Araştırma Makalesi
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Nicotiana tabaccum L. katalaz proteininin in siliko analizi

Yıl 2022, Cilt: 24 Sayı: 2, 818 - 829, 08.07.2022
https://doi.org/10.25092/baunfbed.1114706

Öz

Katalazlar, hidrojen peroksitin su ve oksijene ayrışmasından sorumlu olan antioksidan enzimlerdir. Katalaz aktivitelerinin çevresel faktörlerden ve stres koşullarından etkilendiği gösterilmiştir. Bu çalışmada Nicotiana tabaccum L. katalaz proteininin biyoinformatik araçlarla in siliko analizi yapılmıştır. Bu araştırmanın sonuçları, NtCAT-1 geninin ORF'sinin 1479 bp olduğunu ve 492 amino asitlik bir polipeptidi kodladığını göstermiştir. Öngörülen polipeptit, 6.27'lik bir pl ile 56.82 kDa'lık bir protein olarak ortaya çıkmıştır. Polipeptit, 71.52'lik bir alifatik indekse ve -0.519'luk büyük hidropatisite (GRAVY) ortalamasına sahiptir. NtCAT-1 proteini hidrofiliktir ve peroksizomda lokalizedir. NtCAT-1, 18-399 ve 421 ve 486 pozisyonlarında iki korunmuş domaine sahiptir. 54-70 pozisyonunda katalaz aktivite motifine (CAM) ve 344-352 pozisyonunda heme-bağlama bölgesine (HBS) sahiptir. Son derece güvenilir bir 3B yapı elde edilmiş ve Ramachandran çizim analizinden, en çok tercih edilen bölgelere düşen rezidülerin %97.23 olduğu bulunmuştur. Bu çalışmanın sonuçları, farklı bitki türlerinde katalaz proteini ile ilgili in siliko çalışmalarında daha ileri araştırmalar için temel bilgiler sağlayacaktır.

Kaynakça

  • Cruz de Carvalho M. H. Drought stress and reactive oxygen species: Production, scavenging and signaling, Plant signaling & behavior, 3, 3, 156–165, (2008).
  • Sachdev. S., Ansari, S.A., Ansari. M.I., Fujita. M., Hasanuzzaman. M. Abiotic Stress and Reactive Oxygen Species: Generation, Signaling, and Defense Mechanisms, Antioxidants (Basel), 10, 2, 277, (2021).
  • Sharma, P., Jha, A.B., Dubey, R.S. and Pessarakli, M. Reactive Oxygen Species, Oxidative Damage, and Antioxidative Defense Mechanism in Plants under Stressful Conditions, Journal of Botany, 1, 26, (2012).
  • Dat J.F., Inzé, D., Van Breusegem, F. Catalase-deficient tobacco plants: tools for in planta studies on the role of hydrogen peroxide, Redox Report, 6, 1, 37-42, (2001).
  • Zamocky, M., Furtmüller, P. G., and Obinger, C. Evolution of catalases from bacteria to humans, Antioxidants & redox signaling, 10, 9, 1527–1548, (2008).
  • Wutipraditkul, N., Boonkomrat, S. and Buaboocha, T. Cloning and characterization of catalases from rice, Oryza sativa L., Bioscience, Biotechnology, and Biochemistry, 75, 10, 1900-6, (2011).
  • Sofo, A., Scopa, A., Nuzzaci, M., Vitti, A. Ascorbate Peroxidase and Catalase Activities and Their Genetic Regulation in Plants Subjected to Drought and Salinity Stresses, International Journal of Molecular Sciences, 12, 16, 6, 13561-78, (2015).
  • Polidoros, A.N., Mylona, P.V. and Scandalios, J.G. Transgenic tobacco plants expressing the maize Cat2 gene have altered catalase levels that affect plant-pathogen interactions and resistance to oxidative stress, Transgenic Research, 10, 6, 555-69, (2001).
  • Lukasik, I. Changes in activity of superoxide dismutase and catalase within cereal aphids in response to plant o-dihydroxyphenols. Journal of Applied Entomology, 131, 209-214, (2007).
  • Havir, E.A. and McHale, N.A. Regulation of Catalase Activity in Leaves of Nicotiana sylvestris by High CO(2), Plant Physiology, 8, 3, 952-957, (1989).
  • Isman, M.B. Botanical insecticides: for richer, for poorer, Pest Management Science, 64, 8-11, (2008).
  • Sayers, E.W., Bolton, E.E., Brister, J.R., Canese, K., Chan, J., Comeau, D.C., Connor, R., Funk, K., Kelly, C., Kim, S., Madej, T., Marchler-Bauer, A., Lanczycki, C., Lathrop, S., Lu, Z., Thibaud-Nissen, F., Murphy, T., Phan, L., Skripchenko, Y., Tse, T., Wang, J., Williams, R., Trawick, B.W., Pruitt, K.D., Sherry, S.T. Database resources of the national center for biotechnology information, Nucleic Acids Research, 50, D1, D20-D26, (2022).
  • Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; Protein Identification and Analysis Tools on the ExPASy Server; (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). pp. 571-607
  • Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E., Tosatto, S., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., Bateman, A. Pfam: The protein families database in 2021. Nucleic acids research, 49(D1), D412–D419, (2021).
  • Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N.J., Oinn, T.M., Pagni, M., Servant, F., Sigrist, C.J., Zdobnov, E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites, Nucleic Acids Research, 1, 29, 37-40, (2001).
  • Kuo-Chen, Chou and Hong-Bin, Shen. Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization, PLoS ONE, 5, e11335, (2010).
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., Zhang, Y. The I-TASSER Suite: protein structure and function prediction, Nature Methods, 12, 7-8, (2015).
  • Chen, V.B., Arendall, W.B. 3rd, Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., Richardson, D.C. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D Biological Crystallography, 66(Pt 1), 12-21 (2009).
  • Blom, N., Gammeltoft, S., and Brunak, S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites, Journal of Molecular Biology, 294, 5, 1351–1362, (1999).
  • Pagni, M., Ioannidis, V., Cerutti, L., Zahn-Zabal, M., Jongeneel, C.V., Falquet, L. MyHits: a new interactive resource for protein annotation and domain identification, Nucleic Acids Research, 32(Web Server issue), W332-5, (2004).
  • Hall, T.A. BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98, (1999).
  • Sudhir, K.,, Glen S., Michael L., Christina K., Koichiro T. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms, Molecular Biology and Evolution, 35, 1547-1549, (2018).
  • Yong, B., Wang, X., Xu, P., Zheng, H., Fei, X., Hong, Z., Ma, Q., Miao, Y., Yuan, X., Jiang, Y., Shao, H. Isolation and Abiotic Stress Resistance Analyses of a Catalase Gene from Ipomoea batatas (L.) Lam, BioMed Research International, 2017, 6847532, (2017).
  • Zhou, Y., Liu, S., Yang, Z., Yang, Y., Jiang, L., Hu, L. CsCAT3 , a catalase gene from Cucumis sativus , confers resistance to a variety of stresses to Escherichia coli, Biotechnology & Biotechnological Equipment, 31, 1-11, (2017).
  • Kamigaki, A., Mano, S., Terauchi, K., Nishi, Y., Tachibe-Kinoshita, Y., Nito, K., Kondo, M., Hayashi, M., Nishimura, M., Esaka, M. Identification of peroxisomal targeting signal of pumpkin catalase and the binding analysis with PTS1 receptor, The Plant Journal, 33, 161–175, (2003).
  • Hillisch, A. and Hilgenfeld, R. The role of protein 3D-structures in the drug discovery process, Experientia Supplementum, 93, 157-81, (2003).
  • Yang, L., Yanli, Y., Xiaowen, H., Shulian, X., Lei, X. Cloning and allelic variation of two novel catalase genes (SoCAT-1 and SsCAT-1) in Saccharum officinarum L. and Saccharum spontaneum L., Biotechnology & Biotechnological Equipment, 29, 3, 431-440, (2015).
  • Olsen, J.V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks, Cell, 3, 127, 3, 635-48, (2006). doi: 10.1016/j.cell.2006.09.026. PMID: 17081983.
  • Ardito, F., Giuliani, M., Perrone, D., Troiano, G., Lo Muzio, L. The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review), International Journal Of Molecular Medicine, 40, 2, 271–280, (2017).
  • de la Fuente van Bentem, S., and Hirt, H. Protein tyrosine phosphorylation in plants: More abundant than expected?, Trends in Plant Science, 14, 2, 71-76, (2009).
  • Selvakumar, P., Lakshmikuttyamma, A., & Sharma, R. K. Biochemical characterization of bovine brain myristoyl-CoA:protein N-myristoyltransferase type 2, Journal of Biomedicine & Biotechnology, 907614, (2009).
  • Rusin, S.F., Adamo, M.E., Kettenbach, A.N. Identification of Candidate Casein Kinase 2 Substrates in Mitosis by Quantitative Phosphoproteomics, Frontiers in Cell and Developmental Biology, 22, 5, 97, (2017).
  • Afiyanti, M. and Chen, H.-J. Catalase activity is modulated by calcium and calmodulin in detached mature leaves of sweet potato, Journal of Plant Physiology, 171, 2, 35–47, (2014).

In silico analysis on catalase protein from Nicotiana tabaccum L.

Yıl 2022, Cilt: 24 Sayı: 2, 818 - 829, 08.07.2022
https://doi.org/10.25092/baunfbed.1114706

Öz

Catalases are antioxidant enzymes which are responsible for decomposition of hydrogen peroxide to water and oxygen. Catalase activities have been shown to be influenced by environmental factors and stress conditions. In this study, in silico analysis of Nicotiana tabaccum L. was performed via bioinformatic tools. The results of this sudy suggested that the ORF of NtCAT-1 gene is 1479 bp and encodes a polypeptide of 492 amino acids. The predicted polypeptide was revealed as a 56.82 kDa protein with a pI of 6.27. The polypeptide had an aliphatic index of 71.52 and the grand average of hydropathicity (GRAVY) of -0.519. NtCAT-1 protein is hydrophilic and localised in Peroxisome. NtCAT-1 had two conserved domains at the positions of 18-399 and 421 and 486. had the catalase activity motif (CAM) at the position of 54–70 and heme-binding site (HBS) at the position of 344– 352. A highly reliable 3D structure was obtained and from Ramachandran plot analysis it was found that the portion of residues falling into the most favoured regions was 97.23%. The results of this study will provide fundamental information for further research in silico studies on catalase protein in different plant species.

Kaynakça

  • Cruz de Carvalho M. H. Drought stress and reactive oxygen species: Production, scavenging and signaling, Plant signaling & behavior, 3, 3, 156–165, (2008).
  • Sachdev. S., Ansari, S.A., Ansari. M.I., Fujita. M., Hasanuzzaman. M. Abiotic Stress and Reactive Oxygen Species: Generation, Signaling, and Defense Mechanisms, Antioxidants (Basel), 10, 2, 277, (2021).
  • Sharma, P., Jha, A.B., Dubey, R.S. and Pessarakli, M. Reactive Oxygen Species, Oxidative Damage, and Antioxidative Defense Mechanism in Plants under Stressful Conditions, Journal of Botany, 1, 26, (2012).
  • Dat J.F., Inzé, D., Van Breusegem, F. Catalase-deficient tobacco plants: tools for in planta studies on the role of hydrogen peroxide, Redox Report, 6, 1, 37-42, (2001).
  • Zamocky, M., Furtmüller, P. G., and Obinger, C. Evolution of catalases from bacteria to humans, Antioxidants & redox signaling, 10, 9, 1527–1548, (2008).
  • Wutipraditkul, N., Boonkomrat, S. and Buaboocha, T. Cloning and characterization of catalases from rice, Oryza sativa L., Bioscience, Biotechnology, and Biochemistry, 75, 10, 1900-6, (2011).
  • Sofo, A., Scopa, A., Nuzzaci, M., Vitti, A. Ascorbate Peroxidase and Catalase Activities and Their Genetic Regulation in Plants Subjected to Drought and Salinity Stresses, International Journal of Molecular Sciences, 12, 16, 6, 13561-78, (2015).
  • Polidoros, A.N., Mylona, P.V. and Scandalios, J.G. Transgenic tobacco plants expressing the maize Cat2 gene have altered catalase levels that affect plant-pathogen interactions and resistance to oxidative stress, Transgenic Research, 10, 6, 555-69, (2001).
  • Lukasik, I. Changes in activity of superoxide dismutase and catalase within cereal aphids in response to plant o-dihydroxyphenols. Journal of Applied Entomology, 131, 209-214, (2007).
  • Havir, E.A. and McHale, N.A. Regulation of Catalase Activity in Leaves of Nicotiana sylvestris by High CO(2), Plant Physiology, 8, 3, 952-957, (1989).
  • Isman, M.B. Botanical insecticides: for richer, for poorer, Pest Management Science, 64, 8-11, (2008).
  • Sayers, E.W., Bolton, E.E., Brister, J.R., Canese, K., Chan, J., Comeau, D.C., Connor, R., Funk, K., Kelly, C., Kim, S., Madej, T., Marchler-Bauer, A., Lanczycki, C., Lathrop, S., Lu, Z., Thibaud-Nissen, F., Murphy, T., Phan, L., Skripchenko, Y., Tse, T., Wang, J., Williams, R., Trawick, B.W., Pruitt, K.D., Sherry, S.T. Database resources of the national center for biotechnology information, Nucleic Acids Research, 50, D1, D20-D26, (2022).
  • Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; Protein Identification and Analysis Tools on the ExPASy Server; (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). pp. 571-607
  • Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E., Tosatto, S., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., Bateman, A. Pfam: The protein families database in 2021. Nucleic acids research, 49(D1), D412–D419, (2021).
  • Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N.J., Oinn, T.M., Pagni, M., Servant, F., Sigrist, C.J., Zdobnov, E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites, Nucleic Acids Research, 1, 29, 37-40, (2001).
  • Kuo-Chen, Chou and Hong-Bin, Shen. Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization, PLoS ONE, 5, e11335, (2010).
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., Zhang, Y. The I-TASSER Suite: protein structure and function prediction, Nature Methods, 12, 7-8, (2015).
  • Chen, V.B., Arendall, W.B. 3rd, Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., Richardson, D.C. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D Biological Crystallography, 66(Pt 1), 12-21 (2009).
  • Blom, N., Gammeltoft, S., and Brunak, S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites, Journal of Molecular Biology, 294, 5, 1351–1362, (1999).
  • Pagni, M., Ioannidis, V., Cerutti, L., Zahn-Zabal, M., Jongeneel, C.V., Falquet, L. MyHits: a new interactive resource for protein annotation and domain identification, Nucleic Acids Research, 32(Web Server issue), W332-5, (2004).
  • Hall, T.A. BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98, (1999).
  • Sudhir, K.,, Glen S., Michael L., Christina K., Koichiro T. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms, Molecular Biology and Evolution, 35, 1547-1549, (2018).
  • Yong, B., Wang, X., Xu, P., Zheng, H., Fei, X., Hong, Z., Ma, Q., Miao, Y., Yuan, X., Jiang, Y., Shao, H. Isolation and Abiotic Stress Resistance Analyses of a Catalase Gene from Ipomoea batatas (L.) Lam, BioMed Research International, 2017, 6847532, (2017).
  • Zhou, Y., Liu, S., Yang, Z., Yang, Y., Jiang, L., Hu, L. CsCAT3 , a catalase gene from Cucumis sativus , confers resistance to a variety of stresses to Escherichia coli, Biotechnology & Biotechnological Equipment, 31, 1-11, (2017).
  • Kamigaki, A., Mano, S., Terauchi, K., Nishi, Y., Tachibe-Kinoshita, Y., Nito, K., Kondo, M., Hayashi, M., Nishimura, M., Esaka, M. Identification of peroxisomal targeting signal of pumpkin catalase and the binding analysis with PTS1 receptor, The Plant Journal, 33, 161–175, (2003).
  • Hillisch, A. and Hilgenfeld, R. The role of protein 3D-structures in the drug discovery process, Experientia Supplementum, 93, 157-81, (2003).
  • Yang, L., Yanli, Y., Xiaowen, H., Shulian, X., Lei, X. Cloning and allelic variation of two novel catalase genes (SoCAT-1 and SsCAT-1) in Saccharum officinarum L. and Saccharum spontaneum L., Biotechnology & Biotechnological Equipment, 29, 3, 431-440, (2015).
  • Olsen, J.V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks, Cell, 3, 127, 3, 635-48, (2006). doi: 10.1016/j.cell.2006.09.026. PMID: 17081983.
  • Ardito, F., Giuliani, M., Perrone, D., Troiano, G., Lo Muzio, L. The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review), International Journal Of Molecular Medicine, 40, 2, 271–280, (2017).
  • de la Fuente van Bentem, S., and Hirt, H. Protein tyrosine phosphorylation in plants: More abundant than expected?, Trends in Plant Science, 14, 2, 71-76, (2009).
  • Selvakumar, P., Lakshmikuttyamma, A., & Sharma, R. K. Biochemical characterization of bovine brain myristoyl-CoA:protein N-myristoyltransferase type 2, Journal of Biomedicine & Biotechnology, 907614, (2009).
  • Rusin, S.F., Adamo, M.E., Kettenbach, A.N. Identification of Candidate Casein Kinase 2 Substrates in Mitosis by Quantitative Phosphoproteomics, Frontiers in Cell and Developmental Biology, 22, 5, 97, (2017).
  • Afiyanti, M. and Chen, H.-J. Catalase activity is modulated by calcium and calmodulin in detached mature leaves of sweet potato, Journal of Plant Physiology, 171, 2, 35–47, (2014).
Toplam 33 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Araştırma Makalesi
Yazarlar

Görkem Deniz Sönmez 0000-0002-3613-0195

Yayımlanma Tarihi 8 Temmuz 2022
Gönderilme Tarihi 10 Mayıs 2022
Yayımlandığı Sayı Yıl 2022 Cilt: 24 Sayı: 2

Kaynak Göster

APA Deniz Sönmez, G. (2022). In silico analysis on catalase protein from Nicotiana tabaccum L. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 24(2), 818-829. https://doi.org/10.25092/baunfbed.1114706
AMA Deniz Sönmez G. In silico analysis on catalase protein from Nicotiana tabaccum L. BAUN Fen. Bil. Enst. Dergisi. Temmuz 2022;24(2):818-829. doi:10.25092/baunfbed.1114706
Chicago Deniz Sönmez, Görkem. “In Silico Analysis on Catalase Protein from Nicotiana Tabaccum L”. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 24, sy. 2 (Temmuz 2022): 818-29. https://doi.org/10.25092/baunfbed.1114706.
EndNote Deniz Sönmez G (01 Temmuz 2022) In silico analysis on catalase protein from Nicotiana tabaccum L. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 24 2 818–829.
IEEE G. Deniz Sönmez, “In silico analysis on catalase protein from Nicotiana tabaccum L”., BAUN Fen. Bil. Enst. Dergisi, c. 24, sy. 2, ss. 818–829, 2022, doi: 10.25092/baunfbed.1114706.
ISNAD Deniz Sönmez, Görkem. “In Silico Analysis on Catalase Protein from Nicotiana Tabaccum L”. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 24/2 (Temmuz 2022), 818-829. https://doi.org/10.25092/baunfbed.1114706.
JAMA Deniz Sönmez G. In silico analysis on catalase protein from Nicotiana tabaccum L. BAUN Fen. Bil. Enst. Dergisi. 2022;24:818–829.
MLA Deniz Sönmez, Görkem. “In Silico Analysis on Catalase Protein from Nicotiana Tabaccum L”. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, c. 24, sy. 2, 2022, ss. 818-29, doi:10.25092/baunfbed.1114706.
Vancouver Deniz Sönmez G. In silico analysis on catalase protein from Nicotiana tabaccum L. BAUN Fen. Bil. Enst. Dergisi. 2022;24(2):818-29.