Molecular Characterization, Regioselective and Synergistic Action of First Recombinant Type III α-L-arabinofuranosidase of Family 43 Glycoside Hydrolase (PsGH43_12) from Pseudopedobacter saltans

Microbial α-L-arabinofuranosidases: diversity, properties, and biotechnological applications

Arabinoxylans (AXs) are hemicellulosic polysaccharides consisting of a linear backbone of β-1,4-linked xylose residues branched by high content of α-L-arabinofuranosyl (Araf) residues along with other side-chain substituents, and are abundantly found in various agricultural crops especially cereals. The efficient bioconversion of AXs into monosaccharides, oligosaccharides and/or other chemicals depends on the synergism of main-chain enzymes and de-branching enzymes. Exo-α-L-arabinofuranosidases (ABFs) catalyze the hydrolysis of terminal non-reducing α-1,2-, α-1,3- or α-1,5- linked α-L-Araf residues from arabinose-substituted polysaccharides or oligosaccharides. ABFs are critically de-branching enzymes in bioconversion of agricultural biomass, and have received special attention due to their application potentials in biotechnological industries. In recent years, the researches on microbial ABFs have developed quickly in the aspects of the gene mining, properties of novel members, catalytic mechanisms, methodologies, and application technologies. In this review, we systematically summarize the latest advances in microbial ABFs, and discuss the future perspectives of the enzyme research.

Molecular dynamics-based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans

CONTEXT

The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)₈-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of - 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm²), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm²) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of - 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector.

METHODS

The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.

Discovery of a bifunctional xylanolytic enzyme with arabinoxylan arabinofuranohydrolase-d3 and endo-xylanase activities and its application in the hydrolysis of cereal arabinoxylans

Xylanolytic enzymes, with both endo-xylanase and arabinoxylan arabinofuranohydrolase (AXH) activities, are attractive for the economically feasible conversion of recalcitrant arabinoxylan. However, their characterization and utilization of these enzymes in biotechnological applications have been limited. Here, we characterize a novel bifunctional enzyme, rAbf43A, cloned from a bacterial consortium that exhibits AXH and endo-xylanase activities. Hydrolytic pattern analyses revealed that the AXH activity belongs to AXHd3 because it attacked only the C(O)-3-linked arabinofuranosyl residues of double-substituted xylopyranosyl units of arabinoxylan and arabinoxylan-derived oligosaccharides, which are usually resistant to hydrolysis. The enzyme rAbf43A also liberated a series of xylo-oligosaccharides (XOSs) from beechwood xylan, xylohexaose and xylopentaose, indicating that rAbf43A exhibited endo-xylanase activity. Homology modelling based on AlphaFold2 and site-directed mutagenesis identified three non-catalytic residues (H161, A270 and L505) located in the substrate-binding pocket essential for its dual-functionality, while the mutation of A117 located in the -1 subsite to the proline residue only affected its endo-xylanase activity. Additionally, rAbf43A showed significant synergistic action with the bifunctional xylanase/feruloyl esterase rXyn10A/Fae1A from the same bacterial consortium on insoluble wheat arabinoxylan and de-starched wheat bran degradation. When rXyn10A/Fae1A was added to the rAbf43A pre-hydrolyzed reactions, the amount of released reducing sugars, xylose and ferulic acid increased by 9.43% and 25.16%, 189.37% and 93.54%, 31.39% and 32.30%, respectively, in comparison with the sum of hydrolysis products released by each enzyme alone. The unique characteristics of rAbf43A position it as a promising candidate not only for designing high-performance enzyme cocktails but also for investigating the structure-function relationship of GH43 multifunctional enzymes.

Cloning, expression and characterization of a glycoside hydrolase family 51 α-l-arabinofuranosidase from Thermoanaerobacterium thermosaccharolyticum DSM 571

The present study focused on the characterization of a glycoside hydrolase 51 family α-l-arabinofuranosidase named TtAbf51 from thermophile Thermoanaerobacterium thermosaccharolyticum DSM 571. The recombinant TtAbf51 with 497 amino acids was successfully expressed in Escherichia coli BL21(DE3) and purified via nickel affinity chromatography, and native protein was a dimer verified by size exclusion chromatography. The TtAbf51 showed an optimum pH and temperature of 5.5 and 55 °C, and was relatively stable at pH 5.0-8.0 and up to 60 °C for 2 h of incubation. In addition, TtAbf51 was significantly inhibited by Cu²⁺, Zn²⁺ and 1 mM or 10 mM SDS. In the presence of 800 mM arabinose, the residual activity remained over 40% of the initial activity. In addition, the recombinant enzyme possessed a good catalytic effect for both synthesized and natural substrates, and the specific enzyme activity toward CM-linear arabinan reached 426.5 μmol min^-1 mg^-1. In summary, this study provides an α-l-arabinofuranosidase with potential in the synergistic hydrolysis of hemicellulose to fermentable sugars in applications such as liquid biofuels, food and beverages, and related industries.

Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass

The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.

Enzymatic upgrading of heteroxylans for added-value chemicals and polymers

Xylan is one of the most abundant, natural polysaccharides, and much recent interest focuses on upgrading heteroxylan to make use of its unique structures and chemistries. Significant progress has been made in the discovery and application of novel enzymes for debranching and modifying heteroxylans. Debranching enzymes include acetylxylan esterases, α-l-arabinofuranosidases and α-dglucuronidases that release side groups from the xylan backbone to recover both biochemicals and less substituted xylans for polymer applications in food packaging or drug delivery systems. Besides esterases and hydrolases, many oxidoreductases including carbohydrate oxidases, lytic polysaccharide monooxygenases, laccases and peroxidases have been also applied to alter different types of xylans for improved physical and chemical properties. This review will highlight the recent discovery and application of enzymes for upgrading xylans for use as added-value chemicals and in functional polymers.

Molecular modification, structural characterization, and biological activity of xylans

The differences in the source and structure of xylans make them have various biological activities. However, due to their inherent structural limitations, the various biological activities of xylans are far lower than those of commercial drugs. Currently, several types of molecular modification methods have been developed to address these limitations, and many derivatives with specific biological activity have been obtained. Further research on structural characteristics, structure-activity relationship and mechanism of action is of great significance for the development of xylan derivatives. Therefore, the major molecular modification methods of xylans are introduced in this paper, and the primary structure and conformation characteristics of xylans and their derivatives are summarized. In addition, the biological activity and structure-activity relationship of the modified xylans are also discussed.

Two-Step Saccharification of the Xylan Portion of Sugarcane Waste by Recombinant Xylanolytic Enzymes for Enhanced Xylose Production

Sugarcane bagasse (SB) and sugarcane trash (SCT) containing 30% hemicellulose content are the waste from the sugarcane industry. Hemicellulose being heterogeneous, more complex, and less abundant than cellulose remains less explored. The optimized conditions for the pretreatment of SB and SCT for maximizing the delignification are soaking in aqueous ammonia (SAA), 18.5 wt %, followed by heating at 70 °C for 14 h. The optimization of hydrolysis of SAA pretreated (ptd) SB and SCT by the Box-Behnken design in the first step of saccharification by xylanase (CtXyn11A) and α-l-arabinofuranosidase (PsGH43_12) resulted in the total reducing sugar (TRS) yield of xylooligosaccharides (TRS_(XOS)) of 93.2 mg/g ptd SB and 85.1 mg/g ptd SCT, respectively. The second step of saccharification by xylosidase (BoGH43) gave the TRS yield of 164.7 mg/g ptd SB and 147.2 mg/g ptd SCT. The high-performance liquid chromatography analysis of hydrolysate obtained after the second step of saccharification showed 69.6% xylan-to-xylose conversion for SB and 64.1% for SCT. This study demonstrated the optimization of the pretreatment method and of the enzymatic saccharification by recombinant xylanolytic enzymes, resulting in the efficient saccharification of ptd hemicellulose to TRS by giving 73.5% conversion for SB and 71.1% for SCT. These optimized conditions for the pretreatment and saccharification of sugarcane waste can also be used at a large scale.