alberda van Ekenstein (LA) rearrangement, and much work has been directed toward improving the conversion efficiency in terms of lactulose yield and purity by using new chemo-catalysts and integrated catalytic-purification systems. Lactulose can also be produced by an enzymatic route offering a potentially greener alternative to chemo-catalysis with fewer side products. Compared to the controlled trans-galactosylation by β-galactosidase, directed isomerization of lactose with high isomerization efficiency catalyzed by the most efficient lactulose-producing enzyme, cellobiose 2-epimerase (CE), has gained much attention in recent decades. To further facilitate the industrial translation of CE-based lactulose biotransformation, numerous studies have been reported on improving biocatalytic performance through enzyme mediated molecular modification. This review summarizes recent developments in the chemical and enzymatic production of lactulose. Related catalytic mechanisms are also highlighted and described in detail. Emerging techniques that aimed at advancing lactulose production, such as the boronate affinity-based technique and molecular biological techniques, are reviewed. Finally, perspectives on challenges and opportunities in lactulose production and purification are also discussed.

Advances in Rational Protein Engineering toward Functional Architectures and Their Applications in Food Science

Protein biomolecules including enzymes, cagelike proteins, and specific peptides have been continuously exploited as functional biomaterials applied in catalysis, nutrient delivery, and food preservation in food-related areas. However, natural proteins usually function well in physiological conditions, not industrial conditions, or may possess undesirable physical and chemical properties. Currently, rational protein design as a valuable technology has attracted extensive attention for the rational engineering or fabrication of ideal protein biomaterials with novel properties and functionality. This article starts with the underlying knowledge of protein folding and assembly and is followed by the introduction of the principles and strategies for rational protein design. Basic strategies for rational protein engineering involving experienced protein tailoring, computational prediction, computation redesign, and de novo protein design are summarized. Then, we focus on the recent progress of rational protein engineering or design in the application of food science, and a comprehensive summary ranging from enzyme manufacturing to cagelike protein nanocarriers engineering and antimicrobial peptides preparation is given. Overall, this review highlights the importance of rational protein engineering in food biomaterial preparation which could be beneficial for food science.

Trends in lactose-derived bioactives: synthesis and purification

Lactose obtained from cheese whey is a low value commodity despite its great potential as raw material for the production of bioactive compounds. Among them, prebiotics stand out as valuable ingredients to be added to food matrices to build up functional foods, which currently represent the most active sector within the food industry. Functional foods market has been growing steadily in the recent decades along with the increasing awareness of the World population about healthy nutrition, and this is having a strong impact on lactose-derived bioactives. Most of them are produced by enzyme biocatalysis because of molecular precision and environmental sustainability considerations. The current status and outlook of the production of lactose-derived bioactive compounds is presented with special emphasis on downstream operations which are critical because of the rather modest lactose conversion and product yields that are attainable. Even though some of these products have already an established market, there are still several challenges referring to the need of developing better catalysts and more cost-effective downstream operations for delivering high quality products at affordable prices. This technological push is expected to broaden the spectrum of lactose-derived bioactive compounds to be produced at industrial scale in the near future.

Graphical abstract

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.

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.

What regulates the catalytic activities in AGE catalysis? An answer from quantum mechanics/molecular mechanics simulations

The AGE superfamily (AGEs) is made up of kinds of isomerase which are very important both physiologically and industrially. One of the most intriguing aspects of AGEs has to do with the mechanism that regulates their activities in single conserved active pocket. In order to clarify the relationship among single conserved active pocket and two activities in AGEs, results for the epimerization activity catalyzed by RaCE and the isomerization activity catalyzed by SeYihS were obtained by using QM/MM umbrella sampling simulations and 2D-FES calculations. Our results show that both of them have similar enzyme-substrate combination mode for inner pyranose ring in single conserved active pocket even though they have different substrate specificity. This means that the pathways of ring opening catalyzed by them are similar. However, one non-conserved residue (Leu183 in RaCE, Met175 in SeYihS) in the active site, which has different steric hindrance, causes a small but effective change in the direction of ring opening in stage 1. And then this change will induce a fundamentally different catalytic activity for RaCE and SeYihS in stage 2. Our results give a novel viewpoint about the regulatory mechanism between CE and YihS in AGEs, and may be helpful for further experiments of rational enzyme design based on the (α/α)₆-barrel basic scaffold.

Characterisation of a novel cellobiose 2-epimerase from thermophilic Caldicellulosiruptor obsidiansis for lactulose production

BACKGROUND

Lactulose, a bioactive lactose derivative, has been widely used in food and pharmaceutical industries. Isomerisation of lactose to lactulose by cellobiose 2-epimerase (CE) has recently attracted increasing attention, since CE produces lactulose with high yield from lactose as a single substrate. In this study, a new lactulose-producing CE from Caldicellulosiruptor obsidiansis was extensively characterised.

RESULTS

The recombinant enzyme exhibited maximal activity at pH 7.5 and 70 °C. It displayed high thermostability with T_m of 86.7 °C. The half-life was calculated to be 8.1, 2.8 and 0.6 h at 75, 80, and 85 °C, respectively. When lactose was used as substrate, epilactose was rapidly produced in a short period, and afterwards both epilactose and lactose were steadily isomerised to lactulose, with a final ratio of 35:11:54 for lactose:epilactose:lactulose. When the reverse reaction was investigated using lactulose as substrate, both lactose and epilactose appeared to be steadily produced from the start.

CONCLUSION

The recombinant CE showed both epimerisation and isomerisation activities against lactose, making it an alternative promising biocatalyst candidate for lactulose production. © 2016 Society of Chemical Industry.

Improvingthecatalytic properties and stability of immobilized γ-glutamyltranspeptidase by post-immobilization with PharmalyteMT 8-10.5

γ-Glutamyltranspeptidase (GGT) is a dimeric protein that specifically catalyzes the transfer of γ-glutamyl in the optimum pH range of 8.5-9.0, but has poor in vitro stability under the alkaline conditions. In the present work, GGT was immobilized on a mesoporoustitania oxide whisker (MTWs) carrier to afford MTWs-GGT that was further modified with Pharmalyte^MT (Phar) 8.0-10.5 to yield MTWs-GGT-Phar. Phar absorbed on MTWs-GGT to form a buffering layer with an isoelectric point of ∼9.2 that isolated the immobilized enzyme from the liquid bulk and significantly in proved the pH tolerance and stability of the immobilized GGT. The MTWs-GGT-Phar exhibited a stable enzyme activity in the pH range of 6.0-11.0 and an optimum temperature 10°C higher than GGT. Its pH stability at pH 11.0 and thermal stability at 50°C were respectively 23.7 times and 19.4 times higher than those of GGT. In addition, the affinity constant of MTWs-GGT-Phar towards GpNA (K_m) was 0.597mM, slightly lower than that of free GGT, indicating that Phar had a protective effect on the structure of GGT.

Hidden Reaction: Mesophilic Cellobiose 2-Epimerases Produce Lactulose

Lactulose (4-O-β-d-galactopyranosyl-d-fructofuranose) is a prebiotic sugar derived from the milk sugar lactose (4-O-β-d-galactopyranosyl-d-glucopyranose). In our study we observed for the first time that known cellobiose 2-epimerases (CEs; EC 5.1.3.11) from mesophilic microorganisms were generally able to catalyze the isomerization reaction of lactose into lactulose. Commonly, CEs catalyze the C2-epimerization of d-glucose and d-mannose moieties at the reducing end of β-1,4-glycosidic-linked oligosaccharides. Thus, epilactose (4-O-β-d-galactopyranosyl-d-mannopyranose) is formed with lactose as substrate. So far, only four CEs, exclusively from thermophilic microorganisms, have been reported to additionally catalyze the isomerization reaction of lactose into lactulose. The specific isomerization activity of the seven CEs in this study ranged between 8.7 ± 0.1 and 1300 ± 37 pkat/mg. The results indicate that very likely all CEs are able to catalyze both the epimerization as well as the isomerization reaction, whereby the latter is performed at a comparatively much lower reaction rate.