Single-Point Mutation Near Active Center Increases Substrate Affinity of Alginate Lyase AlgL-CD

Recent Advances in Alginate Lyase Engineering for Efficient Conversion of Alginate to Value-Added Products

Alginate lyases depolymerize alginate and generate alginate oligosaccharides (AOS) and eventually 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), a monosaccharide. Recently, alginate lyases have garnered significant attention due to the increasing demand for AOS, which exhibit bioactivities beneficial to human health, livestock productivity, and agricultural efficiency. Additionally, these enzymes play a crucial role in producing DEH, essential in alginate catabolism in bacteria. This review explains the industrial value of AOS and DEH, which contribute broadly to industries ranging from the food industry to biorefinery processes. This review also highlights recent advances in alginate lyase applications and engineering, including domain truncation, chimeric enzyme design, rational mutagenesis, and directed evolution. These approaches have enhanced enzyme performance for efficient AOS and DEH production. We also discuss current challenges and future directions toward industrial-scale bioconversion of alginate-rich biomass.

Rational design of alginate lyase ALYI1 for improving the antioxidant activity of the alginate oligosaccharides

To achieve the cost-effective alginate oligosaccharides production, we have developed a novel rational design strategy that optimized capture behavior, orientation movement and hydrogen bond interaction of substrate in alginate lyase ALYI1. This approach led to S56D and G258Q advantageous variants balancing the trade-off challenge, particularly S56D, which exhibited a 1.56-fold increase in specific activity and 23.11 % higher activity at 45 °C for 1 h compared to ALYI1. The variants exhibited reduced binding fluctuation and more favorable binding energy compared to ALYI1, which was ascribed to more favorable dynamic hydrogen bonds and binding energy distribution. Furthermore, we innovatively found that alginate oligosaccharides produced by S56D and G258Q displayed increasing ABTS+ and DPPH• radical scavenging efficiencies than those produced by ALYI1. Especially, S56D degradation product demonstrated 10.80 % higher ABTS+ radical and 29.75 % higher DPPH• radical scavenging activities at 1.0 mg/mL. This was attributed to the improved disaccharides and trisaccharides ratios in the product. Our findings provide critical insights and establish a robust foundation for the development of superior biocatalysts for the industrial production of AOS.

Molecular Engineering of Alginate Lyases and the Potential Agricultural Applications of Their Enzymatic Products

Alginate lyases, enzymes that degrade alginate into unsaturated oligosaccharides, have attracted significant attention for their potential applications across various fields, particularly in agriculture. This review focuses on the molecular engineering of alginate lyases to enhance their activity, stability, and specificity as well as the agricultural applications of the resulting enzymatic products, known as alginate oligosaccharides (AOS). We start by summarizing the sources and classification of alginate lyases, followed by recent advances in their engineering through directed evolution, rational design, truncation of noncatalytic domains, and conserved domain reconstruction. We then explore the diverse agricultural applications of AOS, including their ability to promote plant growth, to increase the content of active plant components, to extend fruit shelf life, and to enhance plant resistance to abiotic stresses. Furthermore, the potential value of AOS as feed additives and preservatives in shrimp-based products is also assessed. This review will not only lay a solid theoretical foundation but also serve as a catalyst for the innovative development and practical application of high-value enzymatic preparations and utilization of AOS-related products, providing new solutions for sustainable agriculture and the food industry.

Direct Influence of the Conserved Motif in PL7 Family Alginate Lyases on Enzyme Cold Adaptability

Alginate lyase, a vital component of polysaccharide lyases, is instrumental in the efficient degradation of alginate and the production of single oligosaccharides. Although numerous alginate lyases have been characterized, only a few display extreme cold adaptability in the range of 0-20 °C. In this study, we identified a novel cold-adapted alginate lyase, Aly423, from Tamlana laminarinivorans PT2-4 isolated from Sargassum. Phylogenetic classification, enzyme structure, and catalytic property analyses confirmed that Aly423 could be classified as a member of subfamily 5 of the PL7 family and exhibited significant cold adaptability at low temperatures. Further analysis of the secondary structure and homology modeling of several cold-adapted enzymes revealed two variable amino acid sites in the conserved amino acid motif (YFK*G*Y) of Aly423, which may affect the cold adaptation mechanism. Point mutation experiments demonstrated that mutant A304T significantly altered the temperature adaptation of Aly423, highlighting the critical role of this amino acid site in the cold-adaptation mechanism of the enzyme. In summary, we effectively enhanced the enzymatic activity of the PL7 alginate cold-adapted enzyme through a rational design using computational methods. This advancement is of significant importance for the efficient utilization of sodium alginate in the food, agricultural, and pharmaceutical industries under low-temperature conditions.

De Novo Biosynthesis of a Polyene-Type Ginsenoside Precursor Dammaradienol in Saccharomyces cerevisiae

Typical dammarane-type ginsenosides are well-known tetracyclic triterpenoids with significant pharmacological effects including antitumor, cardiovascular protection, and neuroprotection. Polyene-type ginsenosides exhibit stronger biological activities than common ginsenosides; however, their contents are low, and most are converted from ginsenosides through a series of processing steps, resulting in higher preparation costs. In this study, a dammaradienol synthase, AarOSC20433, was identified for the first time from Artemisia argyi H. Lév. & Vaniot (A. argyi). The high-yielding squalene strain constructed in this study was used as the chassis strain. Yeast heterologous biosynthesis of the polyene-type ginsenoside precursor dammaradienol was achieved via metabolic engineering strategies, including optimization of the terpene supply, increase in copy number of AarOSC20433, and rational enzyme design. Eventually, through replenishment and batch fermentation, the titer of dammaradienol reached 1.037 g/L (4.3 mg/L/OD), laying a solid foundation for the construction of a polyene-type ginsenoside cell factory.

Identification and characterization of a novel thermostable PL7 alginate lyase from a submarine volcanic metagenomic library

Seaweed biomass is as an abundant and renewable source of complex polysaccharides, including alginate which has a variety of applications. A sustainable method for exploiting alginate towards the production of valuable oligosaccharides is through enzymatic processing, using alginate lyases. Industrial refinement methods demand robust enzymes. Metagenomic libraries from extreme environments are a new source of unique enzymes with great industrial potential. Herein we report the identification of a new thermostable alginate lyase with only 58 % identity to known sequences, identified by mining a metagenomic library obtained from the hydrothermal vents of the volcano Kolumbo in the Aegean Sea (Kolumbo Alginate Lyase, KAlLy). Sequence analysis and biochemical characterization of KAlLy showed that this new alginate lyase is a Polysaccharide Lyase of family 7 (PL7) enzyme with endo- and exo-action on alginate and poly-mannuronic acid, with high activity at 60°C (56 ± 8 U/mg) and high thermostability (half-life time of 30 h at 50°C). The response surface methodology analysis revealed that the reaction optimum conditions with poly-mannuronic acid as substrate are 44°C, pH of 5.5 with 440 mM NaCl. This novel alginate lyase is a valuable addition to the toolbox of alginate modifying enzymes, due to its diverse sequence and its good thermal stability.

The two-step strategy for enhancing the specific activity and thermostability of alginate lyase AlyG2 with mechanism for improved thermostability

To overcome the trade-off challenge encountered in the engineering of alginate lyase AlyG2 from Seonamhaeicola algicola Gy8T and to expand its potential industrial applications, we devised a two-step strategy encompassing activity enhancement followed by thermal stability engineering. To enhance the specific activity of efficient AlyG2, we strategically substituted residues with bulky steric hindrance proximal to the active pocket with glycine or alanine. This led to the generation of three promising positive mutants, with particular emphasis on the T91S mutant, exhibiting a 1.91-fold specific activity compared to the wild type. To mitigate the poor thermal stability of T91S, mutants with negative ΔΔG values in the thermal flexibility region were screened out. Notably, the S72Ya mutant not only displayed 17.96 % further increase in specific activity but also exhibited improved stability compared to T91S, manifesting as a remarkable 30.97 % increase in relative activity following a 1-hour incubation at 42 °C. Furthermore, enhanced kinetic stability was observed. To gain deeper insights into the mechanism underlying the enhanced thermostability of the S72Ya mutant, we conducted molecular dynamics simulations, principal component analysis (PCA), dynamic cross-correlation map (DCCM), and free energy landscape (FEL) analysis. The results unveiled a reduction in the flexibility of the surface loop, a stronger correlation dynamic and a narrower motion subspace in S72Ya system, along with the formation of more stable hydrogen bonds. Collectively, our findings suggest amino acids substitutions resulting in smaller side chains proximate to the active site can positively impact enzyme activity, while reducing the flexibility of surface loops emerges as a pivotal factor in conferring thermal stability. These insights offer valuable guidance and a framework for the engineering of other enzyme types.

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.

Characterization and Mechanism Study of a Novel PL7 Family Exolytic Alginate Lyase from Marine Bacteria Vibrio sp. W13

Alginate lyase can degrade alginate into oligosaccharides through β-elimination for various biological, biorefinery, and agricultural purposes. Here, we report a novel PL7 family exolytic alginate lyase VwAlg7A from marine bacteria Vibrio sp. W13 and achieve the heterologous expression in E. coli BL21 (DE3). VwAlg7A is 348aa with a calculated molecular weight of 36 kDa, containing an alginate lyase 2 domain. VwAlg7A exhibits specificity towards poly-guluronate. The optimal temperature and pH of VwAlg7A are 30 °C and 7.0, respectively. The activity of VwAlg7A can be significantly inhibited by the Ni2+, Zn2+, and NaCl. The Km and Vmax of VwAlg7A are 36.9 mg/ml and 395.6 μM/min, respectively. The ESI and HPAEC-PAD results indicate that VwAlg7A cleaves the sugar bond in an exolytic mode. Based on the molecular docking and mutagenesis results, we further confirmed that R98, H169, and Y303 are important catalytic residues.

Role of distal sites in enzyme engineering

The limitations associated with natural enzyme catalysis have triggered the rise of the field of protein engineering. Traditional rational design was based on the analysis of protein structural information and catalytic mechanisms to identify key active sites or ligand binding sites to reshape the substrate pocket. The role and significance of functional sites in the active center have been studied extensively. With a deeper understanding of the structure-catalysis relationship map, the entire protein molecule can be filled with residues that play a substantial role in its structure and function. However, the catalytic mechanism underlying distal mutations remains unclear. The aim of this review was to highlight the criticality of the distal site in enzyme engineering based on the following three aspects: What can distal mutations exert on function from mutability landscape? How do distal sites influence enzyme function? How to predict and design distal mutations? This review provides insights into the catalytic mechanism of enzymes from the global interaction network, knowledge from sequence-structure-dynamics-function relationships, and strategies for distal mutation-based protein engineering.

Cloning, expression, and characterization of a novel endo-type alginate lyase from Microbulbifer sp. BY17

BACKGROUND

Alginate oligosaccharides (AOS), with various physiological effects, have been widely used in the food, agricultural, and pharmaceutical industries. The biological enzymatic method of preparing AOS, using alginate lyase, has more advantages compared with physical and chemical methods. Cloning and heterologously expressing alginate lyase are therefore very important.

RESULTS

A novel alginate lyase, BY17PV7, from Microbulbifer sp. BY17, isolated from Gracilaria, was cloned and expressed in Escherichia coli BL21(DE3). BY17PV7 was about 27 KDa. BY17PV7 showed the greatest activity (150.42 ± 3.32 U/mg) at 43 °C and pH 8.9. It could be activated by Ca²⁺ , Mn²⁺ , Co²⁺ , Fe³⁺ , Na⁺ , and inhibited by Mg²⁺ , Zn²⁺ , Ba²⁺ , Cu²⁺ , sodium dodecyl sulfate (SDS), ethylene diamine tetraacetic acid (EDTA). BY17PV7 had a wide range of substrate specificity and good degradation effects for poly β-D-mannuronate (polyM) and poly α-L-guluronate (polyG), demonstrating that it is a bifunctional alginate lyase. The kinetic parameters showed that BY17PV7 had a greater affinity for polyG. BY17PV7 released AOS with a degree of polymerization (DP) of 3-4 in an endolytic manner from sodium alginate. Alginate oligosaccharides showed strong antioxidant ability of reducing Fe³⁺ and scavenging radicals such as hydroxyl, 2,2-azion-bia (3-ethylbenzo-thiazoline-6-sulfonic acid diammonium salt) (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH).

CONCLUSION

A novel bifunctional alginate lyase, BY17PV7, was expressed and characterized in Escherichia coli BL21(DE3). The results were helpful for the analysis of the molecular mechanisms of degrading patterns in the polysaccharide lyase (PL) family. © 2022 Society of Chemical Industry.

Biochemical Characterization of a Carrageenase, Car1383, Derived From Associated Bacteria of Antarctic Macroalgae

A carrageenase gene, car1383, was obtained from the metagenome of Antarctic macroalgae-associated bacteria. The amino acid sequence of its product showed up to 33% similarity with other carrageenases and contained a GH16-family motif. The recombinant Car1383 was heterologously expressed in Eschericia coli and exhibited maximal activity at 50°C and pH 6.0, with a K_m of 6.51 mg/ml and a V_max of 55.77 U/mg. Its activity was enhanced by some cations (Na⁺, K⁺, and Fe²⁺), but inhibited or inactivated by others (Sr²⁺, Ca²⁺, Ni²⁺, Ba²⁺, Mn²⁺, Cu²⁺, Fe³⁺, and Mg²⁺). Car1383 degraded carrageenan into neocarrabiose and neocarratetraose. Site-directed mutagenesis indicated that putative active sites, E₁₉₀ and E₁₉₅, conserved sites, W₁₈₃ and G₂₅₅, play important roles in Car1383 activity. This study provides a new candidate for the industrial preparation of bioactive algal oligosaccharides.

Evolving strategies for marine enzyme engineering: recent advances on the molecular modification of alginate lyase

Alginate, an acidic polysaccharide, is formed by β-d-mannuronate (M) and α-l-guluronate (G). As a type of polysaccharide lyase, alginate lyase can efficiently degrade alginate into alginate oligosaccharides, having potential applications in the food, medicine, and agriculture fields. However, the application of alginate lyase has been limited due to its low catalytic efficiency and poor temperature stability. In recent years, various structural features of alginate lyase have been determined, resulting in modification strategies that can increase the applicability of alginate lyase, making it important to summarize and discuss the current evidence. In this review, we summarized the structural features and catalytic mechanisms of alginate lyase. Molecular modification strategies, such as rational design, directed evolution, conserved domain recombination, and non-catalytic domain truncation, are also described in detail. Lastly, the application of alginate lyase is discussed. This comprehensive summary can inform future applications of alginate lyases.

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.

Design of a PL18 alginate lyase with flexible loops and broader entrance to enhance the activity and thermostability

Alginate oligosaccharides are enzymolysis products of alginate with versatile bioactivities and their industrial preparation was limited by the insufficient activity and unsatisfying thermostability of alginate lyases. The structure-function information about PL18 alginate lyases was seldom reported since which few positive mutants of PL18 alginate lyases were generated. In present study, a mutant of PL18 alginate lyase E226K was expressed intracellularly and taken as parent for further modification. Site I211 at the lid loop 1 and sites E276, Y292 and R294 at the predicted entrance were chosen as engineering targets based on the E226K-PM4 binding mode in prereaction-state MD simulation and 29 mutants were constructed, from those, the variant E226K/I211T/R294V was screened out as the best mutant (showing 4.78-fold increased catalytic efficiency and the half-time t_1/2^45℃ increased up to 557 min from 89 min). MD simulations indicated that the affinity of E226K/I211T/R294V towards alginate was improved due to the optimized energy distribution of active center, more flexible loops around catalytic cleft and larger substrate entrance. The more efficient proton transmitting endowed E226K/I211T/R294V higher activity and the more complicated intraprotein interactions together with stronger backbone rigidity were responsible for the improved thermostability of E226K/I211T/R294V than E226K. The success in this study enriches the structure-function information of PL18 alginate lyases and provides hints for their further design.

Potential applications of alginate oligosaccharides for biomedicine - A mini review

Extensive research on marine algae, especially on their health-promoting properties, has been conducted. Various ingredients with potential biomedical applications have been discovered and extracted from marine algae. Alginate oligosaccharides are low molecular weight alginate polysaccharides present in cell walls of brown algae. They exhibit various health benefits such as anti-inflammatory, anti-microbial, anti-oxidant, anti-tumor and immunomodulation. Their low-toxicity, non-immunogenicity, and biodegradability make them an excellent material in biomedicine. Alginate oligosaccharides can be chemically or biochemically modified to enhance their biological activity and potential in pharmaceutical applications. This paper provides a brief overview on alginate oligosaccharides characteristics, modification patterns and highlights their vital health promoting properties.