Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24

Ferritin-tagged ulva polysaccharide lyase for efficient degradation of biomass polysaccharides into reducing sugars

Enhancing the stability and the reusability of ulva polysaccharide lyase (UPL) is crucial for the efficient production of reducing sugars from ulva polysaccharides, which are vital for their broad applications in functional foods. In this study, we innovatively developed a self-immobilized UPL by fusing the enzyme with ferritin, leading to the spontaneous formation of micron-sized ulva polysaccharide lyase supraparticles (mUPLSPs). This novel system streamlines the enzyme purification and immobilization process into a single step, effectively circumventing the need for conventional, laborious chromatographic methods. The mUPLSPs exhibited superior stability and reusability, maintaining over 80% of their initial activity after five cycles of use. When compared to free UPLs, mUPLSPs displayed enhanced thermal and pH stability, resulting in a 252% increase in the yield of reducing sugars after a 40-hour reaction period. The ferritin-tagged, self-immobilization strategy not only provides a scalable and cost-efficient approach to the sustainable production of reducing sugars from ulva polysaccharides but also holds significant potential for industrial-scale applications.

Complete genome sequence of Alteromonas sp. OM2203, a marine bacterium degrading Ulva prolifera polysaccharides

Green algae Ulva prolifera cause successive green tides in the Yellow Sea, China, leading to harmful ecological impacts and economic losses. Bacterial degradation of U. prolifera polysaccharides could accelerate the breakdown of its biomass and transition to the waning phase of green tides. In this study, the strain Alteromonas sp. OM2203 was isolated from seawater samples in the coastal area of Qingdao during a U. prolifera bloom. The genome of strain OM2203 contains one circular chromosome totaling 4,556,409 bp, with a mean GC content of 44.05%. Genomic analysis revealed that Alteromonas sp. OM2203 contains 6 ulvan lyase genes, indicating its potential to degrade U. prolifera polysaccharides and expedite the decomposition of algal biomass. Collectively, the genome of Alteromonas sp. OM2203 provides insights into the role of Alteromonas bacteria in U. prolifera polysaccharide degradation.

Complete genome sequence of Alteromonas marina OM2201, a marine bacterium degrading Ulva prolifera polysaccharides isolated from surface of the Yellow Sea

As a consequence of marine eutrophication, there has been an exponential growth of Ulva prolifera, culminating in the yearly emergence of a massive green tide along the shores of Qingdao. This phenomenon exerts a detrimental impact on the marine ecosystem. As reported, the expression level of Alteromonas enzymes involved in U. prolifera polysaccharides degradation is increased during the green tide outbreak period, potentially accelerating the breakdown of U. prolifera biomass. This enhanced degradation could facilitate the transition to the waning phase of the green tide event. In this study, strain Alteromonas marina OM2201 was isolated from seawater samples taken during an U. prolifera bloom in the coastal waters of Qingdao. Its genome contains a ring chromosome and two plasmids. The length of the circular chromosome was 4,489,073 bp with GC content of 44.21 mol%, and the length of plasmid 1 was 233,636 bp with GC content of 42.24 mol%, and the length of plasmid 2 was 5594 bp with GC content of 39.61 mol%. Genomic analysis showed that Alteromonas marina OM2201 contained a variety of ulvan lyase genes, indicating that it could promote the degradation of U. prolifera polysaccharides. This genetic makeup potentially enables the strain to expedite the decomposition of U. prolifera biomass. Therefore, this study broadens our understanding of the Alteromonas bacteria that can degrade U. prolifera polysaccharides during the outbreak period.

Directed preparation of algal oligosaccharides with specific structures by algal polysaccharide degrading enzymes

Seaweed polysaccharides have a wide range of sources and rich content, with various biological activities such as anti-inflammatory, anti-tumor, anticoagulant, and blood pressure lowering. They can be applied in fields such as food, agriculture, and medicine. However, the poor solubility of macromolecular seaweed polysaccharides limits their further application. Reports have shown that some biological activities of seaweed oligosaccharides are more extensive and superior to that of seaweed polysaccharides. Therefore, reducing the degree of polymerization of polysaccharides will be the key to the high value utilization of seaweed polysaccharide resources. There are three main methods for degrading algal polysaccharides into algal oligosaccharides, physical, chemical and enzymatic degradation. Among them, enzymatic degradation has been a hot research topic in recent years. Various types of algal polysaccharide hydrolases and related glycosidases are powerful tools for the preparation of algal oligosaccharides, including α-agarases, β-agaroses, α-neoagarose hydrolases and β-galactosidases that are related to agar, κ-carrageenases, ι-carrageenases and λ-carrageenases that are related to carrageenan, β-porphyranases that are related to porphyran, funoran hydrolases that are related to funoran, alginate lyases that are related to alginate and ulvan lyases related to ulvan. This paper describes the bioactivities of agar oligosaccharide, carrageenan oligosaccharide, porphyran oligosaccharide, funoran oligosaccharide, alginate oligosaccharide and ulvan oligosaccharide and provides a detailed review of the progress of research on the enzymatic preparation of these six oligosaccharides. At the same time, the problems and challenges faced are presented to guide and improve the preparation and application of algal oligosaccharides in the future.

Sustainable Production of Ulva Oligosaccharides via Enzymatic Hydrolysis: A Review on Ulvan Lyase

Ulvan is a water-soluble sulfated polysaccharide extracted from the green algae cell wall. Compared with polysaccharides, oligosaccharides have drawn increasing attention in various industries due to their enhanced biocompatibility and solubility. Ulvan lyase degrades polysaccharides into low molecular weight oligosaccharides through the β-elimination mechanism. The elucidation of the structure, catalytic mechanism, and molecular modification of ulvan lyase will be helpful to obtain high value-added products from marine biomass resources, as well as reduce environmental pollution caused by the eutrophication of green algae. This review summarizes the structure and bioactivity of ulvan, the microbial origin of ulvan lyase, as well as its sequence, three-dimensional structure, and enzymatic mechanism. In addition, the molecular modification of ulvan lyase, prospects and challenges in the application of enzymatic methods to prepare oligosaccharides are also discussed. It provides information for the preparation of bioactive Ulva oligosaccharides through enzymatic hydrolysis, the technological bottlenecks, and possible solutions to address these issues within the enzymatic process.

Biochemical Characterization of a Novel Thermostable Ulvan Lyase from Tamlana fucoidanivorans CW2-9

Ulvan is a complex sulfated polysaccharide extracted from Ulva, and ulvan lyases can degrade ulvan through a β-elimination mechanism to obtain oligosaccharides. In this study, a new ulvan lyase, EPL15085, which belongs to the polysaccharide lyase (PL) 28 family from Tamlana fucoidanivorans CW2-9, was characterized in detail. The optimal pH and salinity are 9.0 and 0.4 M NaCl, respectively. The Km and Vmax of recombinant EPL15085 toward ulvan are 0.80 mg·mL-1 and 11.22 μmol·min -1 mg-1·mL-1, respectively. Unexpectedly, it is very resistant to high temperatures. After treatment at 100 °C, EPL15085 maintained its ability to degrade ulvan. Molecular dynamics simulation analysis and site-directed mutagenesis analysis indicated that the strong rigidity of the disulfide bond between Cys74-Cys102 in the N-terminus is related to its thermostability. In addition, oligosaccharides with disaccharides and tetrasaccharides were the end products of EPL15085. Based on molecular docking and site-directed mutagenesis analysis, Tyr177 and Leu134 are considered to be the crucial residues for enzyme activity. In conclusion, our study identified a new PL28 family of ulvan lyases, EPL15085, with excellent heat resistance that can expand the database of ulvan lyases and provide the possibility to make full use of ulvan.

Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography

Gum arabic (GA) is widely used as an emulsion stabilizer and edible coating and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidic chains of GA and modify their properties are valuable for structural analysis and industrial application. Cryogenic X-ray crystal structure of GA-specific L-rhamnose-α-1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1), belonging to the polysaccharide lyase (PL) family 42, has been previously reported. To determine the specific reaction mechanism based on its hydrogen-containing enzyme structure, we performed joint X-ray/neutron crystallography of FoRham1. Large crystals were grown in the presence of L-rhamnose (a reaction product), and neutron and X-ray diffraction datasets were collected at room temperature at 1.80 and 1.25 Å resolutions, respectively. The active site contained L-rhamnose and acetate, the latter being a partial analog of glucuronate. Incomplete H/D exchange between Arg166 and acetate suggested that a strong salt-bridge interaction was maintained. Doubly deuterated His105 and deuterated Tyr150 supported the interaction between Arg166 and the acetate. The unique hydrogen-rich environment functions as a charge neutralizer for glucuronate and stabilizes the oxyanion intermediate. The NE2 atom of His85 was deprotonated and formed a hydrogen bond with the deuterated O1 hydroxy of L-rhamnose, indicating the function of His85 as the base/acid catalyst for bond cleavage via β-elimination. Asp83 functions as a pivot between the two catalytic histidine residues by bridging them. This His-His-Asp structural motif is conserved in the PL 24, 25, and 42 families.

Biochemical characterisation of a PL24 ulvan lyase from seaweed-associated Vibrio sp. FNV38

Ulvan is a green macroalgal cell wall polysaccharide that has tremendous potential for valorisation due to its unique composition of sulphated rhamnose, glucuronic acid, iduronic acid and xylose. Several potential applications such as production of biofuels, bioplastics and other value-added products necessitate the breakdown of the polysaccharide to oligomers or monomers. Research on ulvan saccharifying enzymes has been continually increasing over the last decade, with the increasing focus on valorisation of seaweed biomass for a biobased economy. Lyases are the first of several enzymes that are involved in saccharifying the polysaccharide and several ulvan lyases have been structurally and biochemically characterised to enable their effective use in the valorisation processes. This study investigates the whole genome of Vibrio sp. FNV38, an ulvan metabolising organism and biochemical characteristics of a PL24 ulvan lyase that it possesses. The genome of Vibrio sp. FNV38 has a diverse CAZy profile with several genes involved in the metabolism of ulvan, cellulose, agar, and alginate. The enzyme exhibits optimal activity at pH 8.5 in 100 mM Tris-HCl buffer and 30 °C. However, its thermal stability is poor with significant loss of activity after 2 h of incubation at temperatures above 25 °C. Breakdown product analysis reveals that the enzyme depolymerised the polysaccharide predominantly to disaccharides and tetrasaccharides.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10811-023-03136-3.

Ulvan and Ulva oligosaccharides: a systematic review of structure, preparation, biological activities and applications

Ulva is one of the main green algae causing green tide disasters. Ulvan is the primarily component polysaccharide of the cell wall of Ulva and its complex structure and monosaccharide composition resulted in various biological activities. However, the high-value and effective utilization of extracted ulvan have been obstructed by limitations ranging from large molecular weight and low solubility to poor bioavailability. Ulva oligosaccharide obtained by degrading ulvan can not only ideally retain the various biological activities of ulvan very well but also effectively solve the problems of low solubility and poor bioavailability. The preparation and biological activity studies of ulvan and Ulva oligosaccharides have become a hot spot in the field of marine biological resources development research. At present, the comprehensive reviews of ulvan and Ulva oligosaccharides are still scarce. What are overviewed in this paper are the chemical composition, structure, extraction, and purification of ulvan and Ulva oligosaccharides, where research progress on the biological activities of ulvan and Ulva oligosaccharides is summarized and prospected. A theoretical and practical basis has been provided for further research on ulvan and Ulva oligosaccharides, as well as the high-value development and effective utilization of marine algae resources.

Biochemical Properties of a New Polysaccharide Lyase Family 25 Ulvan Lyase TsUly25B from Marine Bacterium Thalassomonas sp. LD5

Marine macroalgae, contributing much to the bioeconomy, have inspired tremendous attention as sustainable raw materials. Ulvan, as one of the main structural components of green algae cell walls, can be degraded by ulvan lyase through the β-elimination mechanism to obtain oligosaccharides exhibiting several good physiological activities. Only a few ulvan lyases have been characterized until now. This thesis explores the properties of a new polysaccharide lyase family 25 ulvan lyase TsUly25B from the marine bacterium Thalassomonas sp. LD5. Its protein molecular weight was 54.54 KDa, and it was most active under the conditions of 60 °C and pH 9.0. The Km and kcat values were 1.01 ± 0.05 mg/mL and 10.52 ± 0.28 s-1, respectively. TsUly25B was salt-tolerant and NaCl can significantly improve its thermal stability. Over 80% of activity can be preserved after being incubated at 30 °C for two days when the concentration of NaCl in the solution is above 1 M, while 60% can be preserved after incubation at 40 °C for 10 h with 2 M NaCl. TsUly25B adopted an endolytic manner to degrade ulvan polysaccharides, and the main end-products were unsaturated ulvan disaccharides and tetrasaccharides. In conclusion, our research enriches the ulvan lyase library and advances the utilization of ulvan lyases in further fundamental research as well as ulvan oligosaccharides production.