Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities

Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library

Xylanases are key biocatalysts in the degradation of the β-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.

pCold-assisted expression of a thermostable xylanase from Bacillus amyloliquefaciens: cloning, expression and characterization

The biotechnological application of bacterial xylanases requires a high thermostability, a catalytically active state for a broad pH range. The Bacillus amyloliquefaciens (MTCC 1270) xynA gene was amplified and cloned into the pCold vector and was expressed in Escherichia coli to evaluate the expressed proteins' thermostability. The pCold, compared to other similar vectors, has unique properties-including pH and temperature tolerance due to the presence of the cspA promoter. The recombinant xynA-pCold (rxynApC) showed the expression of xynA gene with a molecular weight of ~ 27 kDa, confirmed on SDS-PAGE. The rxynApC exhibits optimal activity at 70 °C and pH 8.0. The residual activity of the recombinant enzyme was 90% at pH 8.0. The thermal decomposition temperature (T d) value for the rxynApC enzyme was 93.33 °C obtained from the thermogravimetric analysis, indicating the potent stability of the cloned enzyme. The specific activity of native xylanase and rxynApC under optimal conditions was 32.35 and 105.5 U/mg, respectively. The structural model of the xynA gene was predicted using the in silico tool along with the active site (containing four important Tyr-166, Gly-7, Try-69 and Arg-112 amino acids). The predicted biophysical parameters of the in silico model were similar to the experimental results. The unique feature of the cspA promoter is that it gave a high expression of rxynApC enzyme having alkali and thermostable properties with high yield in surrogate host E. coli. Thus, the recombinant xynA gene can potentially be applied to different industrial needs by looking at its thermostability and enhanced enzyme activity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03315-y.

Biochemical and Thermodynamic Studies on a Novel Thermotolerant GH10 Xylanase from Bacillus safensis

Xylanases have a broad range of applications in agro-industrial processes. In this study, we report on the discovery and characterization of a new thermotolerant GH10 xylanase from Bacillus safensis, designated as BsXyn10. The xylanase gene (bsxyn10) was cloned from Bacillus safensis and expressed in Escherichia coli. The reduced molecular mass of BsXyn10 was 48 kDa upon SDS-PAGE. Bsxyn10 was optimally active at pH 7.0 and 60 °C, stable over a broad range of pH (5.0–8.0), and also revealed tolerance toward different modulators (metal cations, EDTA). The enzyme was active toward various xylans with no activity on the glucose-based polysaccharides. K_M, v_max, and k_cat for oat spelt xylan hydrolysis were found to be 1.96 g·L⁻¹, 58.6 μmole·min⁻¹·(mg protein)⁻¹, and 49 s⁻¹, respectively. Thermodynamic parameters for oat spelt xylan hydrolysis at 60 °C were ΔS* = −61.9 J·mol⁻¹·K⁻¹, ΔH* = 37.0 kJ·mol⁻¹ and ΔG* = 57.6 kJ·mol⁻¹. BsXyn10 retained high levels of activity at temperatures up to 60 °C. The thermodynamic parameters (ΔH*_D, ΔG*_D, ΔS*_D) for the thermal deactivation of BsXyn10 at a temperature range of 40–80 °C were: 192.5 ≤ ΔH*_D ≤ 192.8 kJ·mol⁻¹, 262.1 ≤ ΔS*_D ≤ 265.8 J·mol⁻¹·K⁻¹, and 99.9 ≤ ΔG*_D ≤ 109.6 kJ·mol⁻¹. The BsXyn10-treated oat spelt xylan manifested the catalytic release of xylooligosaccharides of 2–6 DP, suggesting that BsXyn10 represents a promising candidate biocatalyst appropriate for several 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.

Improving the Extraction of Active Ingredients from Medicinal Plants by XynA Modification

Active ingredients of medicinal plants have unique pharmacological and clinical effects. However, conventional extraction technology has many disadvantages, such as long-time and low-efficiency. XynA-assisted extraction may overcome such problems, since the plant cell wall is mainly composed of cellulose. Based on the three-dimensional protein structure, we found the C-terminal domain and N-terminal domain twisted together and resulted in more flexibility. We carried out a series of truncations, with XynA_ΔN36 getting more yields of active ingredients. As shown by HPLC analysis, the efficiencies for extraction of salvianic acid A and berberine from Salvia miltiorrhiza and Phellodendron chinense were increased by approximately 38.14% and 35.20%, respectively, compared with the conventional extraction protocol. The yields of the two compounds reached 2.84 ± 0.05 mg g−1 and 3.52 ± 0.14 mg g−1, respectively. Above all, XynA_ΔN36 can be applied to the extraction of salvianic acid A and berberine, and this study provides a novel enzyme for the extraction technology, which aids rational utilization and quality control of medicinal plants.