Abstract
Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly identified and constituted 54% of the current soybean phosphosite repository. These phosphosites were converted into the highly conserved kinase docking sites by bioinformatics analysis, which predicted six kinase families that matched with those newly found nine kinase families. The overly post-translationally modified proteins (OPP) occupies 2.1% of these leading phosphoproteins. Most of these OPPs are photoreceptors, mRNA-, histone-, and phospholipid-binding proteins, as well as protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of phosphosites of phosphoproteins follows the exponential decay law, Y = 4.13e−0.098X − 0.04. Out of 218 significantly regulated unique phosphopeptide groups, 188 phosphoproteins were regulated by the drought-tolerant cultivar under the water loss condition. These significantly regulated phosphoproteins (SRP) are mainly enriched in the biological functions of water transport and deprivation, methionine metabolic processes, photosynthesis/light reaction, and response to cadmium ion, osmotic stress, and ABA response. Seventeen and 15 SRPs are protein kinases/phosphatases and transcription factors, respectively. Bioinformatics analysis again revealed that three members of the calcium dependent protein kinase family (CAMK family), GmSRK2I, GmCIPK25, and GmAKINβ1 kinases, constitute a phosphor-relay-mediated signal transduction network, regulating ion channel activities and many nuclear events in this drought-tolerant cultivar, which presumably contributes to the development of the soybean drought tolerance under water deprivation process.
Highlights
Soybean (Glycine Max (L.) Merr), similar to maize, wheat, rice, and cotton crops, is an important agricultural crop traded in global commodity markets [1]
To investigate the phosphoproteomic changes associated with the drought-tolerant cultivar, both the drought-tolerant and -sensitive cultivars were subjected to a mild drought treatment (60% humidity in soil; Figure S1A; [51,53]), during which, both the soil humidity level and plant tissue water content were measured every two days
In the case of post-translational modification (PTM) proteomes, we have previously reported that the correlation between the abundance of phosphoprotein and the number of phosphosite on phosphoprotein obeys a power law (Y(X) = a × X−k ) based on the phosphoproteomics data collected from Arabidopsis [59]
Summary
Soybean (Glycine Max (L.) Merr), similar to maize, wheat, rice, and cotton crops, is an important agricultural crop traded in global commodity markets [1]. Soybean seeds are widely consumed as human food, animal feed, and industrial material supplies [2]. The productivity of this cash crop has a profound and direct impact on the market price of this legume crop, and consumption behaviors of people, and on the trading activities between countries. The production of soybean has been curtailed by numerous harsh environmental stresses, especially drought, a water deficit state of soil [9]. Application of molecular biology and genetics studies in the model plant
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