Integrated Proteomics and Metabolomics Analysis Highlights Correlative Metabolite-Protein Networks in Soybean Seeds Subjected to Warm-Water Soaking

Abstract

Soaking of soybean seeds is a prerequisite for the production of soy foods, and it has been shown that the extent of water absorbed during different imbibition conditions directly affects the quality of the subsequent soybean seed products by yet unknown mechanisms. In order to elucidate the molecular changes in soybean seeds during different soaking temperatures, we performed an integrated proteomics and metabolomics analysis of seeds soaked at 4, 25, and 55 °C. Proteomics analysis revealed that various enzymes related to carbohydrate and protein hydrolysis were activated in soybean seeds during water soaking at 55 °C. Interestingly, results obtained from this integrated proteomics and metabolomics study showed changes in various metabolites, including isoflavones, amino acids, and sugars, that were positively correlated with proteome changes occurring upon soaking at 55 °C. Furthermore, soaking of soybean seeds at 55 °C resulted in degradation of indigestible anti-nutrients such as raffinose oligosaccharides. Taken together, our results suggest that the seed soaking at a high temperature (55 °C) increases the nutritional value of soybean seeds by decreasing the contents of some of the common anti-nutrients.

A TMT-based quantitative proteomic analysis provides insights into the protein changes in the seeds of high- and low- protein content soybean cultivars

“…Moreover, a previous report revealed that LAPs related to various major metabolism in filling and matured stages of soybean seeds were successfully enriched and identified in PS-S fraction using TMT-based quantitative analysis (Min et al 2020b). Therefore, here we utilized the PS precipitation method in combination with TMT-based quantification to identify the differential proteins from the seeds of Daewon and Saedanbaek differing in total protein contents (Gupta et al 2020;Min et al, 2020aMin et al, , 2020b. This approach led to the identification of 1,146 significantly modulated proteins (FDR < 0.05, FC > 1.5) by the comparison between Daewon and Saedanbaek cultivars.…”

“…Finally, the PS-S fraction was dissolved in 80% acetone containing 0.07% β-mercaptoethanol and stored -20°C until further analysis. Trypsin digestion by filter-aided sample preparation (FASP), TMT labeling and peptide pre-fractionation by basic pH reverse phase chromatography were carried out as described previously (Gupta et al 2020;Kim et al 2018;Min et al 2020a;Wiśniewski et al 2009). A total of 12 peptide fractions were collected, lyophilized in a vacuum centrifuge and stored at -80°C until further LC-MS/MS analysis.…”

“…Statistical analysis was carried out using Perseus software (ver. 1.5.8.5) and R software as described previous report (Min et al 2020a;Tyanova et al 2016b). For removing the batch effect within TMT-6plex, data normalization was carried out using an internal reference scaling method as described previously (Plubell et al 2017;Gupta et al 2019) Missing values imputation was carried out from a normal distribution (width: 0.3, downshift: 1.8) using Perseus software (Tyanova et al 2016b).…”

“…To investigate the differential modulation of soybean seed proteome in high-and low-protein containing cultivars, seed proteins were isolated from Daewon and Saedanbaek and subjected to protamine sulfate precipitation method for depletion of major seed storage proteins (SSPs) (Kim et al 2015). SSPs depleted fraction, referred as PS-S fraction, from two different cultivars (marked by DS; Daewon PS-S fraction and SS; Saedanbaek PS-S fraction, respectively) were sequentially subjected to trypsin digestion by filter-aided sample preparation (FASP) method and TMT-6plex labeling in the same manner as reported previously (Min et al 2020a(Min et al , 2020b (Fig. 1A).…”

Liver Metabolome and Proteome Response of Turbot (Scophthalmus maximus) to Lysine and Leucine in Free and Dipeptide Forms

“…Omics approaches in those studies were often used separatelyproteomics and metabolomics-and an integrated analysis using these approaches was rarely conducted in fish nutrition. Thus, in order to provide more metabolic information to explain the relationship between dietary nutrition and fish growth, it was necessary to combine metabolomics with proteomics in nutritional studies with fish (Guo et al, 2019;Min et al, 2020;Yu et al, 2020).…”