Bioinformatics Studies and Examining the Tissue Distribution of Glutathione Reductase and Glucose-6-Phosphate Dehydrogenase Genes to Investigate Gender Differences in Differences in Stress Tolerance in Zebrafish (Danio rerio)

Yıl 2023, Cilt: 12 Sayı: 3, 352 - 369, 28.09.2023

Burcu Naz Uzun Mehtap Bayır

https://doi.org/10.33714/masteb.1337231

Öz

The study aimed to investigate the bioinformatics of zebrafish glutathione reductase (gsr) and glucose-6-phosphate dehydrogenase (g6pd) genes, as well as their tissue-specific distribution. To achieve this, samples of various tissues were taken from female and male zebrafish and total RNA was extracted to obtain cDNA. qPCR was performed to determine the transcripts of gsr and g6pd genes. The structure of the genes, conserved gene maps, and phylogenetic tree were also designed. The results showed that the liver was the most dominant tissue for both gsr and g6pd genes in both female and male zebrafish. The expression of gsr gene was significantly higher in male zebrafish's liver, intestine, heart, eye, gills, and gonad tissues compared to female fish, while g6pd gene transcription was found to be significantly higher in the male liver, intestine, muscle, brain, eye, gill, kidney, stomach, and gonad tissues. Overall, this study provides valuable insights into the bioinformatics of gsr and g6pd genes in zebrafish and their tissue-specific distribution, which could help in understanding their roles in various physiological and pathological processes in zebrafish and other related species.

Anahtar Kelimeler

Zebrafish, In silico analysis, gsr, g6pd, Gene expression

Destekleyen Kurum

Atatürk University

Proje Numarası

FYL-2021-955

Teşekkür

The present research was financially supported by Atatürk University Scientific Research Project (FYL-2021-955).

Kaynakça

• Apel, K., & Hirt, H. (2004). Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annual Review of Plant Biology, 55, 373-399. https://doi.org/10.1146/annurev.arplant.55.031903.141701
• Barbazuk, W. B., Korf, I., Kadavi, C., Heyen, J., Tate, S., Wun, E., Bedel, J. A., Pherson, M. C., & Johnson, S. L. (2000). The syntenic relationship of the zebrafish and human genomes. Genome Research, 10(9), 1351-1358. https://doi.org/10.1101/gr.144700
• Bayır, M., & Arslan, G. (2021). Bioinformatics of Nile tilapia (Oreochromis niloticus) lymphocyte cytosolic protein 1 (lcp1) gene Nil tilapia (Oreochromis niloticus) lenfosit sitosolik protein 1 (lcp1). Ege Journal of Fisheries and Aquatic Sciences, 38(1), 63-68. https://doi.org/10.12714/egejfas.38.1.07
• Bayır, M., Arslan, G., & Oğuzhan Yıldız, 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. https://doi.org/10.33714/masteb.660220
• Blount, J. D. (2004). Carotenoids and life-history evolution in animals. Archives of Biochemistry and Biophysics, 430(1), 10-15. https://doi.org/10.1016/j.abb.2004.03.039
• Braasch, I., & Postlethwait, J. H. (2012). Polyploidy in fish and the teleost genome duplication. In Soltis, P., & Soltis, D. (Eds.), Polyploidy and Genome Evolution (pp. 341-383). Springer. https://doi.org/10.1007/978-3-642-31442-1_17
• Catoni, C., Peters, A., & Schaefer, H. M. (2008). Life history trade-offs are influenced by the diversity, availability and interactions of dietary antioxidants. Animal Behaviour, 76(4), 1107-1119. https://doi.org/10.1016/j.anbehav.2008.05.027
• 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. https://doi.org/10.1126/science.282.5389.682
• Dowling, D. K., & Simmons, L. W. (2009). Reactive oxygen species as universal constraints in life-history evolution. Proceedings of the Royal Society B: Biological Sciences, 276(1663), 1737-1745. https://doi.org/10.1098/rspb.2008.1791
• Espinosa-Diez, C., Miguel, V., Mennerich, D., Kietzmann, T., Sánchez-Pérez, P., Cadenas, S., & Lamas, S. (2015). Antioxidant responses and cellular adjustments to oxidative stress. Redox Biology, 6, 183-197. https://doi.org/10.1016/j.redox.2015.07.008
• García-Meilán, I., Tort, L., & Khansari, A. R. (2022). Rainbow trout integrated response after recovery from short-term acute hypoxia. Frontiers in Physiology, 21(13), 1021927. https://doi.org/10.3389/fphys.2022.1021927
• Glasauer, S. M., & Neuhauss, S. C. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6), 1045-1060. https://doi.org/10.1007/s00438-014-0889
• Gromiha, M. M. (2010). Protein Bioinformatics: From Sequence to Function. Academic Press.
• Hill, G. E. (2014). The evolution of ornaments and armaments. In Yasukawa, K. (Ed.), Animal Behavior: How and Why Animals Do the Things They Do, 2. Volume 2: Function and Evolution (pp. 145-172). Praeger.
• Kari, G., Rodeck, U., & Dicker, A. P. (2007). Zebrafish: an emerging model system for human disease and drug discovery. Clinical Pharmacology & Therapeutics, 82(1), 70-80. https://doi.org/10.1038/sj.clpt.6100230
• Kumar, S., Dudley, J., Nei, M., & Tamura, K. (2008). MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics, 9(4), 299-306. https://doi.org/10.1093/bib/bbn017
• Li, C., Wei, M., Ge, Y., Zhao, J., Chen, Y., Hou, J., Cheng, Y., Chen, J., & Li, J. (2020). The role of glucose-6-phosphate dehydrogenase in reactive oxygen species metabolism in apple exocarp induced by acibenzolar-S-methyl, Food Chemistry, 308, 125663. https://doi.org/10.1016/j.foodchem.2019.125663
• 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 in Cell Biology, 11(6), 699-704. https://doi.org/10.1016/S0955-0674(99)00039-3
• Nandi, A., Yan, L. J., Jana, C. K., & Das, N. (2019). Role of catalase in oxidative stress- and age- diseases. Oxidative Medicine and Cellular Longevity, 2019, 9613090. https://doi.org/10.1155/2019/9613090
• Osman, A. (2012). Biomarkers in associated degenerative Nile Tilapia Oreochromis niloticus niloticus (Linnaeus, 1758) to assess the impacts of River Nile pollution: Bioaccumulation, biochemical and tissues biomarkers, Journal of Environmental Protection, 3(8A), 966-977. https://doi.org/10.4236/jep.2012.328112
• Ozdemir, E., & Bayır, M. (2022). 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, 2022, 1–11. https://doi.org/10.1080/10495398.2022.2061505
• Parmar, M. B., Venkatachalam, A. B., & Wright, J. M. (2012). The evolutionary relationship of the transcriptionally active fabp11a (intronless) and fabp11b genes of medaka with fabp11 genes of other teleost fishes. The FEBS Journal, 279(13), 2310-2321. https://doi.org/10.1111/j.1742-4658.2012.08611.x
• 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 Research, 10(12), 1890-1902. https://doi.org/10.1101/gr.164800
• Postlethwait, J. H., Yan, Y. L., Gates, M. A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E. S., Force, A., Gong, Z., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T. S., Yelick, P., Beier, D., Joly, J. S., Larhammar, D., Rosa, F., Westerfield, M., Zon, L. I., Johnson, S. L., & Talbot, W. S. (1998). Vertebrate genome evolution and the zebrafish gene map. Nature Genetics, 18(4), 345-349. https://doi.org/10.1038/ng0498-345
• Puppel, K., Kapusta, A., & Kuczynska, B. (2015). The etiology of oxidative stress in the various species of animals, a review. Journal of the Science of Food and Agriculture, 95(11), 2179-2184. https://doi.org/10.1002/jsfa.7015
• Schieber, M., & Chandel, N. S. (2014). ROS function in redox signaling and oxidative stress. Current Biology, 24(10), R453-R462. https://doi.org/10.1016/j.cub.2014.03.034
• Szudrowicz, H., Kamaszewski, M., Adamski, A., Skrobisz, M., Frankowska-Łukawska, J., Wójcik, M., Bochenek, J., Kawalski, K., Martynow, J., & Bujarski, P. (2022). The effects of seven-day exposure to silver nanoparticles on fertility and homeostasis of zebrafish (Danio rerio). International Journal of Molecular Sciences, 23(19), 11239. https://doi.org/10.3390/ijms231911239
• Taylor, J. S., Braasch, I., Frickey, T., Meyer, A., & Van de Peer, Y. (2001). Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Research, 11(12), 240-250. https://doi.org/10.1101/gr.194001
• Taylor, J. S., Van de Peer, Y., & Meyer, A. (2003). Genome duplication, divergent resolution and speciation. Trends in Genetics, 19(5), 259-266. https://doi.org/10.1016/S0168-9525(03)00080-6
• 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
• Torstensen, B. E., Nanton, D. A., Olsvik, P. A., Sundvold, H., & Stubhaug, I., (2009). Gene expression of fatty acid-binding proteins, fatty acid transport proteins (cd36 and FATP) and ß-oxidation-related genes in Atlantic salmon (Salmo salar L.) fed fish oil or vegetable oil. Aquaculture Nutrition, 15(4), 440–451. https://doi.org/10.1111/j.1365- 2095.2008.00609.x
• Traverso, N., Ricciarelli, R., Nitti, M., Marengo, B., Furfaro, A. L., Pronzato, M. A., & Marinari, U. M. (2013). Role of glutathione in cancer progression and chemoresistance. Oxidative Medicine and Cellular Longevity, 2013, 972913. https://doi.org/10.1155/2013/972913
• Veldman, M. & Lin, S. (2008). Zebrafish as a developmental model organism for pediatric research. Pediatric Research, 64, 470-476. https://doi.org/10.1203/PDR.0b013e318186e609
• Wolff, J. N., Ladoukakis, E. D., Enríquez, J. A., & Dowling, D. K. (2014). Mitonuclear interactions: evolutionary consequences over multiple biological scales. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1646), 20130443. https://doi.org/10.1098/rstb.2013.0443
• Xu, D., Li, L., & Li, C. (2020). Glutathione reductase gene in zebrafish: Characterization and expression analysis under heavy metal exposure. International Journal of Molecular Sciences, 21(17), 6143. https://doi.org/10.3390/ijms21176143
• Zorov, D. B., Juhaszova, M., & Sollott, S. J. (2014). Mitochondrial reactive oxygen species (ROS) and ROS-induced ROS release. Physiological Reviews, 94(3), 909-950. https://doi.org/10.1016/j.bbabio.2006.04.029