Improvement of cold adaptation of Bacillus alcalophilus alkaline protease by directed evolution

Exploring the molecular mechanism of cold-adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network

Psychrophilic proteases have attracted enormous attention in past decades, due to their high catalytic activity at low temperatures in a wide range of industrial processes, especially in the detergent and leather industries. Among them, H5 is an alkaline protease mutant, which featuring psychrophilic-like behavior, but the reasons that H5 with higher activity at low temperatures are still poorly understood. Herein, the molecular dynamics (MD) simulations combined with residue interaction network (RIN) were utilized to investigate the mechanisms of the cold-adaption of mutant H5. The results demonstrated that two loops involved in the substrate binding G100-S104 and S125-S129 in H5 had higher mobility, and the distance enlargement between the two loops modulated the substrate's accessibility compared with wild type counterpart. Besides, H5 enhanced conformational flexibility by weakening salt bridges and increasing interaction with the solvent. In particular, the absence of Lys251-Asp197-Arg247 salt bridge network may contribute to the structural mobility. Based on the free energy landscape and molecular mechanics Poisson-Boltzmann surface area of the wild type and H5, it was elucidated that H5 possessed a large population of interconvertible conformations, resulting in the weaker substrate binding free energy. The calculated RIN topology parameters such as the average degree, average cluster coefficient, and average path length further verified that the mutant H5 attenuated residue-to-residue interactions. The investigation of the mechanisms by which how the residue mutation affects the stability and activity of enzymes provides a theoretical basis for the development of cold-adapted protease.

Bioengineered Enzymes and Precision Fermentation in the Food Industry

Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.

The last 25 years of research on bioflocculants for kaolin flocculation with recent trends and technical challenges for the future

The generation of kaolin-containing wastewater is an inevitable consequence in a number of industries including mining, wastewater treatment, and bitumen processing. In some cases, the production of kaolin tailings waste during the production of bitumen or phosphate is as high as 3 times greater than the actual produced product. The existing inventory of nearly five billion barrels of oil sands tailings alone represents a massive storage and reclamation challenge, as well as a significant economic and environmental liability. Current reclamation options like inorganic coagulants and organic synthetic polymers may settle kaolin effectively, but may themselves pose an additional environmental hazard. Bioflocculants are an emerging alternative, given the inherent safety and biodegradability of their bio-based compositions. This review summarizes the different research attempts towards a better bioflocculant of kaolin, with a focus on the bioflocculant source, composition, and effective flocculating conditions. Bacillus bacteria were the most prevalent single species for bioflocculant production, with wastewater also hosting a large number of bioflocculant-producing microorganisms while serving as an inexpensive nutrient. Effective kaolin flocculation could be obtained over a broad range of pH values (1-12) and temperatures (5-95°C). Uronic acid and glutamic acid were predominant sugars and amino acids, respectively, in a number of effective bioflocculants, potentially due to their structural and charge similarities to effective synthetic polymers like polyacrylamide. Overall, these results demonstrate that bioflocculants can be produced from a wide range of microorganisms, can be composed of polysaccharides, protein or glycoproteins and can serve as effective treatment options for kaolin. In some cases, the next obstacle to their wide-spread application is scaling to industrially relevant volumes and their deployment strategies.

Novel Detection Method for Evaluating the Activity of an Alkaline Serine Protease from Bacillus clausii

Until now, the detection methods for serine proteases have been quite time-consuming or cannot indicate the "real" protease activity. Here, a rapid and simple method for determining the "real" activity of serine proteases toward AAPX (a kind of mixed polypeptide substrates, with X representing 20 standard amino acids) was developed. This AAPX method has high reliability, sensitivity, and repeatability and can be used for detecting the serine protease activity spectrophotometrically. Additionally, the site-directed saturation mutagenesis library of alkaline serine protease PRO (BcPRO) from Bacillus clausii was screened with this AAPX method. Three beneficial mutants S99R, S99H, and S99W were identified, and S99W displayed the highest activity. In comparison to wild-type BcPRO, S99W exhibited enhanced catalytic performance toward eight AAPX monomers, and the molecular dynamics simulation revealed the mechanism responsible for its improved activity toward AAPM. Consequently, this work provides an efficient method for detecting, characterizing, mining, and high-throughput screening of serine proteases.

Production of subtilisin proteases in bacteria and yeast

In this review, we discuss the progress in the study and modification of subtilisin proteases. Despite longstanding applications of microbial proteases and a large number of research papers, the search for new protease genes, the construction of producer strains, and the development of methods for their practical application are still relevant and important, judging by the number of citations of the research articles on proteases and their microbial producers. This enzyme class represents the largest share of the industrial production of proteins worldwide. This situation can explain the high level of interest in these enzymes and points to the high importance of designing domestic technologies for their manufacture. The review covers subtilisin classification, the history of their discovery, and subsequent research on the optimization of their properties. An overview of the classes of subtilisin proteases and related enzymes is provided too. There is a discussion about the problems with the search for (and selection of) subtilases from natural strains of various microorganisms, approaches to (and specifics of) their modification, as well as the relevant genetic engineering techniques. Details are provided on the methods for expression optimization of industrial subtilases of various strains: the details of the most important parameters of cultivation, i.e., composition of the media, culture duration, and the influence of temperature and pH. Also presented are the results of the latest studies on cultivation techniques: submerged and solid-state fermentation. From the literature data reviewed, we can conclude that native enzymes (i.e., those obtained from natural sources) currently hardly have any practical applications because of the decisive advantages of the enzymes modified by genetic engineering and having better properties: e.g., thermal stability, general resistance to detergents and specific resistance to various oxidants, high activity in various temperature ranges, independence from metal ions, and stability in the absence of calcium. The vast majority of subtilisin proteases are expressed in producer strains belonging to different species of the genus Bacillus. Meanwhile, there is an effort to adapt the expression of these enzymes to other microbes, in particular species of the yeast Pichia pastoris.

Isolation and characterization of a new cold-active protease from psychrotrophic bacteria of Western Himalayan glacial soil

As an approach to the exploration of cold-active enzymes, in this study, we isolated a cold-active protease produced by psychrotrophic bacteria from glacial soils of Thajwas Glacier, Himalayas. The isolated strain BO1, identified as Bacillus pumilus, grew well within a temperature range of 4-30 °C. After its qualitative and quantitative screening, the cold-active protease (Apr-BO1) was purified. The Apr-BO1 had a molecular mass of 38 kDa and showed maximum (37.02 U/mg) specific activity at 20 °C, with casein as substrate. It was stable and active between the temperature range of 5-35 °C and pH 6.0-12.0, with an optimum temperature of 20 °C at pH 9.0. The Apr-BO1 had low K_m value of 1.0 mg/ml and V_max 10.0 µmol/ml/min. Moreover, it displayed better tolerance to organic solvents, surfactants, metal ions and reducing agents than most alkaline proteases. The results exhibited that it effectively removed the stains even in a cold wash and could be considered a decent detergent additive. Furthermore, through protein modelling, the structure of this protease was generated from template, subtilisin E of Bacillus subtilis (PDB ID: 3WHI), and different methods checked its quality. For the first time, this study reported the protein sequence for psychrotrophic Apr-BO1 and brought forth its novelty among other cold-active proteases.

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.

Molecular biology interventions for activity improvement and production of industrial enzymes

Metagenomics and directed evolution technology have brought a revolution in search of novel enzymes from extreme environment and improvement of existing enzymes and tuning them towards certain desired properties. Using advanced tools of molecular biology i.e. next generation sequencing, site directed mutagenesis, fusion protein, surface display, etc. now researchers can engineer enzymes for improved activity, stability, and substrate specificity to meet the industrial demand. Although many enzymatic processes have been developed up to industrial scale, still there is a need to overcome limitations of maintaining activity during the catalytic process. In this article recent developments in enzymes industrial applications and advancements in metabolic engineering approaches to improve enzymes efficacy and production are reviewed.

Directed evolution of a β-mannanase from Rhizomucor miehei to improve catalytic activity in acidic and thermophilic conditions

BACKGROUND

β-Mannanase randomly cleaves the β-1,4-linked mannan backbone of hemicellulose, which plays the most important role in the enzymatic degradation of mannan. Although the industrial applications of β-mannanase have tremendously expanded in recent years, the wild-type β-mannanases are still defective for some industries. The glycoside hydrolase (GH) family 5 β-mannanase (RmMan5A) from Rhizomucor miehei shows many outstanding properties, such as high specific activity and hydrolysis property. However, owing to the low catalytic activity in acidic and thermophilic conditions, the application of RmMan5A to the biorefinery of mannan biomasses is severely limited.

RESULTS

To overcome the limitation, RmMan5A was successfully engineered by directed evolution. Through two rounds of screening, a mutated β-mannanase (mRmMan5A) with high catalytic activity in acidic and thermophilic conditions was obtained, and then characterized. The mutant displayed maximal activity at pH 4.5 and 65 °C, corresponding to acidic shift of 2.5 units in optimal pH and increase by 10 °C in optimal temperature. The catalytic efficiencies (k_cat/K_m) of mRmMan5A towards many mannan substrates were enhanced more than threefold in acidic and thermophilic conditions. Meanwhile, the high specific activity and excellent hydrolysis property of RmMan5A were inherited by the mutant mRmMan5A after directed evolution. According to the result of sequence analysis, three amino acid residues were substituted in mRmMan5A, namely Tyr233His, Lys264Met, and Asn343Ser. To identify the function of each substitution, four site-directed mutations (Tyr233His, Lys264Met, Asn343Ser, and Tyr233His/Lys264Met) were subsequently generated, and the substitutions at Tyr233 and Lys264 were found to be the main reason for the changes of mRmMan5A.

CONCLUSIONS

Through directed evolution of RmMan5A, two key amino acid residues that controlled its catalytic efficiency under acidic and thermophilic conditions were identified. Information about the structure-function relationship of GH family 5 β-mannanase was acquired, which could be used for modifying β-mannanases to enhance the feasibility in industrial application, especially in biorefinery process. This is the first report on a β-mannanase from zygomycete engineered by directed evolution.

Current Technological Improvements in Enzymes toward Their Biotechnological Applications

Enzymes from extremophiles are creating interest among researchers due to their unique properties and the enormous power of catalysis at extreme conditions. Since community demands are getting more intensified, therefore, researchers are applying various approaches viz. metagenomics to increase the database of extremophilic species. Furthermore, the innovations are being made in the naturally occurring enzymes utilizing various tools of recombinant DNA technology and protein engineering, which allows redesigning of the enzymes for its better fitment into the process. In this review, we discuss the biochemical constraints of psychrophiles during survival at the lower temperature. We summarize the current knowledge about the sources of such enzymes and their in vitro modification through mutagenesis to explore their biotechnological potential. Finally, we recap the microbial cell surface display to enhance the efficiency of the process in cost effective way.