Molecular characterization, catalytic, kinetic and thermodynamic properties of protease produced by a mutant of Bacillus cereus-S6-3

Exploration of urease-aided calcium carbonate mineralization by enzyme analyses of Neobacillus mesonae strain NS-6

Urease containing nickel cofactor is crucial for urea-hydrolytic induced calcium carbonate (CaCO3) precipitation (UICP). However, limited information exists regarding the influence of amino acid residues interacting with nickel ions in its structure on induced CaCO3 mineralization. Herein, RT-qPCR was used to demonstrate that the addition of NiCl2 dramatically upregulated the expression of urease structural gene ureC that was correlated with nickel binding in Neobacillus mesonae strain NS-6. Homology modeling and molecular docking were employed to construct the three-dimensional structure of urease and seek the key residues involved in nickel binding process, and virtual mutation technology was adopted to inform three key residues coordinated with nickel ions and urea, His249, His275, and Asp363. Four metrics, including root mean square deviation values for mutations of those key residues in urease-urea complexes severally and wild-type, were calculated by molecular dynamics simulations when they were mutated into alanine, respectively. Subsequently, the mutations of H249A, H275A, and D363A were characterized using western blotting to reveal a decrease in the relative expression and activity of urease, along with a corresponding reduction in CaCO3 precipitation. Ultimately, the mutations also exhibited that they had lower substrate affinity and catalytic efficiency for urea through enzymatic properties analysis. The findings suggested that those residues played a pivotal role in UICP of strain NS-6, which would expand the theoretical basis for modulating urease activity.IMPORTANCEUrease-producing bacterium is of great importance in diverse application fields, such as environmental remediation, due to its key driving characteristics in catalyzing urea hydrolysis via urea-hydrolytic induced CaCO3 precipitation (UICP). As essential cofactors of urease, nickel ions play a crucial role in regulating urease catalysis and maintaining structural stability. Numerous investigations have emphasized the impact of nickel ions on urease activity in recent years, to our best knowledge, only a few literatures have studied the molecular-level regulation of nickel-ligand residues. This study focused on the highly urease-producing bacterial Neobacillus mesonae NS-6 to explore the effects of specific nickel-ligand residues on the urease-aided CaCO3 mineralization process using molecular simulation predictions and targeted mutation experiments. The aim was to provide a molecular-level understanding of the interactive effects between urea and critical residues associated with the urease active center, as well as propose an effective modification strategy to enhance the application of UICP in future environmental areas.

Molecular expression, purification and structural characterization of recombinant L-Glutaminase from Streptomyces roseolus

The present research reports the anti-cancer potential of recombinant L-Glutaminase from Streptomyces roseolus. L-Glutaminase gene was synthesized by codon-optimization, cloned and successfully expressed in E. coli BL21 (DE3). Affinity purified recombinant L-Glutaminase revealed a molecular mass of 32 kDa. Purified recombinant L-Glutaminase revealed stability at pH 7.0-8.0 with optimum activity at 70 °C further indicating its thermostable nature based on thermodynamic characterization. Recombinant L-Glutaminase exhibited profound stability in the presence of several biochemical parameters and demonstrated its metalloenzyme nature and was also found to be highly specific towards favorable substrate (l-Glutamine) based on kinetics. It demonstrated antioxidant property and pronounced cytotoxic effect against breast cancer (MCF-7 cell lines) in a dose dependent behavior with IC50 of 40.68 μg/mL. Matrix-assisted laser desorption ionization-time of flight-mass spectroscopy (MALDI-TOF-MS) analysis of desired mass peaks ascertained the recombinant L-Glutaminase identity. N-terminal amino acid sequence characterization through Edman degradation revealed highest resemblance for L-glutaminase within the Streptomyces sp. family. The purified protein was characterized structurally and functionally by employing spectroscopic methods like Raman, circular dichroism and nuclear magnetic resonance. The thermostability was assessed by thermogravimetric analysis. The outcomes of the study, suggests the promising application of recombinant L-Glutaminase as targeted therapeutic candidate for breast cancer.

Therapeutic potential of proteases in acute lung injury and respiratory distress syndrome via TLR4/Nrf2/NF-kB signaling modulation

The COVID-19 pandemic has drawn attention to acute lung injury and respiratory distress syndrome as major causes of death, underscoring the urgent need for effective treatments. Protease enzymes possess a wide range of beneficial effects, including antioxidant, anti-inflammatory, antifibrotic, and fibrinolytic effects. This study aimed to evaluate the potential therapeutic effects of bacterial protease and chymotrypsin in rats in mitigating acute lung injury induced by lipopolysaccharide. Molecular docking was employed to investigate the inhibitory effect of bacterial protease and chymotrypsin on TLR-4, the receptor for lipopolysaccharide. Bacterial protease restored TLR-4, Nrf2, p38 MAPK, NF-kB, and IKK-β levels to normal levels, while chymotrypsin normalized TLR-4, IKK-β, IL-6, and IL-17 levels. The expression of TGF-β, caspase-3, and VEGF in the bacterial protease- and chymotrypsin-treated groups was markedly reduced. Our results suggest that both therapies ameliorate LPS-induced acute lung injury and modulate the TLR4/Nrf2/NF-k signaling pathway. Each protease exhibited distinct mechanisms, with bacterial protease showing a better response to oxidative stress, edema, and fibrosis, whereas chymotrypsin provided a better response in the acute phase and innate immunity. These findings highlight the potential of each protease as a promising therapeutic option for acute lung injury and respiratory distress syndrome.

Evaluation of a novel purified and characterized alkaline protease from the extremophile Exiguobacterium alkaliphilum VLP1 as a detergent additive

This study focused on the isolation and identification of a novel alkaline protease-producing strain from Lake Van, the largest soda lake on Earth. The objective was to purify, characterize, and investigate the potential application of protease in the detergent industry. Through a combination of classical and molecular methods, the most potent protease producer was identified as Exiguobacterium alkaliphilum VLP1. The purification process, involving ammonium sulfate precipitation, ultrafiltration, and anion exchange chromatography, resulted in a 45-fold purification with a yield of 6.4% and specific activity of 1169 U mg-1 protein. The enzyme exhibited a molecular weight of 69 kDa, a Km value of 0.4 mm, and a maximal velocity (Vmax ) value of 2000 U mg-1 . The optimum activity was observed at 40°C and potential of hydrogen (pH) 9, while the enzyme also exhibited remarkable stability in the ranges of 30-60°C and pH 9-12. Notably, this study represents the first report of an alkaline protease isolated and characterized from E. alkaliphilum. This study also highlighted the potential of the enzyme as a detergent additive, as it showed compatibility with commercial detergents and effectively removed blood and chocolate stains from fabrics.

Evaluating the industrial potential of naturally occurring proteases: A focus on kinetic and thermodynamic parameters

Thermodynamic and kinetic parameters, such as enthalpy, entropy, and free energy, are crucial in evaluating enzyme stability and activity. These parameters, including the free energy of activation (ΔG#) and the Gibbs free energy of inactivation (ΔG*), are important for predicting energy requirements and reaction rates. However, relying solely on these parameters is insufficient in selecting an enzyme for industrial processes. Numerous studies have explored the measurement of thermodynamic parameters for proteases. Unfortunately, some of the definitions and calculations of key parameters such as ΔG#, ΔG*, and substrate-binding free energy have contained significant errors. In this study, these mistakes have been addressed and corrected. Additionally, a new parameter called δ, defined as the difference between ΔG* and ΔG#, has been introduced for the first time. It is argued that δ provides a more reliable measure for predicting the potential industrial application of enzymes. The highest calculated value for δ was found to be 39.6 kJ·mol-1 at 55 °C. Furthermore, this study also presents a comprehensive collection and determination of all thermodynamic and kinetic parameters for proteases, providing researchers and professionals in the field with a valuable resource to compare and understand the relationships between these parameters and the industrial potential of enzymes.

Structure prediction, docking studies and molecular cloning of novel Pichia kudriavzevii YK46 metalloprotease (MetPr) for improvement of feather waste biodegradation

This study addresses the environmental risks associated with the accumulation of keratin waste from poultry, which is resistant to conventional protein degradation methods. To tackle this issue, microbial keratinases have emerged as promising tools for transforming resilient keratin materials into valuable products. We focus on the Metalloprotease (MetPr) gene isolated from novel Pichia kudriavzevii YK46, sequenced, and deposited in the NCBI GenBank database with the accession number OQ511281. The MetPr gene encodes a protein consisting of 557 amino acids and demonstrates a keratinase activity of 164.04 U/ml. The 3D structure of the protein was validated using Ramachandran's plot, revealing that 93% and 97.26% of the 557 residues were situated within the most favoured region for the MetPr proteins of template Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Computational analyses were employed to determine the binding affinities between the deduced protein and beta keratin. Molecular docking studies elucidated the optimal binding affinities between the metalloprotease (MetPr) and beta-keratin, yielding values of - 260.75 kcal/mol and - 257.02 kcal/mol for the template strains Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Subsequent molecular cloning and expression of the MetPr gene in E. coli DH5α led to a significantly higher keratinase activity of 281 ± 12.34 U/ml. These findings provide valuable insights into the potential of the MetPr gene and its encoded protein for keratin waste biotransformation, with implications for addressing environmental concerns related to keratinous waste accumulation.

The catalytic and kinetic characterization of Bacillus subtilis MK775302 milk clotting enzyme: comparison with calf rennet as a coagulant in white soft cheese manufacture

BACKGROUND

Calf rennet is considered the traditional source of milk clotting enzyme (MCE). However, increasing cheese consumption with decreasing the calf rennet supply had encouraged the quest for new rennet alternatives. The purpose of this study is to acquire more information about the catalytic and kinetic properties of partially purified Bacillus subtilis MK775302 MCE and to assess the role of enzyme in cheese manufacture.

RESULTS

B. subtilis MK775302 MCE was partially purified by 50% acetone precipitation with 5.6-fold purification. The optimum temperature and pH of the partially purified MCE were 70 °C and 5.0, respectively. The activation energy was calculated as 47.7 kJ/mol. The calculated Km and Vmax values were 36 mg/ml and 833 U/ml, respectively. The enzyme retained full activity at NaCl concentration of 2%. Compared to the commercial calf rennet, the ultra-filtrated white soft cheese produced from the partially purified B. subtilis MK775302 MCE exhibited higher total acidity, higher volatile fatty acids, and improved sensorial properties.

CONCLUSIONS

The partially purified MCE obtained in this study is a promising milk coagulant that can replace calf rennet at a commercial scale to produce better-quality cheese with improved texture and flavor.

Bacterial protease alleviate chronic liver fibrosis induced by thioacetamide through suppression of hepatic stellate cells consequently decrease its proliferative index

In chronic liver diseases, liver fibrosis occurs due to excessive extracellular matrix (ECM) protein accumulation. Approximately 2 million deaths occur yearly due to liver disease, while cirrhosis is the 11th most common cause of death. Therefore, newer compounds or biomolecules must be synthesized to treat chronic liver diseases. In this aspect, the present study focuses on the assessment of the anti-inflammatory and antioxidant impact of Bacterial Protease (BP) produced by a new mutant strain of bacteria (Bacillus cereus S6-3/UM90) and 4,4'-(2,5-dimethoxy-1,4-phenylene) bis (1-(3-ethoxy phenyl)-1H-1,2,3-triazole) (DPET) in the treatment of early stage of liver fibrosis induced by thioacetamide (TAA). Sixty male rats were divided into six groups, ten rats each as follows: (1) Control group, (2) BP group, (3) TAA group, (4) TAA-Silymarin (S) group, (5) TAA-BP group, and (6) TAA-DPET group. Liver fibrosis significantly elevated liver function ALT, AST, and ALP, as well as anti-inflammatory interleukin 6 (IL-6) and VEGF. The oxidative stress parameters (MDA, SOD, and NO) were significantly increased with a marked reduction in GSH. Expression of MAPK and MCP-1 was unregulated in the TAA group, with downregulation of Nrf₂ was observed. TAA caused histopathological alterations associated with hepatic vacuolation and fibrosis, increasing collagen fibers and high immuno-expression of VEGF. On the other hand, treatment with BP successfully improved the severe effects of TAA on the liver and restored histological architecture. Our study concluded the protective potentials of BP for attenuating liver fibrosis and could be used as adjuvant therapy for treating hepatic fibrosis.

Lipopolysaccharide induced neuroprotective effects of bacterial protease against Alzheimer's disease in male Wistar albino rats

Alzheimer's disease (AD) is a highly severe neurodegenerative condition that affects the hippocampus and is characterized by memory loss and dementia. This investigation aims to determine the potential of a bacterial protease enzyme produced by a new mutant strain of bacteria (Bacillus cereus S6-3/UM90) to influence the rat behavioural, biochemical, histological, and immuno-histochemical functions induced by lipopolysaccharides (LPS) experimentally. The administration of LPS exhibited a decline in memory performance via Morris' Water Maze test along with an elevation of IL-6, IL-17, amino acid neurotransmitters, Adenosine monophosphate (AMP), and 8-OHdG, whereas a decrease in ATP (Adenosine Triphosphate), monoamine transmitters, AChE (acetylcholinesterase) and PC (phosphatidylcholine). Additionally, there was a notable increase in GFAP (glial fibrillary acidic protein) and p-Tau protein immuno-expression levels along with obvious histological lesions in the hippocampal CA3 region. Moreover, the administration of protease or Donepezil restored the measured parameters to nearly normal levels and improved the histological architecture of the hippocampus and ameliorated memory impairments. In conclusion, the study provides evidence that the treatment with Bacterial protease can improve the memory and learning impairments of LPS-induced AD and may be used as a promising therapeutic agent to manage AD since it has anti-inflammatory and antioxidant effects.

Overexpression of Bacillus circulans alkaline protease in Bacillus subtilis and its potential application for recovery of protein from soybean dregs

Proteases are important for decomposition of proteins to generate peptides or amino acids and have a broad range of applications in different industries. Herein, a gene encoding an alkaline protease (AprBcp) from Bacillus circulans R1 was cloned and bioinformatics analyzed. In addition, a series of strategies were applied to achieve high-level expression of AprBcp in Bacillus subtilis. The maximum activity of AprBcp reached 165,870 U/ml after 60 h fed-batch cultivation in 50 l bioreactor. The purified recombinant AprBcp exhibited maximum activity at 60°C and pH 10.0, and remained stable in the range from pH 8.0 to 11.0 and 30 to 45°C. Metal ions Ca²⁺, Mn²⁺, and Mg²⁺ could improve the stability of AprBcp. Furthermore, the recombinant AprBcp displayed great potential application on the recovery of protein from soybean dregs. The results of this study will provide an effective method to prepare AprBcp in B. subtilis and its potential application on utilization of soybean dregs.

Inflammatory Modulation of miR-155 Inhibits Doxorubicin-Induced Testicular Dysfunction via SIRT1/FOXO1 Pathway: Insight into the Role of Acacetin and Bacillus cereus Protease

Doxorubicin (DOX) is a chemotherapeutic agent that can disrupt testicular function leading to male infertility. This study examined the protective role of natural flavone, acacetin (ACA), and a protease of Bacillus cereus bacteria (B. cereus) as well as the potential role of miR-155/SIRT1/FOXO1 network in DOX-induced testicular injury. Twenty-four male Wistar rats were randomly allocated into four groups and treated as follows: Control, DOX (1 mg/kg, i.p) every other day for 21 days with a total dose equal to 10 mg/kg throughout the experiment, and pre-treated groups that received ACA (5 mg/kg/day, p.o) or B. cereus protease (36 mg/kg/day, p.o) for a week prior to DOX administration. DOX challenge reduced the testis weight coefficient, serum testosterone, and testicular 17β-hydroxysteroid dehydrogenase (17β-HSD). DOX caused a significant increase in testicular oxidative stress, inflammatory, and apoptotic markers. Aberrant testicular miR-34c, a germ-specific miRNA, and miR-155 expressions were observed, along with decreased protein expression of sirtuin1 (SIRT1) dependent forkhead box 1 (FOXO1) acetylation which induces apoptosis. Besides, abnormal histopathological architecture and a marked reduction in the testicular expression of proliferating cell nuclear antigen (PCNA) were observed. ACA or protease administration significantly improved the histopathological and immunohistochemical pictures compared with DOX alone and renovated testicular functions. Interestingly, treatment with protease was more significant than treatment with ACA in ameliorating DOX-induced testicular injury. Taken together, this study reveals the prophylactic role of these two regimens on male fertility by exhibiting antioxidant, anti-inflammatory, and anti-apoptotic effects against DOX-elicited testicular damage, possibly via modulating miR-155/SIRT1/FOXO1 network.

Novel Feather Degrading Keratinases from Bacillus cereus Group: Biochemical, Genetic and Bioinformatics Analysis

In this study, five keratinolytic bacteria were isolated from poultry farm waste of Eastern Province, Saudi Arabia. The highest keratinase activity was obtained at 40–45 °C, pH 8–9, feather concentration 0.5–1%, and using white chicken feather as keratin substrate for 72 h. Enhancement of keratinase activity through physical mutagen UV radiation and/or chemical mutagen ethyl methanesulfonate (EMS) resulted in five mutants with 1.51–3.73-fold increased activity over the wild type. When compared with the wild type, scanning electron microscopy validated the mutants’ effectiveness in feather degradation. Bacterial isolates are classified as members of the S8 family peptidase Bacillus cereus group based on sequence analysis of the 16S rRNA and keratinase genes. Interestingly, keratinase KerS gene shared 95.5–100% identity to keratinase, thermitase alkaline serine protease, and thermophilic serine protease of the B. cereus group. D₁₃₇N substitution was observed in the keratinase KerS gene of the mutant strain S13 (KerS13uv+ems), and also seven substitution variations in KerS26 and KerS26uv of strain S26 and its mutant S26uv. Functional analysis revealed that the subtilisin-like serine protease domain containing the Asp/His/Ser catalytic triad of KerS gene was not affected by the predicted substitutions. Prediction of physicochemical properties of KerS gene showed instability index between 17.5–19.3 and aliphatic index between 74.7–75.7, which imply keratinase stability and significant thermostability. The docking studies revealed the impact of substitutions on the superimposed structure and an increase in binding of mutant D₁₃₇N of KerS13uv+ems (affinity: −7.17; S score: −6.54 kcal/mol) and seven mutants of KerS26uv (affinity: −7.43; S score: −7.17 kcal/mol) compared to the wild predicted structure (affinity: −6.57; S score: −6.68 kcal/mol). Together, the keratinolytic activity, similarity to thermostable keratinases, and binding affinity suggest that keratinases KerS13uv+ems and KerS26uv could be used for feather processing in the industry.

Use of a Sequential Fermentation Method for the Production of Aspergillus tamarii URM4634 Protease and a Kinetic/Thermodynamic Study of the Enzyme

Microbial proteases are commonly produced by submerged (SmF) or solid-state fermentation (SSF), whose combination results in an unconventional method, called sequential fermentation (SF), which has already been used only to produce cellulolytic enzymes. In this context, the aim of the present study was the development of a novel SF method for protease production using wheat bran as a substrate. Moreover, the kinetic and thermodynamic parameters of azocasein hydrolysis were estimated, thus providing a greater understanding of the catalytic reaction. In SF, an approximately 9-fold increase in protease activity was observed compared to the conventional SmF method. Optimization of glucose concentration and medium volume by statistical means allowed us to achieve a maximum protease activity of 180.17 U mL−1. The obtained enzyme had an optimum pH and temperature of 7.0 and 50 °C, respectively. Kinetic and thermodynamic parameters highlighted that such a neutral protease is satisfactorily thermostable at 50 °C, a temperature commonly used in many applications in the food industry. The results obtained suggested not only that SF could be a promising alternative to produce proteases, but also that it could be adapted to produce several other enzymes.