Alginate degrading enzymes: an updated comprehensive review of the structure, catalytic mechanism, modification method and applications of alginate lyases

Elucidation of Domain Function of a Novel Multifunctional Glycoside Hydrolase and Its Use in Efficient Preparation of Oligosaccharides from Kelp Powder

Kelp contained laminarin, cellulose, and alginate as major polysaccharides and could be utilized as functional oligosaccharides. A new multifunctional glycoside hydrolase CelA was identified and characterized for the efficient degradation of kelp powder. It displayed cellulase (2308.38 U/mg), alginate lyase (578.68 U/mg), and laminarinase (720.97 U/mg) activities. It exhibited maximal activity on both sodium alginate and laminarin at 50 °C and pH 8.0, while it could degrade sodium carboxymethylcellulose (CMC-Na) by maximal activity at 40 °C and pH 7.0. The action mode analysis by thin layer chromatography and electrospray ionization mass spectrometry indicated that CelA adopted an endolytic manner to degrade CMC-Na, sodium alginate, and laminarin releasing oligosaccharides with degrees of polymerization (Dps) of 2-5. According to domain analysis, CelA contained a GH5 module and a PL6 module, and both of them exhibited glycoside hydrolase and polysaccharide lyase activity. The docking results revealed that Glu163 and Glu250 are essential in cellulose and laminarin degradation. As to the degradation of alginate, Asn376, Lys436, Arg464, Asp496, and Asn551 could bind alginate and Tyr492 and Lys529 acted as catalytic sites. CelA displayed high hydrolysis efficiency for cellulose, β-glucan, laminarin, alginate, and kelp powder. Thus, it has strong potential in food and feed industries as a catalyst for bioconversion of algal biomass into value-added products oligosaccharides.

A bifunctional endolytic alginate lyase with two different lyase catalytic domains from Vibrio sp. H204

Alginate lyases can fully degrade alginate into various size-defined unsaturated oligosaccharide products by β-elimination. Here, we identified the bifunctional endolytic alginate lyase Aly35 from the marine bacterium Vibrio sp. Strain H204. The enzyme Aly35 is classified into the polysaccharide lyase 7 superfamily and contains two alginate lyase catalytic domains. The relationship and function of the two lyase domains are not well known. Thus, the full-length recombinant enzyme and its truncated proteins Aly35-CD1 (catalytic domain 1), Aly35-CD2 (catalytic domain 2 domain) were constructed. The three enzymes showed similar biochemical characteristics and exhibited temperature and pH stability. Further research showed that Aly35 and Aly35-CD2 can efficiently degrade alginate, polymannuronate (PM) and polyguluronate (PG) into a series of unsaturated oligosaccharides, while Aly35-CD1 exhibits greater PM-degrading activity than that of Aly35-CD2 but can not degraded PG efficiently. The results suggest that the domain (Trp295-His582) is critical for PG-degrading activity, the domain has (Leu53-Lys286) higher PM-degrading activity, both catalytic domains together confer increased alginate (including M-blocks and G blocks)-degrading activity. The enzyme Aly35 and its truncations Aly35-CD1 and Aly35-CD2 will be useful tools for structural analyses and for preparing bioactive oligosaccharides, especially Aly35-CD1 can be used to prepare G unit-rich oligosaccharides from alginate.

Alginate catabolic systems in marine bacteria

Brown algae, constituting the second largest group of marine macroalgae, fix significant amounts of inorganic carbon into alginate, the most abundant polysaccharide found in their cell walls. Alginate serves as an important macromolecular carbon source for marine bacteria. The catabolism of alginate by bacteria is an important step in the marine carbon cycle, and this area of research has attracted growing interests over the past decade. Here, we provide an overview of the recent advances in our understanding of marine bacterial alginate catabolic systems, both in individual organisms and within bacterial consortia, discuss the possibility of additional alginate metabolic pathways in light of the present findings, and highlight the future research foci.

Alginate-Degrading Modes, Oligosaccharide-Yielding Properties, and Potential Applications of a Novel Bacterial Multifunctional Enzyme, Aly16-1

Relatively little is known about enzymes with broad substrate spectra, leading to limited applications and progress. Herein, we elucidate Aly16-1 of Streptomyces sp. strain CB16 as a novel multifunctional member of the eighth polysaccharide lyase (PL8) family, although it shared few sequence identities with the characterized enzymes. The recombinant enzyme rAly16-1 showed lyase activities against several acidic polysaccharides, including many glycosaminoglycan types, xanthan, and alginate. It was mannuronate (M)-preferred, endolytic, and optimal at 50 °C and pH 6.0. The smallest substrate was an ∆M-terminal (∆: unsaturated monosaccharide) trisaccharide, and the minimal product was ∆. In the final alginate digestions by rAly16-1, the fractions larger than disaccharides were ∆G-terminal (G: guluronate), while the disaccharides were mainly ∆M, showing an oligosaccharide-yielding property under the succession law. However, when degrading various oligosaccharides, rAly16-1 continued producing ∆M from the non-reducing end even when the substrates increased their sizes, quite different from the elucidated alginate lyases with variable alginate-degrading modes. Thus, co-determined by its M-preference, Aly16-1 is novel for its ∆M-yielding property in oligosaccharide preparations. Additionally, rAly16-1 can be applied in sequencing unsaturated trisaccharides, whether ∆M- or ∆G-terminal. This study provides novel insights into the characteristics and applications of a multifunctional enzyme within the PL8 family for resource explorations.

Degradation of Natural Undaria pinnatifida into Unsaturated Guluronic Acid Oligosaccharides by a Single Alginate Lyase

Here, we report on a bifunctional alginate lyase (Vnalg7) expressed in Pichia pastoris, which can degrade natural Undaria pinnatifida into unsaturated guluronic acid di- and trisaccharide without pretreatment. The enzyme activity of Vnalg7 (3620.00 U/mL-culture) was 15.81-fold higher than that of the original alg (228.90 U/mL-culture), following engineering modification. The degradation rate reached 52.75%, and reducing sugar reached 30.30 mg/mL after combining Vnalg7 (200.00 U/mL-culture) and 14% (w/v) U. pinnatifida for 6 h. Analysis of the action mode indicated that Vnalg7 could degrade many substrates to produce a variety of unsaturated alginate oligosaccharides (AOSs), and the minimal substrate was tetrasaccharide. Site-directed mutagenesis showed that Glu238, Glu241, Glu312, Arg236, His307, Lys414, and Tyr418 are essential catalytic sites, while Glu334, Glu344, and Asp311 play auxiliary roles. Mechanism analysis revealed the enzymatic degradation pattern of Vnalg7, which mainly recognizes and attacks the third glycosidic linkage from the reducing end of oligosaccharide substrate. Our findings provide a novel alginate lyase tool and a sustainable and commercial production strategy for value-added biomolecules using seaweeds.

Characterization and elucidation of a novel M-specific alginate lyase Aly7Aq with strict recognition at subsites ±2

A novel alginate lyase Aly7Aq was cloned and heterologous expressed by a combination of bioinformatics and molecular biology. Aly7Aq was an M-specific alginate lyase, exhibiting optimum reaction conditions at 50 °C and pH 10.0. Aly7Aq was determined to degrade polysaccharides in a random endo-acting manner. The minimum reaction substrate was tetrasaccharide, and Aly7Aq mainly attacked the third glycosidic linkage from the reducing end of oligosaccharide substrates. The disaccharide product of Aly7Aq was ΔM and the trisaccharide products were ΔMM and ΔMG, which differed from all previously characterized M-specific alginate lyases. The degradation products demonstrated that the ±2 subsites of Aly7Aq strictly recognized M units, while the -1 subsite accommodated both M and G units. Therefore, the substrate specificity of Aly7Aq was derived from the specificity of ±2 subsites. This is the first report on the specificity at subsite ±2 of M-specific alginate lyase. The novel M-specific Aly7Aq could serve as a potential tool in the specific degradation of alginate and targeted preparation of oligosaccharide.

Biomedical potentials of alginate via physical, chemical, and biological modifications

Alginate is a linear polysaccharide with a modifiable structure and abundant functional groups, offers immense potential for tailoring diverse alginate-based materials to meet the demands of biomedical applications. Given the advancements in modification techniques, it is significant to analyze and summarize the modification of alginate by physical, chemical and biological methods. These approaches provide plentiful information on the preparation, characterization and application of alginate-based materials. Physical modification generally involves blending and physical crosslinking, while chemical modification relies on chemical reactions, mainly including acylation, sulfation, phosphorylation, carbodiimide coupling, nucleophilic substitution, graft copolymerization, terminal modification, and degradation. Chemical modified alginate contains chemically crosslinked alginate, grafted alginate and oligo-alginate. Biological modification associated with various enzymes to realize the hydrolysis or grafting. These diverse modifications hold great promise in fully harnessing the potential of alginate for its burgeoning biomedical applications in the future. In summary, this review provides a comprehensive discussion and summary of different modification methods applied to improve the properties of alginate while expanding its biomedical potentials.

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.

Efficient Production of an Alginate Lyase in Bacillus subtilis with Combined Strategy: Vector and Host Selection, Promoter and Signal Peptide Screening, and Modification of a Translation Initiation Region

Alginate lyases (ALys) whose degrading products, alginate oligosaccharides, exhibit various outstanding biochemical activities have aroused increasing interest of researchers in the marine bioresource field. However, their predominant sourcing from marine bacteria, with limited yields and unclear genetic backgrounds, presents a challenge for industrial production. In this study, ALys (Aly01) from Vibrio natriegens SK 42.001 was expressed in Bacillus subtilis (B. subtilis), a nonpathogenic microorganism recognized as generally safe (GRAS). This accomplishment was realized through a comprehensive strategy involving vector and host selection, promoter and signal peptide screening, and engineering of the ribosome binding site (RBS) and the N-terminal coding sequence (NCS). The optimal combination was identified as the pP43NMK and B. subtilis WB600. Among the 19 reported strong promoters, PnprE exhibited the best performance, showing intracellular enzyme activities of 4.47 U/mL. Despite expectations, dual promoter construction did not yield a significant increase. Further, SPydhT demonstrated the highest extracellular activity (1.33 U/mL), which was further improved by RBS/NCS engineering, reaching 4.58 U/mL. Finally, after fed-batch fermentation, the extracellular activity reached 18.01 U/mL, which was the highest of ALys with a high molecular weight expressed in B. subtilis. These findings are expected to offer valuable insights into the heterologous expression of ALys in B. subtilis.

Automatic high-throughput and non-invasive selection of sperm at the biochemical level

BACKGROUND

Sperm selection, a key step in assisted reproductive technology (ART), has long been restrained at the preliminary physical level (morphology or motility); however, subsequent fertilization and embryogenesis are complicated biochemical processes. Such an enormous "gap" poses tough problems for couples dealing with infertility, especially patients with severe/total asthenozoospermia .

METHODS

We developed a biochemical-level, automatic-screening/separation, smart droplet-TO-hydrogel chip (BLASTO-chip) for sperm selection. The droplet can sense the pH change caused by sperm's respiration products and then transforms into a hydrogel to be selected out.

FINDINGS

The BLASTO-chip system can select biochemically active sperm with an accuracy of over 90%, and its selection efficiency can be flexibly tuned by nearly 10-fold. All the substances in the system were proven to be biosafe via evaluating mice fertilization and offspring health. Live sperm down to 1% could be enriched by over 76-fold to 76%. For clinical application to patients with severe/total asthenozoospermia, the BLASTO-chip could select live sperm from human semen samples containing 10% live but 100% immotile sperm. The rates of fertilization, cleavage, early embryos, and blastocysts were drastically elevated from 15% to 70.83%, 10% to 62.5%, 5% to 37.5%, and 0% to 16.67%, respectively.

CONCLUSIONS

The BLASTO-chip represents a real biochemical-level technology for sperm selection that is completely independent of sperm's motility. It can be a powerful tool in ART, especially for patients with severe/total asthenozoospermia.

FUNDING

This work was funded by the Ministry of Science and Technology of China, the Ministry of Education of China, and the Shenzhen-Hong Kong Hetao Cooperation Zone.

Advances in alginate lyases and the potential application of enzymatic prepared alginate oligosaccharides: A mini review

Alginate is mainly a linear polysaccharide composed of randomly arranged β-D-mannuronic acid and α-L-guluronic acid linked by α, β-(1,4)-glycosidic bonds. Alginate lyases degrade alginate mainly adopting a β-elimination mechanism, breaking the glycosidic bonds between the monomers and forming a double bond between the C4 and C5 sugar rings to produce alginate oligosaccharides consisting of 2-25 monomers, which have various physiological functions. Thus, it can be used for the continuous industrial production of alginate oligosaccharides with a specific degree of polymerization, in accordance with the requirements of green exploitation of marine resources. With the development of structural analysis, the quantity of characterized alginate lyase structures is progressively growing, leading to a concomitant improvement in understanding the catalytic mechanism. Additionally, the use of molecular modification methods including rational design, truncated expression of non-catalytic domains, and recombination of conserved domains can improve the catalytic properties of the original enzyme, enabling researchers to screen out the enzyme with the expected excellent performance with high success rate and less workload. This review presents the latest findings on the catalytic mechanism of alginate lyases and outlines the methods for molecular modifications. Moreover, it explores the connection between the degree of polymerization and the physiological functions of alginate oligosaccharides, providing a reference for enzymatic preparation development and utilization.

A Novel Bifunctional Alginate Lyase and Antioxidant Activity of the Enzymatic Hydrolysates

Alginate lyase Aly448, a potential new member of the polysaccharide lyase (PL) 7 family, which was cloned and identified from the macroalgae-associated bacterial metagenomic library, showed bifunctionality. The molecular docking results revealed that Aly448 has two completely different binding sites for alginate (polyMG), poly-α-l-guluronic acid (polyG), and poly-β-d-mannuronic acid (polyM) substrates, respectively, which might be the molecular basis for the enzyme's bifunctionality. Truncational results confirmed that predicted key residues affected the bifunctionality of Aly448, but did not wholly explain. Besides, Aly448 presented excellent biochemical characteristics, such as higher thermal stability and pH tolerance. Degradation of polyMG, polyM, and polyG substrates by Aly448 produced tetrasaccharide (DP4), disaccharide (DP2), and galactose (DP1), which exhibited excellent antioxidant activity. These findings provide novel insights into the substrate recognition mechanism of bifunctional alginate lyases and pave a new path for the exploitation of natural antioxidant agents.

Computer-Aided Rational Design Strategy to Improve the Thermal Stability of Alginate Lyase AlyMc

Alginate lyase degrades alginate by the β-elimination mechanism to produce unsaturated alginate oligosaccharides (UAOS), which have better bioactivities than saturated AOS. Enhancing the thermal stability of alginate lyases is crucial for their industrial applications. In this study, a feasible and efficient rational design strategy was proposed by combining the computer-aided ΔΔG value calculation with the B-factor analysis. Two thermal stability-enhanced mutants, Q246V and K249V, were obtained by site-directed mutagenesis. Particularly, the t1/2, 50 °C for mutants Q246V and K249V was increased from 2.36 to 3.85 and 3.65 h, respectively. Remarkably, the specific activities of Q246V and K249V were enhanced to 2.41- and 2.96-fold that of alginate lyase AlyMc, respectively. Structural analysis and molecular dynamics simulations suggested that mutations enhanced the hydrogen bond networks and the overall rigidity of the molecular structure. Notably, mutant Q246V exhibited excellent thermal stability among the PL-7 alginate lyase family, especially considering the heightened enzymatic activity. Moreover, the rational design strategy used in this study can effectively improve the thermal stability of enzymes and has important significance in advancing applications of alginate lyase.

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.

A repertoire of alginate lyases in the alginate polysaccharide utilization loci of marine bacterium Wenyingzhuangia fucanilytica: biochemical properties and action pattern

BACKGROUND

Alginate lyases are important tools for alginate biodegradation and oligosaccharide production, which have great potential in food and biofuel fields. The alginate polysaccharide utilization loci (PUL) typically encode a series of alginate lyases with a synergistic action pattern. Exploring valuable alginate lyases and revealing the synergistic effect of enzymes in the PUL is of great significance.

RESULTS

An alginate PUL was discovered from the marine bacterium Wenyingzhuangia fucanilytica CZ1127T , and a repertoire of alginate lyases within it was cloned, expressed and characterized. The four alginate lyases in PUL demonstrated similar optimal reaction conditions: maximum enzyme activity at 35-50 °C and pH 8.0-9.0. The results of action pattern indicated that they were two PL7 endolytic bifunctional enzymes (Aly7A and Aly7B), a PL6 exolytic bifunctional enzyme (Aly6A) and a PL17 exolytic M-specific enzyme (Aly17A). Ultra-performance liquid chromatography-mass spectrometry was employed to reveal the synergistic effect of the four enzymes. The end products of Aly7A were further degraded by Aly7B and eventually generated oligosaccharides, from disaccharide to heptasaccharide. The oligosaccharide products were completely degraded to monosaccharides by Aly6A, but it was unable to directly degrade alginate. Aly17A could also produce monosaccharides by cleaving the M-blocks of oligosaccharide products, as well as the M-blocks of polysaccharides. The combination of these enzymes resulted in the complete degradation of alginate to monosaccharides.

CONCLUSION

A new alginate PUL was mined and four novel alginate lyases in the PUL were expressed and characterized. The four cooperative alginate lyases provide novel tools for alginate degradation and biological fermentation. © 2023 Society of Chemical Industry.

Identification and characterization of a critical loop for the high activity of alginate lyase VaAly2 from the PL7_5 subfamily

As the major component in the cell wall of brown algae, alginates are degradable by alginate lyases via β-elimination. Alginate lyases can be categorized into various polysaccharide lyase (PL) families, and PL7 family alginate lyases are the largest group and can be divided into six subfamilies. However, the major difference among different PL7 subfamilies is not fully understood. In this work, a marine alginate lyase, VaAly2, from Vibrio alginolyticus ATCC 17749 belonging to the PL7_5 subfamily was identified and characterized. It displayed comparatively high alginolytic activities toward different alginate substrates and functions as a bifunctional lyase. Molecular docking and biochemical analysis suggested that VaAly2 not only contains a key catalyzing motif (HQY) conserved in the PL7 family but also exhibits some specific characters limited in the PL7_5 subfamily members, such as the key residues and a long loop1 structure around the active center. Our work provides insight into a loop structure around the center site which plays an important role in the activity and substrate binding of alginate lyases belonging to the PL7_5 subfamily.

Rational design for thermostability improvement of a novel PL-31 family alginate lyase from Paenibacillus sp. YN15

Currently, alginate oligosaccharides (AOS) become attractive due to their excellent physiological effects. AOS has been widely used in food, pharmaceutical, and cosmetic industries. Generally, AOS can be produced from alginate using alginate lyase (ALyase) as the biocatalyst. However, most ALyase display poor thermostability. In this study, a thermostable ALyase from Paenibacillus sp. YN15 (Payn ALyase) was characterized. It belonged to the polysaccharide lyase (PL) 31 family and displayed poly β-D-mannuronate (Poly M) preference. Under the optimum condition (pH 8.0, 55 °C, 50 mM NaCl), it exhibited maximum activity of 90.3 U/mg and efficiently degraded alginate into monosaccharides and AOS with polymerization (DP) of 2-4. Payn ALyase was relatively stable at 55 °C, but the thermostability dropped rapidly at higher temperatures. To further improve its thermostability, rational design mutagenesis was carried out based on a combination of FireProt, Consensus Finder, and PROSS analysis. Finally, a triple-point mutant K71P/Y129G/S213G was constructed. The optimum temperature was increased from 55 to 70 °C, and the Tm was increased from 62.7 to 64.1 °C. The residual activity after 30 min incubation at 65 °C was enhanced from 36.0 % to 83.3 %. This study provided a promising ALyase mutant for AOS industrial production.

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

Three novel strains designated ABR2-5T, BKB1-1T, and WSW4-B4T belonging to the genus Reichenbachiella of the phylum Bacteroidota were isolated from algae and mud samples collected in the West Sea, Korea. All three strains were enriched for genes encoding up to 216 carbohydrate-active enzymes (CAZymes), which participate in the degradation of agar, alginate, carrageenan, laminarin, and starch. The 16S rRNA sequence similarities among the three novel isolates were 94.0%-94.7%, and against all three existing species in the genus Reichenbachiella they were 93.6%-97.2%. The genome sizes of the strains ABR2-5T, BKB1-1T, and WSW4-B4T were 5.5, 4.4, and 5.0 Mb, respectively, and the GC content ranged from 41.1%-42.0%. The average nucleotide identity and the digital DNA-DNA hybridization values of each novel strain within the isolates and all existing species in the genus Reichenbachiella were in a range of 69.2%-75.5% and 17.7-18.9%, respectively, supporting the creation of three new species. The three novel strains exhibited a distinctive fatty acid profile characterized by elevated levels of iso-C15:0 (37.7%-47.4%) and C16:1 ω5c (14.4%-22.9%). Specifically, strain ABR2-5T displayed an additional higher proportion of C16:0 (13.0%). The polar lipids were phosphatidylethanolamine, unidentified lipids, aminolipids, and glycolipids. Menaquinone-7 was identified as the respiratory quinone of the isolates. A comparative genome analysis was performed using the KEGG, RAST, antiSMASH, CRISPRCasFinder, dbCAN, and dbCAN-PUL servers and CRISPRcasIdentifier software. The results revealed that the isolates harbored many key genes involved in central metabolism for the synthesis of essential amino acids and vitamins, hydrolytic enzymes, carotenoid pigments, and antimicrobial compounds. The KEGG analysis showed that the three isolates possessed a complete pathway of dissimilatory nitrate reduction to ammonium (DNRA), which is involved in the conservation of bioavailable nitrogen within the ecosystem. Moreover, all the strains possessed genes that participated in the metabolism of heavy metals, including arsenic, copper, cobalt, ferrous, and manganese. All three isolated strains contain the class 2 type II subtype C1 CRISPR-Cas system in their genomes. The distinguished phenotypic, chemotaxonomic, and genomic characteristics led us to propose that the three strains represent three novel species in the genus Reichenbachiella: R. ulvae sp. nov. (ABR2-5T = KCTC 82990T = JCM 35839T), R. agarivorans sp. nov. (BKB1-1T = KCTC 82964T = JCM 35840T), and R. carrageenanivorans sp. nov. (WSW4-B4T = KCTC 82706T = JCM 35841T).

Modulating in vitro fecal fermentation behavior of sodium alginate by Ca2+ cross-linking

Slow fermentable dietary fibers can be utilized by human gut microbiota in the distal region of the colon and thus exert a sufficient short-chain fatty acids (SCFAs) supplement in the distal region of the human colon. Alginate (Alg) based microgels are widely fabricated and used to control their digestion by digestive enzymes releasing active substances site-specifically. Herein, sodium alginate microgels with gradient calcium-ion (Ca2+) cross-linking densities were developed, restricting their degradation by gut microbiota. Alg microgels were prepared using high-speed shearing after Alg was cross-linked with 10, 40, and 60 mmol/L Ca2+, respectively (named 10-Alg, 40-Alg, and 60-Alg). The fluorescence and atomic force microscopic results showed that the 40-Alg particle has the densest structure among the three cross-linked Alg. In vitro human fecal fermentation results revealed that the Ca2+ cross-linking exerted more restricting effects than delaying effects on the fermentation of Alg, and the 40-Alg exhibited the slowest fermentation rate and the least fermentation extent, by characterizing the residual total carbohydrate content, residual monosaccharide content, pH, and total short-chain fatty acids. The 16S rRNA gene sequencing results indicated that cross-linking structures shaped a high specifical Bacteroides-type microbial community and that OTU205 (Bacteroides_xylanisolvens) highly correlated to the cross-linking density (R = 0.65, p = 0.047). In sum, Ca2+ cross-linking generated a dense and compact structure of sodium alginate that facilitated a more restricted fermentation property and specificity-targeting microbial community structure in comparison to the original sodium alginate.

A Recombinant Alginate Lyase Algt1 with Potential in Preparing Alginate Oligosaccharides at High-Concentration Substrate

Alginate lyase has been demonstrated as an efficient tool in the preparation of functional oligosaccharides (AOS) from alginate. The high viscosity resulting from the high concentration of alginate poses a limiting factor affecting enzymatic hydrolysis, particularly in the preparation of the fragments with low degrees of polymerization (DP). Herein, a PL7 family alginate lyase Algt from Microbulbifer thermotolerans DSM 19189 was developed and expressed in Pichia pastoris. The recombinant alginate lyase Algt1 was constructed by adopting the structural domain truncation strategy, and the enzymatic activity towards the alginate was improved from 53.9 U/mg to 212.86 U/mg compared to Algt. Algt1 was stable when incubated at 40 °C for 90 min, remaining with approximately 80.9% of initial activity. The analyses of thin-layer chromatography (TLC), fast protein liquid chromatography (FPLC), and electrospray ionization mass spectrometry (ESI-MS) demonstrated that the DP of the minimum identifiable substrate of Algt1 was five, and the main hydrolysis products were AOS with DP 1-4. Additionally, 1-L the enzymatic hydrolysis system demonstrated that Algt1 exhibited an effective degradation at alginate concentrations of up to 20%, with the resulting products of monosaccharides (14.02%), disaccharides (21.10%), trisaccharides (37.08%), and tetrasaccharides (27.80%). These superior properties of Algt1 make it possible to efficiently generate functional AOS with low DP in industrial processing.

Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.

Genome Sequencing-Based Mining and Characterization of a Novel Alginate Lyase from Vibrio alginolyticus S10 for Specific Production of Disaccharides

Alginate oligosaccharides prepared by alginate lyases attracted great attention because of their desirable biological activities. However, the hydrolysis products are always a mixture of oligosaccharides with different degrees of polymerization, which increases the production cost because of the following purification procedures. In this study, an alginate lyase, Alg4755, with high product specificity was identified, heterologously expressed, and characterized from Vibrio alginolyticus S10, which was isolated from the intestine of sea cucumber. Alg4755 belonged to the PL7 family with two catalytic domains, which was composed of 583 amino acids. Enzymatic characterization results show that the optimal reaction temperature and pH of Alg4755 were 35 °C and 8.0, respectively. Furthermore, Alg4755 was identified to have high thermal and pH stability. Moreover, the final hydrolysis products of sodium alginate catalyzed by Alg4755 were mainly alginate disaccharides with a small amount of alginate trisaccharides. The results demonstrate that alginate lyase Alg4755 could have a broad application prospect because of its high product specificity and desirable catalytic properties.

Functional carbohydrate-based hydrogels for diabetic wound therapy

Diabetes wound are grave and universal complications of diabetes. Owing to poor treatment course, high amputation rate and mortality, diabetes wound treatment and care have become a global challenge. Wound dressings have received much attention due to their ease of use, good therapeutic effect, and low costs. Among them, carbohydrate-based hydrogels with excellent biocompatibility are considered to be the best candidates for wound dressings. Based on this, we first systematically summarized the problems and healing mechanism of diabetes wounds. Next, common treatment methods and wound dressings were discussed, and the application of various carbohydrate-based hydrogels and their corresponding functionalization (antibacterial, antioxidant, autoxidation and bioactive substance delivery) in the treatment of diabetes wounds were emphatically introduced. Ultimately, the future development of carbohydrate-based hydrogel dressings was proposed. This review aims to provide a deeper understanding of wound treatment and theoretical support for the design of hydrogel dressings.

Three marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading alginate, chitin, laminarin, starch, and xylan

Bacteroidota is a group of marine polysaccharide degraders, which play a crucial role in the carbon cycle in the marine ecosystems. In this study, three novel gliding strains, designated as SS9-22^T, W9P-11^T, and SW1-E11^T, isolated from algae and decaying wood were proposed to represent three novel species of the genus Fulvivirga. We identified a large number of genes encoding for carbohydrate-active enzymes, which potentially participate in polysaccharide degradation, based on whole genome sequencing. The 16S rRNA sequence similarities among them were 94.4-97.2%, and against existing species in the genus Fulvivirga 93.1-99.8%. The complete genomes of strains SS9-22^T, W9P-11^T, and SW1-E11^T comprised one circular chromosome with size of 6.98, 6.52, and 6.39 Mb, respectively; the GC contents were 41.9%, 39.0%, and 38.1%, respectively. The average nucleotide identity and the digital DNA-DNA hybridization values with members in the genus Fulvivirga including the isolates were in a range of 68.9-85.4% and 17.1-29.7%, respectively, which are low for the proposal of novel species. Genomic mining in three genomes identified hundreds of carbohydrate-active enzymes (CAZymes) covering up to 93 CAZyme families and 58-70 CAZyme gene clusters, exceeding the numbers of genes present in the other species of the genus Fulvivirga. Polysaccharides of alginate, chitin, laminarin, starch, and xylan were degraded in vitro, highlighting that the three strains are rich sources of CAZymes of polysaccharide degraders for biotechnological applications. The phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of three novel species in the genus Fulvivirga, for which the names Fulvivirga ulvae sp. nov. (SS9-22^T = KCTC 82072^T = GDMCC 1.2804^T), Fulvivirga ligni sp. nov. (W9P-11^T = KCTC 72992^T = GDMCC 1.2803^T), and Fulvivirga maritima sp. nov. (SW1-E11^T = KCTC 72832^T = GDMCC 1.2802^T) are proposed.

A novel alginate lyase and its domain functions for the preparation of unsaturated monosaccharides

Brown algae are considered promising crops for the production of sustainable biofuels. However, the commercial application has been limited by lack of efficient methods for converting alginate into fermentable sugars. Herein, we cloned and characterized a novel alginate lyase AlyPL17 from Pedobacter hainanensis NJ-02. It possessed outstanding catalytic efficiency toward polymannuronic acid (polyM), polyguluronic acid (polyG), and alginate sodium, with k_cat of 39.42 ± 1.9 s^-1, 32.53 ± 0.88 s^-1, and 38.30 ± 2.12 s^-1, respectively. AlyPL17 showed maximum activity at 45 °C and pH 9.0. The domain truncation did not change the optimal temperature and optimal pH, but greatly reduced the activity. In addition, AlyPL17 degrades alginate through the cooperative action of two structural domains in an exolytic mode. The minimal degradation substrate of AlyPL17 is a disaccharide. Furthermore, AlyPL17 and AlyPL6 can synergistically degrade alginate to prepare unsaturated monosaccharides that can be converted to 4-deoxy-L-erythron-5-hexoseuloseuronate acid (DEH). DEH is reduced to KDG by DEH reductase (Sdr), which enters the Entner-Doudoroff (ED) pathway as a common metabolite and is converted to bioethanol. KEY POINTS: • Biochemical characterization of alginate lyase from Pedobacter hainanensis NJ-02 and its truncated form. • Degradation patterns of AlyPL17 and the role of its domains in product distribution and mode of action. • Potential of synergistic degradation system for efficient preparation of unsaturated monosaccharides.

Characterization of a thermostable PL-31 family alginate lyase from Paenibacillus ehimensis and its application for alginate oligosaccharides bioproduction

Currently, people pay more attention to marine sugars, because of their unique physiological effects. Alginate oligosaccharides (AOS) are the degradation products of alginate and have been used in food, cosmetic, and medicine fields. AOS display good physical characteristics (low relative molecular weight, good solubility, high safety, and high stability) and excellent physiological functions (immunomodulatory, antioxidant, antidiabetic, and prebiotic activities). Alginate lyase plays a key role in the AOS bioproduction. In this study, a novel PL-31 family alginate lyase from Paenibacillus ehimensis (paeh-aly) was identified and characterized. It was extracellularly secreted in E. coli and exhibited a preference for the substrate poly β-D-mannuronate. Using sodium alginate as the substrate, it showed the maximum catalytic activity (125.7 U/mg) at pH 7.5 and 55 °C with 50 mM NaCl. Compared with other alginate lyases, paeh-aly exhibited good stability. About 86.6% and 61.0% residual activity could be maintained after 5 h incubation at 50 and 55 °C respectively, and its T_m value was 61.5 °C. The degradation products were AOS with DP 2-4. Paeh-aly demonstrated strong promise for AOS industrial production because of its excellent thermostability and efficiency.

Characterisation of marine bacterium Microbulbifer sp. ALW1 with Laminaria japonica degradation capability

Marine bacterium Microbulbifer sp. ALW1 was revealed to be able to effectively degrade Laminaria japonica thallus fragments into fine particles. Polysaccharide substrate specificity analysis indicated that ALW1 could produce extracellular alginate lyase, laminarinase, fucoidanase and cellulase. Based on alignment of the 16 S rRNA sequence with other reference relatives, ALW1 showed the closest relationship with Microbulbifer aggregans CCB-MM1T. The cell morphology and some basic physiological and biochemical parameters of ALW1 cells were characterised. ALW1 is a Gram-negative, rod- or oval-shaped, non-spore-forming and non-motile bacterium. The DNA–DNA relatedness values of ALW1 with type strains of M. gwangyangensis (JCM 17,800), M. aggregans (JCM 31,875), M. maritimus (JCM 12,187), M. okinawensis (JCM 16,147) and M. rhizosphaerae (DSM 28,920) were 28.9%, 43.3%, 41.2%, 35.4% and 45.6%, respectively. The major cell wall sugars of ALW1 were determined to be ribose and galactose, which differed from other closely related species. These characteristics indicated that ALW1 could be assigned to a separate species of the genus Microbulbifer. The complete genome of ALW1 contained one circular chromosome with 4,682,287 bp and a GC content of 56.86%. The putative encoded proteins were categorised based on their functional annotations. Phenotypic, physiological, biochemical and genomic characterisation will provide insights into the many potential industrial applications of Microbulbifer sp. ALW1.

Key points.

Biochemical Characterization and Elucidation of the Hybrid Action Mode of a New Psychrophilic and Cold-Tolerant Alginate Lyase for Efficient Preparation of Alginate Oligosaccharides

Alginate lyases with unique biochemical properties have irreplaceable value in food and biotechnology industries. Herein, the first new hybrid action mode Thalassotalea algicola-derived alginate lyase gene (TAPL7A) with both psychrophilic and cold-tolerance was cloned and expressed heterologously in E. coli. With the highest sequence identity (43%) to the exolytic alginate lyase AlyA5 obtained from Zobellia galactanivorans, TAPL7A was identified as a new polysaccharide lyases family 7 (PL7) alginate lyase. TAPL7A has broad substrate tolerance with specific activities of 4186.1 U/mg, 2494.8 U/mg, 2314.9 U/mg for polyM, polyG, and sodium alginate, respectively. Biochemical characterization of TAPL7A showed optimal activity at 15 °C, pH 8.0. Interestingly, TAPL7A exhibits both extreme psychrophilic and cold tolerance, which other cold-adapted alginate lyase do not possess. In a wide range of 5–30 °C, the activity can reach 80–100%, and the residual activity of more than 70% can still be maintained after 1 h of incubation. Product analysis showed that TAPL7A adopts a hybrid endo/exo-mode on all three substrates. FPLC and ESI-MS confirmed that the final products of TAPL7A are oligosaccharides with degrees of polymerization (Dps) of 1–2. This study provides excellent alginate lyase candidates for low-temperature environmental applications in food, agriculture, medicine and other industries.

Alginate oligosaccharides: The structure-function relationships and the directional preparation for application

Alginate oligosaccharides (AOS) are degradation products of alginate extracted from brown algae. With low molecular weight, high water solubility, and good biological activity, AOS present anti-inflammatory, antimicrobial, antioxidant, and antitumor properties. They also exert growth-promoting effects in animals and plants. Three types of AOS, mannuronate oligosaccharides (MAOS), guluronate oligosaccharides (GAOS), and heterozygous mannuronate and guluronate oligosaccharides (HAOS), can be produced from alginate by enzymatic hydrolysis. Thus far, most studies on the applications and biological activities of AOS have been based mainly on a hybrid form of HAOS. To improve the directional production of AOS for practical applications, systematic studies on the structures and related biological activities of AOS are needed. This review provides a summary of current understanding of structure-function relationships and advances in the production of AOS. The current challenges and opportunities in the application of AOS is suggested to guide the precise application of AOS in practice.

Toward Understanding the Alginate Catabolism in Microbulbifer sp. ALW1 by Proteomics Profiling

The bacterial strain of Microbulbifer sp. ALW1 has demonstrated visible ability of degrading the cell wall of Laminaria japonica, and biochemical characterization has been performed on some individual enzymes to elucidate its genetic basis. However, it still remains elusive how strain ALW1 successfully breaks down the major cell wall component alginate polysaccharide and colonizes on its marine host. In this study, a mass spectrometry-based quantitative analysis of the extracellular and intracellular proteomes was introduced to elucidate the alginate degradation pathway in ALW1 strain. Mass spectrometry and biochemical assays indicated that strain ALW1 could effectively degrade alginate polysaccharide into disaccharides and trisaccharides within 12 h. Proteome analysis identified 156 and 1,047 proteins exclusively localized in extracellular and intracellular compartments, respectively, with 1,086 protein identities of dual localization. Functional annotation of the identified proteins suggested the involvement of diverse catalytic enzymes and non-catalytic molecules for the cleavage and metabolism of alginate polysaccharide. A simplified pathway was constructed to demonstrate the extracellular digestion, active transport, and intracellular conversion of alginate polysaccharide and its fragmented oligosaccharides, casting a picture of genetic loci controlling alginate catabolism by ALW1 strain. This study aims to provide a guide for utilization and genetic manipulation of the bacterial strain ALW1 for efficient alginate oligosaccharides production by fermentation.

Recent Advances in Bioutilization of Marine Macroalgae Carbohydrates: Degradation, Metabolism, and Fermentation

Marine macroalgae are considered renewable natural resources due to their high carbohydrate content, which gives better utilization value in biorefineries and higher value conversion than first- and second-generation biomass. However, due to the diverse composition, complex structure, and rare metabolic pathways of macroalgae polysaccharides, their bioavailability needs to be improved. In recent years, enzymes and pathways related to the degradation and metabolism of macroalgae polysaccharides have been continuously developed, and new microbial fermentation platforms have emerged. Aiming at the bioutilization and transformation of macroalgae resources, this review describes the latest research results from the direction of green degradation, biorefining, and metabolic pathway design, including summarizing the the latest biorefining technology and the fermentation platform design of agarose, alginate, and other polysaccharides. This information will provide new research directions and solutions for the biotransformation and utilization of marine macroalgae.

Structure Characteristics, Biochemical Properties, and Pharmaceutical Applications of Alginate Lyases

Alginate, the most abundant polysaccharides of brown algae, consists of various proportions of uronic acid epimers α-L-guluronic acid (G) and β-D-mannuronic acid (M). Alginate oligosaccharides (AOs), the degradation products of alginates, exhibit excellent bioactivities and a great potential for broad applications in pharmaceutical fields. Alginate lyases can degrade alginate to functional AOs with unsaturated bonds or monosaccharides, which can facilitate the biorefinery of brown algae. On account of the increasing applications of AOs and biorefinery of brown algae, there is a scientific need to explore the important aspects of alginate lyase, such as catalytic mechanism, structure, and property. This review covers fundamental aspects and recent developments in basic information, structural characteristics, the structure-substrate specificity or catalytic efficiency relationship, property, molecular modification, and applications. To meet the needs of biorefinery systems of a broad array of biochemical products, alginate lyases with special properties, such as salt-activated, wide pH adaptation range, and cold adaptation are outlined. Withal, various challenges in alginate lyase research are traced out, and future directions, specifically on the molecular biology part of alginate lyases, are delineated to further widen the horizon of these exceptional alginate lyases.

Purification and Characterization of a Novel Alginate Lyase from a Marine Streptomyces Species Isolated from Seaweed

Alginate, a natural polysaccharide derived from brown seaweed, is finding multiple applications in biomedicine via its transformation through chemical, physical, and, increasingly, enzymatic processes. In this study a novel alginate lyase, AlyDS44, was purified and characterized from a marine actinobacterium, Streptomyces luridiscabiei, which was isolated from decomposing seaweed. The purified enzyme had a specific activity of 108.6 U/mg, with a molecular weight of 28.6 kDa, and was composed of 260 amino acid residues. AlyDS44 is a bifunctional alginate lyase, active on both polyguluronate and polymannuronate, though it preferentially degrades polyguluronate. The optimal pH of this enzyme is 8.5 and the optimal temperature is 45 °C. It is a salt-tolerant alginate lyase with an optimal activity at 0.6 M NaCl. Metal ions Mn²⁺, Co²⁺, and Fe²⁺ increased the alginate degrading activity, but it was inhibited in the presence of Zn²⁺ and Cu²⁺. The highly conserved regions of its amino acid sequences indicated that AlyDS44 belongs to the polysaccharide lyase family 7. The main breakdown products of the enzyme on alginate were disaccharides, trisaccharides, and tetrasaccharides, which demonstrated that this enzyme acted as an endo-type alginate lyase. AlyDS44 is a novel enzyme, with the potential for efficient production of alginate oligosaccharides with low degrees of polymerization.