A GH51 α-L-arabinofuranosidase from Talaromyces leycettanus strain JCM12802 that selectively drives synergistic lignocellulose hydrolysis

Unlocking the distinctive enzymatic functions of the early plant biomass deconstructive genes in a brown rot fungus by cell-free protein expression

Saprotrophic fungi that cause brown rot of woody biomass evolved a distinctive mechanism that relies on reactive oxygen species (ROS) to kick-start lignocellulosic polymers' deconstruction. These ROS agents are generated at incipient decay stages through a series of redox relays that shuttle electrons from fungus's central metabolism to extracellular Fenton chemistry. A list of genes has been suggested encoding the enzyme catalysts of the redox processes involved in ROS's function. However, navigating the functions of the encoded enzymes has been challenging due to the lack of a rapid method for protein synthesis. Here, we employed cell-free expression system to synthesize four redox or degradative enzymes, which were identified, by transcriptomic data, as conserved players of the ROS oxidation phase across brown rot fungal species. All four enzymes were successfully expressed and showed activities that enable confident assignment of function, namely, benzoquinone reductase (BQR), ferric reductase, α-L-arabinofuranosidase (ABF), and heme-thiolate peroxidase (HTP). Detailed analysis of their catalytic features within the context of brown rot environments allowed us to interpret their roles during ROS-driven wood decomposition. Specifically, we validated the functions of BQR as the driver redox enzyme of Fenton cycles and reconstructed its interactions with the co-occurring HTP or laccase and ABF. Taken together, this research demonstrated that the cell-free expression platform is adequate for synthesizing functional fungal enzymes and provided an alternative route for the rapid characterization of fungal proteins, escalating our understanding of the distinctive biocatalyst system for plant biomass conversion.IMPORTANCEBrown rot fungi are efficient wood decomposers in nature, and their unique degradative systems harbor untapped catalysts pursued by the biorefinery and bioremediation industries. While the use of "omics" platforms has recently uncovered the key "oxidative-hydrolytic" mechanisms that allow these fungi to attack lignocellulose, individual protein characterization is lagging behind due to the lack of a robust method for rapid synthesis of crucial fungal enzymes. This work delves into the studies of biochemical functions of brown rot enzymes using a rapid, cell-free expression platform, which allowed the successful depictions of enzymes' catalytic features, their interactions with Fenton chemistry, and their roles played during the incipient stage of brown rot when fungus sets off the reactive oxygen species for oxidative degradation. We expect this research could illuminate cell-free protein expression system's use to fulfill the increasing need for functional studies of fungal enzymes, advancing the discoveries of novel biomass-converting catalysts.

Characterization of a novel thermostable α-l-arabinofuranosidase for improved synergistic effect with xylanase on lignocellulosic biomass hydrolysis without prior pretreatment

Utilizing thermostable enzymes in biomass conversion processes presents a promising approach to bypass pretreatment, garnering significant attention from the biorefinery industry. A novel discovered α-l-arabinofuranosidase, Abf4980, exhibits exceptional thermostability by maintaining full activity after 24 h of incubation at 70 °C. It effectively acts on polyarabinosides, cleaving α-1,2- and α-1,3-linked arabinofuranose side chains from water-soluble wheat arabinoxylan while releasing xylose. When synergistically combined with the thermostable bifunctional xylanase/β-glucanase CbXyn10C from Caldicellulosiruptor bescii at an enzyme-activity ratio of 6:1, Abf4980 achieves the highest degradation efficiency for wheat arabinoxylan. Furthermore, Abf4980 and CbXyn10C demonstrated remarkable efficacy in hydrolyzing unmodified wheat bran and corn cob to generate arabinose and xylooligosaccharides. This discovery holds promising opportunities for improving the efficiency of lignocellulosic biomass conversion into fermentable sugars.

The ileal and total tract digestibility fibre and nutrients in pigs fed high-fibre cereal-based diets provided without and with a carbohydrase complex

The effect of carbohydrase can be variable according to the complexity of cereal grains and co-products. Studies on the effect of carbohydrase on cereal diets varying in complexity are scarce. This study was conducted to investigate the apparent ileal (AID) and total tract digestibility (ATTD) of energy, fibre and nutrients in pigs fed diets based on cereal grains and co-products without and with supplementation with a carbohydrase complex in the form of xylanase, arabinofuranosidase and β-glucanase. The experiment was carried out as an 8 × 4 Youden Square design (eight diets and four periods by two blocks) using 16 growing pigs (33.3 ± 0.8 kg) surgically fitted with a T-cannula in the terminal ileum. The pigs were fed eight experimental diets based on either - maize, wheat, rye, or a wheat and rye mix that were provided with or without enzyme supplementation. The AID and ATTD of DM, organic matter, energy, CP, fat, starch, and soluble and insoluble non-starch polysaccharides (NSPs) were studied using titanium dioxide as an indigestible marker. There was a cereal type effect (P < 0.05) of the AID of most of the nutrients investigated but ash and NSP and some of its constituents but with no interactions between cereal types and carbohydrase supplementation (P > 0.05). The ATTD of nutrients in the large intestine was mainly influenced by the fibre composition and was significantly lower (P < 0.001) for NSP, protein and energy for the Maize than the other diets. Supplementation of the cereal diets with the carbohydrase complex partially degrades arabinoxylan (AX) and β-glucan giving rise to a generally higher AID of high-molecular weight arabinoxylan (P = 0.044), starch (P = 0.042), a tendency (P < 0.10) of higher AID of non-cellulosic polysaccharide glucose residue (β-glucan) and soluble arabinoxylan (AX) whereas none of the other components were affected (P > 0.05). Collectively, the results indicate that the carbohydrase complex degrades AX in the stomach and small intestine, leading to a higher AID but with no influence on the ATTD of fibres, nutrients, and energy.

Expression and characterization of α-L-arabinofuranosidase derived from Aspergillus awamori and its enzymatic degradation of corn byproducts with xylanase

In this study, α-L-arabinofuranosidase (AF) from Aspergillus awamori was heterologously expressed in Pichia pastoris X33, with a 1-fold increase in AF activity after codon and vector optimization. AF remained stable at 60-65 °C and displayed a broad pH stability range of 2.5-8.0. It also demonstrated considerable resistance to pepsin and trypsin. Furthermore, compared with xylanase alone, AF with xylanase exhibited a marked synergistic effect in the degradation of expanded corn bran, corn bran, and corn distillers' dried grains with solubles, reducing sugars by 3.6-fold, 1.4-fold, and 6.5-fold, respectively, with the degree of synergy increasing to 4.61, 2.44, and 5.4, respectively, while in vitro dry matter digestibility values were 17.6%, 5.2%, and 8.8%, respectively. After enzymatic saccharification, corn byproducts were converted to prebiotic xylo-oligosaccharides and arabinoses, thereby demonstrating the favorable properties of AF in the degradation of corn biomass and its byproducts.

Structure and function characterization of the α-L-arabinofuranosidase from the white-rot fungus Trametes hirsuta

α-L-Arabinofuranosidases (Abfs) play a crucial role in the degradation of hemicelluloses, especially arabinoxylans (AX). Most of the available characterized Abfs are from bacteria, while fungi, as natural decomposers, contain Abfs with little attention given. An arabinofuranosidase (ThAbf1), belonging to the glycoside hydrolase 51 (GH51) family, from the genome of the white-rot fungus Trametes hirsuta, was recombinantly expressed, characterized, and functionally determined. The general biochemical properties showed that the optimal conditions for ThAbf1 were pH 6.0 and 50°C. In substrate kinetics assays, ThAbf1 preferred small fragment arabinoxylo-oligosaccharides (AXOS) and could surprisingly hydrolyze di-substituted 2³,3³-di-L-arabinofuranosyl-xylotriose (A^2,3XX). It also synergized with commercial xylanase (XYL) and increased the saccharification efficiency of arabinoxylan. The crystal structure of ThAbf1 indicated the presence of an adjacent cavity next to the catalytic pocket which led to the ability of ThAbf1 to degrade di-substituted AXOS. The narrow binding pocket prevents ThAbf1 from binding larger substrates. These findings have strengthened our understanding of the catalytic mechanism of GH51 family Abfs and provided a theoretical foundation for the development of more efficient and versatile Abfs to accelerate the degradation and biotransformation of hemicellulose in biomass. KEY POINTS: • ThAbf1 from Trametes hirsuta degraded di-substituted arabinoxylo-oligosaccharide. • ThAbf1 performed detailed biochemical characterization and kinetics. • ThAbf1 structure has been obtained to illustrate the substrate specificity.

Debranching enzymes decomposed corn arabinoxylan into xylooligosaccharides and achieved prebiotic regulation of gut microbiota in broiler chickens

BACKGROUND

Corn arabinoxylan (AX) is a complicated and multibranched antinutritional factor, thereby proving the use of endo-xylanase (EX) to be marginally valid. This study focused on specific types of AX-degrading enzymes (ADEs) to exert the synergy of debranching enzymes and track the prebiotic potential of enzymatic hydrolysates. This study investigated the effects of ADEs on the growth performance, intestinal histomorphology, absorption functions, changes in polysaccharide components, fermentation, and gut microbiota of broiler chickens. Five hundred seventy-six five-day-old Arbor Acres male broiler chickens were randomly allocated into eight treatments with six replicates each. Corn basal diets supplemented with or without enzymes were fed for a 21-day period, specifically including EX, its compatible use with arabinofuranosidase (EXA) or ferulic acid esterase (EXF), and compound groups with the above three enzymes (XAF).

RESULTS

Specific ADEs stimulated the jejunal villus height and goblet cell number and evidently decreased the crypt depth (P < 0.05), while the ratio of ileal villus height to crypt depth was significantly increased in EXF (P < 0.05). Maltase activities of ileal mucosa in XAF groups were extremely enhanced (P < 0.01), and EX boosted the activity of Na⁺-K⁺ ATPase in the small intestine (P < 0.01). The insoluble AX concentrations comparatively lessened, thereby notably raising the sundry xylooligosaccharide (XOS) yield in the ileal chyme (P < 0.05), which was dominant in xylobiose and xylotriose. Improvements in the abundance and diversity of ileal microbial communities within the EXA, EXF, and XAF treatments were observed (P < 0.05). Positive correlations between microbiota and XOS were revealed, with xylobiose and xylotriose being critical for ten beneficial bacteria (P < 0.05). EXF increased the BWG and FCR of broiler chickens in this phase (P < 0.05), which was attributed to the thriving networks modified by Lactobacillus. The intracecal contents of acetic acid, butyric acid, and propionic acid were greatly enhanced in most ADE groups, such as EXF (P < 0.05).

CONCLUSIONS

Debranching enzymes appreciably targeted corn AX to release prebiotic XOS in the posterior ileum and facilitated intracaecal fermentation. It was beneficial for improving gut development, digestion and absorption and modulating the microflora to promote the early performance of broiler chickens.

Effectiveness of ruminal xylanase with an extra proline-rich C-terminus on lignocellulosic biomass degradation

The efficient degradation of plant polysaccharides in agricultural waste requires xylanases with high catalytic activity. In this study, the C-terminal proline-rich GH10 xylanase XynA from sheep rumen was investigated using product analysis, structural characterization, truncated and site-directed mutagenesis, molecular dynamics simulation, and application evaluation, revealing that the proline-rich C-terminus contributes to the interaction at the substrate-binding pocket to reduce the binding free energy. Compared to the C-terminally truncated enzyme XynA-Tr, XynA has a more favorable conformation for proton transfer and affinity attack, facilitating the degradation of oligomeric and beechwood xylan without altering the hydrolysis pattern. Moreover, both the reduced sugar yield and weight loss of the pretreated wheat bran, corn cob, and corn stalk hydrolyzed by XynA for 12 h increased by more than 30 %. These findings are important to better understand the relationship between enzyme activities and their terminal regions and suggest candidate materials for lignocellulosic biomass utilization.

Structural and functional analyses of GH51 alpha-L-arabinofuranosidase of Geobacillus vulcani GS90 reveal crucial residues for catalytic activity and thermostability

Alpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid-base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C-C bond between C171 and C213 by becoming closer to each other.

GH10 and GH11 endoxylanases in Penicillium subrubescens: comparative characterization and synergy with GH51, GH54, GH62 α-L-arabinofuranosidases from the same fungus

Penicillium subrubescens has an expanded set of genes encoding putative endoxylanases (PsXLNs) compared to most other Penicillia and other fungi. In this study, all GH10 and GH11 PsXLNs were produced heterologously in Pichia pastoris and characterized. They were active towards beech wood xylan (BWX) and wheat flour arabinoxylan (WAX), and showed stability over a wide pH range. Additionally, PsXLNs released distinct oligosaccharides from WAX, and showed significant cooperative action with P. subrubescens α-L-arabinofuranosidases (PsABFs) from GH51 or GH54 for WAX degradation, giving insight into a more diverse XLN and ABF system for the efficient degradation of complex hemicelluloses. Homology modelling analysis pointed out differences in the catalytic center of PsXLNs, which are discussed in view of the different modes of action observed. These findings facilitate understanding of structural requirements for substrate recognition to contribute to recombinant XLN engineering for biotechnological applications.

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.

Bioprospecting of xylanase producing fungal strains: Multilocus phylogenetic analysis and enzyme activity profiling

The study aims to explore potential xylanase-producing indigenous fungi isolated from soil and vegetable wastes containing plant degraded matter, reporting multilocus phylogenetic analysis and xylanase enzyme activity from selective strains. Four potential xylanolytic fungi were identified through distinct primary and secondary screening of 294 isolates obtained from the samples. Morphological characterization and multigene analysis (ITS rDNA, 18S rDNA, LSU rDNA, β-tubulin, and actin gene) confirmed them as Aspergillus sp. AUMS56, Aspergillus tubingensis AUMS60 and AUMS64, and Aspergillus fumigatus AUKEMS24; achieving crude xylanase activities (through submerged fermentation using corn cobs) of 18.9, 32.29, 30.68, and 15.82 U ml^-1 , respectively. AUMS60 and AUMS64 (forming lineage with A. tubingensis and Aspergillus niger in the same phylogroup with 100% Bayesian posterior probability support) secreted single xylanase (Xyn60; 36 kDa) and multiple xylanases (Xyn64A and Xyn64B; 33.4 and 19.8 kDa) respectively, having pH optima of 6.0 and exhibiting maximal activity at 60°C. These enzymes were highly stable at 40°C (120 h) and retained more than 70% activity at 50°C and at pH 5-6 (upon 72 h incubation). Our analysis suggested these enzymes to be endoxylanases demonstrating substrate hydrolysis within 15 min of reaction and maximum efficiency of xylanases from AUMS60 and AUMS64 achieving 51.1% (13 h) and 52.2% (24 h) saccharification, respectively. They also showed enhanced catalytic activity with various cations. Based on our investigation on xylan hydrolysis, we believe that these xylanases may find significant industrial applications as they have a real potential of working as a bio-catalytic cocktail (patent file number: IN E1/38213/2020-DEL) for the enhanced saccharification of lignocelluloses.

Complete Genome Sequence of Pedobacter sp. PAMC26386 and Their Low Temperature Application in Arabinose-containing Polysaccharides Degradation

Pedobacter are a representative genus of soil-associated bacteria. Here we have provided the complete genome sequence of Pedobacter sp. PAMC26386 isolated from Antarctic soil, and functionally annotated the genome, describing the unique features of carbohydrate active enzymes (CAZymes) and α-L-arabinofuranosidase (α-L-ABF). The genome of Pedobacter sp. PAMC26386 is circular and comprises 4,796,773 bp, with a 38.2% GC content. The genome encodes 4,175 genes, including 7 rRNA and 44 tRNA genes. We identified 172 genes (8 auxiliary activities, 8 carbohydrate binding modules, 23 carbohydrate esterases, 86 glycoside hydrolases, 42 glycosyl transferases, and 5 polysaccharide lyases) related to CAZymes using the dbCAN2 tool. We checked enzyme activity on 11 substrates using the AZCL assay and obtained strong activity for arabinooligosaccharide and hemicellulose. This includes information regarding α-L-ABF, which is active at low temperatures, based on the annotation results. Our findings on Pedobacter sp. PAMC26386 provide the basis for research in the future. The favorable properties of Pedobacter sp. PAMC26386 make it a good candidate for industrial applications involving low temperatures.

Characterization and functional analysis of two novel thermotolerant α-L-arabinofuranosidases belonging to glycoside hydrolase family 51 from Thielavia terrestris and family 62 from Eupenicillium parvum

Abstract

Arabinofuranose substitutions on xylan are known to interfere with enzymatic hydrolysis of this primary hemicellulose. In this work, two novel α-l-arabinofuranosidases (ABFs), TtABF51A from Thielavia terrestris and EpABF62C from Eupenicillium parvum, were characterized and functionally analyzed. From sequences analyses, TtABF51A and EpABF62C belong to glycoside hydrolase (GH) families 51 and 62, respectively. Recombinant TtABF51A showed high activity on 4-nitrophenyl-α-l-arabinofuranoside (83.39 U/mg), low-viscosity wheat arabinoxylan (WAX, 39.66 U/mg), high-viscosity rye arabinoxylan (RAX, 32.24 U/mg), and sugarbeet arabinan (25.69 U/mg), while EpABF62C preferred to degrade arabinoxylan. For EpABF62C, the rate of hydrolysis of RAX (94.10 U/mg) was 2.1 times that of WAX (45.46 U/mg). The optimal pH and reaction temperature for the two enzymes was between 4.0 and 4.5 and 65 °C, respectively. Calcium played an important role in the thermal stability of EpABF62C. TtABF51A and EpABF62C showed the highest thermal stabilities at pH 4.5 or 5.0, respectively. At their optimal pHs, TtABF51A and EpABF62C retained greater than 80% of their initial activities after incubation at 55 °C for 96 h or 144 h, respectively. ¹H NMR analysis indicated that the two enzymes selectively removed arabinose linked to C-3 of mono-substituted xylose residues in WAX. Compared with the singular application of the GH10 xylanase EpXYN1 from E. parvum, co-digestions of WAX including TtABF51A and/or EpABF62C released 2.49, 3.38, and 4.81 times xylose or 3.38, 1.65, and 2.57 times of xylobiose, respectively. Meanwhile, the amount of arabinose released from WAX by TtABF51A with EpXYN1 was 2.11 times the amount with TtABF51A alone.

Key points

• Two novel α-l-arabinofuranosidases (ABFs) displayed high thermal stability.

• The thermal stability of GH62 family EpABF62C was dependent on calcium.

• Buffer pH affects the thermal stability of the two ABFs.

• Both ABFs enhance the hydrolysis of WAX by a GH10 xylanase.

Electronic supplementary material

The online version of this article (10.1007/s00253-020-10867-7) contains supplementary material, which is available to authorized users.

N-Terminal Fused Signal Peptide Prompted Extracellular Production of a Bacillus-Derived Alkaline and Thermo Stable Xylanase in E. coli Through Cell Autolysis

Xylanases are extensively used as industrial enzymes for its ability of hydrolyzing xylan to oligosaccharides. Here, XynHB, a thermo and alkaline stable xylanase derived from Bacillus pumilus HBP8, was extracellularly produced in E. coli cells through N-terminal-fused signal peptides. We found that the matured XynHB itself could be auto-secreted out of E. coli BL21(DE3) cells at a very low level, and two Sec-pathway signal peptides, PelB and OmpA, and one dual Sec-Tat-pathway signal peptide, FhuD, could effectively prompt its extracellular production up to 12-fold. Our results showed that PelB signal peptide led to the highest extracellular production of XynHB for approximately 54.1 μg/mL, and FhuD-fused XynHB possessed the highest specific activity of 1746.0 U/mg at 70 °C. Meanwhile, our studies also indicated that PelB- and FhuD-fused XynHB might disrupt E. coli cells' periplasm during their secretion process, thus causing cell lysis to facilitate their extracellular production. Moreover, further characterization revealed that the extracellular production of XynHB was not affected by the outer membrane permeability of E. coli cells. Our studies provided an advantageous strategy for the extracellular production of xylanase in E. coli, which may also be used for E. coli autolysis in the future.

Rozhkova A, N. Zorov I, Korotkova O, P. Sinitsyn A, Schwaneberg U, D. Davari M. Engineering Robust Cellulases for Tailored Lignocellulosic Degradation Cocktails

Lignocellulosic biomass is a most promising feedstock in the production of second-generation biofuels. Efficient degradation of lignocellulosic biomass requires a synergistic action of several cellulases and hemicellulases. Cellulases depolymerize cellulose, the main polymer of the lignocellulosic biomass, to its building blocks. The production of cellulase cocktails has been widely explored, however, there are still some main challenges that enzymes need to overcome in order to develop a sustainable production of bioethanol. The main challenges include low activity, product inhibition, and the need to perform fine-tuning of a cellulase cocktail for each type of biomass. Protein engineering and directed evolution are powerful technologies to improve enzyme properties such as increased activity, decreased product inhibition, increased thermal stability, improved performance in non-conventional media, and pH stability, which will lead to a production of more efficient cocktails. In this review, we focus on recent advances in cellulase cocktail production, its current challenges, protein engineering as an efficient strategy to engineer cellulases, and our view on future prospects in the generation of tailored cellulases for biofuel production.