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 (TBKS) 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

Received: 4 October 2017/Accepted: 18 January 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 (TBKS) mempunyai kandungan gula yang tinggi, maka ia sesuai digunakan untuk penghasilan bahan kimia ringkas dan bahan bakar bio. Peningkatan kandungan gula pada sap daripada TBKS yang disimpan telah dilaporkan. Walau bagaimanapun, setakat ini, kajian terhadap perubahan profil protein TBKS semasa penyimpanan masih belum diterokai. Maka dalam kajian ini, pengekspresan protein TBKS 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 kawal atur eskpresi molekul protein sap TBKS.

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

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*Corresponding authors; email: nabihah@ukm.edu.my