Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis

Area of Science:

• Plant Proteomics
• Biochemistry
• Molecular Biology

Background:

• Protein solubility is crucial for proteomics analysis, particularly in oil palm studies focused on fatty acid biosynthesis.
• Urea/thiourea and CHAPS are common solubilization buffers, but alternatives are sought to improve efficiency and data quality.
• Understanding oil palm fatty acid biosynthesis is key to enhancing palm oil's economic value and sustainability.

Purpose of the Study:

• To evaluate sodium deoxycholate as an alternative protein solubilization buffer for oil palm mesocarp proteomics.
• To compare the efficiency of sodium deoxycholate against traditional urea/thiourea/CHAPS buffers.
• To assess the impact of sodium deoxycholate on protein identification, gene ontology enrichment, and post-translational modifications.

Main Methods:

• Comparative analysis of protein solubilization using different buffer systems: urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate, and sodium deoxycholate.
• Evaluation based on protein yield and electrophoretic profiles.
• Mass spectrometric and statistical analyses to identify and quantify proteins and peptides.
• Assessment of gene ontology enrichment and carbamylated lysine residues.

Main Results:

• Sodium deoxycholate buffer demonstrated comparable protein yields to urea/thiourea/CHAPS, with insignificant differences.
• Mass spectrometry revealed that sodium deoxycholate increased the number of identified proteins and enriched their gene ontologies.
• Sodium deoxycholate reduced carbamylated lysine residues by over 67.0% compared to urea/thiourea/CHAPS.
• While 62.0% of proteins were shared, 38.0% unique proteins were identified with sodium deoxycholate, offering new insights.

Conclusions:

• Sodium deoxycholate is an effective and applicable buffer for solubilizing proteins from oil palm mesocarps.
• It offers higher efficiency and significant advantages over the traditional urea/thiourea/CHAPS buffer for proteomics analysis.
• Potential interference with protein quantitation by sodium deoxycholate can be overcome by a 4-fold dilution.