The GH10 and GH48 dual-functional catalytic domains from a multimodular glycoside hydrolase synergize in hydrolyzing both cellulose and xylan

Functional studies on tandem carbohydrate-binding modules of a multimodular enzyme possessing two catalytic domains

Although functional studies on carbohydrate-binding module (CBM) have been carried out extensively, the role of tandem CBMs in the enzyme containing multiple catalytic domains (CDs) is unclear. Here, we identified a multidomain enzyme (Lc25986) with a novel modular structure from lignocellulolytic bacterial consortium. It consists of a mannanase domain, two CBM65 domains (LcCBM65-1/LcCBM65-2), and an esterase domain. To investigate CBM function and domain interactions, full-length Lc25986 and its variants were constructed and used for enzymatic activity, binding, and bioinformatic analyses. The results showed that LcCBM65-1 and LcCBM65-2 both bind mannan and xyloglucan but not cellulose or β-1,3-1,4-glucan, which differs from the ligand specificity of reported CBM65s. Compared to LcCBM65-2, LcCBM65-1 showed a stronger ligand affinity and a preference for acetylation sites. Both CBM65s stimulated the enzymatic activities of their respective neighboring CDs against acetylated mannan, but did not contribute to the activities of the distal CDs. The time course of mannan hydrolysis indicated that the full-length Lc25986 was more effective in the complete degradation of mixed acetyl/non-acetyl substrates than the mixture of single-CD mutants. When acting on complex substrates, LcCBM65-1 not only improved the enzymatic activity of the mannanase domain, but also directed the esterase domain to the acetylated polysaccharides. LcCBM65-2 adopted a low affinity to reduce interference with the catalysis of the mannanase domain. These results demonstrate the importance of CBMs for the synergism between the two CDs of a multidomain enzyme and suggest that they contribute to the adequate degradation of complex substrates such as plant cell walls.

IMPORTANCE

Lignocellulolytic enzymes, particularly those of bacterial origin, often harbor multiple carbohydrate-binding modules (CBMs). However, the function of CBM multivalency remains poorly understood. This is especially true for enzymes that contain more than one catalytic domain (CD), as the interactions between CDs, CBMs, and CDs and CBMs can be complex. Our research demonstrates that homogeneous CBMs can have distinct functions in a multimodular enzyme. The tandem CBMs coordinate the CDs in catalytic conflict through their differences in binding affinity, ligand preference, and arrangement within the full-length enzyme. Additionally, although the synergism between mannanase and esterase is widely acknowledged, our study highlights the benefits of integrating the two enzymes into a single entity for the degradation of complex substrates. In summary, these findings enhance our understanding of the intra-synergism of a multimodular enzyme and emphasize the significance of multiple CBMs in this context.

The Discovery of a Multidomain Mannanase Containing Dual-Catalytic Domain of the Same Activity: Biochemical Properties and Synergistic Effect

In recent years, the wide application of mannan has driven the demand for the exploration of mannanase. As one of the main components of hemicellulose, mannan is an important polysaccharide that ruminants need to degrade and utilize, making rumen a rich source of mannanases. In this study, gene mining of mannanases was performed using bioinformatics, and potential dual-catalytic domain mannanases were heterologously expressed to analyze their properties. The hydrolysis pattern and enzymatic products were identified by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). A dual-catalytic domain mannanase Man26/5 with the same function as the substrate was successfully mined from the genome of cattle rumen microbiota. Compared to the single-catalytic domain, its higher thermal stability (≤50 °C) and catalytic efficiency confirm the synergistic effect between the two catalytic domains. It exhibited a unique "crab-like" structure where the CBM located in the middle is responsible for binding, and the catalytic domains at both ends are responsible for cutting. The exploration of its multidomain structure and synergistic patterns could provide a reference for the artificial construction and molecular modification of enzymes.

Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities

Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.

Synergy of the Two Alginate Lyase Domains of a Novel Alginate Lyase from Vibrio sp. NC2 in Alginate Degradation

Alginate lyases play a vital role in the degradation of alginate, an important marine carbon source. Alginate is a complex macromolecular substrate, and the synergy of alginate lyases is important for the alginate utilization by microbes and the application of alginate lyases in biotechnology. Although many studies have focused on the synergy between different alginate lyases, the synergy between two alginate lyase domains of one alginate lyase has not been reported. Here, we report the synergism between the two catalytic domains of a novel alginate lyase, AlyC6', from the marine alginate-degrading bacterium Vibrio sp. NC2. AlyC6' contains two PL7 catalytic domains (CD1 and CD2) that have no sequence similarity. While both CD1 and CD2 are endo-lyases with the highest activity at 30°C, pH 8.0, and 1.0 M NaCl, they also displayed some different properties. CD1 was PM-specific, but CD2 was PG-specific. Compared with CD2, CD1 had higher catalytic efficiency, but lower substrate affinity. In addition, CD1 had a smaller minimal substrate than CD2, and the products from CD2 could be further degraded by CD1. These distinctions between the two domains enable them to synergize intramolecularly in alginate degradation, resulting in efficient and complete degradation of various alginate substrates. The bioinformatics analysis revealed that diverse alginate lyases have multiple catalytic domains, which are widespread, especially abundant in Flavobacteriaceae and Alteromonadales, which may secret multimodular alginate lyases for alginate degradation. This study provides new insight into bacterial alginate lyases and alginate degradation and is helpful for designing multimodular enzymes for efficient alginate depolymerization. IMPORTANCE Alginate is a major component in the cell walls of brown algae. Alginate degradation is carried out by alginate lyases. Until now, while most characterized alginate lyases contain one single catalytic domain, only a few have been shown to contain two catalytic domains. Furthermore, the synergy of alginate lyases has attracted increasing attention since it plays important roles in microbial alginate utilization and biotechnological applications. Although many studies have focused on the synergy between different alginate lyases, the synergy between two catalytic domains of one alginate lyase has not been reported. Here, a novel alginate lyase, AlyC6', with two functional alginate lyase domains was biochemically characterized. Moreover, the synergism between the two domains of AlyC6' was revealed. Additionally, the distribution of the alginate lyases with multiple alginate lyase domains was investigated based on the bioinformatics analysis. This study provides new insight into bacterial alginate lyases and alginate degradation.

Characterization of a Novel Alginate Lyase with Two Alginate Lyase Domains from the Marine Bacterium Vibrio sp. C42

Alginate is abundant in the cell walls of brown algae. Alginate lyases can degrade alginate, and thus play an important role in the marine carbon cycle and industrial production. Currently, most reported alginate lyases contain only one functional alginate lyase domain. AlyC8 is a putative alginate lyase with two alginate lyase domains (CD1 and CD2) from the marine alginate-degrading strain Vibrio sp. C42. To characterize AlyC8 and its two catalytic domains, AlyC8 and its two catalytic domain-deleted mutants, AlyC8-CD1 and AlyC8-CD2, were expressed in Escherichia coli. All three proteins have noticeable activity toward sodium alginate and exhibit optimal activities at pH 8.0-9.0 and at 30-40 °C, demonstrating that both CD1 and CD2 are functional. However, CD1 and CD2 showed opposite substrate specificity. The differences in substrate specificity and degradation products of alginate between the mutants and AlyC8 demonstrate that CD1 and CD2 can act synergistically to enable AlyC8 to degrade various alginate substrates into smaller oligomeric products. Moreover, kinetic analysis indicated that AlyC8-CD1 plays a major role in the degradation of alginate by AlyC8. These results demonstrate that AlyC8 is a novel alginate lyase with two functional catalytic domains that are synergistic in alginate degradation, which is helpful for a better understanding of alginate lyases and alginate degradation.

Fusion of a proline-rich oligopeptide to the C-terminus of a ruminal xylanase improves catalytic efficiency

Xylanases are widely used in the degradation of lignocellulose and are important industrial enzymes. Therefore, increasing the catalytic activity of xylanases can improve their efficiency and performance. In this study, we introduced the C-terminal proline-rich oligopeptide of the rumen-derived XynA into XylR, a GH10 family xylanase. The optimum temperature and pH of the fused enzyme (XylR-Fu) were consistent with those of XylR; however, its catalytic efficiency was 2.48-fold higher than that of XylR. Although the proline-rich oligopeptide did not change the enzyme hydrolysis mode, the amount of oligosaccharides released from beechwood xylan by XylR-Fu was 17% higher than that released by XylR. This increase may be due to the abundance of proline in the oligopeptide, which plays an important role in substrate binding. Furthermore, circular dichroism analysis indicated that the proline-rich oligopeptide might increase the rigidity of the overall structure, thereby enhancing the affinity to the substrate and catalytic activity of the enzyme. Our study shows that the proline-rich oligopeptide enhances the catalytic efficiency of GH10 xylanases and provides a better understanding of the C-terminal oligopeptide-function relationships. This knowledge can guide the rational design of GH10 xylanases to improve their catalytic activity and provides clues for further applications of xylanases in industry.

A novel chicory fructanase can degrade common microbial fructan product profiles and displays positive cooperativity

Fructan metabolism in bacteria and plants relies on fructosyltransferases and fructanases. Plant fructanases (fructan exohydrolase, FEH) only hydrolyse terminal fructose residues. Levan (β-2,6 linkages) is the most abundant fructan type in bacteria. Dicot fructan accumulators, such as chicory (Cichorium intybus), accumulate inulin (β-2,1 linkages), harbouring several 1-FEH isoforms for their degradation. Here, a novel chicory fructanase with high affinity for levan was characterized, providing evidence that such enzymes widely occur in higher plants. It is adapted to common microbial fructan profiles, but has low affinity towards chicory inulin, in line with a function in trimming of microbial fructans in the extracellular environment. Docking experiments indicate the importance of an N-glycosylation site close to the active site for substrate specificity. Optimal pH and temperature for levan hydrolysis are 5.0 and 43.7 °C, respectively. Docking experiments suggested multiple substrate binding sites and levan-mediated enzyme dimerization, explaining the observed positive cooperativity. Alignments show a single amino acid shift in the position of a conserved DXX(R/K) couple, typical for sucrose binding in cell wall invertases. A possible involvement of plant fructanases in levan trimming is discussed, in line with the emerging 'fructan detour' concepts, suggesting that levan oligosaccharides act as signalling entities during plant-microbial interactions.

Recent advances in the enzymatic production and applications of xylooligosaccharides

The majority of lignocellulosic biomass on the planet originates from plant cell walls, which are complex structures build up mainly by cellulose, hemicellulose and lignin. The largest part of hemicellulose, xylan, is a polymer with a β-(1→4)-linked xylose residues backbone decorated with α-D-glucopyranosyl uronic acids and/or L-arabinofuranose residues. Xylan is the second most abundant biopolymer in nature, which can be sustainably and efficiently degraded into decorated and undecorated xylooligosaccharides (XOS) using combinations of thermochemical pretreatments and enzymatic hydrolyses, that have broad applications in the food, feed, pharmaceutical and cosmetic industries. Endo-xylanases from different complex carbohydrate-active enzyme (CAZyme) families can be used to cleave the backbone of arabino(glucurono)xylans and xylooligosaccharides and degrade them into short XOS. It has been shown that XOS with a low degree of polymerization have enhanced prebiotic effects conferring health benefits to humans and animals. In this review we describe recent advances in the enzymatic production of XOS from lignocellulosic biomass arabino- and glucuronoxylans and their applications as food and feed additives and health-promoting ingredients. Comparative advantages of xylanases from different CAZy families in XOS production are discussed and potential health benefits of different XOS are presented.

Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity

Endoxylanases active under extreme conditions of temperature and alkalinity can replace the use of highly pollutant chemicals in the pulp and paper industry. Searching for enzymes with these properties, we carried out a comprehensive bioinformatics study of the GH10 family. The phylogenetic analysis allowed the construction of a radial cladogram in which protein sequences putatively ascribed as thermophilic and alkaliphilic appeared grouped in a well-defined region of the cladogram, designated TAK Cluster. One among five TAK sequences selected for experimental analysis (Xyn11) showed extraordinary xylanolytic activity under simultaneous conditions of high temperature (90 °C) and alkalinity (pH 10.5). Addition of a carbohydrate binding domain (CBM2) at the C-terminus of the protein sequence further improved the activity of the enzyme at high pH. Xyn11 structure, which has been solved at 1.8 Å resolution by X-ray crystallography, reveals an unusually high number of hydrophobic, ionic and hydrogen bond atomic interactions that could account for the enzyme’s extremophilic nature.

A Conserved Glycoside Hydrolase Family 7 Cellobiohydrolase PsGH7a of Phytophthora sojae Is Required for Full Virulence on Soybean

Phytopathogens deploy glycoside hydrolases (GHs) to disintegrate plant cell walls for nutrition and invasion. However, the pathogenic mechanisms of the majority of GHs in virulence remain unknown, especially in oomycetes. In this study, a Phytophthora sojae gene encodes a GH7 family cellobiohydrolase, named PsGH7a, was identified. PsGH7a was highly induced during the cyst germination and infection stages. PsGH7a is conserved in oomycetes, and shares a high amino acid sequence identity (>85%) within Phytophthora genus. The recombinant PsGH7a catalyzes the hydrolysis of β-1,4-glucan and avicel, which represent the major components of cellulose in plant cell wall. The mutation of catalytic residue Glu236 to alanine resulted in a lower catalytic activity. In addition, the PsGH7a promotes Phytophthora invasion, while the mutant can not. Notably, PsGH7a protein triggers hypersensitive cell death in diverse plants. PsGH7a knockout mutants were generated via CRISPR/Cas9 system, to investigate its biological function. Compared to wild-type strain P6497, the mutants showed reduced virulence on susceptible soybean, indicates PsGH7a is indispensable to P. sojae virulence.