Computational analysis of collagenase from different Vibrio, Clostridium and Bacillus strains to find new enzyme sources

Navid Nezafat, Manica Negahdaripour, Ahmad Gholami, Younes Ghasemi


Collagenase is one the important enzyme, which is applied in varied fields ranging from tannery, food and cosmetic industries to clinical therapies. Currently, the commercially available collagenase enzyme has been produced by Clostridium histolyticum bacteria. In our study, in order to find new sources of collagenase producer, 30 collagenases from different species of Clostridium, Vibrio and Bacillus were evaluated from the view of phylogenetic relation, domain architecture and Physiochemical features. Totally our results indicate that the non-pathogenic C. novyi (NT) with the aliphatic index (80.68), instability index (27), pI (6.54), Mw (112.838 kDa) and two PPC domain could be suggested as potent bacteria for industrial production of collagenase.

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Lee CH, Singla A, Lee Y. Biomedical applications of collagen. International journal of pharmaceutics. 2001;221(1):1-22.

Ferreira AM, Gentile P, Chiono V, Ciardelli G. Collagen for bone tissue regeneration. Acta biomaterialia. 2012;8(9):3191-200.

Peng W-j, Yan J-w, Wan Y-n, Wang B-x, Tao J-h, Yang G-j, et al. Matrix Metalloproteinases: A Review of Their Structure and Role in Systemic Sclerosis. J Clin Immunol. 2012;32(6):1409-14.

Gutiérrez-Fernández A, Inada M, Balbín M, Fueyo A, Pitiot AS, Astudillo A, et al. Increased inflammation delays wound healing in mice deficient in collagenase-2 (MMP-8). The FASEB Journal. 2007 August 1, 2007;21(10):2580-91.

Beltran JA, Bonnet M, Ouali A. Collagenase Effect on Thermal Denaturation of Intramuscular Collagen. Journal of Food Science. 1991;56(6):1497-9.

Kanth SV, Venba R, Madhan B, Chandrababu NK, Sadulla S. Studies on the influence of bacterial collagenase in leather dyeing. Dyes and Pigments. 2008;76(2):338-47.

Vellard M. The enzyme as drug: application of enzymes as pharmaceuticals. Current Opinion in Biotechnology. 2003;14(4):444-50.

Watanabe K. Collagenolytic proteases from bacteria. Appl Microbiol Biotechnol. 2004;63(5):520-6.

Takeuchi H, Shibano Y, Morihara K, Fukushima J, Inami S, Keil B, et al. Structural gene and complete amino acid sequence of Vibrio alginolyticus collagenase. Biochem J. 1992;281:703-8.

Teramura N, Tanaka K, Iijima K, Hayashida O, Suzuki K, Hattori S, et al. Cloning of a novel collagenase gene from the gram-negative bacterium Grimontia (Vibrio) hollisae 1706B and its efficient expression in Brevibacillus choshinensis. Journal of bacteriology. 2011;193(12):3049-56.

Miyoshi S-i, Nitanda Y, Fujii K, Kawahara K, Li T, Maehara Y, et al. Differential gene expression and extracellular secretion of the collagenolytic enzymes by the pathogen Vibrio parahaemolyticus. FEMS microbiology letters. 2008;283(2):176-81.

Houle M-A, Grenier D, Plamondon P, Nakayama K. The collagenase activity of Porphyromonas gingivalis is due to Arg-gingipain. FEMS microbiology letters. 2003;221(2):181-5.

Awad MM, Ellemor DM, Bryant AE, Matsushita O, Boyd RL, Stevens DL, et al. Construction and virulence testing of a collagenase mutant of Clostridium perfringens. Microbial pathogenesis. 2000;28(2):107-17.

Jung C-M, Matsushita O, Katayama S, Minami J, Sakurai J, Okabe A. Identification of Metal Ligands in theClostridium histolyticum ColH Collagenase. Journal of bacteriology. 1999;181(9):2816-22.

Wu Q, Li C, Li C, Chen H, Shuliang L. Purification and characterization of a novel collagenase from Bacillus pumilus Col-J. Applied biochemistry and biotechnology. 2010;160(1):129-39.

Tran LH, Nagano H. Isolation and Characteristics of Bacillus subtilis CN2 and its Collagenase Production. Journal of Food Science. 2002;67(3):1184-7.

Preet Kaur S, Azmi W. Cost Effective Production of a Novel Collagenase from a Non-Pathogenic Isolate Bacillus tequilensis. Current Biotechnology. 2013;2(1):17-22.

Petrova D, Derekova A, Vlahov S. Purification and properties of individual collagenases fromStreptomyces sp. strain 3B. Folia Microbiol. 2006;51(2):93-8.

Abdel-Fattah A. Production and partial characterization of collagenase from marine Nocardiopsis dassonvillei NRC2aza using chitin wastes. Egyptian Pharmaceutical Journal. 2013;12(2):109.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of molecular biology. 1990;215(3):403-10.

Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic acids research. 2014;42(W1):W320-W4.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution. 2013;30(12):2725-9.

Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server: Springer; 2005.

Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, et al. CDD: NCBI's conserved domain database. Nucleic acids research. 2014:gku1221.

Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic acids research. 2013:gkt953.

Demina N. Cosmetic product for removing rough skin and reducing wrinkles comprises the microbial collagenase preparation ultralysin. WO2009002208-A1 WORU000522. 2007;27.

Nakayama T, Tsuruoka N, Akai M, Nishino T. Thermostable collagenolytic activity of a novel thermophilic isolate, Bacillus sp. strain NTAP-1. Journal of bioscience and bioengineering. 2000;89(6):612-4.

Nezafat N, Ghasemi Y, Javadi G, Khoshnoud MJ, Omidinia E. A novel multi-epitope peptide vaccine against cancer: an in silico approach. Journal of theoretical biology. 2014;349:121-34.

Zamani M, Nezafat N, Negahdaripour M, Dabbagh F, Ghasemi Y. In silico evaluation of different signal peptides for the secretory production of human growth hormone in E. coli. International Journal of Peptide Research and Therapeutics. 2015:1-8.

Gholami A, Shahin S, Mohkam M, Nezafat N, Ghasemi Y. Cloning, Characterization and Bioinformatics Analysis of Novel Cytosine Deaminase from Escherichia coli AGH09. International Journal of Peptide Research and Therapeutics.1-10.

Ghasemi Y, Dabbagh F, Rasoul-Amini S, Haghighi AB, Morowvat MH. The possible role of HSPs on Behçet's disease: A bioinformatic approach. Computers in biology and medicine. 2012;42(11):1079-85.



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