Quantitative Proteomics Reveals the Flooding-Tolerance Mechanism in Mutant and Abscisic Acid-Treated Soybean

Wheat TaNACα18 functions as a positive regulator of high-temperature adaptive responses and improves cell defense machinery

Global wheat production amounted to >780 MMT during 2022-2023 whose market size are valued at >$128 billion. Wheat is highly susceptible to high-temperature stress (HTS) throughout the life cycle and its yield declines 5-7% with the rise in each degree of temperature. Previously, we reported an array of HTS-response markers from a resilient wheat cv. Unnat Halna and described their putative role in heat acclimation. To complement our previous results and identify the key determinants of thermotolerance, here we examined the cytoplasmic proteome of a sensitive cv. PBW343. The HTS-triggered metabolite reprograming highlighted how proteostasis defects influence the formation of an integrated stress-adaptive response. The proteomic analysis identified several promising HTS-responsive proteins, including a NACα18 protein, designated TaNACα18, whose role in thermotolerance remains unknown. Dual localization of TaNACα18 suggests its crucial functions in the cytoplasm and nucleus. The homodimerization of TaNACα18 anticipated its function as a transcriptional coactivator. The complementation of TaNACα18 in yeast and overexpression in wheat demonstrated its role in thermotolerance across the kingdom. Altogether, our results suggest that TaNACα18 imparts tolerance through tight regulation of gene expression, cell wall remodeling and activation of cell defense responses.

Biochemical Analysis to Understand the Flooding Tolerance of Mutant Soybean Irradiated with Gamma Rays

Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic DNA were then analyzed based on oppositely changed proteins between the wild type and the mutant line under flooding stress. They were associated with cell organization, RNA metabolism, and protein degradation according to proteomic analysis. Immunoblot analysis confirmed that the accumulation of beta-tubulin/beta-actin increased in the wild type under flooding stress and recovered to the control level in the mutant line; however, alpha-tubulin increased in both the wild type and the mutant line under stress. Ubiquitin was accumulated and genomic DNA was degraded by flooding stress in the wild type; however, they were almost the same as control levels in the mutant line. On the other hand, the gene expression level of RNase H and 60S ribosomal protein did not change in either the wild type or the mutant line under flooding stress. Furthermore, chlorophyll a/b decreased and increased in the wild type and the mutant line, respectively, under flooding stress. These results suggest that the regulation of cell organization and protein degradation might be an important factor in the acquisition of flooding tolerance in soybean.

Subcellular Proteomics to Elucidate Soybean Response to Abiotic Stress

Climate change jeopardizes soybean production by declining seed yield and quality. In this review, the morphophysiological alterations of soybean in response to abiotic stress are summarized, followed by illustrations of cellular metabolisms and regulatory mechanisms to organellar stress based on subcellular proteomics. This highlights the communications associated with reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments. Given the complexity of climate change and the limitations of plants in coping with multiple abiotic stresses, a generic response to environmental constraints is proposed between calcium and abscisic acid signals in subcellular organelles. This review summarizes the findings of subcellular proteomics in stressed soybean and discusses the future prospects of subcellular proteomics for promoting the improvement of climate-tolerant crops.

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review

Abiotic stresses and climate changes cause severe loss of yield and quality of crops and reduce the production area worldwide. Flooding stress curtails soybean growth, yield, and quality and ultimately threatens the global food supply chain. Flooding tolerance is a multigenic trait. Tremendous research in molecular breeding explored the potential genomic regions governing flood tolerance in soybean. The most robust way to develop flooding tolerance in soybean is by using molecular methods, including quantitative trait loci (QTL) mapping, identification of transcriptomes, transcription factor analysis, CRISPR/Cas9, and to some extent, genome-wide association studies (GWAS), and multi-omics techniques. These powerful molecular tools have deepened our knowledge about the molecular mechanism of flooding stress tolerance. Besides all this, using conventional breeding methods (hybridization, introduction, and backcrossing) and other agronomic practices is also helpful in combating the rising flooding threats to the soybean crop. The current review aims to summarize recent advancements in breeding flood-tolerant soybean, mainly by using molecular and conventional tools and their prospects. This updated picture will be a treasure trove for future researchers to comprehend the foundation of flooding tolerance in soybean and cover the given research gaps to develop tolerant soybean cultivars able to sustain growth under extreme climatic changes.

Enolase, a cadmium resistance related protein from hyperaccumulator plant Phytolacca americana, increase the tolerance of Escherichia coli to cadmium stress

Phytolacca americana is a Cd hyperaccumulator plant that accumulates significant amounts of Cd in leaves, making it a valuable phytoremediation plant species. Our previous research found enolase (ENO) may play an important part in P. americana to cope with Cd stress. As a multifunctional enzyme, ENO was involved not only in glycolysis but also in the response of plants to various environmental stresses. However, there are few studies on the function of PaENO (P. americana enolase) in coping with Cd stress. In this study, the PaENO gene was isolated from P. americana, and the expression level of PaENO gene significantly increased after Cd treatment. The enzymatic activity analysis showed PaENO had typical ENO activity, and the 42-position serine was essential to the enzymatic activity of PaENO. The Cd resistance assay indicated the expression of PaENO remarkably enhanced the resistance of E. coli to Cd, which was achieved by reducing the Cd content in E. coli. Moreover, both the expression of inactive PaENO and PaMBP-1 (alternative translation product of PaENO) can improve the tolerance of E. coli to Cd. The results indicated PaENO may be alternatively translated into the transcription factor PaMBP-1 to participate in the response of P. americana to Cd stress.

The Role of Phytohormones in Plant Response to Flooding

Climatic variations influence the morphological, physiological, biological, and biochemical states of plants. Plant responses to abiotic stress include biochemical adjustments, regulation of proteins, molecular mechanisms, and alteration of post-translational modifications, as well as signal transduction. Among the various abiotic stresses, flooding stress adversely affects the growth of plants, including various economically important crops. Biochemical and biological techniques, including proteomic techniques, provide a thorough understanding of the molecular mechanisms during flooding conditions. In particular, plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by an elaborate hormonal signaling network. With the help of these findings, the main objective is to identify plant responses to flooding and utilize that information for the development of flood-tolerant plants. This review provides an insight into the role of phytohormones in plant response mechanisms to flooding stress, as well as different mitigation strategies that can be successfully administered to improve plant growth during stress exposure. Ultimately, this review will expedite marker-assisted genetic enhancement studies in crops for developing high-yield lines or varieties with flood tolerance.

Deep sequencing of suppression subtractive library identifies differentially expressed transcripts of Saccharum spontaneum exposed to salinity stress

Saccharum spontaneum, a wild relative of sugarcane, is highly tolerant to drought and salinity. The exploitation of germplasm resources for salinity tolerance is a major thrust area in India. In this study, we utilized suppression subtractive hybridization (SSH) followed by sequencing for the identification of upregulated transcripts during salinity stress in S. spontaneum clones coming from different geographical regions of India. Our sequencing of the SSH library revealed that 95% of the transformants contained inserts of size 200-1500 bp. We have identified 314 differentially expressed transcripts in the salinity-treated samples after subtraction, which were subsequently validated by quantitative real-time polymerase chain reaction. Functional annotation and pathway analysis revealed that the upregulated transcripts were a result of protein modifications, stress, and hormone signaling along with cell wall development and lignification. The prominently upregulated transcripts included UDP glucose dehydrogenase, cellulose synthase, ribulose, cellulose synthase COBRA, leucine-rich protein, NAC domain protein, pectin esterase, ABA-responsive element binding factor 1, and heat stress protein. Our results is a step forward the understanding of the molecular response of S. spontaneum under salinity stress, which will lead to the identification of genes and transcription factors as novel targets for salinity tolerance in sugarcane.

Morphophysiological and Proteomic Responses on Plants of Irradiation with Electromagnetic Waves

Electromagnetic energy is the backbone of wireless communication systems, and its progressive use has resulted in impacts on a wide range of biological systems. The consequences of electromagnetic energy absorption on plants are insufficiently addressed. In the agricultural area, electromagnetic-wave irradiation has been used to develop crop varieties, manage insect pests, monitor fertilizer efficiency, and preserve agricultural produce. According to different frequencies and wavelengths, electromagnetic waves are typically divided into eight spectral bands, including audio waves, radio waves, microwaves, infrared, visible light, ultraviolet, X-rays, and gamma rays. In this review, among these electromagnetic waves, effects of millimeter waves, ultraviolet, and gamma rays on plants are outlined, and their response mechanisms in plants through proteomic approaches are summarized. Furthermore, remarkable advancements of irradiating plants with electromagnetic waves, especially ultraviolet, are addressed, which shed light on future research in the electromagnetic field.

Proteomic and Biochemical Analyses of the Mechanism of Tolerance in Mutant Soybean Responding to Flooding Stress

To investigate the mechanism of flooding tolerance of soybean, flooding-tolerant mutants derived from gamma-ray irradiated soybean were crossed with parent cultivar Enrei for removal of other factors besides the genes related to flooding tolerance in primary generated mutant soybean. Although the growth of the wild type was significantly suppressed by flooding compared with the non-flooding condition, that of the mutant lines was better than that of the wild type even if it was treated with flooding. A two-day-old mutant line was subjected to flooding for 2 days and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins in abundance between the wild type and mutant line under flooding stress were associated in endoplasmic reticulum according to gene-ontology categorization. Immunoblot analysis confirmed that calnexin accumulation increased in both the wild type and mutant line; however, calreticulin accumulated in only the mutant line under flooding stress. Furthermore, although glycoproteins in the wild type decreased by flooding compared with the non-flooding condition, those in the mutant line increased even if it was under flooding stress. Alcohol dehydrogenase accumulated in the wild type and mutant line; however, this enzyme activity significantly increased and mildly increased in the wild type and mutant line, respectively, under flooding stress compared with the non-flooding condition. Cell death increased and decreased in the wild type and mutant line, respectively, by flooding stress. These results suggest that the regulation of cell death through the fermentation system and glycoprotein folding might be an important factor for the acquisition of flooding tolerance in mutant soybean.

Proteomic analysis reveals the effects of melatonin on soybean root tips under flooding stress

Flooding constrains soybean growth, while melatonin enhances the ability of plants to tolerate abiotic stresses. To interpret the melatonin-mediated flooding response in soybeans, proteomic analysis was performed in root tips. Retarded growth and severe cell death were observed in flooded soybeans, but these phenotypes were ameliorated by melatonin treatment. A total of 634, 1401, and 1205 proteins were identified under control, flood, and flood plus melatonin conditions, respectively; and these proteins were predominantly associated with metabolism of protein, RNA, and the cell wall. Among these melatonin-induced proteins, eukaryotic aspartyl protease family protein was increased after flood compared with melatonin treatment group, in accordance with its upregulated transcript levels during stress. Eukaryotic translation initiation factor 5A was decreased after flood compared with melatonin. When stress was prolonged, its transcript levels were upregulated by flood, while they were not changed by melatonin. Furthermore, 13-hydroxylupanine O-tigloyltransferase was decreased by flood compared with melatonin; however, its transcription was upregulated by melatonin. In addition, reduced lignification in root tips of flooded soybeans was restored by melatonin. These results suggest that factors related to protein degradation and functional states of RNA play critical roles in promoting the effects of melatonin on soybean plants under flooding. SIGNIFICANCE: Flooding stress threatens soybean growth, while melatonin treatment enhances plant tolerance to stress stimuli. To examine the effects of melatonin on flooded soybeans, morphological analysis was performed. Melatonin promoted soybean growth as judged from greater fresh weight of plant, longer seedling length, and less evident cell death in flooding-stressed soybeans treated with melatonin than those plants exposed to flood alone. Proteomic analysis was conducted to explore the promoting effects of melatonin on soybeans under flooding stress. As a result, metabolism of protein metabolism, RNA regulation, and cell wall was enriched by proteins identified under control, flood, and flood plus melatonin conditions. Among these melatonin-induced proteins, abundance of eukaryotic aspartyl protease family protein, eukaryotic translation initiation factor 5A, and 13-hydroxylupanine O-tigloyltransferase displayed similar change patterns between the control and melatonin compared with flood; and transcript levels of genes encoding these proteins responded to flooding stress and melatonin treatment. In addition, activated cell degradation, expanded intercellular spaces, and reduced lignification in root tips of flooded soybeans were ameliorated by melatonin treatment.

Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]

Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.

Integrative omic and transgenic analyses reveal the positive effect of ultraviolet-B irradiation on salvianolic acid biosynthesis through upregulation of SmNAC1

Salvianolic acids (SalAs), a group of secondary metabolites in Salvia miltiorrhiza, are widely used for treating cerebrovascular diseases. Their biosynthesis is modulated by a variety of abiotic factors, including ultraviolet-B (UV-B) irradiation; however, the underlying mechanisms remain largely unknown. Here, an integrated metabolomic, proteomic, and transcriptomic approach coupled with transgenic analyses was employed to dissect the mechanisms underlying UV-B irradiation-induced SalA biosynthesis. Results of metabolomics showed that 28 metabolites, including 12 SalAs, were elevated in leaves of UV-B-treated S. miltiorrhiza. Meanwhile, the contents of several phytohormones, including jasmonic acid and salicylic acid, which positively modulate the biosynthesis of SalAs, also increased in UV-B-treated S. miltiorrhiza. Consistently, 20 core biosynthetic enzymes and numerous transcription factors that are involved in SalA biosynthesis were elevated in treated samples as indicated by a comprehensive proteomic analysis. Correlation and gene expression analyses demonstrated that the NAC1 gene, encoding a NAC transcriptional factor, was positively involved in UV-B-induced SalA biosynthesis. Accordingly, overexpression and RNA interference of NAC1 increased and decreased SalA contents, respectively, through regulation of key biosynthetic enzymes. Furthermore, ChIP-qPCR and Dual-LUC assays showed that NAC1 could directly bind to the CATGTG and CATGTC motifs present in the promoters of the SalA biosynthesis-related genes PAL3 and TAT3, respectively, and activate their expression. Our results collectively demonstrate that NAC1 plays a crucial role in UV-B irradiation-induced SalA biosynthesis. Taken together, our findings provide mechanistic insights into the UV-B-induced SalA biosynthesis in S. miltiorrhiza, and shed light on a great potential for the development of SalA-abundant varieties through genetic engineering.

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.

The beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana

The nascent polypeptide-associated (NAC) complex was described in yeast as a heterodimer composed of two subunits, α and β, and was shown to bind to the nascent polypeptides newly emerging from the ribosomes. NAC function was widely described in yeast and several information are also available about its role in plants. The knock down of individual NAC subunit(s) led usually to a higher sensitivity to stress. In Arabidopsis thaliana genome, there are five genes encoding NACα subunit, and two genes encoding NACβ. Double homozygous mutant in both genes coding for NACβ was acquired, which showed a delayed development compared to the wild type, had abnormal number of flower organs, shorter siliques and greatly reduced seed set. Both NACβ genes were characterized in more detail-the phenotype of the double homozygous mutant was complemented by a functional NACβ copy. Then, both NACβ genes were localized to nuclei and cytoplasm and their promoters were active in many organs (leaves, cauline leaves, flowers, pollen grains, and siliques together with seeds). Since flowers were the most affected organs by nacβ mutation, the flower buds' transcriptome was identified by RNA sequencing, and their proteome by gel-free approach. The differential expression analyses of transcriptomic and proteomic datasets suggest the involvement of NACβ subunits in stress responses, male gametophyte development, and photosynthesis.

An Integrated Approach of Proteomics and Computational Genetic Modification Effectiveness Analysis to Uncover the Mechanisms of Flood Tolerance in Soybeans

Flooding negatively affects the growth of soybeans. Recently, omic approaches have been used to study abiotic stress responses in plants. To explore flood-tolerant genes in soybeans, an integrated approach of proteomics and computational genetic modification effectiveness analysis was applied to the soybean (Glycine max L. (Merrill)). Flood-tolerant mutant and abscisic acid (ABA)-treated soybean plants were used as the flood-tolerant materials. Among the primary metabolism, glycolysis, fermentation, and tricarboxylic acid cycle were markedly affected under flooding. Fifteen proteins, which were related to the affected processes, displayed similar protein profiles in the mutant and ABA-treated soybean plants. Protein levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), aconitase 1, and 2-oxoglutarate dehydrogenase were higher in flood-tolerant materials than in wild-type soybean plants under flood conditions. These three proteins were positioned in each of the three enzyme groups revealed by our computational genetic modification effectiveness analysis, and the three proteins configured a candidate set of genes to promote flood tolerance. Additionally, transcript levels of GAPDH were similar in flood-tolerant materials and in unstressed plants. These results suggest that proteins related to energy metabolism might play an essential role to confer flood tolerance in soybeans.

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.

Metabolic profiles of flooding-tolerant mechanism in early-stage soybean responding to initial stress

KEY MESSAGE

Metabolomic analysis of flooding-tolerant mutant and abscisic acid-treated soybeans suggests that accumulated fructose might play a role in initial flooding tolerance through regulation of hexokinase and phosphofructokinase. Soybean is sensitive to flooding stress, which markedly reduces plant growth. To explore the mechanism underlying initial-flooding tolerance in soybean, mass spectrometry-based metabolomic analysis was performed using flooding-tolerant mutant and abscisic-acid treated soybeans. Among the commonly-identified metabolites in both flooding-tolerant materials, metabolites involved in carbohydrate and organic acid displayed same profile at initial-flooding stress. Sugar metabolism was highlighted in both flooding-tolerant materials with the decreased and increased accumulation of sucrose and fructose, respectively, compared to flooded soybeans. Gene expression of hexokinase 1 was upregulated in flooded soybean; however, it was downregulated in both flooding-tolerant materials. Metabolites involved in carbohydrate/organic acid and proteins related to glycolysis/tricarboxylic acid cycle were integrated. Increased protein abundance of phosphofructokinase was identified in both flooding-tolerant materials, which was in agreement with its enzyme activity. Furthermore, sugar metabolism was pointed out as the tolerant-responsive process at initial-flooding stress with the integration of metabolomics, proteomics, and transcriptomics. Moreover, application of fructose declined the increased fresh weight of plant induced by flooding stress. These results suggest that fructose might be the critical metabolite through regulation of hexokinase and phosphofructokinase to confer initial-flooding stress in soybean.

Proteomic Analysis of Calcium Effects on Soybean Root Tip under Flooding and Drought Stresses

Flooding and drought are disadvantageous environmental conditions that induce cytosolic calcium in soybean. To explore the effects of flooding- and drought-induced increases in calcium, a gel-free/label-free proteomic analysis was performed. Cytosolic calcium was decreased by blocking calcium channels in the endoplasmic reticulum (ER) and plasma membrane under both stresses. Calnexin, protein disulfide isomerase, heat shock proteins and thioredoxin were predominantly affected as the ER proteins in response to calcium, and ER-associated degradation-related proteins of HCP-like superfamily protein were up-regulated under stress exposure and then down-regulated. Glycolysis, fermentation, the tricarboxylic acid cycle and amino acid metabolism were mainly induced as the types of cellular metabolism in response to calcium under both stresses. Pyruvate decarboxylase was increased and decreased under flooding and drought, respectively, and was further decreased by the reduction of cytosolic calcium; however, it was recovered by exogenous calcium under both stresses. Furthermore, pyruvate decarboxylase activity was increased under flooding, but decreased under drought. These results suggest that calcium is involved in protein folding in the ER, and ER-associated degradation might alleviate ER stress during the early stage of both stresses. Furthermore, calcium appears to modify energy metabolism, and pyruvate decarboxylase may be a key enzyme in this process under flooding and drought.

Organ-specific proteomics of soybean seedlings under flooding and drought stresses

Organ-specific analyses enrich the understanding of plant growth and development under abiotic stresses. To elucidate the cellular responses in soybean seedlings exposed to flooding and drought stresses, organ-specific analysis was performed using a gel-free/label-free proteomic technique. Physiological analysis indicated that enzyme activities of alcohol dehydrogenase and delta-1-pyrroline-5-carboxylate synthase were markedly increased in leaf and root of plants treated with 6days of flooding and drought stresses, respectively. Proteins related to photosynthesis, RNA, DNA, signaling, and the tricarboxylic acid cycle were predominately affected in leaf, hypocotyl, and root in response to flooding and drought. Notably, the tricarboxylic acid cycle was suppressed in leaf and root under both stresses. Moreover, 17 proteins, including beta-glucosidase 31 and beta-amylase 5, were identified in soybean seedlings under both stresses. The protein abundances of beta-glucosidase 31 and beta-amylase 5 were increased in leaf and root under both stresses. Additionally, the gene expression of beta-amylase 5 was upregulated in leaf exposed to the flooding and drought, and the expression level was highly correlated with the protein abundance. These results suggest that beta-amylase 5 may be involved in carbohydrate mobilization to provide energy to the leaf of soybean seedlings exposed to flooding and drought.

BIOLOGICAL SIGNIFICANCE

This study examined the effects of flooding and drought on soybean seedlings in different organs using a gel-free/label-free proteomic approach. Physiological responses indicated that enzyme activities of alcohol dehydrogenase and delta-1-pyrroline-5-carboxylate synthase were increased in leaf and root of soybean seedlings exposed to flooding and drought for 6days. Functional analysis of acquired protein profiles exhibited that proteins related to photosynthesis, RNA, DNA, signaling, and the tricarboxylic acid cycle were predominated affected in leaf, hypocotyl, and root under both stresses. Moreover, the tricarboxylic acid cycle was suppressed in leaf and root of stressed soybean seedlings. Additionally, increased protein abundance of beta-amylase 5 was consistent with upregulated gene expression in the leaf under both stresses, suggesting that carbohydrate metabolism might be governed in response to flooding and drought of soybean seedlings.

Proteomic analysis of injured storage roots in cassava (Manihot esculenta Crantz) under postharvest physiological deterioration

Postharvest physiological deterioration (PPD) is a global challenge in the improvement of cassava value chain. However, how to reduce cassava spoilage and reveal the mechanism of injured cassava storage roots in response to PPD were poorly understood. In the present study, we investigated the activities of antioxidant enzymes of cassava injured storage roots in PPD-susceptible (SC9) and PPD-tolerant (QZ1) genotypes at the time-points from 0h to 120h, and further analyzed their proteomic changes using two-dimensional electrophoresis (2-DE) in combination with MALDI-TOF-MS/MS. Ninety-nine differentially expressed proteins were identified from SC9 and QZ1 genotypes in the pairwise comparison of 24h/0h, 48h/0h, 72h/0h and 96h/0h. Of those proteins were associated with 13 biological functions, in which carbohydrate and energy metabolism related proteins were the biggest amount differential proteins in both genotypes, followed by chaperones, DNA and RNA metabolism, and defense system. We speculated that SOD in combination with CAT activities would be the first line of defense against PPD to support PPD-tolerant cassava varieties. The four hub proteins including CPN60B, LOS2, HSC70-1 and CPN20B, produced from the network of protein-protein interaction, will be the candidate key proteins linked with PPD. This study provides a new clue to improve cassava PPD-tolerant varieties and would be helpful to much better understand the molecular mechanism of PPD of cassava injured storage roots.

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.

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein-protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future.