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Research Article
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Bioinformatics studies and comparison of mRNA transcription of glutathione S-transferase gene in some tissues of common carp (Cyprinus carpio) and brown trout (Salmo trutta)

Year 2023, Volume: 40 Issue: 4, 266 - 275, 15.12.2023

Badrul Islam Elsevar , Mehtap Bayır

https://doi.org/10.12714/egejfas.40.4.05
Cited By: 1

Abstract

Bioinformatics has revolutionized the way we study gene expression and regulation, enabling researchers to analyze large-scale genomic data with unprecedented speed and precision. In this study, we use bioinformatics tools and methods to compare mRNA transcription of glutathione S-transferase (gstr) gene in two different fish species: common carp and brown trout. In this study, liver, intestine, muscle, brain, heart, eye, spleen, gill, kidney, stomach, ovary and testis samples were taken from male and female brown trout and common carp, and total RNA was isolated from each tissue to synthesize cDNA from these tissues. Then, the transcript amounts of the gstr gene were determined by qPCR from all tissue samples. Gene structures, conserved gene synteny design, phyogenetic tree analyzes and similarity-identity ratios with other vertebrates were determined. When the transcriptional differences between male and female tissues for the brown trout gstr gene were examined, it was seen that the intestine, gill, kidney, stomach, muscle and gonads were significantly higher in male fish (p<0.05), but the differences between other tissues were not statistically significant. It has been determined that the highest gene expression was liver (p<0.05) and brain, eye, spleen, kidney, heart and spleen tissues have significantly lower gstr gene expression than other tissues in both male and female in common carp. In addition, the in-silico analysis determined that the brown trout gstr gene shared the highest similarity and identity ratio with rainbow trout, and the common carp gstr gene shared the highest similarity and identity ratio with goldfish.
Keywords: Brown trout, common carp, in silico analysis, gstr, gene expression

Keywords

Brown trout common carp, in silico analysis gstr gene expression

Ethical Statement

The research adhered to all relevant international, national, and institutional guidelines for the ethical care and use of animals. Approval was granted by the Local Ethics Committee for Animal Experiments of Atatürk University (27.05.2021/No:127)

Project Number

FYL-2021-9372

Thanks

We thank Atatürk University for providing financial support for this study

References

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  • Arlinghaus, R., & Mehner, T. (2003). Socio-economic characterisation of specialised common carp (Cyprinus carpio L.) anglers in Germany, and implications for inland fisheries management and eutrophication control. Fisheries Research, 61(1-3), 373-389. https://doi.org/10.1016/S0165-7836(02)00243-6
  • Aubrecht, J., & Caba, E. (2005). Gene expression profile analysis: An emerging approach to investigate mechanisms of genotoxicity. Pharmacogenomics, 6(4), 419. https://doi.org/10.1517/14622416.6.4.419
  • Bayat, A. (2002). Science, medicine, and the future: Bioinformatics. British Medical Journal, ;324(7344), 1018 22. https://doi.org/10.1136/bmj.324.7344.1018
  • Braasch, I., & Postlethwait, J.H. (2012). Polyploidy in fish and the teleost genome duplication. In P.S. Soltis, D.E. Soltis (Eds.), Polyploidy and Genome Evolution, 341-383. https://doi.org/10.1007/978-3-642-31442-1_17
  • Chen, B., Peng, W., Xu, J., Feng, J., Dong, C., & Xu, P. (2017). Genomic analysis of glutathione S-transferases (GST) family in common carp: Identification, phylogeny and expression. Pakistan Journal of Zoology, 49(4), 1437 1448. https://doi.org/10.17582/journal.pjz/2017.49.4.1437.1448
  • Chen, L., Xu, J., Sun, X., & Xu, P. (2021). Research advances and future perspectives of genomics and genetic improvement in allotetraploid common carp. Reviews in Aquaculture, 13(1), 16 26. https://doi.org/10.1111/RAQ.12636
  • Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376. https://doi.org/10.1007/BF01734359
  • Franěk, R., Kašpar, V., Shah, M.A., Gela, D., & Pšenička, M. (2021). Production of common carp donor-derived offspring from goldfish surrogate broodstock. Aquaculture, 534, 736252. https://doi.org/10.1016/j.aquaculture.2020.736252
  • Glisic, B., Mihaljevic, I., Popovic, M., Zaja, R., Loncar, J., Fent, K., Kovacevic, R., & Smital, T. 2015. Characterization of glutathione-S-transferases in zebrafish (Danio rerio). Aquatic Toxicology, 158, 50 62. https://doi.org/10.1016/j.aquatox.2014.10.013
  • Guo, C., Duan, Y., Ye, W., Zhang, W., Cheng, Y., Shi, M., & Xia, X.Q. (2023). FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization. iScience, 26(4), 106539. https://doi.org/10.1016/j.isci.2023.106539
  • Keiz, K., Ulrich, S., Wenderlein, J., Keferloher, P., Wiesinger, A., Neuhaus, K., Lagkouvardos, I., Wedekind, H., & Straubinger, R.K. (2023). The development of the bacterial community of Brown Trout (Salmo trutta) during ontogeny. Microorganisms, 11(1), 211. https://doi.org/10.3390/microorganisms11010211
  • Kim, J.H., Dahms, H.U., Rhee J.S., Lee, Y.M., Lee J., Han, K.N., Lee,J.S. 2010. Expression profiles of seven glutathione S-transferase (GST) genes in cadmium-exposed river pufferfish (Takifugu obscurus). Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 151(1), 99 106. https://doi.org/10.1016/j.cbpc.2009.09.001
  • Larsen, P.F., Schulte, P.M., & Nielsen, E.E. (2010). Gene expression analysis for the identification of selection and local adaptation in fishes. Journal of Fish Biology, 77(9), 1745 1776. https://doi.org/10.1111/j.1095-8649.2010.02834.x
  • Liang, X.F., Li, G.G., He, S., & Huang Y., 2007. Transcriptional responses of alpha- and rho-class glutathione S-transferase genes in the liver of three freshwater fishes intraperitoneally injected with microcystin-LR: Relationship of inducible expression and tolerance. Journal of Biochemical and Molecular Toxicology, 21(5), 289-98. https://doi.org/10.1002/jbt.20188
  • Lynch, A.J., Cooke, S.J., Deines, A.M., Bower, S.D., Bunnell, D.B., Cowx, I.G., Nguyen, V.M., Nohner, J., Phouthavong, K., Riley, B., Rogers, M.W., Taylor, W.W., & Woelmer, W. (2016). The social, economic, and environmental importance of inland fish and fisheries. Environmental Reviews, 24(1), 75-91. https://doi.org/10.1139/er-2015-0064
  • Özdemir, E., & Bayır, M. (2023). Molecular cloning and characterization of Cu-Zn superoxide dismutase (sod1) gene in brown trout and its expression in response to acute aquaculture stressors. Animal Biotechnology, 34(6), 1968 1978. https://doi.org/10.1080/10495398.2022.2061505
  • Pandi, P., Madhuvandhi, J., Priya, K.K., Thiagarajan, R., Gopalakrishnan, S., Elumalai, S., & Thilagam, H. (2022). Weathered polyethylene microplastics exposure leads to modulations in glutathione-S-transferase activity in fish. Frontiers in Marine Science, 9, 1521. https://doi.org/10.3389/fmars.2022.990351
  • Papin, J. A., Price, N. D., Wiback, S. J., Fell, D. A., & Palsson, B. O. (2003). Metabolic pathways in the post-genome era. Trends in Biochemical Sciences, 28(5), 250 258. https://doi.org/10.1016/S0968 0004(03)00064-1
  • Qian, X., Ba, Y., Zhuang, Q., & Zhong, G. (2014). RNA-Seq technology and its application in fish transcriptomics. OMICS: A Journal of Integrative Biology, 18(2), 98–110. https://doi.org/10.1089/omi.2013.0110
  • Rojas-Hernandez, N., Véliz, D., & Vega-Retter, C. (2019). Selection of suitable reference genes for gene expression analysis in gills and liver of fish under field pollution conditions. Scientific Reports, 9, 3459. https://doi.org/10.1038/s41598-019-40196-3
  • Rudneva, I.I., Kuzminova, N.S., & Skuratovskaya E. N., 2010. Glutathione-S-Transferase Activity in Tissues of Black Sea Fish Species. Asian Journal of Experimental Biological Sciences, 1(1),141-150.
  • Thompson, J. D., Higgins, D. G., Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  • Tierbach, A., Groh, K.J., Schönenberger, R., Schirmer, K., & Suter, M.J. (2018). Glutathione S-transferase protein expression in different life stages of zebrafish (Danio rerio). Toxicological Sciences, 162(2), 702–712. https://doi.org/10.1093/toxsci/kfx293
  • Voelker, D., Vess, C., Tillmann, M., Nagel, R., Otto, G. W., Geisler, R., Schirmer, K., & Scholz, S. (2007). Differential gene expression as a toxicant-sensitive endpoint in zebrafish embryos and larvae. Aquatic Toxicology, 81(4), 355 364. https://doi.org/10.1016/j.aquatox.2006.12.014

Year 2023, Volume: 40 Issue: 4, 266 - 275, 15.12.2023

Badrul Islam Elsevar , Mehtap Bayır

https://doi.org/10.12714/egejfas.40.4.05
Cited By: 1

Abstract

Project Number

FYL-2021-9372

References

  • Adamek, M., Matras, M., Surachetpong, W., Rakus, K., Stachnik, M., Bauer, J., Falco, A., Jung-Schroers, V., Piewbang, C., Techangamsuwan, S., Abd El Rahman, S., Paley, R., Reichert, M., & Steinhagen, D. (2023). How susceptible are rainbow trout and brown trout to infection with tilapia lake virus at increased water temperature – Is there any potential for climate change driven host jump? Aquaculture, 571, 739469. https://doi.org/10.1016/j.aquaculture.2022.739469
  • Arlinghaus, R., & Mehner, T. (2003). Socio-economic characterisation of specialised common carp (Cyprinus carpio L.) anglers in Germany, and implications for inland fisheries management and eutrophication control. Fisheries Research, 61(1-3), 373-389. https://doi.org/10.1016/S0165-7836(02)00243-6
  • Aubrecht, J., & Caba, E. (2005). Gene expression profile analysis: An emerging approach to investigate mechanisms of genotoxicity. Pharmacogenomics, 6(4), 419. https://doi.org/10.1517/14622416.6.4.419
  • Bayat, A. (2002). Science, medicine, and the future: Bioinformatics. British Medical Journal, ;324(7344), 1018 22. https://doi.org/10.1136/bmj.324.7344.1018
  • Braasch, I., & Postlethwait, J.H. (2012). Polyploidy in fish and the teleost genome duplication. In P.S. Soltis, D.E. Soltis (Eds.), Polyploidy and Genome Evolution, 341-383. https://doi.org/10.1007/978-3-642-31442-1_17
  • Chen, B., Peng, W., Xu, J., Feng, J., Dong, C., & Xu, P. (2017). Genomic analysis of glutathione S-transferases (GST) family in common carp: Identification, phylogeny and expression. Pakistan Journal of Zoology, 49(4), 1437 1448. https://doi.org/10.17582/journal.pjz/2017.49.4.1437.1448
  • Chen, L., Xu, J., Sun, X., & Xu, P. (2021). Research advances and future perspectives of genomics and genetic improvement in allotetraploid common carp. Reviews in Aquaculture, 13(1), 16 26. https://doi.org/10.1111/RAQ.12636
  • Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376. https://doi.org/10.1007/BF01734359
  • Franěk, R., Kašpar, V., Shah, M.A., Gela, D., & Pšenička, M. (2021). Production of common carp donor-derived offspring from goldfish surrogate broodstock. Aquaculture, 534, 736252. https://doi.org/10.1016/j.aquaculture.2020.736252
  • Glisic, B., Mihaljevic, I., Popovic, M., Zaja, R., Loncar, J., Fent, K., Kovacevic, R., & Smital, T. 2015. Characterization of glutathione-S-transferases in zebrafish (Danio rerio). Aquatic Toxicology, 158, 50 62. https://doi.org/10.1016/j.aquatox.2014.10.013
  • Guo, C., Duan, Y., Ye, W., Zhang, W., Cheng, Y., Shi, M., & Xia, X.Q. (2023). FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization. iScience, 26(4), 106539. https://doi.org/10.1016/j.isci.2023.106539
  • Keiz, K., Ulrich, S., Wenderlein, J., Keferloher, P., Wiesinger, A., Neuhaus, K., Lagkouvardos, I., Wedekind, H., & Straubinger, R.K. (2023). The development of the bacterial community of Brown Trout (Salmo trutta) during ontogeny. Microorganisms, 11(1), 211. https://doi.org/10.3390/microorganisms11010211
  • Kim, J.H., Dahms, H.U., Rhee J.S., Lee, Y.M., Lee J., Han, K.N., Lee,J.S. 2010. Expression profiles of seven glutathione S-transferase (GST) genes in cadmium-exposed river pufferfish (Takifugu obscurus). Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 151(1), 99 106. https://doi.org/10.1016/j.cbpc.2009.09.001
  • Larsen, P.F., Schulte, P.M., & Nielsen, E.E. (2010). Gene expression analysis for the identification of selection and local adaptation in fishes. Journal of Fish Biology, 77(9), 1745 1776. https://doi.org/10.1111/j.1095-8649.2010.02834.x
  • Liang, X.F., Li, G.G., He, S., & Huang Y., 2007. Transcriptional responses of alpha- and rho-class glutathione S-transferase genes in the liver of three freshwater fishes intraperitoneally injected with microcystin-LR: Relationship of inducible expression and tolerance. Journal of Biochemical and Molecular Toxicology, 21(5), 289-98. https://doi.org/10.1002/jbt.20188
  • Lynch, A.J., Cooke, S.J., Deines, A.M., Bower, S.D., Bunnell, D.B., Cowx, I.G., Nguyen, V.M., Nohner, J., Phouthavong, K., Riley, B., Rogers, M.W., Taylor, W.W., & Woelmer, W. (2016). The social, economic, and environmental importance of inland fish and fisheries. Environmental Reviews, 24(1), 75-91. https://doi.org/10.1139/er-2015-0064
  • Özdemir, E., & Bayır, M. (2023). Molecular cloning and characterization of Cu-Zn superoxide dismutase (sod1) gene in brown trout and its expression in response to acute aquaculture stressors. Animal Biotechnology, 34(6), 1968 1978. https://doi.org/10.1080/10495398.2022.2061505
  • Pandi, P., Madhuvandhi, J., Priya, K.K., Thiagarajan, R., Gopalakrishnan, S., Elumalai, S., & Thilagam, H. (2022). Weathered polyethylene microplastics exposure leads to modulations in glutathione-S-transferase activity in fish. Frontiers in Marine Science, 9, 1521. https://doi.org/10.3389/fmars.2022.990351
  • Papin, J. A., Price, N. D., Wiback, S. J., Fell, D. A., & Palsson, B. O. (2003). Metabolic pathways in the post-genome era. Trends in Biochemical Sciences, 28(5), 250 258. https://doi.org/10.1016/S0968 0004(03)00064-1
  • Qian, X., Ba, Y., Zhuang, Q., & Zhong, G. (2014). RNA-Seq technology and its application in fish transcriptomics. OMICS: A Journal of Integrative Biology, 18(2), 98–110. https://doi.org/10.1089/omi.2013.0110
  • Rojas-Hernandez, N., Véliz, D., & Vega-Retter, C. (2019). Selection of suitable reference genes for gene expression analysis in gills and liver of fish under field pollution conditions. Scientific Reports, 9, 3459. https://doi.org/10.1038/s41598-019-40196-3
  • Rudneva, I.I., Kuzminova, N.S., & Skuratovskaya E. N., 2010. Glutathione-S-Transferase Activity in Tissues of Black Sea Fish Species. Asian Journal of Experimental Biological Sciences, 1(1),141-150.
  • Thompson, J. D., Higgins, D. G., Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  • Tierbach, A., Groh, K.J., Schönenberger, R., Schirmer, K., & Suter, M.J. (2018). Glutathione S-transferase protein expression in different life stages of zebrafish (Danio rerio). Toxicological Sciences, 162(2), 702–712. https://doi.org/10.1093/toxsci/kfx293
  • Voelker, D., Vess, C., Tillmann, M., Nagel, R., Otto, G. W., Geisler, R., Schirmer, K., & Scholz, S. (2007). Differential gene expression as a toxicant-sensitive endpoint in zebrafish embryos and larvae. Aquatic Toxicology, 81(4), 355 364. https://doi.org/10.1016/j.aquatox.2006.12.014
There are 25 citations in total.

Details

Primary Language English
Subjects Fish Physiology and Genetics
Journal Section Articles
Authors

Badrul Islam Elsevar 0000-0003-3447-0628

Mehtap Bayır 0000-0002-7794-1058

Project Number FYL-2021-9372
Early Pub Date December 8, 2023
Publication Date December 15, 2023
Submission Date August 14, 2023
Published in Issue Year 2023 Volume: 40 Issue: 4

Cite

APA Elsevar, B. I., & Bayır, M. (2023). Bioinformatics studies and comparison of mRNA transcription of glutathione S-transferase gene in some tissues of common carp (Cyprinus carpio) and brown trout (Salmo trutta). Ege Journal of Fisheries and Aquatic Sciences, 40(4), 266-275. https://doi.org/10.12714/egejfas.40.4.05

Cited By

Computational analysis of superoxide dismutase genes (sod1, sod2, and sod3) and comprehensive tissue-specific gene expression profiling in Tetraodon (Tetraodon nigroviridis)
Ege Journal of Fisheries and Aquatic Sciences
https://doi.org/10.12714/egejfas.41.4.02