เปรียบเทียบลำดับกรดอะมิโนและคุณสมบัติทางชีวเคมีของเอนไซม์เพอร์ออกซิเดสในพืช ยีสต์ แบคทีเรีย และมนุษย์: A Comparative Computational analysis of Amino Acid Sequences and Biochemical Properties of Peroxidase Enzymes in Plants, Yeast, Bacteria, and Humans

Patsarawadee Paojinda; Napat Pimsiri; Nunthawadee Niamnuy; Piya Wongyanin; Pramoon Arooncharus; Nittiya Chowchaikong; Ranida Tuanudom; Waranya Imprasittichai

Authors

Patsarawadee Paojinda Medical Technology Program, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok
Napat Pimsiri Medical Technology Program, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok
Nunthawadee Niamnuy Medical Technology Program, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok
Piya Wongyanin Medical Technology Program, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok
Pramoon Arooncharus Medical Technology Program, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok
Nittiya Chowchaikong Faculty of Medical Technology, Rangsit University, Phathum Thani
Ranida Tuanudom Preclinic Health Science Center, Faculty of Medicine, Bangkokthonburi University, Bangkok
Waranya Imprasittichai Department of Basic Medical Science, Faculty of Medicine Vajira hospital, Navamindradhiraj University, Bangkok

Keywords:

peroxidase , amino acid sequences , bioinformatics

Abstract

Peroxidases (E.C.1.11.1.7) are commonly found in natural oxidoreductases and can oxidize with various reactants such as guaiacol, pyrogallol, etc. It is popular for use in immunology research, as well as the treatment of phenolic compounds in wastewater, peroxides elimination from raw materials in the food industry, and as biosensor. The objectives of this research were to compare the amino acid sequences and biochemical properties of peroxidase in plants, yeast, bacteria and humans in 7 types including Arabidopsis thaliana, Armoracia rusticana, Escherichia coli, Glycine max, Homo sapiens, Ipomoea batatas, and Saccharomyces cerevisiae from the NCBI database (http://www.ncbi.nlm.nih.gov/protein). The software of the ExPASy SIB Bioinformatics SOPMA tool was used to analyze the physicochemical data by comparing similarities among protein chains, while the ClustalW software was used to analyze the phylogenetic relationships. The lengths of amino acid sequences for peroxidase in plants, yeast, bacteria, and humans were found to be in the ranges of 58 – 352, theoretical pI 4.72-8.76, negative charge (Asp + Glu) 2-45, positive charge (Arg + Lys) 3-32, extinction coefficient 8980-32680, instability index 26.05-59.62, and grand average of hydropathicity (GRAVY) -0.442-0.190. In the comparison of amino acid sequences for peroxidase among Armoracia rusticana, Arabidopsis thaliana, Escherichia coli, Glycine max, Homo sapiens, Ipomoea batatas, and Saccharomyces cerevisiae, the highest percent identity was found in Arabidopsis thaliana at 65.70%. In the analysis of the phylogenetic relationships, short phylogenetic branches were found in 4 living things including Armoracia rusticana, Arabidopsis thaliana, Glycine max, and Ipomoea batatas, indicating close phylogenetic relationships. The results from this study provide insight into the role of peroxidase in the development of enzymatic engineering to promote the potential of industry, medicine, and bioremediation.

Downloads

Download data is not yet available.

References

Hiraga S, Sasaki K, Ito H, Ohashi Y, Matsui H. A large family of class III plant peroxidases. Plant and Cell Physiology 2001;42(5):462-8.

O'Brien PJ. Peroxidases. Chemico-Biological Interactions 2000;129(1-2):113-39.

Pandey VP, Awasthi M, Singh S. A comprehensive review on function and application of plant peroxidases. Biochem Anal Biochem 2017;6(1):308.

Krainer FW, Glieder A. An updated view on horseradish peroxidases: recombinant production and biotechnological applications. Appl Microbiol Biotechnol 2015;99:1611-25.

Flohe L, Ursini F. Peroxidase: a term of many meanings. Antioxid Redox Signal 2008;10(9):1485-90.

Rompel A, Albers M, Naseri JI, Gerdemann C, Büldt-Karentzopoulos K, Jasper B, et al. Purification, cloning and characterization of a novel peroxidase isozyme from sweetpotatoes (Ipomoea batatas). Biochim Biophys Acta 2007;1774(11):1422-30.

Henriksen A, Mirza O, Indiani C, Teilum K, Smulevich G, Welinder KG, et al. Structure of soybean seed coat peroxidase: a plant peroxidase with unusual stability and haem-apoprotein interactions. Protein Sci 2001;10(1):108-15.

Welinder KG. Superfamily of plant fungal and bacterial peroxidase. Curr Opin Struct Biol 1992;2(3):388-93.

Passardi F, Penel C, Dunand C. Performing the paradoxical: how plant peroxidases modify the cell wall. Trends Plant Sci 2004;9(11):534-40.

Welinder KG. Covalent structure of the glycoprotein horseradish peroxidase (EC 1.11.1.7). FEBS Lett 1976;72(1):19-23.

Chauhan V, Kumari V, Kanwa SS. Comparative analysis of amino acid sequence diversity and physiochemical properties of peroxidase superfamily. J Protein Res Bioinform 2020;2(003):1-8.

Spadiut O, Rossetti L, Dietzsch C, Herwig C. Purification of a recombinant plant peroxidase produced in Pichia pastoris by a simple 2-step strategy. Protein Expr Purif 2012;86(2):89-97.

Tognolli M, Penel C, Greppin H, Simon P. Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana. Gene 2002;288(1-2):129-38.

Passardi F, Theiler G, Zamocky M, Cosio C, Rouhier N, Teixera F, et al. Peroxibase: the peroxidase database. Phytochemistry 2007;68(12):1605-11.

Duvaud S, Gabella C, Lisacek F, Stockinger H, Ioannidis V, Durinx C. Expasy, the swiss bioinformatics resource portal, as designed by its users. Nucleic Acids Res 2021;49(W1):216-27.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatic 2007;23(21):2947-48.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools. Nucleic Acids Res 1997;25(24): 4876-82.

Sievers F, Higgins DG. The Clustal Omega Multiple Alignment Package. Methods Mol Biol 2021;2231:3-16.

Ajawatanawong P. Sequence analysis: from sequence to information [internet]. Bangkok; 2010 [updated 2010 Feb 1; cited 2021 Oct 13] Available from: http://thaibioinfonetwork.blogspot.com/2010/02/sequence-analysis-from-sequence-to.html

Hillis DM. Phylogenetic analysis. Curr Biol 1997;7(3):129-31.

Dutta B, Banerjee A, Chakraborty P, Bandopadhyay R. In silico studies on bacterial xylanase enzyme: Structural and functional insight. J Genet Eng Biotechnol 2018;16(2):749-56.

A Comparative Computational analysis of Amino Acid Sequences and Biochemical Properties of Peroxidase Enzymes in Plants, Yeast, Bacteria, and Humans