Improvement of GH10 family xylanase thermostability by introducing of an extra α-helix at the C-terminal

Improvement of thermostability and catalytic efficiency of xylanase from Myceliophthora thermophilar by N-terminal and C-terminal truncation

Introduction

Extracting xylanase from thermophilic filamentous fungi is a feasible way to obtain xylanase with good thermal stability.

Methods

The transcriptomic data of Myceliophthora thermophilic destructive ATCC42464 were differentially expressed and enriched. By comparing the sequences of Mtxylan2 and more than 10 xylanases, the N-terminal and C-terminal of Mtxylan2 were truncated, and three mutants 28N, 28C and 28NC were constructed.

Results and discussion

GH11 xylan Mtxylan2 was identified by transcriptomic analysis, the specific enzyme activity of Mtxylan2 was 104.67 U/mg, and the optimal temperature was 65°C. Molecular modification of Mtxylan2 showed that the catalytic activity of the mutants was enhanced. Among them, the catalytic activity of 28C was increased by 9.3 times, the optimal temperature was increased by 5°C, and the residual enzyme activity remained above 80% after 30 min at 50-65°C, indicating that redundant C-terminal truncation can improve the thermal stability and catalytic performance of GH11 xylanase.

Microbial agents obtained from tomato straw composting effectively promote tomato straw compost maturation and improve compost quality

Appropriate management of agricultural organic waste (AOW) presents a significant obstacle in the endeavor to attain sustainable agricultural development. The proper management of AOW is a necessity for sustainable agricultural development. This can be done skillfully by incorporating microbial agents in the composting procedure. In this study, we isolated relevant bacteria strains from tomato straw AOW, which demonstrated efficient degradation of lignocellulose without any antagonistic effects in them. These strains were then combined to create a composite microbial agent called Zyco Shield (ZS). The performance of ZS was compared with a commercially effective microorganism (EM) and a control CK. The results indicate that the ZS treatment significantly prolonged the elevated temperature phase of the tomato straw pile, showing considerable degradation of lignocellulosic material. This substantial degradation did not happen in the EM and CK treatments. Moreover, there was a temperature rise of 4-6 ℃ in 2 days of thermophilic phase, which was not the case in the EM and CK treatments. Furthermore, the inoculation of ZS substantially enhanced the degradation of organic waste derived from tomato straw. This method increased the nutrient content of the resulting compost and elevated the enzymatic activity of lignocellulose-degrading enzymes, while reducing the urease enzyme activity within the pile. The concentrations of NH4+-N and NO3--N showed increases of (2.13% and 47.51%), (14.81% and 32.17%) respectively, which is again very different from the results of the EM and CK treatments. To some extent, the alterations observed in the microbial community and the abundance of functional microorganisms provide indirect evidence supporting the fact that the addition of ZS microbial agent facilitates the composting process of tomato straw. Moreover, we confirmed the degradation process of tomato straw through X-ray diffraction, Fourier infrared spectroscopy, and by scanning electron microscopy to analyze the role of ZS microbial inoculum composting. Consequently, reinoculation compost strains improves agricultural waste composting efficiency and enhances product quality.

Digestion-Resistant Linear Epitopes as Dominant Contributors to Strong Allergenicity of Tropomyosin in Antarctic Krill (Euphausia superba)

Although tropomyosin has been identified as a major allergen in Antarctic krill, the digestive fate of Antarctic krill tropomyosin and its relationship with allergenicity are unknown. In this study, Antarctic krill tropomyosin was administered to BALB/c mice via both gavage and intraperitoneal injection to explore its sensitizing and eliciting capacity, and its digestion products were analyzed for structural changes and digestion-resistant linear epitopes. Mice gavaged with tropomyosin exhibited lower levels of specific IgE and IgG1, mast cell degranulation, vascular permeability, and anaphylaxis symptoms than those in the intraperitoneal injection group. This may be due to the destruction of macromolecular aggregates, loose expansion of the tertiary structure, complete disappearance of α-helix, and significant changes in molecular force upon the digestion of tropomyosin. Nevertheless, the intragastric administration of Antarctic krill tropomyosin still triggered strong allergic reactions, which was attributed to the existence of seven digestion-resistant linear epitopes (Glu26-His44, Thr111-Arg125, Glu157-Glu164, Glu177-Gly186, Val209-Ile225, Arg244-Arg255, and Val261-Ile270).

Investigating the effect of substrate binding on the catalytic activity of xylanase

XynAF1 from Aspergillus fumigatus Z5 is an efficient thermophilic xylanase belonging to glycoside hydrolase family 10 (GH10). The non-catalytic amino acids N179 and R246 in its catalytic center formed one and three intermolecular H-bonds with the substrate in the aglycone region, respectively. Here we purified XynAF1-N179S and XynAF1-R246K, and obtained the protein-product complex structures by X-ray diffraction. The snapshots indicated that mutations at N179 and R246 had decreased the substrate-binding ability in the aglycone region. XynAF1-N179S, XynAF1-R246K, and XynAF1-N179S-R246K lost one, three, and four H-bonds with the substrate in comparison with the wild-type XynAF1, respectively, but this had little influence on the protein structure. As expected, N179S, R246K, and N179S-R246K led to a gradual decrease of substrate affinity of XynAF1. Interestingly, the enzyme assay showed that N179S increased catalytic efficiency, while both R246K and N179S-R246K had decreased catalytic efficiency. KEY POINTS: • The non-catalytic amino acids of XynAF1 could form H-bonds with the substrate. • The protein-product complex structures were obtained by X-ray diffraction. • The enzyme-substrate-binding capacity could affect enzyme catalytic efficiency.

Role of N-Terminal Extensional Long α-Helix in the Arylesterase from Lacticaseibacillus rhamnosus GG on Catalysis and Stability

In the α/β hydrolases superfamily, the extra module modulated enzymatic activity, substrate specificity, and stability. The functional role of N-terminal extensional long α-helix (Ala2-Glu29, designated as NEL-helix) acting as the extra module in the arylesterase LggEst from Lacticaseibacillus rhamnosus GG had been systemically investigated by deletion mutagenesis, biochemical characterization, and biophysical methods. The deletion of the NEL-helix did not change the overall structure of this arylesterase. The deletion of the NEL-helix led to the shifting of optimal pH into the acidity and the loss of thermophilic activity. The deletion of the NEL-helix produced a 10.6-fold drop in catalytic activity towards the best substrate pNPC10. NEL-Helix was crucial for the thermostability, chemical resistance, and organic solvents tolerance. The deletion of the NEL-helix did not change the overall rigidity of enzyme structure and only reduced the local rigidity of the active site. Sodium deoxycholate might partially replenish the loss of activity caused by the deletion of the NEL-helix. Our research further enriched the functional role of the extra module on catalysis and stability in the α/β hydrolase fold superfamily.

Effects of thermophiles inoculation on the efficiency and maturity of rice straw composting

The present study investigated the effects of separately or simultaneously inoculating thermophilic fungus Aspergillus fumigatus Z5 and bacterium Geobacillus stearothermophilus B5 on lignocellulose degradation, enzyme activities and humification during rice straw composting. The results indicated that inoculation of Z5 accelerated the rise of temperature in the mesophilic phase, and the degradation degree of cellulose and hemicellulose was increased by 25.3% and 20.7%, respectively, due to the higher activities of lignocellulolytic enzymes. Inoculation of B5 increased 5-7 °C of the compost temperature in the thermophilic phase, and also prolonged the duration from 33 to 41 days. Inoculated simultaneously, the secreted hydrolases of Z5 generated more nutrition and promoted the growth of B5. B5 maintained and increased the compost temperature, thus presenting a better hydrolysis environment for extracellular hydrolases. Thermophilic inoculation altered the main physicochemical factors and improved efficiency and maturity in rice straw composting.

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.

A multifaceted enzyme conspicuous in fruit juice clarification: An elaborate review on xylanase

Xylanase enzyme has been classified as an enzyme belonging to the glycoside hydrolase family. The catalytic action of xylanase is focused on the degradation of xylan, a substrate for this enzyme comprising of a complex arrangement of monosaccharides interlinked with the help of ester and glycosidic bonds. Xylan represents the second most profuse renewable polysaccharide present on earth. Breakage of the β- 1, 4-glycoside linkage in the xylan polymer is what makes xylanase enzyme an important biocatalyst favoring various applications including treatment of pulp for improving paper quality, improvement of bread quality, treatment of lignocelluloses waste, production of xylose sugar and production of biological fuels. Most recently, xylanase has been exploited in the food industry for the purpose of fruit juice clarification. Turbidity caused by the colloidal polysaccharides present in the freshly squeezed fruit juice poses a setback to the fruit juice industry since the commercial product must be clear and free of excess polysaccharides to improve juice quality and storage life. This review gives an overview of the recent advancements made in regards to xylanase enzyme being used commercially with main focus on its role in fruit juice clarification.

Biochemical characterization of a GH10 xylanase from the anaerobic rumen fungus Anaeromyces robustus and application in bread making

Anaeromyces robustus is an anaerobic rumen microorganism which can produce plant cell wall degrading enzymes. In this study, a new GH10 xylanase gene xylAr10 from A. robustus was identified, cloned and expressed in Pichia pastoris GS115. The recombinant protein ArXyn10 was characterized after being purified by Ni-NTA. The optimal pH and temperature of ArXyn10 was determined at 5.5 and 40 °C, respectively. ArXyn10 was stable at the pH range of 4.0-8.0, and could maintain high stability from 35 to 45 °C. The hydrolysis products released from beechwood xylan by ArXyn10 showed chromatographic mobility similar to xylobiose and xylotriose according to thin-layer chromatography analysis. It was shown that the addition of 7.5 mg of ArXyn10 in 100 g high-gluten wheat flour during bread making could increase the reducing sugar content by 10.80%, indicating that xylo-oligosaccharides were produced. With the addition of ArXyn10, the hardness and chewiness of the bread decreased and the quality was improved. The new discovered xylanase ArXyn10 have potential application prospect in bread making.

Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges

Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.

Improve thermostability of Bacillus sp. TS chitosanase through structure-based alignment

Chitosanases can catalyze the release of chitooligosaccharides which have a number of medical applications. Therefore, Chitosanases are good candidates for large-scale enzymatic synthesis due to their favorable thermostability properties and high catalytic efficiency. To further improve the thermostability of a chitosanase from Bacillus sp. TS, which has a half-life of 5.32 min, we mutated specific serine residues that we identified as potentially relevant through structure comparison with thermophilic CelA from Clostridium thermocellum. Out of a total of 15 mutants, three, namely S265G, S276A, and S347G, show higher thermostability. Their half-lives at 60 °C were calculated as 34.57 min, 36.79 min and 7.2 min. The K_m values of S265G, S276A and S347G mutants show substrate binding ability comparable to that of the wild-type enzyme, while the S265G mutant displays a significant decrease of enzymatic activities. Additionally, we studied the synergistic effects of combined mutations, observing that all double mutants and the triple mutant are more stable than the wild-type enzyme and single mutants. Finally, we investigated the mechanisms which might give a reasonable explanation for the improved thermostability via comparative analysis of the resulting 3D structures.

Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design

Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.

A novel thermostable xylanase from Geobacillus vulcani GS90: Production, biochemical characterization, and its comparative application in fruit juice enrichment

Xylanases have great attention to act as a potential role in agro-industrial processes. In this study, production, characterization, and fruit juice application of novel xylanase from thermophilic Geobacillus vulcani GS90 (GvXyl) were performed. GvXyl was purified via acetone precipitation and gel-filtration chromatography. The results showed that GvXyl had 1,671.4 U/mg of specific activity and optimally worked at pH 8 and 55°C. It was also active in a wide pH (3-9) and temperature (30-90ºC) ranges. GvXyl was highly stable at 90ºC and relatively stable at pH 3-9. The kinetic parameters of GvXyl were obtained as K_m , V_max , and k_cat ; 10.2 mg/ml, 4,104 µmol min^-1  mg^-1 , and 3,542.6 s^-1 , respectively. GvXyl had higher action than commercial xylanase in fruit juice enrichment. These results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability. PRACTICAL APPLICATIONS: Polysaccharides include starch, pectin, and hemicellulose create problems by lowering fruit juice quality in beverages. To overcome this problem, various clarification processes might be applied to natural fruit juices. Even though chemicals are widely used for this purpose, recently enzymes including xylanases are preferred for obtaining high-quality products. In this study, we reported the production and biochemical characterization of novel thermostable xylanase from thermophilic G. vulcani GS90 (GvXyl). Also, apple and orange juice enrichment were performed with the novel xylanase to increase the quality in terms of yield, clarity, and reducing sugar substance. The improved quality features of apple and orange juices with GvXyl was then compared to commercially available β-1,4-xylanase. The results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability.

A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera

The worldwide dependence of population on fossil fuels continues to have several harmful implications for the environment. Bioethanol is an excellent option for renewable fuel to replace the current greenhouse gas emitters. In addition, its production by enzymatic route has gained space among the industrial processes because it replaces the traditional acid treatment. Due to its high versatility, the xylanase family is used in this process as an accessory enzyme for degrading the lignocellulosic substrate of biomass. A chimera built by a xylanolytic domain (Xyl) and a xylose-binding protein (XBP) showed an experimentally improved catalytic efficiency and interdomain allosteric modulation after xylose binding. In this context, we performed a quantum biochemistry characterization of the interactions between these domains and dynamic cross-correlation (DCC) analysis after performing molecular dynamics (DM) simulations of the systems in the presence and absence of xylose in the XBP active site. We used the density functional theory (DFT) within the molecular fractionation with the conjugated caps (MFCC) approach to describe the pair energies, and the corresponding energy difference between the chimera domains responsible for the allosteric effect and amino acid DCC to evaluate the interdomain coupling differences between the energy states. The detailed energetic investigation together with the related structural and dynamics counterparts revealed the molecular mechanisms of chimeric improvement of the xylanase activity observed experimentally. This mechanism was correlated with greater stability and high connectivity at the interdomain interface in the xylose bound relative to the free chimera. We identify the contributions of hydrogen bonds, hydrophobic interactions and water-mediated interactions in the interdomain region responsible for stability together with the structural and dynamical elements related to the allosteric effect. Taken together, these observations led to a comprehensive understanding of the chimera's modulatory action that occurs through the formation of a highly connected interface that makes the essential movements related to xylanolytic activity in xylanase correlated to those of the xylose-binding protein.