Thermostability improvement of the glucose oxidase from Aspergillus niger for efficient gluconic acid production via computational design

Improving glucose oxidase catalysis in Aspergillus niger via Vitreoscilla hemoglobin fusion protein

Oxygen is crucial for converting glucose to gluconic acid catalyzed by glucose oxidase (Gox). However, industrial gluconic acid production faces oxygen supply limitations. To enhance Gox efficiency, Vitreoscilla hemoglobin (VHb) has been considered as an efficient oxygen transfer carrier. This study identified GoxA, a specific isoform of Gox in the industrial gluconic acid-producing strain of Aspergillus niger. Various forms of VHb expression in A. niger were tested to improve GoxA's catalytic efficiency. Surprisingly, the expression of free VHb, both intracellularly and extracellularly, did not promote gluconic acid production during shake flask fermentation. Then, five fusion proteins were constructed by linking Gox and VHb using various methods. Among these, VHb-GS1-GoxA, where VHb's C-terminus connected to GoxA's N-terminus via the flexible linker GS1, demonstrated a significantly higher Kcat/Km value (96% higher) than GoxA. Unfortunately, the expression of VHb-GS1-GoxA in A. niger was limited, resulting in a low gluconic acid production of 3.0 g/L. To overcome the low expression problem, single- and dual-strain systems were designed with tools of SpyCatcher/SpyTag and SnoopCatcher/SnoopTag. In these systems, Gox and VHb were separately expressed and then self-assembled into complex proteins. Impressively, the single-strain system outperformed the GoxA overexpression strain S1971, resulting in 23% and 9% higher gluconic acid production under 0.6 vvm and 1.2 vvm aeration conditions in the bioreactor fermentation, respectively. The successful construction of Gox and VHb fusion or complex proteins, as proposed in this study, presents promising approaches to enhance Gox catalytic efficiency and lower aerodynamic costs in gluconic acid production. KEY POINTS: • Overexpressing free VHb in A. niger did not improve the catalytic efficiency of Gox • The VHb-GS1-GoxA showed an increased Kcat/Km value by 96% than GoxA • The single-strain system worked better in the gluconic acid bioreactor fermentation.

Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation

The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.

Cost-effective, scalable production of glucose oxidase using Casuarina equisetifolia biomass and its application in the bio-Fenton oxidation process for the removal of trace organic contaminants from wastewater

This study focuses on using Casuarina equisetifolia biomass for pilot-scale glucose oxidase production from Aspergillus niger and its application in the removal of trace organic contaminants (TrOCs) from municipal wastewater through the bio-Fenton oxidation. The cost of glucose oxidase was 0.005 $/U, including the optimum production parameters, 10% biomass, 7% sucrose, 1% peptone, and 3% CaCO₃ at 96 h with an enzyme activity of 670 U/mL. Optimized conditions for H₂O₂ were 1 M glucose, 100 U/mL glucose oxidase, and 120 mins of incubation, resulting in 544.3 mg/L H₂O₂. Thus, H₂O₂ produced under these conditions lead to bio-Fenton oxidation resulting in the removal of 36-92% of nine TrOCs in municipal wastewater at pH 7.0 in 360 mins. Therefore, this work establishes the cost-effective glucose oxidase-producing H₂O₂ as an attractive bioremediating agent to enhance the removal of TrOCs in wastewater at neutral pH.

Low pH Stress Enhances Gluconic Acid Accumulation with Enzymatic Hydrolysate as Feedstock Using Gluconobacter oxydans

Gluconic acid has been increasingly in demand in recent years due to the wide applications in the food, healthcare and construction industries. Plant-derived biomass is rich in biopolymers that comprise glucose as the monomeric unit, which provide abundant feedstock for gluconic acid production. Gluconobacter oxydans can rapidly and incompletely oxidize glucose to gluconic acid and it is regarded as ideal industrial microorganism. Once glucose is depleted, the gluconic acid will be further bio-oxidized to 2-ketogluconic acid by Gluconobacter oxydans. The endpoint is difficult to be controlled, especially in an industrial fermentation process. In this study, it was found that the low pH environment (2.5~3.5) could limit the further metabolism of gluconic acid and that it resulted in a yield over 95%. Therefore, the low pH stress strategy for efficiently producing gluconic acid from biomass-derived glucose was put forward and investigated with enzymatic hydrolysate. As a result, 98.8 g/L gluconic acid with a yield of 96% could be obtained from concentrated corncob enzymatic hydrolysate that initially contained 100 g/L glucose with 1.4 g/L cells loading of Gluconobacter oxydans. In addition, the low pH stress strategy could effectively control end-point and decrease the risk of microbial contamination. Overall, this strategy provides a potential for industrial gluconic acid production from lignocellulosic materials.

Recent advances and perspectives on production of value-added organic acids through metabolic engineering

Organic acids are important consumable materials with a wide range of applications in the food, biopolymer and chemical industries. The global consumer organic acids market is estimated to increase to $36.86 billion by 2026. Conventionally, organic acids are produced from the chemical catalysis process with petrochemicals as raw materials, which posts severe environmental concerns and conflicts with our sustainable development goals. Most of the commonly used organic acids can be produced from various organisms. As a state-of-the-art technology, large-scale fermentative production of important organic acids with genetically-modified microbes has become an alternative to the chemical route to meet the market demand. Despite the fact that bio-based organic acid production from renewable cheap feedstock provides a viable solution, low productivity has impeded their industrial-scale application. With our deeper understanding of strain genetics, physiology and the availability of strain engineering tools, new technologies including synthetic biology, various metabolic engineering strategies, omics-based system biology tools, and high throughput screening methods are gradually established to bridge our knowledge gap. And they were further applied to modify the cellular reaction networks of potential microbial hosts and improve the strain performance, which facilitated the commercialization of consumable organic acids. Here we present the recent advances of metabolic engineering strategies to improve the production of important organic acids including fumaric acid, citric acid, itaconic acid, adipic acid, muconic acid, and we also discuss the current challenges and future perspectives on how we can develop a cost-efficient, green and sustainable process to produce these important chemicals from low-cost feedstocks.

Agro-Industrial Food Waste as a Low-Cost Substrate for Sustainable Production of Industrial Enzymes: A Critical Review

The grave environmental, social, and economic concerns over the unprecedented exploitation of non-renewable energy resources have drawn the attention of policy makers and research organizations towards the sustainable use of agro-industrial food and crop wastes. Enzymes are versatile biocatalysts with immense potential to transform the food industry and lignocellulosic biorefineries. Microbial enzymes offer cleaner and greener solutions to produce fine chemicals and compounds. The production of industrially important enzymes from abundantly present agro-industrial food waste offers economic solutions for the commercial production of value-added chemicals. The recent developments in biocatalytic systems are designed to either increase the catalytic capability of the commercial enzymes or create new enzymes with distinctive properties. The limitations of low catalytic efficiency and enzyme denaturation in ambient conditions can be mitigated by employing diverse and inexpensive immobilization carriers, such as agro-food based materials, biopolymers, and nanomaterials. Moreover, revolutionary protein engineering tools help in designing and constructing tailored enzymes with improved substrate specificity, catalytic activity, stability, and reaction product inhibition. This review discusses the recent developments in the production of essential industrial enzymes from agro-industrial food trash and the application of low-cost immobilization and enzyme engineering approaches for sustainable development.

Molecular Dynamics Simulation of E412 Catalytic Residue Mutation of GOx-IPBCC

The enzyme glucose oxidase from Aspergillus niger has a homodimeric structure, consisting of two identical subunits with a molecular weight of 150,000 Daltons. In this study, we used the structure of the enzyme glucose oxidase from Aspergillus niger IPBCC.08.610 (GOx-IPBCC), this enzyme had a total activity of 92.87 U (μmol/min) and a Michaelis-Menten constant (Km) of 2.9 mM (millimolar). This study was conducted to predict the molecular dynamics of E412 (Glu412) residue catalytic mutation belonging to the GOx-IPBCC enzyme was determine the effect of changes in the catalytic residue on substrate binding (β-D-glucose). The results of molecular docking of 19 mutant structures, six E412 mutant homologous structures were selected (E412C, E412K, E412Q, E412T, E412, E412V, and E412W), which were evaluated using molecular dynamics simulation for 50 ns. The results showed a decrease in ∆G values in two mutant structures is E412C and E412T, and there is one mutant structure that increased ∆G values, namely E412W, these three mutant structures showed the best stability, bond interaction, and salt bridge profile according to molecular dynamics simulation.

Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy

Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t_1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t_1/2 at 35 °C and a 5.7 °C increase in melting temperature (T_m). Unexpectedly, its specific activity and catalytic efficiency (k_cat/K_m) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.

Insights into the Structures, Inhibitors, and Improvement Strategies of Glucose Oxidase

Glucose oxidase, which uses molecular oxygen as an electron acceptor to specifically catalyze the conversion of β-d-glucose to gluconic acid and hydrogen peroxide (H₂O₂), has been considered an important enzyme in increasing environmental sustainability and food security. However, achieving the high yield, low price and high activity required for commercial viability remains challenging. In this review, we first present a brief introduction, looking at the sources, characteristics, catalytic process, and applications of glucose oxidase. Then, the predictive structures of glucose oxidase from two different sources are comparatively discussed. We summarize the inhibitors of glucose oxidase. Finally, we highlight how the production of glucose oxidase can be improved by optimizing the culture conditions and microbial metabolic engineering.

Review of glucose oxidase as a feed additive: production, engineering, applications, growth-promoting mechanisms, and outlook

The regulation and prohibition of antibiotics used as growth promoters (AGP) in the feed field are increasing because they cause antimicrobial resistance and drug residue issues and threaten community health. Recently, glucose oxidase (GOx) has attracted increasing interest in the feed industry as an alternative to antibiotics. GOx specifically catalyzes the production of gluconic acid (GA) and hydrogen peroxide (H₂O₂) by consuming molecular oxygen, and plays an important role in relieving oxidative stress, preserving health, and promoting animal growth. To expand the application of GOx in the feed field, considerable efforts have been made to mine new genetic resources. Efforts have also been made to heterologously overexpress relevant genes to reduce production costs and to engineer proteins by modifying enzyme properties, both of which are bottleneck problems that limit industrial feed applications. Herein, the: different sources, diverse biochemical properties, distinct structural features, and various strategies of GOx engineering and heterologous overexpression are summarized. The mechanism through which GOx promotes growth in animal production, including the improvement of antioxidant capacity, maintenance of intestinal microbiota homeostasis, and enhancement of gut function, are also systematically addressed. Finally, a new perspective is provided for the future development of GOx applications in the feed field.

Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production

Glucose oxidase (GOD) is an oxidoreductase enzyme that catalyzes the oxidation of glucose to gluconolactone and hydrogen peroxide. Then, gluconolactone will be hydrolyzed to gluconic acid. The wide application of gluconic acid in various industries has increased production demand. However, glucose concentrations higher than 40% (w/w) inhibited the conversion of glucose to gluconic acid due to a decrease in the oxygen solubility concentration at pH 6, 30℃, and 1 bar pressure. Therefore, decreasing the value of Km is predicted to reduce saturation and enhance gluconic acid production. This study aimed to analyze the interaction between the IPBCC.08.610 GOD mutant with β-D-Glucose in improving gluconic acid production by decreasing the Km value. Mutations were performed in silico using Chimera and then docked using AutoDock Vina. The mutations resulted in distinct ligand poses in the binding pocket, different -OH conformations of the ligands, and changes in the T554M/D578P mutant’s hydrophobicity index (554 mutated from threonine to methionine, and 578 mutated from aspartate to proline), and decreased ΔG and Km values in the H559D mutant (559 mutated from histidine to aspartate), D578P and T554M/D578P. This decrease might strengthen the ligand-receptor interaction, increasing gluconic acid production. The H559D was the best mutant to increase production based on the ΔG, Km value, and stability due to the addition of hydrogen bonds.

Production of Gluconic Acid and Its Derivatives by Microbial Fermentation: Process Improvement Based on Integrated Routes

Gluconic acid (GA) and its derivatives, as multifunctional biological chassis compounds, have been widely used in the food, medicine, textile, beverage and construction industries. For the past few decades, the favored production means of GA and its derivatives are microbial fermentation using various carbon sources containing glucose hydrolysates due to high-yield GA production and mature fermentation processes. Advancements in improving fermentation process are thriving which enable more efficient and economical industrial fermentation to produce GA and its derivatives, such as the replacement of carbon sources with agro-industrial byproducts and integrated routes involving genetically modified strains, cascade hydrolysis or micro- and nanofiltration in a membrane unit. These efforts pave the way for cheaper industrial fermentation process of GA and its derivatives, which would expand the application and widen the market of them. This review summarizes the recent advances, points out the existing challenges and provides an outlook on future development regarding the production of GA and its derivatives by microbial fermentation, aiming to promote the combination of innovative production of GA and its derivatives with industrial fermentation in practice.

Refactoring transcription factors for metabolic engineering

Due to the ability to regulate target metabolic pathways globally and dynamically, metabolic regulation systems composed of transcription factors have been widely used in metabolic engineering and synthetic biology. This review introduced the categories, action principles, prediction strategies, and related databases of transcription factors. Then, the application of global transcription machinery engineering technology and the transcription factor-based biosensors and quorum sensing systems are overviewed. In addition, strategies for optimizing the transcriptional regulatory tools' performance by refactoring transcription factors are summarized. Finally, the current limitations and prospects of constructing various regulatory tools based on transcription factors are discussed. This review will provide theoretical guidance for the rational design and construction of transcription factor-based metabolic regulation systems.

Molecular Cloning, Expression, and Enzyme Activity of Glucose Oxidase Gene from Soil Thermophilic Streptomyces

Background

Glucose oxidase is an oxidoreductase that depletes oxygen in food processing and is used in biosensors, glucose diagnostic kits, food processing, cosmetics, and chemical industries. This enzyme is often isolated from fungi, such as Penicillium and Aspergillus Niger.

Objectives

The objective of this study was to clone and express a full-length GOX gene from soil thermophilic streptomyces for bioinformatic and enzyme activity evaluations.

Materials and Methods

After collecting samples from the Gandom Beryan area of Kerman province, Iran, Streptomyces strains were identified with specific biochemical and molecular tests. Streptomyces strains with glucose oxidase gene were detected by PCR, and the amplified gene fragment was cloned into Escherichia coli host bacterium using TA cloning technique. The expression of the cloned GOX gene in the host bacterium was measured using real-time PCR, and the recombinant plasmids were sequenced. The enzymatic activity was measured in the extracts of E. coli cells carrying the plasmids.

Results

After screening the samples, 12 strains of Streptomyces were identified, 4 of which carried the GOX gene. The GOX open reading frame, obtained by PCR, was cloned into a vector and transformed into Escherichia coli origami to generate GOX-producing bacteria. Enzyme activity was confirmed and a phylogenetic tree showed the degree of kinship between Streptomyces species and other species, including Streptomyces SP MI02-7b. The expression levels of GOX genes mRNA were found to be approximately 4-fold higher in transformed E. coli than in soil thermophilic Streptomyces (P <0.001).

Conclusion

This study showed that natural thermostable streptomyces producing glucose oxidase enzyme could be found in Iran. The enzyme gene was successfully transformed into Escherichia coli generating a recombinant host with high yield capability that can be a major step towards the production of this enzyme from indigenous strains. It should be emphasized that the GOX enzyme produced by these strains is profitable due to high production levels correlated to the optimum condition in cheap culture media, short fermentation cycles, high expression capability, and ease of growth.

Structural basis for molecular recognition of G protein-coupled estrogen receptor by selected bisphenols

Complicated ligand-dependent signaling pathways of bisphenol A (BPA) and its analogues involve not only intranuclear estrogen receptor but also membrane receptor G protein-coupled estrogen receptor (GPER). However, the structural basis for molecular recognition of GPER by the environmental chemicals remains unknown. To reveal the structural dependence of GPER recognition by bisphenols, a systematic molecular dynamics simulation study was performed for selected bisphenols with different electron hybrid orbitals and substituents on their C atoms connecting two phenol rings. BPA was used as a control, bisphenol C(BPC) as an example for a connecting C with sp² hybrid orbitals to provide more ligand rigidity, bisphenol E(BPE) and bisphenol F(BPF) for decreased steric hindrance and hydrophobicity around the connecting C, and bisphenol B(BPB) and bisphenol AF(BPAF) for increased hydrophobicity and steric hindrance. All the tested bisphenols can bind with GPER at its classic orthosteric site to obtain GPER-ligand complexes, while van der Waals interactions and direct inter-molecular electrostatic energies provide the driving forces for ligand binding. Bulky substituents and structural rigidity of the connecting C dramatically impair hydrogen bonding between GPER and the bisphenols, which results in decreased contribution of both favorable intermolecular hydrogen bonds and unfavorable polar solvation effect to complex stability of BPB and BPC since decreased number of key residues is expected. Increase in substituent lipophilicity enhances the van der Waals interactions and favorable non-polar solvation effect. The six bisphenols of high structural similarity shared two key recognition residues, Leu137^TM3 and Trp272^TM6, the latter of which was in the highly conserved CWxP motif of TM6 and has been reported as key residue for G protein-coupled receptor activation. Based on the obtained knowledge, GPER affinity and relevant toxicity of BPA alternatives can be easily predicted, and the calculated binding free energies are consistent with the available experimental observations.

Protein engineering of stable IsPETase for PET plastic degradation by Premuse

Poly(ethylene terephthalate) (PET) is used widely by human beings, but is very difficult to degrade. Up to now, the PET degradation effect of PETase from Ideonella sakaiensis 201-F6 (IsPETase) variants with low stability and activity was not ideal. In this study, a mutation design tool, Premuse, was developed to integrate the sequence alignment and quantitative selection of the preferred mutations based on natural sequence evolution. Ten single point mutants were selected from 1486 homologous sequences using Premuse, and then two mutations (W159H and F229Y) with improved stability were screened from them. The derived double point mutant, W159H/F229Y, exhibited a strikingly enhanced enzymatic performance. Its T_m and catalytic efficiency values (k_cat/K_m) respectively increased by 10.4 °C and 2.0-fold using p-NPP as the substrate compared with wild type. The degradation activity for amorphous PET was increased by almost 40-fold in comparison with wild type at 40 °C in 24 h. Additionally, the variant could catalyze biodegradation of PET bottle preform at a mean rate of 23.4 mg_PET/h/mg_enzyme. This study allowed us to design the mutation more efficiently, and provides a tool for achieving biodegradation of PET pollution under mild natural environments.

Exploiting the activity-stability trade-off of glucose oxidase from Aspergillus niger using a simple approach to calculate thermostability of mutants

Glucose oxidase (Gox) is a biocatalyst that is widely applied in the food industry, as well as other biotechnological industries. However, the industrial application of Gox is hampered by its low thermostability and activity. Here, we aimed to improve the thermostability of GoxM4 from Aspergillus niger without reducing its activity due to the activity-stability trade-off. A simple and effective approach combining enzyme activity and structure stability was adopted to evaluate the thermostability of GoxM4 and its mutants. After four rounds of computer-aided rational design, the best mutant, GoxM8, was obtained. The melting temperature (T_m) of GoxM8 was increased by 9 °C compared with GoxM4. The catalytic efficiency of GoxM8 was similar to GoxM4, suggesting that the enzyme activity-stability trade-off was counteracted. To explore its mechanism, we performed molecular dynamics simulations of GoxM4 and its mutants. Our findings provided a typical example for researching the enzyme activity-stability trade-off.

The vast repertoire of carbohydrate oxidases: An overview

Carbohydrates are widely abundant molecules present in a variety of forms. For their biosynthesis and modification, nature has evolved a plethora of carbohydrate-acting enzymes. Many of these enzymes are of particular interest for biotechnological applications, where they can be used as biocatalysts or biosensors. Among the enzymes catalysing conversions of carbohydrates are the carbohydrate oxidases. These oxidative enzymes belong to different structural families and use different cofactors to perform the oxidation reaction of CH-OH bonds in carbohydrates. The variety of carbohydrate oxidases available in nature reflects their specificity towards different sugars and selectivity of the oxidation site. Thanks to their properties, carbohydrate oxidases have received a lot of attention in basic and applied research, such that nowadays their role in biotechnological processes is of paramount importance. In this review we provide an overview of the available knowledge concerning the known carbohydrate oxidases. The oxidases are first classified according to their structural features. After a description on their mechanism of action, substrate acceptance and characterisation, we report on the engineering of the different carbohydrate oxidases to enhance their employment in biocatalysis and biotechnology. In the last part of the review we highlight some practical applications for which such enzymes have been exploited.

Computational design of new enzymes for hydrolysis and synthesis of third-generation cephalosporin antibiotics

Engineering active sites in inert scaffolds to catalyze chemical transformations with unnatural substrates is still a great challenge for enzyme catalysis. In this research, a p-nitrobenzyl esterase from Bacillus subtilis was identified from the structural database, and a double mutant E115A/E188A was designed to afford catalytic activities toward the hydrolysis of ceftizoxime. A quadruple mutant E115A/E188A/L362S/I270A with enhanced catalytic efficiency was created to catalyze the condensation reaction of ethyl-2-methoxy-amino-2-(2-aminothiazole-4-yl) acetate with 7-amino-3-nor-cephalosporanic acid to produce ceftizoxime in a fully aqueous medium. The catalytic efficiencies of the computationally designed mutants E115A/E188A/L362S/I270A and E115A/Y118 K/E188 V/I270A/L362S can be taken as starting points to further improve their properties towards the practical application in designing more ecology-friendly production of third-generation cephalosporins.

Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering

Enzyme instability is an important limitation for the investigation and application of enzymes. Therefore, methods to rapidly and effectively improve enzyme stability are highly appealing. In this study we applied a computational method (FRESCO) to guide the engineering of an alcohol dehydrogenase. Of the 177 selected mutations, 25 mutations brought about a significant increase in apparent melting temperature (ΔTm ≥ +3 °C). By combining mutations, a 10-fold mutant was generated with a Tm of 94 °C (+51 °C relative to wild type), almost reaching water's boiling point, and the highest increase with FRESCO to date. The 10-fold mutant's structure was elucidated, which enabled the identification of an activity-impairing mutation. After reverting this mutation, the enzyme showed no loss in activity compared to wild type, while displaying a Tm of 88 °C (+45 °C relative to wild type). This work demonstrates the value of enzyme stabilization through computational library design.