Microbial α-galactosidases: Efficient biocatalysts for bioprocess technology

Multidimensional computational strategies enhance the thermostability of alpha-galactosidase

Alpha-Galactosidase has significant industrial application value in food processing, animal nutrition and medical applications. Microbial-derived α-galactosidases predominate industrial implementation due to high productivity, yet their inherent thermal instability necessitates systematic protein engineering. In this study, we established a dual-strategy protein engineering framework to enhance the thermostability of Aspergillus tubingensis α-galactosidase (AtWU_04653). Strategy I employed integrative computational design tools (ABACUS2/PROSS/DBD2) for mutational library construction, which yielded the dominant mutant A169P exhibiting remarkable performance: 78.52 % enhancement in thermal half-life at 55 °C (pH 4.0) and 52.04 % increase in catalytic efficiency (kcat /Km). Strategy II implemented a physics-based computational methodology combining GROMACS molecular dynamics simulations with Rosetta unfolding free energy calculations and SPIRED machine learning predictions, successfully deriving three stabilized variants (E429I, N380L, T64P) displaying 57.33 %, 67.17 %, and 41.34 % extended half-lives respectively. Notably, E429I and T64P demonstrated concurrent 85.25 % and 65.90 % catalytic activity augmentation (kcat /Km). Both strategies achieved substantial reduction in experimental screening workload while enabling synergistic thermostability-activity optimization. This study uses sequence conservation analysis, unfolding free energy calculation, molecular dynamics simulation, and innovative protein prediction models to establish multidimensional computational strategies for designing mutants, providing new and important technical references for computational design and functional optimization of enzymes.

Functional characterization of two GH27 ɑ-galactosidases from Penicillium parvum 4-14 and their differential capabilities upon plant biomass degradation

Two new ɑ-galactosidases PpAgl27B and PpAgl27C from Penicillium parvum 4-14 were functionally investigated in this study. Based on the analysis of catalytic domain and phylogenetic tree, PpAgl27B (435 aa) and PpAgl27C (543 aa) belong to glycoside hydrolase (GH) 27 family. After expression in Pichia pastoris, the recombinant PpAgl27B and PpAgl27C showed the highest activities at pH 3.5 and 65 °C, or 4.0 and 45 °C, respectively. Using p-nitrophenyl-α-d-galactopyranoside (pNPGal) as substrate, the Michaelis constant were 0.90 mM for PpAgl27B and 2.54 mM for PpAgl27C. PpAgl27C had a low catalytic activity toward pNPGal and negligible activities on various natural substrates. Differently, PpAgl27B efficiently released galactose from the artificial substrate, raffinose family oligosaccharides, or galactomannans. Hydrolysis of corn bran arabinoxylan (CBAX) 1 or 2 were conducted by PpAgl27B alone or in combination with the enzyme blend E_CBAX1. PpAgl27B released a small amount of galactose (1.7-3.0 mg/g) from the both substrates. Compared with the individual enzymes, the liberations of galactose, xylose and arabinose from the substrates were significantly enhanced by combing PpAgl27B and E_CBAX1. The degrees of synergy of the enzyme combination for the saccharification of CBAX1 or CBAX2 were 1.20 and 1.13, respectively. PpAgl27B showed promising potential for the valorization of galactose-rich feedstocks as well as CBAX.

A review on the expanding biotechnological frontier of Pedobacter

The genus Pedobacter consists of Gram-negative bacteria with a broad geographic distribution, isolated from diverse habitats, including water, soil, plants, wood, rocks and animals. However, characterization efforts have been limited to a small number of species. Likewise, in the context of natural products (NP), only a small fraction of Pedobacter -derived NPs have been characterized so far. In contrast, in silico analysis of the increasing number of available genomes in the databases, suggests a wealth of yet to be discovered compounds. Notable biotechnological applications described so far include the production of heparinases and chondroitinases for therapeutic purposes, phytases and galactosidases as aquaculture feed supplements, alginate lyases for biofuel production, and secondary metabolites such as pedopeptins and isopedopeptins with antimicrobial properties. Further research integrating synthetic biology approaches, holds great promise for unlocking the hidden potential of members of this genus, thus expanding its industrial applications.

Prebiotic Effects of α- and β-Galactooligosaccharides: The Structure-Function Relation

Oligosaccharides containing galactosyl moieties belong to two main groups: raffinose family oligosaccharides (RFO, α-GOS) and lactose-type β-galactooligosaccharides (β-GOS), both well-known for their prebiotic effect. The present review investigates the vast amounts of recent research on the structures of GOS and their beneficial impact. It focuses on the molecular interactions between GOS and probiotics in vitro and in vivo, the enzymology of the processes, and the genetic prerequisites for the synthesis and degradation of GOS by probiotic bacteria. The preferences of probiotic strains belonging to the Bifidobacterium and Lactobacillus genera are elucidated to form and degrade GOS of a certain length, structure, and linkages between monomers. A brief overview of the industrial production of β-GOS by natural and recombinant strains included the methods and production efficiency evaluation.

Application of an α-galactosidase from Bacteroides fragilis on structural analysis of raffinose family oligosaccharides

Raffinose family oligosaccharides (RFOs) have diverse structures and exhibit various biological activities. When using RFOs as prebiotics, their structures need to be identified. If we first knew whether an RFO was classical or non-classical, structural identification would become much easier. Here, we cloned and expressed an α-galactosidase (BF0224) from Bacteroides fragilis which showed strict specificity for hydrolyzing α-Gal-(1 → 6)-Gal linkages in RFOs. BF0224 efficiently distinguished classical from non-classical RFOs by identifying the resulting hydrolyzed oligo- and mono-saccharides with HPAEC-PAD-MS. Using this strategy, we identified a non-classical RFO from Pseudostellaria heterophylla (Miquel) Pax with DP6 (termed PHO-6), as well as a classical RFO from Lycopus lucidus Turcz. with DP7 (termed LTO-7). To characterize these RFO structures, we employed four other commercial or reported α-galactosidases in combination with NMR and methylation analysis. Using this approach, we elucidated the accurate chemical structure of PHO-6 and LTO-7. Our study provides an efficient analytical approach to structurally analyze RFOs. This enzyme-based strategy also can be applied to structural analysis of other glycans.

Activity-based metaproteomics driven discovery and enzymological characterization of potential α-galactosidases in the mouse gut microbiome

The gut microbiota offers an extensive resource of enzymes, but many remain uncharacterized. To distinguish the activities of similar annotated proteins and mine the potentially applicable ones in the microbiome, we applied an effective Activity-Based Metaproteomics (ABMP) strategy using a specific activity-based probe (ABP) to screen the entire gut microbiome for directly discovering active enzymes and their potential applications, not for exploring host-microbiome interactions. By using an activity-based cyclophellitol aziridine probe specific to α-galactosidases (AGAL), we successfully identified and characterized several gut microbiota enzymes possessing AGAL activities. Cryo-electron microscopy analysis of a newly characterized enzyme (AGLA5) revealed the covalent binding conformations between the AGAL5 active site and the cyclophellitol aziridine ABP, which could provide insights into the enzyme's catalytic mechanism. The four newly characterized AGALs have diverse potential activities, including raffinose family oligosaccharides (RFOs) hydrolysis and enzymatic blood group transformation. Collectively, we present a ABMP platform that facilitates gut microbiota AGALs discovery, biochemical activity annotations and potential industrial or biopharmaceutical applications.

Recent advances in modifications of exudate gums: Functional properties and applications

Gums are high-molecular-weight compounds with hydrophobic or hydrophilic characteristics, which are mainly comprised of complex carbohydrates called polysaccharides, often associated with proteins and minerals. Various innovative modification techniques are utilized, including ultrasound-assisted and microwave-assisted techniques, enzymatic alterations, electrospinning, irradiation, and amalgamation process. These methods advance the process, reducing processing times and energy consumption while maintaining the quality of the modified gums. Enzymes like xanthan lyases, xanthanase, and cellulase can selectively modify exudate gums, altering their structure to enhance their properties. This precise enzymatic approach allows for the use of exudate gums for specific applications. Exudate gums have been employed in nanotechnology applications through techniques like electrospinning. This enables the production of nanoparticles and nanofibers with improved properties, making them suitable for the drug delivery system, tissue engineering, active and intelligient food packaging. The resulting modified exudate gums exhibit improved rheological, emulsifying, gelling, and other functional properties, which expand their potential applications. This paper discusses novel applications of these modified gums in the pharmaceutical, food, and industrial sectors. The ever-evolving field presents diverse opportunities for sustainable innovation across these sectors.

Purification and characterization of α-galactosidase isolated from Klebsiella pneumoniae in the human oral cavity

The enzyme α-Galactosidase (α-D-galactoside galactohydrolase [EC 3.2.1.22]) is an exoglycosidase that hydrolyzes the terminal α-galactosyl moieties of glycolipids and glycoproteins. It is ubiquitous in nature and possesses extensive applications in the food, pharma, and biotechnology industries. The present study aimed to purify α-galactosidase from Klebsiella pneumoniae, a bacterium isolated from the human oral cavity. The purification steps involved ammonium sulfate precipitation (70 %), dialysis, ion exchange chromatography using a DEAE-cellulose column, and affinity monolith chromatography. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis was used to determine the molecular weight of the purified enzyme. The kinetic constants, Michaelis constant (Km) and maximal velocity (Vmax), for this enzyme were determined by using p-nitrophenyl-α-D-galactopyranoside as substrate. The results showed that the purification fold, specific activity, and yield were 126.52, 138.58 units/mg, and 21.5 %, respectively. The SDS-PAGE showed that the molecular weight of the purified enzyme was 75 kDa. The optimum pH and temperature of the purified α-galactosidase were detected at pH 6.0 and 50 °C, respectively. The kinetic constants, Michaelis constant (Km) and maximal velocity (Vmax), for this enzyme were 4.6 mM and 769.23 U/ml, respectively. α-galactosidase from Klebsiella pneumoniae was purified and characterized. (SDS-PAGE) analysis showed that the purified enzyme appeared as single band with a molecular weight of 75 kDa.

Microbial production and applications of β-glucosidase-A review

β-Glucosidase exists in all areas of living organisms, and microbial β-glucosidase has become the main source of its production because of its unique physicochemical properties and the advantages of high-yield production by fermentation. With the rise of the green circular economy, the production of enzymes through the fermentation of waste as the substrate has become a popular trend. Lignocellulosic biomass is an easily accessible and sustainable feedstock that exists in nature, and the production of biofuels from lignocellulosic biomass requires the involvement of β-glucosidase. This review proposes ways to improve β-glucosidase yield and catalytic efficiency. Optimization of growth conditions and purification strategies of enzymes can increase enzyme yield, and enzyme immobilization, genetic engineering, protein engineering, and whole-cell catalysis provide solutions to enhance the catalytic efficiency and activity of β-glucosidase. Besides, the diversified industrial applications, challenges and prospects of β-glucosidase are also described.

Protein composition and nutritional aspects of pea protein fractions obtained by a modified isoelectric precipitation method using fermentation

Pea albumins are promising for their nutritional, biological, and techno-functional properties. However, this fraction is usually discarded in the industry due to its low protein content compared to globulin fraction and the presence of some anti-nutritional compounds. In the present study, we used an alternative method of pea protein extraction based on alkaline solubilization/isoelectric precipitation in which the reduction of pH was achieved by lactic acid fermentation using specific starters instead of mineral acids. Hence, the main objective of this study was to examine the protein profile and the content of anti-nutritional and nutritional active compounds in pea albumin-rich fractions obtained by the isoelectric extraction method without (control) or with fermentation with different lactic acid bacteria (Streptococcus thermophilus, Lactiplantibacillus plantarum, and their co-culture). Different pea cultivars (Cartouche, Ascension, and Assas) were used here for their differences in protein profile. The results revealed a higher total nitrogen content in albumin-rich fraction for fermented samples and, in particular, for co-culture. The majority of total nitrogen was determined as non-protein (~50%), suggesting the degradation of proteins by LAB to small peptides and amino acids, which were solubilized in the soluble fraction (albumin) as confirmed by size exclusion chromatography (SEC-HPLC) analysis. Moreover, the higher antioxidant activity of fermented albumin samples was attributed to the production of small peptides during extraction. Lactic acid fermentation also resulted in a significant reduction of trypsin inhibitor activity, α-galactoside, and phytic acid content of this fraction compared to control.

Towards an understanding of the enzymatic degradation of complex plant mannan structures

Plant cell walls are composed of a heterogeneous mixture of polysaccharides that require several different enzymes to degrade. These enzymes are important for a variety of biotechnological processes, from biofuel production to food processing. Several classical mannanolytic enzyme functions of glycoside hydrolases (GH), such as β-mannanase, β-mannosidase and α-galactosidase activities, are helpful for efficient mannan hydrolysis. In this light, we bring three enzymes into the model of mannan degradation that have received little or no attention. By linking their three-dimensional structures and substrate specificities, we have predicted the interactions and cooperativity of these novel enzymes with classical mannanolytic enzymes for efficient mannan hydrolysis. The novel exo-β-1,4-mannobiohydrolases are indispensable for the production of mannobiose from the terminal ends of mannans, this product being the preferred product for short-chain mannooligosaccharides (MOS)-specific β-mannosidases. Second, the side-chain cleaving enzymes, acetyl mannan esterases (AcME), remove acetyl decorations on mannan that would have hindered backbone cleaving enzymes, while the backbone cleaving enzymes liberate MOS, which are preferred substrates of the debranching and sidechain cleaving enzymes. The nonhydrolytic expansins and swollenins disrupt the crystalline regions of the biomass, improving their accessibility for AcME and GH activities. Finally, lytic polysaccharide monooxygenases have also been implicated in promoting the degradation of lignocellulosic biomass or mannan degradation by classical mannanolytic enzymes, possibly by disrupting adsorbed mannan residues. Modelling effective enzymatic mannan degradation has implications for improving the saccharification of biomass for the synthesis of value-added and upcycling of lignocellulosic wastes.

Biopharmaceutical applications of α-galactosidases

α-Galactosidases are exoglycosidases that are active on galactose-containing side chains in oligosaccharides, polysaccharides, glycolipids, and glycoproteins. α-Galactosidases are gaining increased interest in human medicine, especially in the enzyme replacement therapy for Fabry's disease. α-Galactosidases with regioselectivity toward α-1,3-linked galactose find application in xenotransplantation and blood group transformation. The use of α-galactosidases as a therapeutic agent in alleviating the postprandial symptoms of irritable bowel syndrome is much acclaimed. The excellent therapeutic applications of α-galactosidases have led to an upwelling of worldwide research interventions to identify novel α-galactosidases with improved catalytic efficiency. In addition to these therapeutic applications, α-galactosidases also have interesting applications in the industrial sectors like food, feed, probiotics, sugar, and paper pulp. The current review focuses on the diverse therapeutic applications of α-galactosidases and their prospects.

Molecular advances in microbial α-galactosidases: challenges and prospects

α-Galactosidase (α-D-galactosidase galactohydrolase; EC 3.2.1.22), is an industrially important enzyme that hydrolyzes the galactose residues in galactooligosaccharides and polysaccharides. The industrial production of α-galactosidase is currently insufficient owing to the high production cost, low production efficiency and low enzyme activity. Recent years have witnessed an increase in the worldwide research on molecular techniques to improve the production efficiency of microbial α-galactosidases. Cloning and overexpression of the gene sequences coding for α-galactosidases can not only increase the enzyme yield but can confer industrially beneficial characteristics to the enzyme protein. This review focuses on the molecular advances in the overexpression of α-galactosidases in bacterial and yeast/fungal expression systems. Recombinant α-galactosidases have improved biochemical and hydrolytic properties compared to their native counterparts. Metabolic engineering of microorganisms to produce high yields of α-galactosidase can also assist in the production of value-added products. Developing new variants of α-galactosidases through directed evolution can yield enzymes with increased catalytic activity and altered regioselectivity. The bottlenecks in the recombinant production of α-galactosidases are also discussed. The knowledge about the hurdles in the overexpression of recombinant proteins illuminates the emerging possibilities of developing a successful microbial cell factory and widens the opportunities for the production of industrially beneficial α-galactosidases.