Proteome profiling and molecular dynamics simulation of Malaysian upland rice
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Date
2017
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Universiti Teknologi Malaysia
Abstract
Rice is one of the most consumed cereals all over the world. Unfortunately, its production has been decreasing since the past few decades due to several constraints primarily due to biotic and abiotic stresses. Hence, upland rice would be a good alternative as it is a stress-tolerant plant that possessed many excellent qualities and could survive under harsh condition. To date, there is no proteomics study reported for Malaysian upland rice. Hence, the present study employed three approaches; One-dimensional (1D), Two-Dimensional (2D) proteomics and bioinformatics to analyze the leaf proteome of Malaysian upland rice. A total of 205 proteins has been identified using modified trichloroacetic acid /acetone extraction protocol, tryptic digestion and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. These proteins were further classified according to gene ontology (GO) biological process of GoMapMan database. From the result obtained, over 50% of the leaf proteome identified are stress-responsive proteins. This information strongly underlines their importance in growth, development and survival of the plant. Moreover, the expression level of protein from vegetative to reproductive stage was studied using Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and PDQuest software analysis. Based on the findings, 10 proteins were found to be differentially expressed where seven (Fructose-1,6- bisphosphatase (FBPase), Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RuBisCO large subunit), Triosephosphate isomerase (TPI), Glyoxalase I, Translational elongation factor Tu-like protein (EF-Tu), GSH-dependent dehydroascorbate reductase 1 (GSH-DHAR 1), Peroxiredoxin 5 (PRX 5) of them are stress-responsive proteins. Additionally, the ability of two stress-responsive proteins; Heat shock cognate 70 (HSC 70) and Superoxide dismutase [Cu-Zn] (SOD [Cu-Zn]) to withstand high-temperature condition was determined by employing molecular dynamics (MD) study. The three-dimensional (3D) protein model generated using MODELLER was simulated using GROningen Machine for Chemical Simulations (GROMACS) software at three different temperatures (311 K, 315 K, 319 K). The MD simulation analysis (root mean square deviation (RMSD), root mean square fluctuation (RMSF), gyration (Rg), hydrogen bond, protein secondary structure, salt bridge) has revealed that the stress-responsive proteins could withstand temperature as high as 315 K. Taken together, the findings presented provide a snapshot of upland rice leaf proteome, particularly the one in relation to stress response. This information could serve as a preliminary platform in providing better understanding of upland rice function and expression which influence its response towards stress condition. In addition, the information could be utilized for the development of protein biomarker and efficient breeding program
Description
Thesis (Ph.D (Biosciences))
Keywords
Plant proteomics, Plant molecular biology