Research Article
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In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene

Year 2023, Volume: 12 Issue: 2, 212 - 224, 30.06.2023

Esra Can Çapan Gökhan Arslan Mehtap Bayır

https://doi.org/10.33714/masteb.1266381

Abstract

The present study focused on conducting in silico analysis and investigating the tissue-specific distribution and expression of the catalase gene in platyfish (Xiphophorus maculatus), which can be used as a model organism for studying stress responses in fish. Assay of the steady-state levels of cat gene transcripts by real time PCR revealed. The steady-state level of platyfish cat transcript was abundant liver (2162.21) compared with the level of cat transcript in intestine (1270.94), heart (1241.25), muscle (419.157), brain (46.205), eye (47.57), swimming bladder (28.99), gills (81.18), spleen (95.45), kidney (20.25) ovary (91.16) and testis (113.22). The results suggest that the liver is the major site of cat expression in platyfish, with significantly higher expression levels compared to other tissues. In addition, the research involved using bioinformatics tools to analyze the genetic sequence of the catalase gene and predict its structure and function. The results of the study indicated that the cat in Platyfish shares a high sequence identity and similarity with its orthologs in other teleost species, including medaka, fugu, and zebrafish. This observation suggests that the cat gene is conserved among these fish species, and the gene’s function and regulatory mechanisms are likely to be similar. The high conservation of the cat gene among teleost fish species highlights the importance of this gene in the antioxidant defense system and its potential role in responding to environmental stressors. Platyfish cat gene exhibits a conserved gene structure, as evidenced by its conserved gene synteny with the orthologous cat/CAT genes in other teleost fish and humans. Overall, the study provides evidence for the highly conserved gene structure of the cat gene in platyfish, which contributes to its functional stability and the maintenance of its critical role in antioxidant defense and stress response mechanisms.

Keywords

Bioinformatics Catalase Gene expression Platyfish

Thanks

This manuscript is produced from Esra Can Çapan’s master thesis.

References

  • Arthington, A. H. (1989). Diet of Gambusia affinis holbrooki, Xiphorus helleri, X. maculatus and Poecilia reticulata (Pisces: Peociliidae) in streams of southeastern Queensland, Australia. Asian Fisheries Science, 2(2), 193-212.
  • Balasch, J. C., & Tort, L. (2019). Netting the stress responses in fish. Frontiers in Endocrinology, 10, 62. https://doi.org/10.3389/fendo.2019.00062
  • Bopp, S. K., Abicht, H. K., & Knauer, K. (2008). Copper-induced oxidative stress in rainbow trout gill cells. Aquatic Toxicology, 86(2), 197–204. https://doi.org/10.1016/j.aquatox.2007.10.014
  • Chance, B., & Maehly, A. C. (1955). Assay of catalases and peroxidases. Methods in Enzymology, 2, 764-775. https://doi.org/10.1016/S0076-6879(55)02300-8
  • Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376. https://doi.org/10.1007/BF01734359
  • Gotoh, O. (2012). Evolution of cytochrome p450 genes from the viewpoint of genome informatics. Biological and Pharmaceutical Bulletin, 35(6), 812-817. https://doi.org/10.1248/bpb.35.812
  • Heston, W. E. (1982). Genetics: Animal tumors (pp. 47-71). In Becker, F. F. (Ed.), Etiology: Chemical and physical carcinogenesis. Cancer, a comprehensive treatise. Plenum Press. https://doi.org/10.1007/978-1-4615-6598-7_2
  • Howe, K., Clark, M. D., Torroja, C. F., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G. -J., White, S., … Stemple, D. L. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature, 496, 498–503. https://doi.org/10.1038/nature12111
  • Iwamatsu, T. (2004). Stages of normal development in the medaka Oryzias latipes. Mechanisms of Development, 121(7-8), 605-618. https://doi.org/10.1016/j.mod.2004.03.012
  • Kang, J. H., Schartl, M., Walter, R. B., & Meyer, A. (2013). Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily. BMC Evolutionary Biology, 13, 25. https://doi.org/10.1186/1471-2148-13-25
  • Kell, M. J., Riccio, R. E., Baumgartner, E. A., Compton, Z. J., Pecorin, P. J., Mitchell, T. A, Topczewski, J., & LeClair, E. E. (2018). Targeted deletion of the zebrafish actin-bundling protein L-plastin (lcp1). PLoS ONE, 13(1), e0190353. https://doi.org/10.1371/journal.pone.0190353
  • Keşan, S., Bayır, M., & Arslan, G. (2022). Fatty acid composition and mRNA expression of fatty acid binding protein genes (fabp3 and fabp6) in rainbow trout fed camelina seed oil (Camelina sativa)-based diets. Marine Science and Technology Bulletin, 11(2), 144-157. https://doi.org/10.33714/masteb.1082427
  • Mirvaghefi, A., Ali, M., & Poorbagher, H. (2016). Effects of vitamin C on oxidative stress parameters in rainbow trout exposed to diazinon. Ege Journal of Fisheries and Aquatic Sciences, 33(2), 113-120. https://doi.org/10.12714/egejfas.2016.33.2.04
  • Pan, L., Luo, Y., Wang, J., Li, X., Tang, B., Yang, H., Hou, X., Liu, F., & Zhou, X. (2022). Evolution and functional diversification of catalase genes in the green lineage. BMC Genomics, 23, 411. https://doi.org/10.1186/s12864-022-08621-6
  • Schartl, M. (2014). Beyond the zebrafish: Diverse fish species for modeling human disease. Disease Models & Mechanisms, 7(2), 181-192. https://doi.org/10.1242/dmm.012245
  • Schartl, M., Walter, R. B., Shen, Y., Garcia, T., Catchen, J., Amores, A., Braasch, I., Chalopin, D., Volff, J. -N., Lesch, K. -P., Bisazza, A., Minx, P., Hillier, L., Wilson, R. K., Fuerstenberg, S., Boore, J., Searle, S., Postlethwait, J. H., & Warren, W. C. (2013). The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics, 45(4), 567-72. https://doi.org/10.1038/ng.2604
  • Sies, H. (2017). Hydrogen peroxide as a central redox signaling molecule in physiological oxidative stress: Oxidative eustress. Redox Biology, 11, 613-619. https://doi.org/10.1016/j.redox.2016.12.035
  • Tamura, K., Stecher, A., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
  • 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
  • Volff, J. -N. (2005). Genome evolution and biodiversity in teleost fish. Heredity, 94(3), 280-294. https://doi.org/10.1038/sj.hdy.6800635
  • Zaret, T. M. (Ed.) (1984). Evolutionary ecology of neotropical freshwater fishes: Proceedings of the 1st international symposium on systematics and evolutionary ecology of neotropical freshwater fishes, held at DeKalb, Illinois, U.S.A., June 14-18, 1982. Springer Science+Business Media, B.V.

Year 2023, Volume: 12 Issue: 2, 212 - 224, 30.06.2023

Esra Can Çapan Gökhan Arslan Mehtap Bayır

https://doi.org/10.33714/masteb.1266381

Abstract

References

  • Arthington, A. H. (1989). Diet of Gambusia affinis holbrooki, Xiphorus helleri, X. maculatus and Poecilia reticulata (Pisces: Peociliidae) in streams of southeastern Queensland, Australia. Asian Fisheries Science, 2(2), 193-212.
  • Balasch, J. C., & Tort, L. (2019). Netting the stress responses in fish. Frontiers in Endocrinology, 10, 62. https://doi.org/10.3389/fendo.2019.00062
  • Bopp, S. K., Abicht, H. K., & Knauer, K. (2008). Copper-induced oxidative stress in rainbow trout gill cells. Aquatic Toxicology, 86(2), 197–204. https://doi.org/10.1016/j.aquatox.2007.10.014
  • Chance, B., & Maehly, A. C. (1955). Assay of catalases and peroxidases. Methods in Enzymology, 2, 764-775. https://doi.org/10.1016/S0076-6879(55)02300-8
  • Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376. https://doi.org/10.1007/BF01734359
  • Gotoh, O. (2012). Evolution of cytochrome p450 genes from the viewpoint of genome informatics. Biological and Pharmaceutical Bulletin, 35(6), 812-817. https://doi.org/10.1248/bpb.35.812
  • Heston, W. E. (1982). Genetics: Animal tumors (pp. 47-71). In Becker, F. F. (Ed.), Etiology: Chemical and physical carcinogenesis. Cancer, a comprehensive treatise. Plenum Press. https://doi.org/10.1007/978-1-4615-6598-7_2
  • Howe, K., Clark, M. D., Torroja, C. F., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G. -J., White, S., … Stemple, D. L. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature, 496, 498–503. https://doi.org/10.1038/nature12111
  • Iwamatsu, T. (2004). Stages of normal development in the medaka Oryzias latipes. Mechanisms of Development, 121(7-8), 605-618. https://doi.org/10.1016/j.mod.2004.03.012
  • Kang, J. H., Schartl, M., Walter, R. B., & Meyer, A. (2013). Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily. BMC Evolutionary Biology, 13, 25. https://doi.org/10.1186/1471-2148-13-25
  • Kell, M. J., Riccio, R. E., Baumgartner, E. A., Compton, Z. J., Pecorin, P. J., Mitchell, T. A, Topczewski, J., & LeClair, E. E. (2018). Targeted deletion of the zebrafish actin-bundling protein L-plastin (lcp1). PLoS ONE, 13(1), e0190353. https://doi.org/10.1371/journal.pone.0190353
  • Keşan, S., Bayır, M., & Arslan, G. (2022). Fatty acid composition and mRNA expression of fatty acid binding protein genes (fabp3 and fabp6) in rainbow trout fed camelina seed oil (Camelina sativa)-based diets. Marine Science and Technology Bulletin, 11(2), 144-157. https://doi.org/10.33714/masteb.1082427
  • Mirvaghefi, A., Ali, M., & Poorbagher, H. (2016). Effects of vitamin C on oxidative stress parameters in rainbow trout exposed to diazinon. Ege Journal of Fisheries and Aquatic Sciences, 33(2), 113-120. https://doi.org/10.12714/egejfas.2016.33.2.04
  • Pan, L., Luo, Y., Wang, J., Li, X., Tang, B., Yang, H., Hou, X., Liu, F., & Zhou, X. (2022). Evolution and functional diversification of catalase genes in the green lineage. BMC Genomics, 23, 411. https://doi.org/10.1186/s12864-022-08621-6
  • Schartl, M. (2014). Beyond the zebrafish: Diverse fish species for modeling human disease. Disease Models & Mechanisms, 7(2), 181-192. https://doi.org/10.1242/dmm.012245
  • Schartl, M., Walter, R. B., Shen, Y., Garcia, T., Catchen, J., Amores, A., Braasch, I., Chalopin, D., Volff, J. -N., Lesch, K. -P., Bisazza, A., Minx, P., Hillier, L., Wilson, R. K., Fuerstenberg, S., Boore, J., Searle, S., Postlethwait, J. H., & Warren, W. C. (2013). The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics, 45(4), 567-72. https://doi.org/10.1038/ng.2604
  • Sies, H. (2017). Hydrogen peroxide as a central redox signaling molecule in physiological oxidative stress: Oxidative eustress. Redox Biology, 11, 613-619. https://doi.org/10.1016/j.redox.2016.12.035
  • Tamura, K., Stecher, A., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
  • 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
  • Volff, J. -N. (2005). Genome evolution and biodiversity in teleost fish. Heredity, 94(3), 280-294. https://doi.org/10.1038/sj.hdy.6800635
  • Zaret, T. M. (Ed.) (1984). Evolutionary ecology of neotropical freshwater fishes: Proceedings of the 1st international symposium on systematics and evolutionary ecology of neotropical freshwater fishes, held at DeKalb, Illinois, U.S.A., June 14-18, 1982. Springer Science+Business Media, B.V.
There are 21 citations in total.

Details

Primary Language English
Subjects Industrial Biotechnology
Journal Section Research Article
Authors

Esra Can Çapan 0000-0003-3817-7576

Gökhan Arslan 0000-0002-8634-8598

Mehtap Bayır 0000-0002-7794-1058

Early Pub Date June 20, 2023
Publication Date June 30, 2023
Submission Date March 16, 2023
Acceptance Date June 12, 2023
Published in Issue Year 2023 Volume: 12 Issue: 2

Cite

APA Çapan, E. C., Arslan, G., & Bayır, M. (2023). In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene. Marine Science and Technology Bulletin, 12(2), 212-224. https://doi.org/10.33714/masteb.1266381
AMA Çapan EC, Arslan G, Bayır M. In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene. Mar. Sci. Tech. Bull. June 2023;12(2):212-224. doi:10.33714/masteb.1266381
Chicago Çapan, Esra Can, Gökhan Arslan, and Mehtap Bayır. “In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus Maculatus) Catalase Gene”. Marine Science and Technology Bulletin 12, no. 2 (June 2023): 212-24. https://doi.org/10.33714/masteb.1266381.
EndNote Çapan EC, Arslan G, Bayır M (June 1, 2023) In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene. Marine Science and Technology Bulletin 12 2 212–224.
IEEE E. C. Çapan, G. Arslan, and M. Bayır, “In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene”, Mar. Sci. Tech. Bull., vol. 12, no. 2, pp. 212–224, 2023, doi: 10.33714/masteb.1266381.
ISNAD Çapan, Esra Can et al. “In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus Maculatus) Catalase Gene”. Marine Science and Technology Bulletin 12/2 (June 2023), 212-224. https://doi.org/10.33714/masteb.1266381.
JAMA Çapan EC, Arslan G, Bayır M. In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene. Mar. Sci. Tech. Bull. 2023;12:212–224.
MLA Çapan, Esra Can et al. “In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus Maculatus) Catalase Gene”. Marine Science and Technology Bulletin, vol. 12, no. 2, 2023, pp. 212-24, doi:10.33714/masteb.1266381.
Vancouver Çapan EC, Arslan G, Bayır M. In Silico Analysis and Tissue-Specific Transcription of Platyfish (Xiphophorus maculatus) Catalase Gene. Mar. Sci. Tech. Bull. 2023;12(2):212-24.
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