Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars

• Published in: Molecular & cellular proteomics Vol. 15; no. 1; pp. 266 - 288
• Main Authors: Pi, Erxu, Qu, Liqun, Hu, Jianwen, Huang, Yingying, Qiu, Lijuan, Lu, Hongfei, Jiang, Bo, Liu, Cong, Peng, Tingting, Zhao, Ying, Wang, Huizhong, Tsai, Sau-Na, Ngai, Saiming, Du, Liqun
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.01.2016; The American Society for Biochemistry and Molecular Biology
• Subjects: Acyltransferases - genetics; Acyltransferases - metabolism; Arabidopsis thaliana; Chromatography, Liquid; Cytochrome P-450 Enzyme System - genetics; Cytochrome P-450 Enzyme System - metabolism; Electrophoresis, Gel, Two-Dimensional; Gene Expression Profiling - methods; Glycine max - classification; Glycine max - genetics; Glycine max - metabolism; Intramolecular Lyases - genetics; Intramolecular Lyases - metabolism; Phosphoproteins - genetics; Phosphoproteins - metabolism; Phosphorylation; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Roots - genetics; Plant Roots - metabolism; Proteome - genetics; Proteome - metabolism; Proteomics - methods; Reverse Transcriptase Polymerase Chain Reaction; Salt Tolerance - genetics; Species Specificity; Tandem Mass Spectrometry; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1535-9476; 1535-9484
• DOI: 10.1074/mcp.M115.051961

Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by chalcone isomerase and cytochrome P450 monooxygenase. A novel salt tolerance pathway involving chalcone metabolism, mostly mediated by phosphorylated MYB transcription factors, was proposed based on our findings. (The mass spectrometry raw data are available via ProteomeXchange with identifier PXD002856).