Multifactorial level of extremostability of proteins: can they be exploited for protein engineering?

Computer-Aided Reconstruction and Application of Bacillus halodurans S7 Xylanase with Heat and Alkali Resistance

β-1,4-Endoxylanase is the most critical hydrolase for xylan degradation during lignocellulosic biomass utilization. However, its poor stability and activity in hot and alkaline environments hinder its widespread application. In this study, BhS7Xyl from Bacillus halodurans S7 was improved using a computer-aided design through isothermal compressibility (βT) perturbation engineering and by combining three thermostability prediction algorithms (ICPE-TPA). The best variant with remarkable improvement in specific activity, heat resistance (70 °C), and alkaline resistance (both pH 9.0 and 70 °C), R69F/E137M/E145L, exhibited a 4.9-fold increase by wild-type in specific activity (1368.6 U/mg), a 39.4-fold increase in temperature half-life (458.1 min), and a 57.6-fold increase in pH half-life (383.1 min). Furthermore, R69F/E137M/E145L was applied to the hydrolysis of agricultural waste (corncob and hardwood pulp) to efficiently obtain a higher yield of high-value xylooligosaccharides. Overall, the ICPE-TPA strategy has the potential to improve the functional performance of enzymes under extreme conditions for the high-value utilization of lignocellulosic biomass.

Thermostability improvement of sucrose isomerase PalI NX-5: a comprehensive strategy

OBJECTIVE

To increase the thermal stability of sucrose isomerase from Erwinia rhapontici NX-5, we designed a comprehensive strategy that combines different thermostabilizing elements.

RESULTS

We identified 19 high B value amino acid residues for site-directed mutagenesis. An in silico evaluation of the influence of post-translational modifications on the thermostability was also carried out. The sucrose isomerase variants were expressed in Pichia pastoris X33. Thus, for the first time, we report the expression and characterization of glycosylated sucrose isomerases. The designed mutants K174Q, L202E and K174Q/L202E, showed an increase in their optimal temperature of 5 °C, while their half-lives increased 2.21, 1.73 and 2.89 times, respectively. The mutants showed an increase in activity of 20.3% up to 25.3%. The Km values for the K174Q, L202E, and K174Q/L202E mutants decreased by 5.1%, 7.9%, and 9.4%, respectively; furthermore, the catalytic efficiency increased by up to 16%.

CONCLUSIONS

With the comprehensive strategy followed, we successfully obtain engineered mutants more suitable for industrial applications than their counterparts: native (this research) and wild-type from E. rhapontici NX-5, without compromising the catalytic activity of the molecule.

Analyzing structural features of proteins from deep-sea organisms

Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.

Structural and functional adaptation in extremophilic microbial α-amylases

Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.

Kinetic characterization and thermostability of C. elegans cytoplasmic and mitochondrial malate dehydrogenases

Malate dehydrogenase (MDH) catalyzes the conversion of NAD⁺ and malate to NADH and oxaloacetate in the citric acid cycle. Eukaryotes have one MDH isozyme that is imported into the mitochondria and one in the cytoplasm. We overexpressed and purified Caenorhabditis elegans cytoplasmic MDH-1 and mitochondrial MDH-2 in E. coli. Our goal was to compare the kinetic and structural properties of these enzymes because C. elegans can survive adverse environmental conditions, such as lack of food and elevated temperatures. In steady-state enzyme kinetics assays, we measured K_M values for oxaloacetate of 54 and 52 μM and K_M values for NADH of 61 and 107 μM for MDH-1 and MDH-2, respectively. We partially purified endogenous MDH-1 and MDH-2 from a mixed population of worms and separated them using anion exchange chromatography. Both endogenous enzymes had a K_M for oxaloacetate similar to that of the corresponding recombinant enzyme. Recombinant MDH-1 and MDH-2 had maximum activity at 40 °C and 35 °C, respectively. In a thermotolerance assay, MDH-1 was much more thermostable than MDH-2. Protein homology modeling predicted that MDH-1 had more intersubunit salt-bridges than mammalian MDH1 enzymes, and these ionic interactions may contribute to its thermostability. In contrast, the MDH-2 homology model predicted fewer intersubunit ionic interactions compared to mammalian MDH2 enzymes. These results suggest that the increased stability of MDH-1 may facilitate its ability to remain active in adverse environmental conditions. In contrast, MDH-2 may use other strategies, such as protein binding partners, to function under similar conditions.

Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity

Endoxylanases active under extreme conditions of temperature and alkalinity can replace the use of highly pollutant chemicals in the pulp and paper industry. Searching for enzymes with these properties, we carried out a comprehensive bioinformatics study of the GH10 family. The phylogenetic analysis allowed the construction of a radial cladogram in which protein sequences putatively ascribed as thermophilic and alkaliphilic appeared grouped in a well-defined region of the cladogram, designated TAK Cluster. One among five TAK sequences selected for experimental analysis (Xyn11) showed extraordinary xylanolytic activity under simultaneous conditions of high temperature (90 °C) and alkalinity (pH 10.5). Addition of a carbohydrate binding domain (CBM2) at the C-terminus of the protein sequence further improved the activity of the enzyme at high pH. Xyn11 structure, which has been solved at 1.8 Å resolution by X-ray crystallography, reveals an unusually high number of hydrophobic, ionic and hydrogen bond atomic interactions that could account for the enzyme’s extremophilic nature.

Computational design of noncanonical amino acid-based thioether staples at N/C-terminal domains of multi-modular pullulanase for thermostabilization in enzyme catalysis

Enzyme thermostabilization is considered a critical and often obligatory step in biosynthesis, because thermostability is a significant property of enzymes that can be used to evaluate their feasibility for industrial applications. However, conventional strategies for thermostabilizing enzymes generally introduce non-covalent interactions and/or natural covalent bonds caused by natural amino acid substitutions, and the trade-off between the activity and stability of enzymes remains a challenge. Here, we developed a computationally guided strategy for constructing thioether staples by incorporating noncanonical amino acid (ncAA) into the more flexible N/C-terminal domains of the multi-modular pullulanase from Bacillus thermoleovorans (BtPul) to enhance its thermostability. First, potential thioether staples located in the N/C-terminal domains of BtPul were predicted using RosettaMatch. Next, eight variants involving stable thioether staples were precisely predicted using FoldX and Rosetta ddg_monomer. Six positive variants were obtained, of which T73(O2beY)-171C had a 157% longer half-life at 70 °C and an increase of 7.0 °C in T m, when compared with the wild-type (WT). T73(O2beY)-171C/T126F/A72R exhibited an even more improved thermostability, with a 211% increase in half-life at 70 °C and a 44% enhancement in enzyme activity compared with the WT, which was attributed to further optimization of the local interaction network. This work introduces and validates an efficient strategy for enhancing the thermostability and activity of multi-modular enzymes.

Extracellular Production, Characterization, and Engineering of a Polyextremotolerant Subtilisin-Like Protease From Feather-Degrading Thermoactinomyces vulgaris Strain CDF

Here, the gene encoding a subtilisin-like protease (protease Als) was cloned from Thermoactinomyces vulgaris strain CDF and expressed in Escherichia coli. The recombinant enzyme was released into the culture medium of E. coli as a mature form (mAls). Purified mAls displayed optimal activity at 60–70°C and pH 10.0 using azo-casein as the substrate, and showed a half-life of 13.8 h at 70°C. Moreover, the activity of thermostable mAls was comparable to or higher than those of mesophilic subtilisin Carlsberg and proteinase K at low temperatures (10–30°C). Protease Als was also stable in several organic solvents and showed high compatibility with commercial laundry detergents. Notably, mAls exhibited approximately 100% of its activity at 3 M NaCl, and showed enhanced thermostability with the increase of NaCl concentration up to 3 M. Protease Als possesses an excess of solvent-accessible acidic amino acid residues, which may account for the high halotolerance of the enzyme. Compared with homologous protease C2 from the same strain, protease Als exhibits substantially lower activity toward insoluble keratin substrates but efficiently hydrolyzes soluble keratin released from chicken feathers. Additionally, direct substitution of the substrate-binding site of protease Als with that of protease C2 improves its activity against insoluble keratin substrates. By virtue of its polyextremotolerant attribute and kerationolytic capacity, protease Als may find broad applications in various industries such as laundry detergents, food processing, non-aqueous biocatalysis, and feather processing.

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.

On the Thermal Stability of O6-Methylguanine-DNA Methyltransferase from Archaeon Pyrococcus kodakaraensis by Molecular Dynamics Simulations

We have employed molecular dynamics simulations to analyze the thermal stability of the O⁶-methylguanine-DNA methyltransferase (MGMT) protein, both hyperthermophilic archaeon Pyrococcus kodakaraensis (Pk-MGMT) and its mesophilic homologue pair, obtained from enterobacterium Escherichia coli (AdaC). This theoretical study was done at three different temperatures: 302, 371, and 450 K. The molecular dynamics has been performed in explicit aqueous solvent during a period of time of 95 ns, including periodic boundary conditions and constant pressure. The same procedure has been used for both proteins, and each simulation has been carried out by triplicate. Hence, we performed 18 simulations. In this way, we have done different analyses to explore the factors that may affect the thermal stability of Pk-MGMT. The structural behavior was analyzed using indicators such as root-mean-square deviation, radius of gyration, solvent-accessible surface area, hydrogen bonds, native contacts, secondary structure, and salt bridge formation. The results showed that when the temperature increases, the global atomic fluctuations increase too, which suggests that both proteins lose thermal stability, but as expected, this fact is highlighted in AdaC. Moreover, the contacts of the native state in AdaC are considerably lower than those found in Pk-MGMT at 450 K. Also, the structural studies showed that conserved and nonconserved salt bridges kept close contacts with the Pk-MGMT protein at high temperatures. These interaction types act as molecular staples and are mainly responsible to provide thermostability to the hyperthermophilic protein.

Unique Features of a New Baeyer–Villiger Monooxygenase from a Halophilic Archaeon

Type I Baeyer–Villiger monooxygenases (BVMOs) are flavin-dependent monooxygenases that catalyze the oxidation of ketones to esters or lactones, a reaction otherwise performed in chemical processes by employing hazardous and toxic peracids. Even though various BVMOs are extensively studied for their promising role in industrial biotechnology, there is still a demand for enzymes that are able to retain activity at high saline concentrations. To this aim, and based on comparative in silico analyses, we cloned HtBVMO from the extremely halophilic archaeon Haloterrigena turkmenica DSM 5511. When expressed in standard mesophilic cell factories, proteins adapted to hypersaline environments often behave similarly to intrinsically disordered polypeptides. Nevertheless, we managed to express HtBVMO in Escherichia coli and could purify it as active enzyme. The enzyme was characterized in terms of its salt-dependent activity and resistance to some water–organic-solvent mixtures. Although HtBVMO does not seem suitable for industrial applications, it provides a peculiar example of an alkalophilic and halophilic BVMO characterized by an extremely negative charge. Insights into the behavior and structural properties of such salt-requiring may contribute to more efficient strategies for engineering the tuned stability and solubility of existing BVMOs.

Structure and function of the Ts2631 endolysin of Thermus scotoductus phage vB_Tsc2631 with unique N-terminal extension used for peptidoglycan binding

To escape from hosts after completing their life cycle, bacteriophages often use endolysins, which degrade bacterial peptidoglycan. While mesophilic phages have been extensively studied, their thermophilic counterparts are not well characterized. Here, we present a detailed analysis of the structure and function of Ts2631 endolysin from thermophilic phage vB_Tsc2631, which is a zinc-dependent amidase. The active site of Ts2631 consists of His30, Tyr58, His131 and Cys139, which are involved in Zn²⁺ coordination and catalysis. We found that the active site residues are necessary for lysis yet not crucial for peptidoglycan binding. To elucidate residues involved in the enzyme interaction with peptidoglycan, we tested single-residue substitution variants and identified Tyr60 and Lys70 as essential residues. Moreover, substitution of Cys80, abrogating disulfide bridge formation, inactivates Ts2631, as do substitutions of His31, Thr32 and Asn85 residues. The endolysin contains a positively charged N-terminal extension of 20 residues that can protrude from the remainder of the enzyme and is crucial for peptidoglycan binding. We show that the deletion of 20 residues from the N-terminus abolished the bacteriolytic activity of the enzyme. Because Ts2631 exhibits intrinsic antibacterial activity and unusual thermal stability, it is perfectly suited as a scaffold for the development of antimicrobial agents.

Deciphering the rationale behind specific codon usage pattern in extremophiles

Protein stability is affected at different hierarchies – gene, RNA, amino acid sequence and structure. Gene is the first level which contributes via varying codon compositions. Codon selectivity of an organism differs with normal and extremophilic milieu. The present work attempts at detailing the codon usage pattern of six extremophilic classes and their harmony. Homologous gene datasets of thermophile-mesophile, psychrophile-mesophile, thermophile-psychrophile, acidophile-alkaliphile, halophile-nonhalophile and barophile-nonbarophile were analysed for filtering statistically significant attributes. Relative abundance analysis, 1–9 scale ranking, nucleotide compositions, attribute weighting and machine learning algorithms were employed to arrive at findings. AGG in thermophiles and barophiles, CAA in mesophiles and psychrophiles, TGG in acidophiles, GAG in alkaliphiles and GAC in halophiles had highest preference. Preference of GC-rich and G/C-ending codons were observed in halophiles and barophiles whereas, a decreasing trend was reflected in psychrophiles and alkaliphiles. GC-rich codons were found to decrease and G/C-ending codons increased in thermophiles whereas, acidophiles showed equal contents of GC-rich and G/C-ending codons. Codon usage patterns exhibited harmony among different extremophiles and has been detailed. However, the codon attribute preferences and their selectivity of extremophiles varied in comparison to non-extremophiles. The finding can be instrumental in codon optimization application for heterologous expression of extremophilic proteins.