In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis

Cells

CheolWoo Min¹  Ravi Gupta¹  SunTae Kim¹  Joonho Park²  Youngsoo Kim²  Pingfang Yang³  JinWoo Bae⁴  GaneshKumar Agrawal⁵  Randeep Rakwal⁵ 

[1] Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea;Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal;

关键词: soybean;    basic pH reverse phase;    filter-aided sample preparation;    low-abundance proteins;    maxquant;    protamine sulfate precipitation;   

DOI  :  10.3390/cells9061517

来源: DOAJ

【 摘 要 】

Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.

【 授权许可】

Unknown