High-temperature behavior of hyperthermostable Thermotoga maritima xylanase XYN10B after designed and evolved mutations

A hyperthermostable xylanase XYN10B from Thermotoga maritima (PDB code 1VBR, GenBank accession number KR078269) was subjected to site-directed and error-prone PCR mutagenesis. From the selected five mutants, the two site-directed mutants (F806H and F806V) showed a 3.3-3.5-fold improved enzyme half-life at 100 °C. The mutant XYNA generated by error-prone PCR showed slightly improved stability at 100 °C and a lower K_m. In XYNB and XYNC, the additional mutations over XYNA decreased the thermostability and temperature optimum, while elevating the K_m. In XYNC, two large side-chains were introduced into the protein's interior. Micro-differential scanning calorimetry (DSC) showed that the melting temperature (T_m) dropped in XYNB and XYNC from 104.9 °C to 93.7 °C and 78.6 °C, respectively. The detrimental mutations showed that extremely thermostable enzymes can tolerate quite radical mutations in the protein's interior and still retain high thermostability. The analysis of mutations (F806H and F806V) in a hydrophobic area lining the substrate-binding region indicated that active site hydrophobicity is important for high activity at extreme temperatures. Although polar His at 806 provided higher stability, the hydrophobic Phe at 806 provided higher activity than His. This study generates an understanding of how extreme thermostability and high activity are formed in GH10 xylanases. KEY POINTS: • Characterization and molecular dynamics simulations of TmXYN10B and its mutants • Explanation of structural stability of GH10 xylanase.

Biological cellulose saccharification using a coculture of Clostridium thermocellum and Thermobrachium celere strain A9

Abstract

An anaerobic thermophilic bacterial strain, A9 (NITE P-03545), that secretes β-glucosidase was newly isolated from wastewater sediments by screening using esculin. The 16S rRNA gene sequence of strain A9 had 100% identity with that of Thermobrachium celere type strain JW/YL-NZ35. The complete genome sequence of strain A9 showed 98.4% average nucleotide identity with strain JW/YL-NZ35. However, strain A9 had different physiological properties from strain JW/YL-NZ35, which cannot secrete β-glucosidases or grow on cellobiose as the sole carbon source. The key β-glucosidase gene (TcBG1) of strain A9, which belongs to glycoside hydrolase family 1, was characterized. Recombinant β-glucosidase (rTcBG1) hydrolyzed cellooligosaccharides to glucose effectively. Furthermore, rTcBG1 showed high thermostability (at 60°C for 2 days) and high glucose tolerance (IC₅₀ = 0.75 M glucose), suggesting that rTcBG1 could be used for biological cellulose saccharification in cocultures with Clostridium thermocellum. High cellulose degradation was observed when strain A9 was cocultured with C. thermocellum in a medium containing 50 g/l crystalline cellulose, and glucose accumulation in the culture supernatant reached 35.2 g/l. In contrast, neither a monoculture of C. thermocellum nor coculture of C. thermocellum with strain JW/YL-NZ35 realized efficient cellulose degradation or high glucose accumulation. These results show that the β-glucosidase secreted by strain A9 degrades cellulose effectively in combination with C. thermocellum cellulosomes and has the potential to be used in a new biological cellulose saccharification process that does not require supplementation with β-glucosidases.

Key points

• Strain A9 can secrete a thermostable β-glucosidase that has high glucose tolerance

• A coculture of strain A9 and C. thermocellum showed high cellulose degradation

• Strain A9 achieves biological saccharification without addition of β-glucosidase

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11818-0.

Immobilization of Baeyer-Villiger monooxygenase from acetone grown Fusarium sp

OBJECTIVE

A novel biocatalyst for Baeyer-Villiger oxidations is necessary for pharmaceutical and chemical industries, so this study aims to find a Baeyer-Villiger monooxygenase (BVMO) and to improve its stability by immobilization.

RESULTS

Acetone, the simplest ketone, was selected as the only carbon source for the screening of microorganisms with a BVMO. A eukaryote, Fusarium sp. NBRC 109816, with a BVMO (FBVMO), was isolated from a soil sample. FBVMO was overexpressed in E. coli and successfully immobilized by the organic-inorganic nanocrystal formation method. The immobilization improved the thermostability of FBVMO. Substrate specificity investigation revealed that both free and immobilized FBVMO were found to show catalytic activities not only for Baeyer-Villiger oxidation of ketones to esters but also for oxidation of sulfides to sulfoxides. Furthermore, a preparative scale reaction using immobilized FBVMO was successfully conducted.

CONCLUSIONS

FBVMO was discovered from an environmental sample, overexpressed in E. coli, and immobilized by the organic-inorganic nanocrystal formation method. The immobilization successfully improved its thermostability.

A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants

Extradiol dioxygenases (EDOs) catalyze the meta cleavage of catechol into 2-hydroxymuconaldehyde, a critical step in the degradation of aromatic compounds in the environment. In the present work, a novel thermophilic extradiol dioxygenase from Thermomonospora curvata DSM43183 was cloned, expressed, and characterized by phylogenetic and biochemical analyses. This enzyme exhibited excellent thermo-tolerance, displaying optimal activity at 50 °C, remaining >40% activity at 70 °C. Structural modeling and molecular docking demonstrated that both active center and pocket-construction loops locate at the C-terminal domain. Site-specific mutants D285A, H205V, F301V based on a rational design were obtained to widen the entrance of substrates; resulting in significantly improved catalytic performance for all the 3 mutants. Compared to the wild-type, the mutant D285A showed remarkably improved activities with respect to the 3,4-dihydroxyphenylacetic acid, catechol, and 3-chlorocatechol, by 17.7, 6.9, and 3.7-fold, respectively. The results thus verified the effectiveness of modeling guided design; and confirmed that the C-terminal loop structure indeed plays a decisive role in determining catalytic ring-opening efficiency and substrate specificity of the enzyme. This study provided a novel thermostable dioxygenase with a broad substrate promiscuity for detoxifying environmental pollutants and provided a new thinking for further enzyme engineering of EDOs.

Improving the catalytic efficiency and dimeric stability of Cu,Zn superoxide dismutase by combining structure-guided consensus approach with site-directed mutagenesis

Superoxide dismutase (SOD) leads the front line of defense against injuries mediated by the reactive oxygen species (ROS). The SOD from a high-altitude plant Potentilla atrosanguinea is a unique thermostable enzyme. In this study, we applied a structure-guided consensus approach on Cu,Zn SOD from Potentilla atrosanguinea plant, to improve its enzymatic properties. The polar uncharged amino acid (threonine) at position 97 of wild-type (WT) SOD was selected as a target residue for substitution by aspartate (T97D) through site-directed mutagenesis. The WT and T97D were examined by a combinative approach consisting of robust computational and experimental tools. The in-silico analysis indicated improved dimeric stability in T97D as compared to the WT. The strong interactions between the monomers were related to improved dimerization and enhanced catalytic efficiency of T97D. These results were validated by in-vitro assays showing improved dimer stability and catalytic efficiency in T97D than WT. Moreover, the mutation also improved the thermostability of the enzyme. The combined structural and functional data described the basis for improved specific activity and thermostability. This study could expand the scope of interface residue to be explored as targets for designing of SODs with improved kinetics.

Ancestral Sequence Reconstruction of Ancient Lipase from Family I.3 Bacterial Lipolytic Enzymes

Family I.3 lipase is distinguished from other families by the amino acid sequence and secretion mechanism. Little is known about the evolutionary process driving these differences. This study attempt to understand how the diverse temperature stabilities of bacterial lipases from family I.3 evolved. To achieve that, eighty-three protein sequences sharing a minimum 30% sequence identity with Antarctic Pseudomonas sp. AMS8 lipase were used to infer phylogenetic tree. Using ancestral sequence reconstruction (ASR) technique, the last universal common ancestor (LUCA) sequence of family I.3 was reconstructed. A gene encoding LUCA was synthesized, cloned and expressed as inclusion bodies in E. coli system. Insoluble form of LUCA was refolded using urea dilution method and then purified using affinity chromatography. The purified LUCA exhibited an optimum temperature and pH at 70℃ and 10 respectively. Various metal ions increased or retained the activity of LUCA. LUCA also demonstrated tolerance towards various organic solvents in 25% v/v concentration. The finding from this study could support the understanding on temperature and environment during ancient time. In overall, reconstructed ancestral enzymes have improved physicochemical properties that make them suitable for industrial applications and ASR technique can be employed as a general technique for enzyme engineering.

A Native PAGE Assay for the Biochemical Characterization of G Protein Coupling to GPCRs

G protein-coupled receptors (GPCRs) are a large family of membrane-embedded receptors that have diverse roles in physiology and are major drug targets. GPCRs transduce an agonist binding signal across the membrane to activate intracellular heterotrimeric G proteins. The dynamic nature of the receptors and the complexity of their interactions with agonists and G proteins present significant challenges for biochemical studies. Most biochemical/biophysical methods that have been employed to study GPCR-G protein coupling require purified receptors and are technically difficult. Here, we provide a protocol for a relatively simple and time- and cost-effective membrane protein native PAGE assay, to visualize and biochemically characterize agonist-dependent coupling of detergent-solubilized GPCRs to purified G protein surrogate "mini-G" proteins, which stabilize the receptor in an active state. The assay was developed for our studies of the calcitonin receptor-like receptor, a class B GPCR that mediates the actions of calcitonin gene-related peptide and adrenomedullin peptide agonists. It does not require a purified receptor and it can be used in a screening format with transiently-transfected adherent mammalian cell cultures, to quickly identify detergent-stable complexes amenable to study, or in a quantitative format with membrane preparations, to determine apparent affinities of agonists for the mini-G-coupled receptor and apparent affinities of mini-G proteins for the agonist-occupied receptor. The latter provides a partial measure of agonist efficacy. The method should be applicable to other GPCRs, and has the potential to be adapted to the study of other challenging membrane proteins and their complexes with binding partners. Graphic abstract: Visualizing agonist-dependent mini-G protein coupling and determining apparent binding affinities using the native PAGE assay quantitative formats.

SA-COO by random mutagenesis

To enhance the thermal stability of Streptomyces Sp. SA-COO cholesterol oxidase, random mutagenesis was used. A random mutant library was generated using two types of error-prone PCR (single step and serial dilution) and two mutants (ChOA-M1 and ChOA-M2) with improved thermostability were obtained. The best mutant ChOA-M1 acquired three amino acid substitutions (G49T, W52K, and F62V) and improved thermostability (at 50 °C for 5 h) by 40% and increased the kcat/Km value by 23%. The optimum pH was desirably changed to encompass a broad range from alkali to acid and circular dichroism revealed no significant secondary structure changes in mutants against wild type. These findings indicated that random mutagenesis was an effective technique for optimizing cholesterol oxidase properties and make a foundation for practical applications of Cholesterol oxidase in clinical diagnosis and industrial fields.

Enhancement of thermostability of GH10 xylanase E Penicillium canescens directed by ΔΔG calculations and structure analysis

Hydrolytic enzymes are highly demanded in the industry. Thermostability is an important property of enzymes that affects the economic costs of the industrial processes. The rational design of GH10 xylanase E (XylE) Penicillium canescens for the thermostability improvement was directed by ΔΔG calculations and structure analysis. Amino acid substitutions with stabilizing values of ΔΔG and providing an increase in side-chain volume of buried residues were performed experimentally. From the six designed substitutions, four substitutions appeared to be stabilizing, one - destabilizing, and one - neutral. For the improved XylE variants, values of T_m were increased by 1.1-3.1 °C, and times of half-life at 70 °C were increased in 1.3-1.7-times. Three of the four stabilizing substitutions were located in the N- or the C-terminus region. This highlights the importance of N- and C-terminus for the thermostability of GH10 xylanases and also enzymes with (β/α)₈ TIM barrel type of structure. The criteria of stabilizing values of ΔΔG and increased side-chain volume of buried residues for selection of substitutions may be applied in the rational design for thermostability improvement.

Two C1-oxidizing AA9 lytic polysaccharide monooxygenases from Sordaria brevicollis differ in thermostability, activity, and synergy with cellulase

Cellulolytic fungi usually have multiple genes for C1-oxidizing auxiliary activity 9 (AA9) lytic polysaccharide monooxygenases (LPMOs) in their genomes, but their potential functional differences are less understood. In this study, two C1-oxidizing AA9 LPMOs, SbLPMO9A and SbLPMO9B, were identified from Sordaria brevicollis, and their differences, particularly in terms of thermostability, reducing agent specificity, and synergy with cellulase, were explored. The two enzymes exhibited weak binding to cellulose and intolerance to hydrogen peroxide. Their oxidative activity was influenced by cellulose crystallinity and surface morphology, and both enzymes tended to oxidize celluloses of lower crystallinity and high surface area. Comparably, SbLPMO9A had much better thermostability than SbLPMO9B, which may be attributed to the presence of a carbohydrate binding module 1 (CBM1)-like sequence at its C-terminus. In addition, the two enzymes exhibited different specificities and responsivities toward electron donors. SbLPMO9A and SbLPMO9B were able to boost the catalytic efficiency of endoglucanase I (EGI) on physically and chemically pretreated substrates but with different degrees of synergy. Substrate- and enzyme-specific synergism was observed by comparing the synergistic action of SbLPMO9A or SbLPMO9B with commercial Celluclast 1.5L on three kinds of cellulosic substrates. On regenerated amorphous cellulose and PFI (Papirindustriens Forskningsinstitut)-fibrillated bleached eucalyptus pulp, SbLPMO9B showed a higher synergistic effect than SbLPMO9A, while on delignified wheat straw, the synergistic effect of SbLPMO9A was higher than that of SbLPMO9B. On account of its excellent thermostability and boosting effect on the enzymatic hydrolysis of delignified wheat straw, SbLPMO9A may have high application potential in biorefineries for lignocellulosic biomass. KEY POINTS: • C1-oxidizing SbLPMO9A displayed higher thermostability than SbLPMO9B, probably due to the presence of a CBM1-like module. • The oxidative activity of the two SbLPMO9s on celluloses increased with decreasing cellulose crystallinity or increasing beating degree. • The two SbLPMO9s boosted the catalytic efficiency of cellulase, but the synergistic effect was substrate- and enzyme-specific.

Thermostable and organic solvent-tolerant acid pectinase from Aspergillus terreus FP6: purification, characterization and evaluation of its phytopigment extraction potential

The present study discusses the purification, characterization and application of pectinase from Aspergillus terreus FP6 in fruit pigment extraction. By the four-step purification involving precipitation, dialysis, ion-exchange chromatography, gel filtration chromatography, a 20.85-fold purification of the enzyme to homogeneity was achieved. The apparent molecular mass of the pectinase was 47 kDa, as found by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The optimum activity of the enzyme was recorded at pH 6.0 and 50 °C. The enzyme retained 80.3% and 79.1% residual activity, respectively at pH 6.0 and 50 °C for 90 min. The pectinase was best functional in the presence of toluene and retained its activity for 30 min. Cu²⁺ and Co²⁺ acted as enzyme activators, while Ca²⁺, β-mercaptoethanol, dimethyl sulfoxide and ethylenediaminetetraacetic acid proved to be the inhibitors. The K _m and V _max values of the pectinase with pectin as substrate were 0.002 mM and 27.39 U/mL, respectively thus indicating the high enzyme affinity towards the substrate. After 30-min treatment of the grape skin with the partially purified enzyme, microscopic observation revealed that a short time of the enzymatic treatment resulted in substantial loss of pigment and shrinkage of the grape skin cells thereby highlighting the high efficiency of the pectinase. The current study implies that the A. terreus FP6 pectinase may be applied as a bio-agent in the food and beverage industries and has the potential to replace harmful solvents by promoting a greener approach to extract plant pigments.

Enhanced catalytic efficiency and thermostability of glucose isomerase from Thermoanaerobacter ethanolicus via site-directed mutagenesis

Glucose isomerase (GI) is a key enzyme in the preparation of high fructose corn syrup (HFCS). In this study, a mutant TEGI-M-L38 M/V137 L (TEGI-M2) of glucose isomerase (TEGI-M) originated from Thermoanaerobacter ethanalicus CCSD1 was obtained by site-directed mutagenesis. The TEGI-M2 showed an optimal activity at 85 ℃ and pH 6.5 with the divalent cations Co²⁺ and Mg²⁺. The structural differences between TEGI-M and TEGI-M2 were investigated based on the homology modeling and molecular docking, to elucidate the mechanism of improvement in the enzymatic properties. Compared with the original enzyme, the TEGI-M2 showed a 2.0-fold increased enzyme activity and a decreased K_m from 234.2 mM to 85.9 mM. Finally, the application of mutant TEGI-M2 in HFCS one-step biosynthesis was attempted, resulting in a d-fructose yield of 67.3 %, which was 14.3 % higher than that of TEGI-M. This improved catalytic performance of TEGI-M2 was of great importance for the industrial preparation of d-fructose in one-step process.

Extraction and characterization of an exopolysaccharide from a marine bacterium

The marine bacterial exopolysaccharides (EPS) have transfigured the biotech sector with their myriad applications and prospects. This work was carried out to characterize and analyze the functional and biochemical properties of an EPS (EPS-DR3A) produced by a marine bacterium, Pseudoalteromonas sp. YU16-DR3A. The bacterium was cultured in Zobell marine broth for the production of EPS. The extracted EPS designated as EPS-DR3A was composed of 69% carbohydrates and 7.6% proteins with a molecular weight of 20 kDa. FT-IR spectra showed the presence of different functional groups. The monosaccharide analysis performed using GC-MS showed the presence of fucose, erythrotetrose, ribose, and glucose as monomers. EPS-DR3A showed excellent emulsifying activity against the tested hydrocarbons and food oils with stable emulsions. Rheological analysis of EPS-DR3A revealed the pseudoplastic behavior. The EPS-DR3A displayed good thermal stability with a degradation temperature of 249 °C and a melting point at 322 °C. Further, it had the ability to scavenge DPPH and nitric oxide free radicals with good total antioxidant activity. The in vitro biocompatibility study of EPS-DR3A showed high degree of biocompatibility with human dermal fibroblast cells at the tested concentrations. Taken together, the findings such as thermostability, emulsifying activity, pseudoplasticity, antioxidant activity, and biocompatibility of EPS-DR3A make this biomolecule an important candidate for a wide range of biomedical applications.

Design of a PL18 alginate lyase with flexible loops and broader entrance to enhance the activity and thermostability

Alginate oligosaccharides are enzymolysis products of alginate with versatile bioactivities and their industrial preparation was limited by the insufficient activity and unsatisfying thermostability of alginate lyases. The structure-function information about PL18 alginate lyases was seldom reported since which few positive mutants of PL18 alginate lyases were generated. In present study, a mutant of PL18 alginate lyase E226K was expressed intracellularly and taken as parent for further modification. Site I211 at the lid loop 1 and sites E276, Y292 and R294 at the predicted entrance were chosen as engineering targets based on the E226K-PM4 binding mode in prereaction-state MD simulation and 29 mutants were constructed, from those, the variant E226K/I211T/R294V was screened out as the best mutant (showing 4.78-fold increased catalytic efficiency and the half-time t_1/2^45℃ increased up to 557 min from 89 min). MD simulations indicated that the affinity of E226K/I211T/R294V towards alginate was improved due to the optimized energy distribution of active center, more flexible loops around catalytic cleft and larger substrate entrance. The more efficient proton transmitting endowed E226K/I211T/R294V higher activity and the more complicated intraprotein interactions together with stronger backbone rigidity were responsible for the improved thermostability of E226K/I211T/R294V than E226K. The success in this study enriches the structure-function information of PL18 alginate lyases and provides hints for their further design.

Improvements in xylose stability and thermalstability of GH39 β-xylosidase from Dictyoglomus thermophilum by site-directed mutagenesis and insights into its xylose tolerance mechanism

β-Xylosidases are often inhibited by its reaction product xylose or inactivated by high temperature environment, which limited its application in hemicellulosic biomass conversion to fuel and food processing. Remarkably, some β-xylosidases from GH39 family are tolerant to xylose. Therefore, it is of great significance to elucidate the effect mechanism of xylose on GH39 β-xylosidases to improve their application. In this paper, based on the homologous model and prediction of protein active pocket constructed by I-TASSA and PyMOL, two putative xylose tolerance relevant sites (283 and 284) were mutated at the bottom of the protein active pocket, where xylose sensitivity and thermostability of Dictyoglomus thermophilum β-xylosidase Xln-DT were improved by site-directed mutagenesis. The Xln-DT mutant Xln-DT-284ASP and Xln-DT-284ALA showed high xylose tolerance, with the K_i values of 4602 mM and 3708 mM, respectively, which increased by 9-35% compared with the wildtype Xln-DT. The thermostability of mutant Xln-DT-284ASP was significantly improved at 75 and 85 °C, while the activity of the wild enzyme Xln-DT decreased to 40-20%, the activity of the mutant enzyme still remained 100%. The mutant Xln-DT-284ALA showed excellent stability at pH 4.0-7.0, but Xln-DT-284ASP showed slightly decreased activity. Furthermore, in order to explore the key sites and mechanism of xylose's effect on β-xylosidase activity, the interaction between xylose and enzyme was simulated by molecular docking. Besides binding to the active sites at the bottom of the substrate channel, xylose can also bind to sites in the middle or entrance of the channel with different affinities, which may determine the xylose inhibition of β-xylosidase. In conclusion, the improved xylose tolerance of mutant enzyme could be more advantageous in the degradation of hemicellulose and the biotransformation of other natural active substances containing xylose. This study supplies new insights into general mechanism of xylose effect on the activity of GH 39 β-xylosidases as well as related enzymes that modulate their activity via feedback control mechanism.

Improvement of thermostability and catalytic efficiency of glucoamylase from Talaromyces leycettanus JCM12802 via site-directed mutagenesis to enhance industrial saccharification applications

BACKGROUND

Glucoamylase is an important industrial enzyme in the saccharification of starch into glucose. However, its poor thermostability and low catalytic efficiency limit its industrial saccharification applications. Therefore, improving these properties of glucoamylase is of great significance for saccharification in the starch industry.

RESULTS

In this study, a novel glucoamylase-encoding gene TlGa15B from the thermophilic fungus Talaromyces leycettanus JCM12802 was cloned and expressed in Pichia pastoris. The optimal temperature and pH of recombinant TlGa15B were 65 ℃ and 4.5, respectively. TlGa15B exhibited excellent thermostability at 60 ℃. To further improve thermostability without losing catalytic efficiency, TlGa15B-GA1 and TlGa15B-GA2 were designed by introducing disulfide bonds and optimizing residual charge-charge interactions in a region distant from the catalytic center. Compared with TlGa15B, mutants showed improved optimal temperature, melting temperature, specific activity, and catalytic efficiency. The mechanism underlying these improvements was elucidated through molecular dynamics simulation and dynamics cross-correlation matrices analysis. Besides, the performance of TlGa15B-GA2 was the same as that of the commercial glucoamylase during saccharification.

CONCLUSIONS

We provide an effective strategy to simultaneously improve both thermostability and catalytic efficiency of glucoamylase. The excellent thermostability and high catalytic efficiency of TlGa15B-GA2 make it a good candidate for industrial saccharification applications.

Exploring the factors that affect the themostability of barley limit dextrinase - Inhibitor complex

Barley Limit dextrinase (Hordeum vulgare HvLD) is the unique endogenous starch-debranching enzyme, determining the production of a high degree of fermentation. The activity of HvLD is regulated by an endogenous LD inhibitor protein (LDI). In beer production, free LD is easy to inactivate in mashing process under the condition of high temperature. The binding of LD with LDI protects it against heat inactivation. Exploring the factors affecting the themostability of HvLD-LDI complex is important for beer production. In this work, the themostability of HvLD-LDI complex at different NaCl concentrations and temperatures were explored by molecular dynamics simulation and binding free energy calculation. In NaCl solution, the complex exhibits higher conformational stability at 343 K and 363 K than those in pure water. Root mean square fluctuation (RMSF) analysis identified the thermal sensitive regions of HvLD and LDI. The binding free energy results suggest that the LD-LDI complex is more stable in NaCl solution than those in pure water at high temperature. The residues with high contribution to the complex were identified. The structural and dynamic details will help us to understand the driving forces that lead to the themostability of HvLD-LDI complex at different temperatures and different salt concentrations, which will facilitate the optimization conditions of beer production for maintaining the thermal stability and activity of HvLD.

Characterization and Modeling of Thermostable GH50 Agarases from Microbulbifer elongatus PORT2

Viewing the considerable potential of marine agar as a source for the sustainable production of energy as well as nature-derived pharmaceutics, this work investigated the catalytic activity of three novel GH50 agarases from the mesophilic marine bacterium Microbulbifer elongatus PORT2 isolated from Indonesian coastal seawaters. The GH50 agarases AgaA50, AgaB50, and AgaC50 were identified through genome analysis; the corresponding genes were cloned and expressed in Escherichia coli BL21 (DE3). All recombinant agarases hydrolyzed β-p-nitrophenyl galactopyranoside, indicating β-glycosidase characteristics. AgaA50 and AgaB50 were able to cleave diverse natural agar species derived from Indonesian agarophytes, indicating a promising tolerance of these enzymes for substrate modifications. All three GH50 agarases degraded agarose, albeit with remarkable diversity in their catalytic activity and mode of action. AgaA50 and AgaC50 exerted exolytic activity releasing differently sized neoagarobioses, while AgaB50 showed additional endolytic activity in dependence on the substrate size. Surprisingly, AgaA50 and AgaB50 revealed considerable thermostability, retaining over 75% activity after 1-h incubation at 50 °C. Considering the thermal properties of agar, this makes these enzymes promising candidates for industrial processing.

Isolation and thermo-acclimation of thermophilic bacteria in hyperthermophilic fermentation system

Hyperthermophilic microorganisms play a key role in the hyper-thermophilic composting (HTC) technique. However, little information is available about the hyperthermophilic microorganisms prevalent in HTC systems, except for the Calditerricola satsumensis, Calditerricola yamamurae, and Thermaerobacter. To obtain effective hyper-thermophilic microorganisms, a continuous thermo-acclimation of the suitable thermophilic microorganisms was demonstrated in this study. Bacillus thermoamylovorans with high-temperature endurance (70 °C) were newly isolated from sludge composting, and an adequate slow heating rate (2 °C per cycle) was applied to further improve its thermostability. Finally, a strain with a maximum growth temperature of 80 °C was obtained. Moreover, structural and hydrophobic changes in cell proteins, the special amino acid content ratio, and the membrane permeability of the thermophilic bacterium after thermo-acclimation were evaluated for improved thermostability. In addition, the acclimated hyperthermophilic bacterium was further inoculated into the HTC system, and an excellent performance with a maximum operating temperature of 82 °C was observed.

Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome

Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical "right hand" architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity. KEY POINTS: • A hyperthermophilic xylanase with high activity was discovered using the metatranscriptomic method. • The mechanisms of thermophilicity and high activity were revealed using X-ray crystallography, mutagenesis, and molecular dynamics simulations. • The thermostability and activity were further improved by introducing a disulfide bond.

Covalent Immobilization of Chondrostereum purpureum Endopolygalacturonase on Ferromagnetic Nanoparticles: Catalytic Properties and Biotechnological Application

Pectinases are widely used in a variety of industrial processes. However, their application is limited by low catalytic processivity, reduced stability, high cost, and poor re-use compatibility. These drawbacks may be overcome by enzyme immobilization with ferromagnetic nanoparticles, which are easily recovered by a magnetic field. In this work, an endopolygalacturonase from Chondrostereum purpureum (EndoPG_Cp) expressed in Pichia pastoris was immobilized on glutaraldehyde-activated chitosan ferromagnetic nanoparticles (EndoPG_Cp-MNP) and used to supplement a commercial enzyme cocktail. No significant differences in biochemical and kinetic properties were observed between EndoPG_Cp-MNP and EndoPG_Cp, although the EndoPG_Cp-MNP showed slightly increased thermostability. Cocktail supplementation with EndoPG_Cp-MNP increased reducing sugar release from orange wastes by 1.8-fold and showed a synergistic effect as compared to the free enzyme. Furthermore, EndoPG_Cp-MNP retained 65% of the initial activity after 7 cycles of re-use. These properties suggest that EndoPG_Cp-MNP may find applications in the processing of pectin-rich agroindustrial residues.

Development of thermostable sucrose phosphorylase by semi-rational design for efficient biosynthesis of alpha-D-glucosylglycerol

Abstract

Sucrose phosphorylase (SPase) can specifically catalyze transglycosylation reactions and can be used to enzymatically synthesize α-D-glycosides. However, the low thermostability of SPase has been a bottleneck for its industrial application. In this study, a SPase gene from Leuconostoc mesenteroides ATCC 12,291 (LmSPase) was synthesized with optimized codons and overexpressed successfully in Escherichia coli. A semi-rational design strategy that combined the FireProt (a web server designing thermostable proteins), structure–function analysis, and molecular dynamic simulations was used to improve the thermostability of LmSPase. Finally, one single-point mutation T219L and a combination mutation I31F/T219L/T263L/S360A (Mut4) with improved thermostability were obtained. The half-lives at 50 °C of T219L and Mut4 both increased approximately two-fold compared to that of wild-type LmSPase (WT). Furthermore, the two variants T219L and Mut4 were used to produce α-D-glucosylglycerol (αGG) from sucrose and glycerol by incubating with 40 U/mL crude extracts at 37 °C for 60 h and achieved the product concentration of 193.2 ± 12.9 g/L and 195.8 ± 13.1 g/L, respectively, which were approximately 1.3-fold higher than that of WT (150.4 ± 10.0 g/L). This study provides an effective strategy for improving the thermostability of an industrial enzyme.

Key points

• Predicted potential hotspot residues directing the thermostability of LmSPase by semi-rational design

• Screened two positive variants with higher thermostability and higher activity

• Synthesized α-D-glucosylglycerol to a high level by two screened positive variants

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11551-0.

Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges

Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.

Unexpectedly high thermostability of an NADP-dependent malic enzyme from a psychrophilic bacterium, Shewanella livingstonensis Ac10

Psychrophilic enzymes are generally active at low temperatures, and their functions have attracted much interest in food processing, biochemical research, and chemical industry. However, their activities are usually lost above their growth temperature because of their flexible and unstable structure. Here, we unexpectedly found that a homodimeric NADP-dependent malic enzyme from a psychrophilic bacterium, Shewanella livingstonensis Ac10 (SL-ME) showed sufficient activity with 60°C treatment, similar to its counterpart from mesophilic Escherichia coli (MaeB). Consistently, SL-ME and MaeB irreversibly denatured at 71.9°C and 64.5°C, respectively. Therefore, SL-ME shows robust catalytic activity, which appears to be advantageous for its application in the bioconversion of NADP to NADPH, an essential ingredient for membrane phospholipid synthesis.

Impacts of Ca2+ cation and temperature on bovine α-lactalbumin secondary structures and foamability - Insights from computational molecular dynamics

We used computational molecular dynamics (MD) to assess molecular conformations of apo- and holo-forms (respectively without and with Ca²⁺) of bovine α-lactalbumin (α-La) at different temperatures, and to correlate them with the protein's foaming properties. At 4 °C and 25 °C no major protein conformation changes occurred. At 75 °C, lots of changes were evidenced: the Ca²⁺ depletion triggered the complete loss of h2b, h3c helices and S1, S2 and S3 β-sheets, and partial losses of H1, H2 and H3 α-helices. The absence of Ca²⁺ in apo-α-La and its leaving from holo-α-La triggered electrostatic repulsion among Asp82, Asp84 and Asp87, leading to the formation of a hydrophobic cluster involving Phe9, Phe31, Ile1, Va42, Ile55, Phe80 and Leu81. These conformational changes were related to an interfacial tension decrease and to a foaming capacity increase, for both apo-α-La and holo-α-La. This study exemplifies how powerful MD is as a tool to provide a better understanding of the molecular origins of food proteins' techno-functionalities.

Characterization of a Stable Form of Carboxypeptidase G2 (Glucarpidase), a Potential Biobetter Variant, From Acinetobacter sp. 263903-1

Carboxypeptidase G2 (CPG2) is a bacterial enzyme widely used to detoxify methotrexate (MTX) and in enzyme/prodrug therapy for cancer treatment. However, several drawbacks, such as instability, have limited its efficiency. Herein, we have evaluated the properties of a putative CPG2 from Acinetobacter sp. 263903-1 (AcCPG2). AcCPG2 is compared with a CPG2 derived from Pseudomonas sp. strain RS-16 (PsCPG2), available as an FDA-approved medication called glucarpidase. After modeling AcCPG2 using the I-TASSER program, the refined model was validated by PROCHECK, VERIFY 3D and according to the Z score of the model. Using computational analyses, AcCPG2 displayed higher thermodynamic stability and a lower aggregation propensity than PsCPG2. AcCPG2 showed an optimum pH of 7.5 against MTX and was stable over a pH range of 5-10. AcCPG2 exhibited optimum activity at 50 °C and higher thermal stability at a temperature range of 20-70 °C compared to PsCPG2. The K_m value of the purified AcCPG2 toward folate and MTX was 31.36 µM and 44.99 µM, respectively. The V_max value of AcCPG2 for folate and MTX was 125.80 µmol/min/mg and 48.90  µmol/min/mg, respectively. Accordingly, thermostability and pH versatility makes AcCPG2 a potential biobetter variant for therapeutic applications.

Evaluation of the stability of a spray-dried tuberculosis vaccine candidate designed for dry powder respiratory delivery

Particle engineering via spray drying was used to develop a dry powder presentation of an adjuvanted tuberculosis vaccine candidate. This presentation utilizing a trileucine-trehalose excipient system was designed to be both thermostable and suitable for respiratory delivery. The stability of the spray-dried vaccine powder was assessed over one year at various storage temperatures (-20, 5, 25, 40, 50 °C) in terms of powder stability, adjuvant stability, and antigen stability. A formulation without trileucine was included as a control. The results showed that the interior particle structure and exterior particle morphology of the powder was maintained for one year at 40 °C, while the control case exhibited a small extent of particle fusing under the same storage conditions. Moisture content was maintained, and powder solid state remained amorphous for all storage temperatures. Aerosol performance was assessed with a commercial dry powder inhaler in combination with a human mouth-throat model. The emitted dose and lung dose were maintained for all samples after one year at temperatures up to 40 °C. Nanoemulsion size and oil content of the adjuvant system were maintained after one year at temperatures up to 40 °C, and the agonist content was maintained after one year at temperatures up to 25 °C. The antigen was completely degraded in the control formulation at seven months of storage at 40 °C; by contrast, 45% of the antigen was still present in the trehalose-trileucine formulation after one year of storage at 50 °C. Comparatively, the antigen was completely degraded in a liquid sample of the vaccine candidate after only one month of storage at 37 °C. The spray-dried trehalose-trileucine vaccine powder clearly maintained its inhalable properties after one year's storage at high temperatures and improved overall thermostability of the vaccine.

Recombinant Expression and Purification of Cannabinoid Receptor CB2, a G Protein-Coupled Receptor

G protein-coupled receptors (GPCR) are integral membrane proteins that regulate multiple cellular processes. To obtain insights into structural properties of GPCR and mechanism of activity, these proteins should be isolated in significant (milligram) quantities, in a pure, homogenous, and stable form. Here we describe the expression and purification of type II human cannabinoid receptor CB₂, a class A GPCR, in two different types of expression hosts: in Escherichia coli and in mammalian suspension cell culture Expi293. Our method allows preparation of milligram quantities of the purified receptors suitable for a wide array of downstream applications including high-resolution structural studies and functional assays.

A Thermostable Aluminum-Tolerant Protease Produced by Feather-Degrading Bacillus thuringiensis Isolated from Tea Plantation

BACKGROUND

Proteases with keratinolytic activity are widely used in biotechnologies. The feather-degrading Bacillus thuringensis isolated from soil sample of a tea plantation produced high level of extracellular keratinase.

OBJECTIVE

This study aimed to analyze the properties by biochemical and enzymological methods to gain information for better utilization of the enzyme.

METHODS

The enzyme was purified with ion exchange and size exclusion chromatography. The substrate preference, optimal pH and temperature, and the effects of organic solvents and ions were checked. Circular dichroism was performed to compare the secondary structures of the native and apo-enzyme.

RESULTS

The enzyme worked best at 50°C, and it was an acidic serine protease with an optimal pH of 6.2. Ions Ca²⁺ and Mg²⁺ were essential for its activity. Organic solvents and other metal ions generally deactivated the enzyme in a concentration-dependent manner. However, Mn²⁺ and DMSO, which were frequently reported as inhibitors of protease, could activate the enzyme at low concentration (0.01 to 2 mmol/L of Mn²⁺; DMSO <2%, v/v). The enzyme exhibited high resistance to Al³⁺, which might be explained by the soil properties of its host's residence. Circular dichroism confirmed the contribution of ions to the structure and activity.

CONCLUSION

The enzyme was a thermostable aluminum-tolerant serine protease with unique biochemical properties.

Studies of multifunctional DNA polymerase I from the extremely radiation resistant Deinococcus radiodurans: Recombinant expression, purification and characterization of the full-length protein and its large fragment

Deinococcus radiodurans is a bacterium with extreme resistance to desiccation and radiation. Although the origins of this extreme resistance have not been fully elucidated, an efficient DNA repair machinery that includes the enzyme DNA polymerase I, is potentially crucial as part of a protection mechanism. Here we have cloned and performed small, medium, and large-scale expression of full-length D. radiodurans DNA polymerase I (DrPolI) as well as the large/Klenow fragment (DrKlenow). We then carried out functional characterization of 5' exonuclease, DNA strand displacement and polymerase activities of these proteins using gel-based and molecular beacon-based biochemical assays. With the same expression and purification strategy, we got higher yield in the production of DrKlenow than of the full-length protein, approximately 2.5 mg per liter of culture. Moreover, we detected a prominent 5' exonuclease activity of DrPolI in vitro. This activity and, DrKlenow strand displacement and DNA polymerase activities are preferentially stimulated at pH 8.0-8.5 and are reduced by addition of NaCl. Interestingly, both protein variants are more thermostable at pH 6.0-6.5. The characterization of DrPolI's multiple functions provides new insights into the enzyme's role in DNA repair pathways, and how the modulation of these functions is potentially used by D. radiodurans as a survival strategy.

Improving the enzyme property of D-allulose 3-epimerase from a thermophilic organism of Halanaerobium congolense through rational design

The rare sugar d-allulose is an attractive sucrose substitute due to its sweetness and ultra-low caloric value. It can be produced from D-fructose using d-allulose 3-epimerase (DAE) as the biocatalyst. However, most of the reported DAEs show low catalytic efficiency and poor thermostability, which limited their further use in food industrial. Here, a putative d-allulose 3-epimerase from a thermophilic organism of Halanaerobium congolense (HcDAE) was characterized, showing optimal activity at pH 8.0 and 70 °C in the presence of Mg²⁺. Saturation mutagenesis of Y7, C66, and I108, the putative residues responsible for substrate recognition at the O-4, -5, and -6 atoms of D-fructose was performed, and it yielded the triple mutant Y7H/C66L/I108A with improved activity toward D-fructose (345 % of wild-type enzyme). The combined mutant Y7H/C66L/I108A/R156C/K260C exhibited a half-half (t_1/2) of 5.2 h at 70 °C and an increase of the T_m value by 6.5 °C due to the introduction of disulfide bridges between intersubunit with increased interface interactions. The results indicate that mutants could be used as industrial biocatalysts for d-allulose production.

Improvement Thermal Stability of D-Lactate Dehydrogenase by Hydrophobin-1 and in Silico Prediction of Protein-Protein Interactions

Hydrophobins are small surface-active proteins. They can connect to hydrophobic or hydrophilic regions and oligomerize in solution to form massive construction. In nature, these proteins are produced by filamentous fungi at different stages of growth. So far, researchers have used them in various fields of biotechnology. In this study, recombinant hydrophobin-1 (rHFB1, 7.5 kDa) was used to stabilize recombinant D-lactate dehydrogenase (rD-LDH, 35 kDa). rD-LDH is a sensitive enzyme deactivated and oxidized by external agents such as O₂ and lights. So, its stabilization with rHFB1 can be the best index to demonstrate the positive effect of rHFB1 on preserving and improving enzyme's activity. The unique ability of rHFB1 for interacting with hydrophobic regions of rD-LDH was predicted by protein-protein docking study with ClusPro and PIC servers and confirmed by fluorescence experiments, and Colorless Native-PAGE. Measurement of thermodynamic parameters allows for authenticating the role of rHFB1 as a thermal stabilizer in the protein-protein complex (rD-LDH@rHFB1). Interaction between rHFB1 and rD-LDH improved half-life of enzyme 2.25-fold at 40 °C. Investigation of the kinetic parameters proved that the presence of rHFB1 along with the rD-LDH enhancement strongly the affinity of the enzyme for pyruvate. Furthermore, an increase of Kcat/Km for complex displayed the effect of rHFB1 for improving the enzyme's catalytic efficiency.

Design of Bacillus fastidious Uricase Mutants Bearing Long Lagging Phases Before Exponential Decreases of Activities Under Physiological Conditions

Under physiological conditions, Bacillus fastidious uricase (BFU) activity shows negligible lagging phase before the exponential decrease; mutants are thus designed for long lagging phases before exponential activity decreases. On homodimer surface of BFU (4R8X.pdb), the last fragment ANSEYVAL at the C-terminus forms a loop whose Y319 is H-bonded by the buried D257 in the same monomer. Within 1.5 nm from the α-carboxyl group of the last leucine (L322), E30, K26, D257, R258, E311, K312 and E318 from the same monomer plus D126 and K127 from a monomer of the other homodimer generate an electrostatic interaction network. Within 1.5 nm from Y319, D307 and R310 in the same monomer interact with ionized residues around the inter-chain β-sheet in the same homodimer. Mutagenesis of Y319R is designed to strengthen the original interactions and concomitantly generate new electrostatic attractions between homodimers. Under physiological conditions, the mutant V144A/Y319R showed an approximately 4 week lagging phase before the exponential activity decrease, an apparent half-life of activity nearly three folds of mutant V144A, but comparable activity. The introduction of ionizable residues into the C-terminus contacting the other homodimer for additional and/or stronger electrostatic attractions between homodimers may be a universal approach to thermostable mutants of uricases.

Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design

Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.

0602 to improve thermostability

BACKGROUND

Ramie degumming is often carried out at high temperatures; therefore, thermostable alkaline pectate lyase (PL) is beneficial for ramie degumming for industrial applications. Thermostable PLs are usually obtained by exploring new enzymes or reconstructing existing enzyme by rational design. Here, we improved the thermostability of an alkaline pectate lyase (PelN) from Paenibacillus sp. 0602 with rational design and structure-based engineering.

RESULTS

From 26 mutants, two mutants of G241A and G241V showed a higher thermostability compared with the wild-type PL. The mutant K93I showed increasing specific activity at 45 °C. Subsequently, we obtained combinational mutations (K93I/G241A) and found that their thermostability and specific activity improved simultaneously. The K93I/G241A mutant showed a half-life time of 15.9 min longer at 60 °C and a melting temperature of 1.6 °C higher than those of the wild PL. The optimum temperature decreased remarkably from 67.5 °C to 60 °C, accompanied by a 57% decrease in Km compared with the Km value of the wild-type strain. Finally, we found that the intramolecular interaction in PelN was the source in the improvements of molecular properties by comparing the model structures. Rational design of PelN was performed by stabilizing the α-helices with high conservation and increasing the stability of the overall structure of the protein. Two engineering strategies were applied by decreasing the mutation energy calculated by Discovery Studio and predicting the free energy in the process of protein folding by the PoPMuSiC algorithm.

CONCLUSIONS

The results demonstrated that the K93I/G241A mutant was more suitable for industrial production than the wild-type enzyme. Furthermore, the two forementioned strategies could be extended to reveal engineering of other kinds of industrial enzymes.

Enhanced recombinant Sulfurihydrogenibium yellowstonense carbonic anhydrase activity and thermostability by chaperone GroELS for carbon dioxide biomineralization

Biological carbon fixation is a feasible strategy to reduce atmospheric carbon dioxide levels (CO₂). In this platform, carbonic anhydrase (CA) enzyme is employed to accelerate the sequestration of CO₂. The present work explored the effect of chaperone GroELS and TrxA-tag on improving soluble expression of the recombinant Sulfurihydrogenibium yellowstonense CA which activity and biomineralization capability were taken into consideration. At first, the expression of GroELS using the inducible T7 promoter and constitutive J23100 promoter were investigated. The results indicated that 1.4 folds increment of soluble protein and 100% of CA activity enhancement were achieved with GroELS co-expression driven by J23100 promoter. Furthermore, the involvement of TrxA fusion tag displayed a significant enhancement of soluble protein production which was about 2.67 times higher than that of original SyCA. Besides, co-expression with GroELS intensified the thermostability of SyCA at 60 °C owing to changes in the structural conformation of the protein, which was proved by an in vitro assay. The SyCA was further entrapped and immobilized into polyacrylamide gel (i.e., PAGE-SyCA). The biomineralization capability of the PAGE-SyCA and whole-cell (WC) was compared in a two-column system. After 5 cycles of reuse, PAGE-SyCA maintained 29.8% activity and formed 774 mg of CaCO₃ solids in the B::JG strain. This study presents the recombinant engineering strategies to improve SyCA productivity, activity, thermostability, and effective carbon dioxide conversion.

Molecular cloning and characterization of a thermostable and halotolerant endo-β-1,4-glucanase from Microbulbifer sp. ALW1

The bacterium Microbulbifer sp. ALW1 was previously characterized with the capability to break down the cell wall of brown algae into fine pieces. The biological functions of strain ALW1 were yet to be elucidated. In this study, a gene, namely MaCel5A, was isolated from the ALW1 strain genome, encoding an endo-β-1,4-glucanase. MaCel5A was phylogenetically categorized under the glycoside hydrolase family GH5, with the highest identity to a putative cellulase of Microbulbifer thermotolerans. The recombinant MaCel5A protein purified from heterologous expression in E. coli exhibited maximum activity at 50 °C and pH 6.0, respectively, and functioned selectively toward carboxymethyl cellulose and barley β-glucan. Recombinant MaCel5A demonstrated considerable tolerance to the exposure to high temperature up to 80 °C for 30 min retaining 49% residual activity. In addition, MaCel5A showed moderate stability against pH 5.0-11.0 and strong stability in the presence of nonionic surfactant. MaCel5A exhibited strong halo-stability and halotolerance. The activity of the enzyme increased about tenfold at 0.5 M NaCl, and about fivefold even at 4.0 M NaCl compared to the enzyme activity without the addition of salt. The two conserved glutamic acid residues in MaCel5A featured the typical catalytic acid/base and nucleophile machinery of glycoside hydrolases. These characteristics highlight the industrial application potential of MaCel5A.

A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures

Mycobacterium hassiacum is so far the most thermophilic among mycobacteria as it grows optimally at 50 °C and up to 65 °C in a glycerol-based medium, as verified in this study. Since this and other nontuberculous mycobacteria (NTM) thrive in diverse natural and artificial environments, from where they may access and infect humans, we deemed essential to probe M. hassiacum resistance to heat, a strategy routinely used to control microbial growth in water-supply systems, as well as in the food and drink industries. In addition to possibly being a threat in its own right in rare occasions, M. hassiacum is also a good surrogate for studying other NTM species more often associated with opportunistic infection, namely Mycobacterium avium and Mycobacterium abscessus as well as their strictly pathogenic counterparts Mycobacterium tuberculosis and Mycobacterium leprae. In this regard, this thermophilic species is likely to be useful as a source of stable proteins that may provide more detailed structures of potential drug targets. Here, we investigate M. hassiacum growth at near-pasteurization temperatures and at different pHs and also characterize its thermostable glucosyl-3-phosphoglycerate synthase (GpgS), an enzyme considered essential for M. tuberculosis growth and associated with both nitrogen starvation and thermal stress in different NTM species.

Extra disulfide and ionic salt bridge improves the thermostability of lignin peroxidase H8 under acidic condition

The development of a lignin peroxidase (LiP) that is thermostable even under acidic pH conditions is a main issue for efficient enzymatic lignin degradation due to reduced repolymerization of free phenolic products at acidic pH (< 3). Native LiP under mild conditions (half-life (t_1/2) of 8.2 days at pH 6) exhibits a marked decline in thermostability under acidic conditions (t_1/2 of only 14 min at pH 2.5). Thus, improving the thermostability of LiP in acidic environments is required for effective lignin depolymerization in practical applications. Here, we show the improved thermostability of a synthetic LiPH8 variant (S49C/A67C/H239E, PDB: 6ISS) capable of strengthening the helix-loop interactions under acidic conditions. This variant retained excellent thermostability at pH 2.5 with a 10-fold increase in t_1/2 (2.52 h at 25 °C) compared with that of the native enzyme. X-ray crystallography analysis showed that the recombinant LiPH8 variant is the only unique lignin peroxidase containing five disulfide bridges, and the helix-loop interactions of the synthetic disulfide bridge and ionic salt bridge in its structure are responsible for stabilizing the Ca²⁺-binding region and heme environment, resulting in an increase in overall structural resistance against acidic conditions. Our work will allow the design of biocatalysts for ligninolytic enzyme engineering and for efficient biocatalytic degradation of plant biomass in lignocellulose biorefineries.

Factors deciding the assembly and thermostability of the DmrB cage

Dihydromethanopterin reductase (DmrB), is a naturally occurring cage protein found in various archaeal and a few bacterial species. It exists as 24mer with cubic geometry where 8 trimeric subunits are present at the corners of each cube. Each trimer is made up of three monomeric units and six FMN, where two molecules of FMN are present at the interface of each monomer. DmrB is involved in the conversion of dihydromethanopterin to tetrahydromethanopterin using FMN as a redox equivalent. In the present study, we have used spectroscopic and biochemical techniques along with complementary bio-informatic work to understand the assembly principles of the DmrB. Our results show a concentration dependant self-assembly of DmrB which is mediated by ionic interactions. The co-factor FMN stabilizes and preserves the secondary and quaternary structure of DmrB against thermal insult, indicating that the higher order assembly of DmrB is very thermostable. Our work provides an interesting piece of information regarding the role of the co-factors in the thermostability of these classes of cage proteins. The understanding of the assembly and disassembly of this thermostable cage would enable the downstream usage of this system in various nano-biotechnological applications.

Next-Generation COVID-19 Vaccines Should Take Efficiency of Distribution into Consideration

The dire need for safe and effective coronavirus disease (COVID-19) vaccines is met with many vaccine candidates being evaluated in pre-clinical and clinical studies. The COVID-19 vaccine candidates currently in phase 3 or phase 2/3 clinical trials as well as those that recently received emergency use authorization (EUA) from the United States Food and Drug Administration (FDA) and/or other regulatory agencies worldwide require either cold (i.e., 2–8°C) or even freezing temperatures as low as −70°C for storage and distribution. Thus, existing cold chain will struggle to support both the standard national immunization programs and COVID-19 vaccination. The requirement for cold chain is now a major challenge towards worldwide rapid mass vaccination against COVID-19. In this commentary, we stress that thermostabilizing technologies are available to enable cold chain-free vaccine storage and distribution, as well as potential needle-free vaccination. Significant efforts on thermostabilizing technologies must now be applied on next-generation COVID-19 vaccines for more cost-effective worldwide mass vaccination and COVID-19 eradication.

Stability of lyophilized and spray dried vaccine formulations

Liquid formulations of vaccines are subject to instabilities that result from degradation processes that proceed via a variety of physical and chemical pathways. In dried formulations, such as those prepared by lyophilization or spray drying, many of these degradation pathways may be avoided or inhibited. Thus, the stability of vaccine formulations can be enhanced significantly in the absence of bulk water. Potential advantages of dry vaccine formulations include extended shelf lives and less stringent cold-chain storage requirements, both of which offer possibilities of reduced vaccine wastage and facilitated distribution to resource-poor areas. Lyophilization and spray drying represent the most common methods of stabilizing vaccines through drying. This article reviews several lyophilized and spray dried vaccines that address a diverse set of pathogens, as well as some of the assays used to quantify their stability. Recent dry vaccine trends include needle-free delivery of dry powder via non-parenteral routes of administration and the incorporation of advanced vaccine adjuvants into formulations, which further contribute to the goal of increasing vaccine distribution to resource-poor areas. Challenges associated with development of these newer technologies are also discussed.

Thermal denaturation and autoxidation profiles of carangid fish myoglobins

Although myoglobin (Mb) has been considered to be one of the well-characterized proteins, screening of post-genomic era databases revealed the lack of adequate information on teleost Mbs. The present study was aimed to investigate stability and functional features of Mbs from three teleosts of the same family. To unfold how primary structure influences the stability and function of proteins, Mbs were purified from the dark muscles of three carangids, namely, yellowtail, greater amberjack, and silver trevally. Thermostabilities measured by circular dichroism (CD) spectrometry revealed species-specific thermal denaturation pattern, i.e., silver trevally > yellowtail > greater amberjack Mbs. On the other hand, autoxidation rate constants of the ferrous forms of those three carangid Mbs showed positive correlation between the ferrous state of the heme iron and rising temperature. The order of autoxidation rate was in the order of greater amberjack > yellowtail > silver trevally Mbs. The finding of the present study denotes that the thermal stability is not necessarily correlated with the functional stability of carangid Mbs even though their primary structures shared high homology (84-94%).

Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris

BACKGROUND

Phytases are widely used commercially as dietary supplements for swine and poultry to increase the digestibility of phytic acid. Enzyme development has focused on increasing thermostability to withstand the high temperatures during industrial steam pelleting. Increasing thermostability often reduces activity at gut temperatures and there remains a demand for improved phyases for a growing market.

RESULTS

In this work, we present a thermostable variant of the E. coli AppA phytase, ApV1, that contains an extra non-consecutive disulfide bond. Detailed biochemical characterisation of ApV1 showed similar activity to the wild type, with no statistical differences in k_cat and K_M for phytic acid or in the pH and temperature activity optima. Yet, it retained approximately 50% activity after incubations for 20 min at 65, 75 and 85 °C compared to almost full inactivation of the wild-type enzyme. Production of ApV1 in Pichia pastoris (Komagataella phaffi) was much lower than the wild-type enzyme due to the presence of the extra non-consecutive disulfide bond. Production bottlenecks were explored using bidirectional promoters for co-expression of folding chaperones. Co-expression of protein disulfide bond isomerase (Pdi) increased production of ApV1 by ~ 12-fold compared to expression without this folding catalyst and restored yields to similar levels seen with the wild-type enzyme.

CONCLUSIONS

Overall, the results show that protein engineering for enhanced enzymatic properties like thermostability may result in folding complexity and decreased production in microbial systems. Hence parallel development of improved production strains is imperative to achieve the desirable levels of recombinant protein for industrial processes.

Improving the activity and stability of Bacillus clausii alkaline protease using directed evolution and molecular dynamics simulation

Detergent enzymes have been developed extensively as eco-friendly substitutes for the harmful chemicals in detergent. Among them, alkaline protease accounts for a large share of detergent enzyme sales. Thus, improving the specific activity of alkaline protease could play an important role in reducing the cost of detergent enzymes. In our study, alkaline protease from Bacillus clausii (PRO) was used to construct a mutant library through directed evolution using error-prone PCR, and a variant (G95P) with 9-fold enhancement in specific activity was obtained. After incubation at a pH of 11.0 for 70 h, G95P maintained 67 % of its maximal activity, which was 46 % more than wild-type PRO (WT), indicating that G95P has better alkaline stability than WT. The thermostability of G95P was also enhanced, as G95P achieved 17 % initial activity after incubation for 50 h at 60 °C, while WT lost its activity. The MD simulation results verified that variant G95P possessed improved stability of its Gly95-Gly100 loop region and Arg19-Asp265 salt bridge, leading to enhanced stability and catalytic efficiency. This work enhances the understanding of the structure-function relationship of PRO and provides an academic foundation for improving the enzymatic properties of PRO to satisfy industrial requirements using protein engineering.

Effect of introducing a disulfide bridge on the thermostability of microbial transglutaminase from Streptomyces mobaraensis

Microbial transglutaminase (MTG) has been used extensively in academic research and the food industry through cross-linking or posttranslational modification of proteins. In our previous paper, the activity-increased MTG mutants were obtained by means of rational mutagenesis and random mutagenesis coupled with the newly developed screening system. In addition, the improvement of heat resistance of MTG is needed to expand further its industrial applications. Here, a structure-based rational enzyme engineering approach was applied to improve the thermostability of MTG by introducing an artificial disulfide bridge. As a result of narrowing down candidates using a rational approach, we successfully engineered a disulfide bridge into the N-terminal region of MTG by substituting Thr-7 and Glu-58 with cysteine. The T7C/E58C mutant was observed to have a de novo disulfide bridge and showed an increased melting temperature (Tm value) of 4.3 °C with retained enzymatic activity. To address the benefit-gained reason, we focused on the Cβ temperature factor of the amino-acid residues that might form a disulfide bridge in MTG. Introducing the disulfide bridge had no remarkable effect on the mutant aiming to stabilize the high temperature factor. On the other hand, the mutation was effective on the relatively stable region. The introduction of a disulfide bridge may therefore be effective to stabilize further the relatively stable part. This finding is considered to be useful for the rational design of mutants aiming at heat resistance of proteins.Key Points• Microbial transglutaminase (MTG) is used as a binder in the food industry.• MTG has the potential for use in the manufacturing of various commercial materials.• Enhanced thermostability was observed for the disulfide bridge mutant, T7C/G58C.

DiRect: Site-directed mutagenesis method for protein engineering by rational design

Site-directed mutagenesis (SDM), an indispensable method in molecular biology and protein engineering, is rather time-consuming and laborious. Protein engineering, especially that of enzymes, nowadays increasingly relies on rational design approaches in which both SDM and protein expression are the bottlenecks because they are generally based on the recombinant DNA technology. Here, we developed a new PCR-based mutagenesis method, DiRect, that achieves high performance in product quality (≥99% substitution) without recombinant DNA technology. We applied DiRect in combination with a cell-free protein expression system to an industrially relevant enzyme, nicotinamide adenine dinucleotide phosphate-dependent 3-quinuclidinone reductase from Rhodotorula rubra. In a single round of screening, 90 newly designed mutant proteins were produced within two days, and an unreported mutant (Q135I) exhibiting much higher thermostability than the wild-type enzyme was successfully identified within one extra day. Thus, DiRect is a simple, efficient, and potentially scalable SDM method.

The desirable salt bridges in amylases: Distribution, configuration and location

The α-amylases are the most widely used industrial enzymes, and are particularly useful as liquifying enzymes in industrial processes based upon starch. Since starch liquefication is carried out at evaluated temperatures, typically above 60 °C, there is substantial demand for thermostable α -amylases. Most naturally occurring α -amylases exhibit moderate thermostability, so substantial effort has been invested in attempts to increase their thermostability. One structural feature that has the potential to increase protein thermostability is the introduction of salt bridges. However, not every salt bridge contributes to protein thermostability. The salt bridges in amylases have their characteristics in terms of distribution, configuration and location. The summary of these features helps to introduce new salt bridges based on the characteristics. This review focuses on salt bridges of α-amylases, both naturally present and introduced using mutagenesis. Its aim is to provide a bird's eye view of distribution, configuration, location of desirable salt bridges.

A thermostable Fe/Mn SOD of Geobacillus sp. PCH100 isolated from glacial soil of Indian trans-Himalaya exhibits activity in the presence of common inhibitors

Superoxide dismutases are the enzymes involved in dismutation of superoxide radicals into oxygen and hydrogen peroxide. The present work reports a thermostable Fe/Mn SOD of Geobacillus sp. strain PCH100 (GsSOD) isolated from glacial soil. Purified recombinant GsSOD is a dimeric protein of ~57 kDa that exhibited highest activity at a temperature of 10 °C and pH of 7.8. Maximum enzyme velocity and Michaelis constant of the GsSOD were 1098.90 units/mg and 0.62 μM, respectively. At 80 °C, thermal inactivation rate constant and half-life of GsSOD were 3.33 × 10^-3 min^-1 and 208 min, respectively. Interestingly, GsSOD tolerated a temperature of 100 °C and 130 °C up to 15 min and 5 min, respectively. Circular dichroism and differential scanning calorimetry confirmed thermostable nature of GsSOD. Apoenzyme of GsSOD regained enzymatic activity in the presence of Fe²⁺ and Mn²⁺ as metal ion cofactors. GsSOD was stable under varying concentrations of chemicals, namely ethylenediaminetetraacetic acid, potassium cyanide, hydrogen peroxide, chloroform-ethanol, 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate, Tween-20, Triton X-100, urea, and guanidine hydrochloride. The enzyme exhibited >70% activity in presence of 10 mM metal ions. Owing to its thermostable nature and resistance to chemical inhibitors, GsSOD is a potential enzyme for industrial applications.