Proteomic and Metabolomic Analyses of Soybean Root Tips Under Flooding Stress

Abstract

Flooding is one of the serious problems for soybean plants because it inhibits growth. Proteomic and metabolomic techniques were used to determine whether proteins and metabolites are altered in the root tips of soybeans under flooding stress. Two-day-old soybean plants were flooded for 2 days, and proteins and metabolites were extracted from root tips. Flooding-responsive proteins were identified using two-dimensional- or SDS-polyacrylamide gel electrophoresis- based proteomics techniques. Using both techniques, 172 proteins increased and 105 proteins decreased in abundance in the root tips of flood-stressed soybean. The abundance of methionine synthase, heat shock cognate protein, urease, and phosphoenol pyruvate carboxylase was significantly increased by flooding stress. Furthermore, 73 flooding-responsive metabolites were identified using capillary electrophoresis-mass spectrometry. The levels of gamma-aminobutyric acid, glycine, NADH2, and phosphoenol pyruvate were increased by flooding stress. Taken together, these results suggest that synthesis of phosphoenol pyruvate by way of oxaloacetate produced in the tricarboxylic acid cycle is activated in soybean root tips in response to flooding stress, and that flooding stress also leads to modulation of the urea cycle in the root tips.

Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress

“…To characterize the glycoproteome of soybean roots submitted to a flooding stress, we have in the present work used a protocol previously described in our studies (Komatsu et al, 2013 , 2014 ; Nanjo et al, 2013 ; Yin et al, 2014 ). In this protocol, soybean seeds were germinated under optimal control conditions for 2 days and growth is then continued either in control conditions or in flooding stress conditions.…”

Metabolomics: A Way Forward for Crop Improvement

“…In metabolomics, no single technique or tool can be used to analyze all the metabolites present in a metabolome; instead, a set of different technologies are required to provide the greatest amount of metabolite coverage. Different metabolomics techniques include mass spectrometry (MS) [20], non-destructive nuclear magnetic resonance spectroscopy (NMR) [21], high-performance thin-layer chromatography (HPTLC), capillary electrophoresis-mass spectrometry (CE-MS) [22], gas chromatography-mass spectrometry (GC-MS) [23], liquid chromatography-mass spectrometry (LC-MS) [24], direct infusion mass spectrometry (DIMS), ultra-performance liquid chromatography (UPLC), high-resolution mass spectrometry (HRMS) [25], and Fourier transform ion cyclotron resonance mass spectrometry (FI-ICR-MS) [26]. Out of these, CE-MS, LC-MS, GC-MS, and NMR-based integrated approaches have been extensively applied for metabolomics analysis.…”

“…In another experiment, metabolic profiling of soybean root tips under waterlogging was performed with capillary electrophoresis MS that unveiled 73 metabolites. The concentrations of phosphoenolpyruvate, nicotinamide adenine dinucleotide (NADH2), glycine, and gamma-aminobutyric acid were elevated under waterlogging conditions [22]. Herzog and colleagues used GC/MS and LC/MS to study the submergence tolerance mechanism in two wheat cultivars, identifying lysine, proline, methionine, and tryptophan as important biomarkers for waterlogging tolerance [153].…”

‘Omics’ techniques and their use to identify how soybean responds to flooding

“…Soybean proteins affected by flooding stress have been identified in the cell wall (Komatsu and Yanagawa 2013;Komatsu et al 2010), endoplasmic reticulum (Komatsu et al 2012b), mitochondria (Komatsu et al 2011a;Komatsu et al 2011b), plasma membrane (Komatsu et al 2009b), and nucleus (Komatsu et al 2013b(Komatsu et al , 2014bOh et al 2014) (Figure 1). Improved protocols for the purification of subcellular proteins allow in-depth proteomic studies to generate detailed information about the intrinsic mechanisms underlying stress responses.…”

“…It is not known whether nuclear function such as transcription factors is altered. However, Komatsu et al (2013bKomatsu et al ( , 2014b suggested that the accumulation of RACK1 in the soybean nucleus has an important role under flooding, and several nuclear-related proteins and their mRNAs were decreased in the root tip of soybean under flooding.…”