Galactomannan Degrading Enzymes from the Mannan Utilization Gene Cluster of Alkaliphilic Bacillus sp. N16-5 and Their Synergy on Galactomannan Degradation

Exploring the mechanism of seed shattering in Psathyrostachys juncea through histological analysis and comparative transcriptomics

BACKGROUND

Seed shattering (SS) negatively impacts seed yield in Psathyrostachys juncea. Understanding and improving the SS trait requires elucidating the regulatory mechanisms of SS and identifying the key genes involved.

RESULTS

This study presents a comprehensive analysis of the abscission zone (AZ) structures at four developmental stages in two P. juncea genotypes. High-SS P. juncea (H) exhibited a significantly higher SS rate than low-SS P. juncea (L) at all four developmental stages. Anatomical analysis revealed that the degree of lignification in the AZ cell walls is related to the integrity of the abscission structure. The degradation of the AZ in H occurred earlier and was more severe compared to L. At different developmental stages of the AZ, H exhibited higher cellulase and polygalacturonase activities and higher abscisic acid contents compared to L. Conversely, L showed higher lignin, cytokinin, auxin, and gibberellin contents than H. Transcriptomic analysis identified key metabolic pathways related to SS in P. juncea, such as phenylpropanoid biosynthesis, fructose and mannose metabolism, galactose metabolism, and pentose and glucuronate interconversions. The integration of morphological, histological, physiochemical, and metabolic data led to the identification of critical genes, including AUX1, CKX, ABF, GH3, 4CL, CCoAOMT, BGAL, Gal, and PG. The roles of these genes were involved in the regulation of plant hormones and in the synthesis and degradation of cell walls within the AZ.

CONCLUSIONS

This study provides an in-depth understanding of the regulatory mechanisms of SS in P. juncea through comparative transcriptomic analysis. The SS in P. juncea may result from the degradation of the cell wall regulated by cell wall hydrolases genes. The genes identified in this study provide a basis for the genetic improvement of SS traits and serve as a reference for research on other grass species.

Biochemical analyses of a novel acidophilic GH5 β-mannanase from Trichoderma asperellum ND-1 and its application in mannooligosaccharides production from galactomannans

In this study, an acidophilic GH5 β-mannanase (TaMan5) from Trichoderma asperellum ND-1 was efficiently expressed in Pichia pastoris (a 2.0-fold increase, 67.5 ± 1.95 U/mL). TaMan5 displayed the highest specificity toward locust bean gum (K_m = 1.34 mg/mL, V_max = 749.14 μmol/min/mg) at pH 4.0 and 65°C. Furthermore, TaMan5 displayed remarkable tolerance to acidic environments, retaining over 80% of its original activity at pH 3.0-5.0. The activity of TaMan5 was remarkably decreased by Cu²⁺, Mn²⁺, and SDS, while Fe²⁺/Fe³⁺ improved the enzyme activity. A thin-layer chromatography (TLC) analysis of the action model showed that TaMan5 could rapidly degrade mannan/MOS into mannobiose without mannose via hydrolysis action as well as transglycosylation. Site-directed mutagenesis results suggested that Glu²⁰⁵, Glu³¹³, and Asp³⁵⁷ of TaMan5 are crucial catalytic residues, with Asp¹⁵² playing an auxiliary function. Additionally, TaMan5 and commercial α-galactosidase displayed a remarkable synergistic effect on the degradation of galactomannans. This study provided a novel β-mannanase with ideal characteristics and can be considered a potential candidate for the production of bioactive polysaccharide mannobiose.

Functional exploration of the glycoside hydrolase family GH113

β-Mannans are a heterogeneous group of polysaccharides with a common main chain of β-1,4-linked mannopyranoside residues. The cleavage of β-mannan chains is catalyzed by glycoside hydrolases called β-mannanases. In the CAZy database, β-mannanases are grouped by sequence similarity in families GH5, GH26, GH113 and GH134. Family GH113 has been under-explored so far with six enzymes characterized, all from the Firmicutes phylum. We undertook the functional characterization of 14 enzymes from a selection of 31 covering the diversity of the family GH113. Our observations suggest that GH113 is a family with specificity towards mannans, with variations in the product profiles and modes of action. We were able to assign mannanase and mannosidase activities to four out of the five clades of the family, increasing by 200% the number of characterized GH113 members, and expanding the toolbox for fine-tuning of mannooligosaccharides.

Reshaping the binding channel of a novel GH113 family β-mannanase from Paenibacillus cineris (PcMan113) for enhanced activity

Endo-β-mannanases are important enzymes for degrading lignocellulosic biomass to generate mannan, which has significant health effects as a prebiotic that promotes the development of gut microbiota. Here, a novel endo-β-mannanase belonging to glycoside hydrolase (GH) family 113 from Paenibacillus cineris (PcMan113) was cloned, expressed and characterized, as one of only a few reported GH113 family β-mannanases. Compared to other functionally and structurally characterized GH113 mannanases, recombinant PcMan113 showed a broader substrate spectrum and a better performance. Based on a structural homology model, the highly active mutant PcMT3 (F110E/N246Y) was obtained, with 4.60- and 5.53-fold increases of enzyme activity (towards KG) and catalytic efficiency (kcat/Km, against M5) compared with the WT enzyme, respectively. Furthermore, molecular dynamics (MD) simulations were conducted to precisely explore the differences of catalytic activity between WT and PcMT3, which revealed that PcMT3 has a less flexible conformation, as well as an enlarged substrate-binding channel with decreased steric hindrance and increased binding energy in substrate recognition. In conclusion, we obtained a highly active variant of PcMan113 with potential for commercial application in the manufacture of manno-oligosaccharides.

Functional and structural investigation of a novel β-mannanase BaMan113A from Bacillus sp. N16-5

Mannan is an important renewable resource whose backbone can be hydrolyzed by β-mannanases to generate manno-oligosaccharides of various sizes. Only a few glycoside hydrolase (GH) 113 family β-mannanases have been functionally and structurally characterize. Here, we report the function and structure of a novel GH113 β-mannanase from Bacillus sp. N16-5 (BaMan113A). BaMan113A exhibits a substrate preference toward manno-oligosaccharides and releases mannose and mannobiose as main hydrolytic products. The crystal structure of BaMan113A suggest that the enzyme shows a semi-enclosed substrate-binding cleft and the amino acids surrounding the +2 subsite form a steric barrier to terminate the substrate-binding tunnel. Based on these structural features, we conducted mutagenesis to engineer BaMan113A to remove the steric hindrance of the substrate-binding tunnel. We found that F101E and N236Y variants exhibit increased specific activity toward mannans comparing to the wild-type enzyme. Meanwhile, the product profiles of these two variants toward polysaccharides changed from mannose to a series of manno-oligosaccharides. The crystal structure of variant N236Y was also determined to illustrate the molecular basis underlying the mutation. In conclusion, we report the functional and structural features of a novel GH113 β-mannanase, and successfully improved its endo-acting activity by using structure-based engineering.

Carbohydrate-binding modules targeting branched polysaccharides: overcoming side-chain recalcitrance in a non-catalytic approach

Extensive decoration of backbones is a major factor resulting in resistance of enzymatic conversion in hemicellulose and other branched polysaccharides. Employing debranching enzymes is the main strategy to overcome this kind of recalcitrance at present. A carbohydrate-binding module (CBM) is a contiguous amino acid sequence that can promote the binding of enzymes to various carbohydrates, thereby facilitating enzymatic hydrolysis. According to previous studies, CBMs can be classified into four types based on their preference in ligand type, where Type III and IV CBMs prefer to branched polysaccharides than the linear and thus are able to specifically enhance the hydrolysis of substrates containing side chains. With a role in dominating the hydrolysis of branched substrates, Type III and IV CBMs could represent a non-catalytic approach in overcoming side-chain recalcitrance.

Bagasse minority pathway expression: Real time study of GH2 β-mannosidases from bacteroidetes

After being isolated from a sugarcane pile, the bacterium Chitinophaga sp. CB10 demonstrated to be a rich source of carbohydrases, with 350 predicted CAZyme domains. CB10 was able to grow on carbohydrates of different structural complexities: glucose, carboxymethylcellulose, corn starch, galactomannan, Aloe vera gum and sugarcane bagasse. The sugarcane bagasse is a rich source of complex polymers, and the diversity of metabolites released by its enzymatic hydrolysis has an important role for green chemistry, including minority pathways such as the degradation of mannan conjugates. In this sense, CB10 demonstrated considerable levels of gene expression for mannanases, and was stable for a period of 96-144 hours in the presence of sugarcane bagasse as sole carbon source. The bacterium showed respectively 4.8x and 5.6x expression levels for two genes predicted for GH2 β-mannosidase: one located within a gene cluster identified as "polysaccharide utilization loci" (PUL), and another a classic β-mannosidase. These enzymes shared less than 45% of identity with enzymes characterized from the genus Chitinophaga belonging to the phylum Bacteroidetes. The degree of novelty-as demonstrated by the low identity with previously characterized enzymes; the remarkable capability to grow in different substrates; mannanase activity, evidenced by the release of residual oligosaccharides in the cultivation with galactomannan (HPLC-RID, 12.3 mMol); associated to the ability of mannanases expression in a low concentration of inductor conditions (sugarcane bagasse, 0.2%) indicate the high potential for the application of CB10 as a source of enzymes in the production of oligosaccharides from biomass. This capacity might prove to be very valuable for the biorefinery process of pre-biotic precursors and other functional oligosaccharides focused on the food and pharmaceutical industries.

Prebiotic mannooligosaccharides: Synthesis, characterization and bioactive properties

Functional oligosaccharides are non-digestible food ingredients that confer numerous health benefits. Among these, mannooligosaccharides (MOS) are emerging prebiotics that have characteristic potential bio-active properties. Microbial mannanases can be used to break down mannan rich agro-residues to yield MOS. Various applications of MOS as health promoting functional food ingredient may open up newer opportunities in food and feed industry. Enzymatic hydrolysis is the widely preferred method over chemical hydrolysis for MOS production. Presently, commercial MOS is being derived from yeast cell wall mannan and is widely used as prebiotic in feed supplements for poultry and aquaculture. Apart from stimulating the growth of probiotic microflora, MOS impart anticancer and immunomodulatory effects by inducing different gene markers in colon cells. This review summarizes recent developments and future prospects of enzymatic synthesis of MOS from various mannans, their structural characteristics and their potential health benefits.

Biochemical analyses of a novel thermostable GH5 endo β-1,4-mannanase with minor β-1,4-glucosidic cleavage activity from Bacillus sp. KW1 and its synergism with a commercial α-galactosidase on galactomannan hydrolysis

A novel GH5 endo-1,4-β-mannanase (BaMan5A) was identified from Bacillus sp. KW1, it shares the highest sequence identity (86%) with another characterized Bacillus endo-1,4-β-mannanase. The recombinant BaMan5A displayed maximum activity at pH 7.0 and 70 °C, it was stable at a broad pH range (pH 3.5-11.0) after 12-h incubation at 25 °C, and exhibited good thermostability, retaining about 100% and 85% activity after incubating at 60 °C for 12 h and 65 °C for 8 h, respectively. The results of polysaccharide hydrolysis revealed that the enzyme can only hydrolyze mannan substrates, including carob galactomannan, konjac glucomannan, 1,4-β-D-mannan, locust bean gum, and guar gum, yielding mannose, mannobiose, mannotriose, and some other oligosaccharides. The best substrate was carob galactomannan, the corresponding specific activity and K_m value were 10,886 μmol/min/μmol and 3.31 mg/mL, respectively. Interestingly, BaMan5A was capable to hydrolyze both manno-oligosaccharides and cello-oligosaccharides, including mannotetraose, mannopentaose, mannohexaose, cellopentaose and cellohexaose. Furthermore, BaMan5A acted synergistically with a commercial α-galactosidase (CbAgal) on galactomannan depolymerization, a best synergy degree of 1.58 was achieved after optimizing enzyme ratios. This study not only expands the diversity of Bacillus GH5 β-mannanase, but also discloses the potential of BaMan5A in industrial application.

A Recombinant β-Mannanase from Thermoanaerobacterium aotearoense SCUT27: Biochemical Characterization and Its Thermostability Improvement

β-Mannanase was expressed in Thermoanaerobacterium aotearoense SCUT27 induced by locust bean gum (LBG). The open reading frame encoding a GH26 β-mannanase was identified and encoded a preprotein of 515 amino acids with a putative signal peptide. The enzyme without a signal sequence (Man25) was overexpressed in Escherichia coli with a specific activity of 1286.2 U/mg. Moreover, a facile method for β-mannanase activity screening was established based on agar plates. The optimum temperature for the purified Man25 using LBG as a substrate was 55 °C. The catalytic activity and thermostability of Man25 displayed a strong dependence on calcium ions. Through saturation mutagenesis at the putative Ca²⁺ binding sites in Man25, the best mutant ManM3-3 (D143A) presented improvements in thermostability with 3.6-fold extended half-life at 55 °C compared with that of the wild-type. The results suggest that mutagenesis at metal binding sites could be an efficient approach to increase enzyme thermostability.

Recombinant production and characterization of six novel GH27 and GH36 α-galactosidases from Penicillium subrubescens and their synergism with a commercial mannanase during the hydrolysis of lignocellulosic biomass

α-Galactosidases are important industrial enzymes for hemicellulosic biomass degradation or modification. In this study, six novel extracellular α-galactosidases from Penicillium subrubescens were produced in Pichia pastoris and characterized. All α-galactosidases exhibited high affinity to pNPαGal, and only AglE was not active towards galacto-oligomers. Especially AglB and AglD released high amounts of galactose from guar gum, carob galactomannan and locust bean, but combining α-galactosidases with an endomannanase dramatically improved galactose release. Structural comparisons to other α-galactosidases and homology modelling showed high sequence similarities, albeit significant differences in mechanisms of productive binding, including discrimination between various galactosides. To our knowledge, this is the first study of such an extensive repertoire of extracellular fungal α-galactosidases, to demonstrate their potential for degradation of galactomannan-rich biomass. These findings contribute to understanding the differences within glycoside hydrolase families, to facilitate the development of new strategies to generate tailor-made enzymes for new industrial bioprocesses.