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bioRxiv · 10.1101/2020.07.01.183475

All-in-one comprehensive extraction of metabolites, proteins and ribonucleic acids for the rapid analysis of oil palm systems biology

Shahwan, S.·Othman, A.·Zain, N.·Rozali, N. L.·Ramli, U. S.
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Abstract

Oil palm (Elaeis guineensis Jacq.) systems biology offers a comprehensive view of the plant system by employing a holistic multi-omics approach encompassing the molecular data at various hierarchical levels. Sample limitation and the importance of integrating all molecular data with minimal variation, led to the development of sequential extraction of biomolecule fractions from a single undivided biological sample. This article describes a workflow for the comprehensive isolation of metabolites, proteins and ribonucleic acids from oil palm root. Samples were subjected to solvent extraction with methanol-chloroform-water to recover metabolites of diverse polarity. The resultant pellet was subjected to buffer and solvent partitioning to obtain RNA and proteins. RNA extracted from the oil palm root showed a recovery of 180.25 ng mg-1, with a A260:A280 ratio ranging between1.9-2.0 and a RIN value of 6.7. Co-extracted proteins resulted in a recovery of 29.28 μg mg-1 and revealed a total of 1852 identified proteins. Polar metabolites revealed approximately 40 metabolite peaks, and non-polar metabolites with two major fatty acid groups i.e. saturated and unsaturated fatty acids at 55.4% and 38.6%, respectively. This protocol demonstrated an advancement of extraction protocols for oil palm root biomolecules, which will consecutively expedite the establishment of various multi-omics platforms.Highlight Metabolites, proteins and RNA are co-extracted from oil palm root using the all-in-one extraction protocol which provides biomolecule extracts for various omics platforms.AbbreviationsRNARibonucleic acidLC-MS/MSliquid chromatographytandem mass spectrometryGC-FIDgas chromatography-flame ionization detectorSDS-PAGEsodium dodecyl sulphate-polyacrylamide gel electrophoresisFAMEfatty acid methyl estersView Full Text

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Shahwan, S., Othman, A., Zain, N., Rozali, N. L., Ramli, U. S.. 2020-07-02. All-in-one comprehensive extraction of metabolites, proteins and ribonucleic acids for the rapid analysis of oil palm systems biology. https://doi.org/10.1101/2020.07.01.183475

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