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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)

Year 2019, Volume: 5 Issue: 1, 16 - 35, 27.06.2019

Büşra Özkan Buket Ustaoğlu Tevfik Hasan Can Mehmet Cengiz Baloglu Yasemin Celik Altunoglu

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

References

  • [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 ] Verspoor, E., Stradmeyer, L., & Nielsen, J. L. (Eds.). The Atlantic salmon: genetics, conservation and management. John Wiley & Sons, 2008.
  • [3] Kottelat, M. and J. Freyhof,. Handbook of European freshwater fishes. Berlin, 2007, 646 pp.
  • [4] Courtenay, Walter R.; Welcomme, R. L., "International Introductions of Inland Aquatic Species". Copeia. 1989 (2): 520.
  • [5] Balon, Eugene K., "Probable Origin of Domestication", Domestication of the carp Cyprinus caprio L., Royal Ontario Museum, 1974, pp. 16–18.
  • [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] McCrimmon, H., Carp in Canada. Fisheries Research Board Of Canada, 1968.
  • [8] Fornshell, G.. Rainbow trout—challenges and solutions. Reviews in Fisheries Science, 2002, 10(3-4), 545-557.
  • [9] Hardy, R. W., Rainbow trout, Oncorhynchus mykiss. Nutrient requirements and feeding of finfish for aquaculture, 2002,184-202.
  • [10] Thieringer, H. A., Jones, P. G., & Inouye, M., Cold shock and adaptation. Bioessays, 1998, 20(1), 49-57.
  • [11] Phadtare, S., Alsina, J., & Inouye, M., Cold-shock response and cold-shock proteins. Current opinion in microbiology, 1999, 2(2), 175-180.
  • [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] 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] 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] 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] Fry, F. E. J., Effects of the environment on animal activity. Publ. Out. Fish. Res. Lab., 1947, 55(68), 1-62.1
  • [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] 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] 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] 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] Bailey, T. L., & Elkan, C., Fitting a mixture model by expectation maximization to discover motifs in bipolymers, 1994.
  • [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] Conesa, A., & Götz, S., Blast2GO: A comprehensive suite for functional analysis in plant genomics. International journal of plant genomics, 2008.
  • [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] 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.

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)

Year 2019, Volume: 5 Issue: 1, 16 - 35, 27.06.2019

Büşra Özkan Buket Ustaoğlu Tevfik Hasan Can Mehmet Cengiz Baloglu Yasemin Celik Altunoglu

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] 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 ] Verspoor, E., Stradmeyer, L., & Nielsen, J. L. (Eds.). The Atlantic salmon: genetics, conservation and management. John Wiley & Sons, 2008.
  • [3] Kottelat, M. and J. Freyhof,. Handbook of European freshwater fishes. Berlin, 2007, 646 pp.
  • [4] Courtenay, Walter R.; Welcomme, R. L., "International Introductions of Inland Aquatic Species". Copeia. 1989 (2): 520.
  • [5] Balon, Eugene K., "Probable Origin of Domestication", Domestication of the carp Cyprinus caprio L., Royal Ontario Museum, 1974, pp. 16–18.
  • [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] McCrimmon, H., Carp in Canada. Fisheries Research Board Of Canada, 1968.
  • [8] Fornshell, G.. Rainbow trout—challenges and solutions. Reviews in Fisheries Science, 2002, 10(3-4), 545-557.
  • [9] Hardy, R. W., Rainbow trout, Oncorhynchus mykiss. Nutrient requirements and feeding of finfish for aquaculture, 2002,184-202.
  • [10] Thieringer, H. A., Jones, P. G., & Inouye, M., Cold shock and adaptation. Bioessays, 1998, 20(1), 49-57.
  • [11] Phadtare, S., Alsina, J., & Inouye, M., Cold-shock response and cold-shock proteins. Current opinion in microbiology, 1999, 2(2), 175-180.
  • [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] 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] 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] 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] Fry, F. E. J., Effects of the environment on animal activity. Publ. Out. Fish. Res. Lab., 1947, 55(68), 1-62.1
  • [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] 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] 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] 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] Bailey, T. L., & Elkan, C., Fitting a mixture model by expectation maximization to discover motifs in bipolymers, 1994.
  • [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] Conesa, A., & Götz, S., Blast2GO: A comprehensive suite for functional analysis in plant genomics. International journal of plant genomics, 2008.
  • [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] 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.
There are 25 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Research Articles
Authors

Büşra Özkan This is me

Buket Ustaoğlu This is me

Tevfik Hasan Can This is me

Mehmet Cengiz Baloglu This is me

Yasemin Celik Altunoglu

Publication Date June 27, 2019
Submission Date May 11, 2019
Published in Issue Year 2019 Volume: 5 Issue: 1

Cite

APA Özkan, B., Ustaoğlu, B., Can, T. H., Baloglu, M. C., et al. (2019). 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). Kastamonu University Journal of Engineering and Sciences, 5(1), 16-35.
AMA Özkan B, Ustaoğlu B, Can TH, Baloglu MC, Celik Altunoglu Y. 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). KUJES. June 2019;5(1):16-35.
Chicago Özkan, Büşra, Buket Ustaoğlu, Tevfik Hasan Can, Mehmet Cengiz Baloglu, and Yasemin Celik Altunoglu. “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)”. Kastamonu University Journal of Engineering and Sciences 5, no. 1 (June 2019): 16-35.
EndNote Özkan B, Ustaoğlu B, Can TH, Baloglu MC, Celik Altunoglu Y (June 1, 2019) 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). Kastamonu University Journal of Engineering and Sciences 5 1 16–35.
IEEE B. Özkan, B. Ustaoğlu, T. H. Can, M. C. Baloglu, and Y. Celik Altunoglu, “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)”, KUJES, vol. 5, no. 1, pp. 16–35, 2019.
ISNAD Özkan, Büşra et al. “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)”. Kastamonu University Journal of Engineering and Sciences 5/1 (June 2019), 16-35.
JAMA Özkan B, Ustaoğlu B, Can TH, Baloglu MC, Celik Altunoglu Y. 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). KUJES. 2019;5:16–35.
MLA Özkan, Büşra et al. “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)”. Kastamonu University Journal of Engineering and Sciences, vol. 5, no. 1, 2019, pp. 16-35.
Vancouver Özkan B, Ustaoğlu B, Can TH, Baloglu MC, Celik Altunoglu Y. 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). KUJES. 2019;5(1):16-35.
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