Genome-Wide Determination, Characterization and Bioinformatic Analysis of Cold Shock Protein (CSP) Genes In Atlantic Salmon (Salmo salar), Carp (Cyprinus carpio) and Rainbow Trout (Oncorhynchus mykiss)

Abstract

Atlantic salmon (Salmo salar) is the symbol of the underwater world; carp (Cyprinus carpio) is a freshwater fish that gives its name to the Cyprinidae family and rainbow trout (Oncorhynchus mykiss) is a species of Salmonidae family, like as salmon. These three types of fish are important in the world because they are made of fish farming. The cold shock proteins (CSP) were first described in Escherichia coli and are the conserved proteins that have the activity to protect the organism against cold temperatures. They can be characterized by general stress response in fish. There is no comprehensive study related to the identification of CSPs in fish genomes. In this study, determination, characterization and bioinformatics analysis of CSPs were carried out in the genomes of salmon, carp and rainbow trout. The study results represent preliminary knowledge about understanding of the effects of these proteins in cold tolerance in economically important fish species.

Keywords

• Atlantic Salmon
• Carp
• Rainbow Trout
• Cold Shock Protein

Genome-Wide Determination, Characterization and Bioinformatic Analysis of Cold Shock Protein (CSP) Genes In Atlantic Salmon (Salmo salar), Carp (Cyprinus carpio) and Rainbow Trout (Oncorhynchus mykiss)

Abstract

Atlantik somonu (Salmo salar) sualtı dünyasının simgesidir; sazan balığı (Cyprinus carpio), sazangiller (Cyprinidae) familyasına adını veren tatlı su balığıdır ve gökkuşağı alabalığı (Oncorhynchus mykiss) somon gibi Salmonidae ailesine ait bir balık türüdür. Bu üç balık türü dünyada en çok çiftçiliği yapılan balık türlerinden olduğu için önemlidir. Soğuk şoku proteinleri (CSP) ise ilk kez Escherichia coli'de tanımlanmış olup organizmayı soğuğa karşı koruma aktivitesine sahip olan korunmuş proteinlerdir. Bunlar, balıklardaki genel stres tepkisi ile karakterize edilebilir. Balık genomlarında CSP proteinlerinin tanımlanması ile ilgili kapsamlı bir çalışma yoktur. Bu çalışmada, Atlantik somonu, sazan balığı ve gökkuşağı alabalığı genomlarında CSP proteinlerinin belirlenmesi karakterizasyonu ve biyoinformatik analizleri gerçekleştirilmiştir. Çalışma sonuçları, ekonomik öneme sahip balık türlerinde bu proteinlerin soğuk toleransındaki etkilerinin anlaşılması için ön bilgi sunmaktadır.

Keywords

• Somon Balığı
• Sazan Balığı
• Gökkuşağı Alabalığı
• Biyoinformatik
• Soğuk Şoku Proteini

References

1. [1] Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., and Grammes, F.. The Atlantic salmon genome provides insights into rediploidization. Nature, 533(7602), 200, 2016.
2. [2 ] Verspoor, E., Stradmeyer, L., & Nielsen, J. L. (Eds.). The Atlantic salmon: genetics, conservation and management. John Wiley & Sons, 2008.
3. [3] Kottelat, M. and J. Freyhof,. Handbook of European freshwater fishes. Berlin, 2007, 646 pp.
4. [4] Courtenay, Walter R.; Welcomme, R. L., "International Introductions of Inland Aquatic Species". Copeia. 1989 (2): 520.
5. [5] Balon, Eugene K., "Probable Origin of Domestication", Domestication of the carp Cyprinus caprio L., Royal Ontario Museum, 1974, pp. 16–18.
6. [6] Banarescu, P., B. Coad., Cyprinids of Euroasia. in I Winfield, J Nelson, eds. Cyprinids Fishes, London: Chapman and Hall, 1991, Pp 127-155.
7. [7] McCrimmon, H., Carp in Canada. Fisheries Research Board Of Canada, 1968.
8. [8] Fornshell, G.. Rainbow trout—challenges and solutions. Reviews in Fisheries Science, 2002, 10(3-4), 545-557.

9. [9] Hardy, R. W., Rainbow trout, Oncorhynchus mykiss. Nutrient requirements and feeding of finfish for aquaculture, 2002,184-202.
10. [10] Thieringer, H. A., Jones, P. G., & Inouye, M., Cold shock and adaptation. Bioessays, 1998, 20(1), 49-57.
11. [11] Phadtare, S., Alsina, J., & Inouye, M., Cold-shock response and cold-shock proteins. Current opinion in microbiology, 1999, 2(2), 175-180.
12. [12] Lindquist, J. A., & Mertens, P. R., Cold shock proteins: from cellular mechanisms to pathophysiology and disease. Cell Communication and Signaling, 2018, 16(1), 63.
13. [13] Keto-Timonen, R., Hietala, N., Palonen, E., Hakakorpi, A., Lindström, M., & Korkeala, H., Cold shock proteins: a minireview with special emphasis on Csp-family of enteropathogenic Yersinia. Frontiers in microbiology, 2016, 7, 1151.
14. [14] Crawshaw, L. I., Physiological and behavioral reactions of fishes to temperature change. Journal of the Fisheries Board of Canada, 1977, 34(5), 730-734.
15. [15] Tanck, M. W. T., Booms, G. H. R., Eding, E. H., Bonga, S. W., & Komen, J., Cold shocks: a stressor for common carp. Journal of fish Biology, 2000, 57(4), 881-894.
16. [16] Fry, F. E. J., Effects of the environment on animal activity. Publ. Out. Fish. Res. Lab., 1947, 55(68), 1-62.1
17. [17] Donaldson, M. R., Cooke, S. J., Patterson, D. A., & Macdonald, J. S., Cold shock and fish. Journal of Fish Biology, 2008, 73(7), 1491-1530.
18. [18] Kumar, S., Stecher, G., & Tamura, K., MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution, 2016, 33(7), 1870-1874.
19. [19] Hu B., Jin J., Guo A.Y., Zhang H., Luo J. and Gao G., GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 2015, 31(8), 1296-1297.
20. [20] Saitou, N., & Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 1987, 4(4), 406-425.
21. [21] Bailey, T. L., & Elkan, C., Fitting a mixture model by expectation maximization to discover motifs in bipolymers, 1994.
22. [22] Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., & Lopez, R.,. InterProScan: protein domains identifier. Nucleic acids research, 2005, 33(suppl_2), W116-W120.
23. [23] Conesa, A., & Götz, S., Blast2GO: A comprehensive suite for functional analysis in plant genomics. International journal of plant genomics, 2008.
24. [24] Kelley, L. A., & Sternberg, M. J., Protein structure prediction on the Web: a case study using the Phyre server. Nature protocols, 2009, 4(3), 363.
25. [25] Jones-Rhoades, M. W., & Bartel, D. P., Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular cell, 2004, 14(6), 787-799.