Engineering a carbohydrate-binding module to increase the expression level of glucoamylase in Pichia pastoris

Enhancing activity and stability of a GH8 chitosanase through conserved N-terminal and peripheral residue mutations for bioactive chitooligosaccharide production

Chitosan, the second most abundant biopolymer after cellulose, has vast application potential. However, its high viscosity and poor solubility have limited its full utilization. Chitosan degradation primarily depends on GH46 family chitosanases, while the more stable GH8 family chitosanases have received less attention. This study, for the first time, reveals the critical role of the conserved N-terminal region in the catalytic activity and substrate binding of the GH8 family chitosanase BcCn8A using truncation mutagenesis and molecular dynamics simulations. Through evolutionary analysis and computationally assisted semi-rational design, the optimized mutant BcCn8A-ΔN4-V319L was obtained, showing a 310 % increase in specific activity and a 5 °C increase in optimal temperature. The engineered enzyme efficiently hydrolyzes chitosan into chitooligosaccharides (COSs) with antioxidant and anti-browning properties, making it suitable for applications like juice preservation. This work provides new insights into the regulatory roles of the N-terminal region and distal amino acid residues in GH8 family chitosanases, advancing their potential in functional oligosaccharide production.

Structural Stabilization and Activity Enhancement of Glucoamylase via the Machine-Learning Technique and Immobilization

Glucoamylases (GLL) hydrolyze starch to glucose syrup without yielding intermediate oligosaccharides, but their lack of stability under industrial conditions poses a major limiting factor. Using consensus- and ancestral-based machine-learning tools, a functional GLL with six mutations (GLLI73l/T130V/N212V/D238G/N327M/S332P) was constructed that exhibited superior hydrolytic activity relative to the wild-type (WT-GLL). An oxidized multi-walled carbon nanotube (oMW-CNT) was used as a solid support to immobilize the WT-GLL with an immobilization capacity of 211.28 mg/g. The specific activity of mutant GLL-6M and GLL@oMW-CNTII was improved by 2.5-fold and 3.9-fold respectively, with both retaining 64.5% residual activity after incubation at 50 °C for 2 h compared to the WT-GLL with 42.6% activity. GLL and GLL-6M were however completely inactivated at 55 °C in 30 min while oMW-CNTII retained ∼43.1% activity. Our results demonstrate that employing a machine-learning approach for enzyme redesign and immobilization is a practicable alternative for improving enzyme performance and stability for industrial applications.

Carbohydrate-binding modules enhance H2O2 tolerance by promoting lytic polysaccharide monooxygenase active site H2O2 consumption

Lytic polysaccharide monooxygenases (LPMOs) oxidatively depolymerize recalcitrant polysaccharides, which is important for biomass conversion. The catalytic domains of many LPMOs are linked to carbohydrate-binding modules (CBMs) through flexible linkers, but the function of these CBMs in LPMO catalysis is not well understood. In this study, we utilized MtLPMO9L and MtLPMO9G derived from Myceliophthora thermophila to investigate the impact of CBMs on LPMO activity, with particular emphasis on their influence on H2O2 tolerance. Using truncated forms of MtLPMO9G generated by removing the CBM, we found reduced substrate binding affinity and enzymatic activity. Conversely, when the CBM was fused to the C terminus of the single-domain MtLPMO9L to create MtLPMO9L-CBM, we observed a substantial improvement in substrate binding affinity, enzymatic activity, and notably, H2O2 tolerance. Furthermore, molecular dynamics simulations confirmed that the CBM fusion enhances the proximity of the active site to the substrate, thereby promoting multilocal cleavage and impacting the exposure of the copper active site to H2O2. Importantly, the fusion of CBM resulted in more efficient consumption of H2O2 by LPMO, leading to improved enzymatic activity and reduced auto-oxidative damage of the copper active center.

Flow-cytometric cell sorting coupled with UV mutagenesis for improving pectin lyase expression

Introduction: Alkaline pectin lyase is an important enzyme with a wide range of applications in industrial production, It has been widely used in many important fields such as fruit juice processing and extraction, the dyeing and processing of cotton and linen textiles, degumming plant fibers, environmental industrial wastewater treatment, and pulp and paper production. PGLA-rep4 was previously generated as a modified alkaline pectin lyase with high specific activity at pH 11.0°C and 70°C. However, the pre-constructed high-activity pectin lyase expression strains are still difficult to apply in industrial production due to their limited enzymatic activity. We hope to solve these problems by combining modern breeding techniques with high-throughput equipment to rapidly screen alkaline pectin lyase with higher enzymatic activity and lower cost. Methods: We fused the genes encoding PGLA-rep4 and fluorescent protein egfp using a flexible linker peptide and ligated them into a temperature-sensitive plasmid, pKD46. The constructed screening plasmid pKD46-PGLA-rep4-egfp was then transformed into an expression host and screened via flow-cytometric cell sorting coupled with UV mutagenesis. Results: Following mutagenesis, primary screening, and secondary screening, the high-expression strain, named Escherichia coli BL21/1G3, was obtained. The screening plasmid pKD46-PGLA-rep4-egfp was eliminated, and the original expression plasmid pET28a-PGLA-rep4 was then retransformed into the mutant strains. After induction and fermentation, pectin lyase activity in E. coli BL21/1G3 was significantly increased (1.37-fold relative to that in the parental E. coli BL21/PGLA-rep4 strain, p < 0.001), and the highest activity was 230, 240 U/mL at 144 h. Genome sequencing revealed that genes encoding ribonuclease E (RNase E) and diadenosine tetraphosphatase (ApaH) of E. coli BL21/1G3 were mutated compared to the sequence in the original E. coli BL21 (DE3) strain, which could be associated with increased enzyme expression. Discussion: Our work provides an effective method for the construction of strains expressing pectin lyase at high levels.

Novel Design of an α-Amylase with an N-Terminal CBM20 in Aspergillus niger Improves Binding and Processing of a Broad Range of Starches

In the starch processing industry including the food and pharmaceutical industries, α-amylase is an important enzyme that hydrolyses the α-1,4 glycosidic bonds in starch, producing shorter maltooligosaccharides. In plants, starch molecules are organised in granules that are very compact and rigid. The level of starch granule rigidity affects resistance towards enzymatic hydrolysis, resulting in inefficient starch degradation by industrially available α-amylases. In an approach to enhance starch hydrolysis, the domain architecture of a Glycoside Hydrolase (GH) family 13 α-amylase from Aspergillus niger was engineered. In all fungal GH13 α-amylases that carry a carbohydrate binding domain (CBM), these modules are of the CBM20 family and are located at the C-terminus of the α-amylase domain. To explore the role of the domain order, a new GH13 gene encoding an N-terminal CBM20 domain was designed and found to be fully functional. The starch binding capacity and enzymatic activity of N-terminal CBM20 α-amylase was found to be superior to that of native GH13 without CBM20. Based on the kinetic parameters, the engineered N-terminal CBM20 variant displayed surpassing activity rates compared to the C-terminal CBM20 version for the degradation on a wide range of starches, including the more resistant raw potato starch for which it exhibits a two-fold higher Vmax underscoring the potential of domain engineering for these carbohydrate active enzymes.