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Nil tilapiası (Oreochromis niloticus) lenfosit sitosolik protein 1 (lcp1) geninin biyoinformatiği

Year 2021, Volume 38, Issue 1, 63 - 68, 15.03.2021
https://doi.org/10.12714/egejfas.38.1.07

Abstract



Bu çalışmada, deneysel çalışmalarda model organizma olarak kullanılan tilapia (Oreochromis niloticus) 'da lenfosit sitozolik protein 1 (lcp1) geninin biyoinformatik çalışmaları yapılmıştır. Bu amaçla, lcp1'in karakterizasyonu ve tanımlaması yapılmış ve lcp1 geninin yapısını tasarlamak için ensembl veri tabanı kullanılmıştır. Ayrıca tilapia lcpl geninin üzerinde yer aldığı kromozom bölgesi ve lcpl geni ile aynı bölgedeki diğer genler ile bu genlerin de yerleri belirlenmiştir. Ayrıca belirlenen bu genlerin kromozom bölgeleri, tilapianın ortologları olan zebra balığı ve insanda da tespit edilmiştir. Bu kromozomal bölgelere göre manuel olarak korunmuş gen yapısı dizayn edilmiştir. Bunlara ilaveten, tilapia ile diğer omurgalılar arasındaki filogenetik ilişkinin belirlenmesi amacıyla UNIPROT, ENSEMBL ve NCBI gibi bazı biyoinformatik veritabanları kullanılarak lcp1 geni tarafından sentezlenen amino asit sekanslarına ulaşılmış ve bu seklanslar kullanılark filogenetik ağaç, Mega programı yardımıyla, Maksimum Olasılık Metodu’na göre oluşturulmuştur. Zebra balığı, gökkuşağı alabalığı, insan, fare ve plati balığı lcp1/Lcp1 ile tilapia lcp1 geninin sekans benzerlik-özdeşlik oranı BLOSUM62 matris algoritması kullanılarak hesaplanmıştır. Bu çalışma, tilapiada lcp1 geninin in-siliko analizinin tamamlanması için büyük önem taşımaktadır. Çünkü tilapia, sucul bir model organizmadır ve ekonomik su ürünleri türleri arasında önemli bir yere sahiptir. Bu nedenlerle, yapılan bu çalışma, balıklarda moleküler stres yanıtı üzerine yapılacak çalışmalar için temel oluşturacak ve her zaman başvurulacak bilgiler sağlamaktadır.




References

  • Adams, A.E., Shen, W., Lin, C. S., Leavitt, J. & Matsudaira, P. (1995). Isoform-specific complementation of the yeast sac6 null mutation by human fimbrin. Molecular and Cellular Biology, 15, 69-75.
  • Amores, A., Force, A., Yan, Y.L., Joly, L., Amemiya, C., Fritz, A., Ho R.K., Langeland, J., PrinceV., Wang, Y.L., Westerfield, M., Wang, M.E., Y.L. Postlethwait, J. H. (1998). Zebrafish hox clusters and vertebrate genome evolution. Science, 282 (5394), 1711-1714. https://doi.org/10.1126/science.282.5394.1711
  • Bayır, M., Arslan, G., Yıldız Oğuzhan, P. (2020). Characterization, identification and phylogeny of the cretaine kinase (ckma) gene in medaka (Oryzias latipes). Marine Science and Technology Bulletin, 9(1), 15-22.
  • Braasch, I. & Postlethwait, J.H.I. (2012). Polyploidy in fish and the teleost genome duplication. In: Soltis, P.S., Soltis, D.E. (eds.), Polyploidy and Genome Evolution, 341-383. DOI:10.1007/9783-642-31442-1_17
  • Bretscher, A. (1981). Fimbrin is a cytoskeletal protein that crosslinks F-actin in vitro. Proceeeding of the National Academy of Sciences, 78,6849–6853. DOI:10.1073/pnas.78.11.6849
  • Chung, I. & Deisseroth, A.B. (2004). Recombinant adenoviral vector containing tumor-specific L-plastin promoter fused to cytosine deaminase gene as a transcription unit: Generation and functional test. Archives of Pharmacal Research, 27(6), 633-9. PubMed PMID: WOS:000222363000011. PMID: 15283466
  • 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. DOI:10.1126/science.282.5389.682
  • Çapan, E.C. (2019). Plati balığı (Xiphophorus maculatus)’nda katalaz enzim geninin biyoenformatiği ve doku spesifik dağılımı. Master Thesis. Atatürk University, Erzurum. 77 pp.
  • Donaldson, E. M. 1979. Hormonal enhancement of growth. Fish Physiology, 8, 456-597.
  • Ergene, S., Kaya, F., Pekcan, Y. & Oral, A. (1998). A Karyological Analysis of Oreochromis niloticus (L., 1758) (Pisces, Cichlidae) Used in Aquaculture, First International Symposium on Fisheries and Ecology, 1(10), 2-4, Trabzon.
  • Felsenstein, J. (1989). PHYLIP-Phylogeny inference package. Cladistics, 5, 164-166.
  • Goldstein, D., Djeu, J., Latter, G., Burbeck, S. & Leavitt, J. (1985). Abundant synthesis of the transformation-induced protein of neoplastic human fibroblasts, plastin, in normal lymphocytes. Cancer Res.; 45(11 Pt 2), 5643-7. PMID: 4053036.
  • Guyon, R., Rakotomanga, M., Azzouzi, N., Coutanceau, J.P., Bonillo, C., D'Cotta, H., Pepey E, Soler, L., Rodier-Goud, M., D’Hont, A., Conte, M.A., van Bers, N. E.M., Penman, D.J., Hitte, C., Crooijmans, R.P.M.A., Kocher, T.D., Ozouf-Costaz, C., Baroiller, J.F. & Galibert F. (2012). A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. BMC Genomics,6(13), 222. doi: 10.1186/1471-2164-13-222.
  • Kaya, H., Akbulut, M. (2012). Kurşuna Maruz Bırakılan Tilapia (Oreochromis mossambicus)’nın Eritrosit Morfolojisinde Görülen Değişimler, 22(B), 10-15.
  • Kell, A.J.E., Yamins, D.L.K., Shook, E. N. & Norman-Haignere, S.V. (2018). A Task-Optimized Neural Network Replicates Human Auditory Behavior, Predicts Brain Responses, and Reveals a Cortical Processing Hierarchy. Neron, 98(3), 630-644.
  • Li, J. & Zhao, R. (2011). Expression and clinical significance of L-plastin in colorectal carcinoma. Journal of Gastrointestinal Surgery, 15(11), 1982-1988. DOI: 10. 1007/s11605-011-1678-4
  • Lin, C.S., Aebersold, R. H., Kent, S. B., Varma, M. & Leavitt, J. (1988). Molecular cloning and characterization of plastin, a human leukocyteprotein expressed in transformed human fibroblasts. Molecular and Cellular Biology, 8, 4659-4668.
  • Margaret, J.K., Rachel, E.R., Emily A. B., Zachary J. C., Paul J.P., Taylor A. M., Jacek T. & Elizabeth, E.L. (2017). Targeted deletion of the zebrafish actinbundling protein L-plastin (lcp1). PLoS ONE, 13(1) . DOI:10.1371/journal. pone.0190353
  • 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. DOI:10.1016/s0955-0674(99)00039-3
  • Otsuka, M., Kato, M., Yoshikawa, T., Chen, H., Brown, E.J., …Masuho, Y. (2001). Differential expression of the L-plastin gene in human colorectal cancer progression and metastasis. Biochemical and Biophysical Research Communications. 289(4), 876-81. PubMed PMID: WOS:000173212200017. Park, T.S., Chen, Z.P. & Leavitt, J. (1994). Activation of the leukocyte plastin gene occurs in most human cancer cells. Cancer Research, 54(7), 1775-1781. PubMed PMID: WOS:A1994ND23800032. PMID: 8137292
  • Peng, X.Y., Won, J.H., Rutherford, T., Fujii, T., Zelterman, D., Pizzorno, G., Sapi, E., Leavitt, J., Kacinski, B., Crystal, R., Schwartz P. & Deisseroth, A. (2001). The use of the L-plastin promoter for adenoviral-mediated, tumor-specific gene expression in ovarian and bladder cancer cell lines. Cancer Research, 61(11), 4405–13. PubMedPMID: WOS:000169051100022. PMID: 11389068
  • Postlethwait, J.H., Woods, I.G., Ngo-Hazelett, P., Yan, Y.L., Kelly, P.D., Chu, F., Huang, H., Force, A. H., Talbot, W.S. (2000). Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Research, 10,1890-1902. doi:10.1101/gr.164800
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar S, (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30 (12): 2725-2729. doi: 10.1093/molbev/mst197
  • Tekelioğlu, N., Sarıhan, E., Polat, A. & Işık, O. (1991). Tilapyaların (Tilapia zilli) Çukurova Koşullarında Sera İçerisinde Kışlatılmaları ve Cinsiyetlerinin Hormonlu Yemlerle Değiştirilmesi. Ege Üni. Su Ür. Fak. Eğitiminin 10. Yılında Su Ürünleri Sempozyumu (12-14 Kasım), İzmir, 534-541 s.
  • Thompson, J.D., Higgins, D.G. & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. DOI:10.1093/nar/22.22.4673
  • Urch, M. (1996). Spotligt turns on Tilapia: ‘the fish of the 21st Century’ Seafood International June pp 25-27.

Bioinformatics of Nile tilapia (Oreochromis niloticus) lymphocyte cytosolic protein 1 (lcp1) gene

Year 2021, Volume 38, Issue 1, 63 - 68, 15.03.2021
https://doi.org/10.12714/egejfas.38.1.07

Abstract



Bioinformatics analysis of lymphocyte cytosolic protein 1 (lcp1) gene in tilapia (Oreochromis niloticus) which is a model organism in experimental studies were completed in this study. For this purpose, characterization and identification of lcp1 has been completed and ensembl database has been used to design the structure of lcp1 gene. In addition, the chromosome region of tilapia lcp1 and other genes in the same region with lcp1were determined. The chromosome of these genes were detected in zebrafish and human which are identical orthologos of tilapia. Conserved gene synteny designed manually according to these chromosomal regions. In addition, amino acid sequences synthesized by lcp1 gene in some vertebrates were determined using some bioinformatics databases such as UNIPROT, ENSEMBL and NCBI before determine the phylogenetic relationship between these organisms and tilapia. Sequence similarity-identity rate of tilapia lcp1 gene with zebrafish, rainbow trout, human, mouse and platyfish lcp1/Lcp1 was calculated using BLOSUM62 matrix algorithm. This study is of great importance for the completion of in silico analysis of lcp1 gene in tilapia because it is an aquatic model organism and it has an important place among economic aquaculture species. However this study provides the basic pioneering information for the future studies on molecular stress response in fish.


References

  • Adams, A.E., Shen, W., Lin, C. S., Leavitt, J. & Matsudaira, P. (1995). Isoform-specific complementation of the yeast sac6 null mutation by human fimbrin. Molecular and Cellular Biology, 15, 69-75.
  • Amores, A., Force, A., Yan, Y.L., Joly, L., Amemiya, C., Fritz, A., Ho R.K., Langeland, J., PrinceV., Wang, Y.L., Westerfield, M., Wang, M.E., Y.L. Postlethwait, J. H. (1998). Zebrafish hox clusters and vertebrate genome evolution. Science, 282 (5394), 1711-1714. https://doi.org/10.1126/science.282.5394.1711
  • Bayır, M., Arslan, G., Yıldız Oğuzhan, P. (2020). Characterization, identification and phylogeny of the cretaine kinase (ckma) gene in medaka (Oryzias latipes). Marine Science and Technology Bulletin, 9(1), 15-22.
  • Braasch, I. & Postlethwait, J.H.I. (2012). Polyploidy in fish and the teleost genome duplication. In: Soltis, P.S., Soltis, D.E. (eds.), Polyploidy and Genome Evolution, 341-383. DOI:10.1007/9783-642-31442-1_17
  • Bretscher, A. (1981). Fimbrin is a cytoskeletal protein that crosslinks F-actin in vitro. Proceeeding of the National Academy of Sciences, 78,6849–6853. DOI:10.1073/pnas.78.11.6849
  • Chung, I. & Deisseroth, A.B. (2004). Recombinant adenoviral vector containing tumor-specific L-plastin promoter fused to cytosine deaminase gene as a transcription unit: Generation and functional test. Archives of Pharmacal Research, 27(6), 633-9. PubMed PMID: WOS:000222363000011. PMID: 15283466
  • 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. DOI:10.1126/science.282.5389.682
  • Çapan, E.C. (2019). Plati balığı (Xiphophorus maculatus)’nda katalaz enzim geninin biyoenformatiği ve doku spesifik dağılımı. Master Thesis. Atatürk University, Erzurum. 77 pp.
  • Donaldson, E. M. 1979. Hormonal enhancement of growth. Fish Physiology, 8, 456-597.
  • Ergene, S., Kaya, F., Pekcan, Y. & Oral, A. (1998). A Karyological Analysis of Oreochromis niloticus (L., 1758) (Pisces, Cichlidae) Used in Aquaculture, First International Symposium on Fisheries and Ecology, 1(10), 2-4, Trabzon.
  • Felsenstein, J. (1989). PHYLIP-Phylogeny inference package. Cladistics, 5, 164-166.
  • Goldstein, D., Djeu, J., Latter, G., Burbeck, S. & Leavitt, J. (1985). Abundant synthesis of the transformation-induced protein of neoplastic human fibroblasts, plastin, in normal lymphocytes. Cancer Res.; 45(11 Pt 2), 5643-7. PMID: 4053036.
  • Guyon, R., Rakotomanga, M., Azzouzi, N., Coutanceau, J.P., Bonillo, C., D'Cotta, H., Pepey E, Soler, L., Rodier-Goud, M., D’Hont, A., Conte, M.A., van Bers, N. E.M., Penman, D.J., Hitte, C., Crooijmans, R.P.M.A., Kocher, T.D., Ozouf-Costaz, C., Baroiller, J.F. & Galibert F. (2012). A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. BMC Genomics,6(13), 222. doi: 10.1186/1471-2164-13-222.
  • Kaya, H., Akbulut, M. (2012). Kurşuna Maruz Bırakılan Tilapia (Oreochromis mossambicus)’nın Eritrosit Morfolojisinde Görülen Değişimler, 22(B), 10-15.
  • Kell, A.J.E., Yamins, D.L.K., Shook, E. N. & Norman-Haignere, S.V. (2018). A Task-Optimized Neural Network Replicates Human Auditory Behavior, Predicts Brain Responses, and Reveals a Cortical Processing Hierarchy. Neron, 98(3), 630-644.
  • Li, J. & Zhao, R. (2011). Expression and clinical significance of L-plastin in colorectal carcinoma. Journal of Gastrointestinal Surgery, 15(11), 1982-1988. DOI: 10. 1007/s11605-011-1678-4
  • Lin, C.S., Aebersold, R. H., Kent, S. B., Varma, M. & Leavitt, J. (1988). Molecular cloning and characterization of plastin, a human leukocyteprotein expressed in transformed human fibroblasts. Molecular and Cellular Biology, 8, 4659-4668.
  • Margaret, J.K., Rachel, E.R., Emily A. B., Zachary J. C., Paul J.P., Taylor A. M., Jacek T. & Elizabeth, E.L. (2017). Targeted deletion of the zebrafish actinbundling protein L-plastin (lcp1). PLoS ONE, 13(1) . DOI:10.1371/journal. pone.0190353
  • 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. DOI:10.1016/s0955-0674(99)00039-3
  • Otsuka, M., Kato, M., Yoshikawa, T., Chen, H., Brown, E.J., …Masuho, Y. (2001). Differential expression of the L-plastin gene in human colorectal cancer progression and metastasis. Biochemical and Biophysical Research Communications. 289(4), 876-81. PubMed PMID: WOS:000173212200017. Park, T.S., Chen, Z.P. & Leavitt, J. (1994). Activation of the leukocyte plastin gene occurs in most human cancer cells. Cancer Research, 54(7), 1775-1781. PubMed PMID: WOS:A1994ND23800032. PMID: 8137292
  • Peng, X.Y., Won, J.H., Rutherford, T., Fujii, T., Zelterman, D., Pizzorno, G., Sapi, E., Leavitt, J., Kacinski, B., Crystal, R., Schwartz P. & Deisseroth, A. (2001). The use of the L-plastin promoter for adenoviral-mediated, tumor-specific gene expression in ovarian and bladder cancer cell lines. Cancer Research, 61(11), 4405–13. PubMedPMID: WOS:000169051100022. PMID: 11389068
  • Postlethwait, J.H., Woods, I.G., Ngo-Hazelett, P., Yan, Y.L., Kelly, P.D., Chu, F., Huang, H., Force, A. H., Talbot, W.S. (2000). Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Research, 10,1890-1902. doi:10.1101/gr.164800
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar S, (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30 (12): 2725-2729. doi: 10.1093/molbev/mst197
  • Tekelioğlu, N., Sarıhan, E., Polat, A. & Işık, O. (1991). Tilapyaların (Tilapia zilli) Çukurova Koşullarında Sera İçerisinde Kışlatılmaları ve Cinsiyetlerinin Hormonlu Yemlerle Değiştirilmesi. Ege Üni. Su Ür. Fak. Eğitiminin 10. Yılında Su Ürünleri Sempozyumu (12-14 Kasım), İzmir, 534-541 s.
  • Thompson, J.D., Higgins, D.G. & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. DOI:10.1093/nar/22.22.4673
  • Urch, M. (1996). Spotligt turns on Tilapia: ‘the fish of the 21st Century’ Seafood International June pp 25-27.

Details

Primary Language English
Subjects Fisheries
Journal Section Articles
Authors

Mehtap BAYIR (Primary Author)
ATATURK UNIVERSITY
0000-0002-7794-1058
Türkiye


Gökhan ARSLAN
ATATURK UNIVERSITY
0000-0002-8634-8598
Türkiye

Publication Date March 15, 2021
Application Date February 6, 2020
Acceptance Date October 6, 2020
Published in Issue Year 2021, Volume 38, Issue 1

Cite

APA Bayır, M. & Arslan, G. (2021). Bioinformatics of Nile tilapia (Oreochromis niloticus) lymphocyte cytosolic protein 1 (lcp1) gene . Ege Journal of Fisheries and Aquatic Sciences , 38 (1) , 63-68 . DOI: 10.12714/egejfas.38.1.07