Preparation of linear maltodextrins using a hyperthermophilic amylopullulanase with cyclodextrin- and starch-hydrolysing activities

Simultaneously improving the activity and thermostability of hyperthermophillic pullulanase by modifying the active-site tunnel and surface lysine

Pullulanases are important starch-debranching enzymes that mainly hydrolyze the α-1,6-glycosidic linkages in pullulan, starch, and oligosaccharides. Nevertheless, their practical applications are constrained because of their poor activity and low thermostability. Moreover, the trade-off between activity and thermostability makes it challenging to simultaneously improve them. In this study, an engineered pullulanase was developed through reshaping the active-site tunnel and engineering the surface lysine residues using the pullulanase from Pyrococcus yayanosii CH1 (PulPY2). The specific activity of the engineered pullulanase was increased 3.1-fold, and thermostability was enhanced 1.8-fold. Moreover, the engineered pullulanase exhibited 11.4-fold improvement in catalytic efficiency (kcat/Km). Molecular dynamics simulations demonstrated an anti-correlated movement around the entrance of active-site tunnel and stronger interactions between the surface residues in the engineered pullulanase, which would be beneficial to the activity and thermostability improvement, respectively. The strategies used in this study and dynamic evidence for insight into enzyme performance improvement may provide guidance for the activity and thermostability engineering of other enzymes.

Progress in cyclodextrins as important molecules regulating catalytic processes of glycoside hydrolases

Cyclodextrins (CDs) are important starch derivatives and commonly comprise α-, β-, and γ-CDs. Their hydrophilic surface and hydrophobic inner cavity enable regulation of enzyme catalysis through direct or indirect interactions. Clarifying interactions between CDs and enzyme is of great value for enzyme screening, mechanism exploration, regulation of catalysis, and applications. We summarize the interactions between CDs and glycoside hydrolases (GHs) according to two aspects: 1) CD as products, substrates, inhibitors and activators of enzymes, directly affecting the reaction process; 2) CDs indirectly affecting the enzymatic reaction by solubilizing substrates, relieving substrate/product inhibition, increasing recombinant enzyme production and storage stability, isolating and purifying enzymes, and serving as ligands in crystal structure to identify functional amino acid residues. Additionally, CD enzyme mimetics are developed and used as catalysts in traditional artificial enzymes as well as nanozymes, making the application of CDs no longer limited to GHs. This review concerns the regulation of GHs catalysis by CDs, and gives insights into research on interactions between enzymes and ligands.

Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications

(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.

Improved Stability and Hydrolysates of Hyperthermophilic GH57 Type II Pullulanase from the Deep-Sea Archaeon Thermococcus siculi HJ21 by Truncation

Pullulanase (EC 3.2.1.41) belongs to the amylase family and is often used alone or in combination with other amylases in the industrial production of starch-based products. This enzyme is often required in industrial production because of its better stability. We here truncated the pullulanase gene from the deep-sea hydrothermal anaerobic archaeon Thermococcus siculi HJ21 and obtained Pul-HJΔ782, which is a member of the α-amylase family GH57. The results revealed that the optimum temperature for Pul-HJΔ782 was 100 °C, and its thermostability at 100 °C improved after truncation. Less than 15% of its enzyme activity was lost after 1 h of incubation at 100 °C, and 57% activity remained after 5 h of treatment. Truncation significantly improved the overall pH tolerance range of Pul-HJΔ782, and its stability in the pH range 4–8 was over 80% relative activity from an average of 60%. The sequence and structural model of Pul-HJΔ782 was analyzed, and its instability index was reduced significantly. Furthermore, the hydrolysates of the truncated and wild-type pullulanase were analyzed, and the enzymatic digestion efficiency of the truncated Pul-HJΔ782 was higher.

Modulating the pH profile of the pullulanase from Pyrococcus yayanosii CH1 by synergistically engineering the active center and surface

A preferable pullulanase with high thermostability and catalytic activity at pH 4.5-5 is desired to match with glucoamylase in the starch-saccharification process. However, most of them exhibit low activity under such low pH conditions. Here, the optimal pH of the hyperthermostable pullulanase from Pyrococcus yayanosii (Pul_PY2) was successfully shifted from 6.4 to 5 with a 2-fold increase in the specific activity based on synergistic engineering of the active center and surface. Synergistic engineering was performed by introducing histidine within 6 Å of the active sites, and by enhancing negative charges on the enzymatic surface. Two single-site mutants of Pul_PY2-Q13H and Pul_PY2-I25E with higher hydrolytic activity were obtained, the optimal pH of which was shifted to pH 5 and 5.4, respectively; the combined mutant Pul_PY2-Q13H/I25E exhibited the optimal pH of 5, 3.2-fold increasing catalytic efficiency at pH 5, and high thermostability compared to Pul_PY2. These results not only obtained an applicable pullulanase for industrial application, but also provided a strategy for shifting the optimal pH of the enzyme based on synergistic engineering of the active center and surface.

Characterization of a novel type of glycogen-degrading amylopullulanase from Lactobacillus crispatus

Glycogen is one of the major carbohydrates utilized by the human vaginal microbiota, which is commonly dominated by Lactobacillus, especially L. crispatus. An in silico analysis predicted that a type I pullulanase was involved in glycogen degradation in L. crispatus. The biochemical and genetic properties of the pullulanase still need to be determined. Here, we de novo identified the glycogen (Glg)-utilization enzyme (named GlgU) from L. crispatus through a biochemical assay. GlgU was optimally active at acidic pH, approximately 4.0 ~ 4.5, and was able to hydrolyze glycogen into low-molecular-weight malto-oligosaccharides. Actually, GlgU was a type II pullulanase (amylopullulanase) with just one catalytic domain that possessed substrate specificity toward both α-1,4 and α-1,6-glucosidic bonds. Phylogenetically, GlgU was obviously divergent from the known amylases and pullulanases (including amylopullulanases) in lactobacilli. In addition, we confirmed the catalytic activity of glgU in a nonglycogen-utilizing lactobacilli strain, demonstrating the essential role of glgU in glycogen metabolism. Overall, this study characterized a novel type of amylopullulanases, contributing to the knowledge of the glycogen utilization mechanism of the dominant species of human vaginal microbiota. KEY POINTS: • GlgU was a type II pullulanase, not a type I pullulanase predicted before. • GlgU was able to completely hydrolyze glycogen into malto-oligosaccharides. • GlgU played a key role in the metabolism of extracellular glycogen.

Microbial starch debranching enzymes: Developments and applications

Starch debranching enzymes (SDBEs) hydrolyze the α-1,6 glycosidic bonds in polysaccharides such as starch, amylopectin, pullulan and glycogen. SDBEs are also important enzymes for the preparation of sugar syrup, resistant starch and cyclodextrin. As the synergistic catalysis of SDBEs and other starch-acting hydrolases can effectively improve the raw material utilization and production efficiency during starch processing steps such as saccharification and modification, they have attracted substantial research interest in the past decades. The substrate specificities of the two major members of SDBEs, pullulanases and isoamylases, are quite different. Pullulanases generally require at least two α-1,4 linked glucose units existing on both sugar chains linked by the α-1,6 bond, while isoamylases require at least three units of α-1,4 linked glucose. SDBEs mainly belong to glycoside hydrolase (GH) family 13 and 57. Except for GH57 type II pullulanse, GH13 pullulanases and isoamylases share plenty of similarities in sequence and structure of the core catalytic domains. However, the N-terminal domains, which might be one of the determinants contributing to the substrate binding of SDBEs, are distinct in different enzymes. In order to overcome the current defects of SDBEs in catalytic efficiency, thermostability and expression level, great efforts have been made to develop effective enzyme engineering and fermentation strategies. Herein, the diverse biochemical properties and distinct features in the sequence and structure of pullulanase and isoamylase from different sources are summarized. Up-to-date developments in the enzyme engineering, heterologous production and industrial applications of SDBEs is also reviewed. Finally, research perspective which could help understanding and broadening the applications of SDBEs are provided.

Cyclodextrinase from Thermococcus sp expressed in Bacillus subtilis and its application in the preparation of maltoheptaose

Background

Maltoheptaose as malto-oligosaccharides with specific degree of polymerization, has wide applications in food, medicine and cosmetics industries. Currently, cyclodextrinase have been applied as prepared enzyme to prepare maltoheptaose. However, the yield and proportion of maltoheptaose was lower, which is due to limited substrate and product specificity of cyclodextrinase (CDase). To achieve higher maltoheptaose yield, cyclodextrinase with high substrate and product specificity should be obtained.

Results

In this study, cyclodextrinase derived from Thermococcus sp B1001 (TsCDase) was successfully expressed and characterized in Bacillus subtilis for the first time. The specific activity of TsCDase was 637.95 U/mg under optimal conditions of 90 °C and pH 5.5, which exhibited high substrate specificity for cyclodextrins (CDs). When the concentration of β-CD was 8%, the yield of maltoheptaose achieved by TsCDase was 82.33% across all reaction products, which exceeded the yields of maltoheptaose in other recent reports. Among malto-oligosaccharides generated as reaction products, maltoheptaose was present in the highest proportion, about 94.55%.

Conclusions

This study provides high substrate and product specificity of TsCDase. TsCDase is able to prepare higher yield of maltoheptaose through conversion of β-CD in the food industry.

Industrially produced pullulanases with thermostability: Discovery, engineering, and heterologous expression

Pullulanases (EC 3.2.1.41) are well-known starch-debranching enzymes widely used to hydrolyze α-1,6-glucosidic linkages in starch, pullulan, amylopectin, and other oligosaccharides, with application potentials in food, brewing, and pharmaceutical industries. Although extensive studies are done to discover and express pullulanases, only few are available with desirable characteristics for industrial applications. This raises the challenge to mine new enzyme sources, engineer proteins based on sequence/structure, and regulate expressions. We review here the identification of extremophilic and mesophilic microbes as sources of industrial pullulanases with desirable characteristics, including acid-resistance, thermostability, and psychrotrophism. We present current advances in site-directed mutagenesis and sequence/structure-guided protein engineering of pullulanases. In addition, we discuss heterologous expression of pullulanases in prokaryotic and eukaryotic microbial systems, and address the effectiveness of the expression elements and their regulation of enzyme production. Finally, we indicate future research needs to develop desired industrial pullulanases.

In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities

Glycoside hydrolases (GHs) have been classified in the CAZy database into 153 GH families. Currently, there might be four α-amylase families: the main family GH13, the family GH57 with related GH119 and, eventually, also GH126. The family GH57 was established in 1996 as the second and smaller α-amylase family. In addition to α-amylase, it contains 4-α-glucanotransferase, α-glucan branching enzyme, amylopullulanase, dual-specificity amylopullulanase–cyclomaltodextrinase, non-specified amylase, maltogenic amylase and α-galactosidase. The family GH57 enzymes employ the retaining reaction mechanism, share five typical conserved sequence regions and possess catalytic (β/α)₇-barrel succeeded by a four-helix bundle with the catalytic machinery consisting of catalytic nucleophile and proton donor (glutamic acid and aspartic acid at strands β4 and β7, respectively). The present bioinformatics study delivers a detailed sequence comparison of 1602 family GH57 sequences with the aim to highlight the uniqueness of each enzyme’s specificity and all eventual protein groups. This was achieved by creating the evolutionary tree focused on both the enzyme specificities and taxonomical origin. The substantial increase of numbers of sequences from recent comparisons done more than 5 years ago has allowed to refine the details of the sequence logos for the individual enzyme specificities. The study identifies a new evolutionary distinct group of α-galactosidase-related enzymes with until-now-undefined enzyme specificity but positioned on the evolutionary tree on a branch adjacent to α-galactosidases. The specificity of α-galactosidase is, moreover, the only one of the entire family GH57 for which there is no structural support for the proposal of the proton donor based on sequence analysis. The analysis also suggests a few so-called “like” protein groups related to some family GH57 enzyme specificities but lacking one or both catalytic residues.

Characterization of a thermostable glycoside hydrolase (CMbg0408) from the hyperthermophilic archaeon Caldivirga maquilingensis IC-167

BACKGROUND

Hyperthermophilic archaea capable of functioning optimally at very high temperatures are a good source of unique and industrially important thermostable enzymes.

RESULTS

A glycoside hydrolase family 1 β-galactosidase gene (BglB) from a hyperthermophilic archaeon Caldivirga maquilingensis IC-167 was cloned and expressed in Escherichia coli. The recombinant enzyme (CMbg0408) displayed optimum activity at 110 °C and pH 5.0. It also retained 92% and 70% of its maximal activity at 115 and 120 °C, respectively. The enzyme was completely thermostable and active after 120 min of incubation at 80 and 90 °C. It also showed broad substrate specificity with activities of 8876 ± 185 U mg^-1 for p-nitrophenyl-β-d-galactopyranoside, 4464 ± 172 U mg^-1 for p-nitrophenyl-β-d-glucopyranoside, 1486 ± 68 U mg^-1 for o-nitrophenyl-β-d-galactopyranoside, 2250 ± 86 U mg^-1 for o-nitrophenyl-β-d-xylopyranoside and 175 ± 4 U mg^-1 for lactose. A catalytic efficiency (k_cat /K_m ) of 3059 ± 122 mmol L^-1  s^-1 and K_m value of 8.1 ± 0.08 mmol L^-1 were displayed towards p-nitrophenyl-β-d-galactopyranoside.

CONCLUSION

As a result of its remarkable thermostability and high activity at high temperatures, this novel β-galactosidase may be useful for food and pharmaceutical applications. © 2016 Society of Chemical Industry.

Structure and function of α-glucan debranching enzymes

α-Glucan debranching enzymes hydrolyse α-1,6-linkages in starch/glycogen, thereby, playing a central role in energy metabolism in all living organisms. They belong to glycoside hydrolase families GH13 and GH57 and several of these enzymes are industrially important. Nine GH13 subfamilies include α-glucan debranching enzymes; isoamylase and glycogen debranching enzymes (GH13_11); pullulanase type I/limit dextrinase (GH13_12-14); pullulan hydrolase (GH13_20); bifunctional glycogen debranching enzyme (GH13_25); oligo-1 and glucan-1,6-α-glucosidases (GH13_31); pullulanase type II (GH13_39); and α-amylase domains (GH13_41) in two-domain amylase-pullulanases. GH57 harbours type II pullulanases. Specificity differences, domain organisation, carbohydrate binding modules, sequence motifs, three-dimensional structures and specificity determinants are discussed. The phylogenetic analysis indicated that GH13_39 enzymes could represent a "missing link" between the strictly α-1,6-specific debranching enzymes and the enzymes with dual specificity and α-1,4-linkage preference.