Shotgun Proteomic Analysis of Germinated Rice (Oryza sativa L.) under Salt Stress
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Published:
Feb 19, 2020
Keywords:
Proteomics GeLC-MS Thai rice Salt stress Germination
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Abstract
Rice (Oryza sativa L.) is an important staple crop that feeds more than one half of the world’s population. However, salt stress caused a dramatic decline of rice production. Proteome study of salt tolerant mechanism supplied a span-new viewpoint and valuable clue to rice tolerant improvement. In this study, the salt tolerant capacity and stress response proteins of seven Thai rice cultivars at the germination stage were determined. Pathumthani, Phitsanulok2, RD29, RD31, RD41, RD47, and Riceberry rice cultivars were germinated under 200 mm NaCl for 4 days. Based on germination rate, Pathumthani, Phitsanulok2 and RD31 cultivars were categorized as tolerant, while RD29, RD41 and Riceberry were moderately tolerant and RD47 as susceptible. Shotgun proteome analysis of total proteins prepared from 7 rice seeds grown under salt stress identified 1339 proteins, 51 of which were expressed only in salt tolerant cultivars including Pathumthani, Phitsanulok2 and RD31. These proteins played role in development, protein modification, signal transduction, stress response, transport and transcription. Proteome mechanism during the process of seed germination under salt stress was proposed. This data may be used for not only improvement of rice yield under salinity stress but also enhancing salinity stress tolerance in this important crop.
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Li, R., Chaicherdsakul, T., Kunathigan, V., Roytrakul, S., Paemanee, A., & Kittisenachai, S. (2020). Shotgun Proteomic Analysis of Germinated Rice (Oryza sativa L.) under Salt Stress. Applied Science and Engineering Progress, 13(1), 76–85. Retrieved from https://ph02.tci-thaijo.org/index.php/ijast/article/view/240018
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References
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[21] G.-L. Wang, F. Que, Z.-S. Xu, F. Wang, and A.-S. Xiong, “Exogenous gibberellin altered morphology, anatomic and transcriptional regulatory networks of hormones in carrot root and shoot,” BMC Plant Biology, vol. 15, no.1, p. 290, Dec. 2015.
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[26] T. Van der Heide, M. C. A. Stuart, and B. Poolman, “On the osmotic signal and osmosensing mechanism of an ABC transport system for glycine betaine,” EMBO Journal, vol. 20, no. 24, pp. 7022–7032, Dec. 2001.
[27] Y. Guo, U. Halfter, M. Ishitani, and J.-K. Zhu, “Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance,” The Plant Cell, vol.13, no. 6, pp. 1383–1400, Jun 2001.
[28] A. Shimada, M. Ueguchi-Tanaka, T. Sakamoto, S. Fujioka, S. Takatsuto, S. Yoshida, T. Sazuka, M. Ashikari, and M. Matsuoka, “The rice SPINDLY gene functions as a negative regulator ofgibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis,” The Plant Journal, vol. 48, no. 3, pp. 390–402, Nov. 2006.
[29] G. Miller, N. Suzuki, S. Ciftci-Yilmaz, and R. Mittler, “Reactive oxygen species homeostasis and signalling during drought and salinity,” Plant Cell and Environment, vol. 33, no. 4, pp. 453–467, Apr. 2010.
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[31] S. Razzaque, S. M. Elias, S. Biswas, T. Haque, and Z. I. Seraj, “Cloning of the plasma membrane sodium/ hydrogen antiporter SOS1 for its over expression in rice,” Plant Tissue Culture and Biotechnology, vol. 23, no. 2, pp. 263–273, Dec. 2013.
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[33] H. Chen, R. An, J.-H. Tang, X.-H. Cui, F.-H. Hao, J. Chen, and X.-C. Wang, “Over-expression of a vacuolar Na+/H+ antiporter gene improves salt tolerance in an upland rice,” Molecular Breeding, vol. 19, no. 3, pp. 215–225, Apr. 2007.
[34] A. Fukuda, A. Nakamura, A. Tagiri, H. Tanaka, A. Miyao, H. Hirochika, and Y. Tanaka, “Function, intracellular localization and the importance in salt tolerance of a vacuolar Na+/H+ antiporter from rice,” Plant Cell and Physiology, vol. 45, no. 2, pp. 146–159, Feb. 2004.
[35] Q. S. Qiu, Y. Guo, M. A. Dietrich, K. S. Schumaker, and J. K. Zhu, “Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3,” in Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 12, pp. 8436–8441, Jun. 2002.
[2] B. Titapiwatanakun, (2012, Jan.). The Rice Situation in Thailand. Asian Development Bank. Manila, Philippines [Online]. Available: https://www.adb.org/sites/default/files/projectdocument/ 73082/43430-012-reg-tacr-03.pdf
[3] L. Zeng and M. C. Shannon, “Salinity effects on seedling growth and yield components of rice,” Crop Science, vol. 40, no. 4, pp. 996–1003, Jul. 2000.
[4] E. V. Maas and S. R. Grattan, Crop Yields as Affected by Salinity. Madison, WI: Agricultural Drainage, 1999, pp. 55–108.
[5] P. Deepa Sankar, M. A. Arabi Mohammed Saleh, and C. I. Selvaraj, “Rice breeding for salt tolerance,” Research in Biotechnology, vol. 2, no. 2, pp. 1–10, Apr. 2011.
[6] O. K. Lowry, N. J. Rosbrough, A. L. Farr, and R. J. Randall, “Protein measurement with the folin phenol reagent,” Journal of Biological Chemistry, vol. 193, no. 1, p. 265, Nov. 1951.
[7] U. K. Laemmli, “Cleavage of structural proteins during the assembly of the head of bacteriophage T4,” Nature, vol. 227, no. 5259, pp. 680–685, Aug. 1970.
[8] I. Syrový and Z. Hodný, “Staining and quantification of proteins separated by polyacrylamide gel electrophoresis,” Journal of Chromatography B, vol. 569, no. 1–2, pp. 175–196, Sep. 1991.
[9] A. Paemanee, N. Wikan, S. Roytrakul, and D. R. Smith, “Application of GelC-MS/MS to proteomic profiling of Chikungunya virus infection: Preparation of peptides for analysis,” Methods in Molecular Biolology, vol. 1426, pp. 179–193, 2016.
[10] C. Johansson, J. Samskog, L. Sundstrom, H. Wadensten, L. Bjorkesten, and J. Flensburg, “Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data,” Proteomics, vol. 6, no. 16, pp. 4475–4485, Aug. 2006.
[11] A. Thorsell, E. Portelius, K. Blennow, and B. A. Westman, “Evaluation of sample fractionation using microscale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment,” Rapid Communication in Mass Spectrometry, vol. 21, no. 5, pp. 771–778, Mar. 2007.
[12] D. N. Perkins, D. J. C. Pappin, D. M. Creasy, and J. S. Cottrell, “Probability-based protein identification by searching sequence databases using mass spectrometry data,” Electrophoresis, vol. 20, no. 18, pp. 3551–3567, Dec. 1999.
[13] M. Kuhn, D. Szklarczyk, S. Pletscher-Frankild, T. H. Blicher, C. von Mering, L. J. Jensen, and P. Bork, “STITCH 4: Integration of proteinchemical interactions with user data,” Nucleic Acids Research, vol. 42, no. D1, pp. D401–D407, Nov. 2013.
[14] P. Bardou, J. Mariette, F. Escudié, C. Djemiel, C. Klopp, “jvenn: An interactive Venn diagram viewer,” BMC Bioinformatics, vol. 15, no. 1, p. 293, Dec. 2014.
[15] S. Chutipaijit, S. Cha-um, and K. Sompornpailin, “Differential accumulations of proline and flavonoids in indica rice varieties against salinity,” Pakistan Journal of Botany, vol. 41, no. 5, pp. 2497–2506, Oct. 2009.
[16] P. Wanichananan, C. Kirdmanee, and C. Vutiyano, “Effect of salinity on biochemical and physiological characteristics in correlation to selection of salt- tolerance in aromatic rice (Oryza sativa L.),” Science Asia, vol. 29, no. 4, pp. 333–339, Dec. 2003.
[17] S. Hasthanasombut, N. Paisarnwipatpong, K. Triwitayakorn, C. Kirdmanee, and K. Supaibulwatana, “Expression of OsBADH1 gene in Indica rice (Oryza sativa L.) in correlation with salt, plasmolysis, temperature and light stresses,” Plant Omics Journal, vol. 4, no. 7, pp. 400–407, Dec. 2011.
[18] F. Worede, T. Sreewongchai, C. Phumichai, and P. Sripichitt, “Genetic diversity analysis of rice cultivars from various origins using simple sequence repeat (SSR) markers,” African Journal of Biotechnology, vol. 12, no. 26, pp. 4074–4081, Jun. 2013.
[19] W. H. McDonald, R. Ohi, D. T. Miyamoto, T. J. Mitchison, and J. R. Yates Iii, “Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: Single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT,” International Journal of Mass Spectrometry, vol. 219, no. 1, pp. 245–251, Aug 2002.
[20] A. Gómez-Cadenas, R. Zentella, M. K. Walker- Simmons, and T.-H.D. Ho, “Gibberellin/abscisic acid antagonism in barley aleurone cells: Site of action of the protein kinase PKABA1 in relation to gibberellin signaling molecules,” The Plant Cell, vol. 13, no. 3, pp. 667–679, Mar. 2001.
[21] G.-L. Wang, F. Que, Z.-S. Xu, F. Wang, and A.-S. Xiong, “Exogenous gibberellin altered morphology, anatomic and transcriptional regulatory networks of hormones in carrot root and shoot,” BMC Plant Biology, vol. 15, no.1, p. 290, Dec. 2015.
[22] M. Geisler, J. J. Blakeslee, R. Bouchard, O. R. Lee, V. Vincenzetti, A. Bandyopadhyay, B. Titapiwatanakun, W. A. Peer, A. Bailly, E. L. Richards, K. F. Ejendal, A. P. Smith, C. Baroux, U. Grossniklaus, A. Müller, C. A. Hrycyna, R. Dudler, A. S Murphy, and E. Martinoia, “Cellular efflux of auxin catalyzed by the Arabidopsis MDR/PGP transporter AtPGP1,” The Plant Journal, vol. 44, no. 2, pp. 179–194, Oct. 2005.
[23] G. Akbari, S. A. Sanavy, and S. Yousefzadeh, “Effect of auxin and salt stress (NaCl) on seed germination of wheat cultivars (Triticum aestivum L.),” Pakistan Journal of Biological Science, vol. 10, no. 15, pp. 2557–2561, Aug. 2007.
[24] G. Wu, D. R. Lewis, and E. P. Spalding, “Mutations in Arabidopsis multidrug resistance-like ABC transporters separate the roles of acropetal and basipetal auxin transport in lateral root development,” The Plant Cell, vol. 19, no. 6, pp. 1826–1837, Jun. 2007.
[25] M. Monroe-Augustus, B. K. Zolman, and B. Bartel, “IBR5, a dual-specificity phosphataselike protein modulating auxin and abscisic acid responsiveness in Arabidopsis,” The Plant Cell, vol. 15, no. 12, pp. 2979–2991, Dec. 2003.
[26] T. Van der Heide, M. C. A. Stuart, and B. Poolman, “On the osmotic signal and osmosensing mechanism of an ABC transport system for glycine betaine,” EMBO Journal, vol. 20, no. 24, pp. 7022–7032, Dec. 2001.
[27] Y. Guo, U. Halfter, M. Ishitani, and J.-K. Zhu, “Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance,” The Plant Cell, vol.13, no. 6, pp. 1383–1400, Jun 2001.
[28] A. Shimada, M. Ueguchi-Tanaka, T. Sakamoto, S. Fujioka, S. Takatsuto, S. Yoshida, T. Sazuka, M. Ashikari, and M. Matsuoka, “The rice SPINDLY gene functions as a negative regulator ofgibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis,” The Plant Journal, vol. 48, no. 3, pp. 390–402, Nov. 2006.
[29] G. Miller, N. Suzuki, S. Ciftci-Yilmaz, and R. Mittler, “Reactive oxygen species homeostasis and signalling during drought and salinity,” Plant Cell and Environment, vol. 33, no. 4, pp. 453–467, Apr. 2010.
[30] E. Blumwald, “Sodium transport and salt tolerance in plants,” Current Opinion in Cell Biology, vol. 12, no. 4, pp. 431–434, Aug. 2000.
[31] S. Razzaque, S. M. Elias, S. Biswas, T. Haque, and Z. I. Seraj, “Cloning of the plasma membrane sodium/ hydrogen antiporter SOS1 for its over expression in rice,” Plant Tissue Culture and Biotechnology, vol. 23, no. 2, pp. 263–273, Dec. 2013.
[32] H. Shi, B.-H. Lee, S.-J. Wu, and J.-K. Zhu, “Overexpression of a plasma membrane Na+/ H+ antiporter gene improves salt tolerance in Arabidopsis thaliana,” Nature Biotechnology, vol. 21, no. 1, pp. 81–85, Jan. 2003.
[33] H. Chen, R. An, J.-H. Tang, X.-H. Cui, F.-H. Hao, J. Chen, and X.-C. Wang, “Over-expression of a vacuolar Na+/H+ antiporter gene improves salt tolerance in an upland rice,” Molecular Breeding, vol. 19, no. 3, pp. 215–225, Apr. 2007.
[34] A. Fukuda, A. Nakamura, A. Tagiri, H. Tanaka, A. Miyao, H. Hirochika, and Y. Tanaka, “Function, intracellular localization and the importance in salt tolerance of a vacuolar Na+/H+ antiporter from rice,” Plant Cell and Physiology, vol. 45, no. 2, pp. 146–159, Feb. 2004.
[35] Q. S. Qiu, Y. Guo, M. A. Dietrich, K. S. Schumaker, and J. K. Zhu, “Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3,” in Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 12, pp. 8436–8441, Jun. 2002.