Properties of a fibrinolytic enzyme secreted by Bacillus subtilis JS2 isolated from saeu (small shrimp) jeotgal

Computational analysis to comprehend the structure-function properties of fibrinolytic enzymes from Bacillus spp for their efficient integration into industrial applications

Background

The fibrinolytic enzymes from Bacillus sp. are proposed as therapeutics in preventing thrombosis. Computational-based analyses of these enzymes' amino acid composition, basic physiological properties, presence of functional domain and motifs, and secondary and tertiary structure analyses can lead to developing a specific enzyme with improved catalytic activity and other properties that may increase their therapeutic potential.

Methods

The nucleotide sequences of fibrinolytic enzymes produced by the genus Bacillus and its corresponding protein sequences were retrieved from the NCBI database and aligned using the PRALINE programme. The varied physiochemical parameters and structural and functional analysis of the enzyme sequences were carried out with the ExPASy-ProtParam tool, MEME server, SOPMA, PDBsum tool, CYS-REC tool, SWISS-MODEL, SAVES servers, TMHMM program, GlobPlot, and peptide cutter software. The assessed in-silico data were compared with the published experimental results for validation.

Results

The alignment of sixty fibrinolytic serine protease enzymes (molecular mass 12-86 kDa) sequences showed 49 enzymes possess a conserved domain with a catalytic triad of Asp196, His242, and Ser569. The predicted instability and aliphatic indexes were 1.94-37.77, and 68.9-93.41, respectively, indicating high thermostability. The random coil means value suggested the predominance of this secondary structure in these proteases. A set of 50 amino acid residues representing motif 3 signifies the Peptidase S8/S53 domain that was invariably observed in 56 sequences. Additionally, 28 sequences have transmembrane helices, with two having the most disordered areas, and they pose 25 enzyme cleavage sites. A comparative analysis of the experimental work with the results of in-silico study put forward the characteristics of the enzyme sequences JF739176.1 and MF677779.1 to be considered when creating a potential mutant enzyme as these sequences are stable at high pH with thermostability and to exhibit αβ-fibrinogenase activity in both experimental and in-silico studies.

Purification and Characterization of a Novel Fibrinolytic Enzyme from Marine Bacterium Bacillus sp. S-3685 Isolated from the South China Sea

A novel fibrinolytic enzyme, BSFE1, was isolated from the marine bacterium Bacillus sp. S-3685 (GenBank No.: KJ023685) found in the South China Sea. This enzyme, with a molecular weight of approximately 42 kDa and a specific activity of 736.4 U/mg, exhibited its highest activity at 37 °C in a phosphate buffer at pH 8.0. The fibrinolytic enzyme remained stable over a pH range of 7.5 to 10.0 and retained about 76% of its activity after being incubated at 37 °C for 2 h. The Km and Vmax values of the enzyme at 37 °C were determined to be 2.1 μM and 49.0 μmol min-1 mg-1, respectively. The fibrinolytic activity of BSFE1 was enhanced by Na+, Ba2+, K+, Co2+, Mn2+, Al3+, and Cu2+, while it was inhibited by Fe3+, Ca2+, Mg2+, Zn2+, and Fe2+. These findings indicate that the fibrinolytic enzyme isolated in this study exhibits a strong affinity for fibrin. Moreover, the enzyme we have purified demonstrates thrombolytic enzymatic activity. These characteristics make BSFE1 a promising candidate for thrombolytic therapy. In conclusion, the results obtained from this study suggest that our work holds potential in the development of agents for thrombolytic treatment.

Diverse origins of fibrinolytic enzymes: A comprehensive review

Fibrinolytic enzymes cleave fibrin which plays a crucial role in thrombus formation which otherwise leads to cardiovascular diseases. While different fibrinolytic enzymes have been purified, only a few have been utilized as clinical and therapeutic agents; hence, the search continues for a fibrinolytic enzyme with high specificity, fewer side effects, and one that can be mass-produced at a lower cost with a higher yield. In this context, this review discusses the physiological mechanism of thrombus formation and fibrinolysis, and current thrombolytic drugs in use. Additionally, an overview of the optimization, production, and purification of fibrinolytic enzymes and the role of Artificial Intelligence (AI) in optimization and the patents granted is provided. This review classifies microbial as well as non-microbial fibrinolytic enzymes isolated from food sources, including fermented foods and non-food sources, highlighting their advantages and disadvantages. Despite holding immense potential for the discovery of novel fibrinolytic enzymes, only a few fermented food sources limited to Asian countries have been studied, necessitating the research on fibrinolytic enzymes from fermented foods of other regions. This review will aid researchers in selecting optimal sources for screening fibrinolytic enzymes and is the first one to provide insights and draw a link between the implication of source selection and in vivo application.

Fermented Foods of Korea and Their Functionalities

Fermented foods are loved and enjoyed worldwide and are part of a tradition in several regions of the world. Koreans have traditionally had a healthy diet since people in this region have followed a fermented-foods diet for at least 5000 years. Fermented-product footprints are evolving beyond boundaries and taking the lead in the world of food. Fermented foods, such as jang (fermented soybean products), kimchi (fermented vegetables), jeotgal (fermented fish), and vinegar (liquor with grain and fruit fermentation), are prominent fermented foods in the Korean culture. These four major fermented foods have been passed down through the generations and define Korean cuisine. However, scientific advancements in the fermentation process have increased productivity rates and facilitated global exports. Recently, Korean kimchi and jang have garnered significant attention due to their nutritional and health-beneficial properties. The health benefits of various Korean fermented foods have been consistently supported by both preclinical and clinical research. Korean fermented foods effectively reduce the risk of cardiovascular and chronic metabolic diseases, such as immune regulation, memory improvement, obesity, diabetes, and high blood pressure. Additionally, kimchi is known to prevent and improve multiple metabolic diseases, including irritable bowel syndrome (IBS), and improve beneficial intestinal bacteria. These functional health benefits may reflect the synergistic effect between raw materials and various physiologically active substances produced during fermentation. Thus, fermented foods all over the world not only enrich our dining table with taste, aroma, and nutrition, but also the microorganisms involved in fermentation and metabolites of various fermentations have a profound effect on human health. This article describes the production and physiological functions of Korean fermented foods, which are anticipated to play a significant role in the wellness of the world’s population in the coming decades.

Purification, biochemical characterization and fibrinolytic potential of proteases produced by bacteria of the genus Bacillus: a systematic literature review

Thrombosis is a hematological disorder characterized by the formation of intravascular thrombi, which contributes to the development of cardiovascular diseases. Fibrinolytic enzymes are proteases that promote the hydrolysis of fibrin, promoting the dissolution of thrombi, contributing to the maintenance of adequate blood flow. The characterization of new effective, safe and low-cost fibrinolytic agents is an important strategy for the prevention and treatment of thrombosis. However, the development of new fibrinolytics requires the use of complex methodologies for purification, physicochemical characterization and evaluation of the action potential and toxicity of these enzymes. In this context, microbial enzymes produced by bacteria of the Bacillus genus are promising and widely researched sources to produce new fibrinolytics, with high thrombolytic potential and reduced toxicity. Thus, this review aims to provide a current and comprehensive understanding of the different Bacillus species used for the production of fibrinolytic proteases, highlighting the purification techniques, biochemical characteristics, enzymatic activity and toxicological evaluations used.

DNA Shuffling of aprE Genes to Increase Fibrinolytic Activity and Thermostability

Four aprE genes encoding alkaline serine proteases from B. subtilis strains were used as template genes for family gene shuffling. Shuffled genes obtained by DNase I digestion followed by consecutive primerless and regular PCR reactions were ligated with pHY300PLK, an E. coli-Bacillus shuttle vector. The ligation mixture was introduced into B. subtilis WB600 and one transformant (FSM4) showed higher fibrinolytic activity. DNA sequencing confirmed that the shuffled gene (aprEFSM4) consisted of DNA mostly originated from either aprEJS2 or aprE176 in addition to some DNA from either aprE3-5 or aprESJ4. Mature AprEFSM4 (275 amino acids) was different from mature AprEJS2 in 4 amino acids and mature AprE176 in 2 amino acids. aprEFSM4 was overexpressed in E. coli BL21 (DE3) by using pET26b(+) and recombinant AprEFSM4 was purified. The optimal temperature and pH of AprEFSM4 were similar to those of parental enzymes. However, AprEFM4 showed better thermostability and fibrinogen hydrolytic activity than the parental enzymes. The results indicated that DNA shuffling could be used to improve fibrinolytic enzymes from Bacillus sp. for industrial applications.

Marine Microbial Fibrinolytic Enzymes: An Overview of Source, Production, Biochemical Properties and Thrombolytic Activity

Cardiovascular diseases (CVDs) have emerged as a major threat to global health resulting in a decrease in life expectancy with respect to humans. Thrombosis is one of the foremost causes of CVDs, and it is characterized by the unwanted formation of fibrin clots. Recently, microbial fibrinolytic enzymes due to their specific features have gained much more attention than conventional thrombolytic agents for the treatment of thrombosis. Marine microorganisms including bacteria and microalgae have the significant ability to produce fibrinolytic enzymes with improved pharmacological properties and lesser side effects and, hence, are considered as prospective candidates for large scale production of these enzymes. There are no studies that have evaluated the fibrinolytic potential of marine fungal-derived enzymes. The current review presents an outline regarding isolation sources, production, features, and thrombolytic potential of fibrinolytic biocatalysts from marine microorganisms identified so far.

Fibrinolytic and ACE Inhibitory Activity of Nattokinase Extracted from Bacillus subtilis VITMS 2: A Strain Isolated from Fermented Milk of Vigna unguiculata

The current research work aims at optimization, production, purification and evaluation of fibrinolytic extracellular protease from Bacillus subtilis VITMS2 isolated from fermented milk of Vigna unguiculata. The optimal production was achieved at 4.0% inoculum, pH7.0, 30 °C with (1% w/v) sucrose, (2% w/v) soya bean meal and (2% w/v) malt extract and 10 mM of CaCl_2, MgSO_4, Na₂HPO₄ and K₂HPO₄. The clear cell-free supernatant was purified using conventional ammonium sulphate salt fractionation (75%), ultrafiltration, ion-exchange (DEAE Sepharose FF) and gel filtration (Sephadex G-50). The molecular mass was determined to be 29 kDa using SDS-PAGE analysis. The purified enzyme showed strong fibrinolytic activity with a specific activity of 2418.85 U/mg and has a yield of 12.01%. The enzyme was highly stable up to 60 °C and a pH range of 10.0 until 72 h of incubation. The purified enzyme showed 97.4% in vitro thrombolytic activity. The K_m and V_max values of the enzyme was determined to be 0.0114 mM and 147.8 µmol min^-1 using the chromogenic substrate S-7388. IC₅₀ of ace inhibition was assessed to be 0.06 mg/mL suggesting anti-hypertensive property of the fibrinolytic enzyme. The above-obtained ace-inhibition results was supported by in silico molecular docking studies which revealed better binding affinity of nattokinase with a HADDOCK score of - 22.0 ± 8.5 confirms affinity towards angiotensin converting enzyme.

Isolation of Bacillus spp. with High Fibrinolytic Activity and Performance Evaluation in Fermented Douchi

ABSTRACT

Fibrinolytic enzymes are effective and highly safe in treating cardiovascular and cerebrovascular diseases. Therefore, screening fibrinolytic enzyme-producing microbial strains with excellent fermentation performance is of great value to industrial applications. The fibrin plate method was used in screening strains with high yields of fibrinolytic enzymes from different fermented food products, and the screened strains were preliminarily identified using molecular biology. Then, the strains were used for solid-state fermentation of soybeans. Moreover, the fermentation product douchi was subjected to fibrinolytic activity measurement, sensory evaluation, and biogenic amine content determination. The fermentation performance of each strain was comprehensively evaluated through principal component analysis. Finally, the target strain was identified based on strain morphology, physiological and biochemical characteristics, 16S rDNA sequence, and phylogenetic analysis results. A total of 15 Bacillus species with high fibrinolysin activity were selected. Their fibrinolytic enzyme-producing activity levels were higher than 5,500 IU/g. Through molecular biology analysis, we found 4 strains of Bacillus subtilis, 10 strains of Bacillus amyloliquefaciens, and 1 strain of Bacillus velezensis. The principal component analysis results showed that SN-14 had the best fermentation performance and reduced the accumulation of histamine and total amine, the fibrinolytic activity of fermented douchi reached 5,920.5 ± 107.7 IU/g, and the sensory score was 4.6 ± 0.3 (out of 5 points). Finally, the combined results of physiological and biochemical analyses showed SN-14 was Bacillus velezensis. The high-yield fibrinolytic and excellent fermentation performance strain Bacillus velezensis SN-14 has potential industrial application.

HIGHLIGHTS

Protease from Mucor subtilissimus UCP 1262: Evaluation of several specific protease activities and purification of a fibrinolytic enzyme

The industrial demand for proteolytic enzymes is stimulating the search for new enzyme sources. Fungal enzymes are preferred over bacterial enzymes, and more effective and easier to extract. The aim of this work was to evaluate the potential of protease production by solid state fermentation (SSF) of Mucor subtilissimus UCP 1262, evaluate different specific activities, purify and partially characterize the enzyme in terms of biochemical as to the optimal pH and temperature. Initially, the enzyme crude extract was screened for 3 different proteolytic activities, collagenolytic (161.4 U/mL), keratinolytic (39.6 U/mL) and fibrinolytic (26.1 U/mL) in addition to conventional proteinase activity. After ammonium sulfate precipitation, the active fractions with fibrinolytic activity were dialyzed in 15 mM Tris-HCl buffer, pH 8, loaded onto DEAE-Sephadex A50 ion-exchange column and gel filtrated through Superdex 75 HR10/300. The enzyme showed a fibrinolytic maximum activity at 40 C and pH 9,0. The purified enzyme showed activity against a chromogenic chymotrypsin substrate, SDS-PAGE showing a molecular mass of approximately 70 kDa and, the specific activity of 25.93 U/mg. These characteristics suggest that the enzyme could be and efficiently produced in a simple and low-cost way using Mucor subtilissimus UCP 1262 in SSF.

Purification, physicochemical properties, and statistical optimization of fibrinolytic enzymes especially from fermented foods: A comprehensive review

Fibrinolytic enzymes are proteases responsible for cleavage of fibrin mesh in thrombus clots, which are the primary causative agents in cardiovascular diseases. Developing safe, effective and cheap thrombolytic agents are important for prevention and cure of thrombosis. Although a wide variety of sources have been discovered for fibrinolytic enzymes, only few of them have been employed in clinical and therapeutic applications due to the drawbacks such as high cost of production, low stability of enzyme or therapeutic side effects. However, the discovery of new fibrinolytic enzymes requires complex purification stages and characterization, which gives an insight into their diverse modes of action. Post-discovery, approaches such as a) statistical optimization for fermentative bioprocessing and b) genetic engineering are advantageous in providing economic viability by finding simple and cost-effective medium, strain development with sufficient nutrient supplements for stable and high-level production of recombinant enzyme. This review provides a comprehensive understanding of different sources, purification techniques, production through genetic engineering approaches and statistical optimization of fermentation parameters as proteases have a wide variety of industrial and biotechnological applications making 60% of total enzyme market worldwide. New strategies targeting increased enzyme yields, non-denaturing environments, improved stability, enzyme activity and strain improvement have been discussed.

A novel fibrinolytic enzymes from the Korean traditional fermented food-Jotgal: Purification and characterization

The fibrinolytic activity in Korean traditional fermented food, Jotgal (pickled fish) was identified. Though the fibrinolytic activity could vary in different kinds of Jotgal, this activity seems to be produced by microorganisms during the natural fermentation stage. From Gonjaengijot (pickled opossum shrimp), two novel fibrinolytic enzymes named by JP-I and JP-II, have been purified by ethanol precipitation, Bio-GEL P-100 gel filtration, and DEAE-cellulose ion-exchange chromatography. Compared to the crude enzyme extract, the specific activity of the JP-I and JP-II increased 258, 85-fold with the recovery of 22.1, 8.5%, respectively. The molecular weights of both enzymes were estimated as 36 kDa on sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimal condition for fibrinolytic activity of JP-I was at 50°C and pH 8.1, while that of JP-II was at 45°C and 9.9. Both enzymes were stable at a broad range of pH (5.0 to 10.5) and have metalloprotease nature. From these results, it concludes that these enzymes could be a novel potent thrombolytic agent. PRACTICAL APPLICATIONS: The fibrinolytic enzyme is one of the clinical agents for cardiovascular diseases which is the leading cause of morbidity and mortality worldwide with 17 million deaths every year. A variety of fibrinolytic enzymes are found and characterized from various sources such as plants, animals, and microorganisms, and new sources for fibrinolytic enzymes continue to be explored. Jotgal, widely used in Korean people's diet, is a traditional Korean seafood prepared from many different types of fishes, fish eggs, fish intestines, and shellfishes. Through an amount of research, some of fibrinolytic enzymes were found and purified from Jotgal, however, no studies have been done on fibrinolytic enzyme from opossum shrimp. In this study, the purification, enzymatic characteristics, and fibrinolytic activity of the proteases, originated from Korean traditional fermented food, Jotgal were reported. These enzymes could be novel potent thrombolytic agent.

Prospects of fibrinolytic proteases of bacteria from sea cucumber fermentation products as antithrombotic agent

Cardiovascular disease is among the largest contributors of premature mortality in the world caused by inflammation of blood vessels. The abnormalities provoke thrombus formation or thrombosis blocking blood vessels leading to strokes, heart attacks and coronary artery diseases. Increasing percentage of cardiovascular cases and deaths due to thrombosis has attracted researchers to look for newer thrombolysis agents. Commonly used drugs to treat thrombosis has been limited due to various side effects. Therefore, the search for sources of safer and cheaper fibrinolytic enzymes for handling thrombolysis continues. This study aimed to evaluate potentials of fibrinolytic protease of bacteria isolated from fermented seafood (sea cucumber) products as antithrombotic agents. Information was initially gathered from scientific publications identified using web-based tools including PubMed (National Center for Biotechnology Information), Science Direct (Scopus) and Web of Science (Thomson Reuters) using combinations of search terms including “fibrinolytic enzyme protease”, “endopeptidase”, “fermented food”, “sea cucumber”, “thrombolysis therapy,” “thrombolytic agent,” “fibrinolytic bacteria,” “fibrinolysis,” “protease producing bacteria,” “fibrin degradation,” “holothurians,” etc. We also searched for these terms in national and international organization technical reports and databases. This literature review reveals the prospects of fibrinolytic protease enzymes from bacteria from fermented seafood, particularly sea cucumber as novel antithrombotic agents.