Mass Spectrometry-Based Analysis of Proteomic Changes in the Root Tips of Flooded Soybean Seedlings

Abstract

Flooding injury is a major problem in soybean cultivation. A proteomics approach was used to clarify the occurrence of changes in protein expression level and phosphorylation in soybeans under flooding stress. Two-day-old seedlings were flooded for 1 day, proteins were extracted from root tips of the seedlings and digested with trypsin, and their expression levels and phosphorylation states were compared to those of untreated controls using mass spectrometry-based proteomics techniques. Phosphoproteins were enriched using a phosphoprotein purification column prior to digestion and mass spectrometry. The expression of proteins involved in energy production increased as a result of flooding, while expression of proteins involved in protein folding and cell structure maintenance decreased. Flooding induced changes of phosphorylation status of proteins involved in energy generation, protein synthesis and cell structure maintenance. The response to flooding stress may be regulated by both modulation of protein expression and phosphorylation state. Energy-demanding and production-related metabolic pathways may be particularly subject to regulation by changes in protein phosphorylation during flooding.

Proteomic analysis of soybean root including hypocotyl during recovery from drought stress

“…Protein extracts (150 μg) were precipitated with methanol and chloroform to remove any detergent from the sample solutions, as previously described [27]. Briefly, 150 μL sample was mixed with 600 μL methanol, and the resulting suspension was further mixed with 150 μL chloroform and 450 μL water.…”

Proteomic analysis of flooded soybean root exposed to aluminum oxide nanoparticles

“…In this study, the abundance of this protein was increased under flooding stress compared to the control condition, but was reduced by the exposure of flooding-stressed plants to Al 2 O 3 nanoparticles. This reduction in glyceraldehyde-3-phosphate dehydrogenase levels induced by Al 2 O 3 nanoparticles may lead to a metabolic shift towards aerobic pathways.Several previous studies in soybean have revealed that proteins related to fermentation, scavenging, and glycolysis are affected by flooding stress(48,21), which limits the available oxygen supply(49). Low oxygen conditions limit ATP generation and shift plant metabolism from oxidative pathways, such as carbohydrate metabolism, towards anaerobic pathways(50).Komatsu et al (45) reported the activation of a fermentative pathway in the early stage of flooding stress as a stress tolerance mechanism in soybean.…”

Datasets of mung bean proteins and metabolites from four different cultivars

“…Peptide identification was performed by nanoliquid chromatography (LC) MS/MS with a nanospray LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) coupled to an Ultimate 3000 nanoLC system (Dionex). Full-scan mass spectra were acquired in the mass spectrometer over 400–1500 m/z with a resolution of 30,000 in a data dependent mode as previously described [2], [3]. Proteins were identified by Mascot search engine (version 2.5.1, Matrix Science, London, UK) of a soybean peptide database (55,787 sequences) constructed from the Phytozome (version 9.1; http://www.phytozome.net/soybean).…”