Cloning and characterization of a novel chondroitinase ABC categorized into a new subfamily of polysaccharide lyase family 8

Biochemical Characterization and Mechanism of Thermostability of the Thermophilic Hyaluronate Lyase TcHly8D

Hyaluronate lyases are widely used in medicine and biochemical engineering and are also applied as a tool enzyme to prepare oligosaccharides with various biological activities. To date, only a few hyaluronate lyases are on sale with poor thermostability. In this study, a PL8 hyaluronate lyase, TcHly8D, was found from Thermasporomyces composti and expressed in Escherichia coli with a maximum yield of 1.77 × 109 U/L (3.14 g/L) in a 5-L bioreactor. The recombinant TcHly8D exhibited a high hyaluronate lyase activity of 5.64 × 105 U/mg and an excellent thermostability with half-lives of 184.9 h at 60 °C. Fifty micrograms of TcHly8D could catalyze 5 g of hyaluronic acid with an oligosaccharide yield of 84.8% in 4 h. The salt bridges, hydrogen bonds, and proline residues, but not disulfide bonds, played important roles in the thermostability of TcHly8D. These findings provide insights into the multifunctional application potential of TcHly8D in agriculture, medicine, and the food industry.

A comprehensive review on microbial hyaluronan-degrading enzymes: from virulence factors to biotechnological tools

Hyaluronan (HA), a natural high molecular weight polysaccharide, has extensive applications in cosmetology and medical treatment. Hyaluronan-degrading enzymes (Hyals) act as molecular scissors that cleave HA by breaking the glucosidic linkage. Hyals are present in diverse organisms, including vertebrates, invertebrates and microorganisms, and play momentous roles in biological processes. In recent years, microbial Hyals (mHyals) have gained considerable attention for their exceptional performance in the production and processing of HA. Moreover, the applications of mHyals have been greatly extended to various biomedical fields. To explore the potential applications of mHyals, a thorough comprehension is imperative. In this context, this review systematically summarizes the sources, structures, mechanisms and enzymatic properties of mHyals and discusses their biological functions in host invasion, disease development, and regulation of intestinal flora. Furthermore, versatile applications inspired by their biological functions in medicine development, molecular biology, and industrial biotechnology are comprehensively reviewed. Finally, prospects are presented to emphasize the importance of exploration, expression and characterization of mHyals and the necessity of excavating their potential in biotechnological fields.

Engineering of Substrate-Binding Domain to Improve Catalytic Activity of Chondroitin B Lyase with Semi-Rational Design

Dermatan sulfate and chondroitin sulfate are dietary supplements that can be utilized as prophylactics against thrombus formation. Low-molecular-weight dermatan sulfate (LMWDS) is particularly advantageous due to its high absorbability. The enzymatic synthesis of low-molecular-weight dermatan sulfates (LMWDSs) using chondroitin B lyase is a sustainable and environmentally friendly approach to manufacturing. However, the industrial application of chondroitin B lyases is severely hampered by their low catalytic activity. To improve the activity, a semi-rational design strategy of engineering the substrate-binding domain of chondroitin B lyase was performed based on the structure. The binding domain was subjected to screening of critical residues for modification using multiple sequence alignments and molecular docking. A total of thirteen single-point mutants were constructed and analyzed to assess their catalytic characteristics. Out of these, S90T, N103C, H134Y, and R159K exhibited noteworthy enhancements in activity. This study also examined combinatorial mutagenesis and found that the mutant H134Y/R159K exhibited a substantially enhanced catalytic activity of 1266.74 U/mg, which was 3.21-fold that of the wild-type one. Molecular docking revealed that the enhanced activity of the mutant could be attributed to the formation of new hydrogen bonds and hydrophobic interactions with the substrate as well as neighbor residues. The highly active mutant would benefit the utilization of chondroitin B lyase in pharmaceuticals and functional foods.

Efficient Expression and Characterization of an Endo-Type Lyase HCLase_M28 and Its Gradual Scale-Up Fermentation for the Preparation of Chondroitin Sulfate Oligosaccharides

Glycosaminoglycan (GAG) lyases have been critical in structural and functional studies of GAGs. HCLase_M28, a lyase identified from the genome of Microbacterium sp. M28 was heterologously expressed, enzymatically characterized, and prepared in large-scale fermentation for the production of chondroitin sulfate (CS) oligosaccharides. Results showed that the expression of HCLase_M28 in Escherichia coli BL21 (DE3)-pET24a-HCLase_M28opt1 and Bacillus subtilis W800-pSTOP1622-HCLase_M28opt2 were 108-fold and 25-fold that of wide strain. The optimal lytic reaction of HCLase_M28 happened in 20 mM Tris-HCl (pH 7.2) at 50 °C with a specific activity of 190.9 U/mg toward CS-A. The degrading activity was slightly simulated in presence of 1 mM Ca2+ and Mn2+ while severely inhibited by Hg+, Cu2+, Fe3+, and SDS. TLC and ESI-MS analysis proved HCLase_M28 was an endolytic lyase and degraded CS and hyaluronic acid into unsaturated disaccharides. Through a gradual scale-up of fermentation in 5 L, 100 L, and 1000 L, a highly efficient intracellular expression of HCLase_M28 with an activity of 3.88 × 105 U/L achieved within a 34 h of cultivation. Through ultrafiltration, CS oligosaccharides with DP of 2 to 8 as the main components could be controllably prepared. The successful large-scale fermentation made HCLase_M28 a promising enzyme for industrial production of CS oligosaccharides.

Heparinase III with High Activity and Stability: Heterologous Expression, Biochemical Characterization, and Application in Depolymerization of Heparin

A novel heparinase III from Pedobacter schmidteae (PsHep-III) with high activity and good stability was successfully cloned, expressed, and characterized. PsHep-III displayed the highest specific activity ever reported of 192.8 U mg-1 using heparin as the substrate. It was stable at 25 °C with a half-life of 323 h in an aqueous solution. PsHep-III was employed for the depolymerization of heparin, and the enzymatic hydrolyzed products were analyzed with gel permeation chromatography and high-performance liquid chromatography. PsHep-III can break glycosidic bonds in heparin like →4]GlcNAc/GlcNAc6S/GlcNS/GlcNS6S/GlcN/GlcN6S(1 → 4)ΔUA/ΔUA2S[1 → and efficiently digest heparin into seven disaccharides including N-acetylated, N-sulfated, and N-unsubstituted modification, with molecular masses of 503, 605, 563, 563, 665, 360, and 563 Da, respectively. These results indicated that PsHep-III with broad substrate specificity could be combined with heparinase I to overcome the low selectivity at the N-acetylated modification binding sites of heparinase I. This work will contribute to the application of PsHep-III for characterizing heparin and producing low-molecular-weight heparin effectively.

The hydrophobic cluster on the surface of protein is the key structural basis for the SDS-resistance of chondroitinase VhChlABC

The application of chondroitinase requires consideration of the complex microenvironment of the target. Our previous research reported a marine-derived sodium dodecyl sulfate (SDS)-resistant chondroitinase VhChlABC. This study further investigated the mechanism of VhChlABC resistance to SDS. Focusing on the hydrophobic cluster on its strong hydrophilic surface, it was found that the reduction of hydrophobicity of surface residues Ala181, Met182, Met183, Ala184, Val185, and Ile305 significantly reduced the SDS resistance and stability. Molecular dynamics (MD) simulation and molecular docking analysis showed that I305G had more conformational flexibility around residue 305 than wild type (WT), which was more conducive to SDS insertion and binding. The affinity of A181G, M182A, M183A, V185A and I305G to SDS was significantly higher than that of WT. In conclusion, the surface hydrophobic microenvironment composed of six residues was the structural basis for SDS resistance. This feature could prevent the binding of SDS and the destruction of hydrophobic packaging by increasing the rigid conformation of protein and reducing the binding force of SDS-protein. The study provides a new idea for the rational design of SDS-resistant proteins and may further promote chondroitinase research in the targeted therapy of lung diseases under the pressure of pulmonary surfactant.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00201-1.

Advances and challenges in biotechnological production of chondroitin sulfate and its oligosaccharides

Chondroitin sulfate (CS) is a member of glycosaminoglycans (GAGs) and has critical physiological functions. CS is widely applied in medical and clinical fields. Currently, the supply of CS relies on traditional animal tissue extraction methods. From the perspective of medical applications, the biggest drawback of animal-derived CS is its uncontrollable molecular weight and sulfonated patterns, which are key factors affecting CS activities. The advances of cell-free enzyme catalyzed systems and de novo biosynthesis strategies have paved the way to rationally regulate CS sulfonated pattern and molecular weight. In this review, we first present a general overview of biosynthesized CS and its oligosaccharides. Then, the advances in chondroitin biosynthesis, 3'-phosphoadenosine-5'-phosphosulfate (PAPS) synthesis and regeneration, and CS biosynthesis catalyzed by sulfotransferases are discussed. Moreover, the progress of mining and expression of chondroitin depolymerizing enzymes for preparation of CS oligosaccharides is also summarized. Finally, we analyze and discuss the challenges faced in synthesizing CS and its oligosaccharides using microbial and enzymatic methods. In summary, the biotechnological production of CS and its oligosaccharides is a promising method in addressing the drawbacks associated with animal-derived CS and enabling the production of CS oligosaccharides with defined structures.

Enzymatic comparison of two homologous enzymes reveals N-terminal domain of chondroitinase ABC I regulates substrate selection and product generation

Chondroitinase ABC-type I (CSase ABC I), which can digest both chondroitin sulfate (CS) and dermatan sulfate (DS) in an endolytic manner, is an essential tool in structural and functional studies of CS/DS. Although a few CSase ABC I have been identified from bacteria, the substrate-degrading pattern and regulatory mechanisms of them have rarely been investigated. Herein, two CSase ABC I, IM3796 and IM1634, were identified from the intestinal metagenome of CS-fed mice. They show high sequence homology (query coverage: 88.00%, percent identity: 90.10%) except for an extra peptide (Met¹-His¹⁰⁹) at the N-terminus in IM1634, but their enzymatic properties are very different. IM3796 prefers to degrade 6-O-sulfated GalNAc residue-enriched CS into tetra- and disaccharides. In contrast, IM1634 exhibits nearly a thousand times more activity than IM3796, and can completely digest CS/DS with various sulfation patterns to produce disaccharides, unlike most CSase ABC I. Structure modeling showed that IM3796 did not contain an N-terminal domain composed of two β-sheets, which is found in IM1634 and other CSase ABC I. Furthermore, deletion of the N-terminal domain (Met¹-His¹⁰⁹) from IM1634 caused the enzymatic properties of the variant IM1634-T109 to be similar to those of IM3796, and conversely, grafting this domain to IM3796 increased the similarity of the variant IM3796-A109 to IM1634. In conclusion, the comparative study of the new CSase ABC I provides two unique tools for CS/DS-related studies and applications and, more importantly, reveals the critical role of the N-terminal domain in regulating the substrate binding and degradation of these enzymes.

Hungatella hathewayi, an Efficient Glycosaminoglycan-Degrading Firmicutes from Human Gut and Its Chondroitin ABC Exolyase with High Activity and Broad Substrate Specificity

An increased understanding of GAG metabolism by intestinal bacteria is critical in identifying the driving factors for the composition, modulation, and homeostasis of the human gut microbiota. In addition, GAG-depolymerizing polysaccharide lyases are highly desired enzymes for the production of GAG oligosaccharides and as therapeutics.

YsHyl8A, an Alkalophilic Cold-Adapted Glycosaminoglycan Lyase Cloned from Pathogenic Yersinia sp. 298

A high enzyme-yield strain Yersinia sp. 298 was screened from marine bacteria harvested from the coastal water. The screening conditions were extensive, utilizing hyaluronic acid (HA)/chondroitin sulfate (CS) as the carbon source. A coding gene yshyl8A of the family 8 polysaccharide lyase (PL8) was cloned from the genome of Yersinia sp. 298 and subjected to recombinant expression. The specific activity of the recombinase YsHyl8A was 11.19 U/mg, with an optimal reaction temperature of 40 °C and 50% of its specific activity remaining after thermal incubation at 30 °C for 1 h. In addition, its optimal reaction pH was 7.5, and while it was most stable at pH 6.0 in Na2HPO4-citric acid buffer, it remained highly stable at pH 6.0–11.0. Further, its enzymatic activity was increased five-fold with 0.1 M NaCl. YsHyl8A, as an endo-lyase, can degrade both HA and CS, producing disaccharide end-products. These properties suggested that YsHyl8A possessed both significant alkalophilic and cold-adapted features while being dependent on NaCl, likely resulting from its marine source. Yersinia is a typical fish pathogen, with glycosaminoglycan lyase (GAG lyase) as a potential pathogenic factor, exhibiting strong hyaluronidase and chondroitinase activity. Further research on the pathogenic mechanism of GAG lyase may benefit the prevention and treatment of related diseases.

Characterization of a Thermostable and Surfactant-Tolerant Chondroitinase B from a Marine Bacterium Microbulbifer sp. ALW1

Chondroitinase plays an important role in structural and functional studies of chondroitin sulfate (CS). In this study, a new member of chondroitinase B of PL6 family, namely ChSase B6, was cloned from marine bacterium Microbulbifer sp. ALW1 and subjected to enzymatic and structural characterization. The recombinant ChSase B6 showed optimum activity at 40 °C and pH 8.0, with enzyme kinetic parameters of Km and Vmax against chondroitin sulfate B (CSB) to be 7.85 µg/mL and 1.21 U/mg, respectively. ChSase B6 demonstrated thermostability under 60 °C for 2 h with about 50% residual activity and good pH stability under 4.0-10.0 for 1 h with above 60% residual activity. In addition, ChSase B6 displayed excellent stability against the surfactants including Tween-20, Tween-80, Trion X-100, and CTAB. The degradation products of ChSase B6-treated CSB exhibited improved antioxidant ability as a hydroxyl radical scavenger. Structural analysis and site-directed mutagenesis suggested that the conserved residues Lys248 and Arg269 were important for the activity of ChSase B6. Characterization, structure, and molecular dynamics simulation of ChSase B6 provided a guide for further tailoring for its industrial application for chondroitin sulfate bioresource development.

Standard Candles for Dating Microbial Lineages

Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.

Microbial Regulation of Deterioration and Preservation of Salted Kelp under Different Temperature and Salinity Conditions

High salinity is an effective measure to preserve kelp, but salted kelp can still deteriorate after long-term preservation. In order to clarify the key conditions and microbial behavior of salted kelp preservation, 10% (S10), 20% (S20), and 30% (S30) salt concentrations were evaluated at 25 °C (T25) and 4 °C (T4). After 30 days storage, these salted kelps showed different states including rot (T25S10), softening (T25S20), and undamaged (other samples). By detecting polysaccharide lyase activity and performing high-throughput sequencing of the prokaryotic 16S rRNA sequence and metagenome, we found that deteriorated kelps (T25S10 and T25S20) had significantly higher alginate lyase activity and bacterial relative abundance than other undamaged samples. Dyella, Saccharophagus, Halomonas, Aromatoleum, Ulvibacter, Rhodopirellula, and Microbulbifer were annotated with genes encoding endonuclease-type alginate lyases, while Bacillus and Thiobacillus were annotated as the exonuclease type. Additionally, no alginate lyase activity was detected in undamaged kelps, whose dominant microorganisms were halophilic archaea without alginate lyase-encoding genes. These results indicated that room-temperature storage may promote salted kelp deterioration due to the secretion of bacterial alginate lyase, while ultra-high-salinity and low-temperature storage can inhibit bacterial alginate lyase and promote the growth of halophilic archaea without alginate lyase, thus achieving the preservation of salted kelp.

Identification and Biochemical Characterization of a Surfactant-Tolerant Chondroitinase VhChlABC from Vibrio hyugaensis LWW-1

Chondroitinases, catalyzing the degradation of chondroitin sulfate (CS) into oligosaccharides, not only play a crucial role in understanding the structure and function of CS, but also have been reported as a potential candidate drug for the treatment of high CS-related diseases. Here, a marine bacterium Vibrio hyugaensis LWW-1 was isolated, and its genome was sequenced and annotated. A chondroitinase, VhChlABC, was found to belong to the second subfamily of polysaccharide lyase (PL) family 8. VhChlABC was recombinant expressed and characterized. It could specifically degrade CS-A, CS-B, and CS-C, and reached the maximum activity at pH 7.0 and 40 °C in the presence of 0.25 M NaCl. VhChlABC showed high stability within 8 h under 37 °C and within 2 h under 40 °C. VhChlABC was stable in a wide range of pH (5.0~10.6) at 4 °C. Unlike most chondroitinases, VhChlABC showed high surfactant tolerance, which might provide a good tool for removing extracellular CS proteoglycans (CSPGs) of lung cancer under the stress of pulmonary surfactant. VhChlABC completely degraded CS to disaccharide by the exolytic mode. This research expanded the research and application system of chondroitinases.

Characterization of a Hyaluronic Acid Utilization Locus and Identification of Two Hyaluronate Lyases in a Marine Bacterium Vibrio alginolyticus LWW-9

Hyaluronic acid (HA) is a negatively charged and linear polysaccharide existing in the tissues and body fluids of all vertebrates. Some pathogenic bacteria target hyaluronic acid for adhesion and/or infection to host cells. Vibrio alginolyticus is an opportunistic pathogen related to infections of humans and marine animals, and the hyaluronic acid-degrading potential of Vibrio spp. has been well-demonstrated. However, little is known about how Vibrio spp. utilize hyaluronic acid. In this study, a marine bacterium V. alginolyticus LWW-9 capable of degrading hyaluronic acid has been isolated. Genetic and bioinformatic analysis showed that V. alginolyticus LWW-9 harbors a gene cluster involved in the degradation, transport, and metabolism of hyaluronic acid. Two novel PL8 family hyaluronate lyases, VaHly8A and VaHly8B, are the key enzymes for the degradation of hyaluronic acid. VaHly8A and VaHly8B have distinct biochemical properties, reflecting the adaptation of the strain to the changing parameters of the aquatic habitats and hosts. Based on genomic and functional analysis, we propose a model for the complete degradation of hyaluronic acid by V. alginolyticus LWW-9. Overall, our study expands our knowledge of the HA utilization paradigm within the Proteobacteria, and the two novel hyaluronate lyases are excellent candidates for industrial applications.