Characterization of an endo-1,3-fucanase from marine bacterium Wenyingzhuangia aestuarii: The first member of a novel glycoside hydrolase family GH174

Structural characterization and fermentation of a novel Moringa oleifera leaves polysaccharide with hypoglycemic effects

Moringa oleifera leaf-derived natural products offer diverse health benefits in metabolic disorders. However, the structural attributes of M. oleifera leaf polysaccharides, their transformations during gastrointestinal digestion, and their influence on gut microbiota and hypoglycemic activity remain insufficiently understood. This study isolated and purified a hypoglycemic polysaccharide (MOP-3) from M. oleifera leaves, primarily composed of arabinose, rhamnose, and galactose, with a molecular weight of 2.019 × 104 Da. Structural analysis identified glycosidic linkages, including →2)-α-L-Fucp-(1→, →2)-α-L-Araf-(1→, →2)-α-L-Rhap-(1→, →3,6)-β-D-Galp-(1→, →6)-β-D-Glcp-(1→, →2)-α-D-Xylp-(1→, →2,4)-β-D-Manp-(1→, →2,3)-α-D-GalpA-6-OMe-(1→, and →4)-β-D-GlcpA-6-OMe-(1→. MOP-3 reshapes gut microbiota by decreasing Firmicutes while increasing Bacteroidetes and Proteobacteria, concurrently stimulating SCFA production, and enhancing GLP-1 secretion in STC-1 cells. The structural characterization and hypoglycemic properties of MOP-3 in this study provide a theoretical basis for further utilization of food polysaccharides.

A novel endo-1,3-fucanase in glycoside hydrolase family 187 provided a biotechnological tool for preparing sulfated fucan oligosaccharides

Sulfated fucan, an important marine polysaccharide frequently presented in echinoderms and brown algae, has gained growing attention owing to its various biological activities. Fucanases are essential tools for degrading sulfated fucan to produce corresponding oligosaccharides. In this context, an endo-1,3-fucanase (Fun187Al) belonging to the GH187 family was successfully expressed in Escherichia coli. Fun187Al showed the highest activity at 30-40 °C and pH 7.5. It hydrolyzed sulfated fucan in a random endo-acting pattern, and displayed a substrate specificity different from the endo-1,3-fucanases of other glycoside hydrolase family. Analyses of ultra-performance liquid chromatography coupled with high-resolution mass spectrometry revealed that tetrasaccharide with two sulfate groups (Fuc4S2), Fuc4S3, and Fuc4S4 were respectively the major components in the end products of Fun187Al against sulfated fucans from Acaudina molpadioides, Thelonota ananas, and Holothuria tubulosa. The capability of Fun187Al to produce oligosaccharides with different degrees of polymerization and sulfation patterns demonstrated that it could be regarded as a favorable tool for establishing the structure-activity relationships of sulfated fucan and its oligosaccharides.

Structural analysis of sulfated fucan from the sea cucumber Holothuria mexicana with the assistance of endo-1,3-fucanase

Sulfated fucan from sea cucumber has received growing interest in recent decades. Insight into the primary structure of sulfated fucan is fundamental to elucidate their bioactivity. The sea cucumber Holothuria mexicana possesses a high market demand, while the structure of its sulfated fucan (Hm-FUC) remains unclear. This study investigates the structural characteristics of Hm-FUC, especially using a tool enzyme of heterologously expressed endo-1,3-fucanase (Fun168D). Hm-FUC demonstrated a 6.12 ± 0.45 % yield from the body wall of dried sea cucumber and a molecular weight of 475.2 ± 0.5 kDa. A set of procedures including enzymatic degradation, glycomics, and NMR analyses were introduced into the structural identification of Hm-FUC. The structure of Hm-FUC was determined to comprise a tetrafucose repeating unit [→3-α-l-Fucp2,4S-1 → 3-α-l-Fucp-1 → 3-α-l-Fucp2S-1 → 3-α-l-Fucp2S-1→]. The well-defined primary structure is beneficial for its application as nutritional component in foods and therapeutic agent in drugs.

The Origin, Properties, Structure, Catalytic Mechanism, and Applications of Fucoidan-Degrading Enzymes

Fucoidanase is a class of enzymes capable of hydrolyzing fucoidan, a complex sulfated polysaccharide found mainly in marine brown algae and some marine invertebrates. Fucoidan (FUC) has a wide range of potential health benefits and therapeutic effects, including antitumor, immunomodulatory, antiviral, and hypoglycemic activities. Fucoidanase can hydrolyze high-molecular-weight fucoidan into medium- and low-molecular-weight fucoidan. The low-molecular-weight fucoidan not only has good solubility, low viscosity, and high absorption rate but also retains the original biological activities of fucoidan. Fucoidanase has received much attention in recent years. This paper reviews the taxonomic origin, structure, enzymatic properties, and applications of fucoidanase to provide a reference for the study of fucoidanase.

Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota

Marine brown algae produce the highly recalcitrant polysaccharide fucoidan, contributing to long-term oceanic carbon storage and climate regulation. Fucoidan is degraded by specialized heterotrophic bacteria, which promote ecosystem function and global carbon turnover using largely uncharacterized mechanisms. Here, we isolate and study two Planctomycetota strains from the microbiome associated with the alga Fucus spiralis, which grow efficiently on chemically diverse fucoidans. One of the strains appears to internalize the polymer, while the other strain degrades it extracellularly. Multi-omic approaches show that fucoidan breakdown is mediated by the expression of divergent polysaccharide utilization loci, and endo-fucanases of family GH168 are strongly upregulated during fucoidan digestion. Enzymatic assays and structural biology studies reveal how GH168 endo-fucanases degrade various fucoidan cores from brown algae, assisted by auxiliary hydrolytic enzymes. Overall, our results provide insights into fucoidan processing mechanisms in macroalgal-associated bacteria.

Characterization of a novel endo-1,3-fucanase from Wenyingzhuangia fucanilytica within glycoside hydrolase family 168

Sulfated fucan has attracted considerable research interest in recent years due to its diverse physiological activities. Fucanase is a critical tool for investigating sulfated fucans. In the present research, a novel endo-1,3-fucanase in the GH168 family, Fun168E, was identified within a sulfated fucan utilization loci from the genome of bacterium Wenyingzhuangia fucanilytica. Fun168E was a processive degrading enzyme and demonstrated a favorable thermostability. Ultra-performance liquid chromatography-mass spectrometry and NMR experiments demonstrated that Fun168E specifically hydrolyzed the α(1 → 3) linkages between Fucp2S and Fucp2S in sulfated fucan from Isostichopus badionotus, and α(1 → 3) linkages between Fucp2S and Fucp2,4S in sulfated fucan from Holothuria tubulosa. Fun168E could accommodate Fucp2S at subsite -1, and accept Fucp2,4S and Fucp2S at subsite +1. The discovery of this novel endo-1,3-fucanase would promote the utilization of sulfated fucans and their oligosaccharides in future applications.

The structure investigation of GH174 endo-1,3-fucanase revealed an unusual glycoside hydrolase fold

Sulfated fucan has attracted increasing research interest due to its various biological activities. Endo-1,3-fucanases are favorable tools for structure investigation and structure-activity relationships establishment of sulfated fucan. However, the three-dimensional structure of enzymes from the GH174 family has not been disclosed, which hinders the understanding of the action mechanism. This study reports the first crystal structure of endo-1,3-fucanase from GH174 family (Fun174A) at a resolution of 1.60 Å. Notably, Fun174A exhibited an unusual distorted β-sandwich fold, which is distinct from other known glycoside hydrolase folds. The conserved amino acid residues D119 and H154 were proposed as the catalytic residues in the family. Molecular docking suggested that Fun174A primarily recognized sulfated fucan through a series of polar amino acid residues around the substrate binding pocket. Furthermore, structural bioinformatics analysis suggested that the structural analogs of Fun174A may be extensively implicated in the bacterial metabolism of polysaccharides, which provided opportunities for the discovery of novel glycoside hydrolases. This study offers new insights into the structural diversity of glycoside hydrolases and will contribute to the establishment of a novel clan of glycoside hydrolases.

A comprehensive review of sulfated fucan from sea cucumber: Antecedent and prospect

Sulfated fucan from sea cucumber is mainly consists of L-fucose and sulfate groups. Recent studies have confirmed that the structure of sulfated fucan mainly consists of repeating units, typically tetrasaccharides. However, there is growing evidence indicating the presence of irregular domains with heterogeneous units that have not been extensively explored. Moreover, as a key contributor to the nutritional benefits of sea cucumbers, sulfated fucan demonstrates a range of biological activities, such as anti-inflammatory, anticancer, hypolipidemic, anti-hyperglycemic, antioxidant, and anticoagulant properties. These biological activities are profoundly influenced by the structural features of sulfated fucan including molecular weight and distribution patterns of sulfate groups. The latest research indicates that sulfated fucan is dispersed in the extracellular matrix of the body wall of sea cucumbers. This article aimed to review the research progress on the in-situ distribution, structures, structural elucidation strategies, functions, and structure-activity relationships of sulfated fucan, especially in the last decade. It also provided insights into the major challenges and potential solutions in the research and development of sulfated fucan. Moreover, the fucanase and carbohydrate binding modules are anticipated to play pivotal roles in advancing this field.

Biochemical characterization and cleavage specificities analyses of three endo-1,3-fucanases within glycoside hydrolase family 174

Sulfated fucans have garnered extensive research interest in recent decades due to their varied bioactivity. Fucanases are important tools for investigating sulfated fucans. This study reported the bioinformatic analysis and biochemical properties of three GH174 family endo-1,3-fucanases. Wherein, Fun174Rm and Fun174Sb showed the highest optimal reaction temperature among the reported fucanases, and Fun174Sb possessed favorable thermostability and catalysis efficiency. Fun174Rm displayed a random endo-acting manner, while Fun174Ri and Fun174Sb hydrolyzed sulfated fucan in processive manners. UPLC-MS and NMR analyses confirmed that the three enzymes catalyze cleavage of the α(1 → 3)-bonds between Fucp2S and Fucp2S in the sulfated fucan from Isostichopus badionotus. These enzymes demonstrated novel cleavage specificities, which could accept α-Fucp2S residues at subsites -1 and + 1. The acquiring of these biotechnological tools would be beneficial to the in-depth research of sulfated fucans.

Advances in the understanding and exploitation of carbohydrate-active enzymes

Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.

Structural investigation of Fun168A unraveling the recognition mechanism of endo-1,3-fucanase towards sulfated fucan

BACKGROUND

Sulfated fucan has gained interest due to its various physiological activities. Endo-1,3-fucanases are valuable tools for investigating the structure and establishing structure-activity relationships of sulfated fucan. However, the substrate recognition mechanism of endo-1,3-fucanases towards sulfated fucan remains unclear, limiting the application of endo-1,3-fucanases in sulfated fucan research.

SCOPE AND APPROACH

This study presented the first crystal structure of endo-1,3-fucanase (Fun168A) and its complex with the tetrasaccharide product, utilizing X-ray diffraction techniques. The novel subsite specificity of Fun168A was identified through glycomics and nuclear magnetic resonance (NMR).

KEY FINDINGS AND CONCLUSIONS

The structure of Fun168A was determined at 1.92 Å. Residues D206 and E264 acted as the nucleophile and general acid/base, respectively. Notably, Fun168A strategically positioned a series of polar residues at the subsites ranging from -2 to +3, enabling interactions with the sulfate groups of sulfated fucan through salt bridges or hydrogen bonds. Based on the structure of Fun168A and its substrate recognition mechanisms, the novel subsite specificities at the -2 and +2 subsites of Fun168A were identified. Overall, this study provided insight into the structure and substrate recognition mechanism of endo-1,3-fucanase for the first time and offered a valuable tool for further research and development of sulfated fucan.

Biochemical characterization of Fsa16295Glu from "Fervidibacter sacchari," the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3

The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a β-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as β-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing β-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.

Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans

Carbohydrate-binding modules (CBMs) are non-catalytic proteins found appended to carbohydrate-active enzymes. Soil and marine bacteria secrete such enzymes to scavenge nutrition, and they often use CBMs to improve reaction rates and retention of released sugars. Here we present a structural and functional analysis of the recently established CBM family 92. All proteins analysed bind preferentially to β-1,6-glucans. This contrasts with the diversity of predicted substrates among the enzymes attached to CBM92 domains. We present crystal structures for two proteins, and confirm by mutagenesis that tryptophan residues permit ligand binding at three distinct functional binding sites on each protein. Multivalent CBM families are uncommon, so the establishment and structural characterisation of CBM92 enriches the classification database and will facilitate functional prediction in future projects. We propose that CBM92 proteins may cross-link polysaccharides in nature, and might have use in novel strategies for enzyme immobilisation.

Action Pattern of a Novel G-Specific Alginate Lyase: Determination of Subsite Specificity by HPAEC-PAD/MS

G-specific alginate lyases are important tools for alginate fragment biodegradation and oligosaccharide production, which have great potential in alginate refining research. In this research, a novel G-specific alginate lyase Aly7Ce was cloned, expressed, and characterized, with the optimal reaction conditions at 30 °C and pH 8.0. By employing the UPSEC-VWD-MS method, Aly7Ce was confirmed as a random endoacting alginate lyase. Its minimum substrate was tetrasaccharide, and the final product majorly consisted of disaccharide to tetrasaccharide. HPAEC-PAD/MS method was employed to investigate the structurally different unsaturated alginate oligosaccharides. The substrate recognition and subsite specificity of Aly7Ce were revealed by detecting the oligosaccharide pattern in the enzymatic products with oligosaccharides or polysaccharides as substrates. Aly7Ce mainly attacked the second glycosidic linkage from the nonreducing end of oligosaccharide substrates. The subsite specificity of Aly7Ce was revealed as -2 (M/G), - 1 (G), + 1 (M/G), and +2 (M/G). The regular oligosaccharide products of Aly7Ce could be applied for the efficient preparation of ΔG, ΔGG, and ΔGGG with high purity. The G-specific alginate lyase Aly7Ce with a well-defined product composition and action pattern provided a novel tool for the modification and structural elucidation of alginate, as well as for the targeted preparation of oligosaccharides.

Discovery of a catalytic domain defines a new glycoside hydrolase family containing endo-1,3-fucanase

Sulfated fucans are important marine polysaccharides with various bioactivities. Fucanases are desirable tools for the structural elucidations and oligosaccharides preparation of sulfated fucans. Herein, a gene with unknown function was screened from a sulfated fucan utilization locus in genome of marine bacterium Wenyingzhuangia aestuarii OF219 with the assistance of a machine learning approach on the structural biology. An undefined catalytic domain that presented in this gene was further cloned and expressed in Escherichia coli. Utilizing a sulfated fucan tetrasaccharide with definite structure as substrate, the endo-acting cleavage point of expressed protein (named Fun187A) was identified as the α-l-1,3-glycosidic bond between Fucp and Fucp(2OSO3-). Fun187A demonstrated a novel cleavage specificity, that is the subsite -1 could tolerate α-l-Fucp, and the subsite +1 could tolerate α-l-Fucp(2OSO3-). A homologue of Fun187A was also validated to display the endo-1,3-fucanse activity. The sequence novelty of Fun187A and its homologue defines a new glycoside hydrolase family, GH187.

The Discovery of the Fucoidan-Active Endo-1→4-α-L-Fucanase of the GH168 Family, Which Produces Fucoidan Derivatives with Regular Sulfation and Anticoagulant Activity

Sulfated polysaccharides of brown algae, fucoidans, are known for their anticoagulant properties, similar to animal heparin. Their complex and irregular structure is the main bottleneck in standardization and in defining the relationship between their structure and bioactivity. Fucoidan-active enzymes can be effective tools to overcome these problems. In the present work, we identified the gene fwf5 encoding the fucoidan-active endo-fucanase of the GH168 family in the marine bacterium Wenyingzhuangia fucanilytica CZ1127T. The biochemical characteristics of the recombinant fucanase FWf5 were investigated. Fucanase FWf5 was shown to catalyze the endo-type cleavage of the 1→4-O-glycosidic linkages between 2-O-sulfated α-L-fucose residues in fucoidans composed of the alternating 1→3- and 1→4-linked residues of sulfated α-L-fucose. This is the first report on the endo-1→4-α-L-fucanases (EC 3.2.1.212) of the GH168 family. The endo-fucanase FWf5 was used to selectively produce high- and low-molecular-weight fucoidan derivatives containing either regular alternating 2-O- and 2,4-di-O-sulfation or regular 2-O-sulfation. The polymeric 2,4-di-O-sulfated fucoidan derivative was shown to have significantly greater in vitro anticoagulant properties than 2-O-sulfated derivatives. The results have demonstrated a new type specificity among fucanases of the GH168 family and the prospects of using such enzymes to obtain standard fucoidan preparations with regular sulfation and high anticoagulant properties.

Characterization of a novel endo-1,3-fucanase from marine bacterium Wenyingzhuangia fucanilytica reveals the presence of diversity within glycoside hydrolase family 168

Sulfated fucans attract increasing research interests in recent decades for their various physiological activities. Fucanases are indispensable tools for the investigation of sulfated fucans. Herein, a novel GH168 family endo-1,3-fucanase was cloned from the genome of marine bacterium Wenyingzhuangia fucanilytica. The expressed protein Fun168D was a processive endo-acting enzyme. Ultra performance liquid chromatography-high resolution mass spectrum and NMR analyses revealed that the enzyme cleaved the α-1 → 3 bonds between α-l-Fucp(2OSO₃^-) and α-l-Fucp(2OSO₃^-) in sulfated fucan from Isostichopus badionotus, and α-1 → 3 bonds between α-l-Fucp(2OSO₃^-) and α-l-Fucp(2,4OSO₃^-) in sulfated fucan from Holothuria tubulosa. Fun168D would prefer to accept α-l-Fucp(2,4OSO₃^-) than α-l-Fucp(2OSO₃^-) at subsite +1, and could tolerate the absence of fucose residue at subsite +2. The novel cleavage specificity and hydrolysis pattern revealed the presence of diversity within the GH168 family, which would facilitate the development of diverse biotechnological tools for the molecule tailoring of sulfated fucan.

Discovery of a sulfated fucan-specific carbohydrate-binding module: The first member of a new carbohydrate-binding module family

Sulfated fucan is an important functional polysaccharide with various physiological activities. Carbohydrate-binding module (CBM) is a representative class of carbohydrate-binding protein, which could be employed as a favorable tool for the investigations and applications of polysaccharides. Nevertheless, only one confirmed sulfated fucan-binding CBM has been hitherto reported. In the present study, an unknown domain with a predicted β-sandwich fold was discovered from a fucanase Fun174A, and further cloned and heterologously expressed in Escherichia coli. The expressed protein Fun174A-CBM displayed a specific binding capacity to sulfated fucan. The bio-layer interferometry assays showed that the protein could bind to the sulfated fucan tetrasaccharide with an affinity constant of 2.83 × 10^-4 M. Fun174A-CBM shared no significant sequence similarity to any identified CBMs, indicating that it represents a new CBM family. The discovery of Fun174-CBM and the novel CBM family would be beneficial to the investigations of sulfated fucan-binding proteins.