Bitki Proteomik Çalışmalarında Kullanılan Yaklaşımlar ve Uygulama Yöntemleri

Year 2020, , 497 - 528, 28.06.2020

Aslihan Gunel , Semra Hasancebi , Talat Yalçın , Mahmut Emir , Yahya Emin Demirci , Melike Dinç , Melda Güray

https://doi.org/10.35193/bseufbd.667838

Abstract

Proteomik yaklaşımları 2000 li yılların başlarına kadar mikroorganizmalar ve hayvansal kaynaklı örneklerde ağırlıklı olarak kullanıldı. Bu dönemde bitki proteomik çalışmaları yok denecek kadar azdır. Bitkisel dokulardaki sert hücre çeperleri, karmaşık ve çok çeşitli sekonder metabolitlerin varlığı, fazla miktardaki pigmentler, proteazlar, polifenoller, polisakkaritler, nişasta ve lipitler total protein örneklerinin hazırlanması ve proteinlerin ayrımı sırasında pek çok soruna neden olmuştur. Ancak her bir sorunun üstesinden gelmek üzere sürdürülen çabalar sayesinde bitki dünyasında da proteomik yaklaşım kullanımı yaygınlaşmıştır. Bu derlemede, örnek hazırlığından protein tanımlamaya kadar tüm basamaklar yöntemsel gelişmeleri de kapsayacak şekilde ayrıntılı olarak ele alınmış ve konuyla ilgili araştırıcıların maksimum yararlanabileceği bir kaynak oluşturulmaya çalışılmıştır.

Keywords

Proteomiks, bitki proteomik, Kütle spektrometresi, 2D-PAGE, 2D-LC

Supporting Institution

Çalışma bir derleme çalışmasıdır.

Approachs and Application Methods in Plant Proteomics Research

Abstract

Proteomics approach was used mainly in the samples for microorganisms and animal tissues until early 2000s, the period during which the plant proteomics studies were scarcely available. Tough nature of cell membranes, existence of complex and diverse range of secondary metabolites, high abundance of pigments, proteases, polyphenols, polysaccharides and lipids caused a number of problems for preparation and resolution of the protein samples. However, proteomics approach in plant area had become widespread with the help of continuous efforts in order to overcome these difficulties. This review is prepared comprehensively from the preparation of the samples to the identification of the proteins and it aims to serve as a detailed source for the researchers interested in plant proteomics, especially for young investigators.

Keywords

Proteomics, plant proteomics, mass spectrometry, 2D-PAGE, 2D-LC

References

• Wilkins, M.R., Pasquali, C., Appel, R.D., Ou, K., et al., (1996). From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Bio/Technology , 14, 61‐65.
• Konishi, T., (2001). Genetic diversity in Hordeum agriocrithon E. Åberg, six-rowed barley with brittle rachis, from Tibet. Genet. Resour. Crop Evol. 110, 145-150.
• Imin, N., Kerim, T., Weinman, J.J., Rolfe, B.G., (2001). Characterisation of rice anther proteins expressed at the young microspore stage. Proteomics, 1, 1149–1161.
• Mandelc, S., Javornik, B., Majeran, W., Cai, Y., et al., (2004). A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization. Proteomics, 14, 311 LP – 325.
• Schubert, M., Petersson, U.A., Haas, B.J., Funk, C., et al., (2002). Proteome map of the chloroplast lumen of Arabidopsis thaliana. J. Biol. Chem, 277, 8354‐8365.
• Shen, S., Matsubae, M., Takao, T., Tanaka, N., Komatsu, S. (2002). A proteomic analysis of leaf sheaths from rice. Journal of biochemistry, 132(4), 613–620.
• Bindschedler, L. V., Burgis, T.A., Mills, D.J.S., Ho, J.T.C., et al., (2009). In planta proteomics and proteogenomics of the biotrophic Barley fungal pathogen Blumeria graminis f. sp. hordei. Mol. Cell. Proteomics, 8, 2368–2381.
• Rampitsch, C., Günel, A., Beimcik, E., Mauthe, W. (2015). Proteome of monoclonal antibody-purified haustoria from Puccinia triticina Race-1. Proteomics, 15, 1307–1315.
• Rampitsch, C., Bykova, N. V., McCallum, B., Beimcik, E., Ens, W. (2006). Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction. Proteomics, 6, 1897–1907.
• Kim, S. T., Kim, S. G., Hwang, D. H., Kang, S. Y., Kim, H. J., Lee, B. H., Lee, J. J., Kang, K. Y. (2004). Proteomic analysis of pathogen-responsive proteins from rice leaves induced by rice blast fungus, Magnaporthe grisea. Proteomics, 4, 3569–3578.
• Gunel, A., Asbahi, A., Ozgazi, N., Akkaya, M.S., (2012). Identification of differentially expressed proteins in wheat after benzothiadiazole treatment. J. Plant Dis. Prot. 119.
• Jung, Y. H., Jeong, S. H., Kim, S. H., Singh, R., Lee, J. E., Cho, Y. S., Agrawal, G. K., Rakwal, R., Jwa, N. S. (2012). Secretome analysis of Magnaporthe oryzae using in vitro systems. Proteomics, 12, 878–900.
• Rampitsch, C., Day, J., Subramaniam, R., Walkowiak, S. (2013). Comparative secretome analysis of Fusarium graminearum and two of its non-pathogenic mutants upon deoxynivalenol induction in vitro. Proteomics, 13, 1913–1921.
• Hochholdinger, F., Guo, L., Schnable, P. S. (2004). Cytoplasmic regulation of the accumulation of nuclear-encoded proteins in the mitochondrial proteome of maize. The Plant journal : for cell and molecular biology, 37, 199–208.
• Lonosky, P. M., Zhang, X., Honavar, V. G., Dobbs, D. L., Fu, A., Rodermel, S. R. (2004). A proteomic analysis of maize chloroplast biogenesis. Plant physiology, 134, 560–574.
• Majeran, W., Cai, Y., Sun, Q., van Wijk, K. J. (2005). Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. The Plant cell, 17, 3111–3140.
• Zhu, J., Alvarez, S., Marsh, E. L., Lenoble, M. E., Cho, I. J., Sivaguru, M., Chen, S., Nguyen, H. T., Wu, Y., Schachtman, D. P., Sharp, R. E. (2007). Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit. Plant physiology, 145, 1533–1548.
• Dunkley, T. P., Hester, S., Shadforth, I. P., Runions, J., Weimar, T., Hanton, S. L., Griffin, J. L., Bessant, C., Brandizzi, F., Hawes, C., Watson, R. B., Dupree, P., Lilley, K. S. (2006). Mapping the Arabidopsis organelle proteome. Proceedings of the National Academy of Sciences of the United States of America, 103, 6518–6523.
• Maltman, D. J., Gadd, S. M., Simon, W. J., Slabas, A. R. (2007). Differential proteomic analysis of the endoplasmic reticulum from developing and germinating seeds of castor (Ricinus communis) identifies seed protein precursors as significant components of the endoplasmic reticulum. Proteomics, 7, 1513–1528.
• Fernando, U., Chatur, S., Joshi, M., Thomas Bonner, C., Fan, T., Hubbard, K., Chabot, D., Rowland, O., Wang, L., Subramaniam, R., Rampitsch, C. (2019). Redox signalling from NADPH oxidase targets metabolic enzymes and developmental proteins in Fusarium graminearum. Molecular plant pathology, 20, 92–106.
• Rampitsch, C., Huang, M., Djuric-Cignaovic, S., Wang, X., Fernando, U. (2019). Temporal Quantitative Changes in the Resistant and Susceptible Wheat Leaf Apoplastic Proteome During Infection by Wheat Leaf Rust (Puccinia triticina). Frontiers in plant science, 10, 1291.
• Fang, X., Chen, J., Dai, L., Ma, H., Zhang, H., Yang, J., Wang, F., Yan, C. (2015). Proteomic dissection of plant responses to various pathogens. Proteomics, 15, 1525–1543.
• Unlü, M., Morgan, M. E., Minden, J. S. (1997). Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis, 18, 2071–2077.
• Wittig, I., Braun, H. P., Schägger, H. (2006). Blue native PAGE. Nature protocols, 1, 418–428.
• Karger, B. L., Guttman, A. (2009). DNA sequencing by CE. Electrophoresis, 30 Suppl 1(Suppl 1), S196–S202.
• Görg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., & Weiss, W. (2000). The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis, 21, 1037–1053.
• Wang, W., Scali, M., Vignani, R., Spadafora, A., Sensi, E., Mazzuca, S., Cresti, M. (2003). Protein extraction for two-dimensional electrophoresis from olive leaf, a plant tissue containing high levels of interfering compounds. Electrophoresis, 24, 2369–2375.
• Neuhoff, V., Arold, N., Taube, D., Ehrhardt, W. (1988). Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis, 9, 255–262.
• Zörb, C., Betsche, T., Langenkämper, G. (2009). Search for diagnostic proteins to prove authenticity of organic wheat grains (Triticum aestivum L.). Journal of agricultural and food chemistry, 57, 2932–2937.
• Finnie, C. 2006. Plant proteomics. Annual Plant Reviews. 28: ISBN:1-405 1-4429-7. Blackwell Yayınevi.
• Demirci, YE., Inan, C., Günel, A., Maytalman, D., Mert, Z., Baykal, AT.,Vural-Korkut,
• S., Arda, N. & Hasançebi S. (2016). Proteome profiling of the compatible interaction between wheat and stripe rust. European Journal of Plant Pathology, 1-22.
• Kim, ST., Cho, KS., Jang YS., Kang YK. (2001) Two dimensional electrophoretic analysis of rice proteins by polyethylene glycol fractionation for protein arrays. Electrophoresis. 22:2103-2109.
• UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017
• Ncbi Resource Coordinators, Database Resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2017
• Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine Anal. Chem. 1987 Richard S. Johnson, Stephen A. Martin, Klaus. Biemann, John T. Stults, and J. Throck. Watson
• An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Jimmy K.EngAshley L.McCormackJohn R.YatesIII, J Am Soc Mass Spectrom 1994
• Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567
• Karas, M.; Bachmann, D.; Bahr, U.; Hillenkamp, F., Matrix-assisted ultraviolet laser desorption of non-volatile compounds. International Journal of Mass Spectrometry and Ion Processes 1987, 78, 53-68.
• Fenn, J.; Mann, M.; Meng, C.; Wong, S.; Whitehouse, C., Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246 (4926), 64-71
• Matthes, A., Köhl K., Schulze, WX., SILAC and alternatives in studying cellular proteomes of plants. Methods Mol Biol. 2014;1188:65‐83. doi:10.1007/978-1-4939-1142-4_6
• Liu, B., Shan, X., Wu, Y., Su, S., Li, S., Liu, H., Han, J., Yuan, Y. (2018). iTRAQ-Based Quantitative Proteomic Analysis of Embryogenic and Non-embryogenic Calli Derived from a Maize (Zea mays L.) Inbred Line Y423. International journal of molecular sciences, 19(12), 4004.
• Van Ness, L. K., Jayaraman, D., Maeda, J., Barrett-Wilt, G. A., Sussman, M. R., Ane, J. M. (2016). Mass spectrometric-based selected reaction monitoring of protein phosphorylation during symbiotic signaling in the model legume, Medicago truncatula. PloS one, 11(5).
• Arsova, B., Watt, M., Usadel, B. (2018). Monitoring of plant protein post-translational modifications using targeted proteomics. Frontiers in plant science, 9, 1168.
• Fuchs, P., Rugen, N., Carrie, C., Elsässer, M., Finkemeier, I., Giese, J., Schallenberg‐Rüdinger, M. (2020). Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics. The Plant Journal, 101, 420-441.
• Niehaus, M., Straube, H., Künzler, P., Rugen, N., Hegermann, J., Giavalisco, P., Herde, M. (2020). Rapid affinity purification of tagged plant mitochondria (Mito-AP) for metabolome and proteome analyses. Plant Physiology, 182, 1194-1210.
• Wang, Y., Li, X., Liu, N., Wei, S., Wang, J., Qin, F., Suo, B. (2020). The iTRAQ-based chloroplast proteomic analysis of Triticum aestivum L. leaves subjected to drought stress and 5-aminolevulinic acid alleviation reveals several proteins involved in the protection of photosynthesis. BMC plant biology, 20, 1-17.
• Wang X. (2019). Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era. International journal of molecular sciences, 20, 5222.