Sains Malaysiana 47(6)(2018): 1259–1268

http://dx.doi.org/10.17576/jsm-2018-4706-22

Proteomic Analysis of Stored Core Oil Palm Trunk (COPT) Sap Identifying Proteins Related to Stress, Disease Resistance and Differential Gene/Protein Expression

(Analisis Proteomik Pengenalpastian Protein Sap Teras Batang Kelapa Sawit (COPT) Tersimpan Berkaitan Tekanan, Pertahanan Penyakit dan Perbezaan Pengekspressan Gen/Protein)

MARHAINI MOSTAPHA¹, NOORHASMIERA ABU JAHAR¹, KAMALRUL AZLAN AZIZAN², SARANI ZAKARIA¹, WAN MOHD AIZAT² & SHARIFAH NABIHAH SYED JAAFAR^1*

¹Bioresources and Biorefinary Laboratory, Faculty of Science and Technology

Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

²Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia

43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

Diserahkan: 4 Oktober 2017/Diterima: 18 Januari 2018

ABSTRACT

Oil palm is the major crop grown and cultivated in various Asian countries such as Malaysia, Indonesia and Thailand. The core of oil palm trunk (COPT) consists of high sugar content, hence suitable for synthesis of fine chemicals and biofuels. Increase of sugar content was reported previously during prolonged COPT storage. However, until now, there has been no report on protein profiles during storage. Therefore, in this study, protein expression of the COPT during the storage period of one to six weeks was investigated using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) coupled with optical density quantification and multivariate analyses for measuring differentially expressed proteins. Accordingly, protein bands were subjected to tryptic digestion followed by tandem mass spectrometry (nanoLC-MS/MS) protein identification. The results from SDS-PAGE showed consistent protein bands appearing across the biological replicates ranging from 10.455 to 202.92 kDa molecular weight (MW) regions. The findings from the principal component analysis (PCA) plot illustrated the separation pattern of the proteins at weeks 4 and 5 of storage, which was influenced mainly by the molecular weights of 14.283, 25.543, 29.757, 30.549, 31.511, 34.585 and 84.395 kDa, respectively. The majority of these proteins are identified as those involved in stress- and defense-related, disease resistance, as well as gene/protein expression processes. Indeed, these proteins were mostly upregulated during the later storage period suggesting that long-term storage may influence the molecular regulation of COPT sap.

Keywords: Densitometry analysis; Elaeis guineensis; LC-MS; principal component analysis; SDS-PAGE

ABSTRAK

Kelapa sawit merupakan antara tanaman utama di negara Asia seperti Malaysia, Indonesia dan Thailand. Teras batang kelapa sawit (COPT) mempunyai kandungan gula yang tinggi, maka ia sesuai digunakan untuk penghasilan bahan kimia ringkas dan bahan bakar bio. Peningkatan kandungan gula pada sap daripada COPT yang disimpan telah dilaporkan. Walau bagaimanapun setakat ini, kajian terhadap perubahan profil protein COPT semasa penyimpanan masih belum diterokai. Maka dalam kajian ini, pengekspresan protein COPT yang tersimpan selama satu hingga enam minggu telah dikaji menggunakan gel elektroforesis 1D (SDS-PAGE) ditambah dengan penentuan ketumpatan optik dan analisis multivariat untuk mengukur jalur protein yang berbeza. Jalur protein ini kemudiannya dipotong menggunakan tripsin diikuti dengan pengenalpastian protein menggunakan spektrometri jisim (nanoLC-MS/MS). Keputusan daripada SDS-PAGE menunjukkan jalur protein yang konsisten merentasi replikasi biologi dengan berat molekul protein daripada 10.455 kepada 202.92 kDa. Keputusan analisis prinsipal komponen utama (PCA) menunjukkan corak pemisahan protein pada minggu ke-4 dan minggu ke-5 penyimpanan dipengaruhi oleh berat molekul 14.283, 25.543, 29.757, 30.549, 31.511, 34.585 dan 84.395 kDa. Majoriti protein yang dikenal pasti merupakan protein yang terlibat dengan tekanan dan pertahanan, protein yang berkaitan dengan perintang penyakit, serta proses pengekspressan gen atau protein. Penambahan tempoh penyimpanan telah menyebabkan protein ini dikawal naik sekaligus mencadangkan kesan tempoh penyimpanan mempengaruhi kawalatur eskpresi molekul protein sap TBKS.

Kata kunci: Analisis densitometri; analisis kumpulan utama; Elaeis guineensis; LC-MS; SDS-PAGE

RUJUKAN

Adeyemi, K.D., Mislan, N., Aghwan, Z.A., Sarah, S.A. & Sazili, A.Q. 2014. Myofibrillar protein profile of Pectoralis major muscle in broiler chickens subjected to different freezing and thawing methods. International Food Research Journal 21(3): 1089-1093.

Al-Obaidi, J.R., Mohd-Yusuf, Y., Razali, N., Jayapalan, J.J., Tey, C.C., Md-Noh, N., Junit, S.M., Othman, R.Y. & Hashim, O.H. 2014. Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense. International Journal of Molecular Sciences 15(3): 5175-5192.

Barkan, A. & Small, I. 2014. Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology 65: 415-442.

Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. & Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Research 28(1): 235-242.

Berrocal-Lobo, M., Ibañez, C., Acebo, P., Ramos, A., Perez- Solis, E., Collada, C., Casado, R., Aragoncillo, C. & Allona I. 2011. Identification of a homolog of Arabidopsis DSP4(SEX4) in chestnut: Its induction and accumulation in stem amyloplasts during winter or in response to the cold. Plant Cell Environment 34(10): 1693-1704.

Bukhari, N.A., Loh, S.K., Bakar, N.A. & Ismail, M. 2017. Hydrolysis of residual starch from sago pith residue and its fermentation to bioethanol. Sains Malaysiana 46(8): 1269-1278.

de Carvalho Silva, R., Carmo, L.S.T., Luis, Z.G., Silva, L.P., Scherwinski-Pereira, J.E. & Mehta, A. 2014. Proteomic identification of differentially expressed proteins during the acquisition of somatic embryogenesis in oil palm (Elaeis guineensis Jacq.). Journal of Proteomics 104: 112-127.

Department of Statistic Malaysia. 2016. Selected Agriculture Indicators, Malaysia 2016. https://www.dosm.gov.my/v1/ index.php?r=column/cthemeByCat&cat=72&bul_id=Z3Nkh LSFk2VjZ5dkdUL1JQUGs4dz09&menu_id=Z0VTZGU1UH BUT1VJMFlpaXRR0xpdz09. Accessed on May 2017.

Desiderio, C., Rossetti, D.V., Iavarone, F., Messana, I. & Castagnola, M. 2010. Capillary electrophoresis-mass spectrometry: Recent trends in clinical proteomics. Journal of Pharmaceutical and Biomedical Analysis 53(5): 1161-1169.

Dickinson, R.J. & Keyse, S.M. 2006. Diverse physiological functions for dual-specificity MAP kinase phosphatases. Journal of Cell Science 119(22): 4607-4615.

Hage, D.S., Anguizola, J.A., Bi, C., Li, R., Matsuda, R., Papastavros, E., Pfaunmiller, E., Vargas, J. & Zheng, X. 2012. Pharmaceutical and biomedical applications of affinity chromatography: Recent trends and developments. Journal of Pharmaceutical and Biomedical Analysis 69: 93-105.

Hashemi, A., Gharechahi, J., Nematzadeh, G., Shekari, F., Hosseini, S.A. & Salekdeh, G.H. 2016. Two-dimensional blue native/SDS-PAGE analysis of whole cell lysate protein complexes of rice in response to salt stress. Journal of Plant Physiology 200: 90-101.

Hood, L. & Rowen, L. 2013. The human genome project: Big science transforms biology and medicine. Genome Medicine 5(9): 79.

Hunter, T. 2009. Tyrosine phosphorylation: Thirty years and counting. Current Opinion in Cell Biology 21(2): 140-146.

Jahar, N.A., Pua, G., Wong, J.C., Mostapha, M., Zakaria, S., Chia, C.H. & Jaafar, S.N.S. 2017. Utilization of core oil palm trunk waste to methyl levuinate: Physical and chemical characterizations. Waste and Biomass Valorization pp. 1-6.

Jeffery Daim, L.D., Ooi, T.E.K., Ithnin, N., Mohd Yusof, H., Kulaveerasingam, H., Abdul Majid, N. & Karsani, S.A. 2015. Comparative proteomic analysis of oil palm leaves infected with Ganoderma boninense revealed changes in proteins involved in photosynthesis, carbohydrate metabolism, and immunity and defense. Electrophoresis 36(15): 1699-1710.

Kushwaha, H.R., Singh, A.K., Sopory, S.K., Singla-Pareek, S.L. & Pareek, A. 2009. Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa L. reveals their developmental and stress regulation. BioMed. Central Genomics 10: 200.

Lai, W.H., Leo, T.K., Zainal, Z. & Daud, F. 2014. Preliminary proteomic characterisation of primodia and vegetative dikaryotic mycelial cells from Tiger’s milk mushroom (Lignosus rhinocerus). Sains Malaysiana 43(8): 1133-1138.

Liu, B., Fan, J., Zhang, Y., Mu, P., Wang, P., Su, J., Lai, H., Li, S., Feng, D., Wang, J. & Wang, H. 2012. OsPFA-DSP1, a rice protein tyrosine phosphatase, negatively regulates drought stress responses in transgenic tobacco and rice plants. Plant Cell Reports 31(6): 1021-1032.

Lurin, C., Andres, C., Aubourg, S., Bellaoui, M., Bitton, F., Bruyere, C., Caboche, M., Debast, C., Gualberto, J., Hoffmann, B., Lecharny, A., Le Ret, M., Martin-Magniette, M.L., Mireau, H., Peeters, N., Renou, J.P., Szurek, B., Taconnat, L. & Small, I. 2004. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. The Plant Cell 16(8): 2089-2103.

Malaysia Palm Oil Board. Malaysia Palm Oil Industry: A report. http://www.palmoilworld.org/about _malaysian-industry. html. Accessed on 20 October 2016.

Martin, G.B., Bogdanove, A.J. & Sessa, G. 2003. Understanding the functions of plant disease resistance proteins. Annual Review of Plant Biology 54(1): 23-61.

Mostapha, M., Jahar, N.A., Chin, S.X., Jaafar, S.N.S., Zakaria, S., Aizat, W.M. & Azizan, K.A. 2016. Effect of zeolite catalyst on sugar dehydration for 5 Hydroxymethylfurfural synthesis. American Institute of Physics Conference Proceedings 1784(1): 040026.

Mostapha, M., Jahar, N.A., Zakaria, S., Aizat, W.M., Azizan, K.A. & Jaafar, S.N.S. 2017. Metabolite profiling of core oil palm trunk (COPT) sap: The effects of different storage durations, conditions and temperatures. Journal of Oil Palm Research 30(1): 111-120.

Nualkaew, S., Saelim, H., Tiwawech, D., Parvez, T.P.I. & Phongdara, A. 2017. Role of cytochrome P450 monooxygenase in the bioactivation of aflatoxin B1. Sains Malaysiana 46(9): 1499-1503.

Nur Azira, T. & Amin, I. 2012. Differentiation of bovine and porcine gelatins in processed products via sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS PAGE) and principal component analysis (PCA) techniques. International Food Research Journal 19(3): 1175-1180.

Segonzac, C., Macho, A.P., Sanmartín, M., Ntoukakis, V., Sánchez-Serrano, J.J. & Zipfel, C. 2014. Negative control of BAK1 by protein phosphatase 2A during plant innate immunity. The European Molecular Biology Organization Journal 33: 2069-2079.

Shankar, A., Agrawal, N., Sharma, M., Pandey, A. & Pandey, G.K. 2015. Role of protein tyrosine phosphatases in plants. Current Genomics 16(4): 224-236.

Smith P., Bustamante, M., Ahammad, H., Clark, H., Dong, H., Elsiddig, E.A., Haberl, H., Harper, R., House, J., Jafari, M., Masera, O., Mbow, C., Ravindranath, N.H., Rice, C.W., Robledo Abad, C., Romanovskaya, A., Sperling, F. & Tubiello, F. 2014. Agriculture, forestry and other land use (AFOLU). In Climate Change 2014: Mitigation of Climate Change. Contribution of Working Group III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, edited by Edenhofer, O., Pichs-Madruga, R., Sokona, Y., Farahani, E., Kadner, S., Seyboth, K., Adler, A., Baum, I., Brunner, S., Eickemeier, P., Kriemann, B., Savolainen, J., Schlömer, S., von Stechow, C., Zwickel, T. & Minx, J.C. Cambridge: Cambridge University Press.

Sun, H. & Tonks, N.K. 1994. The coordinated action of protein tyrosine phosphatases and kinases in cell signaling. Trends in Biochemicals Science 19(11): 480-485.

Wang, W., Vignani, R., Scali, M. & Cresti, M. 2006. A universal and rapid protocol for protein extraction from recalcitrant plant tissues for proteomic analysis. Electrophoresis 27(13): 2782-2786.

Weiser, D.C. & Shenolikar, S. 2003. Use of protein phosphatase inhibitors. Curr. Protoc. Mol. Biol. 62(1): 18.10.1-18.10-13.

Wormit, A., Butt, S.M., Chairam, I., McKenna, J.F., Nunes-Nesi, A., Kjaer, L., O'Donnelly, K., Fernie, A.R., Woscholski, R., Barter, M.C. & Hamann, T. 2012. Osmosensitive changes of carbohydrate metabolism in response to cellulose biosynthesis inhibition. Plant Physiology 159(1): 105-117.

Yamada, H., Tanaka, R., Sulaiman, O., Hashim, R., Hamid, Z.A.A., Yahya, M.K.A., Kosugi, A., Arai, T., Murata, Y., Nirasawa, S., Yamamoto, K., Ohara, S., Yusof, M.N.M., Ibrahim, W.A. & Mori, Y. 2010. Old oil palm trunk: A promising source of sugars for bioethanol production. Biomass and Bioenergy 34: 1608-1613.

Žd'árská, M., Zatloukalová, P., Benítez, M., Šedo, O., Potěšil, D., Novák, O., Svačinová, J., Pešek, B., Malbeck, J., Vašíčková, J., Zdráhal, Z. & Hejátko, J. 2013. Proteome analysis in Arabidopsis reveals shoot- and root-specific targets of cytokinin action and differential regulation of hormonal homeostasis. Plant Physiology 161(2): 918-930.

*Pengarang untuk surat-menyurat; email: nabihah@ukm.edu.my