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Comparative genomic analyses of Bacillus subtilis strains to study the biochemical and molecular attributes of nattokinases

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Abstract

The present research work explores the Nattokinase (NK) producing capacity of five Bacillus subtilis strains (MTCC 2616, MTCC 2756, MTCC 2451, MTCC 1427, and MTCC 7164) using soybean varieties as substrate under solid-state fermentation conditions. Subsequently, the biochemical attributes of NKs were analyzed. Soybean variety didn’t affect the production of NK to a significant extent; however, the five strains differed substantially for their NK producing capacity. NK produced by MTCC 2451 (R3) showed a low Kmvalue implying its higher specificity for fibrin but this strain (MTCC 2451) didn’t produce NK in sufficient quantity. The low Km of MTCC 2451 NK implicates its potential candidature for treating blood clots in cardiovascular patients. The NK produced by MTCC 2616 (R1) was produced in sufficient quantity and showed good fibrin dissolving potential. The aprN of MTCC 2616 substantially varied from the other four strains. The aprN of MTCC 2756 (R2), MTCC 2451 (R3), MTCC 1427 (R4), and MTCC 7164 (R5) shared > 99% sequence identity, but the encoded NKs had significant variations in their Km values. The biochemical-molecular analyses indicate the co-presence of three critical residues (Thr130, Asp140, and Tyr217) as a quintessential attribute in determining the low Km of NK enzymes, and the absence of any one of the three critical residues may affect (highly increase) the Km.

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References

  • Adivitiya, Khasa YP (2017) The evolution of recombinant thrombolytics: current status and future directions. Bioengineered 8(4):331–358

    Article  CAS  PubMed  Google Scholar 

  • Ahmad S, Gromiha MM (2002) NETASA: neural network based prediction of solvent accessibility. Bioinformatics 18(6):819–824

    Article  CAS  PubMed  Google Scholar 

  • Ahmad S, Gromiha M, Fawareh H, Sarai A (2004) ASAView: database and tool for solvent accessibility representation in proteins. BMC Bioinformatics 5(1):1–5

    Article  Google Scholar 

  • Akhmetshin RR (1998) Mechanistic investigations of catalysis by some hemostatic and thrombolytic enzymes. The Catholic University of America

  • Berg JM, Tymoczko JL, Stryer L (2002) Section 8.4 The Michaelis-Menten model accounts for the kinetic properties of many enzymes. In: Freeman WH (ed) Biochemistry. Freeman and Company, New York

    Google Scholar 

  • Bhargav S, Panda BP, Ali M, Javed S (2008) Solid-state fermentation: an overview. Chem Biochem Eng Q 22(1):49–70

    CAS  Google Scholar 

  • Bhatt PC, Kapoor R, Panda BP (2015) Purification and biochemical characterization of menaquione-7 free, pure nattokinase from Bacillus subtilis. MTCC 2616 52:248–253

  • Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016):164–170

    Article  CAS  PubMed  Google Scholar 

  • Chandra S, Khowal S, Wajid S (2014) In-silico scrutiny and molecular docking analysis for beta secretase-1 and presenilin-1. Int J Pharma Bio Sci 5(4):274–292

    Google Scholar 

  • Chang C-T, Fan M-H, Kuo F-C, Sung H-Y (2000) Potent fibrinolytic enzyme from a mutant of Bacillus subtilis IMR-NK1. J Agric Food Chem 48(8):3210–3216

    Article  CAS  PubMed  Google Scholar 

  • Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ et al (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D 66(1):12–21

    Article  CAS  PubMed  Google Scholar 

  • Chen H, McGowan EM, Ren N, Lal S, Nassif N, Shad-Kaneez F et al (2018) Nattokinase: a promising alternative in prevention and treatment of cardiovascular diseases. Biomarker Insights 13:1177271918785130

    Article  PubMed Central  PubMed  Google Scholar 

  • Cho Y-H, Song JY, Kim KM, Kim MK, Lee IY, Kim SB et al (2010) Production of nattokinase by batch and fed-batch culture of Bacillus subtilis. New Biotechnol 27(4):341–346

    Article  CAS  Google Scholar 

  • Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X et al (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35(suppl_2):W375–W383

    Article  PubMed Central  PubMed  Google Scholar 

  • Deepak V, Kalishwaralal K, Ramkumarpandian S, Babu SV, Senthilkumar S, Sangiliyandi G (2008) Optimization of media composition for Nattokinase production by Bacillus subtilis using response surface methodology. Biores Technol 99(17):8170–8174

    Article  CAS  Google Scholar 

  • Deepak V, Kalishwaralal K, Gurunathan S (2009) Purification, immobilization, and characterization of nattokinase on PHB nanoparticles. Biores Technol 100(24):6644–6646

    Article  CAS  Google Scholar 

  • Diaz AB, Blandino A, Webb C, Caro I (2016) Modelling of different enzyme productions by solid-state fermentation on several agro-industrial residues. Appl Microbiol Biotechnol 100(22):9555–9566

    Article  CAS  PubMed  Google Scholar 

  • Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34(suppl_2):W116–W118

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dym O, Eisenberg D, Yeates T (2012) ERRAT

  • Fujita M, Ito Y, Hong K, Nishimuro S (1995) Characterization of nattokinase-degraded products from human fibrinogen or cross-linked fibrin. Fibrinolysis 9(3):157–164

    Article  CAS  Google Scholar 

  • Gaziano TA, Bitton A, Anand S, Abrahams-Gessel S, Murphy A (2010) Growing epidemic of coronary heart disease in low- and middle-income countries. Curr Probl Cardiol 35(2):72–115

    Article  PubMed Central  PubMed  Google Scholar 

  • Geourjon C, Deleage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11:681

    CAS  PubMed  Google Scholar 

  • Gianforcaro A, Kurz M, Guyette FX, Callaway CW, Rittenberger JC, Elmer J (2017) Association of antiplatelet therapy with patient outcomes after out-of-hospital cardiac arrest. Resuscitation 121:98–103

    Article  PubMed Central  PubMed  Google Scholar 

  • Hatakeyama S, Kafuku M, Okamoto T, Kakizaki Y, Shimasaki N, Fujie N et al (2016) studies on the anticancer mechanisms of the natto extract. J Soc Mater Eng Resour Jpn 27:15–19

    Article  Google Scholar 

  • Havranek EP, Mujahid MS, Barr DA, Blair IV, Cohen MS, Cruz-Flores S et al (2015) Social determinants of risk and outcomes for cardiovascular disease: a scientific statement from the American Heart Association. Circulation 132(9):873–898

    Article  PubMed  Google Scholar 

  • Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38

    Article  CAS  PubMed  Google Scholar 

  • Huy D, Hao P, Hung P (2016) Screening and identification of Bacillus sp. isolated from traditional Vietnamese soybean-fermented products for high fibrinolytic enzyme production. Int Food Res J 23(1):326

    CAS  Google Scholar 

  • Jensen GS, Lenninger M, Ero MP, Benson KF (2016) Consumption of nattokinase is associated with reduced blood pressure and von Willebrand factor, a cardiovascular risk marker: results from a randomized, double-blind, placebo-controlled, multicenter North American clinical trial. IBPC 9:95

    Article  CAS  Google Scholar 

  • Kapoor R, Panda BP (2013a) Bioprospecting of soybean for production of nattokinase. Nutrafoods 12(3):89–95

    Article  CAS  Google Scholar 

  • Kapoor R, Panda BP (2013b) Production of nattokinase from Bacillus sp. by solid state fermentation. Int J Med Sci Biotechnol 61–65

  • Kapoor R, Pathak S, Najmi AK, Aeri V, Panda BP (2014) Processing of soy functional food using high pressure homogenization for improved nutritional and therapeutic benefits. Innov Food Sci Emerg Technol 26:490–497

    Article  CAS  Google Scholar 

  • Kapoor R, Harde H, Jain S, Panda AK, Panda BP (2015) Downstream processing, formulation development and antithrombotic evaluation of microbial nattokinase. J Biomed Nanotechnol 11(7):1213–1224

    Article  CAS  PubMed  Google Scholar 

  • Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Khowal S, Siddiqui MZ, Ali S, Khan MT, Khan MA, Naqvi SH et al (2017) A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR. Mol Phylogenet Evol 107:443–454

    Article  CAS  PubMed  Google Scholar 

  • Khowal S, Naqvi SH, Monga S, Jain SK, Wajid S (2018a) Assessment of cellular and serum proteome from tongue squamous cell carcinoma patient lacking addictive proclivities for tobacco, betel nut, and alcohol: case study. J Cell Biochem 119(7):5186–5221

    Article  CAS  PubMed  Google Scholar 

  • Khowal S, Jain SK, Wajid S (2018b) A potential association between mutations in the iNOS cDNA 3′ stretch and oral squamous cell carcinoma-A preliminary study. Meta Gene 16:189–195

    Article  Google Scholar 

  • Khowal S, Monga S, Naqvi SH, Jain SK, Wajid S (2021) Molecular winnowing, expressional analyses and interactome scrutiny of cellular proteomes of oral squamous cell carcinoma. Adv Cancer Biol 2:100003

    Google Scholar 

  • Kou Y, Feng R, Chen J, Duan L, Wang S, Hu Y et al (2020) Development of a nattokinase–polysialic acid complex for advanced tumor treatment. Eur J Pharm Sci 145:105241

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kumar V, Ahluwalia V, Saran S, Kumar J, Patel AK, Singhania RR (2021) Recent developments on solid-state fermentation for production of microbial secondary metabolites: challenges and solutions. Bioresour Technol 323:124566

    Article  CAS  PubMed  Google Scholar 

  • Kurosawa Y, Nirengi S, Homma T, Esaki K, Ohta M, Clark JF et al (2015) A single-dose of oral nattokinase potentiates thrombolysis and anti-coagulation profiles. Sci Rep 5(1):11601

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S et al (2015) The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res 43(W1):W580–W584

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liu J, Xing J, Chang T, Ma Z, Liu H (2005) Optimization of nutritional conditions for nattokinase production by Bacillus natto NLSSE using statistical experimental methods. Process Biochem 40(8):2757–2762

    Article  CAS  Google Scholar 

  • Mahajan PM, Gokhale SV, Lele SS (2010) Production of nattokinase using Bacillus natto NRRL 3666: media optimization, scale up, and kinetic modeling. Food Sci Biotechnol 19(6):1593–1603

    Article  CAS  Google Scholar 

  • Mbah AN, Isokpehi RD (2013) Identification of functional regulatory residues of the β-lactam inducible penicillin binding protein in methicillin-resistant Staphylococcus aureus. Chemother Res Pract 2013:614670

    PubMed Central  PubMed  Google Scholar 

  • McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N et al (2013) Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 41(W1):W597–W600

    Article  PubMed Central  PubMed  Google Scholar 

  • Milner M (2008) Nattokinase: a potent and safe thrombolytic. FOCUS Newsletter 2

  • Milner M, Makise K (2002) Natto and its active ingredient nattokinase: a potent and safe thrombolytic agent. Altern Complement Ther 8(3):157–164

    Article  Google Scholar 

  • Nakamura T, Yamagata Y, Ichishima E (1992) Nucleotide sequence of the subtilisin NAT gene, aprN, of Bacillus subtilis (natto). Biosci Biotechnol Biochem 56(11):1869–1871

    Article  CAS  PubMed  Google Scholar 

  • Nguyen TT, Quyen TD, Le HT (2013) Cloning and enhancing production of a detergent- and organic-solvent-resistant nattokinase from Bacillus subtilis VTCC-DVN-12-01 by using an eight-protease-gene-deficient Bacillus subtilis WB800. Microb Cell Fact. https://doi.org/10.1186/1475-2859-12-79

    Article  PubMed Central  PubMed  Google Scholar 

  • Noori HR, Spanagel R (2013) In silico pharmacology: drug design and discovery’s gate to the future. In Silico Pharmacol. https://doi.org/10.1186/2193-9616-1-1

    Article  PubMed Central  PubMed  Google Scholar 

  • Oriol E, Raimbault M, Roussos S, Viniegra-Gonzales G (1988) Water and water activity in the solid state fermentation of cassava starch by Aspergillus niger. Appl Microbiol Biotechnol 27(5):498–503

    Article  CAS  Google Scholar 

  • Prajapat R, Jain S, Vaishnav MK, Sogani S (2020) Structural modeling and validation of growth/differentiation factor 15 [NP_004855] associated with pregnancy complication-hyperemesis gravidarum. J Krishna Inst Med Sci (JKIMSU) 9(3)

  • Robinson PK (2015) Enzymes: principles and biotechnological applications. Essays Biochem 59:1–41

    Article  PubMed Central  PubMed  Google Scholar 

  • Roth GA, Mensah GA, Johnson CO, Addolorato G, Ammirati E, Baddour LM et al (2020) Global burden of cardiovascular diseases and risk factors, 1990–2019: update from the GBD 2019 study. J Am Coll Cardiol 76(25):2982–3021

    Article  PubMed Central  PubMed  Google Scholar 

  • Sanbrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor

    Google Scholar 

  • Schrödinger L (2016) The PyMOL molecular graphics system, Version 1.8 Schrödinger, LLC

  • Seibert E, Tracy TS (2014) Fundamentals of enzyme kinetics. In: Enzyme kinetics in drug metabolism, pp 9–22

  • Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7(1):539

    Article  PubMed Central  PubMed  Google Scholar 

  • Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17(4):355–362

    Article  CAS  PubMed  Google Scholar 

  • Soares VF, Castilho LR, Bon EP, Freire DM (2005) High-yield Bacillus subtilis protease production by solid-state fermentation. Appl Biochem Biotechnol 121–124:311–319

    Article  PubMed  Google Scholar 

  • Soccol CR, Costa ESF, Letti LAJ, Karp SG, Woiciechowski AL, Vandenberghe LPS (2017) Recent developments and innovations in solid state fermentation. Biotechnol Res Innov 1(1):52–71

    Article  Google Scholar 

  • Stark K, Massberg S (2021) Interplay between inflammation and thrombosis in cardiovascular pathology. Nat Rev Cardiol 18:666–682

    Article  PubMed Central  PubMed  Google Scholar 

  • Sumi H, Hamada H, Tsushima H, Mihara H, Muraki H (1987) A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet. Experientia 43(10):1110–1111

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3):512–526

    CAS  PubMed  Google Scholar 

  • Undas A, Ariëns RAS (2011) Fibrin clot structure and function. Arterioscler Thromb Vasc Biol 31(12):e88–e99

    Article  CAS  PubMed  Google Scholar 

  • Urano T, Ihara H, Umemura K, Suzuki Y, Oike M, Akita S et al (2001) The profibrinolytic enzyme subtilisin NAT purified from Bacillus subtilis cleaves and inactivates plasminogen activator inhibitor Type 1. J Biol Chem 276(27):24690–24696

    Article  CAS  PubMed  Google Scholar 

  • Versteeg HH, Heemskerk JWM, Levi M, Reitsma PH (2013) New fundamentals in hemostasis. Physiol Rev 93(1):327–358

    Article  CAS  PubMed  Google Scholar 

  • Wang S-L, Yeh P-Y (2006) Production of a surfactant-and solvent-stable alkaliphilic protease by bioconversion of shrimp shell wastes fermented by Bacillus subtilis TKU007. Process Biochem 41(7):1545–1552

    Article  CAS  Google Scholar 

  • Wang C, Du M, Zheng D, Kong F, Zu G, Feng Y (2009) Purification and characterization of nattokinase from Bacillus subtilis natto B-12. J Agric Food Chem 57(20):9722–9729

    Article  CAS  PubMed  Google Scholar 

  • Wei X, Luo M, Xie Y, Yang L, Li H, Xu L et al (2012) Strain screening, fermentation, separation, and encapsulation for production of nattokinase functional food. Appl Biochem Biotechnol 168(7):1753–1764

    Article  CAS  PubMed  Google Scholar 

  • Weng M, Deng X, Bao W, Zhu L, Wu J, Cai Y et al (2015) Improving the activity of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation. Biochem Biophys Res Commun 465(3):580–586

    Article  CAS  PubMed  Google Scholar 

  • Weng Y, Yao J, Sparks S, Wang KY (2017) Nattokinase: an oral antithrombotic agent for the prevention of cardiovascular disease. Int J Mol Sci 18(3):523

    Article  PubMed Central  CAS  Google Scholar 

  • Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(suppl_2):W407–W410

    Article  PubMed Central  PubMed  Google Scholar 

  • Wilson K (2001) Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 56(1):2.4.1-2.4.5

    Article  Google Scholar 

  • Wolberg AS (2016) Primed to understand fibrinogen in cardiovascular disease. Arterioscler Thromb Vasc Biol 36(1):4–6

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wright ES, Yilmaz LS, Noguera DR (2012) DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78(3):717–725

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wu S, Feng C, Zhong J, Huan L (2007) Roles of s3 site residues of nattokinase on its activity and substrate specificity. J Biochem 142(3):357–364

    Article  CAS  PubMed  Google Scholar 

  • Yanagisawa Y, Chatake T, Chiba-Kamoshida K, Naito S, Ohsugi T, Sumi H et al (2010) Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto. Acta Crystallogr F 66(12):1670–1673

    Article  CAS  Google Scholar 

  • Yanagisawa Y, Chatake T, Naito S, Ohsugi T, Yatagai C, Sumi H et al (2013) X-ray structure determination and deuteration of nattokinase. J Synchrotron Radiat 20(6):875–879

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yin L-J, Lin H-H, Jiang S-T (2010) Bioproperties of potent nattokinase from Bacillus subtilis YJ1. J Agric Food Chem 58(9):5737–5742

    Article  CAS  PubMed  Google Scholar 

  • Yongmin Y et al (2019) Nattokinase crude extract inhibits hepatocellular carcinoma growth in mice. J Microbiol Biotechnol 29(8):1281–1287

    Article  CAS  Google Scholar 

  • You C, Zhang C, Kong F, Feng C, Wang J (2016) Comparison of the effects of biocontrol agent Bacillus subtilis and fungicide metalaxyl–mancozeb on bacterial communities in tobacco rhizospheric soil. Ecol Eng 91:119–125

    Article  Google Scholar 

  • Zheng Z, Zuo Z, Liu Z, Tsai K, Liu A, Zou G (2005) Construction of a 3D model of nattokinase, a novel fibrinolytic enzyme from Bacillus natto A novel nucleophilic catalytic mechanism for nattokinase. J Mol Graph Model 23(4):373–380

    Article  CAS  PubMed  Google Scholar 

  • Zheng Z, Ye M, Zuo Z, Liu Z, Tai K, Zou G (2006) Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation. Biochem J 395(3):509–515

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgements

The authors acknowledge the Department of Science and Technology, Govt. of India for providing fellowship to research scholar under the INSPIRE programme.

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RK performed fermentation experiments, analyzed the data, conducted manuscript writing, and manuscript finalization. SK performed molecular experiments, in-silico analyses, analyzed the data, conducted manuscript writing, and manuscript finalization. BPP and SW conceived the idea, analyzed the data and reviewed the manuscript.

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Correspondence to Bibhu Prasad Panda or Saima Wajid.

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The aprN sequences of the five bacterial strains have been submitted to GenBank with accession numbers as KJ205599 for R1 (B. subtilis MTCC 2616); KJ205600 for R2 (B. subtilis MTCC 2756); KJ144819 for R3 (B. subtilis MTCC 2451), KJ174339 for R4 (B. subtilis MTCC 1427) and KJ174338 for R5 (B. subtilis MTCC 7164).

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Kapoor, R., Khowal, S., Panda, B.P. et al. Comparative genomic analyses of Bacillus subtilis strains to study the biochemical and molecular attributes of nattokinases. Biotechnol Lett 44, 485–502 (2022). https://doi.org/10.1007/s10529-022-03226-1

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