Enzymatic preparation and structural determination of oligosaccharides derived from sea cucumber (Acaudina molpadioides) fucoidan

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.

Structural characterization of a distinct fucan sulfate from Pattalus mollis through an oligosaccharide mapping approach

The elucidation of the precise structure of fucan sulfate is essential for understanding the structure-activity relationship and promoting potential biomedical applications. In this work, the structure of a distinct fucan sulfate fraction V (PmFS in Ref 15 and FSV in Ref 16 → PFV) from Pattalus mollis was investigated using an oligosaccharide mapping approach. Six size-homogeneous fractions were purified from the mild acid hydrolyzed PFV and identified as fucitols, disaccharides and trisaccharides by 1D/2D NMR and MS analysis. Significantly, the sulfation pattern, glycosidic linkages, and sequences of all the oligosaccharides were unambiguously identified. The common 2-desulfation of the reducing end residue of the oligosaccharides was observed. Overall, the backbone of PFV was composed of L-Fuc2S (major) and L-Fuc3S (minor) linked by α1,4 glycosidic bonds. Importantly, the branches contain both monosaccharide and disaccharide linked to the backbone by α1,3 glycosidic linkages. Thus, the tentative structure of natural PFV was shown to be {-(R-α1,3)-L-Fuc2S-α1,4-(L-Fuc2S/3S-α1,4)x-}n, where R is L-Fuc(2S)4S-α1,3/4-L-Fuc4S(0S)- or L-Fuc(2S)4S-. Our results provide insight into the heterogeneous structure of the fucan sulfate found in sea cucumbers. Additionally, PFV and its fractions showed strong anticoagulant and anti-iXase activities, which may be related to the distinct structure of PFV.

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.

Structural Characterization and Anticoagulant Activities of a Keratan Sulfate-like Polysaccharide from the Sea Cucumber Holothuria fuscopunctata

A sulfated polysaccharide (AG) was extracted and isolated from the sea cucumber H. fuscopunctata, consisting of GlcNAc, GalNAc, Gal, Fuc and lacking any uronic acid residues. Importantly, several chemical depolymerization methods were used to elucidate the structure of the AG through a bottom-up strategy. A highly sulfated galactose (oAG-1) and two disaccharides labeled with 2,5-anhydro-D-mannose (oAG-2, oAG-3) were obtained from the deaminative depolymerized product along with the structures of the disaccharide derivatives (oAG-4~oAG-6) identified from the free radical depolymerized product, suggesting that the repeating building blocks in a natural AG should comprise the disaccharide β-D-GalS-1,4-D-GlcNAc6S. The possible disaccharide side chains (bAG-1) were obtained with mild acid hydrolysis. Thus, a natural AG may consist of a keratan sulfate-like (KS-like) glycosaminoglycan with diverse modifications, including the sulfation types of the Gal residue and the possible disaccharide branches α-D-GalNAc4S6S-1,2-α/β-L-Fuc3S linked to the KS-like chain. Additionally, the anticoagulant activities of the AG and its depolymerized products (dAG1-9) were evaluated in vitro using normal human plasma. The AG could prolong activated partial thromboplastin time (APTT) in a dose-dependent manner, and the activity potency was positively related to the chain length. The AG and dAG1-dAG3 could prolong thrombin time (TT), while they had little effect on prothrombin time (PT). The results indicate that the AG could inhibit the intrinsic and common coagulation pathways.

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.

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

Sulfated fucans are important marine polysaccharides with various biological and biomedical activities. Fucanases are favorable tools to establish the structure-activity relationships of sulfated fucans. Herein, gene fun174A was discovered from the genome of marine bacterium Wenyingzhuangia aestuarii OF219, and none of the pre-defined glycosidic hydrolase domains were predicted in the protein sequence of Fun174A. Recombinant Fun174A demonstrated a low optimal reaction pH at 5.5. It might degrade sulfated fucans in an endo-processive manner. Glycomics and NMR analyses proved that it specifically hydrolyzed α-1,3-l-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber Isostichopus badionotus. D119, E120 and E218 were critical for the activity of Fun174A, as identified by site-directed mutagenesis. Three homologs of Fun174A were confirmed to exhibit endo-1,3-fucanase activities. The novelty on sequences of Fun174A and its homologs reveals a new glycoside hydrolase family, GH174.

Structure Elucidation of Fucan Sulfate from Sea Cucumber Holothuria fuscopunctata through a Bottom-Up Strategy and the Antioxidant Activity Analysis

Fucan sulfate I (FSI) from the sea cucumber Holothuria fuscopunctata was purified and its structure was clarified based on a bottom-up strategy. The unambiguous structures of a series of oligosaccharides including disaccharides, trisaccharides, and tetrasaccharides, which were released from mild acid hydrolysis of FSI, were identified by one-dimensional (1D)/two-dimensional (2D) nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis. All the glycosidic bonds in these oligosaccharides were presented as α1,3 linkages confirmed by correlated signals from their ¹H-¹H ROESY and ¹H-¹³C HMBC spectra. The structural sequence of these oligosaccharides formed by Fuc_2S4S, Fuc_2S, and non-sulfated ones (Fuc_0S), along with the general structural information of FSI, indicated that the structure of FSI could be elucidated as: [-L-Fuc_2S4S-α1,3-L-Fuc_(2S)-α1,3-L-Fuc_2S-α1,3-L-Fuc_0S-α1,3-1-]_n. Moreover, the L-Fuc_0S-α1,3-L-Fuc_2S4S linkage in FSI was susceptible to be cleaved by mild acid hydrolysis. The antioxidant activity assays in vitro showed that FSI and the depolymerized product (dFSI') had potent activities for superoxide radical scavenging activity with IC₅₀ of 65.71 and 83.72 μg/mL, respectively, while there was no scavenging effect on DPPH, hydroxyl and ABTS radicals.

Facile production of chitin from shrimp shells using a deep eutectic solvent and acetic acid

High purity chitin was extracted from shrimp shells by a green, sustainable, and efficient one-pot approach using a deep eutectic solvent consisting of choline chloride and glycerol (ChCl–Gl) combined with a small amount of acetic acid. Under the conditions of an acetic acid concentration of 7.5 wt% and reaction temperature of 120 °C, the purity of isolated chitin was up to 96.1%, which was superior to that of 87.7% obtained by conventional chemical method. In addition, the viscosity-average molecular weight and crystallinity of the extracted chitin were revealed to be larger than for the latter. Moreover, the deep eutectic solvent could be recycled at least three times without losing the quality of the extracted chitin. This facile approach combining recyclable DES with a small amount of acetic acid was expected to be used for the green and sustainable production of chitin from shrimp shells.

High purity chitin was extracted from shrimp shells by a green, sustainable, and efficient one-pot approach using a deep eutectic solvent consisting of choline chloride and glycerol (ChCl–Gl) combined with a small amount of acetic acid.

Discovery and Characterization of an Endo-1,3-Fucanase From Marine Bacterium Wenyingzhuangia fucanilytica: A Novel Glycoside Hydrolase Family

Sulfated fucans are important marine polysaccharides widely distributed in brown algae and echinoderms, which gained increasing research interest for their various biological and biomedical activities. Fucanases could serve as tools in the bioconversion and structural investigation of sulfated fucans. A few gene-defined endo-1,4-fucanases have been characterized, while the sequence of endo-1,3-fucanase remain unstudied. Here, an endo-1,3-fucanase gene funA was screened from the genome of marine bacterium Wenyingzhuangia fucanilytica CZ1127^T using transcriptomics. None of the previously reported glycoside hydrolase domains were predicted in the enzyme FunA, which hydrolyzed sulfated fucans in a random endo-acting manner. Ultrahigh performance size exclusion chromatography-mass spectrometry and nuclear magnetic resonance analyses revealed that FunA specifically cleaves α-1,3 glycosidic linkage between 2-O-sulfated and non-sulfated fucose residues. FunA exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. D206 and E264 were critical for the functioning of FunA as identified by the site-directed mutagenesis. Another five homologs of FunA were confirmed to possess endo-1,3-fucanase activities. This is the first report on the sequence of endo-1,3-fucanase. The novelty of FunA and its homologs in sequences and activity shed light on a novel glycoside hydrolase family, GH168.

Structural characterization of ulvan extracted from Ulva clathrata assisted by an ulvan lyase

Rhamnan-rich sulfated polysaccharides extracted from green algae (ulvan) constitute potentially useful natural materials for drug development. However, the characterization of their complex structures poses a challenge for their application. In this study, the structure of ulvan extracted from Ulva clathrata was analyzed with the assistance of an ulvan lyase belonging to the PL25 family. According to mass spectrometry and nuclear magnetic resonance analysis of the degraded oligosaccharides, the backbone of such a polysaccharide mainly consisted of →4)-β-d-GlcA-(1→4)-α-l-Rha3S-(1→ and →4)-β-d-Xyl-(1→4)-α-l-Rha3S-(1→ disaccharide repeating units, and the ratio is approximately 4:1. In addition, about 4% of the xylose moieties bear sulfate groups. Minor amounts of branches containing hexose and unsaturated glucuronic acid were found during the sequence analysis of hexa- to octasaccharides. These results indicated the presence of a long branch in the ulvan. The clarification of the detailed structure provides a foundation for ulvan modification and its structure-activity relationship studies.

Expression and Characterization of a Novel β-Porphyranase from Marine Bacterium Wenyingzhuangia fucanilytica: A Biotechnological Tool for Degrading Porphyran

Porphyra is one of the most consumed types of red algae. Porphyran is the major polysaccharide extracted from Porphyra, and it is composed of alternating 4-linked α-l-galactopyranose-6-sulfate (L6S) and 3-linked β-d-galactopyranose (G) residues. β-Porphyranases are promising tools for degrading porphyran; however, few enzymes have been reported, and the biochemical properties of porphyranases are still unclear. Here, a novel GH16 β-porphyranase, designated as Por16A_Wf, was cloned from Wenyingzhuangia fucanilytica and expressed in Escherichia coli. Its biochemical properties and hydrolysis pattern were characterized. Por16A_Wf exhibited stable activity on a wide pH scale from 3.5 to 11.0. Glycomics analysis using LC-MS revealed that Por16A_Wf specifically hydrolyzed the glycosidic linkage of G-L6S, whereas it tolerated 3,6-anhydro-α-l-galactopyranose and methyl-d-galactose in -2 and +2 subsites, respectively. Por16A_Wf could be applied as a biotechnological tool for tailoring porphyran, which would serve in directional preparation of its disaccharide, producing products with various molecular weights and facilitating investigation of the structural heterogeneity of Porphyra polysaccharides.

Structure and molecular morphology of a novel moisturizing exopolysaccharide produced by Phyllobacterium sp. 921F

Bacterial exopolysaccharides (EPSs) are widely applied in food, cosmetic, and medical industries. The EPS produced by Phyllobacterium sp. 921F was a novel polysaccharide, which exhibits attractive characteristics of high yield, favorable rheological properties, and excellent moisture retention ability. Considering the complexity of polysaccharide structures, specific enzymatic hydrolysis was employed here to resolve the structure of the EPS. End-products including tetra-, hexa- and octa-saccharides were isolated. According to their mass spectroscopy (MS) and nuclear magnetic resonance (NMR) spectra, the backbone of the EPS was found to be mainly comprising a → 4)-β-d-Glcp-(1 → 3)-α-d-Galp(4,6-S-Pyr)-(1 → disaccharide repeating units. Based on atomic force microscopy results, EPS exhibited characteristics that were consistent with a stiff, elongated molecule with no branches. The length and height of the single molecular chain were approximately 600 and 0.7 nm, respectively. Our clarification of structure and molecular morphology of EPS from Phyllobacterium sp. 921F provide a foundation for the industrial application of this potential moisture-retaining material.

Identification and Antioxidant Activity of Flavonoids Extracted from Xinjiang Jujube (Ziziphus jujube Mill.) Leaves with Ultra-High Pressure Extraction Technology

In this study, the ultra-high pressure extraction (UHPE) conditions for obtaining the maximum flavonoid yield from Xinjiang jujube (Ziziphus jujuba Mill.) leaves (XJL) were optimized by response surface methodology (RSM). Box–Behnken design (BBD) was applied to evaluate the effects of four variables (extraction temperature, pressure, time and liquid-to-solid ratio) on flavonoid yield. The results showed that the optimal flavonoid yield (25.45 ± 0.21 mg/g) was derived at 50.0 °C, 342.39 MPa, 11.56 min, and a liquid-to-solid ratio of 43.95 mL/g. Eight compounds were tentatively identified and quantified as kaempferol and quercetin glycosides with UPLC-ESI-MS. Compared to ultrasound-assisted extraction (UAE), UHPE can obtain higher concentrations of total flavonoids and stronger DPPH and ABTS radical-scavenging activities in a much shorter time. Therefore, UHPE is an alternative to UAE for obtaining flavonoids from XJL, which may be an optional method for large-scale industrial flavonoid extraction from XJL.

Development and application of a HPLC-MS/MS method for quantitation of fucosylated chondroitin sulfate and fucoidan in sea cucumbers

Fucosylated chondroitin sulfate (FCS) and fucoidan (FUC) are two main bioactive polysaccharides in sea cucumbers. A novel method for quantitation of FCS and FUC was developed by detecting chondroitin disaccharide and fucose produced through acid hydrolysis using HPLC-MS/MS. The present method showed satisfactory performance for both saccharides. It was applied to assay sea cucumbers (Stichopus japonicus) reared in pond grow-out or bottom sowing, and the results were compared with those obtained by traditional HPLC method and 1,9-dimethylmethylene blue test, which could only provide the total sea cucumber polysaccharide (SCP) contents. No difference of total SCP content was observed between sea cucumbers reared through different ways, while a higher ratio of FCS to FUC of sea cucumbers of pond grow-out was revealed by the present method. Thus, this novel method is potential to quantify the two polysaccharides and could be a powerful tool for quality evaluation of sea cucumbers.

Purification, expression and characterization of a novel α-l-fucosidase from a marine bacteria Wenyingzhuangia fucanilytica

α-l-Fucosyl residues are frequently found in oligosaccharides, polysaccharides and glycoconjugates which play fundamental roles in various biological processes. α-l-Fucosidases, glycoside hydrolases for catalyzing the removal of α-l-fucose, can serve as desirable tools in the study and the modification of fucose-containing biomolecules. In this study, an α-l-fucosidase named as Alf1_Wf was purified from a marine bacterium Wenyingzhuangia fucanilytica by using a combination of chromatographic procedures. The sequence of Alf1_Wf was identified via proteomics analysis against the predicted proteome of the bacterium. Recombinant Alf1_Wf with 6×His tag was expressed in E. coli and showed α-l-fucosidase activity. Sequence annotation revealed that Alf1_Wf contained a combination of GH29 catalytic domain and CBM35 accessory domain. Alf1_Wf was confirmed as a member of GH29-A subfamily based on the phylogenetic analysis. Furthermore, biochemical properties and kinetic characteristics of the enzyme were also determined. Substrate specificity determination showed that Alf1_Wf was capable in hydrolyzing α1,4-fucosidic linkage and synthetic substrate pNP-fucose. Besides, Alf1_Wf could act on partially degraded fucoidan. This study successfully purified, identified, cloned, expressed and characterized a novel α-l-fucosidase, and meanwhile revealed a new multidomain structure of glycoside hydrolase. The knowledge gained from this study should facilitate the further research and application of α-l-fucosidases.

Extraction, molecular weight distribution, and antioxidant activity of oligosaccharides from longan (Dimocarpus Longan Lour.) pulp

Ultrasonic-microwave synergistic extraction (UMSE) was optimized for the extraction of oligosaccharides from longan pulp (OLP). Box-Behnken design was used to evaluate the effects of temperature (35-55°C), ultrasonic time (5-25 min), and water to material ratio (10-30 mL/g) on the extraction efficiency of crude OLP. A regression model was developed and its validity was statistically demonstrated. Significant interaction between temperature and water to material ratio was observed. The following optimal conditions for the extraction yield of crude OLP were determined: extraction temperature 55°C, ultrasonic time 18.52 min, and water to material ratio 10 mL/g. The extracted OLP were purified for the determination of molecular weight distribution and antioxidant activity. Results of matrix-assisted laser desorption ionization time-of-flight mass spectrometry revealed that the molecular weight distribution of the purified OLP ranged from m/z 495.138 to 795.511. The purified OLP exhibited a dose-dependent behavior in 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity.

Wenyingzhuangia fucanilytica sp. nov., a sulfated fucan utilizing bacterium isolated from shallow coastal seawater

A Gram-staining-negative, rod-shaped, strictly aerobic, non-flagellated, non-gliding and yellow-pigmented bacterial strain, designated as strain CZ1127T, capable of utilizing sulfated fucan, was isolated from shallow coastal seawater of Jiaozhou Bay, Qingdao, PR China. Its taxonomic position was investigated by a polyphasic approach. CZ1127T grew at 15-37 °C (optimum, 25 °C), pH 5.5-9.0 (optimum, pH 6.5-7.5) and in the presence of 0-4 % (w/v) NaCl [optimum, 0-3 % (w/v)]. CZ1127T contained MK-6 as the sole menaquinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c/C16 : 1ω6c and iso-C15 : 0 3-OH as its major fatty acids. The DNA G+C content of strain CZ1127T was 32.2 mol%. Phylogenetic analysis based on the 16S rRNA gene indicated that strain CZ1127T clustered with members of the genus Wenyingzhuangia and was closely related to Wenyingzhuangia marina CGMCC 1.12162T (97.4 % 16S rRNA gene sequence similarity) and Wenyingzhuangia gracilariae KCTC 42246T (96.1 %). The DNA-DNA relatedness between strain CZ1127T and W. marina CGMCC 1.12162T was 41.9±1.5 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, CZ1127T represents a novel species of the genus Wenyingzhuangia, for which the name Wenyingzhuangia fucanilytica sp. nov. is proposed. The type strain is CZ1127T (=CCTCC AB 2015089T=KCTC 42864T).

Fucoidanases

In recent years, the research of fucoidans has steadily increased. The interest in these substances is due to their various biological activities. Despite a wide range of biological activity and the lack of oral toxicity, fucoidans remain relatively unexploited as a source of medicines because of their heterogeneity. Enzymes that degrade polyanionic polysaccharides are widely used for establishing their structures and structure-activity relationships. Sometimes, to obtain preparations of polysaccharides with standard characteristics, for example, medicines and food supplements, enzymatic treatment can be also applied. Only a few sources of enzymes with fucoidanase activity have been described, and only a few studies regarding the isolation and characterization of fucoidanases have been performed. The data on the specificity of fucoidanases: the type of cleaved glycoside bond, the relation between catalytic activity and the degree of substrate sulfation are scarce. The review summarizes achievements in the research of fucoidanases, mechanisms of enzymatic degradation of fucoidans, as well as of structures of sulfated fucooligosaccharides obtained under the action of fucoidanases.

New Cytotoxic Triterpene Glycoside from the East China Sea Cucumber Holothuria nobilis

A new cytotoxic triterpene glycoside named nobiliside E (1) has been obtained from the East China Sea cucumber Holothuria nobilis Selenka. Its structure was determined on the basis of NMR spectroscopic and MS analyses, together with chemical evidence. The new compound showed significant cytotoxicity to eight human tumor cell lines with IC50 values in the range of 0.53–4.06 μg/mL.

Dietary fucoidan of Acaudina molpadioides and its enzymatically degraded fragments could prevent intestinal mucositis induced by chemotherapy in mice

Mucositis is a common problem that results from cancer chemotherapy and is a cause of significant morbidity and occasional mortality.