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

Heteroxylan hydrolysis by a recombinant cellulase-free GH10 xylanase from the alkaliphilic bacterium Halalkalibacterium halodurans C-125

The search for affordable enzymes with exceptional characteristics is fundamental to overcoming industrial and environmental constraints. In this study, a recombinant GH10 xylanase (Xyn10-HB) from the extremely alkaliphilic bacterium Halalkalibacterium halodurans C-125 cultivated at pH 10 was cloned and expressed in E. coli BL21(DE3). Removal of the signal peptide improved the expression, and an overall activity of 8 U/mL was obtained in the cell-free supernatant. The molecular weight of purified Xyn10-HB was estimated to be 42.6 kDa by SDS-PAGE. The enzyme was active across a wide pH range (5-10) with optimal activity recorded at pH 8.5 and 60 °C. It also presented good stability with a half-life of 3 h under these conditions. Substrate specificity studies showed that Xyn10-HB is a cellulase-free enzyme that conventionally hydrolyse birchwood and oat spelts xylans (Apparent Km of 0.46 mg/mL and 0.54 mg/mL, respectively). HPLC analysis showed that both xylans hydrolysis produced xylooligosaccharides (XOS) with a degree of polymerization (DP) ranging from 2 to 9. The conversion yield was 77% after 24 h with xylobiose and xylotriose as the main end-reaction products. When assayed on alkali-extracted wheat straw heteroxylan, the Xyn10-HB produced active XOS with antioxidant activity determined by the DPPH radical scavenging method (IC50 of 0.54 mg/mL after 4 h). Owing to its various characteristics, Xyn10-HB xylanase is a promising candidate for multiple biotechnological applications.

Alternative splicing analysis of lignocellulose-degrading enzyme genes and enzyme variants in Aspergillus niger

Alternative splicing (AS) greatly expands the protein diversity in eukaryotes. Although AS variants have been frequently reported existing in filamentous fungi, it remains unclear whether lignocellulose-degrading enzyme genes in industrially important fungi undergo AS events. In this work, AS events of lignocellulose-degrading enzymes genes in Aspergillus niger under two carbon sources (glucose and wheat straw) were investigated by RNA-Seq. The results showed that a total of 23 out of the 56 lignocellulose-degrading enzyme genes had AS events and intron retention was the main type of these AS events. The AS variant enzymes from the annotated endo-β-1,4-xylanase F1 gene (xynF1) and the endo-β-1,4-glucanase D gene (eglD), noted as XYNF1-AS and EGLD-AS, were characterized compared to their normal splicing products XYNF1 and EGLD, respectively. The AS variant XYNF1-AS displayed xylanase activity whereas XYNF1 did not. As for EGLD-AS and EGLD, neither of them showed annotated endo-β-1,4-glucanase activity. Instead, both showed lytic polysaccharide monooxygenase (LPMO) activity with some differences in catalytic properties. Our work demonstrated that the AS variants in A. niger were good sources for discovering novel lignocellulose-degrading enzymes. KEY POINTS: • AS events were identified in the lignocellulose-degrading enzyme genes of A. niger. • New β-1,4-xylanase and LPMO derived from AS events were characterized.

A novel endo-1,4-β-xylanase from Alicyclobacillus mali FL18: Biochemical characterization and its synergistic action with β-xylosidase in hemicellulose deconstruction

A novel endo-1,4-β-xylanase-encoding gene was identified in Alicyclobacillus mali FL18 and the recombinant protein, named AmXyn, was purified and biochemically characterized. The monomeric enzyme worked optimally at pH 6.6 and 80 °C on beechwood xylan with a specific activity of 440.00 ± 0.02 U/mg and a good catalytic efficiency (kcat/KM = 91.89 s-1mLmg-1). In addition, the enzyme did not display any activity on cellulose, suggesting a possible application in paper biobleaching processes. To develop an enzymatic mixture for xylan degradation, the association between AmXyn and the previously characterized β-xylosidase AmβXyl, deriving from the same microorganism, was assessed. The two enzymes had similar temperature and pH optima and showed the highest degree of synergy when AmXyn and AmβXyl were added sequentially to beechwood xylan, making this mixture cost-competitive and suitable for industrial use. Therefore, this enzymatic cocktail was also employed for the hydrolysis of wheat bran residue. TLC and HPAEC-PAD analyses revealed a high conversion rate to xylose (91.56 %), placing AmXyn and AmβXyl among the most promising biocatalysts for the saccharification of agricultural waste.

Biochemical unravelling of the endoxylanase activity in a bifunctional GH39 enzyme cloned and expressed from thermophilic Geobacillus sp. WSUCF1

The glycoside hydrolase family 39 (GH39) proteins are renowned for their extremophilic and multifunctional enzymatic properties, yet the molecular mechanisms underpinning these unique characteristics continue to be an active subject of research. In this study, we introduce WsuXyn, a GH39 protein with a molecular weight of 58 kDa, originating from the thermophilic Geobacillus sp. WSUCF1. Previously reported for its exceptional thermostable β-xylosidase activity, WsuXyn has recently demonstrated a significant endoxylanase activity (3752 U·mg-1) against beechwood xylan, indicating towards its bifunctional nature. Physicochemical characterization revealed that WsuXyn exhibits optimal endoxylanase activity at 70 °C and pH 7.0. Thermal stability assessments revealed that the enzyme is resilient to elevated temperatures, with a half-life of 168 h. Key kinetic parameters highlight the exceptional catalytic efficiency and strong affinity of the protein for xylan substrate. Moreover, WsuXyn-mediated hydrolysis of beechwood xylan has achieved 77 % xylan conversion, with xylose as the primary product. Structural analysis, amalgamated with docking simulations, has revealed strong binding forces between xylotetraose and the protein, with key amino acid residues, including Glu278, Tyr230, Glu160, Gly202, Cys201, Glu324, and Tyr283, playing pivotal roles in these interactions. Therefore, WsuXyn holds a strong promise for biodegradation and value-added product generation through lignocellulosic biomass conversion.

Production of xylanase by Aspergillus niger GIO and Bacillus megaterium through solid-state fermentation

Xylanase breaks xylan down to xylose, which is used in industries such as pulp and paper, food and feed, among others. The utilization of wastes for xylanase production is economical, hence this work aimed at producing xylanase through solid-state fermentation and characterizing the enzyme. Xylanase-producing strains of Bacillus megaterium and Aspergillus niger GIO were inoculated separately in a 5 and 10 day solid fermentation study on maize straw, rice straw, sawdust, corn cob, sugarcane bagasse, conifer litters, alkaline-pretreated maize straw (APM) and combined alkaline and biological-pretreated maize straw, respectively. The best substrate was selected for xylanase production. The crude enzyme was extracted from the fermentation medium and xylanase activity was characterized using parameters such as temperature, cations, pH and surfactants. Among different substrates, the highest xylanase activity of 3.18 U ml^-1 was recorded when A. niger GIO was grown on APM. The xylanase produced by A. niger GIO and B. megaterium had the highest activities (3.67 U ml^-1 and 3.36 U ml^-1) at 40 °C after 30 and 45 min of incubation, respectively. Optimal xylanase activities (4.58 and 3.58 U ml^-1) of A. niger GIO and B. megaterium , respectively, were observed at pH 5.0 and 6.2. All cations used enhanced xylanase activities except magnesium ion. Sodium dodecyl sulfate supported the highest xylanase activity of 6.13 and 6.90 U ml^-1 for A. niger GIO and B. megaterium , respectively. High yields of xylanase were obtained from A. niger GIO and B. megaterium cultivated on APM. The xylanase activities were affected by pH, temperature, surfactants and cations.

Heterogeneous catalysis mediated by light, electricity and enzyme via machine learning: Paradigms, applications and prospects

Energy crisis and environmental pollution have become the bottleneck of human sustainable development. Therefore, there is an urgent need to develop new catalysts for energy production and environmental remediation. Due to the high cost caused by blind screening and limited valuable computing resources, the traditional experimental methods and theoretical calculations are difficult to meet with the requirements. In the past decades, computer science has made great progress, especially in the field of machine learning (ML). As a new research paradigm, ML greatly accelerates the theoretical calculation methods represented by first principal calculation and molecular dynamics, and establish the physical picture of heterogeneous catalytic processes for energy and environment. This review firstly summarized the general research paradigms of ML in the discovery of catalysts. Then, the latest progresses of ML in light-, electricity- and enzyme-mediated heterogeneous catalysis were reviewed from the perspective of catalytic performance, operating conditions and reaction mechanism. The general guidelines of ML for heterogeneous catalysis were proposed. Finally, the existing problems and future development trend of ML in heterogeneous catalysis mediated by light, electricity and enzyme were summarized. We highly expect that this review will facilitate the interaction between ML and heterogeneous catalysis, and illuminate the development prospect of heterogeneous catalysis.