Highly efficient production of chitooligosaccharides by enzymes mined directly from the marine metagenome

Blue Biotechnology: Marine Bacteria Bioproducts

The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.

Modulation of a Loop Region in the Substrate Binding Pocket Affects the Degree of Polymerization of Bacillus subtilis Chitosanase Products

The hydrolytic products of chitosanase from Streptomyces avermitilis (SaCsn46A) were found to be aminoglucose and chitobiose, whereas those of chitosanase from Bacillus subtilis (BsCsn46A) were chitobiose and chitotriose. Therefore, the sequence alignment between SaCsn46A and BsCsn46A was conducted, revealing that the structure of BsCsn46A possesses an extra loop region (194N-200T) at the substrate binding pocket. To clarify the impact of this loop on hydrolytic properties, three mutants, SC, TJN, and TJA, were constructed. Eventually, the experimental results indicated that SC changed the ratio of chitobiose to chitotriose hydrolyzed by chitosanase from 1:1 into 2:3, while TJA resulted in a ratio of 15:7. This experiment combined molecular research to unveil a crucial loop within the substrate binding pocket of chitosanase. It also provides an effective strategy for mutagenesis and a foundation for altering hydrolysate composition and further applications in engineering chitosanase.

Secretory production and characterization of a highly effective chitosanase from Streptomyces coelicolor A3(2) M145 in Pichia pastoris

In this study, a glycoside hydrolase family 46 chitosanase from Streptomyces coelicolor A3(2) M145 was firstly cloned and expressed in Pichia pastoris GS115 (P. pastoris GS115). The recombinant enzyme (CsnA) showed maximal activity at pH 6.0 and 65°C. Both thermal stability and pH stability of CsnA expressed in P. pastoris GS115 were significantly increased compared with homologous expression in Streptomyces coelicolor A3(2). A stable chitosanase activity of 725.7 ± 9.58 U mL-1 was obtained in fed-batch fermentation. It's the highest level of CsnA from Streptomyces coelicolor expressed in P. pastoris so far. The hydrolytic process of CsnA showed a time-dependent manner. Chitosan oligosaccharides (COSs) generated by CsnA showed antifungal activity against Fusarium oxysporum sp. cucumerinum (F. oxysporum sp. cucumerinum). The secreted expression and hydrolytic performance make the enzyme a desirable biocatalyst for industrial controllable production of chitooligosaccharides with specific degree of polymerization, which have potential to control fungi that cause important crop diseases.

Enhancing the thermostability and catalytic activity of Bacillus subtilis chitosanase by saturation mutagenesis of Lys242

Catalysis activity and thermostability are some of the fundamental characteristic of enzymes, which are of great significance to their industrial applications. Bacillus subtilis chitosanase BsCsn46A is a kind of enzyme with good catalytic activity and stability, which can hydrolyze chitosan to produce chitobiose and chitotriose. In order to further improve the catalytic activity and stability of BsCsn46A, saturation mutagenesis of the C-terminal K242 of BsCsn46A was performed. The results showed that the six mutants (K242A, K242D, K242E, K242F, K242P, and K242T) showed increased catalytic activity on chitosan. The catalytic activity of K242P increased from 12971 ± 597 U mg-1 of wild type to 17820 ± 344 U mg-1 , and the thermostability of K242P increased by 2.27%. In order to elucidate the reason for the change of enzymatic properties, hydrogen network, molecular docking, and molecular dynamics simulation were carried out. The hydrogen network results showed that all the mutants lose their interaction with Asp6 at 242 site, thereby increasing the flexibility of Glu19 at the junction sites of α1 and loop1. Molecular dynamics results showed that the RMSD of K242P was lower at both 313 and 323 K than that of other mutants, which supported that K242P had better thermostability. The catalytic activity of mutant K242P reached 17820.27 U mg-1 , the highest level reported so far, which could be a robust candidate for the industrial application of chitooligosaccharide (COS) production.

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.

Insights into the relationships of modifying methods, structure, functional properties and applications of chitin: A review

Chitin as the second plentiful polysaccharide has arouse widely attention due to its remarkable availability and biocompatibility. While the strong inter/intra molecular hydrogen bonds and crystallinity severely restrict its applications. Recently, multiple emerging technologies are increasingly used to modify chitin structure for the sake of obtaining excellent functional properties, as well as broadening the corresponding applications. Firstly, this review systematically outlines the features of single and combined methods for chitin modification. Then, the impacts of various modifying methods on the structural characteristics of chitin, including molecular weight, degree of acetylation and functional groups, are further summarized. In addition, the effects of these structural characteristics on the functional properties as well as its potential related applications are illustrated. The conclusion of this review provides better understanding of the relationships among the modifying methods, structure, properties and applications, contributing to chitin modification for the targeted purpose in the future study.

An Insight into the Essential Role of Carbohydrate-Binding Modules in Enzymolysis of Xanthan

To date, due to the low accessibility of enzymes to xanthan substrates, the enzymolysis of xanthan remains deficient, which hinders the industrial production of functional oligoxanthan. To enhance the enzymatic affinity against xanthan, the essential role of two carbohydrate binding modules—MiCBMx and PspCBM84, respectively, derived from Microbacterium sp. XT11 and Paenibacillus sp. 62047—in catalytic properties of endotype xanthanase MiXen were investigated for the first time. Basic characterizations and kinetic parameters of different recombinants revealed that, compared with MiCBMx, PspCBM84 dramatically increased the thermostability of endotype xanthanase, and endowed the enzyme with higher substrate affinity and catalytic efficiency. Notably, the activity of endotype xanthanase was increased by 16 times after being fused with PspCBM84. In addition, the presence of both CBMs obviously enabled endotype xanthanase to produce more oligoxanthan, and xanthan digests prepared by MiXen-CBM84 showed better antioxidant activity due to the higher content of active oligosaccharides. The results of this work lay a foundation for the rational design of endotype xanthanase and the industrial production of oligoxanthan in the future.

Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches

β-Chitin has important ecological and physiological roles and potential for widespread applications, but the characterization of chitin-related enzymes from β-chitin producers was rarely reported. Querying against the Tara Oceans Gene Atlas, 4,939 chitin-related unique sequences from 12 Pfam accessions were found in Bacillariophyta metatranscriptomes. Putative chitin synthase (CHS) sequences are decreasingly present in Crustacea (39%), Stramenopiles (16%) and Insecta (14%) from the Marine Atlas of Tara Oceans Unigenes version 1 Metatranscriptomes (MATOUv1+T) database. A CHS gene from the model diatom Thalassiosira pseudonana (Thaps3_J4413, designated TpCHS1) was identified. Homology analysis of TpCHS1 in Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), PhycoCosm, and the PLAZA diatom omics data set showed that Mediophyceae and Thalassionemales species were potential new β-chitin producers besides Thalassiosirales. TpCHS1 was overexpressed in Saccharomyces cerevisiae and Phaeodactylum tricornutum. In transgenic P. tricornutum lines, TpCHS1-eGFP localizes to the Golgi apparatus and plasma membrane and predominantly accumulates in the cleavage furrow during cell division. Enhanced TpCHS1 expression could induce abnormal cell morphology and reduce growth rates in P. tricornutum, which might be ascribed to the inhibition of the G2/M phase. S. cerevisiae was proved to be a better system for expressing large amounts of active TpCHS1, which effectively incorporates UDP-N-acetylglucosamine in radiometric in vitro assays. Our study expands the knowledge on chitin synthase taxonomic distribution in marine eukaryotic microbes, and is the first to collectively characterize an active marine diatom CHS which may play an important role during cell division. IMPORTANCE As the most abundant biopolymer in the oceans, the significance of chitin and its biosynthesis is rarely demonstrated in diatoms, which are the main contributors to the primary productivity of the oceans, ascribed to their huge biomass and efficient photosynthesis. We retrieved genes involved in chitin-based metabolism against the Tara Oceans Gene Atlas to expand our knowledge about their diversity and distribution in the marine environment. Potential new producers of chitin were found from the analysis of various algal transcriptome and genome databases. Heterologous expression confirms that Thalassiosira pseudonana contains an active chitin synthase (CHS) which may play an important role in the cell division process of diatoms. This study provides new insight into CHS geographic and taxonomic distribution in marine eukaryotic microbes, as well as into a new CHS functioning in the biosynthesis of β-chitin in diatoms.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.

Neoroseomonas marina sp. nov., Isolated from a Beach Sand

A pink-pigmented bacterium (strain JC162^T = KCTC 32190^T) was isolated from a beach sand sample. Cells were Gram-stain-negative, coccoid, non-motile, and strictly aerobic. EzBioCloud BLAST search of 16S rRNA gene sequence showed that strain KCTC 32190^T had the highest sequence identity to the members of the genus Neoroseomonas and was closely related to N. oryzicola YC6724^T (99.8%), N. sediminicola FW-3^T (98.5%), N. soli 5N26^T (98.2%), and other members of the genus Neoroseomonas (< 97.9%) in the family Acetobacteriaceae within the class of Alphaproteobacteria. Chemo-organoheterotrophy was the only growth mode and growth was possible on a wide range of organic substrates. Strain KCTC 32190^T was positive for catalase and oxidase. Fatty acid composition of strain KCTC 32190^T includes (in decreasing %) C_18:1ω7c, cyclo-C_19:0ω8c, C_18:02-OH, C_16:0, C_18:03-OH, C_16:1ω7c/C_16:1ω6c, C_16:02-OH and C_16:1ω5c. Polar lipids comprised of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, and three unidentified lipids. The genomic DNA G+C content of the strain KCTC 32190^T was 70.9 mol%. Strain KCTC 32190^T has a low ANI value of < 92.7% and genome reassociation (based on digital DNA-DNA hybridization) value of < 48.8% with the nearest type strains. The genome relatedness is supported by other polyphasic taxonomic data to propose strain KCTC 32190^T as a new species in the genus Neoroseomonas with the name Neoroseomonas marina sp. nov. The type strain is strain JC162^T (KCTC 32190^T = CGMCC1.12364^T).

Chitosan: Sources, Processing and Modification Techniques

Chitosan, a copolymer of glucosamine and N-acetyl glucosamine, is derived from chitin. Chitin is found in cell walls of crustaceans, fungi, insects and in some algae, microorganisms, and some invertebrate animals. Chitosan is emerging as a very important raw material for the synthesis of a wide range of products used for food, medical, pharmaceutical, health care, agriculture, industry, and environmental pollution protection. This review, in line with the focus of this special issue, provides the reader with (1) an overview on different sources of chitin, (2) advances in techniques used to extract chitin and converting it into chitosan, (3) the importance of the inherent characteristics of the chitosan from different sources that makes them suitable for specific applications and, finally, (4) briefly summarizes ways of tailoring chitosan for specific applications. The review also presents the influence of the degree of acetylation (DA) and degree of deacetylation (DDA), molecular weight (M_w) on the physicochemical and biological properties of chitosan, acid-base behavior, biodegradability, solubility, reactivity, among many other properties that determine processability and suitability for specific applications. This is intended to help guide researchers select the right chitosan raw material for their specific applications.

Preparation of the porous carbon-based solid acid from starch for efficient degradation of chitosan to D-glucosamine

Effective degradation of chitosan to D-glucosamine is considered to make a great contribution for the development of the medical industry. To address this issue, a porous carbon-based solid acid catalyst (PCSA) functionalized with -OH, -COOH and -SO₃H groups was successfully prepared. Typically, the physicochemical properties of PCSA were deeply determined by a series of characterization technique including FT-IR, TGA, RM, NH₃-TPD, SEM and Element Analysis. Moreover, the catalytic performances of PCSA towards to D-glucosamine production from chitosan were evaluated. In particular, the effects of catalyst acid density, ratio of acidic groups, chitosan concentration, reaction temperature, reaction time and catalyst dosage on the yield of D-glucosamine were investigated in detail. Interestingly, the experimental results indicated that a yield of D-glucosamine as high as 90.5% was achieved, and no obvious deactivation occurred even after six consecutive cycles. In light of the advantages of superior activity/recyclability and low cost, the starch-derived solid acid developed in this work might possess the broad industrial application prospects.

A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem

Chitin is abundant in nature and its degradation products are highly valuable for numerous applications. Thermophilic chitinases are increasingly appreciated for their capacity to biodegrade chitin at high temperatures and prolonged enzyme stability. Here, using deep learning approaches, we developed a prediction tool, Preoptem, to screen thermophilic proteins. A novel thermophilic chitinase, Chi304, was mined directly from the marine metagenome. Chi304 showed maximum activity at 85 ℃, its Tm reached 89.65 ± 0.22℃, and exhibited excellent thermal stability at 80 and 90 °C. Chi304 had both endo- and exo-chitinase activities, and the (GlcNAc)2 was the main hydrolysis product of chitin-related substrates. The product yields of colloidal chitin degradation reached 97% within 80 min, and 20% over 4 days of reaction with crude chitin powder. This study thus provides a method to mine the novel thermophilic chitinase for efficient chitin biodegradation.

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.

Chitooligosaccharides production from shrimp chaff in chitosanase cell surface display system

Chitin refers to a natural biopolymer, which is economically significant to next-generation biorefineries. In this study, a novel high-yield method with cell surface-display chitosanase (CHI-1) was built to produce chitooligosaccharides (COS) from shrimp chaff through the co-fermentation in the presence of Bacillus subtilis and Acetobacter sp. Under the optimized co-fermentation conditions (5 g/L yeast extracts, 10 g/L KH₂PO₄, 6% ethanol, 50 g/L glucose), the final deproteinization (DP) and demineralization (DM) efficiency and the chitin yield were achieved as 94, 92 and 18%, respectively. The engineered E. coli BL21-pET23b(+)-NICHI maintained 81% of the initial enzyme activity after 40 days at room temperature. The crude CHI-1 was inactivated after one-day interacting with prepared chitosan. Moreover, E. coli BL21-pET23b(+)-NICHI still maintained excellent hydrolysis ability in 7 days, and the COS yield reached 41%. Accordingly, the proposed method exhibited excellent stability and a high hydrolysis efficiency to produce COS with whole engineered cells.

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.

Structure-based rational design of chitosanase CsnMY002 for high yields of chitobiose

Chitosan oligosaccharides (COS) are attractive active molecules for biomedical applications. Currently, the prohibitively high cost of producing fully defined COS hampers extensive studies on their biological activity and restricts their use in various industries. Thus, cost-effective production of pure COS is of major importance. In this report, chitosanase from Bacillus subtilis MY002 (CsnMY002) was prepared for COS production. The structure of apo CsnMY002 displayed an unexpected tunnel-like substrate-binding site and the structure of the CsnMY002_E19A/(GlcN)₆ complex highlighted the "4 + 2″ splitting of hexaglucosamine even though the "3 + 3″ splitting is also observed in the TLC analysis of the enzyme products for hexaglucosamine. Structure based rational design was performed to generate mutants for chitobiose production. The CsnMY002_G21 K mutant produced chitobiose with a relative content > 87 % from chitosan with a low degree of acetylation, and 50.65 mg chitobiose with a purity > 98 % was prepared from 100 mg chitosan. The results provide insight on the catalytic mechanism of chitosanase and underpin future biomedical applications of pure chitobiose.

Review: Advances in preparation of chitooligosaccharides with heterogeneous sequences and their bioactivity

Chitooligosaccharides has attracted increasing attention due to their diverse bioactivities and potential application. Previous studies on the bioactivity of chitooligosaccharides were mostly carried out using a mixture. The structure-function relationship of chitooligosaccharides is not clear. Recently, it is confirmed that chitooligosaccharides with different degrees of polymerization play different roles in many bioactivities. However, heterogeneous chitooligosaccharides with a single degree of polymerization is still a mixture of many uncertain sequences and it is difficult to determine which structure is responsible for biological effects. Therefore, an interesting and challenging field of studying chitooligosaccharides with heterogeneous sequences has emerged. Herein, we reviewed the current methods for preparing heterogeneous chitooligosaccharides, including chemical synthesis, separation techniques and enzymatic methods. Advances in the bioactivities of chitooligosaccharides with heterogeneous sequences are also reviewed.