Classification, mode of action and production strategy of xylanase and its application for biofuel production from water hyacinth

Selection of DNA aptamers for the aptamer-assisted magnetic capture of the purified xylanase from Aspergillus niger

Xylanases are a group of enzymes that catalyze the hydrolysis of xylan. Xylanases have wide industrial applications, and they can produced by various organisms. In this study, we aimed to develop aptamers for the capture of xylanase produced by a wild-type Aspergillus niger strain. Xylanase was produced by Aspergillus niger in a 5-liter stirred-tank bioreactor and then purified by column chromatography. Magnetic bead-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was performed to select DNA aptamers specific to the purified xylanase. After nine rounds of selection, next-generation sequencing (NGS) analysis was performed. Four aptamers, namely AXYL-1, AXYL-2, AXYL-3, and AXYL-4, were identified for further characterization. The binding properties of the selected aptamers were characterized by fluorescence quenching (FQ) analysis and an enzyme-linked aptamer assay (ELAA). The Kd values were found to be in the low μM range. Then, each aptamer was immobilized on streptavidin-coated magnetic particles, and the recovery ratio of xylanase was determined. Although AXYL-1 wasn't effective, AXYL-2, AXYL-3, and AXYL-4 were proven to capture the xylanase. The maximum recovery rate of xylanase was found to be approximately 54 %.

An insight into microbial sources, classification, and industrial applications of xylanases: A rapid review

Endo 1,4-β-d-xylanases (EC3.2.1.8) are one of the key lignocellulose hydrolyzing enzymes. Xylan, which is present in copious amounts on earth, forms the primary substrate of endo-xylanases, which can unchain the constituent monosaccharides linked via β-1,4-glycosidic bonds from the xylan backbone. Researchers have shown keen interest in the xylanases belonging to glycoside hydrolase families 10 and 11, whereas those placed in other glycoside hydrolase families are yet to be investigated. Various microbes such as bacteria and fungi harbor these enzymes for the metabolism of their lignocellulose fibers. These microbes can be used as miniature biofactories of xylanase enzymes for a plethora of environmentally benign applications in pulp and paper industry, biofuel production, and for improving the quality of food in bread baking and fruit juice industry. This review highlights the potential of microbes in production of xylanase for industrial biotechnology.

Structural and biochemical analysis reveals how ferulic acid improves catalytic efficiency of Humicola grisea xylanase

Humicolagrisea var. thermoidea is an aerobic and thermophilic fungus that secretes the GH11 xylanase HXYN2 in the presence of sugarcane bagasse. In this study, HXYN2 was expressed in Pichiapastoris and characterized biochemically and structurally in the presence of beechwood xylan substrate and ferulic acid (FA). HXYN2 is a thermally stable protein, as indicated by circular dichroism, with greater activity in the range of 40–50 °C and pH 5.0–9.0, with optimal temperature and pH of 50 °C and 6.0, respectively. FA resulted in a 75% increase in enzyme activity and a 2.5-fold increase in catalytic velocity, catalytic efficiency, and catalytic rate constant (k_cat), with no alteration in enzyme affinity for the substrate. Fluorescence quenching indicated that FA forms a complex with HXYN2 interacting with solvent-exposed tryptophan residues. The binding constants ranged from moderate (pH 7.0 and 9.0) to strong (pH 4.0) affinity. Isothermal titration calorimetry, structural models and molecular docking suggested that hydrogen bonds and hydrophobic interactions occur in the aglycone region inducing conformational changes in the active site driven by initial and final enthalpy- and entropy processes, respectively. These results indicate a potential for biotechnological application for HXYN2, such as in the bioconversion of plant residues rich in ferulic acid.

Glycosyl hydrolase 11 (xynA) gene with xylanase activity from thermophilic bacteria isolated from thermal springs

Background

Hemicellulose is one of the copious polymer in lignocellulosic biomass (LCB). It is primarily composed of xylan linked by β-1,4 glycosidic bonds. Xylanase preferentially cleaves the β-1,4-glycosidic bonds in the xylan backbone resulting in complete hydrolysis of the biomass. Thermostable variants of glycoside hydrolases act as robust catalysts, not only in degradation but also during processing, to obtain specific carbohydrate-containing chemicals and materials (Ramasamy et al. in Madras Agric J 107(special):1. 10.29321/MAJ.2020.000382, 2020).

Results

The xylanase production by two thermophilic bacteria isolated from thermal springs was evaluated. In addition, the gene encoding this industrially vital enzyme was isolated and characterized, and its protein structure was analyzed. The thermophilic bacteria producing xylanases were isolated from augmented sawdust and banana fiber biomass from hot springs of Himachal Pradesh and identified as Bacillus subtilis VSDB5 and Bacillus licheniformis KBFB4 using 16S rRNA gene sequencing. The persistent xylanase activity revealed that the enzyme is secreted extracellularly with the maximum activity of 0.76 IU mL−1 and 1.0 IU mL−1 at 6 h and 12 h of growth by KBFB4 and VSDB5, respectively, under submerged fermentation. Both the strains exhibited the maximum activity at pH 6 and a temperature of 50 °C. The xylanases of KBFB4 and VSDB5 were thermostable and retained 40% of their activity at 60 °C after incubation for 30 min. Xylanase of VSDB5 had wide thermotolerance and retained 20% of its activity from 60 to 80 °C, whereas xylanase of KBFB4 showed wide alkali tolerance and retained 80% of its activity until pH 10. The xylanase (xynA)-encoding gene (650 bp) cloned from both the strains using specific primers showed 98 to 99% homology to β-1,4-endoxylanase gene. Further in silico analysis predicted that the xylanase protein, with a molecular weight of 23 kDa, had a high pI (9.44–9.65), which explained the alkaline nature of the enzyme and greater aliphatic index (56.29). This finding suggested that the protein is thermostable. Multiple sequence alignment and homology modeling of the protein sequence revealed that the gene product belonged to the GH11 family, indicating its possible application in bioconversion.

Conclusion

The strains B. subtilis VSDB5 and B. licheniformis KBFB4 obtained from hot springs of Himachal Pradesh produced potent and alkali-tolerant thermostable xylanases, which belong to the GH11 family. The enzyme can be supplemented in industrial applications for biomass conversion at high temperatures and pH (or in processes involving alkali treatment).

Graphical Abstract

Enzymatic Bioprospecting of Fungi Isolated from a Tropical Rainforest in Mexico

The humid tropical environment provides an ideal place for developing a high diversity of plants; this is why it is an interesting site for the enzymatic bioprospecting of fungi that are responsible for the recycling of organic matter in an efficient and accelerated way and whose enzymes could have multiple biotechnological applications. For this study, 1250 isolates of macroscopic and microscopic fungal morphotypes were collected from soil, leaf litter, and wood. One hundred and fifty strains (50 from each source) were selected for the enzymatic screening. From the first phase, 51 strains with positive activity for laccase, protease, amylase, xylanase, and lipase enzymes were evaluated, of which 20 were isolated from leaf litter, 18 from the soil, and 13 from wood. The 10 best strains were selected for the enzymatic quantification, considering the potency index and the production of at least two enzymes. High laccase activity was detected for Trametes villosa FE35 and Marasmius sp. CE25 (1179 and 710.66 U/mg, respectively), while Daedalea flavida PE47 showed laccase (521.85 U/mg) and protease activities (80.66 U/mg). Fusarium spp. PH79 and FS400 strains had amylase (14.0 U/mg, 49.23 U/mg) and xylanase activities (40.05 U/mg, 36.03 U/mg) respectively. These results confirm the enzymatic potential of fungi that inhabit little-explored tropical rainforests with applications in industry.

Identification and characterization of a thermostable GH11 xylanase from Paenibacillus campinasensis NTU-11 and the distinct roles of its carbohydrate-binding domain and linker sequence

An extracellular thermostable xylanase (XynNTU) from Paenibacillus campinasensis NTU-11, consisted of a glycoside hydrolase (GH) family 11 catalytic domain, a Gly/Pro-rich linker sequence (LS) and a family 6 carbohydrate-binding module (CBM6), was identified and expressed in E. coli BL21. The purified XynNTU had a specific activity of 2750 U/mg and an optimal activity at 60 °C and pH 7.0, and retained a residual activity of 58.4% after incubation (60 °C, 48 h). Two truncated mutants, CBM6-truncated form XynNTU-CDLS, CBM6 and linker-truncated form XynNTU-CD, possessed similar values of optimum pH and temperature as the native XynNTU. XynNTU-CD displayed a lower thermostability than XynNTU, whereas for XynNTU-CDLS, more than 90% of residual activity was remained (60 °C, 48 h), indicating that this enzyme presented a higher thermostability than that of the majority of reported GH11 xylanases. Furthermore, XynNTU and two mutants maintained more than 70% of residual activity at pH values of 5-9. Kinetic measurements suggested that CBM6 had a crucial function in the ability of the enzyme to bind and hydrolyze xylan substrates, while LS had a relatively mild influence. Collectively, a noticeable thermostability and a high specific activity of XynNTU and its truncated form XynNTU-CDLS highlights their potentials for diverse industrial applications.

Improved Production of Xylanase in Pichia pastoris and Its Application in Xylose Production From Xylan

Xylanases with high specific activity has been focused with great interest as a useful enzyme in biomass utilization. The production of recombinant GH11 xylanase (MYCTH_56237) from Myceliophthora thermophila has been improved through N-terminal signal peptide engineering in P. pastoris. The production of newly recombinant xylanase (termed Mtxyn11C) was improved from 442.53 to 490.7 U/mL, through a replacement of α-factor signal peptide with the native xylanase signal peptide segment (MVSVKAVLLLGAAGTTLA) in P. pastoris. Scaling up of Mtxyn11C production in a 7.5 L fermentor was improved to the maximal production rate of 2503 U/mL. In this study, the degradation efficiency of Mtxyn11C was further examined. Analysis of the hydrolytic mode of action towards the birchwood xylan (BWX) revealed that Mtxyn11C was clearly more effective than commercial xylanase and degrades xylan into xylooligosaccharides (xylobiose, xylotriose, xylotetraose). More importantly, Mtxyn11C in combination with a single multifunctional xylanolytic enzyme, improved the hydrolysis of BWX into single xylose by 40%. Altogether, this study provided strategies for improved production of xylanase together with rapid conversion of xylose from BWX, which provides sustainable, cost-effective and environmental friendly approaches to produce xylose/XOSs for biomass energy or biofuels production.

Paecilomyces variotii xylanase production, purification and characterization with antioxidant xylo-oligosaccharides production

Paecilomyces variotii xylanase was, produced in stirred tank bioreactor with yield of 760 U/mL and purified using 70% ammonium sulfate precipitation and ultra-filtration causing 3.29-fold purification with 34.47% activity recovery. The enzyme purity was analyzed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) confirming its monomeric nature as single band at 32 KDa. Zymography showed xylan hydrolysis activity at the same band. The purified enzyme had optimum activity at 60 °C and pH 5.0. The pH stability range was 5-9 and the temperature stability was up 70 °C. Fe²⁺and Fe³⁺ exhibited inhibition of xylanase enzyme while Cu²⁺, Ca²⁺, Mg²⁺ and Mn²⁺ stimulated its activity. Mercaptoethanol stimulated its activity; however, Na₂-EDTA and SDS inhibited its activity. The purified xylanase could hydrolyze beechwood xylan but not carboxymethyl cellulose (CMC), avicel or soluble starch. Paecilomyces variotii xylanase K_m and V_max for beechwood were determined to be 3.33 mg/mL and 5555 U/mg, respectively. The produced xylanase enzyme applied on beech xylan resulted in different types of XOS. The antioxidant activity of xylo-oligosaccharides increased from 15.22 to 70.57% when the extract concentration was increased from 0.1 to 1.5 mg/mL. The enzyme characteristics and kinetic parameters indicated its high efficiency in the hydrolysis of xylan and its potential effectiveness in lignocellulosic hydrolysis and other industrial application. It also suggests the potential of xylanase enzyme for production of XOS from biomass which are useful in food and pharmaceutical industries.

Water hyacinth for energy and environmental applications: A review

This review is focused on the sustainable management of harvested water hyacinth (WH) via thermochemical conversion to carbonaceous materials (CMs), biofuels, and chemicals for energy and environmental applications. One of the major challenges in thermochemical conversion is to guarantee the phytoremediation performance of biochar and the energy conversion efficiency in biowaste-to-energy processes. Thus, a circular sustainable approach is proposed to improve the biochar and energy production. The co-conversion process can enhance the syngas, heat, and energy productions with high-quality products. The produced biochar should be economically feasible and comparable to available commercial carbon products. The removal and control of heavy and transition metals are essential for the safe implementation and management of WH biochar. CMs derived from biochar are of interest in wastewater treatment, air purification, and construction. It is important to control the size, shape, and chemical compositions of the CM particles for higher-value products like catalyst, adsorbent or conductor.

Structural insights into xylanase mutant 254RL1 for improved activity and lower pH optimum

Xylanases degrade xylan to valuable end products. In our previous study, the alkaline xylanase S7-xyl from Bacillus halodurans S7 was engineered by rational design and the best mutant xylanase 254RL1 exhibited 3.4-fold improvements in specific activity at pH 9.0. Further research found that the enzyme activity at pH 6.0 was almost 2-fold than that at pH 9.0. To elucidate the reason of enhanced performance of 254RL1 at decreased pH optimum, we determined the X-ray crystal structure of 254RL1 at 2.21 Å resolution. The structural analysis revealed that the mutations enlarged the opening of the access tunnel and shortened the tunnel. Moreover, the mutations changed the hydrogen bond network around the catalytic residue and decreased the pK_a value of acid-base catalyst E159 which reduced the pH optimum of the xylanase. The result provided the basis for the acid-alkaline engineering of the glycoside hydrolases.

Enzyme Storage and Recycling: Nanoassemblies of α-Amylase and Xylanase Immobilized on Biomimetic Magnetic Nanoparticles

Immobilization of enzymes has been extensively required in a wide variety of industrial applications as a way to ensure functionality and the potential of enzyme recycling after use. In particular, enzyme immobilization on magnetic nanoparticles (MNPs) could offer reusability by means of magnetic recovery and concentration, along with increased stability and robust activity of the enzyme under different physicochemical conditions. In the present work, microbial α-amylase (AmyKS) and xylanase (XAn11) were both immobilized on different types of MNPs [MamC-mediated biomimetic MNPs (BMNPs) and inorganic MNPs] by using two different strategies (electrostatic interaction and covalent bond). AmyKS immobilization was successful using electrostatic interaction with BMNPs. Instead, the best strategy to immobilize XAn11 was using MNPs through the hetero-crosslinker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS). The immobilization protocols were optimized by varying glutaraldehyde (GA) concentration, enzyme quantity, and reaction time. Under optimal conditions, 92% of AmyKS and 87% of XAn11 were immobilized on BMNPs and MNPs-E/N, respectively (here referred as AmyKS-BMNPs and XAn11-MNPs nanoassemblies). The results show that the immobilization of the enzymes did not extensively alter their functionality and increased enzyme stability compared to that of the free enzyme upon storage at 4 and 20 °C. Interestingly, the immobilized amylase and xylanase were reused for 15 and 8 cycles, respectively, without significant loss of activity upon magnetic recovery of the nanoassemblies. The results suggest the great potential of these nanoassemblies in bioindustry applications.

PoxCbh, a novel CENPB-type HTH domain protein, regulates cellulase and xylanase gene expression in Penicillium oxalicum

The essential transcription factor PoxCxrA is required for cellulase and xylanase gene expression in the filamentous fungus Penicillium oxalicum that is potentially applied in biotechnological industry as a result of the existence of the integrated cellulolytic and xylolytic system. However, the regulatory mechanism of cellulase and xylanase gene expression specifically associated with PoxCxrA regulation in fungi is poorly understood. In this study, the novel regulator PoxCbh (POX06865), containing a centromere protein B-type helix-turn-helix domain, was identified through screening for the PoxCxrA regulon under Avicel induction and genetic analysis. The mutant ∆PoxCbh showed significant reduction in cellulase and xylanase production, ranging from 28.4% to 59.8%. Furthermore, PoxCbh was found to directly regulate the expression of important cellulase and xylanase genes, as well as the known regulatory genes PoxNsdD and POX02484, and its expression was directly controlled by PoxCxrA. The PoxCbh-binding DNA sequence in the promoter region of the cellobiohydrolase 1 gene cbh1 was identified. These results expand our understanding of the diverse roles of centromere protein B-like protein, the regulatory network of cellulase and xylanase gene expression, and regulatory mechanisms in fungi.

Biochemical characterization and molecular docking of cloned xylanase gene from Bacillus subtilis RTS expressed in E. coli

This study employed mesophilic Bacillus subtilis RTS strain isolated from soil with high xylanolytic activity. A 642 bp (xyn) xylanase gene (GenBank accession number MT677937) was extracted from Bacillus subtilis RTS and cloned in Escherichia coli BL21 cells using pET21c expression system. The cloned gene belongs to glycoside hydrolase family 11 with protein size of approximately 23 KDa. The recombinant xylanase showed optimal enzyme activity at 60 °C and at pH 6.5. Thermostability of recombinant xylanase was observed between the temperature range of 30-60 °C. Xylanase also remained stable in different concentration of various organic solvents (ethanol, butanol). This might be due to the formation of protein/organic solvent interface which prevents stripping of essential water molecules from enzyme, thus enzyme conformation and activity remained stable. Finally, the molecular docking analysis through AutoDock Vina showed the involvement of Tyr 108, Arg140 and Pro144 in protein-ligand interaction, which stabilizes this complex. The observed stability of recombinant xylanase at higher temperature and in the presence of organic solvent (ethanol, butanol) suggested possible application of this enzyme in biofuel and other industrial applications.

Improving β-glucosidase and xylanase production in a combination of waste substrate from domestic wastewater treatment system and agriculture residues

Cellulase and hemicellulase activities are considered to the major bottlenecks in the lignocellulosic biorefinery process, especially in an enzyme cocktail lacking β-glucosidase (BGL) and xylanase (XYL). In view of this issue, higher levels of BGL and XYL activities were obtained in the presence of wastewater and activated sludge as an induction medium mixed with 5% of rice straw by Hypocrea sp. W₆₃. The analysis of the ionic content showed that a relatively low sludge dose could enhance the production of BGL and XYL. Most importantly, compared to a medium using freshwater, the proportion of 1:10 sludge to wastewater, which contained nutrient elements, led to 3.4-fold BGL and 3.7-fold XYL production improvements. This research describes the reuse of substrates that are largely and continuously generated from domestic wastewater treatment systems and agriculture residues, which consequently leads to the development of a simultaneous enzyme production process for sustainable biorefinery practices.

Directed evolution of Aspergillus oryzae lipase for the efficient resolution of (R,S)-ethyl-2-(4-hydroxyphenoxy) propanoate

Aspergillus oryzae lipase (AOL) is a potential biocatalyst for industrial application. In this study, a mutant lipase AOL-3^F38N/V230R was screened through two rounds of directed evolution, resulting in a fourfold increase in lipase activity, and threefold in catalytic efficiency (k_cat/K_m), while maintaining its excellent stereoselectivity. AOL-3^F38N/V230R enzyme activity was maximum at pH 7.5 and also at 40 °C. And compared with wild-type AOL-3, AOL-3^F38N/V230R preferentially hydrolyzed the fatty acid ethyl ester carbon chain length from C4 to C6-C10. In the same catalytic reaction conditions, the conversion of (R,S)-ethyl-2-(4-hydroxyphenoxy) propanoate ((R,S)-EHPP) by AOL-3^F38N/V230R can be increased 169.7% compared to the original enzyme. The e.e._s of (R,S)-EHPP achieved 99.4% and conversion about 50.2% with E value being 829.0. Therefore, AOL-3^F38N/V230R was a potential biocatalyst for obtaining key chiral compounds for aryloxyphenoxy propionate (APP) herbicides.

Construction and characterization of a chimeric enzyme of swollenin and xylanase to improve soybean straw hydrolysis

A study was carried out to produce a fusion protein (Swo-Xyn) using the Trichoderma reesei swollenin and Lentinula edodes xylanase and to investigate its characteristics and application in degrading soybean straw. In parallel, L. edodes xylanase (Xyn) alone was used as a control protein in application tests. The Swo-Xyn was recombined, expressed and produced by Pichia pastoris and had the maximum activity at 40 °C and pH 3.0 using xylan as substrate. The Swo-Xyn exhibited preferential hydrolysis of Xylan. The Swo-Xyn had slight low Km value (23.90 vs. 25.36 mg/ml) but significantly low Vmax value (162.4 vs. 227.2 μmol/mg·min) and specific activity (18.82 vs. 38.97 U/mg) relative to the Xyn. The Swo-Xyn activity was enhanced by Zn2+ in dose dependent manners with the peak activity at 30 mM of Zn2+. The Swo-Xyn could tolerate 15% of methanol, ethanol, aceton, and DMSO with >60% residual activity. The Swo-Xyn had the greater tolerance to SDS, EDTA, 2-ME than the Xyn and could be activated by DTT, Triton X-100, and Tween 20. Compared with the Xyn, the hydrolysis and sequent cellulose enzymolysis of soybean straw could be better improved by the Swo-Xyn. The Swo-Xyn should be more useful for improving the utilization of soybean straw.

Current state-of-the-art in ethanol production from lignocellulosic feedstocks

The renewable lignocellulosic biomass is a sustainable feedstock for the production of bioethanol, which shows the potential to replace fossil fuels. Due to the recalcitrant structure of plant cell wall made of cellulose, hemicellulose, and lignin, the biomass conversion process requires the use of efficient pretreatment process before enzymatic hydrolysis and fermentation to degrade the crystallinity of cellulose fibres and to remove lignin from biomass. Proper pretreatment techniques, economical production of cellulolytic enzymes, and effective fermentation of glucose and xylose in the presence of inhibitors are key challenges for the viable production of bioethanol. Although new strains capable of fermenting xylose are being designed, they are often not resistant to toxic compounds in hydrolysates. This paper provides an in-depth review of lignocellulosic bioethanol production via biochemical route, focusing on the most widely used pretreatment technologies and key operational conditions of enzymatic hydrolysis and fermentation considering sugar/ethanol yields. In addition, this review examines the relevant detoxification strategies for the removal of toxic substances and the importance of immobilization. The review also indicates potential usage of engineered microorganisms to improve glucose and xylose fermentation, cellulolytic enzymes production, and response to stress conditions.

Inhibition kinetics of acetosyringone on xylanase in hydrolysis of hemicellulose

Many phenolic compounds, derived from lignin during the pretreatment of lignocellulosic biomass, could obviously inhibit the activity of cellulolytic and hemicellulolytic enzymes. Acetosyringone (AS) is one of the phenolic compounds produced from lignin degradation. In this study, we investigated the inhibitory effects of AS on xylanase activity through kinetic experiments. The results showed that AS could obviously inhibit the activity of xylanase in a reversible and noncompetitive binding manner (up to 50% activity loss). Inhibitory kinetics and constants of xylanase on AS were conducted by the HCH-1 model (β = 0.0090 ± 0.0009 mM^-1). Furthermore, intrinsic and 8-anilino-1-naphthalenesulfonic (ANS)-binding fluorescence results showed that the tertiary structure of AS-mediated xylanase was altered. These findings provide new insights into the role of AS in xylanase activity. Our results also suggest that AS was an inhibitor of xylanase and targeting AS was a potential strategy to increase xylose production.

Heterologous expression and functional characterization of a GH10 endoxylanase from Aspergillus fumigatus var. niveus with potential biotechnological application

Xylanases decrease the xylan content in pretreated biomass releasing it from hemicellulose, thus improving the accessibility of cellulose for cellulases. In this work, an endo-β-1,4-xylanase from Aspergillus fumigatus var. niveus (AFUMN-GH10) was successfully expressed. The structural analysis and biochemical characterization showed this AFUMN-GH10 does not contain a carbohydrate-binding module. The enzyme retained its activity in a pH range from 4.5 to 7.0, with an optimal temperature at 60 °C. AFUMN-GH10 showed the highest activity in beechwood xylan. The mode of action of AFUMN-GH10 was investigated by hydrolysis of APTS-labeled xylohexaose, which resulted in xylotriose and xylobiose as the main products. AFUMN-GH10 released 27% of residual xylan from hydrothermally-pretreated corn stover and 14% of residual xylan from hydrothermally-pretreated sugarcane bagasse. The results showed that environmentally friendly pretreatment followed by enzymatic hydrolysis with AFUMN-GH10 in low concentration is a suitable method to remove part of residual and recalcitrant hemicellulose from biomass.

Purification and characterization of an endo-xylanase from Trichoderma sp., with xylobiose as the main product from xylan hydrolysis

Fungal endo-β-1,4-xylanases (endo-xylanases) can hydrolyze xylan into xylooligosaccharides (XOS), and have potential biotechnological applications for the exploitation of natural renewable polysaccharides. In the current study, we aimed to screen and characterize an efficient fungal endo-xylanase from 100 natural humus-rich soil samples collected in Guizhou Province, China, using extracted sugarcane bagasse xylan (SBX) as the sole carbon source. Initially, 182 fungal isolates producing xylanases were selected, among which Trichoderma sp. strain TP3-36 was identified as showing the highest xylanase activity of 295 U/mL with xylobiose (X2) as the main product when beechwood xylan was used as substrate. Subsequently, a glycoside hydrolase family 11 endo-xylanase, TXyn11A, was purified from strain TP3-36, and its optimal pH and temperature for activity against beechwood xylan were identified to be 5.0 and 55 °C, respectively. TXyn11A was stable across a broad pH range (3.0-10.0), and exhibited strict substrate specificity, including xylan from beechwood, wheat, rye, and sugarcane bagasse, with K_m and V_max values of 5 mg/mL and 1250 μmol/mg min, respectively, toward beechwood xylan. Intriguingly, the main product obtained from hydrolysis of beechwood xylan by TXyn11A was xylobiose, whereas SBX hydrolysis resulted in both X2 and xylotriose. Overall, these characteristics of the endo-xylanase TXyn11A indicate several potential industrial applications.

High-Level Heterologous Expression of Endo-1,4-β-Xylanase from Penicillium citrinum in Pichia pastoris X-33 Directed through Codon Optimization and Optimized Expression

Most common industrial xylanases are produced from filamentous fungi. In this study, the codon-optimized xynA gene encoding xylanase A from the fungus Penicilium citrinum was successfully synthesized and expressed in the yeast Pichia pastoris. The levels of secreted enzyme activity under the control of glyceraldehyde-3-phosphate dehydrogenase (P_GAP) and alcohol oxidase 1 (P_AOX1) promoters were compared. The Pc Xyn11A was produced as a soluble protein and the total xylanase activity under the control of P_GAP and P_AOX1 was 34- and 193-fold, respectively, higher than that produced by the native strain of P. citrinum. The Pc Xyn11A produced under the control of the P_AOX1 reached a maximum activity of 676 U/mL when induced with 1% (v/v) methanol every 24 h for 5 days. The xylanase was purified by ion exchange chromatography and then characterized. The enzyme was optimally active at 55 °C and pH 5.0 but stable over a broad pH range (3.0–9.0), retaining more than 80% of the original activity after 24 h or after pre-incubation at 40 °C for 1 h. With birchwood xylan as a substrate, Pc Xyn11A showed a K_m(app) of 2.8 mg/mL, and a k_cat of 243 s⁻¹. The high level of secretion of Pc Xyn11A and its stability over a wide range of pH and moderate temperatures could make it useful for a variety of biotechnological applications.

Characterization of recombinant endo-1,4-β-xylanase of Bacillus halodurans C-125 and rational identification of hot spot amino acid residues responsible for enhancing thermostability by an in-silico approach

Increased demand of enzymes for industrial use has led the scientists towards protein engineering techniques. In different protein engineering strategies, rational approach has emerged as the most efficient method utilizing bioinformatics tools to produce enzymes with desired reaction kinetics; physiochemical (temperature, pH, half life, etc) and biological (selectivity, specificity, etc.) characteristics. Xylanase is one of the widely used enzymes in paper and food industry to degrade xylan component present in plant pulp. In this study endo 1,4-β-xylanase (Xyl-11A) from Bacillus halodurans C-125 was cloned in pET-22b (+) vector and expressed in Escherichia coli BL21 (DE3) expression strain. The enzyme had Michaelis constant K_m of 1.32 mg ml^-1 birchwoodxylan (soluble form) and maximum reaction velocity (V_max) 73.53 mmol min^-1 mg^-1 with an optimum temperature of 75 °C and pH 9.0. The thermostability analysis showed that enzyme retained more than 80% of its residual activity when incubated at 75 °C for 2 h. In addition, to increase Xyl-11A thermostability, an in-silico analysis was performedto identify the hot spot amino acid residues. Consensus-based amino acid substitution was applied to evaluate multiple sequence alignment of homologs and identified 20 amino acids positions by following Jensen-Shnnon Divergence method. 3D models of 20 selected mutants were analyzed for conformational transition in protein structures by using NMSim server. Two selected mutants T6K and I17M of Xyl-11A retained 40, 60% residual activity respectively, at 85 °C for 120 min as compared to wild type enzyme which retained 37% initial activity under same conditions, confirming the enhanced thermostability of mutants. The present study showed a good approach for the identification of promising amino acid residues responsible for enhancing the thermostability of enzymes of industrial importance.

GH-10 and GH-11 Endo-1,4-β-xylanase enzymes from Kitasatospora sp. produce xylose and xylooligosaccharides from sugarcane bagasse with no xylose inhibition

A novel strategy for the low-cost, high-yield co-production of xylose and xylooligosaccharides together with no xylose inhibition was developed using a novel heterologous expression of XYN10Ks_480 endo-1,4-β-xylanase with a ricin-type β-trefoil type of domain and XYN11Ks_480 endo-1,4-β-xylanase with a CBM 2 superfamily from the Kitasatospora sp in an actinomycetes expression system. Xylose is the main building block for hemicellulose xylan. Our findings demonstrated high levels of expression and catalytic activity for XYN10Ks_480 during hydrolysis of the extracted xylan of bagasse, and three types of xylan-based substrates were used to produce xylose and xylooligosaccharides. However, hydrolysis by XYN11Ks_480 produced xylooligosaccharides without xylose formation. This study demonstrated how integrating sodium hypochlorite-extracted xylan and enzymatic hydrolysis could provide an alternative strategy for the generation of XOS from lignocellulosic material.

Identification of markers at various stages of batch fermentation and improved production of xylanase using Aspergillus niger (KP874102.1)

Improved xylanase production was carried out through optimization of environmental stresses during spore preservation, seed cultivation and batch fermentation and identifies the markers at various stages. The maximum spore size (radius 6.5 µm) of Aspergillus niger was noticed after 28 days of spore preservation. During seed cultivation, the hypha formed alongside of germination tube (length 196.8 µm) was noticed only at pH-7 after 18 h of incubation at 28 °C. Therefore, pH-7 and 28 °C were considered as optimum during seed cultivation. In this stage, the final pH of the medium was found to be 6.2 which can be used as marker for completion of seed culture. The production media was optimized through Taguchi methodology. The maximum xylanase production was found to be 1575.93 U. The optimum concentration for media components was found to be xylan from beechwood of 3 g/l, potassium nitrate of 10 g/l, magnesium sulphate of 5 g/l, di-potassium hydrogen phosphate of 50 mM, calcium carbonate of 2 g/l, 1000× of trace element (1 ml) and sodium chloride of 5 g/l. It is evident that improved production of xylanase can be possible through optimization of environmental stresses during spore preservation, seed cultivation and batch fermentation and can be intensified through identification of markers at various stages of fermentation process.

Characterization of Two Endo-β-1, 4-Xylanases from Myceliophthora thermophila and Their Saccharification Efficiencies, Synergistic with Commercial Cellulase

The xylanases with high specific activity and resistance to harsh conditions are of high practical value for biomass utilization. In the present study, two new GH11 xylanase genes, MYCTH_56237 and MYCTH_49824, have been cloned from thermophilic fungus Myceliophthora thermophila and expressed in Pichia pastoris. The specific activities of purified xylanases reach approximately 1,533.7 and 1,412.5 U/mg, respectively. Based on multiple template-based homology modeling, the structures of their catalytic domains are predicted. Enzyme activity was more effective in 7.5 L fermentor, yielding 2,010.4 and 2,004.2 U/mL, respectively. Both enzymes exhibit optimal activity at 60°C with pH of 6.0 and 7.0, respectively. Their activities are not affected by EDTA and an array of metal ions. The kinetic constants have been determined for MYCTH_56237 (K_m = 8.80 mg/mL, V_max = 2,380 U/mg) and MYCTH_49824 (K_m = 5.67 mg/mL, V_max = 1,750 U/mg). More importantly, both xylanases significantly cooperate with the commercial cellulase Celluclast 1.5 L in terms of the saccharification efficiency. All these biochemical properties of the xylanases offer practical potential for future applications.

Enhanced production of xylanase by Fusarium sp. BVKT R2 and evaluation of its biomass saccharification efficiency

Growth of Fusarium sp. BVKT R2, a potential isolate of forest soils of Eastern Ghats on birchwood xylan in mineral salts medium (MSM) under un-optimized conditions of 30 °C, pH of 5.0, 150 rpm and inoculum size of 5 agar plugs for 7 days, yielded titer of 1290 U/mL of xylanase (EC 3.2.1.8). The effect of various operating parameters such as different substrates and their concentration, additional carbon and nitrogen sources, incubation temperature, initial pH, agitation and inoculum size on the production of xylanase by Fusarium sp. BVKT R2 was studied in shake flask culture by one factor at a time approach. The same culture exhibited higher production of xylanase (4200 U/mL) when grown on birch wood xylan in MSM under optimized conditions with an additional carbon source-sorbitol (1.5%) nitrogen source-yeast extract (1.5%) temperature of 30 °C, pH of 5.0, agitation of 200 rpm and inoculum of 6 agar plugs for only 5 days. There was enhancement in xylanase production under optimized conditions by 3.2 folds over yields under un-optimized conditions. Growth of BVKT R2 culture on locally available lignocelluloses-sawdust, rice straw and cotton stalk-in MSM for 5 days released soluble sugars to the maximum extent of 52.76% with respect to sawdust indicating its greater importance in saccharification essential for biotechnological applications.

Deletion of TpKu70 facilitates gene targeting in Talaromyces pinophilus and identification of TpAmyR involvement in amylase production

Talaromyces pinophilus is a promising filamentous fungus for industrial production of biomass-degrading enzymes used in biorefining, and its genome was recently sequenced and reported. However, functional analysis of genes in T. pinophilus is rather limited owing to lack of genetic tools. In this study, a putative TpKu70 encoding the Ku70 homolog involved in the classic non-homologous end-joining pathway was deleted in T. pinophilus 1-95. ΔTpKu70 displayed no apparent defect in vegetative growth and enzyme production, and presented similar sensitivity to benomyl, bleomycin, and UV, when compared with the wild-type T. pinophilus strain 1-95. Seven genes that encode putative transcription factors, including TpAmyR, were successfully knocked out in ΔTpKu70 at 61.5-100% of homologous recombination frequency, which is significantly higher than that noted in the wild-type. Interestingly, ΔTpAmyR produced approximately 20% of amylase secreted by the parent strain ΔTpKu70 in medium containing soluble starch from corn as the sole carbon source. Real-time quantitative reverse transcription PCR showed that TpAmyR positively regulated the expression of genes encoding α-amylase and glucoamylase. Thus, this study provides a useful tool for genetic analysis of T. pinophilus, and identification of a key role for the transcription factor TpAmyR in amylase production in T. pinophilus.

Raw sugarcane bagasse as carbon source for xylanase production by Paenibacillus species: a potential degrader of agricultural wastes

Paenibacillus species isolated from a variety of natural sources have shown to be important glycoside hydrolases producers. These enzymes play a key role in bio-refining applications, as they are central biocatalysts for the processing of different types of polymers from vegetal biomass. Xylanase production by three native isolates belonging to the genus Paenibacillus was approached by utilizing mineral-based medium and agricultural by-products as a convenient source to produce biocatalysts suitable for their degradation. While varieties of alkali pretreated sugarcane bagasse were useful substrates for the strains from Paenibacillus genus evaluated, raw sugarcane bagasse was the most effective substrate for endoxylanase production by Paenibacillus sp. AR247. This strain was then selected to further improvement of its enzyme production by means of a two-step statistical approach. It was determined that the carbon source, provided as an inexpensive agro-waste, as well as phosphate and magnesium were the culture media components that most influenced the enzyme production, which was improved three times compared to the screening results.

Heterologous Expression and Characterization of an Acidic GH11 Family Xylanase from Hypocrea orientalis

A gene encoding glycoside hydrolase family 11 xylanase (HoXyn11B) from Hypocrea orientalis EU7-22 was expressed in Pichia pastoris with a high activity (413 IU/ml). HoXyn11B was partly N-glycosylated and appeared two protein bands (19-29 kDa) on SDS-PAGE. The recombinant enzyme exhibited optimal activity at pH 4.5 and 55 °C, and retained more than 90% of the original activity after incubation at 50 °C for 60 min. The determined apparent K _m and V _max values using beechwood xylan were 10.43 mg/ml and 3246.75 IU/mg, respectively. The modes of action of recombinant HoXyn11B on xylo-oligosaccharides (XOSs) and beechwood xylan were investigated by thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), which indicated that the modes of action of HoXyn11B are different from HoXyn11A since it is able to release a significant amount of xylose from various substrates. This study provides an opportunity to better understand the hydrolysis mechanisms of xylan by xylanases from Trichoderma.

The efficiency of Eichhornia crassipes in the removal of organic and inorganic pollutants from wastewater: a review

Water is a basic necessity of life, but due to overextraction and heavy input of nutrients from domestic and industrial sources, the contamination level of water bodies increase. In the last few decades, a potential interest has been aroused to treat wastewater by biological methodologies before discharge into the natural water bodies. Phytoremediation using water hyacinth is found to be an effective biological wastewater treatment method. Water hyacinth (Eichhornia crassipes), a notorious weed, being the most promising plant for removal of contaminants from wastewater is studied extensively in this regard. It has been successfully used to accumulate heavy metals, dyes, radionuclides, and other organic and inorganic contaminants from water at laboratory, pilot, and large scale. The plant materials are also being used as sorbent to separate the contaminant from water. Other than phytoremediation, the plant has been explored for various other purposes like ethanol production and generation of biogases and green manures. Such applications of this have been good support for the technocrats in controlling the growth of the plant. The present paper reviews the phytoremedial application of water hyacinth and its capability to remove contaminants in produced water and wastewater from domestic and isndustrial sources either used as a whole live plant grown in water or use of plant body parts as sorbent has been discussed.

Unravelling the capability of Pyrenophora phaeocomes S-1 for the production of ligno-hemicellulolytic enzyme cocktail and simultaneous bio-delignification of rice straw for enhanced enzymatic saccharification

A natural variant of Pyrenophora phaeocomes isolated from natural biodiversity was able to grow on various agricultural residues by co-producing laccase, xylanase and mannanase. Solid state fermentation of rice straw induced the highest productivities corresponding to 10,859.51±46.74, 22.01±1.00 and 10.45±0.128IUgds^-1 for laccase, xylanase and mannanase respectively after 4days. Besides producing the ligno-hemicellulolytic enzyme cocktail, 40days cultivation of P. phaeocomes S-1 on rice straw brought about the 63 and 51% degradation of lignin and hemicellulose. These components were further removed with mild alkali extraction revealing the overall losses amounting to 78 and 60% respectively for lignin, and hemicellulose. The biologically pretreated straw upon enzymatic hydrolysis revealed 50% saccharification efficiency releasing 470mgg^-1 sugars. Application of this knowledge will lead to efficient management of waste rice straw with low cost production of industrially important enzymes cocktail and its biological delignification for effective enzymatic hydrolysis to free sugars.