Kinetic study of the thermal denaturation of a hyperthermostable extracellular α-amylase from Pyrococcus furiosus

Mechanism and kinetic model of microalgal enzymatic hydrolysis for prospective bioethanol conversion

Tetraselmis chuii is a potential microalgae that is in consideration for producing bioethanol owing to its large content of carbohydrates. The glucose production from T. chuii through an enzymatic process with cellulase and xylanase (pretreatment process) and α-amylase and glucoamylase (saccharification process) was studied. The mechanism of the enzymatic process was developed and the kinetic models were then evaluated. For the pretreatment process, enzymes with 30% concentration reacted at 30 °C for 40 min resulted in 35.9% glucose yield. For the saccharification process, the highest glucose yield of 90.03% was obtained using simultaneous α-amylase (0.0006%) and glucoamylase (0.01%) enzymes at 55 °C and for 40 min. The kinetic models fitted well with the experimental data. The model also revealed that the saccharification process performed better than the pretreatment process with a higher kinetic constant and lower activation energy. The proposed kinetic model plays an important role in implementing processes at a larger scale.

Structure-Function Relationships in Temperature Effects on Bacterial Luciferases: Nothing Is Perfect

The evaluation of temperature effects on the structure and function of enzymes is necessary to understand the mechanisms underlying their adaptation to a constantly changing environment. In the current study, we investigated the influence of temperature variation on the activity, structural dynamics, thermal inactivation and denaturation of Photobacterium leiognathi and Vibrio harveyi luciferases belonging to different subfamilies, as well as the role of sucrose in maintaining the enzymes functioning and stability. We used the stopped-flow technique, differential scanning calorimetry and molecular dynamics to study the activity, inactivation rate, denaturation and structural features of the enzymes under various temperatures. It was found that P. leiognathi luciferase resembles the properties of cold-adapted enzymes with high activity in a narrow temperature range and slightly lower thermal stability than V. harveyi luciferase, which is less active, but more thermostable. Differences in activity at the studied temperatures can be associated with the peculiarities of the mobile loop conformational changes. The presence of sucrose does not provide an advantage in activity but increases the stability of the enzymes. Differential scanning calorimetry experiments showed that luciferases probably follow different denaturation schemes.

Optimisation of Xylanase–Pectinase Cocktail Production with Bacillus amyloliquefaciens ADI2 Using a Low-Cost Substrate via Statistical Strategy

An effective statistical tool for increasing and boosting the production of xylanase and pectinase by Bacillus amyloliquefaciens ADI2 during submerged fermentation (SmF) appears to be the response of surface methodology (RSM) using the central composite design (CCD). Optimum production was achieved under fermentation conditions of a temperature of 28 °C, pH of 8.38, inoculum size of 4% (w/v) and agitation speed of 94 rpm for 48 h. The experimental responses demonstrated a near agreement with the expected responses under optimum conditions of independent variables, suggesting the model’s validity. The optimised CCD model had a 1.34-fold, 159 ± 6 U/mL greater xylanase and 5.96-fold, 205 ± 9 U/mL greater pectinase production than the one factor at a time (OFAT) approach. The production of concurrent enzymes of xylanase–pectinase resulted in a ratio of 1:1.3.

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.

The ancient koji mold (Aspergillus oryzae) as a modern biotechnological tool

Aspergillus oryzae (A. oryzae) is a filamentous micro-fungus that is used from centuries in fermentation of different foods in many countries all over the world. This valuable fungus is also a rich source of many bioactive secondary metabolites. Moreover, A. oryzae has a prestigious secretory system that allows it to secrete high concentrations of proteins into its culturing medium, which support its use as biotechnological tool in veterinary, food, pharmaceutical, and industrial fields. This review aims to highlight the significance of this valuable fungus in food industry, showing its generosity in production of nutritional and bioactive metabolites that enrich food fermented by it. Also, using A. oryzae as a biotechnological tool in the field of enzymes production was described. Furthermore, domestication, functional genomics, and contributions of A. oryzae in functional production of human pharmaceutical proteins were presented. Finally, future prospects in order to get more benefits from A. oryzae were discussed.

Aspartic protease-pepstatin A interactions: Structural insights on the thermal inactivation mechanism

Aspartic proteases are the targets for structure-based drug design for their role in physiological processes and pharmaceutical applications. Structural insights into the thermal inactivation mechanism of an aspartic protease in presence and absence of bound pepstatin A have been obtained by kinetics of thermal inactivation, CD, fluorescence spectroscopy and molecular dynamic simulations. The irreversible thermal inactivation of the aspartic protease comprised of loss of tertiary and secondary structures succeeded by the loss of activity, autolysis and aggregation The enthalpy and entropy of thermal inactivation of the enzyme in presence of pepstatin A increased from 81.2 to 148.5 kcal mol^-1, and from 179 to 359 kcal mol^-1 K^-1 respectively. Pepstatin A shifted the mid-point of thermal inactivation of the protease from 58 °C to 77 °C. The association constant (K) for pepstatin A with aspartic protease was 2.5 ± 0.3 × 10 ⁵ M^-1 and ΔG^o value was -8.3 kcal mol^-1. Molecular dynamic simulation studies were able to delineate the role of pepstatin A in stabilizing backbone conformation and side chain interactions. In the Cα-backbone, the short helical segments and the conserved glycines were part of the most unstable segments of the protein. Understanding the mechanism of thermal inactivation has the potential to develop re-engineered thermostable proteases.

Enhanced Production of Soluble Pyrococcus furiosus α-Amylase in Bacillus subtilis through Chaperone Co-Expression, Heat Treatment and Fermentation Optimization

Pyrococcus furiosus α-amylase can hydrolyze α-1,4 linkages in starch and related carbohydrates under hyperthermophilic condition (~ 100°C), showing great potential in a wide range of industrial applications, while its relatively low productivity from heterologous hosts has limited the industrial applications. Bacillus subtilis, a gram-positive bacterium, has been widely used in industrial production for its non-pathogenic and powerful secretory characteristics. This study was conducted to increase production of P. furiosus α-amylase in B. subtilis through three strategies. Initial experiments showed that co-expression of P. furiosus molecular chaperone peptidyl-prolyl cis-trans isomerase through genomic integration mode, using a CRISPR/Cas9 system, increased soluble amylase production. Therefore, considering that native P. furiosus α-amylase is produced within a hyperthermophilic environment and is highly thermostable, heat treatment of intact culture at 90°C for 15 min was performed, thereby greatly increasing soluble amylase production. After optimization of the culture conditions (nitrogen source, carbon source, metal ion, temperature and pH), experiments in a 3-L fermenter yielded a soluble activity of 3,806.7 U/ml, which was 3.3- and 28.2-fold those of a control without heat treatment (1,155.1 U/ml) and an empty expression vector control (135.1 U/ml), respectively. This represents the highest P. furiosus α-amylase production reported to date and should promote innovation in the starch liquefaction process and related industrial productions. Meanwhile, heat treatment, which may promote folding of aggregated P. furiosus α-amylase into a soluble, active form through the transfer of kinetic energy, may be of general benefit when producing proteins from thermophilic archaea.

Identification and characterization of thermophilic amylase producing bacterial isolates from the brick kiln soil

The present experiment was designed to isolate bacterial strains from the brick kiln soil and to check the activity and enzyme kinetics of amylase from these isolates. The bacterial colonies were isolated from soil samples through the serial dilution method. The bacterial isolates were identified through morphological, electron microscopic and molecular analysis. The 16S ribosomal RNA sequences of the isolates IR-1, IR-2, IR-3, IR-8, and IR-9 showed high similarities with Bacillus tequilensis, Bacillus paramycoides, Proteus alimentorum, Bacillus wiedmannii, and Pseudomonas aeruginosa, respectively. All of the bacterial isolates showed a positive catalase activity except IR-9. Furthermore, the isolates showed variable antagonistic effects against different bacterial pathogens. All of the strains produced indole acetic acid (IAA), and the concentrations increased in the presence of tryptophan application. The isolates showed the amylase enzyme activity and maximum activity of isolates was achieved in 4% starch concentration. The IR-9 isolate showed the highest amylase activity of 5.9 U/ml. The V max values of the extracellular amylase from different bacterial isolates ranged between 12.90 and 50.00 IU ml-1. The lowest K m value of 6.33 mg starch was recorded for IR-8 and the maximum K cat value of 2.50 min-1 was observed for IR-3. The amylase activity of the isolates was significantly affected by a range of different incubation time, temperature, and pH values. Further tests are required before the potential utilization of these isolates for amylase production, and in the biopesticide and biofertilizer applications.

A versatile tool in controlling aggregation and Ag nanoparticles assisted in vitro folding of thermally denatured zDHFR

Background

Proteins have tendency to form inactive aggregates at higher temperatures due to thermal instability. Maintenance of thermal stability is essential to gain the protein in sufficient quantity and biologically active form during their commercial production.

Methods

BL21-DE3 Rosetta E. coli cells which contains plasmid pET43.1a vector was used for producing zDHFR protein commercially. The purification of N-terminal Histidine tagged zDHFR was performed by Immobilized Metal Ion chromatography (IMAC). Investigations were performed in existence and non existence of Silver nanoparticles (AgNPs). The inactivation kinetics of zDHFR in existence and non existence of AgNPs were monitored over a range of 40–80 °C as monitored by UV–Visible absorption spectroscopy.

Results

The protein completely lost its activity at 55 °C. Kinetics of inactivated zDHFR follows first order model in presence and absence of AgNPs. Decrease in rate constant (k) values at respective temperatures depicts that AgNPs contribute in the thermostability of the protein. AgNPs also assists in regaining the activity of zDHFR protein.

Conclusions

AgNPs helps in maintaining thermostability and reducing the aggregation propensity of zDHFR protein.

General significance

Result explains that AgNPs are recommended as a valuable system in enhancing the industrial production of biologically active zDHFR protein which is an important component in folate cycle and essential for survival of cells and prevents the protein from being aggregated.

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Recombinant proteins have the ability to get aggregated during their commercial production due to factors like temperature, pH, etc. Aggregation of protein can be prevented with the help of AgNPs by increasing their thermal stability.

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AgNPs maintain the stability of thermally-denatured zDHFR under high temperatures which is confirmed by kinetic and thermodynamic parameters.

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AgNPs also assists in refolding of the thermally-denatured protein which proves that AgNPs plays a supportive role in maintaining the stability of the protein and thus preventing it from being aggregated.

Stability and refolding of Dihydrofolate reductase enhances with nano-conjugation

The nano-conjugation of proteins is an active area of research due to potential biomedical and nanotechnological applications. Many protein-nanoconjugates were designed for various applications, such as drug delivery, molecular imaging, and liquid biopsy etc. However, the challenges remain to ensure protein stability and to retain the conformational state of the protein intact upon nano-conjugation. In this communication we have reported the status of stability and refolding ability of Au-NP conjugated zDHFR protein. The effect of nano-conjugation of zDHFR on the thermal stability and it's refolding from thermally denatured state have been extensively studied. Zebrafish Dihydrofolate reductase (zDHFR) is an essential enzyme which acts as a crucial part in synthesis of purine, thymidylate and various amino acids in cells. We have nano-conjugated zDHFR protein with Au-nanoparticles and studies were conducted for thermally denatured Au-NP conjugated zDHFR and compared with the non-conjugated protein. Refolding experiment of heat denatured Au-NP conjugated zDHFR was carried out to check the status of refolding and the result was compared with the non-conjugated protein. Our observation reveals that nano-conjugation stabilises the zDHFR protein against thermal denaturation. Furthermore, the nano-conjugation promotes refolding process of thermally unfolded DHFR such that the yield of refolding substantially increases.

Random mutagenesis of super Koji (Aspergillus oryzae): improvement in production and thermal stability of α-amylases for maltose syrup production

Background

Alpha-amylases hydrolyze 1,4 α-glycosidic bonds of starch and produce malto-oligosaccharides. It is an important enzyme generally applied in textile, food and brewing industries. Enhancement in thermal stability and productivity of enzymes are the two most sought after properties for industrial use. The Aspergillus oryzae (Koji) has Generally Recognized as Safe (GRAS) status and safe for use in food industry. Hence, Koji strain’s development for the screening of potent mutants, hyper producer of thermostable α-amylases, with desired attributes is the need of the time.

Results

A process has been developed to improve super Koji (A. oryzae cmc1) strain through γ-rays treatment. The doses i.e. 0.60, 0.80, 1.00, 1.20 & 1.40 KGy gave more than 3.0 log kill. Initially, 52 Koji mutants resistant to 1% (w/v) Triton X-100 were selected. 2^nd screening was based on α-amylases hyper production and 23 mutants were sorted out by measuring clearing zones index (CI). Afterwards nine potent mutants, resistant to 2-deoxy D-glucose, were screened based on CI. These were further analyzed for thermal stability and productivity of α-amylase under submerged conditions. The mutants’ M-80(10), M-100(6) & M-120(5) gave about four fold increases in α-amylases productivity. The half life of M-100(6) α-amylase at 55 °C was 52 min and was highest among the mutants. Liquid Chromatography-Mass Spectrometry (LC-MS) analysis confirmed that mutants did not produce aflatoxins. Field Emission Scanning Electron Microscopy (FESEM) of Koji mycelia depicted that exposure to gamma rays increased rigidity of the mycelium. The potent Koji mutant M-100(6) was grown on soluble starch in 10L fermenter and produced 40.0 IU ml^-1 of α-amylases with specific activity of 2461 IU mg^-1 protein. Growth kinetic parameters were: μ = Specific growth rate= 0.069 h^-1, t_d = Biomass doubling time= 10.0 h, Y_p/x = Product yield coefficient with respect to cell mass = 482 U g^-1; q_p= Specific rate of product formation= 33.29 U g^-1 h^-1.

Conclusion

It was concluded that the developed five step screening process has great potential to generate potent mutants for the hyper production of thermostable enzymes through γ-rays mediated physical mutagenesis. The developed thermostable α-amylases of super Koji mutantM-100(6) has immense potential for application in saccharification process for maltose syrup production. Moreover, the developed five step strain’s development process may be used for the simultaneous improvement in productivity and thermal stability of other microbial enzymes.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1345-y) contains supplementary material, which is available to authorized users.

Kinetics and thermodynamics of the thermal inactivation and chaperone assisted folding of zebrafish dihydrofolate reductase

The maintenance of thermal stability is a major issue in protein engineering as many proteins tend to form inactive aggregates at higher temperatures. Zebrafish DHFR, an essential protein for the survival of cells, shows irreversible thermal unfolding transition. The protein exhibits complete unfolding and loss of activity at 50 °C as monitored by UV-Visible, fluorescence and far UV-CD spectroscopy. The heat induced inactivation of zDHFR follows first-order kinetics and Arrhenius law. The variation in the value of inactivation rate constant, k with increasing temperatures depicts faster inactivation at elevated temperatures. We have attempted to study the chaperoning ability of a shorter variant of GroEL (minichaperone) and compared it with that of conventional GroEL-GroES chaperone system. Both the chaperone system prevented the aggregation and assisted in refolding of zDHFR. The rate of thermal inactivation was significantly retarded in the presence of chaperones which indicate that it enhances the thermal stability of the enzyme. As minichaperone is less complex, and does not require high energy co-factors like ATP, for its function as compared to conventional GroEL-GroES system, it can act as a very good in vitro as well as in vivo chaperone model for monitoring assisted protein folding phenomenon.

[Prediction of protein thermostability from their primary structure: the current state and development factors]

The construction of proteins and peptides with desired properties, including resistance to high temperatures, as well as optimization of their amino acid composition, is an important and complex task, which attracts much attention in various branches of the basic sciences, and also in biomedicine and biotechnology. This raises the question: what method is more relevant for the at the pilot stage of research in order to estimate the influence of the planned amino acid substitutions on the thermostability of the resultant protein construct? In this brief review we have classified existing basic practical and theoretical approaches used in studies and predicting the thermal stability of native and recombinant polypeptides. Particular attention has been paid to the predictive potential of statistical methods for studying the thermodynamic parameters of the primary protein structure and prospects of their use.

Biochemical features and kinetic properties of α-amylases from marine organisms

Marine organisms have the ability of producing enzymes with unique properties compared to those of the same enzymes from terrestrial organisms. α-Amylases are among the most important extracellular enzymes found in various groups of organisms such as plants, animals and microorganisms. They play important roles in their carbohydrates metabolism of each organism. Microbial production of α-amylases is more effective than other sources of the enzyme. Many microorganisms are known to produce α-amylase including bacteria, yeasts, fungi and actinomycetes. However, enzymes from fungal and bacterial sources have dominated applications in industrial sectors. This review deals with what is known about the kinetics, biochemical properties and applications of these enzymes that have only been found in them and not in other α-amylases, and discussing their mechanistic and regulatory implications.

Environment-induced conformational and functional changes of L-2-haloacid dehalogenase

2-Haloacid dehalogenases have been highly studied due to their potential applications in chemical industries and bioremediation. Although biochemical and structural characterizations of the enzyme have been detailed, no information was available regarding environmental effects on the structure-function relationship. Here, circular dichroism spectroscopy (CD) was used to investigate the correlation between changes on the conformation and the function of l-2-haloacid dehalogenase (HadL AJ1) from the Pseudomonas putida induced by the environmental factors. Decreased α-helix and increased β-sheet contents were observed in the structure of HadL AJ1 along with activity losses caused by pH, temperature and inhibitors. Regardless of which factor above-mentioned existed, more than 65.0% of HadL AJ1 activity could be remained if its α-helix content was over 12.0%. The maintenance of α-helical structure in HadL AJ1 was indispensable to its catalysis, while β-sheet increase restricts its activity. This study revealed the variation of enzymatic activity due to environmental conditions resulting in structural changes monitored by CD, which contributed to rational modification and was instructive for predicting changes of the enzymatic activity during application.

Characterization of a thermostable and alkali-stable α-amylase from deep-sea bacterium Flammeovirga pacifica

A thermostable α-amylase (designated as Amy16) has been previously identified in Flammeovirga pacifica isolated from deep-sea sediments. The DNA sequence of Amy16 exhibited no significant similarity with those of any known protein, including the glycoside hydrolases. Amino acid sequence analysis revealed that Amy16 belonged to GH13 family and possessed a conserved DXEXD motif, which was essential for its hydrolysis activities. The recombinant Amy16 purified with Ni(+) affinity column after its heterologous expression in Escherichia coli cells was most active at 50 °C and retained more than 81% of its initial activity after incubation at 60 °C for 20 min. The optimal pH for Amy16 was determined to be 6.5, and a good tolerance to alkaline environment was observed. Low concentration of Mg(2+), Sr(2+), Na(+) and K(+) slightly increased the activity of Amy16. Results of thin layer chromatography experiments revealed that Amy16 was able to hydrolyse starch into maltose in a time-dependent manner, suggesting that Amy16 is a liquid-type endoenzyme with starch hydrolysis activities. Therefore, our study presented thermostable and alkali-stable Amy16, which may be suitable for use as an additive in detergents.

Marine extremophiles: a source of hydrolases for biotechnological applications

The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.