Phylogeny, Characterisation and Identification of Creatine Kinase Genes (ckma and ckmb) in Zebrafish (Danio rerio)

Year 2020, Volume: 1 Issue: 1, 12 - 21, 31.12.2020

Gökhan Arslan Erdal Özdemir Mehtap Bayır

Abstract

Creatine kinase genes (ckma and ckmb) in zebrafish (Danio rerio), an aquatic model organism, have been characterized and identified. However, the gene structure is designed using exons, introns, amino acids produced by the exons. TATA boxex, poly A tails and 5' UTR and 3' UTR regions of zebrafish ckma and ckma genes are showed at the gene structure. In addition, chromosomal regions of ckma and ckmb genes were determined. The other genes which are placed in the same region with ckma and ckmb genes were found in medaka and human which are the orthologs of zebrafish, and conserved gene syntheny was designed manually according to these regions. In addition, phylogenetic relationship was determined between zebrafish and it’s some orthologs using ckma and ckmb gene sequences. Genetic affinity between zebrafish and its orthologs was calculated as similarity-identity % rate and given as a table. For all these studies, bioinformatics databases (NCBI database, Ensembl genomic database, Expasy, Reverse Complementary) and programs (MEGA6 program, BLOSUM62 matrix program and BioEdit software) were used. In this study, characterization and identification of ckma and ckmb genes in zebrafish (D. rerio) was completed using bioinformatics tools and some data to be used in the future studies on molecular stress response were presented.

Keywords

Danio rerio, Genomic organisation, Model organism, Bioinformatics

References

• Amores, A., Force A., Yan, Y. L., Joly, L., Amemiya, C., Fritz, A., Ho, R. K., Langeland, J., Prince V., & Wang Y. L. (1998). Zebrafish hox clusters and vertebrate genome evolution. Science, 282: 1711-1714.
• Arslan, H. (2015). Pestisit Sinerjisinin; Gökkuşağı Alabalıklarında (Oncorhynchus mykiss) Yüzme Performansı, Biyokimyasal Hematolojik, Histopatolojik Ve Genotoksik Etkilerinin Araştırılması, Doktora Tezi. Atatürk Üniversitesi, Erzurum, Turkey.
• Basu S., Binder, R. J., Suto, R., Anderson, K. M., & Srivastava, P. K. (2000). Necrotic but not apoptotic heat shock proteins, which deliver a partial maturation signal to dentritic cells and activate the NF-kB pathway. Interntional Immunology, 12: 1539-1546.
• Bayır, M., Arslan, G., & Yıldız Oğuzhan, P. (2020). Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes). Marine Science and Technology Bulletin, 9(1): 15-22.
• Braasch, I., & Postlethwait, J. H. I. (2012). Polyploidy in fish and the teleost genome duplication. In: Soltis, P. S., Soltis, D. E. (eds.), Polyploidy and Genome Evolution. Springer. 341-383.
• Carpio, Y., & Estrada, M. P. (2006). Zebrafish as a Genetic Model organism. Biotecnología Aplicada, 23: 265-270.
• Collins, F. S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R., & Walters, L. (1998). New Goals for the U.S. Human Genome Project: 1998-2003. Science, 282: 682-689.
• Felsenstein, J. (1989). PHYLIP-Phylogeny inference package. Cladistics, 5: 164-166.
• Gilmour, D. T., Jessen, J. R., & Lin, S. (2002). Manipulating gene expression in the zebrafish. In: Zebrafish: A Practical Approach, Nusslein-Volhard C, Dahm R, (eds.). Oxford: Oxford University Press, p: 121-43.
• Gromiha, M. M. (2010). Protein Bioinformatics: From Sequence to Function. Academic Press, 339 p.
• Iwama, G. K., Vijayan, M. M., Forsyth, R. B., & Ackerman, P. A. (1999). Heat shock proteins and physiological stress in fish. American Zoologist, 39: 901-909.
• Kell, A. J. E., Yamins, D. L. K., Shook, E. N., & Norman-Haignere, S. V. (2018). A Task-Optimized Neural Network Replicates Human Auditory Behavior, Predicts Brain Responses, and Reveals a Cortical Processing Hierarchy. Neron, 98(3): 630-644.
• Lieschke, G. J., & Currie, P. D. (2007). Animal models of human disease: zebrafish swim into view. Nature Reviews Genetics, 8: 353-367.
• Ma, C. (2004). Animal models of disease. Modern Drug Discovery, 7(6): 30-36.
• McLean, L., Young, I. S., Doherty, M. K., Robertson, D. H. L., Cossins, A. R., Gracey, A. Y., Beynon, R. J., & Whitfield, P.D. (2007). Global cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics, 7: 2667-2681.
• Meyer, A., & Schartl, M. (1999). Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Current Opinion Cell Biology, 11: 699-704.
• Postlethwait, J. H., Woods, I. G., Ngo-Hazelett, P., Yan, Y. L., Kelly, P. D., Chu, F., Huang, H., Hill-Force, A., & Talbot, W. S. (2000). Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Reserch, 10: 1890-1902.
• Stryer, L. (1995). Biochemistry, W.H. Freemanand Company, 4th. Ed. New York, 1064 p.
• Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30(12): 2725.
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice+++, Nucleic Acids Research, 22: 4673-4680.
• Wu, C. L., Lin, T. H., Chang, T. L., Sun, H. W., Hui, C. F., & Wu, J. L. (2011). Zebrafish HSC70 promoter to express carp muscle-specific creatine kinase for acclimation under cold condition. Transgenic Research, 20: 1217-1226.