In Silico Comparison of Disulfide-Bearing and Disulfide-Free Phytases among Microorganisms

Authors

  • Shirin Ebrahimi Department of Biology, Faculty of Science, Urmia University, Urmia, Iran
  • Rashid Jamei Department of Biology, Faculty of Science, Urmia University, Urmia, Iran
  • Abdolmajid Ghasemian Department of Microbiology, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
  • Seyyed Khalil Shokouhi Mostafavi Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran

DOI:

https://doi.org/10.6000/1927-5951.2017.07.01.4

Keywords:

In silico analysis, phytase, disulfide bond, protein stability

Abstract

Phytases are degrading enzymes that hydrolyze phytate (myo inositol hexa kis phosphate) to release a series of lower phosphate esters of myoinositol and orthophosphate. Phytase successfully used as an animal feed additive to increase the bioavailability of phosphate from phytic acid in the grain-based diets of poultry and swine. In order to investigate structural relationships between disulfide-bearing phytases and disulfide-free phytases, 9 phytases with resolved three-dimensional (3D) structure were retrieved as pdb and FASFA format from Protein Data Bank server and were analyzed using various tools and software. The results showed that 6 out of 9 phytases carry three or more disulfid bonds while the others lack any disulfide bonds. Our results also demonstrated that there is a remarkable correlation between the presence of disulfide bond and the number of amino acid in each phytase which means the larger enzymes contain three or more disulfide bonds whereas the enzymes containing less than 400 amino acids lack any disulfide bond. Additionally, in order to dig out the structure of phytases, some chemical and physical characteristics of phytases such as aliphatic index (AI), isoelectric pH (PI), amino acids percentage, molecular weights (MW) and 3D structure of phytases were analyzed. Results showed that phytases containing disulfide bonds have some identical characteristic including glycine percentage, AI, and 3D structure rather than disulfide-free phytases do. Moreover, evolutionary surveys by means of alignment studies and evaluations were conducted. Evolutionary analysis represented that phytases with disulfide bond most probably exhibited the same evolutionary course.

References

Lei XG, Porres JM, Mullaney EJ, Brinch-Pedersen H. Phytase: source, structure and application, Industrial enzymes, Springer 2007; pp. 505-529. https://doi.org/10.1007/1-4020-5377-0_29

Reddy N, Sathe S, Salunkhe D. Phytates in legumes and cereals. Advances in Food Research 1982; 28: 1-92. https://doi.org/10.1016/S0065-2628(08)60110-X

Ekholm P, Virkki L, Ylinen M, Johansson L. The effect of phytic acid and some natural chelating agents on the solubility of mineral elements in oat bran. Food Chemistry 2003; 80: 165-170. https://doi.org/10.1016/S0308-8146(02)00249-2

Greiner R, Konietzny U. Phytase for food application. Food Technology and Biotechnology 2006; 44: 123-140.

Singh B, Satyanarayana T. Phytase production by a thermophilic mould Sporotrichum thermophile in solid state fermentation and its potential applications. Bioresource Technology 2008; 99: 2824-2830.

Han Y, Wilson DB, gen Lei X. Expression of an Aspergillus nigerphytase gene (phyA) in Saccharomyces cerevisiae. Applied and Environmental Microbiology 1999; 65: 1915-1918.

Kim T, Mullaney EJ, Porres JM, Roneker KR, Crowe S, Rice S, Ko T, Ullah AH, Daly CB, Welch R. Shifting the pH profile of Aspergillus niger PhyA phytase to match the stomach pH enhances its effectiveness as an animal feed additive. Applied and Environmental Microbiology 2006; 72: 4397-4403. https://doi.org/10.1128/AEM.02612-05

Cowieson A, Adeola O. Carbohydrases, protease, and phytase have an additive beneficial effect in nutritionally marginal diets for broiler chicks. Poultry Science 2005; 84: 1860-1867. https://doi.org/10.1093/ps/84.12.1860

Lei X, Ku P, Miller E, Yokoyama M. Supplementing corn-soybean meal diets with microbial phytase linearly improves phytate phosphorus utilization by weanling pigs. Journal of Animal Science 1993; 71: 3359-3367.

Lei X, Ku P, Miller E, Yokoyama M, Ullrey D. Supplementing corn-soybean meal diets with microbial phytase maximizes phytate phosphorus utilization by weanling pigs. Journal of Animal Science 1993; 71: 3368-3375.

Gunasekaran K, Nagarajaram H, Ramakrishnan C, Balaram P. Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals. Journal of Molecular Biology 1998; 275: 917-932. https://doi.org/10.1006/jmbi.1997.1505

Lassen SF, Breinholt J, Østergaard PR, Brugger R, Bischoff A, Wyss M, Fuglsang CC. Expression, gene cloning, and characterization of five novel phytases from four basidiomycete fungi: Peniophora lycii, Agrocybe pediades, a Ceriporia sp., and Trametes pubescens. Applied and Environmental Microbiology 2001; 67: 4701-4707. https://doi.org/10.1128/AEM.67.10.4701-4707.2001

Deutscher MP. Maintaining protein stability. Methods in Enzymology 1990; 182: 83-89. https://doi.org/10.1016/0076-6879(90)82010-Y

Jaenicke R. Protein stability and molecular adaptation to extreme conditions. EJB Reviews 1991, Springer 1992; pp. 291-304.

Betz SF. Disulfide bonds and the stability of globular proteins. Protein Science 1993; 2: 1551-1558. https://doi.org/10.1002/pro.5560021002

Berman HM, Battistuz T, Bhat T, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S. The protein data bank. Acta Crystallographica Section D: Biological Crystallography 2002; 58: 899-907. https://doi.org/10.1107/S0907444902003451

DeLano WL. The PyMOL molecular graphics system 2002.

Schrödinger L. The PyMOL molecular graphics system, version 1.3 r1, Py-MOL. The PyMOL Molecular Graphics System 2010; Version, 1.

DeepView–Swiss P. Home Page. Viewer http://www. expasy. org/spdbv (accessed Jan 2008). (b) Guex N, Peitsch MC. Electrophoresis 1997; 18: 2714-2723.

Guex N, Peitsch MC. SWISS‐MODEL and the Swiss‐Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 1997; 18: 2714-2723. https://doi.org/10.1002/elps.1150181505

Kerr A. Desktop Sequence Analysis: software review, The Bioinformatics Knowledgeblog 2011.

Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server, The proteomics protocols handbook, Springer 2005; pp. 571-607. https://doi.org/10.1385/1-59259-890-0:571

Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T. Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols 2008; 4: 1-13. https://doi.org/10.1038/nprot.2008.197

Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 2003; 31: 3381-3385. https://doi.org/10.1093/nar/gkg520

Bhattacharya D, Cheng J. 3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization. Proteins: Structure, Function, and Bioinformatics 2013; 81: 119-131. https://doi.org/10.1002/prot.24167

Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. Journal of Computational Chemistry 2004; 25: 1849-1857. https://doi.org/10.1002/jcc.20110

Pei J. Multiple protein sequence alignment. Current opinion in Structural Biology, 2008; 18: 382-386. https://doi.org/10.1016/j.sbi.2008.03.007

Baum DA, Smith S, Donovan SS. EVOLUTION The Tree-Thinking Challenge, Science-New York then Washington-, 2005; 310: 979.

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28: 1647-1649. https://doi.org/10.1093/bioinformatics/bts199

Omland KE. Interpretation of Phylogenetic Trees, The Princeton Guide to Evolution 2013; 51.

Woese CR. Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences 2000; 97: 8392-8396. https://doi.org/10.1073/pnas.97.15.8392

Ansari SN, Iliyas S. A comparative study of protein structure visualization tools for various display capabilities. Bioscience Discovery: An International Journal of Life Sciences 2011; 2.

Kumar K, Dixit M, Khire J, Pal S. Atomistic details of effect of disulfide bond reduction on active site of Phytase B from Aspergillus niger: A MD Study. Bioinformation 2013; 9: 963. https://doi.org/10.6026/97320630009963

Arndt T. Visual software tools for bioinformatics. Journal of Visual Languages & Computing 2008; 19: 291-301. https://doi.org/10.1016/j.jvlc.2007.06.001

Atsushi I. Thermostability and aliphatic index of globular proteins. Journal of Biochemistry 1980; 88: 1895-1898.

Pasamontes L, Haiker M, Wyss M, Tessier M, Van Loon A. Gene cloning, purification, and characterization of a heat-stable phytase from the fungus Aspergillus fumigatus. Applied and Environmental Microbiology 1997; 63: 1696-1700.

Neurath H. The role of glycine in protein structure. Journal of the American Chemical Society 1943; 65: 2039-2041. https://doi.org/10.1021/ja01250a504

Nakashima H, Nishikawa K, Tatsuo O. The folding type of a protein is relevant to the amino acid composition Journal of Biochemistry 1986; 99: 153-162.

Huelsenbeck JP. Performance of phylogenetic methods in simulation. Systematic Biology 1995; 44: 17-48. https://doi.org/10.1093/sysbio/44.1.17

Huelsenbeck JP, Hillis DM. Success of phylogenetic methods in the four-taxon case. Systematic Biology 1993; 42: 247-264. https://doi.org/10.1093/sysbio/42.3.247

Huelsenbeck JP, Rannala B. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 1997; 276: 227-232. https://doi.org/10.1126/science.276.5310.227

Diamond R. On the multiple simultaneous superposition of molecular structures by rigid body transformations. Protein Science 1992; 1: 1279-1287. https://doi.org/10.1002/pro.5560011006

Reva BA, Finkelstein AV, Skolnick J. What is the probability of a chance prediction of a protein structure with an rmsd of 6 Å? Folding and Design 1998; 3: 141-147. https://doi.org/10.1016/S1359-0278(98)00019-4

Horovitz A, Matthews JM, Fersht AR. α-Helix stability in proteins: II. Factors that influence stability at an internal position. Journal of Molecular Biology 1992; 227: 560-568. https://doi.org/10.1016/0022-2836(92)90907-2

Anfinsen CB. Principles that govern the folding of protein chains. Science 1973; 181: 223-230. https://doi.org/10.1126/science.181.4096.223

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Published

2017-02-17

How to Cite

Ebrahimi, S., Jamei, R., Ghasemian, A., & Mostafavi, S. K. S. (2017). In Silico Comparison of Disulfide-Bearing and Disulfide-Free Phytases among Microorganisms. Journal of Pharmacy and Nutrition Sciences, 7(1), 24–34. https://doi.org/10.6000/1927-5951.2017.07.01.4

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