Analysis of initial changes in the proteins of soybean root tip under flooding stress using gel-free and gel-based proteomic techniques

Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean

Soybean is highly sensitive to flooding and extreme rainfall. The phenotypic variation of flooding tolerance is a complex quantitative trait controlled by many genes and their interaction with environmental factors. We previously constructed a gene-pool relevant to soybean flooding-tolerant responses from integrated multiple omics and non-omics databases, and selected 144 prioritized flooding tolerance genes (FTgenes). In this study, we proposed a comprehensive framework at the systems level, using competitive (hypergeometric test) and self-contained (sum-statistic, sum-square-statistic) pathway-based approaches to identify biologically enriched pathways through evaluating the joint effects of the FTgenes within annotated pathways. These FTgenes were significantly enriched in 36 pathways in the Gene Ontology database. These pathways were related to plant hormones, defense-related, primary metabolic process, and system development pathways, which plays key roles in soybean flooding-induced responses. We further identified nine key FTgenes from important subnetworks extracted from several gene networks of enriched pathways. The nine key FTgenes were significantly expressed in soybean root under flooding stress in a qRT-PCR analysis. We demonstrated that this systems biology framework is promising to uncover important key genes underlying the molecular mechanisms of flooding-tolerant responses in soybean. This result supplied a good foundation for gene function analysis in further work.

Integrated omic techniques and their genomic features for invasive weeds

Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.

Nutrient Inputs Alleviate Negative Effects of Early and Subsequent Flooding on Growth of Polygonum hydropiper With the Aid of Adventitious Roots

Riparian plants are exposed to harmful stress induced by flooding, which is often accompanied by eutrophication in the Three Gorges Reservoir Region. The phenomenon is mainly caused by domestic sewage discharges, slow water flow, and agricultural fertilizer pollution. Simulating abiotic stress, such as flooding at the initial period, can act as a signal and induce positive responses of plants to subsequent severe stress. In addition, eutrophication supplies nutrients, provides a favorable environment in the early stages of plant, and facilitates good performance in later development. However, whether early flooding (with or without eutrophication) acts as positive cue or as stress on plants at different developmental stages remains unclear. To address this question, seeds of Polygonum hydropiper were collected from low and high elevations in the hydro-fluctuation belt of the Three Gorges Reservoir Region. Plants germinated from these seeds were subjected to shallower and shorter early flooding treatments with or without eutrophication. Subsequently, plants were subjected to deeper and longer flooding treatments with or without eutrophication. Early flooding and eutrophic flooding significantly induced generation of adventitious roots, suggesting morphological adaptation to flooding. Although early flooding and eutrophic flooding treatments did not increase plant biomass in subsequent treatments compared with control, stem length, length and width of the 1st fully expanded leaf, and biomass of plants in the early eutrophic treatment were higher than these of the early flooding treatment plants. These results suggest a negative lag-effect of early flooding, and also indicate that nutrient inputs can alleviate such effects. Similarly, subsequent eutrophic flooding also enhanced plant growth compared with subsequent flooding, showing significantly higher values of leaf traits and adventitious root number. Plants originated from low elevation had significantly higher functional leaf length and stem biomass compared with those from high elevation. These results suggest that nutrient inputs can alleviate negative effects of early and subsequent flooding on growth of P. hydropiper with the generation of adventitious roots.

Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress

Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.

Alteration of proteome in germinating seedlings of piegonpea (Cajanus cajan) after salt stress

Pigeonpea (Cajanus cajan) is an important crop in semi-arid regions and a significant source of dietary proteins in India. The plant is sensitive to salinity stress, which adversely affects its productivity. Based on the dosage-dependent influence of salinity stress on the growth and ion contents in the young seedlings of pigeonpea, a comparative proteome analysis of control and salt stressed (150 mM NaCl) plants was conducted using 7 days-old seedlings. Among various amino acids, serine, aspartate and asparagine were the amino acids that showed increment in the root, whereas serine, aspartate and phenylalanine showed an upward trend in shoots under salt stress. Furthermore, a label-free and gel-free comparative Q-Tof, Liquid Chromatography-Mass spectrometry (LC-MS) revealed total of 118 differentially abundant proteins in roots and shoots with and without salt stress conditions. Proteins related to DNA-binding with one finger (Dof) transcription factor family and glycine betaine (GB) biosynthesis were differentially expressed in the shoot and root of the salinity-stressed seedlings. Exogenous application of choline on GB accumulation under salt stress showed the increase of GB pathway in C. cajan. Gene expression analysis for differentially abundant proteins revealed the higher induction of ethanolamine kinase (CcEthKin), choline-phosphate cytidylyltransferase 1-like (CcChoPh), serine hydroxymethyltransferase (CcSHMT) and Dof protein (CcDof29). The results indicate the importance of, choline precursor, serine biosynthetic pathways and glycine betaine synthesis in salinity stress tolerance. The glycine betaine protects plant from cellular damages and acts as osmoticum under stress condition. Protein interaction network (PIN) analysis demonstrated that 61% of the differentially expressed proteins exhibited positive interactions and 10% of them formed the center of the PIN. Further, The PIN analysis also highlighted the potential roles of the cytochrome c oxidases in sensing and signaling cascades governing salinity stress responses in pigeonpea.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01116-w.

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

A comparative proteomic analysis of engineered and bio synthesized silver nanoparticles on soybean seedlings

Nanoparticles (NPs) are synthesized by different methods and response mechanism of plants varied towards NPs based on their origin. To study the effects of bio synthesized (BS) and chemically synthesized (CS) silver NPs on soybean, a gel-free/ label-free proteomic technique was used. Length of root and hypocotyl was enhanced by BS compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to 1 and 50 ppm. A total of 190 and 173 differentially changed proteins were identified in BS and CS silver NPs treated soybean, respectively. Twenty proteins commonly changed between BS and CS silver NPs treated soybean. Differentially-changed proteins were associated with protein-degradation and stress according to functional categorization. From proteomics, abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs treated soybean. These results suggest that BS silver NPs enhanced the growth of soybean by regulating proteins related to protein-degradation and ATP contents, which are negatively affected by CS silver NPs. BIOLOGICAL SIGNIFICANCE: This study highlighted the response mechanism of soybean towards bio synthesized (BS) and chemically synthesized (CS) silver nanoparticles (NPs) using a gel-free/ label-free proteomics technique. Length of root and hypocotyl was enhanced by BS silver NPs compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to other concentrations. Differentially changed proteins were associated with protein degradation and stress. From the proteomics, the abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs compared to BS silver NPs treated soybean. These results suggest that the BS silver NPs enhanced the growth of soybean by regulating the proteins related to protein degradation and ATP contents, which are negatively affected by the CS silver NPs.

Impact assessment of major abiotic stresses on the proteome profiling of some important crop plants: a current update

Abiotic stresses adversely affect the plant's growth and development leading to loss of crop plants and plant products in terms of both the quality and quantity. Two main strategies are adopted by plants to acclimatize to stresses; avoidance and tolerance. These adaptive strategies of plants at the cellular and metabolic level enable them to withstand such detrimental conditions. Acclimatization is associated with intensive changes in the proteome of plants and these changes are directly involved in plants response to stress. Proteome studies can be used to screen for these proteins and their involvement in plants response to various abiotic stresses evaluated. In this review, proteomic studies of different plants species under different abiotic stresses, particularly drought, salinity, heat, cold, and waterlogging, are discussed. From different proteomic studies, the stress response can be determined by an interaction between proteomic and physiological changes which occur in plants during such stress conditions. These identified proteins from different processes under different abiotic stress conditions definitely add to our understanding for exploiting them in various biotechnological applications in crop improvement.

Proteomic approaches to uncover the flooding and drought stress response mechanisms in soybean

Soybean is the important crop with abundant protein, vegetable oil, and several phytochemicals. With such predominant values, soybean is cultivated with a long history. However, flooding and drought stresses exert deleterious effects on soybean growth. The present review summarizes the morphological changes and affected events in soybean exposed to such extreme-water conditions. Sensitive organ in stressed soybean at different-developmental stages is presented based on protein profiles. Protein quality control and calcium homeostasis in the endoplasmic reticulum are discussed in soybean under both stresses. In addition, the way of calcium homeostasis in mediating protein folding and energy metabolism is addressed. Finally, stress response to flooding and drought is systematically demonstrated. This review concludes the recent findings of plant response to flooding and drought stresses in soybean employed proteomic approaches.

BIOLOGICAL SIGNIFICANCE

Soybean is considered as traditional-health food because of nutritional elements and pharmacological values. Flooding and drought exert deleterious effects to soybean growth. Proteomic approaches have been employed to elucidate stress response in soybean exposed to flooding and drought stresses. In this review, stress response is presented on organ-specific manner in the early-stage plant and soybean seedling exposed to combined stresses. The endoplasmic reticulum (ER) stress is induced by both stresses; and stress-response in the ER is addressed in the root tip of early-stage soybean. Moreover, calcium-response processes in stressed plant are described in the ER and in the cytosol. Additionally, stress-dependent response was discussed in flooded and drought-stressed plant. This review depicts stress response in the sensitive organ of stressed soybean and forms the basis to develop molecular markers related to plant defense under flooding and drought stresses.

Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial-flooding stress

Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, which markedly reduces its growth and yield. Morphological and biochemical changes such as an increase of fresh weight and a decrease of ATP content happen in early-stage soybean at initial-flooding stress, indicating that soybean responses to flooding stress are keys for its survival and seedling growth. Phosphoproteomics and nuclear proteomics are useful tools to detect protein-phosphorylation status and to identify transcriptional factors. In the review, the effect of flooding on soybean response to initial flooding stress is discussed based on recent results of proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies. In addition, soybean survival under flooding stress, which is defined as tolerance mechanism, is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean.

BIOLOGICAL SIGNIFICANCE

Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, especially soybean responses to initial flooding stress is key for its survival and seedling growth. Recently, proteomic techniques are applied to investigate the response and tolerant mechanisms of soybean at initial flooding condition. In this review, the progress in proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies about the initial-flooding response mechanism in early-stage soybean is presented. In addition, the tolerant mechanism in soybean is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. Through this review, the key proteins and genes involved in initial flooding response and tolerance at early stage soybean are summarized and they contribute greatly to uncover response and tolerance mechanism at early stage under stressful environmental conditions in soybean.

Transcriptomic analysis reveals the flooding tolerant mechanism in flooding tolerant line and abscisic acid treated soybean

Soybean is highly sensitive to flooding stress and exhibits markedly reduced plant growth and grain yield under flooding conditions. To explore the mechanisms underlying initial flooding tolerance in soybean, RNA sequencing-based transcriptomic analysis was performed using a flooding-tolerant line and ABA-treated soybean. A total of 31 genes included 12 genes that exhibited similar temporal patterns were commonly changed in these plant groups in response to flooding and they were mainly involved in RNA regulation and protein metabolism. The mRNA expression of matrix metalloproteinase, glucose-6-phosphate isomerase, ATPase family AAA domain-containing protein 1, and cytochrome P450 77A1 was up-regulated in wild-type soybean under flooding conditions; however, no changes were detected in the flooding-tolerant line or ABA-treated soybean. The mRNA expression of cytochrome P450 77A1 was specifically up-regulated in root tips by flooding stress, but returned to the level found in control plants following treatment with the P450 inhibitor uniconazole. The survival ratio and root fresh weight of plants were markedly improved by 3-h uniconazole treatment under flooding stress. Taken together, these results suggest that cytochrome P450 77A1 is suppressed by uniconazole treatment and that this inhibition may enhance soybean tolerance to flooding stress.

Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique

Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.

Gel-Free/Label-Free Proteomic Analysis of Endoplasmic Reticulum Proteins in Soybean Root Tips under Flooding and Drought Stresses

Soybean is a widely cultivated crop; however, it is sensitive to flooding and drought stresses. The adverse environmental cues cause the endoplasmic reticulum (ER) stress due to accumulation of unfolded or misfolded proteins. To investigate the mechanisms in response to flooding and drought stresses, ER proteomics was performed in soybean root tips. The enzyme activity of NADH cytochrome c reductase was two-fold higher in the ER than other fractions, indicating that the ER was isolated with high purity. Protein abundance of ribosomal proteins was decreased under both stresses compared to control condition; however, the percentage of increased ribosomes was two-fold higher in flooding compared to drought. The ER proteins related to protein glycosylation and signaling were in response to both stresses. Compared to control condition, calnexin was decreased under both stresses; however, protein disulfide isomerase-like proteins and heat shock proteins were markedly decreased under flooding and drought conditions, respectively. Furthermore, fewer glycoproteins and higher levels of cytosolic calcium were identified under both stresses compared to control condition. These results suggest that reduced accumulation of glycoproteins in response to both stresses might be due to dysfunction of protein folding through calnexin/calreticulin cycle. Additionally, the increased cytosolic calcium levels induced by flooding and drought stresses might disturb the ER environment for proper protein folding in soybean root tips.

Proteins involved in biophoton emission and flooding-stress responses in soybean under light and dark conditions

To know the molecular systems basically flooding conditions in soybean, biophoton emission measurements and proteomic analyses were carried out for flooding-stressed roots under light and dark conditions. Photon emission was analyzed using a photon counter. Gel-free quantitative proteomics were performed to identify significant changes proteins using the nano LC-MS along with SIEVE software. Biophoton emissions were significantly increased in both light and dark conditions after flooding stress, but gradually decreased with continued flooding exposure compared to the control plants. Among the 120 significantly identified proteins in the roots of soybean plants, 73 and 19 proteins were decreased and increased in the light condition, respectively, and 4 and 24 proteins were increased and decreased, respectively, in the dark condition. The proteins were mainly functionally grouped into cell organization, protein degradation/synthesis, and glycolysis. The highly abundant lactate/malate dehydrogenase proteins were decreased in flooding-stressed roots exposed to light, whereas the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme was increased in both light and dark conditions. Notably, however, specific enzyme assays revealed that the activities of these enzymes and biophoton emission were sharply increased after 3 days of flooding stress. This finding suggests that the source of biophoton emission in roots might involve the chemical excitation of electron or proton through enzymatic or non-enzymatic oxidation and reduction reactions. Moreover, the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme may play important roles in responses in flooding stress of soybean under the light condition and as a contributing factor to biophoton emission.

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin-related verification in apple calli suggested that the regulation of MdMADS1 on anthocyanin biosynthesis was partially independent of fruit ripening process. Taken together, our findings provide insight into the mechanism how ALA regulates anthocyanin accumulation and add new information on transcriptase regulators of fruit coloration.

Comparative Proteomic Analysis of Soybean Leaves and Roots by iTRAQ Provides Insights into Response Mechanisms to Short-Term Salt Stress

Salinity severely threatens land use capability and crop yields worldwide. Understanding the mechanisms that protect soybeans from salt stress will help in the development of salt-stress tolerant leguminous plants. Here we initially analyzed the changes in malondialdehyde levels, the activities of superoxide dismutase and peroxidases, chlorophyll content, and Na(+)/K(+) ratios in leaves and roots from soybean seedlings treated with 200 mM NaCl at different time points. We found that the 200 mM NaCl treated for 12 h was optimal for undertaking a proteomic analysis on soybean seedlings. An iTRAQ-based proteomic approach was used to investigate the proteomes of soybean leaves and roots under salt treatment. These data are available via ProteomeXchange with the identifier PXD002851. In total, 278 and 440 proteins with significantly altered abundances were identified in leaves and roots of soybean, respectively. From these data, a total of 50 proteins were identified in the both tissues. These differentially expressed proteins (DEPs) were from 13 biological processes. Moreover, protein-protein interaction analysis revealed that proteins involved in metabolism, carbohydrate and energy metabolism, protein synthesis and redox homeostasis could be assigned to four high salt stress response networks. Furthermore, semi-quantitative RT-PCR analysis revealed that some of the proteins, such as a 14-3-3, MMK2, PP1, TRX-h, were also regulated by salt stress at the level of transcription. These results indicated that effective regulatory protein expression related to signaling, membrane and transport, stress defense and metabolism all played important roles in the short-term salt response of soybean seedlings.

Gel-free/label-free proteomic analysis of root tip of soybean over time under flooding and drought stresses

Growth in the early stage of soybean is markedly inhibited under flooding and drought stresses. To explore the responsive mechanisms of soybean, temporal protein profiles of root tip under flooding and drought stresses were analyzed using gel-free/label-free proteomic technique. Root tip was analyzed because it was the most sensitive organ against flooding, and it was beneficial to root penetration under drought. UDP glucose: glycoprotein glucosyltransferase was decreased and increased in soybean root under flooding and drought, respectively. Temporal protein profiles indicated that fermentation and protein synthesis/degradation were essential in root tip under flooding and drought, respectively. In silico protein-protein interaction analysis revealed that the inductive and suppressive interactions between S-adenosylmethionine synthetase family protein and B-S glucosidase 44 under flooding and drought, respectively, which are related to carbohydrate metabolism. Furthermore, biotin/lipoyl attachment domain containing protein and Class II aminoacyl tRNA/biotin synthetases superfamily protein were repressed in the root tip during time-course stresses. These results suggest that biotin and biotinylation might be involved in energy management to cope with flooding and drought in early stage of soybean-root tip.

Proteomic Techniques and Management of Flooding Tolerance in Soybean

Climate change is considered a major threat to world agriculture and food security. To improve the agricultural productivity and sustainability, the development of high-yielding stress-tolerant, and climate-resilient crops is essential. Of the abiotic stresses, flooding stress is a very serious hazard because it markedly reduces plant growth and grain yield. Proteomic analyses indicate that the effects of flooding stress are not limited to oxygen deprivation but include many other factors. Although many flooding response mechanisms have been reported, flooding tolerance mechanisms have not been fully clarified for soybean. There were limitations in soybean materials, such as mutants and varieties, while they were abundant in rice and Arabidopsis. In this review, plant proteomic technologies are introduced and flooding tolerance mechanisms of soybeans are summarized to assist in the improvement of flooding tolerance in soybeans. This work will expedite transgenic or marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Using 7 cm immobilized pH gradient strips to determine levels of clinically relevant proteins in wheat grain extracts

The aim of the work was to test a relatively simple proteomics approach based on phenol extraction and two-dimensional gel electrophoresis (2-DE) with 7 cm immobilized pH gradient strips for the determination of clinically relevant proteins in wheat grain. Using this approach, 157 2-DE spots were quantified in biological triplicate, out of which 55 were identified by matrix-assisted laser desorption/ionization - time of flight tandem mass spectrometry. Clinically relevant proteins associated with celiac disease, wheat dependent exercise induced anaphylaxis, baker's asthma, and food allergy, were detected in 24 2-DE spots. However, alcohol-soluble gliadins were not detected with this approach. The comparison with a recent quantitative study suggested that gel-based and gel-free proteomics approaches are complementary for the detection and quantification of clinically relevant proteins in wheat grain.

Proteomic study on the effects of silver nanoparticles on soybean under flooding stress

Flooding negatively affects the soybean growth; however, silver nanoparticles (AgNPs) enhanced the growth under stress. To study the effects of AgNPs on soybean under flooding, a gel-free proteomic technique was used. The morphological analysis of early-stage soybean exposed to flooding with AgNPs of various sizes and concentrations revealed enhanced seedling growth by treatment with 15n m AgNPs at 2 ppm. Differentially changed 107 root proteins were predominantly associated with stress, signaling, and cell metabolism. Hierarchical clustering divided these proteins into 3 clusters. Based on cluster analysis, the abundances of glyoxalase II 3 and fermentation related proteins were time-dependently increased under flooding stress, but decreased in response to AgNPs. Six enzymes involved in metabolic pathways were analyzed at the transcriptional level. The alcohol dehydrogenase 1 and pyruvate decarboxylase 2 genes were up-regulated under flooding stress while down-regulated in response to AgNPs. Moreover, comparatively low transcript level of glyoxalase II 3 under AgNPs treatment implies that less cytotoxic by-products of glycolysis are produced in AgNPs exposed soybeans as compared to flooded soybean. These results suggest that the AgNPs treated soybeans might have experienced less oxygen-deprivation stress, which might be the key factor for better growth performance of AgNPs treated soybeans under flooding stress.

BIOLOGICAL SIGNIFICANCE

This study highlighted the effect of silver nanoparticles (AgNPs) on the soybean under flooding stress. Silver nanoparticles (2 ppm AgNPs, 15 nm in size) treatment facilitate the soybean under flooding stress enhancing seedling growth. A time-course comparative gel-free proteomic study was performed to analyze the changes inproteome profiles in response to AgNPs treatment under flooding. The 107 differentially changed root proteins were predominantly associated with stress, signaling, cell metabolism. The abundances of the glyoxalase II 3 and fermentation related proteins were significantly increased on exposure to flooding; however, decreased by AgNPs treatment. Comparatively low transcript level of glyoxalase II 3 under AgNPs treatment implies that less cytotoxic by-products of glycolysis are produced in AgNPs exposed soybeans as compared to flooded soybean. Moreover, the observed up-regulation of the alcohol dehydrogenase 1 and pyruvate decarboxylase 2 genes under flooding stress condition and its down-regulation in response to AgNPs treatment might be related to a metabolic shift towards normal cellular processes.

Quantitative proteomics of nuclear phosphoproteins in the root tip of soybean during the initial stages of flooding stress

Soybean is sensitive to flooding stress, which has affected many proteins in roots. To identify the upstream events controlling the regulation of flooding-responsive proteins, nuclear phosphoproteomics of soybean-root tip was performed. Nuclei were isolated from the root tip of 2-day-old soybeans treated with flooding for 3h. The purity of nuclear fractions was confirmed by Western blotting and enzyme-activity assays for subcellular-specific enzymes. Phosphopeptides in the fractions were enriched and analyzed using gel-free proteomic technique. Fourteen phosphoproteins significantly changed in root tip in response to flooding stress. Of these phosphoproteins, 10 proteins including 5 protein synthesis-related proteins were predicted to be localized in the nucleus. In particular, zinc finger/BTB domain-containing protein 47, glycine-rich protein, and rRNA processing protein Rrp5, which are related to abscisic acid (ABA) response, were clearly phosphorylated in response to flooding stress. The mRNA expression levels of these nuclear phosphoproteins were down-regulated in root tip exposed to flooding stress with ABA. In addition, the fresh weight of soybean decreased under flooding stress with ABA, although the fresh weight of plant increased during the initial stage of flooding stress. These results suggest that ABA may affect the flooding response of early-stage soybean through the regulation of nuclear-localized phosphoproteins.

BIOLOGICAL SIGNIFICANCE

This study reported nuclear phosphoprotein analysis of root tip under initial flooding stress using gel-free quantitative proteomics. The main findings of this study are as follows: (i) Fourteen nuclear phosphoproteins in soybean root tip cells were significantly changed in the initial stages of flooding stress; (ii) Zinc finger protein, glycine-rich protein, and Rrp5 were phosphorylated in the nuclei of root tip in response to flooding; and (iii) The mRNA expression levels of these genes were down-regulated by ABA under flooding conditions. These results suggest that ABA may be involved in the initial responses of early-stage soybean to flooding stress by altering the phosphorylation of nuclear-localized phosphoproteins. This study provides not only the nuclear phosphoproteomic analysis but also the molecular mechanism underlying the initial flooding responsive nuclear phosphoproteins functions in the root tip of soybean.

Advances in plant proteomics toward improvement of crop productivity and stress resistancex

Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.

Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress

Flooding has severe negative effects on soybean growth. To explore the flooding-responsive mechanisms in early-stage soybean, a phosphoproteomic approach was used. Two-day-old soybean plants were treated without or with flooding for 3, 6, 12, and 24 h, and root tip proteins were then extracted and analyzed at each time point. After 3 h of flooding exposure, the fresh weight of soybeans increased, whereas the ATP content of soybean root tips decreased. Using a gel-free proteomic technique, a total of 114 phosphoproteins were identified in the root tip samples, and 34 of the phosphoproteins were significantly changed with respect to phosphorylation status after 3 h of flooding stress. Among these phosphoproteins, eukaryotic translation initiation factors were dephosphorylated, whereas several protein synthesis-related proteins were phosphorylated. The mRNA expression levels of sucrose phosphate synthase 1F and eukaryotic translation initiation factor 4 G were down-regulated, whereas UDP-glucose 6-dehydrogenase mRNA expression was up-regulated during growth but down-regulated under flooding stress. Furthermore, bioinformatic protein interaction analysis of flooding-responsive proteins based on temporal phosphorylation patterns indicated that eukaryotic translation initiation factor 4 G was located in the center of the network during flooding. Soybean eukaryotic translation initiation factor 4 G has homology to programmed cell death 4 protein and is implicated in ethylene signaling. The weight of soybeans was increased with treatment by an ethylene-releasing agent under flooding condition, but it was decreased when plants were exposed to an ethylene receptor antagonist. These results suggest that the ethylene signaling pathway plays an important role, via the protein phosphorylation, in mechanisms of plant tolerance to the initial stages of flooding stress in soybean root tips.

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

Flooding stress has a negative impact on soybean cultivation because it severely impairs growth and development. To understand the flooding responsive mechanism in early stage soybeans, a glycoproteomic technique was used. Two-day-old soybeans were treated with flooding for 2 days and roots were collected. Globally, the accumulation level of glycoproteins, as revealed by cross-reaction with concanavalin A decreased by 2 days of flooding stress. Glycoproteins were enriched from total protein extracts using concanavalin A lectin resin and analyzed using a gel-free proteomic technique. One-hundred eleven and 69 glycoproteins were identified without and with 2 days of flooding stress, respectively. Functional categorization of these identified glycoproteins indicated that the accumulation level of proteins related to protein degradation, cell wall, and glycolysis increased, while stress-related proteins decreased under flooding stress. Also the accumulation level of glycoproteins localized in the secretory pathway decreased under flooding stress. Out of 23 common glycoproteins between control and flooding conditions, peroxidases and glycosyl hydrolases were decreased by 2 days of flooding stress. mRNA expression levels of proteins in the endoplasmic reticulum and N-glycosylation related proteins were downregulated by flooding stress. These results suggest that flooding might negatively affect the process of N-glycosylation of proteins related to stress and protein degradation; however glycoproteins involved in glycolysis are activated.