New Class of Chitosanase from Bacillus amyloliquefaciens for the Generation of Chitooligosaccharides

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022

The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

Recent Advances in the Degradability and Applications of Tissue Adhesives Based on Biodegradable Polymers

In clinical practice, tissue adhesives have emerged as an alternative tool for wound treatments due to their advantages in ease of use, rapid application, less pain, and minimal tissue damage. Since most tissue adhesives are designed for internal use or wound treatments, the biodegradation of adhesives is important. To endow tissue adhesives with biodegradability, in the past few decades, various biodegradable polymers, either natural polymers (such as chitosan, hyaluronic acid, gelatin, chondroitin sulfate, starch, sodium alginate, glucans, pectin, functional proteins, and peptides) or synthetic polymers (such as poly(lactic acid), polyurethanes, polycaprolactone, and poly(lactic-co-glycolic acid)), have been utilized to develop novel biodegradable tissue adhesives. Incorporated biodegradable polymers are degraded in vivo with time under specific conditions, leading to the destruction of the structure and the further degradation of tissue adhesives. In this review, we first summarize the strategies of utilizing biodegradable polymers to develop tissue adhesives. Furthermore, we provide a symmetric overview of the biodegradable polymers used for tissue adhesives, with a specific focus on the degradability and applications of these tissue adhesives. Additionally, the challenges and perspectives of biodegradable polymer-based tissue adhesives are discussed. We expect that this review can provide new inspirations for the design of novel biodegradable tissue adhesives for biomedical applications.

Improvement of the catalytic performance of chitosanase Csn-PD from Paenibacillus dendritiformis by semi-rational design

Chitooligosaccharides (COS) possess versatile functional properties that have found extensive applications across various fields. Chitosanase can specifically hydrolyze β-1,4 glycosidic bonds in chitosan to produce COS. In this study, Csn-PD, a glycoside hydrolase family 46 chitosanase from Paenibacillus dendritiformis, which produces (GlcN)2 as its main product, was rationally redesigned aiming to improve its catalytic performance. Based on the results of molecular docking analysis and multiple sequence alignment, four amino acid residues in Csn-PD (I101, T120, T220, and Y259) were pinpointed for targeted mutations. Beneficial mutations in terms of enhanced catalytic activity were then combined by site-directed mutagenesis. Notably, the most promising variant, Csn-PDT6 (Csn-PD I101M/T120E/T220G), exhibited an impressive eight-fold surge in activity compared to the wild-type Csn-PD. This heightened enzymatic activity was complemented by an enhanced pH stability profile. A compelling feature of Csn-PDT6 is its preservation of the hydrolytic product profile observed in Csn-PD. This characteristic further accentuates its candidacy for the targeted production of (GlcN)2. The success of our strategic approach is vividly illustrated by the significant improvements achieved in the catalytic performance of the chitosanase, encompassing both its activity and stability. These developments offer a valuable model that may have implications for the semi-rational design of other enzymes.

Recent Progress in Enzymatic Preparation of Chitooligosaccharides with a Single Degree of Polymerization and Their Potential Applications in the Food Sector

Chitosan oligosaccharides (COS), derived from chitin, have garnered considerable attention owing to their diverse biological activities and potential applications. Previous investigations into the bioactivity of COS often encountered challenges, primarily stemming from the use of COS mixtures, making it difficult to discern specific effects linked to distinct degrees of polymerization (DP). Recent progress underscores the significant variation in the biological activities of COS corresponding to different DPs, prompting dedicated research towards synthesizing COS with well-defined polymerization. Among the available methods, enzymatic preparation stands out as a viable and environmentally friendly approach for COS synthesis. This article provides a comprehensive overview of emerging strategies for the enzymatic preparation of single COS, encompassing protein engineering, enzymatic membrane bioreactors, and transglycosylation reactions. Furthermore, the bioactivities of single COS, including anti-tumor, antioxidant, antibacterial, anti-inflammatory, and plant defense inducer properties, exhibit close associations with DP values. The potential applications of single COS, such as in functional food, food preservation, and crop planting, are also elucidated.

MECE: a method for enhancing the catalytic efficiency of glycoside hydrolase based on deep neural networks and molecular evolution

The demand for high efficiency glycoside hydrolases (GHs) is on the rise due to their various industrial applications. However, improving the catalytic efficiency of an enzyme remains a challenge. This investigation showcases the capability of a deep neural network and method for enhancing the catalytic efficiency (MECE) platform to predict mutations that improve catalytic activity in GHs. The MECE platform includes DeepGH, a deep learning model that is able to identify GH families and functional residues. This model was developed utilizing 119 GH family protein sequences obtained from the Carbohydrate-Active enZYmes (CAZy) database. After undergoing ten-fold cross-validation, the DeepGH models exhibited a predictive accuracy of 96.73%. The utilization of gradient-weighted class activation mapping (Grad-CAM) was used to aid us in comprehending the classification features, which in turn facilitated the creation of enzyme mutants. As a result, the MECE platform was validated with the development of CHIS1754-MUT7, a mutant that boasts seven amino acid substitutions. The kcat/Km of CHIS1754-MUT7 was found to be 23.53 times greater than that of the wild type CHIS1754. Due to its high computational efficiency and low experimental cost, this method offers significant advantages and presents a novel approach for the intelligent design of enzyme catalytic efficiency. As a result, it holds great promise for a wide range of applications.

Structure-based mining of a chitosanase with distinctive degradation mode and product specificity

Chitosan derivates with varying degrees of polymerization (DP) have attracted great concern due to their excellent biological activities. Increasing the abundance of chitosanases with different degradation modes contributes to revealing their catalytic mechanisms and facilitating the production of chitosan derivates. However, the identification of endo-chitosanases capable of producing chitobiose and D-glucosamine (GlcN) from chitosan substrates has remained elusive. Herein, an endo-chitosanase (CsnCA) belonging to the GH46 family was identified based on structural analysis in phylogenetic evolution. Moreover, we demonstrate that CsnCA acts in a random endo-acting manner, producing chitosan derivatives with DP ≤ 2. The in-depth analysis of CsnCA revealed that (GlcN)3 serves as the minimal substrate, undergoing cleavage in the mode that occupies the subsites - 2 to + 1, resulting in the release of GlcN. This study succeeded in discovering a chitosanase with distinctive degradation modes, which could facilitate the mechanistic understanding of chitosanases, further empowering the production of chitosan derivates with specific DP. KEY POINTS: • Structural docking and evolutionary analysis guide to mining the chitosanase. • The endo-chitosanase exhibits a unique GlcN-producing cleavage pattern. • The cleavage direction of chitosanase to produce GlcN was identified.

Rational Redesign of Chitosanase to Enhance Thermostability and Catalytic Activity to Produce Chitooligosaccharides with a Relatively High Degree of Polymerization

Chitooligosaccharides (hdpCOS) with a high degree of polymerization (hdp, DP 4-10) generally have greater biological activities than those of low-DP (ldp, DP 2-3) COS. Chitosanase from Bacillus amyloliquefaciens KCP2 (Csn46) can degrade chitosan to more hdpCOS at high temperature (70 °C), but low thermal stability at this temperature makes it unsuitable for industrial application; the wild-type enzyme can only produce COS (DP 2-4) at lower temperatures. Several thermostable mutants were obtained by modifying chitosanase using a comprehensive strategy based on a computer-aided mutant design. A combination of four beneficial single-point mutations (A129L/T175 V/K70T/D34G) to Csn46 was selected to obtain a markedly improved mutant, Mut4, with a half-life at 60 °C extended from 34.31 to 690.80 min, and the specific activity increased from 1671.73 to 3528.77 U/mg. Mut4 produced COS with DPs of 2-4 and 2-7 at 60 and 70 °C, respectively. Therefore, Mut4 has the potential to be applied to the industrial-scale preparation of hdpCOS with high biological activity.

Production, Characterization and Application of a Novel Chitosanase from Marine Bacterium Bacillus paramycoides BP-N07

Chitooligosaccharides (COS), a high-value chitosan derivative, have many applications in food, pharmaceuticals, cosmetics and agriculture owing to their unique biological activities. Chitosanase, which catalyzes the hydrolysis of chitosan, can cleave β-1,4 linkages to produce COS. In this study, a chitosanase-producing Bacillus paramycoides BP-N07 was isolated from marine mud samples. The chitosanase enzyme (BpCSN) activity was 2648.66 ± 20.45 U/mL at 52 h and was able to effectively degrade chitosan. The molecular weight of purified BpCSN was approximately 37 kDa. The yield and enzyme activity of BpCSN were 0.41 mg/mL and 8133.17 ± 47.83 U/mg, respectively. The optimum temperature and pH of BpCSN were 50 °C and 6.0, respectively. The results of the high-performance liquid chromatography (HPLC) and thin-layer chromatography (TLC) of chitosan treated with BpCSN for 3 h showed that it is an endo-chitosanase, and the main degradation products were chitobiose, chitotriose and chitotetraose. BpCSN was used for the preparation of oligosaccharides: 1.0 mg enzyme converted 10.0 g chitosan with 2% acetic acid into oligosaccharides in 3 h at 50 °C. In summary, this paper reports that BpCSN has wide adaptability to temperature and pH and high activity for hydrolyzing chitosan substrates. Thus, BpCSN is a chitosan decomposer that can be used for producing chitooligosaccharides industrially.

Biochemical Characterization of a GH46 Chitosanase Provides Insights into the Novel Digestion Specificity

Endo-chitosanases (EC 3.2.1.132) are generally considered to selectively release functional chito-oligosaccharides (COSs) with degrees of polymerization (DPs) ≥ 2. Although numerous endo-chitosanases have been characterized, the digestion specificity of endo-chitosanases needs to be further explored. In this study, a GH46 endo-chitosanase OUC-CsnPa was cloned, expressed, and characterized from Paenibacillus sp. 1-18. The digestion pattern analysis indicated that OUC-CsnPa could produce monosaccharides from chitotetraose [(GlcN)₄], the smallest recognized substrate, in a random endo-acting manner. Especially, the enzyme specificities during chitosan digestion including the regulation of product abundance through a transglycosylation reaction were also evaluated. It was hypothesized that an insertion region in OUC-CsnPa may form a strong force to be involved in stabilizing (GlcN)₄ at its negative subsite for efficient hydrolysis. This is the first comprehensive report to reveal the digestion specificity and subsite specificity of monosaccharide production by endo-chitosanases. Overall, OUC-CsnPa described here highlights the previously unknown digestion properties of the endo-acting chitosanases and provides a unique example of possible structure-function relationships.

Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations

Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases.

Gene cloning and molecular characterization of a thermostable chitosanase from Bacillus cereus TY24

Background

An important conceptual advance in health and the environment has been recognized that enzymes play a key role in the green processing industries. Of particular interest, chitosanase is beneficial for recycling the chitosan resource and producing chitosan oligosaccharides. Also, chitosan gene expression and molecular characterization will promote understanding of the biological function of bacterial chitosanase as well as explore chitosanase for utilizing chitosan resources.

Results

A chitosanase-producing bacterium TY24 was isolated and identified as Bacillus cereus. Moreover, the chitosanase gene was cloned and expressed in Escherichia coli. Sequence analysis reveals that the recombinant chitosanase (CHOE) belongs to the glycoside hydrolases 8 family. The purified CHOE has a molecular weight of about 48 kDa and the specific activity of 1150 U/mg. The optimal pH and temperature of CHOE were 5.5 and 65 °C, respectively. The enzyme was observed stable at the pH range of 4.5–7.5 and the temperature range of 30–65 °C. Especially, the half-life of CHOE at 65 °C was 161 min. Additionally, the activity of CHOE was remarkably enhanced in the presence of Mn²⁺, Cu²⁺, Mg²⁺ and K⁺, beside Ca²⁺ at 5 mM. Especially, the activity of CHOE was enhanced to more than 120% in the presence of 1% of various surfactants. CHOE exhibited the highest substrate specificity toward colloid chitosan.

Conclusion

A bacterial chitosanase was cloned from B. cereus and successfully expressed in E. coli (BL21) DE3. The recombinant enzyme displayed good stability under acid pH and high-temperature conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-022-00762-6.

Insights into promiscuous chitosanases: the known and the unknown

Chitosanase, a glycoside hydrolase (GH), catalyzes the cleavage of β-1,4-glycosidic bonds in polysaccharides and is widely distributed in nature. Many organisms produce chitosanases, and numerous chitosanases in the GH families have been intensely studied. The reported chitosanases mainly cleaved the inter-glucosamine glycosidic bonds, while substrate specificity is not strictly unique due to the existence of bifunctional or multifunctional activity profiles. The promiscuity of chitosanases is essential for the different pathways of biomass polysaccharide conversion and understanding of the chitosanase evolutionary process. However, the reviews for this aspect are completely unknown. This review provides an overview of the promiscuous activities, also considering the substrate and product specificity of chitosanases observed to date. These contribute to important implications for the future discovery and research of promiscuous chitosanases and applications related to biomass conversion. KEY POINTS: • The promiscuity of chitosanases is reviewed for the first time. • The current review provides insights into the substrate specificity of chitosanases. • The mode-product relationship and prospect of promiscuous chitosanases are highlighted.

New Insights into Bifunctional Chitosanases with Hydrolysis Activity toward Chito- and Cello-Substrates

In the present study, we carried out a comprehensive investigation of glycoside hydrolase (GH) 46 model-chitosanases based on cleavage specificity classification to understand their unknown bifunctional activity. We for the first time show that GH46 chitosanase CsnMHK1 from Bacillus circulans MH-K1, which was previously thought to be strictly exclusive to chitosan, can hydrolyze both chito- and cello-substrates. We determined the digestion direction of bifunctional chitosanase CsnMHK1 from class III and compared it with class II chitosanase belonging to GH8, providing insight into unique substrate specificities and a new perspective on its reclassification. The results lead us to challenge the current understanding of chitosanase substrate specificity based on GH taxonomy classification and suggest that the prevalence from the common bifunctional activity may have occurred. Altogether, these data contribute to the understanding of chitosanase recognition and hydrolysis toward chito- and cello-substrates, which is valuable for future studies on chitosanases.

Biodegradation and Prospect of Polysaccharide from Crustaceans

Marine crustacean waste has not been fully utilized and is a rich source of chitin. Enzymatic degradation has attracted the wide attention of researchers due to its unique biocatalytic ability to protect the environment. Chitosan (CTS) and its derivative chitosan oligosaccharides (COSs) with various biological activities can be obtained by the enzymatic degradation of chitin. Many studies have shown that chitosan and its derivatives, chitosan oligosaccharides (COSs), have beneficial properties, including lipid-lowering, anti-inflammatory and antitumor activities, and have important application value in the medical treatment field, the food industry and agriculture. In this review, we describe the classification, biochemical characteristics and catalytic mechanisms of the major degrading enzymes: chitinases, chitin deacetylases (CDAs) and chitosanases. We also introduced the technology for enzymatic design and modification and proposed the current problems and development trends of enzymatic degradation of chitin polysaccharides. The discussion on the characteristics and catalytic mechanism of chitosan-degrading enzymes will help to develop new types of hydrolases by various biotechnology methods and promote their application in chitosan.

Heterologous Expression of GH5 Chitosanase in Pichia pastoris and Antioxidant Biological Activity of Its Chitooligosacchride Hydrolysate

Chitosanase was widely used in the production of bioactive chitooligosacchride (CHOS) due to their safety, controllability, environmental protection, and biodegradability. Studies showed that the bioactivity of CHOS is closely related to its degree of polymerization. Therefore, the production of ideal polymerized CHOS becomes our primary goal. In this study, the glycosyl hydrolase (GH) family 5 chitosanase was successfully expressed heterologously in Pichia pastoris. After 96h of high-density fermentation, the chitosanase activity reached 90.62 U·mL^-1, the protein content reached 9.76mg·mL^-1. When 2% chitosan was hydrolyzed by crude enzyme (20U/mL), the hydrolysis rate reached 91.2% after 8h, producing a mixture of CHOS with 2-4 desirable degrees of polymerization (DP). Then, the antioxidant activity of CHOS mixture was investigated, and the results showed that the antioxidant effect was concentration-dependent and had great application potential in the field of nutrition.

Biochemical characterization and cleavage pattern analysis of a novel chitosanase with cellulase activity

Chitosanases are critical tools for the preparation of active oligosaccharides, whose composition is related to the cleavage pattern of the enzyme. Although numerous chitosanases have been characterized, the glycoside hydrolase (GH) family 5 chitosanases with other activities have rarely been investigated. Herein, a novel and second GH5 chitosanase OUC-Csngly from Streptomyces bacillaris was cloned and further characterized by expression in Escherichia coli BL21 (DE3). Interestingly, OUC-Csngly possessed dual chitosanase and cellulase activities. Molecular docking analysis showed that the C-2 group of sugar units affected the binding of the enzyme to oligosaccharides, which could result in different cleavage patterns toward chito-oligosaccharides (COSs) and cello-oligosaccharides. Further, we characterized OUC-Csngly's distinctive cleavage patterns toward two different types of oligosaccharides. Meanwhile, endo-type chitosanase OUC-Csngly generated (GlcN) - (GlcN)₄ from chitosan, was significantly different from other chitosanases. To our knowledge, this is the first report to investigate the different cleavage patterns of chitosanase for COSs and cello-oligosaccharides.Key points• The molecular docking showed C-2 group of sugar units in substrate affecting the cleavage pattern.• The first chitosanase exhibited different cleavage patterns towards chito- and cello-oligosaccharides.• The groups at C-2 influence the subsite composition of the enzyme's active cleft.

Expression and Characterization of a Novel Cold-Adapted Chitosanase from Marine Renibacterium sp. Suitable for Chitooligosaccharides Preparation

(1) Background: Chitooligosaccharides (COS) have numerous applications due to their excellent properties. Chitosan hydrolysis using chitosanases has been proposed as an advisable method for COS preparation. Although many chitosanases from various sources have been identified, the cold-adapted ones with high stability are still rather rare but required. (2) Methods: A novel chitosanase named CsnY from marine bacterium Renibacterium sp. Y82 was expressed in Escherichia coli, following sequence analysis. Then, the characterizations of recombinant CsnY purified through Ni-NTA affinity chromatography were conducted, including effects of pH and temperature, effects of metal ions and chemicals, and final product analysis. (3) Results: The GH46 family chitosanase CsnY possessed promising thermostability at broad temperature range (0-50 °C), and with optimal activity at 40 °C and pH 6.0, especially showing relatively high activity (over 80% of its maximum activity) at low temperatures (20-30 °C), which demonstrated the cold-adapted property. Common metal ions or chemicals had no obvious effect on CsnY except Mn2+ and Co2+. Finally, CsnY was determined to be an endo-type chitosanase generating chitodisaccharides and -trisaccharides as main products, whose total concentration reached 56.74 mM within 2 h against 2% (w/v) initial chitosan substrate. (4) Conclusions: The results suggest the cold-adapted CsnY with favorable stability has desirable potential for the industrial production of COS.