Proteomic analysis of seed germination under salt stress in soybeans

Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation

Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.

Multi-Omics Revealed Peanut Root Metabolism Regulated by Exogenous Calcium under Salt Stress

High salinity severely inhibits plant seedling root development and metabolism. Although plant salt tolerance can be improved by exogenous calcium supplementation, the metabolism molecular mechanisms involved remain unclear. In this study, we integrated three types of omics data (transcriptome, metabolome, and phytohormone absolute quantification) to analyze the metabolic profiles of peanut seedling roots as regulated by exogenous calcium under salt stress. (1) exogenous calcium supplementation enhanced the allocation of carbohydrates to the TCA cycle and plant cell wall biosynthesis rather than the shikimate pathway influenced by up-regulating the gene expression of antioxidant enzymes under salt stress; (2) exogenous calcium induced further ABA accumulation under salt stress by up-regulating the gene expression of ABA biosynthesis key enzymes AAO2 and AAO3 while down-regulating ABA glycosylation enzyme UGT71C5 expression; (3) exogenous calcium supplementation under salt stress restored the trans-zeatin absolute content to unstressed levels while inhibiting the root cis-zeatin biosynthesis.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

An ultrasensitive probe-free electrochemical immunosensor for gibberellins employing polydopamine-antibody nanoparticles modified electrode

Gibberellins (GA₃) is an ubiquitous plant hormone, which plays a regulatory role in different growth stages of plants, so it is of great significance to develop a sensitive quantitative analysis method for GA₃. In this study, carboxylated graphene oxide- carboxylated multi-walled carbon nanotubes-Fc (GO-MWNT-Fc) composite material and PDANPs-antibody (PDANPs-Ab) were sequentially modified to screen-printed electrodes (SPEs), and an ultrasensitive probe-free immunosensor for GA₃ was developed. Fc was applied to generate electrochemical signals. GO-COOH and MWNT-COOH can increase the catalytic ability of the sensor and bind the PDANPs-Ab nanoparticles. PDANPs nanomaterial were synthetized by a facile self-polymerization and used to bind with antibody, so as to increase the antibody loading of the sensor. The as-prepared immunosensor has the widest detection range (100 aM-1 mM) and lowest detection limit (17.4 aM) for GA₃ up to date. To our knowledge, it is the first electrochemical immunosensor for GA₃. By changing the GA₃ antibody to ABA antibody, a sensitive and selective immunosensor for ABA was also fabricated. This immunosensor platform is simple, sensitive, and low cost. It opens broad prospect in on-site applications for biosensors in detecting of various biomolecules in precision agriculture.

Effects of drought and salt stress on seed germination of ephemeral plants in desert of northwest China

Seed germination is the most sensitive stage of plant life history. Studying its response to drought and salinity can analysis the response and adaptation characteristics of desert plants to the environment. In this experiment, the seeds of four common desert ephemeral plants in Xinjiang (Ixiolirion tataricum, Nepeta micrantha, Lepidium apetalum, and Plantago minuta) were used as materials. To study the germination characteristics of seeds under drought, we used salt stress, and coupled salt-drought stress under treatments and explored the germination recovery ability of rehydrated seeds after salt and drought stress treatments. The results showed that: (1) Under salt stress, the germination ability of four plant seeds was inhibited in different degrees. Overall, the degree of inhibition was proportional to the concentration of NaCl solution. (2) Drought stress slowed the seed germination process, and the greater the degree of stress, the more pronounced the slowdown; PEG treatment showed no significant effect on the germination of the four seeds at low concentrations and significant inhibition at medium and high concentrations. (3) The coupled salt-drought treatment significantly alleviated the stress effect of one factor and improved the germination characteristics of seeds. (4) Seeds that did not germinate under different concentrations of salt stress, drought stress, and coupled stresses rapidly recover germination when the stress was relieved or lifted. Ephemeral plants are sensitive to environmental changes, and this study aims to provide a reference basis for vegetation restoration and ecological rehabilitation in arid and semi-arid areas.

The Efficiency of Different Priming Agents for Improving Germination and Early Seedling Growth of Local Tunisian Barley under Salinity Stress

The current work aimed to investigate the effect of seed priming with different agents (CaCl₂, KCl, and KNO₃) on germination and seedling establishment in seeds of the barley species of both Hordeum vulgare (L. Manel) and Hordeum maritimum germinated with three salt concentrations (0, 100, and 200 mM NaCl). The results showed that under unprimed conditions, salt stress significantly reduced the final germination rate, the mean daily germination, and the seedling length and dry weight. It led to a decrease in the essential nutrient content (iron, calcium, magnesium, and potassium) against an increase in sodium level in both of the barley species. Moreover, this environmental constraint provoked a membrane injury caused by a considerable increase in electrolyte leakage and the malondialdehyde content (MDA). Data analysis proved that seed priming with CaCl₂, KCl, and KNO₃ was an effective method for alleviating barley seed germination caused by salt stress to varying degrees. Different priming treatments clearly stimulated germination parameters and the essential nutrient concentration, in addition to increasing the seedling growth rate. The application of seed priming reduced the accumulation of sodium ions and mitigated the oxidative stress of seeds caused by salt. This mitigation was traduced by the maintenance of low levels of MDA and electrolyte leakage. We conclude that the priming agents can be classed into three ranges based on their efficacy on the different parameters analyzed; CaCl₂ was placed in the first range, followed closely by KNO₃, while the least effective was KCl, which placed in the third range.

Natural variation in the promoter of GsERD15B affects salt tolerance in soybean

Salt stress has detrimental effects on crop growth and yield, and the area of salt-affected land is increasing. Soybean is a major source of vegetable protein, oil and feed, but considered as a salt-sensitive crop. Cultivated soybean (Glycine max) is domesticated from wild soybean (G. soja) but lost considerable amount of genetic diversity during the artificial selection. Therefore, it is important to exploit the gene pool of wild soybean. In this study, we identified 34 salt-tolerant accessions from wild soybean germplasm and found that a 7-bp insertion/deletion (InDel) in the promoter of GsERD15B (early responsive to dehydration 15B) significantly affects the salt tolerance of soybean. GsERD15B encodes a protein with transcriptional activation function and contains a PAM2 domain to mediate its interaction with poly(A)-binding (PAB) proteins. The 7-bp deletion in GsERD15B promoter enhanced the salt tolerance of soybean, with increased up-regulation of GsERD15B, two GmPAB genes, the known stress-related genes including GmABI1, GmABI2, GmbZIP1, GmP5CS, GmCAT4, GmPIP1:6, GmMYB84 and GmSOS1 in response to salt stress. We propose that natural variation in GsERD15B promoter affects soybean salt tolerance, and overexpression of GsERD15B enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Proteomics analysis of Cyclobalanopsis gilva provides new insights of low seed germination

A valuable plant, Cyclobalanopsis gilva, (C. gilva) has a low germination rate (below 50%) under its natural habitations. In order to examine the reasons for the low germination rate, the seeds of C. gilva (germinated and non-germinated) were evaluated using comparative proteomics analysis. A total of 3078 differentially abundant proteins (DAPs) were identified through a label-free method; most DAPs up-accumulated in germinated seeds were related to carbohydrates metabolism. Furthermore the proteins related to the signals, stress, and protein metabolism showed up-accumulation in germinated and no abundance or down-accumulation in non-germinated seeds. Enzyme activity of HK, PGK, PFK, and PK from glycolysis in SG-Control samples were 1.7-, 1.1-, 1.4-, and 1.3-times higher compared with those in control ones while CS, NAD-MDH, α-KGDH, and ICDH from the TCA cycle in SG-Control samples were 3, 1.1, 1.2, and 1.2 times higher than those in NG-Control ones. The β-amylase activity was 4-fold higher in successfully germinated seeds compared to non-germinated seeds. Interestingly, α-amylase did not show significant changes in protein abundance and enzyme activity among the three samples. The present findings reveal that unsuccessful germination of C. gilva seeds is due to lack of energy.

Glutathione S-transferase: a versatile protein family

Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc. This review article summarizes the recent information of GST evolution, and their distribution and structural features with emphasis on the assorted roles of Ser and Cys GSTs with the signature motifs in their active sites, alongside their recent biotechnological application in the area of agriculture, environment, and nanotechnology have been highlighted.

Integrated physiological and proteomic analysis of embryo and endosperm reveals central salt stress response proteins during seed germination of winter wheat cultivar Zhengmai 366

BACKGROUND

Salinity is a major abiotic stressor that affects seed germination, plant growth, and crop production. Seed germination represents the beginning of plant growth and is closely linked with subsequent crop development and ultimate yield formation. This study attempted to extend findings regarding the potential proteomic dynamics during wheat seed germination under salt stress and to explore the mechanism of crop salt response.

RESULTS

Salt stress significantly affected seed physiological activities during the germination process, resulting in significant decreases in phytohormone and α-amylase activity and significant increases in soluble sugar, starch, and ADP glucose pyrophosphorylase activity. A comparative proteomics approach was applied to analyze the dynamic proteome changes of embryo and endosperm during seed germination in Chinese winter wheat cultivar Zhengmai 366 under salt stress. Two-dimensional electrophoresis identified 92 and 61 differentially accumulated proteins (DAPs) in response to salt stress in embryo and endosperm, respectively. Both organs contained a high proportion of DAPs involved in stress defense, energy metabolism, and protein/amino acid metabolism. The endosperm had more DAPs related to storage proteins and starch metabolism than the embryo, and 2% of DAPs participating in lipid and sterol metabolism were specifically detected in the embryo.

CONCLUSIONS

Seed physiological activities were significantly affected during the germination process when subjected to salt stress. The DAPs involved in stress defense and energy metabolism were upregulated whereas those related to reserve substance degradation and protein/amino acid metabolism were significantly downregulated, leading to delayed seed germination under salt stress. Our proteomic results revealed synergistic regulation of the response to salt stress during seed germination.

Integration of proteomic and genomic approaches to dissect seed germination vigor in Brassica napus seeds differing in oil content

BACKGROUND

Rapeseed (Brassica napus, B. napus) is an important oil seed crop in the world. Previous studies showed that seed germination vigor might be correlated with seed oil content in B. napus, but the regulation mechanism for seed germination has not yet been explained clearly. Dissecting the regulation mechanism of seed germination and germination vigor is necessary.

RESULTS

Here, proteomic and genomic approaches were used to analyze the germination process in B. napus seeds with different oil content. The identification of 165 differentially expressed proteins (DEPs) in the germinating seeds of B. napus with high and low oil content was accomplished by two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE). The comparative proteomic results revealed that seeds with high oil content had higher metabolic activity, especially for sulfur amino acid metabolism. Thirty-one unique genes were shown to be significantly changed during germination between the seeds with high and low oil content, and thirteen of these genes were located within the confidence interval of germination-related quantitative trait locus (QTLs), which might play an important role in regulating seed germination vigor.

CONCLUSIONS

The present results are of importance for the understanding of the regulation mechanism for seed germination vigor in B. napus.

Salt Stress Represses Soybean Seed Germination by Negatively Regulating GA Biosynthesis While Positively Mediating ABA Biosynthesis

Soybean is an important and staple oilseed crop worldwide. Salinity stress has adverse effects on soybean development periods, especially on seed germination and post-germinative growth. Improving seed germination and emergence will have positive effects under salt stress conditions on agricultural production. Here we report that NaCl delays soybean seed germination by negatively regulating gibberellin (GA) while positively mediating abscisic acid (ABA) biogenesis, which leads to a decrease in the GA/ABA ratio. This study suggests that fluridone (FLUN), an ABA biogenesis inhibitor, might be a potential plant growth regulator that can promote soybean seed germination under saline stress. Different soybean cultivars, which possessed distinct genetic backgrounds, showed a similar repressed phenotype during seed germination under exogenous NaCl application. Biochemical analysis revealed that NaCl treatment led to high MDA (malondialdehyde) level during germination and the post-germinative growth stages. Furthermore, catalase, superoxide dismutase, and peroxidase activities also changed after NaCl treatment. Subsequent quantitative Real-Time Polymerase Chain Reaction analysis showed that the transcription levels of ABA and GA biogenesis and signaling genes were altered after NaCl treatment. In line with this, phytohormone measurement also revealed that NaCl considerably down-regulated active GA₁, GA₃, and GA₄ levels, whereas the ABA content was up-regulated; and therefore ratios, such as GA₁/ABA, GA₃/ABA, and GA₄/ABA, are decreased. Consistent with the hormonal quantification, FLUN partially rescued the delayed-germination phenotype caused by NaCl-treatment. Altogether, these results demonstrate that NaCl stress inhibits soybean seed germination by decreasing the GA/ABA ratio, and that FLUN might be a potential plant growth regulator that could promote soybean seed germination under salinity stress.

A Proteomic Approach to Lipo-Chitooligosaccharide and Thuricin 17 Effects on Soybean GerminationUnstressed and Salt Stress

Salt stress is an important abiotic stressor affecting crop growth and productivity. Of the 20 percent of the terrestrial earth's surface available as agricultural land, 50 percent is estimated by the United Nations Environment Program to be salinized to the level that crops growing on it will be salt-stressed. Increased soil salinity has profound effects on seed germination and germinating seedlings as they are frequently confronted with much higher salinities than vigorously growing plants, because germination usually occurs in surface soils, the site of greatest soluble salt accumulation. The growth of soybean exposed to 40 mM NaCl is negatively affected, while an exposure to 80 mM NaCl is often lethal. When treated with the bacterial signal compounds lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17), soybean seeds (variety Absolute RR) responded positively at salt stress of up to 150 mM NaCl. Shotgun proteomics of unstressed and 100 mM NaCl stressed seeds (48 h) in combination with the LCO and Th17 revealed many known, predicted, hypothetical and unknown proteins. In all, carbon, nitrogen and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with signals. PEP carboxylase, Rubisco oxygenase large subunit, pyruvate kinase, and isocitrate lyase were some of the noteworthy proteins enhanced by the signals, along with antioxidant glutathione-S-transferase and other stress related proteins. These findings suggest that the germinating seeds alter their proteome based on bacterial signals and on stress, the specificity of this response plays a crucial role in organ maturation and transition from one stage to another in the plants' life cycle; understanding this response is of fundamental importance in agriculture and, as a result, global food security. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD004106.

Shotgun proteomic analysis of soybean embryonic axes during germination under salt stress

Seed imbibition and radicle emergence are generally less affected by salinity in soybean than in other crop plants. In order to unveil the mechanisms underlying this remarkable salt tolerance of soybean at seed germination, a comparative label-free shotgun proteomic analysis of embryonic axes exposed to salinity during germination sensu stricto (GSS) was conducted. The results revealed that the application of 100 and 200 mmol/L NaCl stress was accompanied by significant changes (>2-fold, P<0.05) of 97 and 75 proteins, respectively. Most of these salt-responsive proteins (70%) were classified into three major functional categories: disease/defense response, protein destination and storage and primary metabolism. The involvement of these proteins in salt tolerance of soybean was discussed, and some of them were suggested to be potential salt-tolerant proteins. Furthermore, our results suggest that the cross-protection against aldehydes, oxidative as well as osmotic stress, is the major adaptive response to salinity in soybean.

Proteomic Dissection of Seed Germination and Seedling Establishment in Brassica napus

The success of seed germination and establishment of a normal seedling are key determinants of plant species propagation. At present, only a few studies have focused on the genetic control of seed germination by using a proteomic approach in Brassica napus. In the present study, the protein expression pattern of seed germination was investigated using differential fluorescence two-dimensional gel electrophoresis in B. napus. One hundred and thirteen differentially expressed proteins (DEPs) that were mainly involved in storage (23.4%), energy metabolism (18.9%), protein metabolism (16.2%), defense/disease (12.6%), seed maturation (11.7%), carbohydrate metabolism (4.5%), lipid metabolism (4.5%), amino acids metabolism (3.6%), cell growth/division (3.6%), and some unclear functions (2.7%) were observed by proteomic analysis. Seventeen genes corresponding to 11 DEPs were identified within or near the associated linkage disequilibrium regions related to seed germination and vigor quantitative traits reported in B. napus in previous studies. The expression pattern of proteins showed that heterotrophic metabolism could be activated in the process of seed germination and that the onset of defense mechanisms might start during seed germination. These findings will help generate a more in-depth understanding of the mobilization of seed storage reserves and regulation mechanisms of the germination process in B. napus.

Association mapping of soybean seed germination under salt stress

Soil salinity is a serious threat to agriculture sustainability worldwide. Seed germination is a critical phase that ensures the successful establishment and productivity of soybeans in saline soils. However, little information is available regarding soybean salt tolerance at the germination stage. The objective of this study was to identify the genetic mechanisms of soybean seed germination under salt stress. One natural population consisting of 191 soybean landraces was used in this study. Soybean seeds produced in four environments were used to evaluate the salt tolerance at their germination stage. Using 1142 single-nucleotide polymorphisms (SNPs), the molecular markers associated with salt tolerance were detected by genome-wide association analysis. Eight SNP-trait associations and 13 suggestive SNP-trait associations were identified using a mixed linear model and the TASSEL 4.0 software. Eight SNPs or suggestive SNPs were co-associated with two salt tolerance indices, namely (1) the ratio of the germination index under salt conditions to the germination index under no-salt conditions (ST-GI) and (2) the ratio of the germination rate under salt conditions to the germination rate under no-salt conditions (ST-GR). One SNP (BARC-021347-04042) was significantly associated with these two traits (ST-GI and ST-GR). In addition, nine possible candidate genes were located in or near the genetic region where the above markers were mapped. Of these, five genes, Glyma08g12400.1, Glyma08g09730.1, Glyma18g47140.1, Glyma09g00460.1, and Glyma09g00490.3, were verified in response to salt stress at the germination stage. The SNPs detected could facilitate a better understanding of the genetic basis of soybean salt tolerance at the germination stage, and the marker BARC-021347-04042 could contribute to future breeding for soybean salt tolerance by marker-assisted selection.

Computed tomography scanning can monitor the effects of soil medium on root system development: an example of salt stress in corn

Seeds and young seedlings often encounter high soluble salt levels in the upmost soil layers, impeding vigorous growth by affecting root establishment. Computed tomography (CT) scanning used at low X-ray doses can help study root development in such conditions non-destructively, because plants are allowed to grow throughout the experiment. Using a high-resolution Toshiba XVision CT scanner, we studied corn (Zea mays L.) root growth under optimal and salt-stressed conditions in 3D and on a weekly basis over 3 weeks. Two groups of three corn plants were grown in the controlled environment of a growth chamber, in mid-sized plastic pots filled with sieved and autoclaved sand. Seedlings were subjected to first CT scanning 1 week after seed planting. Our main research objectives concerning root systems were: (i) to quantify structural complexity from fractal dimensions estimated on skeletal 3-D images built from CT scanning data; (ii) to measure growth from volumes and lengths and the derived relative rates and increments, after isolating primary and secondary roots from the soil medium in CT scanning data; and (iii) to assess differences in complexity and growth per week and over Weeks 1-3 for groups of corn plants. Differences between groups were present from Week 1; starting in Week 2 secondary roots were present and could be isolated, which refined the complexity and growth analyses of root systems. Besides expected Week main effects (P < 0.01 or 0.05), Week × Group interaction (P < 0.05 or 0.10), and Group main effects were observed. Graphical, quantitative, and statistical analyses of CT scanning data were thus completed at an unprecedented level, and provided new and important insights regarding root system development. Repeated CT scanning is the key to a better understanding of the establishment in the soil medium of crop plants such as corn and the assessment of salt stress effects on developing root systems, in complexity, volume, and length.

Catalytic features and crystal structure of a tau class glutathione transferase from Glycine max specifically upregulated in response to soybean mosaic virus infections

The plant tau class glutathione transferases (GSTs) play important roles in biotic and abiotic stress tolerance in crops and weeds. In this study, we systematically examined the catalytic and structural features of a GST isoenzyme from Glycine max (GmGSTU10-10). GmGSTU10-10 is a unique isoenzyme in soybean that is specifically expressed in response to biotic stress caused by soybean mosaic virus (SMV) infections. GmGSTU10-10 was cloned, expressed in Escherichia coli, purified and characterized. The results showed that GmGSTU10-10 catalyzes several different reactions and exhibits wide substrate specificity. Of particular importance is the finding that the enzyme shows high antioxidant catalytic function and acts as hydroperoxidase. In addition, its Km for GSH is significantly lower, compared to other plant GSTs, suggesting that GmGSTU10-10 is able to perform efficient catalysis under conditions where the concentration of reduced glutathione is low (e.g. oxidative stress). The crystal structure of GmGSTU10-10 was solved by molecular replacement at 1.6Å resolution in complex with glutathione sulfenic acid (GSOH). Structural analysis showed that GmGSTU10-10 shares the same overall fold and domain organization as other plant cytosolic GSTs; however, major variations were identified in helix H9 and the upper part of helix H4 that affect the size of the active site pockets, substrate recognition and the catalytic mechanism. The results of the present study provide new information into GST diversity and give further insights into the complex regulation and enzymatic functions of this plant gene superfamily.

Comparative proteomic and physiological analyses reveal the protective effect of exogenous calcium on the germinating soybean response to salt stress

Calcium enhances salt stress tolerance of soybeans. Nevertheless, the molecular mechanism of calcium's involvement in resistance to salt stress is unclear. A comparative proteomic approach was used to investigate protein profiles in germinating soybeans under NaCl-CaCl2 and NaCl-LaCl3 treatments. A total of 80 proteins affected by calcium in 4-day-old germinating soybean cotyledons and 71 in embryos were confidently identified. The clustering analysis showed proteins were subdivided into 5 and 6 clusters in cotyledon and embryo, respectively. Among them, proteins involved in signal transduction and energy pathways, in transportation, and in protein biosynthesis were largely enriched while those involved in proteolysis were decreased. Abundance of nucleoside diphosphate kinase and three antioxidant enzymes were visibly increased by calcium. Accumulation of gamma-aminobutyric acid and polyamines was also detected after application of exogenous calcium. This was consistent with proteomic results, which showed that proteins involved in the glutamate and methionine metabolism were mediated by calcium. Calcium could increase the salt stress tolerance of germinating soybeans via enriching signal transduction, energy pathway and transportation, promoting protein biosynthesis, inhibiting proteolysis, redistributing storage proteins, regulating protein processing in endoplasmic reticulum, enriching antioxidant enzymes and activating their activities, accumulating secondary metabolites and osmolytes, and other adaptive responses. Biological significance Soybean (Glycine max L.), as a traditional edible legume, is being targeted for designing functional foods. During soybean germination under stressful conditions especially salt stress, newly discovered functional components such as gamma-aminobutyric acid (GABA) are rapidly accumulated. However, soybean plants are relatively salt-sensitive and the growth, development and biomass of germinating soybeans are significantly suppressed under salt stress condition. According to previous studies, exogenous calcium counters the harmful effect of salt stress and increases the biomass and GABA content of germinating soybeans. Nevertheless, the precise molecular mechanism underlying the role of calcium in resistance to salt stress is still unknown. This paper is the first study employing comparative proteomic and physiological analyses to reveal the protective effect of exogenous calcium in the germinating soybean response to salt stress. Our study links the biological events with proteomic information and provides detailed peptide information on all identified proteins. The functions of those significantly changed proteins are also analyzed. The physiological and comparative proteomic analyses revealed the putative molecular mechanism of exogenous calcium treatment induced salt stress responses. The findings from this paper are beneficial to high GABA-rich germinating soybean biomass. Additionally, these findings also might be applicable to the genetic engineering of soybean plants to improve stress tolerance.

Organ-specific proteomic analysis of NaCl-stressed germinating soybeans

A comparative proteomic approach was employed to explore proteome expression patterns in germinating soybeans under NaCl stress and NaCl-aminoguanidine treatment. The proteins were extracted from 4-day-old germinating soybean cotyledons and noncotyledons (hypocotyl and radicle) and were separated using two-dimensional polyacrylamide gel electrophoresis. A total of 63 and 72 differentially expressed proteins were confidently identified by MALDI-TOF/TOF in the noncotyledons and cotyledons, respectively. These identified proteins were divided into ten functional groups and most of them were predicted to be cytoplasmic proteins in noncotyledons. Moreover, γ-aminobutyric acid was accumulated while the major allergen (Bd 30K protein) was reduced in the germinating soybeans. The proteins involved in energy metabolism and in protein processing in endoplasmic reticulum were enriched under NaCl stress. Meanwhile, the negative effect of stress was aggravated once polyamine degradation was inhibited. Redistribution of storage proteins under stress indicated that storage proteins might not only function as seed storage reserves but also have additional roles in plant defense.

Progress and challenges for abiotic stress proteomics of crop plants

Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome.

Label-free quantitative proteomic analysis of abscisic acid effect in early-stage soybean under flooding

Flooding is a serious problem for soybean cultivation because it markedly reduces growth. To investigate the role of phytohormones in soybean under flooding stress, gel-free proteomic technique was used. When 2-day-old soybeans were flooded, the content of abscisic acid (ABA) did not decrease in the root, though its content decreased in untreated plant. When ABA was added during flooding treatment, survival ratio was improved compared with that of soybeans flooded without ABA. When 2-day-old soybeans were flooded with ABA, the abundance of proteins related to cell organization, vesicle transport and glycolysis decreased compared with those in root of soybeans flooded without ABA. Furthermore, the nuclear proteins were analyzed to identify the transcriptional regulation. The abundance of 34 nuclear proteins such as histone deacetylase and U2 small nuclear ribonucleoprotein increased by ABA supplementation under flooding; however, 35 nuclear proteins such as importin alpha, chromatin remodeling factor, zinc finger protein, transducin, and cell division 5 protein decreased. Of them, the mRNA expression levels of cell division cycle 5 protein, C2H2 zinc finger protein SERRATE, CCCH type zinc finger family protein, and transducin were significantly down-regulated under the ABA treatment. These results suggest that ABA might be involved in the enhancement of flooding tolerance of soybean through the control of energy conservation via glycolytic system and the regulation on zinc finger proteins, cell division cycle 5 protein and transducin.

Soybean proteomics for unraveling abiotic stress response mechanism

Plant response to abiotic stresses depends upon the fast activation of molecular cascades involving stress perception, signal transduction, changes in gene and protein expression and post-translational modification of stress-induced proteins. Legumes are extremely sensitive to flooding, drought, salinity and heavy metal stresses, and soybean is not an exception of that. Invention of immobilized pH gradient strips followed by advancement in mass spectrometry has made proteomics a fast, sensitive and reliable technique for separation, identification and characterization of stress-induced proteins. As the functional translated portion of the genome plays an essential role in plant stress response, proteomic studies provide us a finer picture of protein networks and metabolic pathways primarily involved in stress tolerance mechanism. Identifying master regulator proteins that play key roles in the abiotic stress response pathway is fundamental in providing opportunities for developing genetically engineered stress-tolerant crop plants. This review highlights recent contributions in the field of soybean biology to comprehend the complex mechanism of abiotic stress acclimation. Furthermore, strengths and weaknesses of different proteomic methodologies of extracting complete proteome and challenges and future prospects of soybean proteome study both at organ and whole plant levels are discussed in detail to get new insights into the plant abiotic stress response mechanism.

Comparative metabolomics in Glycine max and Glycine soja under salt stress to reveal the phenotypes of their offspring

Metabolomics is developing as an important functional genomics tool for understanding plant systems' response to genetic and environmental changes. Here, we characterized the metabolic changes of cultivated soybean C08 (Glycine max L. Merr) and wild soybean W05 (Glycine soja Sieb.et Zucc.) under salt stress using MS-based metabolomics, in order to reveal the phenotypes of their eight hybrid offspring (9H0086, 9H0124, 9H0391, 9H0736, 9H0380, 9H0400, 9H0434, and 9H0590). Total small molecule extracts of soybean seedling leaves were profiled by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-Fourier transform mass spectrometry (LC-FT/MS). We found that wild soybean contained higher amounts of disaccharides, sugar alcohols, and acetylated amino acids than cultivated soybean, but with lower amounts of monosaccharides, carboxylic acids, and unsaturated fatty acids. Further investigations demonstrated that the ability of soybean to tolerate salt was mainly based on synthesis of compatible solutes, induction of reactive oxygen species (ROS) scavengers, cell membrane modifications, and induction of plant hormones. On the basis of metabolic phenotype, the salt-tolerance abilities of 9H0086, 9H0124, 9H0391, 9H0736, 9H0380, 9H0400, 9H0434, and 9H0590 were discriminated. Our results demonstrated that MS-based metabolomics provides a fast and powerful approach to discriminate the salt-tolerance characteristics of soybeans.

Analysis of proteome profile in germinating soybean seed, and its comparison with rice showing the styles of reserves mobilization in different crops

BACKGROUND

Seed germination is a complex physiological process during which mobilization of nutrient reserves happens. In different crops, this event might be mediated by different regulatory and metabolic pathways. Proteome profiling has been proved to be an efficient way that can help us to construct these pathways. However, no such studies have been performed in soybean germinating seeds up to date.

RESULTS

Proteome profiling was conducted through one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy in the germinating seeds of soybean (glycine max). Comprehensive comparisons were also carried out between rice and soybean germinating seeds. 764 proteins belonging to 14 functional groups were identified and metabolism related proteins were the largest group. Deep analyses of the proteins and pathways showed that lipids were degraded through lipoxygenase dependent pathway and proteins were degraded through both protease and 26S proteosome system, and the lipoxygenase could also help to remove the reactive oxygen species during the rapid mobilization of reserves of soybean germinating seeds. The differences between rice and soybean germinating seeds proteome profiles indicate that each crop species has distinct mechanism for reserves mobilization during germination. Different reserves could be converted into starches before they are totally utilized during the germination in different crops seeds.

CONCLUSIONS

This study is the first comprehensive analysis of proteome profile in germinating soybean seeds to date. The data presented in this paper will improve our understanding of the physiological and biochemical status in the imbibed soybean seeds just prior to germination. Comparison of the protein profile with that of germinating rice seeds gives us new insights on mobilization of nutrient reserves during the germination of crops seeds.

Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes

Salinity is one of the major environmental constraints limiting yield of crop plants in many semi-arid and arid regions around the world. To understand responses in soybean seedling to salt stress at proteomic level, the extracted proteins from seedling leaves of salt-sensitive genotype Jackson and salt-tolerant genotype Lee 68 under 150 mM NaCl stress for 1, 12, 72 and 144 h, respectively, were analyzed by 2-DE. Approximately 800 protein spots were detected on 2-DE gels. Among them, 91 were found to be differently expressed, with 78 being successfully identified by MALDI-TOF-TOF. The identified proteins were involved in 14 metabolic pathways and cellular processes. Based on most of the 78 salt-responsive proteins, a salt stress-responsive protein network was proposed. This network consisted of several functional components, including balancing between ROS production and scavenging, accelerated proteolysis and reduced biosynthesis of proteins, impaired photosynthesis, abundant energy supply and enhanced biosynthesis of ethylene. Salt-tolerant genotype Lee 68 possessed the ability of higher ROS scavenging, more abundant energy supply and ethylene production, and stronger photosynthesis than salt-sensitive genotype Jackson under salt stress, which may be the major reasons why it is more salt-tolerant than Jackson.