Comparative proteomic analysis of canola leaves under salinity stress

Integration of Physiological, Transcriptomic, and Metabolomic Analyses Reveal Molecular Mechanisms of Salt Stress in Maclura tricuspidata

Salt stress is a universal abiotic stress that severely affects plant growth and development. Understanding the mechanisms of Maclura tricuspidate's adaptation to salt stress is crucial for developing salt-tolerant plant varieties. This article discusses the integration of physiology, transcriptome, and metabolome to investigate the mechanism of salt adaptation in M. tricuspidata under salt stress conditions. Overall, the antioxidant enzyme system (SOD and POD) of M. tricuspidata exhibited higher activities compared with the control, while the content of soluble sugar and concentrations of chlorophyll a and b were maintained during salt stress. KEGG analysis revealed that deferentially expressed genes were primarily involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, alkaloids, and MAPK signaling pathways. Differential metabolites were enriched in amino acid metabolism, the biosynthesis of plant hormones, butanoate, and 2-oxocarboxylic acid metabolism. Interestingly, glycine, serine, and threonine metabolism were found to be important both in the metabolome and transcriptome-metabolome correlation analyses, suggesting their essential role in enhancing the salt tolerance of M. tricuspidata. Collectively, our study not only revealed the molecular mechanism of salt tolerance in M. tricuspidata, but also provided a new perspective for future salt-tolerant breeding and improvement in salt land for this species.

Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops

Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.

Development and Optimization of Label-Free Quantitative Proteomics under Different Crossing Periods of Bottle Gourd

Bottle gourd, a common vegetable in the human diet, has been valued for its medicinal and energetic properties. In this experiment, the time-resolved analysis of the changes in the proteins' electrophoretic patterning of the seed development at different crossing periods was studied in bottle gourd using label-free quantitative proteomics. Hybrid HBGH-35 had the highest observed protein levels at the 4th week of the crossing period (F₄) compared to the parental lines, viz. G-2 (M) and Pusa Naveen (F). The crossing period is significantly correlated with grain filling and reserve accumulation. The observed protein expression profile after storage was related to seed maturation and grain filling in bottle gourds. A total of 2517 proteins were identified in differentially treated bottle gourd fruits, and 372 proteins were differentially expressed between different crossing periods. Proteins related to carbohydrate and energy metabolism, anthocyanin biosynthesis, cell stress response, and fruit firmness were characterized and quantified. Some proteins were involved in the development, while others were engaged in desiccation and the early grain-filling stage. F4 was distinguished by an increase in the accumulation of low molecular weight proteins and enzymes such as amylase, a serine protease, and trypsin inhibitors. The seed vigor also followed similar patterns of differential expression of seed storage proteins. Our findings defined a new window during seed production, which showed that at F₄, maximum photosynthetic assimilates accumulated, resulting in an enhanced source-sink relationship and improved seed production. Our study attempts to observe the protein expression profiling pattern under different crossing periods using label-free quantitative proteomics in bottle gourd. It will facilitate future detailed investigation of the protein associated with quality traits and the agronomic importance of bottle gourd through selective breeding programs.

Salinity responses and tolerance mechanisms in underground vegetable crops: an integrative review

The present review gives an insight into the salinity stress tolerance responses and mechanisms of underground vegetable crops. Phytoprotectants, agronomic practices, biofertilizers, and modern biotechnological approaches are crucial for salinity stress management. Underground vegetables are the source of healthy carbohydrates, resistant starch, antioxidants, vitamins, mineral, and nutrients which benefit human health. Soil salinity is a serious threat to agriculture that severely affects the growth, development, and productivity of underground vegetable crops. Salt stress induces several morphological, anatomical, physiological, and biochemical changes in crop plants which include reduction in plant height, leaf area, and biomass. Also, salinity stress impedes the growth of the underground organs, which ultimately reduces crop yield. Moreover, salt stress is detrimental to photosynthesis, membrane integrity, nutrient balance, and leaf water content. Salt tolerance mechanisms involve a complex interplay of several genes, transcription factors, and proteins that are involved in the salinity tolerance mechanism in underground crops. Besides, a coordinated interaction between several phytoprotectants, phytohormones, antioxidants, and microbes is needed. So far, a comprehensive review of salinity tolerance responses and mechanisms in underground vegetables is not available. This review aims to provide a comprehensive view of salt stress effects on underground vegetable crops at different levels of biological organization and discuss the underlying salt tolerance mechanisms. Also, the role of multi-omics in dissecting gene and protein regulatory networks involved in salt tolerance mechanisms is highlighted, which can potentially help in breeding salt-tolerant underground vegetable crops.

How salt stress-responsive proteins regulate plant adaptation to saline conditions

An overview is presented of recent advances in our knowledge of candidate proteins that regulate various physiological and biochemical processes underpinning plant adaptation to saline conditions. Salt stress is one of the environmental constraints that restrict plant distribution, growth and yield in many parts of the world. Increased world population surely elevates food demands all over the globe, which anticipates to add a great challenge to humanity. These concerns have necessitated the scientists to understand and unmask the puzzle of plant salt tolerance mechanisms in order to utilize various strategies to develop salt tolerant crop plants. Salt tolerance is a complex trait involving alterations in physiological, biochemical, and molecular processes. These alterations are a result of genomic and proteomic complement readjustments that lead to tolerance mechanisms. Proteomics is a crucial molecular tool that indicates proteins expressed by the genome, and also identifies the functions of proteins accumulated in response to salt stress. Recently, proteomic studies have shed more light on a range of promising candidate proteins that regulate various processes rendering salt tolerance to plants. These proteins have been shown to be involved in photosynthesis and energy metabolism, ion homeostasis, gene transcription and protein biosynthesis, compatible solute production, hormone modulation, cell wall structure modification, cellular detoxification, membrane stabilization, and signal transduction. These candidate salt responsive proteins can be therefore used in biotechnological approaches to improve tolerance of crop plants to salt conditions. In this review, we provided comprehensive updated information on the proteomic data of plants/genotypes contrasting in salt tolerance in response to salt stress. The roles of salt responsive proteins that are potential determinants for plant salt adaptation are discussed. The relationship between changes in proteome composition and abundance, and alterations observed in physiological and biochemical features associated with salt tolerance are also addressed.

Alkaline Salt Inhibits Seed Germination and Seedling Growth of Canola More Than Neutral Salt

Salinity is a major constraint to crop growth and productivity, limiting sustainable agriculture production. Planting canola (Brassica napus L.) variety with salinity-alkalinity tolerance as a green manure on the large area of salinity-affected land in Xinjiang could alleviate feed shortage. To investigate the differential effects of neutral and alkaline salt stress on seed germination and seedling growth of canola, we used two salts at varying concentrations, i.e., NaCl (neutral salt at 100, 150, and 200 mM) and Na₂CO₃ (alkaline salt at 20, 30, and 40 mM). To further explore the effects of Na⁺ and pH on seed germination, we included combined of NaCl (0, 100, 150, and 200 mM) and pH (7.1, 8.0, 9.0, 10.0, and 11.0). Shoot growth was promoted by low concentrations of NaCl and Na₂CO₃ but inhibited at high salt concentrations. Given the same Na⁺ concentration, Na₂CO₃ inhibited seed germination and seedling growth more than NaCl. The results showed that the main factor affecting seed germination and seedling growth is not pH alone, but the interaction between pH and salt ions. Under NaCl stress, canola increased the absorption of K⁺, Ca²⁺, and Mg²⁺ in roots and K⁺ in leaves. However, under Na₂CO₃ stress, canola maintained a high K⁺ concentration and K⁺/Na⁺ ratio in leaves and increased Ca²⁺ and Mg²⁺ in roots. Our study showed that alkaline salts inhibit canola seed germination and seedling growth more significantly than neutral salts and salt species, salt concentration, and pH significantly affected on seed germination and seedling growth. However, pH affected seed germination and seedling growth mainly through an interaction with salt ions.

Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)

BACKGROUND

High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions.

RESULTS

Compared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in "Glycolysis/Gluconeogenesis" (ko00010), "Cutin, suberine and wax biosynthesis" (ko00073), and "phenylpropanoid biosynthesis" (ko00940) in Sujiang 1419, although "cysteine/methionine metabolism" (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties.

CONCLUSIONS

These findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis.

Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants

In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.

The Resistance of Oilseed Rape Microspore-Derived Embryos to Osmotic Stress Is Associated With the Accumulation of Energy Metabolism Proteins, Redox Homeostasis, Higher Abscisic Acid, and Cytokinin Contents

The present study aims to investigate the response of rapeseed microspore-derived embryos (MDE) to osmotic stress at the proteome level. The PEG-induced osmotic stress was studied in the cotyledonary stage of MDE of two genotypes: Cadeli (D) and Viking (V), previously reported to exhibit contrasting leaf proteome responses under drought. Two-dimensional difference gel electrophoresis (2D-DIGE) revealed 156 representative protein spots that have been selected for MALDI-TOF/TOF analysis. Sixty-three proteins have been successfully identified and divided into eight functional groups. Data are available via ProteomeXchange with identifier PXD024552. Eight selected protein accumulation trends were compared with real-time quantitative PCR (RT-qPCR). Biomass accumulation in treated D was significantly higher (3-fold) than in V, which indicates D is resistant to osmotic stress. Cultivar D displayed resistance strategy by the accumulation of proteins in energy metabolism, redox homeostasis, protein destination, and signaling functional groups, high ABA, and active cytokinins (CKs) contents. In contrast, the V protein profile displayed high requirements of energy and nutrients with a significant number of stress-related proteins and cell structure changes accompanied by quick downregulation of active CKs, as well as salicylic and jasmonic acids. Genes that were suitable for gene-targeting showed significantly higher expression in treated samples and were identified as phospholipase D alpha, peroxiredoxin antioxidant, and lactoylglutathione lyase. The MDE proteome profile has been compared with the leaf proteome evaluated in our previous study. Different mechanisms to cope with osmotic stress were revealed between the genotypes studied. This proteomic study is the first step to validate MDE as a suitable model for follow-up research on the characterization of new crossings and can be used for preselection of resistant genotypes.

Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L

Citric acid (CA), as an organic chelator, plays a vital role in alleviating copper (Cu) stress-mediated oxidative damage, wherein a number of molecular mechanisms alter in plants. However, it remains largely unknown how CA regulates differentially abundant proteins (DAPs) in response to Cu stress in Brassica napus L. In the present study, we aimed to investigate the proteome changes in the leaves of B. L. seedlings in response to CA-mediated alleviation of Cu stress. Exposure of 21-day-old seedlings to Cu (25 and 50 μM) and CA (1.0 mM) for 7 days exhibited a dramatic inhibition of overall growth and considerable increase in the enzymatic activities (POD, SOD, CAT). Using a label-free proteome approach, a total of 6345 proteins were identified in differentially treated leaves, from which 426 proteins were differentially expressed among the treatment groups. Gene ontology (GO) and KEGG pathways analysis revealed that most of the differential abundance proteins were found to be involved in energy and carbohydrate metabolism, photosynthesis, protein metabolism, stress and defense, metal detoxification, and cell wall reorganization. Our results suggest that the downregulation of chlorophyll biosynthetic proteins involved in photosynthesis were consistent with reduced chlorophyll content. The increased abundance of proteins involved in stress and defense indicates that these DAPs might provide significant insights into the adaptation of Brassica seedlings to Cu stress. The abundances of key proteins were further verified by monitoring the mRNA expression level of the respective transcripts. Taken together, these findings provide a potential molecular mechanism towards Cu stress tolerance and open a new route in accelerating the phytoextraction of Cu through exogenous application of CA in B. napus.

Recent progress in understanding salinity tolerance in plants: Story of Na+/K+ balance and beyond

High salt concentrations in the growing medium can severely affect the growth and development of plants. It is imperative to understand the different components of salt-tolerant network in plants in order to produce the salt-tolerant cultivars. High-affinity potassium transporter- and myelocytomatosis proteins have been shown to play a critical role for salinity tolerance through exclusion of sodium (Na⁺) ions from sensitive shoot tissues in plants. Numerous genes, that limit the uptake of salts from soil and their transport throughout the plant body, adjust the ionic and osmotic balance of cells in roots and shoots. In the present review, we have tried to provide a comprehensive report of major research advances on different mechanisms regulating plant tolerance to salinity stress at proteomics, metabolomics, genomics and transcriptomics levels. Along with the role of ionic homeostasis, a major focus was given on other salinity tolerance mechanisms in plants including osmoregulation and osmo-protection, cell wall remodeling and integrity, and plant antioxidative defense. Major proteins and genes expressed under salt-stressed conditions and their role in enhancing salinity tolerance in plants are discussed as well. Moreover, this manuscript identifies and highlights the key questions on plant salinity tolerance that remain to be discussed in the future.

Combined Transcriptomic and Metabolomic Analysis Reveals the Role of Phenylpropanoid Biosynthesis Pathway in the Salt Tolerance Process of Sophora alopecuroides

Salt stress is the main abiotic stress that limits crop yield and agricultural development. Therefore, it is imperative to study the effects of salt stress on plants and the mechanisms through which plants respond to salt stress. In this study, we used transcriptomics and metabolomics to explore the effects of salt stress on Sophora alopecuroides. We found that salt stress incurred significant gene expression and metabolite changes at 0, 4, 24, 48, and 72 h. The integrated transcriptomic and metabolomic analysis revealed that the differentially expressed genes (DEGs) and differential metabolites (DMs) obtained in the phenylpropanoid biosynthesis pathway were significantly correlated under salt stress. Of these, 28 DEGs and seven DMs were involved in lignin synthesis and 23 DEGs and seven DMs were involved in flavonoid synthesis. Under salt stress, the expression of genes and metabolites related to lignin and flavonoid synthesis changed significantly. Lignin and flavonoids may participate in the removal of reactive oxygen species (ROS) in the root tissue of S. alopecuroides and reduced the damage caused under salt stress. Our research provides new ideas and genetic resources to study the mechanism of plant responses to salt stress and further improve the salt tolerance of plants.

Gene duplication and stress genomics in Brassicas: Current understanding and future prospects

Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.

Silicon in Horticultural Crops: Cross-talk, Signaling, and Tolerance Mechanism under Salinity Stress

Agricultural land is extensively affected by salinity stress either due to natural phenomena or by agricultural practices. Saline stress possesses two major threats to crop growth: osmotic stress and oxidative stress. The response of these changes is often accompanied by variety of symptoms, such as the decrease in leaf area and internode length and increase in leaf thickness and succulence, abscission of leaves, and necrosis of root and shoot. Salinity also delays the potential physiological activities, such as photosynthesis, transpiration, phytohormonal functions, metabolic pathways, and gene/protein functions. However, crops in response to salinity stress adopt counter cascade mechanisms to tackle salinity stress incursion, whilst continuous exposure to saline stress overcomes the defense mechanism system which results in cell death and compromises the function of essential organelles in crops. To overcome the salinity, a large number of studies have been conducted on silicon (Si); one of the beneficial elements in the Earth's crust. Si application has been found to mitigate salinity stress and improve plant growth and development, involving signaling transduction pathways of various organelles and other molecular mechanisms. A large number of studies have been conducted on several agricultural crops, whereas limited information is available on horticultural crops. In the present review article, we have summarized the potential role of Si in mitigating salinity stress in horticultural crops and possible mechanism of Si-associated improvements in them. The present review also scrutinizes the need of future research to evaluate the role of Si and gaps to saline stress in horticultural crops for their improvement.

Differential proteomics: Effect of growth regulators on salt stress responses in safflower seedlings

Productivity of safflower (Carthamus tinctorius L.) is markedly reduced by salt stress. This study is based on analysis of proteins profile of safflower plants treated with 200 mM NaCl, with exogenously applied salicylic acid (SA) and penconazole (PEN), as growth regulators. Plants were investigated through a gel-based proteomic approach, which resulted in the identification of 17 salt-responsive proteins related to different metabolic modifications. Of these, seven different proteins were up or down regulated by both SA and PEN, suggesting the synergistic and antagonistic effects of SA and PEN. The classification of differentially expressed proteins showed that salt-responsive proteins were mainly involved in photosynthesis, ion homeostasis, and oxidative stress response, as well as nitrogen, protein, and carbohydrate metabolism. The identified stress-responsive proteins in this study could pave the way to develop salt tolerance in safflower, thus sustaining its productivity under salinity. In addition, SA and PEN may be considered as a foliar application to ameliorate salinity effects, due to their low price and availability.

Photochemistry and proteomics of mulberry (Morus alba L.) seedlings under NaCl and NaHCO3 stress

In order to explore the response and adaptation mechanisms of photosynthesis of the leaves of mulberry (Morus alba L.) seedlings to saline-alkali stress. Photosynthetic activity, and the response of related proteomics of M. alba seedling leaves under NaCl and NaHCO₃ stress were studied by using chlorophyll fluorescence and gas exchange technique combined with TMT proteomics. The results showed that NaCl stress had no significant effect on photosystem II (PSII) activity in M. alba seedling leaves. In addition, the expressions of proteins of the PSII oxygen-evolving complex (OEE3-1 and PPD4) and the LHCII antenna (CP24 10A, CP26, and CP29) were increased, and the photosystem I (PSI) activity in the leaves of M. alba seedlings was increased, as well as expressions of proteins, such as PsaF, PsaG, PsaH, PsaL, PsaN, and Ycf4. Under NaHCO₃ stress, the activity of PSII and PSI and the expression of their protein complexes and the electron transfer-related proteins significantly decreased. NaCl stress had little effect on RuBP regeneration during dark reaction in the leaves and the expressions of glucose synthesis related proteins and net photosynthetic rate (P_n) did not decrease significantly. The leaves could adapt to NaCl stress by reducing stomatal conductance (G_s) and increasing water use efficiency (WUE). Under NaHCO₃ stress, the expression of dark reaction-related proteins was mostly down-regulated, while G_s was reduced, which indicated that non-stomatal factors can be responsible for inhibition of carbon assimilation.

Proteomic and physiological responses in mangrove Kandelia candel roots under short-term high-salinity stress

Kandelia candel is one of the mangrove species that are most resistant to environmental stress. As a typical nonsalt-secreting mangrove plant, K. candel is an ideal biological material to analyze the molecular mechanism of salt tolerance in woody plants. In this study, changes in protein abundance and expression profile in K. candel roots under high-salinity stress of 600 mmol L^-1 NaCl were analyzed using isobaric tags for relative and absolute quantification (iTRAQ) assay. Moreover, the physiological parameters associated with metabolic pathways in which the differentially abundant proteins (DAPs) are involved were determined. A total of 5577 proteins were identified by iTRAQ analysis of the K. candel root proteins, of which 227 were DAPs with a fold change ratio >1.2 or a fold change ratio <0.83 and a P-value <0.05. A total of 227 DAPs consisting of 110 up-regulated and 117 down-regulated proteins were identified. Our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DAPs were primarily involved in biological processes including carbohydrate and energy metabolisms, stress response and defense, cell wall structure, and secondary metabolism. The results of the physiological parameters showed that their profile changes were consistent with those of the proteome analysis. The results of the proteome and physiological parameters showed that K. candel roots could resist high-salinity stress by maintaining a normal Embden-Meyerhof-Parnas and tricarboxylic acid (EMP-TCA) pathway, increasing the activities of various antioxidant enzymes and antioxidant contents, stabilizing the cell wall structure, and accumulating secondary metabolites such as triterpenoids.

Recovery aptitude of the halophyte Cakile maritima upon water deficit stress release is sustained by extensive modulation of the leaf proteome

Among the most intriguing features characterizing extremophile plants is their ability to rapidly recover growth activity upon stress release. Here, we investigated the responses of the halophyte C. maritima to drought and recovery at both physiological and leaf proteome levels. Six week-old plants were either cultivated at 100% or at 25% field capacity. After 12 d of treatment, one lot of dehydrated plants was rewatered to 100% FC for 14 d (stress release). Drought stress impaired shoot hydration, photosynthetic activity and chlorophyll content compared to the control, resulting in severe plant growth restriction. This was concomitant with a marked increase in anthocyanin and proline concentrations. Upon stress release, C. maritima rapidly recovered with respect to all measured parameters. Two-dimensional gel-based proteome analysis of leaves revealed 84 protein spots with significantly changed volumes at the compared conditions: twenty-eight protein spots between normally watered plants and stressed plants but even 70 proteins between stressed and recovered plants. Proteins with higher abundance induced upon rewatering were mostly involved in photosynthesis, glycolytic pathway, TCA cycle, protein biosynthesis, and other metabolic pathways. Overall, C. maritima likely adopts a drought-avoidance strategy, involving efficient mechanisms specifically taking place upon stress release, leading to fast and strong recovery.

Silicon attenuates sodium toxicity by improving nutritional efficiency in sorghum and sunflower plants

Salt stress is known to negatively affect the fundamental processes in plants, reducing their growth and yield. The role of Silicon (Si) to protect the sorghum and sunflower plants against salinity stress was assessed. The objective of this study was to evaluate the effects of different forms of Si application on the uptake and use efficiency of macronutrients and micronutrients in sorghum and sunflower plants under salinity stress under greenhouse conditions. Two experiments were conducted using sorghum and sunflower under greenhouse conditions. Four Si levels were applied to plants: no Si application; foliar application of 28.6 mmol.L^-1; root application of 2.0 mmol.L^-1; and combined Si application with both via nutrient solution and foliar spraying. Each Si treatment was applied in the absence and presence of NaCl (100 mM). Thirty days after treatments, sodium (Na⁺) and Si accumulation, nutrient uptake and use efficiency, and the roots and total plant dry weight were measured. Salinity stress induced nutritional imbalance and decreased dry weight production in both plant species. Our results showed that Si application alleviated the salinity stress by decreased Na⁺ uptake and increased nutritional efficiency, thereby favoring the total plant dry weight in sorghum by 27% and sunflower by 41%. This occurred when Si was applied either via root or in combination via root and foliar application, respectively. Collectively, our findings indicate that Si application can attenuate the deleterious effects of salt stress and increase yield in sorghum and sunflower plants in a sustainable manner.

Comparative proteomics and gene expression analyses revealed responsive proteins and mechanisms for salt tolerance in chickpea genotypes

BACKGROUND

Salinity is a major abiotic stress that limits the growth, productivity, and geographical distribution of plants. A comparative proteomics and gene expression analysis was performed to better understand salinity tolerance mechanisms in chickpea.

RESULTS

Ten days of NaCl treatments resulted in the differential expression of 364 reproducible spots in seedlings of two contrasting chickpea genotypes, Flip 97-43c (salt tolerant, T1) and Flip 97-196c (salt susceptible, S1). Notably, after 3 days of salinity, 80% of the identified proteins in T1 were upregulated, while only 41% in S2 had higher expression than the controls. The proteins were classified into eight functional categories, and three groups of co-expression profile. The second co-expressed group of proteins had higher and/or stable expression in T1, relative to S2, suggesting coordinated regulation and the importance of some processes involved in salinity acclimation. This group was mainly enriched in proteins associated with photosynthesis (39%; viz. chlorophyll a-b binding protein, oxygen-evolving enhancer protein, ATP synthase, RuBisCO subunits, carbonic anhydrase, and fructose-bisphosphate aldolase), stress responsiveness (21%; viz. heat shock 70 kDa protein, 20 kDa chaperonin, LEA-2 and ascorbate peroxidase), and protein synthesis and degradation (14%; viz. zinc metalloprotease FTSH 2 and elongation factor Tu). Thus, the levels and/or early and late responses in the activation of targeted proteins explained the variation in salinity tolerance between genotypes. Furthermore, T1 recorded more correlations between the targeted transcripts and their corresponding protein expression profiles than S2.

CONCLUSIONS

This study provides insight into the proteomic basis of a salt-tolerance mechanism in chickpea, and offers unexpected and poorly understood molecular resources as reliable starting points for further dissection.

Salt-stress induced proteomic changes of two contrasting alfalfa cultivars during germination stage

BACKGROUND

Alfalfa (Medicago sativa L.), the primary forage crop throughout the world, is sensitive to salt stress during the germination stage. To investigate the response of alfalfa to salt stress, a comprehensive proteomic analysis was performed comparing alfalfa cultivars that differ in salinity tolerance in the early seedling.

RESULTS

Five cultivars were examined for salt tolerance, and the most salt-tolerant cultivar, ZhongmuNo.3, and the most salt-sensitive cultivar, Daxiyang, were compared in terms of their physiological and proteomic responses. The two alfalfa cultivars seeds were exposed to 0 mmolL^-1 or 200 mmolL^-1 NaCl salt treatment for 10 days. Salt stress significantly reduced young seedling growth and the cotyledons' chlorophyll content; meanwhile, it increased the cotyledons' H₂ O₂ and malondialdehyde (MDA) levels, all of which were less adversely affected in ZhongmuNo.3 than in Daxiyang. A total of 51 spots (24 and 27 protein spots in the salt-sensitive and salt-tolerant cultivars, respectively) were identified as significantly differentially expressed using two-dimensional electrophoresis analysis. The proteins that were associated with salt tolerance included antioxidants/detoxifying enzymes, molecular chaperones, energy metabolic enzymes, a secondary metabolic enzyme, and pathogenesis-related proteins.

CONCLUSIONS

Under salt stress, ZhongmuNo.3 possessed a higher capacity for reactive oxygen species (ROS) scavenging, a more abundant energy supply, and stronger photosynthesis than the salt-sensitive cultivar Daxiyang, and these physiological processes may be the primary contributors to salt tolerance in ZhongmuNo.3. These advanced proteome data expand our knowledge of the physiology of the response of alfalfa to salt stress, providing a potentially valuable foundation for molecular breeding to enhance salt tolerance. © 2018 Society of Chemical Industry.

Proteomic analysis reveals response of differential wheat (Triticum aestivum L.) genotypes to oxygen deficiency stress

BACKGROUND

Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. salt stress, drought stress, heat stress and waterlogging stress). However, only a few proteins related to primary metabolism and signal transduction, such as UDP - glucose dehydrogenase, UGP, beta glucosidases, were reported to response to waterlogging stress in wheat. The differentially expressed proteins between genotypes of wheat in response to waterlogging are less-defined. In this study, two wheat genotypes, one is sensitive to waterlogging stress (Seri M82, named as S) and the other is tolerant to waterlogging (CIGM90.863, named as T), were compared in seedling roots under hypoxia conditions to evaluate the different responses at proteomic level.

RESULTS

A total of 4560 proteins were identified and the number of differentially expressed proteins (DEPs) were 361, 640, 788 in S and 33, 207, 279 in T in 1, 2, 3 days, respectively. These DEPs included 270 common proteins, 681 S-specific and 50 T-specific proteins, most of which were misc., protein processing, DNA and RNA processing, amino acid metabolism and stress related proteins induced by hypoxia. Some specific proteins related to waterlogging stress, including acid phosphatase, oxidant protective enzyme, S-adenosylmethionine synthetase 1, were significantly different between S and T. A total of 20 representative genes encoding DEPs, including 7 shared DEPs and 13 cultivar-specific DEPs, were selected for further RT-qPCR analysis. Fourteen genes showed consistent dynamic expression patterns at mRNA and protein levels.

CONCLUSIONS

Proteins involved in primary metabolisms and protein processing were inclined to be affected under hypoxia stress. The negative effects were more severe in the sensitive genotype. The expression patterns of some specific proteins, such as alcohol dehydrogenases and S-adenosylmethionine synthetase 1, could be applied as indexes for improving the waterlogging tolerance in wheat. Some specific proteins identified in this study will facilitate the subsequent protein function validation and biomarker development.

Comparative proteomic analysis of salt-responsive proteins in canola roots by 2-DE and MALDI-TOF MS

Salinity stress is a major abiotic stress that affects plant growth and limits crop production. Roots are the primary site of salinity perception, and salt sensitivity in roots limits the productivity of the entire plant. To better understand salt stress responses in canola, we performed a comparative proteomic analysis of roots from the salt-tolerant genotype Safi-7 and the salt-sensitive genotype Zafar. Plants were exposed to 0, 150, and 300 mM NaCl. Our physiological and morphological observations confirmed that Safi-7 was more salt-tolerant than Zafar. The root proteins were separated by two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry was applied to identify proteins regulated in response to salt stress. We identified 36 and 25 protein spots whose abundance was significantly affected by salt stress in roots of plants from the tolerant and susceptible genotype, respectively. Functional classification analysis revealed that the differentially expressed proteins from the tolerant genotype could be assigned to 14 functional categories, while those from the susceptible genotype could be classified into 9 functional categories. The most significant differences concerned proteins involved in glycolysis (Glyceraldehyde-3-phosphate dehydrogenase, Fructose-bisphosphate aldolase, Phosphoglycerate kinase 3), stress (heat shock proteins), Redox regulation (Glutathione S-transferase DHAR1, L-ascorbate peroxidase), energy metabolism (ATP synthase subunit B), and transport (V-type proton ATPase subunit B1) which were increased only in the tolerant line under salt stress. Our results provide the basis for further elucidating the molecular mechanisms of salt-tolerance and will be helpful for breeding salt-tolerant canola cultivars.

Comparative Proteomic Analysis Reveals That Antioxidant System and Soluble Sugar Metabolism Contribute to Salt Tolerance in Alfalfa ( Medicago sativa L.) Leaves

Soil salinity poses a serious threat to alfalfa ( Medicago sativa L.) productivity. To characterize the molecular mechanisms of salinity tolerance in Medicago, the comparative proteome of leaves from Medicago sativa cv. Zhongmu No.1 (ZM1, salt-tolerant) and Medicago truncatula cv. Jemalong A17 (A17, salt-sensitive) was performed using the iTRAQ approach. A total of 438 differentially expressed proteins (DEPs) were identified, among which 282 and 120 DEPs were specific to A17 and ZM1, respectively. In salt-tolerant ZM1, key DEPs were primarily enriched in antioxidant system, starch and sucrose metabolism, and secondary metabolism. ZM1 possessed a greater ability to remove reactive oxygen species and methylglyoxal under salt stress, as demonstrated by enhancement of the antioxidant system and secondary metabolism. Moreover, ZM1 orchestrated starch and sucrose metabolism to accumulate various soluble sugars (sucrose, maltose, glucose, and trehalose), which in turn facilitate osmotic homeostasis. Salt stress dramatically inhibited photosynthesis of A17 due to the downregulation of the light-harvesting complex and photosystem II related protein. Quantitative analyses of photochemical efficiency, antioxidant enzyme activities, hydrogen peroxide, malondialdehyde, and soluble sugar contents were consistent with the alterations predicted on the basis of DEP functions. These results shed light on our understanding of the mechanisms underlying the salt tolerance of alfalfa.

Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress

The overall health of a plant is constantly affected by the changing and hostile environment. Due to climate change and the farming pattern of rice (Oryza sativa) and rapeseed (Brassica napus L.), stress from waterlogging poses a serious threat to productivity assurance and the yield of rapeseed in China's Yangtze River basin. In order to improve our understanding of the complex mechanisms behind waterlogging stress and identify waterlogging-responsive proteins, we firstly conducted iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomic analysis of rapeseed roots under waterlogging treatments, for both a tolerant cultivar ZS9 and sensitive cultivar GH01. A total of 7736 proteins were identified by iTRAQ, of which several hundred showed different expression levels, including 233, 365, and 326 after waterlogging stress for 4H, 8H, and 12H in ZS9, respectively, and 143, 175, and 374 after waterlogging stress for 4H, 8H, and 12H in GH01, respectively. For proteins repeatedly identified at different time points, gene ontology (GO) cluster analysis suggested that the responsive proteins of the two cultivars were both enriched in the biological process of DNA-dependent transcription and the oxidation⁻reduction process, and response to various stress and hormone stimulus, while different distribution frequencies in the two cultivars was investigated. Moreover, overlap proteins with similar or opposite tendencies of fold change between ZS9 and GH01 were observed and clustered based on the different expression ratios, suggesting the two genotype cultivars exhibited diversiform molecular mechanisms or regulation pathways in their waterlogging stress response. The following qRT-PCR (quantitative real-time polymerase chain reaction) results verified the candidate proteins at transcription levels, which were prepared for further research. In conclusion, proteins detected in this study might perform different functions in waterlogging responses and would provide information conducive to better understanding adaptive mechanisms under environmental stresses.

Molecular response of canola to salt stress: insights on tolerance mechanisms

Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.

iTRAQ-Based Comparative Proteomic Analysis of Seedling Leaves of Two Upland Cotton Genotypes Differing in Salt Tolerance

Cotton yields are greatly reduced under high salinity stress conditions, although cotton is considered a moderately salt-tolerant crop. Understanding at the molecular level how cotton responds to salt stress will help in developing salt tolerant varieties. Here, we combined physiological analysis with isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics of seedling leaves of 2 genotypes differing in salinity tolerance to 200 mM (18.3 dS/m) NaCl stress. Salt stress produced significant stress symptoms in the sensitive genotype Nan Dan Ba Di Da Hua (N), including lower relative water and chlorophyll contents and higher relative electrolyte leakage and Na⁺/K⁺ ratio in leaf samples, compared with those in the tolerant genotype Earlistaple 7 (Z). A total of 58 differentially abundant salt-responsive proteins were identified. Asp-Glu-Ala-Asp (DEAD)-box ATP-dependent RNA helicase 3 and protochlorophyllide reductase were markedly suppressed after salt treatment, whereas the phosphate-related differentially abundant proteins (DAPs) phosphoethanolamine N-methyltransferase 1 and 14-3-3-like protein E were induced, and all these proteins may play significant roles in salt stress. Twenty-nine salt-responsive proteins were also genotype specific, and 62.1 and 27.6% of these were related to chloroplast and defense responses, respectively. Based on the Arabidopsis thaliana protein interaction database, orthologs of 25 proteins showed interactions in Arabidopsis, and among these, a calmodulin protein was predicted to have 212 functional partners. In addition, the Golgi apparatus and calcium may be important for salt secretion in cotton. Through integrative proteome and transcriptome analysis, 16 DAPs were matched to differentially expressed genes and verified using qRT-PCR. On the basis of these findings, we proposed that some proteins related to chloroplast, ATP, ribosomal, and phosphate metabolism as well as to the Golgi apparatus and calcium may play key roles in the short-term salt stress response of cotton seedling leaves.

Comparative Proteomics Reveals that Phosphorylation of β Carbonic Anhydrase 1 Might be Important for Adaptation to Drought Stress in Brassica napus

Little is known about the mechanism of drought tolerance in rapeseed (Brassica napus L.). In this study, different morphological and physiological responses to drought stress were studied in three rapeseed cultivars. For the cultivar 2AF009 with high drought tolerance, comparative proteomic analyses were conducted to determine the molecular mechanism behind. Approximately 138 differentially abundant proteins (DAPs) and 1232 phosphoproteins containing 4469 phosphopeptides were identified. Furthermore, 337 phosphoproteins containing 547 phosphorylation sites demonstrated significant changes. These drought-responsive DAPs and phosphoproteins were mainly involved in signal transduction, photosynthesis, and glutathione-ascorbate metabolism. Notably, 9 DAPs were also identified as drought-responsive phosphoproteins, especially beta carbonic anhydrase 1 (βCA1), which was represented by eight distinct protein spots with different abundant levels during drought stress. Tyr207 phosphorylated site of βCA1 was down-regulated at the phosphorylation level during drought stress, which was also located in the substrate-binding active region of three-dimensional (3D) structure. Moreover, drought stress inhibited CA activity. We concluded that Tyr207 was the most likely phosphorylation target affecting the enzyme activity, and phosphorylation of βCA1 might be important for the response to drought stress in rapeseed. The study provided a new clue for the drought tolerance mechanism in B.napus.

Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy

The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level.

SIGNIFICANCE

Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.

Salt-stress-responsive chloroplast proteins in Brassica juncea genotypes with contrasting salt tolerance and their quantitative PCR analysis

Brassica juncea is mainly cultivated in the arid and semi-arid regions of India where its production is significantly affected by soil salinity. Adequate knowledge of the mechanisms underlying the salt tolerance at sub-cellular levels must aid in developing the salt-tolerant plants. A proper functioning of chloroplasts under salinity conditions is highly desirable to maintain crop productivity. The adaptive molecular mechanisms offered by plants at the chloroplast level to cope with salinity stress must be a prime target in developing the salt-tolerant plants. In the present study, we have analyzed differential expression of chloroplast proteins in two Brassica juncea genotypes, Pusa Agrani (salt-sensitive) and CS-54 (salt-tolerant), under the effect of sodium chloride. The chloroplast proteins were isolated and resolved using 2DE, which facilitated identification and quantification of 12 proteins that differed in expression in the salt-tolerant and salt-sensitive genotypes. The identified proteins were related to a variety of chloroplast-associated molecular processes, including oxygen-evolving process, PS I and PS II functioning, Calvin cycle and redox homeostasis. Expression analysis of genes encoding differentially expressed proteins through real time PCR supported our findings with proteomic analysis. The study indicates that modulating the expression of chloroplast proteins associated with stabilization of photosystems and oxidative defence plays imperative roles in adaptation to salt stress.

Role of Proteomics in Crop Stress Tolerance

Plants often experience various biotic and abiotic stresses during their life cycle. The abiotic stresses include mainly drought, salt, temperature (low/high), flooding and nutritional deficiency/excess which hamper crop growth and yield to a great extent. In view of a projection 50% of the crop loss is attributable to abiotic stresses. However, abiotic stresses cause a myriad of changes in physiological, molecular and biochemical processes operating in plants. It is now widely reported that several proteins respond to these stresses at pre- and post-transcriptional and translational levels. By knowing the role of these stress inducible proteins, it would be easy to comprehensively expound the processes of stress tolerance in plants. The proteomics study offers a new approach to discover proteins and pathways associated with crop physiological and stress responses. Thus, studying the plants at proteomic levels could help understand the pathways involved in stress tolerance. Furthermore, improving the understanding of the identified key metabolic proteins involved in tolerance can be implemented into biotechnological applications, regarding recombinant/transgenic formation. Additionally, the investigation of identified metabolic processes ultimately supports the development of antistress strategies. In this review, we discussed the role of proteomics in crop stress tolerance. We also discussed different abiotic stresses and their effects on plants, particularly with reference to stress-induced expression of proteins, and how proteomics could act as vital biotechnological tools for improving stress tolerance in plants.

Silicon Mitigates Salinity Stress by Regulating the Physiology, Antioxidant Enzyme Activities, and Protein Expression in Capsicum annuum 'Bugwang'

Silicon- (Si-) induced salinity stress resistance was demonstrated at physiological and proteomic levels in Capsicum annuum for the first time. Seedlings of C. annuum were hydroponically treated with NaCl (50 mM) with or without Si (1.8 mM) for 15 days. The results illustrated that saline conditions significantly reduced plant growth and biomass and photosynthetic parameters and increased the electrolyte leakage potential, lipid peroxidation, and hydrogen peroxide level. However, supplementation of Si allowed the plants to recover from salinity stress by improving their physiology and photosynthesis. During salinity stress, Si prevented oxidative damage by increasing the activities of antioxidant enzymes. Furthermore, Si supplementation recovered the nutrient imbalance that had occurred during salinity stress. Additionally, proteomic analysis by two-dimensional gel electrophoresis (2DE) followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) revealed that Si treatment upregulated the accumulation of proteins involved in several metabolic processes, particularly those associated with nucleotide binding and transferase activity. Moreover, Si modulated the expression of vital proteins involved in ubiquitin-mediated nucleosome pathway and carbohydrate metabolism. Overall, the results illustrate that Si application induced resistance against salinity stress in C. annuum by regulating the physiology, antioxidant metabolism, and protein expression.

Proteomics, photosynthesis and salt resistance in crops: An integrative view

Salinity is a stressful condition that causes a significant decrease in crop production worldwide. Salt stress affects several photosynthetic reactions, including the modulation of several important proteins. Despite these effects, few molecular-biochemical markers have been identified and evaluated for their importance in improving plant salt resistance. Proteomics is a powerful tool that allows the analysis of multigenic events at the post-translational level that has been widely used to evaluate protein modulation changes in plants exposed to salt stress. However, these studies are frequently fragmented and the results regarding photosynthesis proteins in response to salinity are limited. These constraints could be related to the low number of important photosynthetic proteins differently modulated in response to salinity, as has been commonly revealed by conventional proteomics. In this review, we present an evaluation and perspective on the integrated application of proteomics for the identification of photosynthesis proteins to improve salt resistance. We propose the use of phospho-, thiol- and redox-proteomics, associated with the utilization of isolated chloroplasts or photosynthetic sub-organellar components. This strategy may allow the characterization of essential proteins, providing a better understanding of photosynthesis regulation. Furthermore, this may contribute to the selection of molecular markers to improve salt resistance in crops.

Proteome Dynamics and Physiological Responses to Short-Term Salt Stress in Brassica napus Leaves

Salt stress limits plant growth and crop productivity and is an increasing threat to agriculture worldwide. In this study, proteomic and physiological responses of Brassica napus leaves under salt stress were investigated. Seedlings under salt treatment showed growth inhibition and photosynthesis reduction. A comparative proteomic analysis of seedling leaves exposed to 200 mM NaCl for 24 h, 48 h and 72 h was conducted. Forty-four protein spots were differentially accumulated upon NaCl treatment and 42 of them were identified, including several novel salt-responsive proteins. To determine the functional roles of these proteins in salt adaptation, their dynamic changes in abundance were analyzed. The results suggested that the up-accumulated proteins, which were associated with protein metabolism, damage repair and defense response, might contribute to the alleviation of the deleterious effect of salt stress on chlorophyll biosynthesis, photosynthesis, energy synthesis and respiration in Brassica napus leaves. This study will lead to a better understanding of the molecular basis of salt stress adaptation in Brassica napus and provides a basis for genetic engineering of plants with improved salt tolerance in the future.

Elucidation of Cross-Talk and Specificity of Early Response Mechanisms to Salt and PEG-Simulated Drought Stresses in Brassica napus Using Comparative Proteomic Analysis

To understand the cross-talk and specificity of the early responses of plants to salt and drought, we performed physiological and proteome analyses of Brassica napus seedlings pretreated with 245 mM NaCl or 25% polyethylene glycol (PEG) 6000 under identical osmotic pressure (-1.0 MPa). Significant decreases in water content and photosynthetic rate and excessive accumulation of compatible osmolytes and oxidative damage were observed in response to both stresses. Unexpectedly, the drought response was more severe than the salt response. We further identified 45 common differentially expressed proteins (DEPs), 143 salt-specific DEPs and 160 drought-specific DEPs by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The proteome quantitative data were then confirmed by multiple reaction monitoring (MRM). The differences in the proteomic profiles between drought-treated and salt-treated seedlings exceeded the similarities in the early stress responses. Signal perception and transduction, transport and membrane trafficking, and photosynthesis-related proteins were enriched as part of the molecular cross-talk and specificity mechanism in the early responses to the two abiotic stresses. The Ca²⁺ signaling, G protein-related signaling, 14-3-3 signaling pathway and phosphorylation cascades were the common signal transduction pathways shared by both salt and drought stress responses; however, the proteins with executive functions varied. These results indicate functional specialization of family proteins in response to different stresses, i.e., CDPK21, TPR, and CTR1 specific to phosphorylation cascades under early salt stress, whereas STN7 and BSL were specific to phosphorylation cascades under early drought stress. Only the calcium-binding EF-hand family protein and ZKT were clearly identified as signaling proteins that acted as cross-talk nodes for salt and drought signaling pathways. Our study provides new clues and insights for developing strategies to improve the tolerance of crops to complex, multiple environmental stresses.

Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective

Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress

Drought is one of the most widespread stresses leading to retardation of plant growth and development. We examined proteome changes of an important oil seed crop, canola (Brassica napus L.), under drought stress over a 14-day period. Using iTRAQ LC-MS/MS, we identified 1976 proteins expressed during drought stress. Among them, 417 proteins showed significant changes in abundance, and 136, 244, 286, and 213 proteins were differentially expressed in the third, seventh, 10th, and 14th day of stress, respectively. Functional analysis indicated that the number of proteins associated with metabolism, protein folding and degradation, and signaling decreased, while those related to energy (photosynthesis), protein synthesis, and stress and defense increased in response to drought stress. The seventh and 10th-day profiles were similar to each other but with more post-translational modifications (PTMs) at day 10. Interestingly, 181 proteins underwent PTMs; 49 of them were differentially changed in drought-stressed plants, and 33 were observed at the 10th day. Comparison of protein expression changes with those of gene transcription showed a positive correlation in B. napus, although different patterns between transcripts and proteins were observed at each time point. Under drought stress, most protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to protein diversity and functions.

Proteomic and biochemical responses of canola (Brassica napus L.) exposed to salinity stress and exogenous lipoic acid

To evaluate the mitigating effects of exogenous lipoic acid (LA) on NaCl toxicity, proteomic, biochemical and physiological changes were investigated in the leaves of canola (Brassica napus L.) seedlings. Salinity stress decreased the growth parameters and contents of ascorbate (AsA) and glutathione (GSH), and increased the contents of malondialdehyde (MDA), proline, cysteine and the activities of antioxidant enzymes such as superoxide dismutase (SOD), guaiacol peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX). The foliar application of LA alleviated the toxic effects of salinity stress on canola seedlings and notably decreased MDA content and increased growth parameters, cysteine content, and activities of CAT and POD. In the proteomic analyses, total proteins from the leaves of control, LA, NaCl and NaCl+LA treated-seedlings were separated using two-dimensional gel electrophoresis (2-DE). A total of 28 proteins were differentially expressed. Of these, 21 proteins were successfully identified by MALDI-TOF/TOF MS. These proteins had functions related to photosynthesis, stress defense, energy metabolism, signal transduction, protein folding and stabilization indicating that LA might play important roles in salinity through the regulation of photosynthesis, stress defense and signal transduction related proteins. The proteomic findings have provided new insight to reveal the effect of LA on salinity stress for the first time.

Proteomic analysis of canola root inoculated with bacteria under salt stress

Plant-growth promoting bacteria can ameliorate the negative effects of salt stress on canola. To better understand the role of bacteria in canola under salt stress, salt-sensitive (Sarigol) and salt-tolerant (Hyola308) cultivars were inoculated with Pseudomonas fluorescens and protein profiles of roots were compared. Bacterial inoculation increased the dry weight and length of canola roots under salt stress. Using a gel-free proteomic technique, 55 commonly changed proteins were identified in Sarigol and Hyola308 roots inoculated with bacteria under salt stress. In both canola cultivars, proteins related to amino acid metabolism and tricarboxylic acid cycle were affected. Hierarchical cluster analysis divided the identified proteins into three clusters. Proteins related to Clusters II and III, which were secretion-associated RAS super family 1, dynamin-like protein, and histone, were increased in roots of both Sarigol and Hyola308 inoculated with bacteria under salt stress. Based on pathway mapping, proteins related to amino acid metabolism and the tricarboxylic acid cycle significantly changed in canola cultivars inoculated with or without bacteria under salt stress. These results suggest that bacterial inoculation of canola roots increases tolerance to salt stress by proteins related to energy metabolism and cell division.

BIOLOGICAL SIGNIFICANCE

Plant-growth promoting bacteria as an emerging aid can ameliorate the negative effect of salt stress on canola. To understand the role of bacteria in canola under salt stress, salt sensitive Sarigol and tolerant Hyola308 cultivars were used. Dry weight and length of canola root were improved by inoculation of bacteria under salt stress. Using gel-free proteomic technique, 55 commonly changed proteins identified in Sarigol and Hyola308 inoculated with bacteria under salt stress. In both canola cultivars, the number of proteins related to amino acid metabolism and tricarboxylic acid cycle was more than other categories with higher change in protein abundance. Hierarchical cluster analysis divided into 3 clusters. Cluster II including secretion-associated RAS super family 1 and dynamin-like protein and Cluster III including histones H2A were increased by bacterial inoculation in both cultivars. Furthermore, pathway mapping highlighted the importance of S-denosylmethionine synthetase and malate dehydrogenase that decreased in canola inoculated with bacteria under salt stress. These results suggest that bacterial inoculation helps the canola to endure salt stress by modulating the proteins related to energy metabolism and cell division.

Effect of salinity stress on plants and its tolerance strategies: a review

The environmental stress is a major area of scientific concern because it constraints plant as well as crop productivity. This situation has been further worsened by anthropogenic activities. Therefore, there is a much scientific saddle on researchers to enhance crop productivity under environmental stress in order to cope with the increasing food demands. The abiotic stresses such as salinity, drought, cold, and heat negatively influence the survival, biomass production and yield of staple food crops. According to an estimate of FAO, over 6% of the world's land is affected by salinity. Thus, salinity stress appears to be a major constraint to plant and crop productivity. Here, we review our understanding of salinity impact on various aspects of plant metabolism and its tolerance strategies in plants.

Proteomic analysis of changes in the Kandelia candel chloroplast proteins reveals pathways associated with salt tolerance

The plant chloroplast is one of the most sensitive organelles in response to salt stress. Chloroplast proteins extracted from seedling leaves were separated by two-dimensional gel electrophoresis (2-DE). More than 600 protein spots could be distinguished on each gel. Fifty-eight differentially expressed protein spots were detected, of which 46 could be identified through matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). These proteins were found to be involved in multiple aspects of chloroplast metabolism pathways such as photosynthesis, ATP synthesis, detoxification and antioxidation processes, nitrogen assimilation and fixation, protein metabolism, and tetrapyrrole biosynthesis. The results indicated that K. candel could withstand up to 500 mM NaCl stress for a measured period of 3 days, by maintaining normal or high photosynthetic electron transfer efficiency and an only slightly stimulated Calvin cycle. Meanwhile, we found that ROS scavenging, nitrogen assimilation, protein degradation and chaperone function in chloroplasts were also of importance for salt tolerance of K. candel. The ultrastructural and physiological data agree with chloroplast proteome results. These findings allow further exploration of our knowledge on salt adaptation in woody halophytes and may contribute to the development of more salt-tolerant plants in the future.

Physiological and proteomic analysis in chloroplasts of Solanum lycopersicum L. under silicon efficiency and salinity stress

Tomato plants often grow in saline environments in Mediterranean countries where salt accumulation in the soil is a major abiotic stress that limits its productivity. However, silicon (Si) supplementation has been reported to improve tolerance against several forms of abiotic stress. The primary aim of our study was to investigate, using comparative physiological and proteomic approaches, salinity stress in chloroplasts of tomato under silicon supplementation. Tomato seedlings (Solanum lycopersicum L.) were grown in nutrient media in the presence or absence of NaCl and supplemented with silicon for 5 days. Salinity stress caused oxidative damage, followed by a decrease in silicon concentrations in the leaves of the tomato plants. However, supplementation with silicon had an overall protective effect against this stress. The major physiological parameters measured in our studies including total chlorophyll and carotenoid content were largely decreased under salinity stress, but were recovered in the presence of silicon. Insufficient levels of net-photosynthesis, transpiration and stomatal conductance were also largely improved by silicon supplementation. Proteomics analysis of chloroplasts analyzed by 2D-BN-PAGE (second-dimensional blue native polyacrylamide-gel electrophoresis) revealed a high sensitivity of multiprotein complex proteins (MCPs) such as photosystems I (PSI) and II (PSII) to the presence of saline. A significant reduction in cytochrome b6/f and the ATP-synthase complex was also alleviated by silicon during salinity stress, while the complex forms of light harvesting complex trimers and monomers (LHCs) were rapidly up-regulated. Our results suggest that silicon plays an important role in moderating damage to chloroplasts and their metabolism in saline environments. We therefore hypothesize that tomato plants have a greater capacity for tolerating saline stress through the improvement of photosynthetic metabolism and chloroplast proteome expression after silicon supplementation.

Salt stress-induced alterations in the root proteome of Amaranthus cruentus L

Salt stress is one of the major factors limiting crop productivity worldwide. Amaranth is a highly nutritious pseudocereal with remarkable nutraceutical properties; it is also a stress-tolerant plant, making it an alternative crop for sustainable food production in semiarid conditions. A two-dimensional electrophoresis gel coupled with a liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) approach was applied in order to analyze the changes in amaranth root protein accumulation in plants subjected to salt stress under hydroponic conditions during the osmotic phase (1 h), after recovery (24 h), and during the ionic phase of salt stress (168 h). A total of 101 protein spots were differentially accumulated in response to stress, in which 77 were successfully identified by LC-MS/MS and a database search against public and amaranth transcriptome databases. The resulting proteins were grouped into different categories of biological processes according to Gene Ontology. The identification of several protein isoforms with a change in pI and/or molecular weight reveals the importance of the salt-stress-induced posttranslational modifications in stress tolerance. Interestingly stress-responsive proteins unique to amaranth, for example, Ah24, were identified. Amaranth is a stress-tolerant alternative crop for sustainable food production, and the understanding of amaranth's stress tolerance mechanisms will provide valuable input to improve stress tolerance of other crop plants.

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.

Proteomic analysis of salt-responsive proteins in the leaves of mangrove Kandelia candel during short-term stress

Salt stress is a major abiotic stress that limits crop productivity in many regions of the world. A comparative proteomic approach to identify salt stress-responsive proteins and to understand the molecular mechanisms was carried out in the woody halophyte Kandelia candel. Four-leaf-old K. candel seedlings were exposed to 150 (control), 300, 450, and 600 mM NaCl for 3 days. Proteins extracted from the leaves of K. candel seedlings were separated by two-dimensional gel electrophoresis (2-DE). More than 900 protein spots were detected on each gel, and 53 differentially expressed protein spots were located with at least two-fold differences in abundance on 2-DE maps, of which 48 were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). The results showed that K. candel could withstand up to 450 mM NaCl stress by up-regulating proteins that are mainly involved in photosynthesis, respiration and energy metabolism, Na(+) compartmentalization, protein folding and assembly, and signal transduction. Physiological data, including superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR) activities, hydrogen peroxide (H2O2) and superoxide anion radicals (O2(-)) contents, as well as Na(+) content and K(+)/Na(+) ratios all correlated well with our proteomic results. This study provides new global insights into woody halophyte salt stress responses. Identification of differentially expressed proteins promotes better understanding of the molecular basis for salt stress reduction in K. candel.

Physiology and proteome responses of two contrasting rice mutants and their wild type parent under salt stress conditions at the vegetative stage

Salinity is one of the major environmental limiting factors that affects growth and productivity of rice (Oryza sativa L.) worldwide. Rice is among the most sensitive crops to salinity, especially at early vegetative stages. In order to get a better understanding of molecular pathways affected in rice mutants showing contrasting responses to salinity, we exploited the power of 2-DE based proteomics to explore the proteome changes associated with salt stress response. Our physiological observations showed that standard evaluation system (SES) scores, Na+ and K+ concentrations in shoots and Na+/K+ ratio were significantly different in contrasting mutants under salt stress condition. Proteomics analysis showed that, out of 854 protein spots which were reproducibly detected, 67 protein spots showed significant responses to salt stress. The tandem mass spectrometry analysis of these significantly differentially accumulated proteins resulted in identification of 34 unique proteins. These proteins are involved in various molecular processes including defense to oxidative stresses, metabolisms, photosynthesis, protein synthesis and processing, signal transduction. Several of the identified proteins were emerged as key participants in salt stress tolerance. The possible implication of salt responsive proteins in plant adaptation to salt stress is discussed.

Salt-stress induced changes in the leaf proteome of diploid and tetraploid mandarins with contrasting Na+ and Cl- accumulation behaviour

To understand the genotypic variation of citrus to mild salt stress, a proteomic approach has been carried out in parallel on two citrus genotypes ('Cleopatra' and 'Willow leaf' mandarins), which differ for Na(+) and Cl(-) accumulation, and their cognate autotetraploids (4×). Using two-dimensional electrophoresis approximately 910 protein spots were reproducibly detected in control and salt-stressed leaves of all genotypes. Among them, 44 protein spots showing significant variations at least in one genotype were subjected to mass spectrometry analysis for identification. Salt-responsive proteins were involved in several functions, including photosynthetic processes, ROS scavenging, stress defence, and signalling. Genotype factors affect the salt-responsive pattern, especially that of carbon metabolism. The no ion accumulator 'Cleopatra' mandarin genotype showed the highest number of salt-responsive proteins, and up-regulation of Calvin cycle-related proteins. Conversely the ion accumulator 'Willow leaf' mandarin showed high levels of several photorespiration-related enzymes. A common set of proteins (twelve spots) displayed higher levels in salt-stressed leaves of 2× and 4× 'Cleopatra' and 4× 'Willow leaf' mandarin. Interestingly, antioxidant enzymes and heat shock proteins showed higher constitutive levels in 4× 'Cleopatra' mandarin and 4× 'Willow leaf' mandarin compared with the cognate 2× genotype. This work provides for the first time information on the effect of 8 weeks of salt stress on citrus genotypes contrasting for ion accumulation and their cognate autotetraploids. Results underline that genetic factors have a predominant effect on the salt response, although a common stress response independent from genotype was also found.