Salt and genotype impact on plant physiology and root proteome variations in tomato

Response of photosynthetic characteristics and antioxidant system in the leaves of safflower to NaCl and NaHCO3

KEY MESSAGE

Compared with NaCl, NaHCO3 caused more serious oxidative damage and photosynthesis inhibition in safflower by down-regulating the expression of related genes. Salt-alkali stress is one of the important factors that limit plant growth. NaCl and sodium bicarbonate (NaHCO3) are neutral and alkaline salts, respectively. This study investigated the physiological characteristics and molecular responses of safflower (Carthamus tinctorius L.) leaves treated with 200 mmol L-1 of NaCl or NaHCO3. The plants treated with NaCl treatment were less effective at inhibiting the growth of safflower, but increased the content of malondialdehyde (MDA) in leaves. Meanwhile, safflower alleviated stress damage by increasing proline (Pro), soluble protein (SP), and soluble sugar (SS). Both fresh weight and dry weight of safflower was severely decreased when it was subjected to NaHCO3 stress, and there was a significant increase in the permeability of cell membranes and the contents of osmotic regulatory substances. An enrichment analysis of the differentially expressed genes (DEGs) using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes identified significant enrichment of photosynthesis and pathways related to oxidative stress. Furthermore, a weighted gene co-expression network analysis (WGCNA) showed that the darkgreen module had the highest correlation with photosynthesis and oxidative stress traits. Large numbers of transcription factors, primarily from the MYB, GRAS, WRKY, and C2H2 families, were predicted from the genes within the darkgreen module. An analysis of physiological indicators and DEGs, it was found that under saline-alkali stress, genes related to chlorophyll synthesis enzymes were downregulated, while those related to degradation were upregulated, resulting in inhibited chlorophyll biosynthesis and decreased chlorophyll content. Additionally, NaCl and NaHCO3 stress downregulated the expression of genes related to the Calvin cycle, photosynthetic antenna proteins, and the activity of photosynthetic reaction centers to varying degrees, hindering the photosynthetic electron transfer process, suppressing photosynthesis, with NaHCO3 stress causing more pronounced adverse effects. In terms of oxidative stress, the level of reactive oxygen species (ROS) did not change significantly under the NaCl treatment, but the contents of hydrogen peroxide and the rate of production of superoxide anions increased significantly under NaHCO3 stress. In addition, treatment with NaCl upregulated the levels of expression of the key genes for superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), the ascorbate-glutathione cycle, and the thioredoxin-peroxiredoxin pathway, and increased the activity of these enzymes, thus, reducing oxidative damage. Similarly, NaHCO3 stress increased the activities of SOD, CAT, and POD and the content of ascorbic acid and initiated the glutathione-S-transferase pathway to remove excess ROS but suppressed the regeneration of glutathione and the activity of peroxiredoxin. Overall, both neutral and alkaline salts inhibited the photosynthetic process of safflower, although alkaline salt caused a higher level of stress than neutral salt. Safflower alleviated the oxidative damage induced by stress by regulating its antioxidant system.

Transcriptome Analysis for Salt-Responsive Genes in Two Different Alfalfa (Medicago sativa L.) Cultivars and Functional Analysis of MsHPCA1

Alfalfa (Medicago sativa L.) is an important forage legume and soil salinization seriously affects its growth and yield. In a previous study, we identified a salt-tolerant variety 'Gongnong NO.1' and a salt-sensitive variety 'Sibeide'. To unravel the molecular mechanism involved in salt stress, we conducted transcriptomic analysis on these two cultivars grown under 0 and 250 mM NaCl treatments for 0, 12, and 24 h. Totals of 336, and 548 differentially expressed genes (DEGs) in response to NaCl were, respectively, identified in the 'Gongnong NO.1' and 'Sibeide' varieties. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analysis showed that the DEGs were classified in carbohydrate metabolism, energy production, transcription factor, and stress-associated pathway. Expression of MsHPCA1, encoding a putative H2O2 receptor, was responsive to both NaCl and H2O2 treatment. MsHPCA1 was localized in cell membrane and overexpression of MsHPCA1 in alfalfa increased salt tolerance and H2O2 content. This study will provide new gene resources for the improvement in salt tolerance in alfalfa and legume crops, which has important theoretical significance and potential application value.

Effects of Single and Combined Drought and Salinity Stress on the Root Morphological Characteristics and Root Hydraulic Conductivity of Different Winter Wheat Varieties

Water shortages and crop responses to drought and salt stress are related to the efficient use of water resources and are closely related to food security. In addition, PEG or NaCl stress alone affect the root hydraulic conductivity (Lpr). However, the effects of combined PEG and NaCl stress on Lpr and the differences among wheat varieties are unknown. We investigated the effects of combined PEG and NaCl stress on the root parameters, nitrogen (N) and carbon content, antioxidant enzymes, osmotic adjustment, changes in sodium and potassium, and root hydraulic conductivity of Yannong 1212, Heng 4399, and Xinmai 19. PEG and NaCl stress appreciably decreased the root length (RL), root surface area (RS), root volume (RV), K⁺ and N content in shoots and roots, and Lpr of the three wheat varieties, while the antioxidant enzyme activity, malondialdehyde (MDA), osmotic adjustment, nonstructural carbon and Na⁺ content in shoots and roots, etc., remarkably remained increased. Furthermore, the root hydraulic conductivity had the greatest positive association with traits such as RL, RS, and N and K⁺ content in the shoots of the three wheat varieties. Moreover, the RL/RS directly and actively determined the Lpr, and it had an extremely positive effect on the N content in the shoots of wheat seedlings. Collectively, most of the root characteristics in the wheat seedlings decreased under stress conditions, resulting in a reduction in Lpr. As a result, the ability to transport nutrients-especially N-from the roots to the shoots was affected. Therefore, our study provides a novel insight into the physiological mechanisms of Lpr.

A novel selection model based on multivariate methods and arbitrary genetic parameters: a case study on tomato families

BACKGROUND

Selection is one of the essential skills whereby breeders reduce the population size and increase the chance of success. Various selection methods with special applications have been developed. Superior genotypes are assessed according to interesting traits, including univariate, multivariate, phenotypic, genotypic, etc. METHODS: Mathematical calculation of the traits' importance based on the genetic makeup of investigated population (average degree of dominance/additive involved in the action of genes) and arbitrary genetic parameters is functional. In this paper, a general model for multivariate selection has been presented whereby the selection can be made for (a) more than one interesting trait, (b) the trait(s) with complex inheritance, (c) finding superior genotypes from among a large-scale population, (d) finding superior genotypes in segregating generations and (f) finding tolerant genotypes to stresses. This model is developed based on biometric concepts in four steps. MATLAB script is provided for the model, and users can easily apply that to identify the most suitable genotypes after data collection according to the breeding purposes.

RESULTS

The main features of this model are simplicity, precision, repeatability, and speed (improving several traits simultaneously). All the steps and the analysis of the results are explained step by step in a case study.

A comprehensive and conceptual overview of omics-based approaches for enhancing the resilience of vegetable crops against abiotic stresses

Abiotic stresses adversely affect the productivity and production of vegetable crops. The increasing number of crop genomes that have been sequenced or re-sequenced provides a set of computationally anticipated abiotic stress-related responsive genes on which further research may be focused. Knowledge of omics approaches and other advanced molecular tools have all been employed to understand the complex biology of these abiotic stresses. A vegetable can be defined as any component of a plant that is eaten for food. These plant parts may be celery stems, spinach leaves, radish roots, potato tubers, garlic bulbs, immature cauliflower flowers, cucumber fruits, and pea seeds. Abiotic stresses, such as deficient or excessive water, high temperature, cold, salinity, oxidative, heavy metals, and osmotic stress, are responsible for the adverse activity in plants and, ultimately major concern for decreasing yield in many vegetable crops. At the morphological level, altered leaf, shoot and root growth, altered life cycle duration and fewer or smaller organs can be observed. Likewise different physiological and biochemical/molecular processes are also affected in response to these abiotic stresses. In order to adapt and survive in a variety of stressful situations, plants have evolved physiological, biochemical, and molecular response mechanisms. A comprehensive understanding of the vegetable's response to different abiotic stresses and the identification of tolerant genotypes are essential to strengthening each vegetable's breeding program. The advances in genomics and next-generation sequencing have enabled the sequencing of many plant genomes over the last twenty years. A combination of modern genomics (MAS, GWAS, genomic selection, transgenic breeding, and gene editing), transcriptomics, and proteomics along with next-generation sequencing provides an array of new powerful approaches to the study of vegetable crops. This review examines the overall impact of major abiotic stresses on vegetables, adaptive mechanisms and functional genomic, transcriptomic, and proteomic processes used by researchers to minimize these challenges. The current status of genomics technologies for developing adaptable vegetable cultivars that will perform better in future climates is also examined.

Cold acclimation alleviates cold stress-induced PSII inhibition and oxidative damage in tobacco leaves

This study aimed to explore how cold acclimation (CA) modulates cold stress in tobacco leaves and reveal the relationship between CA and cold stress resistance, and the mechanism of CA-induced plant resistance to cold stress. This study examined the effects of CA treatment (at 8-10℃ for 2 d) on the cold tolerance of tobacco leaves under 4°C cold stress treatment using seedlings without CA treatment as the control (NA). In both CA and NA leaves, cold stress treatment resulted in a decrease in maximum photochemical efficiency of PSII (Fv/Fm), increase in relative variable fluorescence (VJ) at 2 ms on the standardized OJIP curve, inhibition of PSII activity, and impairment of electron transfer on the acceptor side. Besides increasing the malondialdehyde (MDA) content and electrolyte leakage rate, the cold stress exacerbated the degree of membrane peroxidation. The CA treatment also induced the accumulation of reactive oxygen species (ROS), including superoxide anion (O2·-) and H2O2, and increased the activities of antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbic acid peroxidase (APX). The CA treatment also enhanced the accumulation of soluble sugar (SS) and soluble protein (SP), cyclic electron flow (CEF), and the proportion of regulatory energy dissipation Y(NPQ). Moreover, CA+ cold stress treatment significantly reduced CEF and Y(NPQ) in tobacco leaves than under NA+ cold stress treatment, thus significantly alleviating the degree of PSII photoinhibition. In conclusion, CA treatment significantly alleviated PSII photoinhibition and oxidative damage in tobacco leaves under cold stress treatment. Improvement in cold resistance of tobacco leaves is associated with the induction of antioxidant enzyme activity, accumulation of osmoregulation substances, and initiation of photoprotective mechanisms.

Mechanism of [CO2] Enrichment Alleviated Drought Stress in the Roots of Cucumber Seedlings Revealed via Proteomic and Biochemical Analysis

Cucumber is one of the most widely cultivated greenhouse vegetables, and its quality and yield are threatened by drought stress. Studies have shown that carbon dioxide concentration ([CO₂]) enrichment can alleviate drought stress in cucumber seedlings; however the mechanism of this [CO₂] enrichment effect on root drought stress is not clear. In this study, the effects of different drought stresses (simulated with 0, 5% and 10% PEG 6000, i.e., no, moderate, and severe drought stress) and [CO₂] (400 μmol·mol^-1 and 800 ± 40 μmol·mol^-1) on the cucumber seedling root proteome were analyzed using the tandem mass tag (TMT) quantitative proteomics method. The results showed that after [CO₂] enrichment, 346 differentially accumulating proteins (DAPs) were found only under moderate drought stress, 27 DAPs only under severe drought stress, and 34 DAPs under both moderate and severe drought stress. [CO₂] enrichment promoted energy metabolism, amino acid metabolism, and secondary metabolism, induced the expression of proteins related to root cell wall and cytoskeleton metabolism, effectively maintained the balance of protein processing and degradation, and enhanced the cell wall regulation ability. However, the extent to which [CO₂] enrichment alleviated drought stress in cucumber seedling roots was limited under severe drought stress, which may be due to excessive damage to the seedlings.

Pretreatment with LEDs regulates antioxidant capacity and polyphenolic profile in two genotypes of basil under salinity stress

In the present study, we evaluated a pretreatment with four LED light sources (red, blue, red + blue, and white) in two genotypes (green and purple) of basil on the growth parameters, stress oxidative markers, non-enzymatic antioxidants, osmoprotectant compounds, ion content, and polyphenolic profile under both control and salinity stress conditions. The results indicated that 150 mM of NaCl decreased biomass, RWC, and K⁺/Na⁺ ratio but increased the content of proline and antioxidant capacity in the leaves of both genotypes of basil grown under GH (greenhouse) conditions. The results suggested that RB LED-exposed plants in the green genotype and R LED-exposed plants in the purple genotype improved accumulation of shoot biomass, K⁺/Na⁺ ratio, proline and soluble sugars, glutathione and ascorbate, polyphenolic profile, and thioredoxin reductase activity in the leaves of basil under both control and salinity stress conditions. NaCl stress (150 mM) increased oxidative markers, which are responsible for disturbance of routine functions of various plant cellular modules. LED light pretreatments diminished these markers under both control and salinity stress conditions. It could be concluded that intensification of non-enzymatic antioxidant systems during light-mediated priming can diminish the deleterious effects of ROS induced by NaCl stress (150 mM) through preventing the lipid peroxidation, scavenging cytotoxic H₂O₂, and enhancement of antioxidant potentials. Therefore, usage of LED lighting systems as a pretreatment or to supplement natural photoperiods under both control and salinity stress conditions may be advantageous for increasing biomass and phytochemical accumulation in basil.

Salt stress decreases seed yield and postpones growth process of canola (Brassica napus L.) by changing nitrogen and carbon characters

Salt stress is a major challenge for plant growth and yield achievement in canola (Brassica napus L.). Nitrogen (N) is considered as an essential nutrient involved in many physiological processes, and carbon (C) is the most component of plant biomass. N and C assimilations of canola plants are always inhibited by salt stress. However, the knowledge of how salt stress affects biomass and seed yield through changing N and C characters is limited. A field experiment was conducted to investigate the growth process, N and C characters, photosynthetic performance, biomass accumulation and seed yield under the low and high soil salt-ion concentration conditions (LSSC and HSSC). The results indicated that HSSC postponed the time of early flowering stage and maturity stage by 4 ~ 5 days and 6 ~ 8 days, respectively, as compared with LSSC. Besides, HSSC decreased the N and C accumulation and C/N at both growing stages, suggesting that salt stress break the balance between C assimilation and N assimilation, with stronger effect on C assimilation. Although the plant N content under HSSC was increased, the photosynthesis rate at early flowering stage was decreased. The leaf area index at early flowering stage was also reduced. In addition, HSSC decreased N translocation efficiency especially in stem, and N utilization efficiency. These adverse effects of HSSC together resulted in reduced biomass accumulation and seed yield. In conclusion, the high soil salt-ion concentration reduced biomass accumulation and seed yield in canola through changing N and C characters.

Metabolomic and transcriptomic changes in mungbean (Vigna radiata (L.) R. Wilczek) sprouts under salinity stress

Mungbean (Vigna radiata) sprouts are consumed globally as a healthy food with high nutritional values, having antioxidant and anticancer capacity. Under mild salinity stress, plants accumulate more secondary metabolites to alleviate oxidative stress. In this study, metabolomic and transcriptomic changes in mungbean sprouts were identified using a reference cultivar, sunhwa, to understand the regulatory mechanisms of secondary metabolites in response to salinity stress. Under salinity conditions, the contents of phenylpropanoid-derived metabolites, including catechin, chlorogenic acid, isovitexin, p-coumaric acid, syringic acid, ferulic acid, and vitexin, significantly increased. Through RNA sequencing, 728 differentially expressed genes (DEGs) were identified and 20 DEGs were detected in phenylpropanoid and flavonoid biosynthetic pathways. Among them, 11 DEGs encoding key enzymes involved in the biosynthesis of the secondary metabolites that increased after NaCl treatment were significantly upregulated, including dihydroflavonol 4-reductase (log₂FC 1.46), caffeoyl-CoA O-methyltransferase (1.38), chalcone synthase (1.15), and chalcone isomerase (1.19). Transcription factor families, such as MYB, WRKY, and bHLH, were also identified as upregulated DEGs, which play a crucial role in stress responses in plants. Furthermore, this study showed that mild salinity stress can increase the contents of phenylpropanoids and flavonoids in mungbean sprouts through transcriptional regulation of the key enzymes involved in the biosynthetic pathways. Overall, these findings will provide valuable information for molecular breeders and scientists interested in improving the nutritional quality of sprout vegetables.

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.

Influence of Blanching on the Gene Expression Profile of Phenylpropanoid, Flavonoid and Vitamin Biosynthesis, and Their Accumulation in Oenanthe javanica

Field blanching is a process used in agriculture to obtain sweet, delicious, and tender stems of water dropwort by obstructing sunlight. The nutritional and transcriptomic profiling of blanched water dropwort has been investigated in our previous studies. However, the effect of blanching on the production of secondary metabolites and different vitamins in water dropwort has not been investigated at the transcriptomic level. This study explored the transcriptomic variations in the phenylpropanoid biosynthesis, flavonoid biosynthesis, and different vitamin biosynthesis pathways under different blanching periods in the water dropwort stems (pre-blanching, mid-blanching, post-blanching, and control). The results show that polyphenol and flavonoid contents decreased; however, the contents of vitamins (A, B1, B2, and C) and antioxidant activity increased significantly after blanching. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of blanched water dropwort showed the downregulation of many important genes involved in phenylpropanoid and flavonoid biosynthesis pathways, and the downregulation of these genes might be the reason for the reduction in polyphenol and flavonoid contents. We also examined and highlighted the genes involved in the higher vitamin content, antioxidant activity, pale color, tenderness, and sweetness of the blanched stem of water dropwort. In conclusion, the present study explored the role of phenylpropanoid and vitamin biosynthesis, and it will provide a basis for future investigation and application in the blanch cultivation of water dropwort.

Multiple Abiotic Stresses Applied Simultaneously Elicit Distinct Responses in Two Contrasting Rice Cultivars

Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes—Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly. Abscisic acid (ABA) levels increased at least five-fold but did not differ significantly between the genotypes. Tandem Mass Tag isotopic labelling quantitative proteomics revealed 6215 reproducibly identified proteins in mature leaves across the two genotypes and three time points (0, 2 and 4 days of stress). Of these, 987 were differentially expressed due to stress (cf. control plants), including 41 proteins that changed significantly in abundance in all stressed plants. Heat shock proteins, late embryogenesis abundant proteins and photosynthesis-related proteins were consistently responsive to stress in both Nipponbare and IAC1131. Remarkably, even after 2 days of stress there were almost six times fewer proteins differentially expressed in IAC1131 than Nipponbare. This contrast in the translational response to multiple stresses is consistent with the known tolerance of IAC1131 to dryland conditions.

Engineering Macromolecular Trafficking Into the Citrus Vasculature

The plant vasculature is a central organ for long-distance transport of nutrients and signaling molecules that coordinate vegetative and reproductive processes, and adaptation response mechanisms to biotic and abiotic stress. In angiosperms, the sieve elements are devoid of nuclei, thus depending on the companion cells for the synthesis of RNA and proteins, which constitute some of the systemic signals that coordinate these processes. Massive analysis approaches have identified proteins and RNAs that could function as long-range signals in the phloem translocation stream. The selective translocation of such molecules could occur as ribonucleoprotein complexes. A key molecule facilitating this movement in Cucurbitaceae is the phloem protein CmPP16, which can facilitate the movement of RNA and other proteins into the sieve tube. The CmPP16 ortholog in Citrus CsPP16 was characterized in silico to determine its potential capacity to associate with other mobile proteins and its enrichment in the vascular tissue. The systemic nature of CsPP16 was approached by evaluating its capacity to provide phloem-mobile properties to antimicrobial peptides (AMPs), important in the innate immune defense. The engineering of macromolecular trafficking in the vasculature demonstrated the capacity to mobilize translationally fused peptides into the phloem stream for long-distance transport. The translocation into the phloem of AMPs could mitigate the growth of Candidatus Liberibacter asiaticus, with important implications for crop defense; this system also opens the possibility of translocating other molecules to modulate traits, such as plant growth, defense, and plant productivity.

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.

Integrated physiological and comparative proteomics analysis of contrasting genotypes of pearl millet reveals underlying salt-responsive mechanisms

Salinity stress poses a significant risk to plant development and agricultural yield. Therefore, elucidation of stress-response mechanisms has become essential to identify salt-tolerance genes in plants. In the present study, two genotypes of pearl millet (Pennisetum glaucum L.) with contrasting tolerance for salinity exhibited differential morpho-physiological and proteomic responses under 150 mM NaCl. The genotype IC 325825 was shown to withstand the stress better than IP 17224. The salt-tolerance potential of IC 325825 was associated with its ability to maintain intracellular osmotic, ionic, and redox homeostasis and membrane integrity under stress. The IC 325825 genotype exhibited a higher abundance of C4 photosynthesis enzymes, efficient enzymatic and non-enzymatic antioxidant system, and lower Na⁺ /K⁺ ratio compared with IP 17224. Comparative proteomics analysis revealed greater metabolic perturbation in IP 17224 under salinity, in contrast to IC 325825 that harbored pro-active stress-responsive machinery, allowing its survival and better adaptability under salt stress. The differentially abundant proteins were in silico characterized for their functions, subcellular-localization, associated pathways, and protein-protein interaction. These proteins were mainly involved in photosynthesis/response to light stimulus, carbohydrate and energy metabolism, and stress responses. Proteomics data were validated through expression profiling of the selected genes, revealing a poor correlation between protein abundance and their relative transcript levels. This study has provided novel insights into salt adaptive mechanisms in P. glaucum, demonstrating the power of proteomics-based approaches. The critical proteins identified in the present study could be further explored as potential objects for engineering stress tolerance in salt-sensitive major crops.

Thylakoid proteome variation of Eutrema salsugineum in response to drought and salinity combined stress

It is well known that plant responses to stress involve different events occurring at different places of the cell/leaf and at different time scales in relation with the plant development. In fact, the organelles proteomes include a wide range of proteins that could include a wide range of proteins showing a considerable change in cellular functions and metabolism process. On this basis, a comparative proteomics analysis and fluorescence induction measurements were performed to investigate the photosynthetic performance and the relative thylakoid proteome variation in Eutrema salsugineum cultivated under salt stress (200 mM NaCl), water deficit stress (PEG) and combined treatment (PEG + NaCl) as a hyperosmotic stress. The obtained results showed a significant decrease of plant growth under drought stress conditions, with the appearance of some toxicity symptoms, especially in plants subjected to combined treatment. Application of salt or water stress alone showed no apparent change in the chlorophyll a fluorescence transients, primary photochemistry (fluorescence kinetics of the O-J phase), the PQ pool state (J-I phase changes), (Fv/Fm) and (Fk/Fj) ratios. However, a considerable decrease of all these parameters was observed under severe osmotic stress (PEG + NaCl). The thylakoid proteome analysis revealed 58 proteins showing a significant variation in their abundance between treatments (up or down regulation). The combined treatment (PEG + NaCl) induced a decrease in the expression of the whole PSII core subunit (D1, D2, CP43, CP47, PsbE and PsbH), whereas the OEC subunits proteins remained constant. An increase in the amount of PsaD, PsaE, PsaF, PsaH, PsaK and PsaN was detected under drought stress (PEG5%). No significant change in the accumulation of Cyt b6 and Cyt f was observed. Some regulated proteins involved in cellular redox homeostasis were detected (glutamine synthetase, phosphoglycerate kinase, transketolase), and showed a significant decrease under the combined treatment. Some oxidative stress related proteins were significantly up-regulated under salt or drought stress and could play a crucial role in the PSI photoprotection and the control of ROS production level.

Salinity tolerance mechanisms and their breeding implications

BACKGROUND

The era of first green revolution brought about by the application of chemical fertilizers surely led to the explosion of food grains, but left behind the notable problem of salinity. Continuous application of these fertilizers coupled with fertilizer-responsive crops make the country self-reliant, but continuous deposition of these led to altered the water potential and thus negatively affecting the proper plant functioning from germination to seed setting.

MAIN BODY

Increased concentration of anion and cations and their accumulation and distribution cause cellular toxicity and ionic imbalance. Plants respond to salinity stress by any one of two mechanisms, viz., escape or tolerate, by either limiting their entry via root system or controlling their distribution and storage. However, the understanding of tolerance mechanism at the physiological, biochemical, and molecular levels will provide an insight for the identification of related genes and their introgression to make the crop more resilient against salinity stress.

SHORT CONCLUSION

Novel emerging approaches of plant breeding and biotechnologies such as genome-wide association studies, mutational breeding, marker-assisted breeding, double haploid production, hyperspectral imaging, and CRISPR/Cas serve as engineering tools for dissecting the in-depth physiological mechanisms. These techniques have well-established implications to understand plants' adaptions to develop more tolerant varieties and lower the energy expenditure in response to stress and, constitutively fulfill the void that would have led to growth resistance and yield penalty.

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.

Comparative proteomic approach to study the salinity effect on the growth of two contrasting quinoa genotypes

The aim of this study was to investigate the effect of NaCl salinity (0, 100 and 300 mM) on the individual response of the quinoa varieties Kcoito (Altiplano Ecotype) and UDEC-5 (Sea-level Ecotype) with physiological and proteomic approaches. Leaf protein profile was performed using two dimensional gel electrophoresis (2-DE). UDEC-5 showed an enhanced capacity to withstand salinity stress compared to Kcoito. In response to salinity, we detected overall the following differences between both genotypes: Toxicity symptoms, plant growth performance, photosynthesis performance and intensity of ROS-defense. We found a mirroring of these differences in the proteome of each genotype. Among the 700 protein spots reproducibly detected, 24 exhibited significant abundance variations between samples. These proteins were involved in energy and carbon metabolism, photosynthesis, ROS scavenging and detoxification, stress defense and chaperone functions, enzyme activation and ATPases. A specific set of proteins predominantly involved in photosynthesis and ROS scavenging showed significantly higher abundance under high salinity (300 mM NaCl). The adjustment was accompanied by a stimulation of various metabolic pathways to balance the supplementary demand for energy or intermediates. However, the more salt-resistant genotype UDEC-5 presented a beneficial and significantly higher expression of nearly all stress-related altered enzymes than Kcoito.

Role of ATP-binding cassette transporters in maintaining plant homeostasis under abiotic and biotic stresses

The ATP-binding cassette (ABC) transporters belong to a large protein family predominantly present in diverse species. ABC transporters are driven by ATP hydrolysis and can act as exporters as well as importers. These proteins are localized in the membranes of chloroplasts, mitochondria, peroxisomes and vacuoles. ABC proteins are involved in regulating diverse biological processes in plants, such as growth, development, uptake of nutrients, tolerance to biotic and abiotic stresses, tolerance to metal toxicity, stomatal closure, shape and size of grains, protection of pollens, transport of phytohormones, etc. In mitochondria and chloroplast, the iron metabolism and its transport across the membrane are mediated by ABC transporters. Tonoplast-localized ABC transporters are involved in internal detoxification of metal ion; thus protecting against the DNA impairment and maintaining cell growth. ABC transporters are involved in the transport of secondary metabolites inside the cells. Microorganisms also engage a large number of ABC transporters to import and expel substrates decisive for their pathogenesis. ABC transporters also suppress the seed embryonic growth until favorable conditions come. This review aims at giving insights on ABC transporters, their evolution, structure, functions and roles in different biological processes for helping the terrestrial plants to survive under adverse environmental conditions. These specialized plant membrane transporters ensure a sustainable economic yield and high-quality products, especially under unfavorable conditions of growth. These transporters can be suitably manipulated to develop 'Plants for the Future'.

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.

Progress in understanding salt stress response in plants using biotechnological tools

Salinization is a worldwide environmental problem, which is negatively impacting crop yield and thus posing a threat to the world's food security. Considering the rising threat of salinity, it is need of time, to understand the salt tolerant mechanism in plants and find avenues for the development of salinity resistant plants. Several plants tolerate salinity in a different manner, thereby halophytes and glycophytes evolved altered mechanisms to counter the stress. Therefore, in this review article, physiological, metabolic, and molecular aspects of the plant adaptation to salt stress have been discussed. The conventional breeding techniques for developing salt tolerant plants has not been much successful, due to its multigenic trait. The inflow of data from plant sequencing projects and annotation of genes led to the identification of many putative genes having a role in salt stress. The bioinformatics tools provided preliminary information and were helpful for making salt stress-specific databases. The microRNA identification and characterization led to unraveling the finer intricacies of the network. The transgenic approach finally paved a way for overexpressing some important genes viz. DREB, MYB, COMT, SOS, PKE, NHX, etc. conferred salt stress tolerance. In this review, we tried to show the effect of salinity on plants, considering ion homeostasis, antioxidant defense response, proteins involved, possible utilization of transgenic plants, and bioinformatics for coping with this stress factor. An overview of previous studies related to salt stress is presented in order to assist researchers in providing a potential solution for this increasing environmental threat.

Phenotyping Tomato Root Developmental Plasticity in Response to Salinity in Soil Rhizotrons

Plants have developed multiple strategies to respond to salt stress. In order to identify new traits related to salt tolerance, with potential breeding application, the research focus has recently been shifted to include root system architecture (RSA) and root plasticity. Using a simple but effective root phenotyping system containing soil (rhizotrons), RSA of several tomato cultivars and their response to salinity was investigated. We observed a high level of root plasticity of tomato seedlings under salt stress. The general root architecture was substantially modified in response to salt, especially with respect to position of the lateral roots in the soil. At the soil surface, where salt accumulates, lateral root emergence was most strongly inhibited. Within the set of tomato cultivars, H1015 was the most tolerant to salinity in both developmental stages studied. A significant correlation between several root traits and aboveground growth parameters was observed, highlighting a possible role for regulation of both ion content and root architecture in salt stress resilience.

Physiological and Differential Proteomic Analyses of Imitation Drought Stress Response in Sorghum bicolor Root at the Seedling Stage

Drought is one of the most important constraints on the growth and productivity of many crops, including sorghum. However, as a primary sensing organ, the plant root response to drought has not been well documented at the proteomic level. In the present study, we compared physiological alteration and differential accumulation of proteins in the roots of sorghum (Sorghum bicolor) inbred line BT×623 response to Polyethylene Glycol (PEG)-induced drought stress at the seedling stage. Drought stress (up to 24 h after PEG treatment) resulted in increased accumulation of reactive oxygen species (ROS) and subsequent lipid peroxidation. The proline content was increased in drought-stressed plants. The physiological mechanism of sorghum root response to drought was attributed to the elimination of harmful free radicals and to the alleviation of oxidative stress via the synergistic action of antioxidant enzymes, such as superoxide dismutase, peroxidase, and polyphenol oxidase. The high-resolution proteome map demonstrated significant variations in about 65 protein spots detected on Coomassie Brilliant Blue-stained 2-DE gels. Of these, 52 protein spots were identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS) representing 49 unique proteins; the levels of 43 protein spots were increased, and 22 were decreased under drought condition. The proteins identified in this study are involved in a variety of cellular functions, including carbohydrate and energy metabolism, antioxidant and defense response, protein synthesis/processing/degradation, transcriptional regulation, amino acid biosynthesis, and nitrogen metabolism, which contribute jointly to the molecular mechanism of outstanding drought tolerance in sorghum plants. Analysis of protein expression patterns and physiological analysis revealed that proteins associated with changes in energy usage; osmotic adjustment; ROS scavenging; and protein synthesis, processing, and proteolysis play important roles in maintaining root growth under drought stress. This study provides new insight for better understanding of the molecular basis of drought stress responses, aiming to improve plant drought tolerance for enhanced yield.

Insights into the Physiological and Biochemical Impacts of Salt Stress on Plant Growth and Development

Climate change is causing soil salinization, resulting in crop losses throughout the world. The ability of plants to tolerate salt stress is determined by multiple biochemical and molecular pathways. Here we discuss physiological, biochemical, and cellular modulations in plants in response to salt stress. Knowledge of these modulations can assist in assessing salt tolerance potential and the mechanisms underlying salinity tolerance in plants. Salinity-induced cellular damage is highly correlated with generation of reactive oxygen species, ionic imbalance, osmotic damage, and reduced relative water content. Accelerated antioxidant activities and osmotic adjustment by the formation of organic and inorganic osmolytes are significant and effective salinity tolerance mechanisms for crop plants. In addition, polyamines improve salt tolerance by regulating various physiological mechanisms, including rhizogenesis, somatic embryogenesis, maintenance of cell pH, and ionic homeostasis. This research project focuses on three strategies to augment salinity tolerance capacity in agricultural crops: salinity-induced alterations in signaling pathways; signaling of phytohormones, ion channels, and biosensors; and expression of ion transporter genes in crop plants (especially in comparison to halophytes).

Physiological and proteomic responses of reactive oxygen species metabolism and antioxidant machinery in mulberry (Morus alba L.) seedling leaves to NaCl and NaHCO3 stress

In this paper, the effects of 100 mM NaCl and NaHCO₃ stress on reactive oxygen species (ROS) and physiological and proteomic aspects of ROS metabolism in mulberry seedling leaves were studied. The results showed that NaCl stress had little effect on photosynthesis and respiration of mulberry seedling leaves. Superoxide dismutase (SOD) activity and the expression of related proteins in leaves increased by varying degrees, and accumulation of superoxide anion (O₂·^-) not observed. Under NaHCO₃ stress, photosynthesis and respiration were significantly inhibited, while the rate of O₂·^- production rate and H₂O₂ content increased. The activity of catalase (CAT) and the expression of CAT (W9RJ43) increased under NaCl stress. In response to NaHCO₃ stress, the activity and expression of CAT were significantly decreased, but the ability of H₂O₂ scavenging of peroxidase (POD) was enhanced. The ascorbic acid-glutathione (AsA-GSH) cycle in mulberry seedling leaves was enhancement in both NaCl and NaHCO₃ stress. The expression of 2-Cys peroxiredoxin BAS1 (2-Cys Prx BAS1), together with thioredoxin F (TrxF), thioredoxin O1 (TrxO1), thioredoxin-like protein CITRX (Trx CITRX), and thioredoxin-like protein CDSP32 (Trx CDSP32) were significantly increased under NaCl stress. Under NaHCO₃ stress, the expression of the electron donor of ferredoxin-thioredoxin reductase (FTR), together with Trx-related proteins, such as thioredoxin M (TrxM), thioredoxin M4 (TrxM4), thioredoxin X (TrxX), TrxF, and Trx CSDP32 were significantly decreased, suggesting that the thioredoxin-peroxiredoxin (Trx-Prx) pathway's function of scavenging H₂O₂ of in mulberry seedling leaves was inhibited. Taken together, under NaCl stress, excessive production of O₂·^- mulberry seedlings leaves was inhibited, and H₂O₂ was effectively scavenged by CAT, AsA-GSH cycle and Trx-Prx pathway. Under NaHCO₃ stress, despite the enhanced functions of POD and AsA-GSH cycle, the scavenging of O₂·^- by SOD was not effective, and that of H₂O₂ by CAT and Trx-Prx pathway were inhibited; and in turn, the oxidative damage to mulberry seedling leaves could not be reduced.

Salt-tolerance diversity in diploid and polyploid cotton (Gossypium) species

The development of salt-tolerant genotypes is pivotal for the effective utilization of salinized land and to increase global crop productivity. Several cotton species comprise the most important source of textile fibers globally, and these are increasingly grown on marginal or increasingly saline agroecosystems. The allopolyploid cotton species also provide a model system for polyploid research, of relevance here because polyploidy was suggested to be associated with increased adaptation to stress. To evaluate the genetic variation of salt tolerance among cotton species, 17 diverse accessions of allopolyploid (AD-genome) and diploid (A- and D-genome) Gossypium were evaluated for a total of 29 morphological and physiological traits associated with salt tolerance. For most morphological and physiological traits, cotton accessions showed highly variable responses to 2 weeks of exposure to moderate (50 mm NaCl) and high (100 mm NaCl) hydroponic salinity treatments. Our results showed that the most salt-tolerant species were the allopolyploid Gossypium mustelinum from north-east Brazil, the D-genome diploid Gossypium klotzschianum from the Galapagos Islands, followed by the A-genome diploids of Africa and Asia. Generally, A-genome accessions outperformed D-genome cottons under salinity conditions. Allopolyploid accessions from either diploid genomic group did not show significant differences in salt tolerance, but they were more similar to one of the two progenitor lineages. Our findings demonstrate that allopolyploidy in itself need not be associated with increased salinity stress tolerance and provide information for using the secondary Gossypium gene pool to breed for improved salt tolerance.

Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses

Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.

Comparative proteomic analysis of okra (Abelmoschus esculentus L.) seedlings under salt stress

Background

Salinization seriously threatens land use efficiency and crop yields across the world. Understanding the mechanisms plants use to protect against salt stress will help breeders develop salt-tolerant vegetable crops. Okra (Abelmoschus esculentus L.) is an important vegetable crop of the mallow family, which is now cultivated in warm regions worldwide. To understand the effects of salt stress on the protein level of okra, a comparative proteomic analysis of okra seedlings grown in the presence of 0 or 300 mmol L^− 1 NaCl treatment was performed using an integrated approach of Tandem Mass Tag labeling and LC-MS/MS integrated approach.

Results

A total of 7179 proteins were identified in this study, for which quantitative information was available for 5774 proteins. In the NaCl/control comparison group, there were 317 differentially expressed proteins (DEPs), of which 165 proteins were upregulated and 152 proteins downregulated in the presence of NaCl. Based on the above data, we carried out a systematic bioinformatics analysis of proteins with information, including protein annotation, domain characteristics, functional classification, and pathway enrichment. Enriched gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEPs were most strongly associated with “response to stress” and “protein processing in endoplasmic reticulum”. Furthermore, several heat shock proteins were identified as DEPs.

Conclusions

This information provides a reference direction for further research on the okra proteome in the downstream of the salt stress response, with our data revealing that the responses of okra to salt stress involves by various pathways.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5737-7) contains supplementary material, which is available to authorized users.

Screening Oat Genotypes for Tolerance to Salinity and Alkalinity

A set of four experiments was conducted to develop methods for screening oat tolerance to salt and alkali and the following results were obtained. (1) In experiment 1, 68.5 mmol L^-1 salt and 22.5 mmol L^-1 alkali were identified as appropriate concentrations for determining oat tolerance to salinity and alkalinity during germination. (2) These concentrations were used in experiment 2 to screen 248 oat genotypes and 21 were identified to be tolerant to salinity and alkalinity in germination. (3) In experiment 3, one salt treatment, 40 L of Na₂SO₄:NaCl (1:1), 150 mmol L^-1, was found to be optimal for screening oat tolerance to salinity during growth and development. For alkalinity tolerance, the optimal treatment was 40 L of Na₂CO₃:NaHCO₃ (1:1) at 75 mmol L^-1. (4) No significant correlation was found between tolerances at the germination and adult stages or between tolerances to salt and alkali. Three lines were found to be tolerant to both salt and alkali in both germination and adult stages. (5) In experiment 4, 25 out of 262 oat genotypes were found to be tolerant to both salinity and alkalinity. (6) GGE biplot analysis was found to be effective in interpreting the multivariate data and the plastic cone-container system was found to be cost-effective system for screening adult plant tolerance to salt and alkali. (7) The symptoms of salt stress and alkali stress were found to be different; alkali stress mainly reduces the chlorophyll content, while salinity mainly disrupts water absorption.

Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

BACKGROUND

Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes.

RESULTS

In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure.

CONCLUSION

We provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.

The influence of chosen fungicides on the activity of aminopeptidases in winter oilseed rape during pods development

Cultivation of oilseed rape requires application of specific fungicides. Besides their protective role, they can potentially influence the expression and activity of crucial enzymes in the plant. Among the large number of enzymes expressed in plants, aminopeptidases play a key role in all crucial physiological processes during the whole life cycle (e.g. storage protein mobilization and thus supplying plant with needed amino acids, as well as plant aging, protection and defense responses). In the present paper, we evaluate for the first time, the influence of the treatment of winter oilseed rape with commercially available fungicides (Pictor 400 SC, Propulse 250 SE and Symetra 325 SC), on the activity of aminopeptidases expressed in each plant organ (flowers, leaves, stems and pods separately). Fungicides were applied once, at one of the three stages of oilseed rape development (BBCH 59-61, BBCH 63-65 and BBCH 67-69). The aminopeptidase activity was determined using six different amino acid p-nitroanilides as substrates. The results have shown, that in control plants, at the beginning of intensive pods development and seeds production, hydrophobic amino acids with bulky side chains (Phe, Leu) were preferentially hydrolysed. In control plants, the activity was ~3.5 times higher in stems and pods, compared to leaves. The treatment with all pesticides caused significant increase in aminopeptidases hydrolytic activity toward small amino acids Gly, Ala as well as proline, mostly in flowers and leaves. These amino acids are proven to be crucial in the mechanisms of delaying of plant aging, development of better resistance to stress and plant defense. It can be suggested, that studied fungicides enhance such mechanisms, by activating the expression of genes coding for aminopeptidases, which are active in hydrolysis of N-terminal amino acids such as Gly, Ala, Pro from storage peptides and proteins. Depending on fungicide, the major increase of aminopeptidase activity was observed after application at BBCH 67-69 (Pictor 400 SC and Symetra 325 SC) and BBCH 63-65 (Propulse 250 SE) stages of development. Our study revealed, that agrochemical treatment and time of application, influenced the expression and activity of aminopeptidases, even though they were not molecular targets of applied fungicides. Since aminopeptidases are widely distributed throughout all organisms and are crucial in many key physiological processes, it can be expected, that factors influencing their expression and activity in plants, can also influence these enzymes in other organisms, especially humans and other mammals.

Proteomic and physiological analyses reveal the role of exogenous spermidine on cucumber roots in response to Ca(NO3)2 stress

The mechanism of exogenous Spd-induced Ca(NO₃)₂ stress tolerance in cucumber was studied by proteomics and physiological analyses. Protein-protein interaction network revealed 13 key proteins involved in Spd-induced Ca(NO₃)₂ stress resistance. Ca(NO₃)₂ stress is one of the major reasons for secondary salinization that limits cucumber plant development in greenhouse. The conferred protective role of exogenous Spd on cucumber in response to Ca(NO₃)₂ stress cues involves changes at the cellular and physiological levels. To investigate the molecular foundation of exogenous Spd in Ca(NO₃)₂ stress tolerance, a proteomic approach was performed in our work. After a 9 days period of Ca(NO₃)₂ stress and/or exogenous Spd, 71 differential protein spots were confidently identified. The resulting proteins were enriched in seven different categories of biological processes, including protein metabolism, carbohydrate and energy metabolism, ROS homeostasis and stress defense, cell wall related, transcription, others and unknown. Protein metabolism (31.2%), carbohydrate and energy metabolism (15.6%), ROS homeostasis and stress defense (32.5%) were the three largest functional categories in cucumber root and most of them were significantly increased by exogenous Spd. The Spd-responsive protein interaction network revealed 13 key proteins, whose accumulation changes could be critical for Spd-induced resistance; all 13 proteins were upregulated by Spd at transcriptional and protein levels in response to Ca(NO₃)₂ stress. Furthermore, accumulation of antioxidant enzymes, non-enzymatic antioxidant and polyamines, along with reduction of H₂O₂ and MDA, were detected after exogenous Spd application during Ca(NO₃)₂ stress. The results of these proteomic and physiological analyses in cucumber root may facilitate a better understanding of the underlying mechanism of Ca(NO₃)₂ stress tolerance mediated by exogenous Spd.

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.

Drought stress impact on leaf proteome variations of faba bean (Vicia faba L.) in the Qinghai-Tibet Plateau of China

Water scarcity is a major abiotic stress factor that strongly influences growth, development and yield of grain legumes in arid and semi-arid area of the world. Drought stress frequently occurs during the seedling stage and finally affects yield of faba bean (Vicia faba L.). However, the responses of plant leaf to drought have not been documented very well at the proteomic level. "Ga da dou" of the drought-tolerant faba bean cultivar was exposed to drought to examine the proteome changes of leaves. In this study, 2-week-old seedlings were subjected to water deficit by 7 days drought stress, whereas control plants were regularly irrigated. After withdrawing water, plants exposed to drought for 7 days and control plants at the same developmental stage were included in quantitative proteomic analysis using two-dimensional electrophoresis gels of proteins in combination with mass spectrometry. Over 300 proteins were detected by 2-DE, 50 differentially expressed proteins were detected by t test and 30 proteins were successfully identified by MALDI-TOF/TOF, in which 25 proteins were clearly downregulated and five proteins were upregulated. The quantified proteins were grouped into five functional groups, mainly regulatory proteins (46.7%), energy metabolism (23.3%), cell cytoskeleton (6.7%), other functions (20%) and unknown function (3.3%). Chitinase was upregulated under drought, suggesting that it was an important part of the plant defense system, playing an important role in stress resistance. 50S ribosomal protein was upregulated under drought, suggesting its role in protecting plants against stress by re-establishing normal protein conformations. The abundance of proteins involved in protein synthesis such as chitinase, Bet protein and glutamate-glyoxylate aminotransferase was upregulated under drought stress. These proteins could play important roles in drought tolerance and contribute to the relatively stronger drought tolerance of "Ga da dou".

Comparative proteomic analysis of Chlamydomonas reinhardtii control and a salinity-tolerant strain revealed a differential protein expression pattern

Proteins involved in membrane transport and trafficking, stress and defense, iron uptake and metabolism, as well as proteolytic enzymes, were remarkably up-regulated in the salinity-tolerant strain of Chlamydomonas reinhardtii. Excessive concentration of NaCl in the environment can cause adverse effects on plants and microalgae. Successful adaptation of plants to long-term salinity stress requires complex cellular adjustments at different levels from molecular, biochemical and physiological processes. In this study, we developed a salinity-tolerant strain (ST) of the model unicellular green alga, Chlamydomonas reinhardtii, capable of growing in medium containing 300 mM NaCl. Comparative proteomic analyses were performed to assess differential protein expression pattern between the ST and the control progenitor cells. Proteins involved in membrane transport and trafficking, stress and defense, iron uptake and metabolism, as well as protein degradation, were remarkably up-regulated in the ST cells, suggesting the importance of these processes in acclimation mechanisms to salinity stress. Moreover, 2-DE-based proteomic also revealed putative salinity-specific post-translational modifications (PTMs) on several important housekeeping proteins. Discussions were made regarding the roles of these differentially expressed proteins and the putative PTMs in cellular adaptation to long-term salinity stress.

Unraveling the Root Proteome Changes and Its Relationship to Molecular Mechanism Underlying Salt Stress Response in Radish (Raphanus sativus L.)

To understand the molecular mechanism underlying salt stress response in radish, iTRAQ-based proteomic analysis was conducted to investigate the differences in protein species abundance under different salt treatments. In total, 851, 706, and 685 differential abundance protein species (DAPS) were identified between CK vs. Na100, CK vs. Na200, and Na100 vs. Na200, respectively. Functional annotation analysis revealed that salt stress elicited complex proteomic alterations in radish roots involved in carbohydrate and energy metabolism, protein metabolism, signal transduction, transcription regulation, stress and defense and transport. Additionally, the expression levels of nine genes encoding DAPS were further verified using RT-qPCR. The integrative analysis of transcriptomic and proteomic data in conjunction with miRNAs was further performed to strengthen the understanding of radish response to salinity. The genes responsible for signal transduction, ROS scavenging and transport activities as well as several key miRNAs including miR171, miR395, and miR398 played crucial roles in salt stress response in radish. Based on these findings, a schematic genetic regulatory network of salt stress response was proposed. This study provided valuable insights into the molecular mechanism underlying salt stress response in radish roots and would facilitate developing effective strategies toward genetically engineered salt-tolerant radish and other root vegetable crops.

Comparative proteomic analysis of alfalfa revealed new salt and drought stress-related factors involved in seed germination

Salinity and drought are two major environmental factors that limit the growth and yield of many forage crops in semi-arid and arid regions. Alfalfa (Medicago sativa L.) is one of the most important forage crops in many countries. We aim to investigate the molecular mechanisms of alfalfa in response to salt and drought stresses in this study. Physiological and proteomic analyses were applied to examine the Zhongmu NO.3 alfalfa seed germination stage with 200 mM NaCl and 180 g·L^-1 polyethylene glycol (PEG) treatments. The germination ability of the seed and the accumulation of osmotic solutes were quite different between the NaCl and PEG treatments. More than 800 protein spots were detected by proteomics technology on two-dimensional electrophoresis (2-DE) gels. The abundance of twenty-eight proteins were decreased or increased after salt and drought stress. Seventeen of these proteins were identified and classified into six functional categories through mass spectrometry (MS). The six groups involved in salt- and PEG-mediated stress included defense response, energy metabolism, protein synthesis and degradation, oxidative stress, carbohydrate metabolism-associated proteins, and unknown proteins. We discovered that some proteins related to carbohydrate metabolism and energy production increased in abundance under salt- and PEG-mediated drought stress. This demonstrates a common mechanism of energy consumption during abiotic stresses. Further study of these proteins with unknown function will provide insights into the molecular mechanisms of abiotic stress and the discovery of new candidate markers.

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.

Proteomic response of oat leaves to long-term salinity stress

Salinity adversely affects plant growth and production. Oat is a moderately salt-tolerant crop and can contribute to improving saline soil. The physiological and molecular responses of the oat plant to long-term salinity were studied. After a 16-day salt treatment (150 mmol L^-1NaCl in Hoagland's solution), photosynthetic rate, maximum photosystem II photochemical efficiency, and actual efficiency of photosystem II decreased. The activities of superoxide dismutase, peroxidase, and catalase significantly increased. We also investigated the protein profiles of oat leaves in response to salinity and detected 30 reproducible protein spots by two-dimensional gel electrophoresis that were differentially abundant. Specifically, one protein was up-regulated and 29 proteins were down-regulated compared with the control. These 29 proteins were identified using MALDI-TOF mass spectrometry, and 19 corresponding genes were further investigated by quantitative real-time PCR. These proteins were involved in four types of biological processes: photosynthesis, carbohydrate metabolism and energy, protein biosynthesis, and folding and detoxification. This study indicates that the lower levels of Calvin cycle-related proteins, 50S ribosomal protein L10 and adenosine-triphosphate regulation-related proteins, and the high levels of antioxidant enzymes play important roles in the response of oat to long-term salinity stress.

Salinity-induced inhibition of growth in the aquatic pteridophyte Azolla microphylla primarily involves inhibition of photosynthetic components and signaling molecules as revealed by proteome analysis

Salinity stress causes adverse physiological and biochemical changes in the growth and productivity of a plant. Azolla, a symbiotic pteridophyte and potent candidate for biofertilizer due to its nitrogen fixation ability, shows reduced growth and nitrogen fixation during saline stress. To better understand regulatory components involved in salinity-induced physiological changes, in the present study, Azolla microphylla plants were exposed to NaCl (6.74 and 8.61 ds/m) and growth, photochemical reactions of photosynthesis, ion accumulation, and changes in cellular proteome were studied. Maximum dry weight was accumulated in control and untreated plant while a substantial decrease in dry weight was observed in the plants exposed to salinity. Exposure of the organism to different concentrations of salt in hydroponic conditions resulted in differential level of Na⁺ and K⁺ ion accumulation. Comparative analysis of salinity-induced proteome changes in A. microphylla revealed 58 salt responsive proteins which were differentially expressed during the salt exposure. Moreover, 42 % spots among differentially expressed proteins were involved in different signaling events. The identified proteins are involved in photosynthesis, energy metabolism, amino acid biosynthesis, protein synthesis, and defense. Downregulation of these key metabolic proteins appears to inhibit the growth of A. microphylla in response to salinity. Altogether, the study revealed that in Azolla, increased salinity primarily affected signaling and photosynthesis that in turn leads to reduced biomass.

Increased water salinity applied to tomato plants accelerates the development of the leaf miner Tuta absoluta through bottom-up effects

Variation in resource inputs to plants may trigger bottom-up effects on herbivorous insects. We examined the effects of water input: optimal water vs. limited water; water salinity: with vs. without addition of 100 mM NaCl; and their interactions on tomato plants (Solanum lycopersicum), and consequently, the bottom-up effects on the tomato leaf miner, Tuta absoluta (Meytick) (Lepidoptera: Gelechiidae). Plant growth was significantly impeded by limited water input and NaCl addition. In terms of leaf chemical defense, the production of tomatidine significantly increased with limited water and NaCl addition, and a similar but non-significant trend was observed for the other glycoalkaloids. Tuta absoluta survival did not vary with the water and salinity treatments, but the treatment “optimal water-high salinity” increased the development rate without lowering pupal mass. Our results suggest that caution should be used in the IPM program against T. absoluta when irrigating tomato crops with saline water.

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.

Genome-wide investigation of the NAC transcription factor family in melon (Cucumis melo L.) and their expression analysis under salt stress

82 melon NAC (CmNAC) genes were identified in melon. We putatively identified the function of CmNAC gene in melon under salt stress. NAC transcription factor proteins play important roles in many biological processes, including plant development and stress responses. To date, few full-length melon NAC proteins have been identified. In this study, 82 melon NAC (CmNAC) genes were identified in the Cucumis melo L. genome. By interrogating our cDNA libraries and transcriptome data from melon under salt stress, and comparison of their phylogenetic relationship with Arabidopsis NAC salt stress-related genes, we putatively identified that the fourth clade of CmNAC genes were involved in the salt stress response, especially the second clade of the group IV of the phylogenetic tree. Expression analysis confirmed that eleven of the twelve CmNAC genes from the group IV were induced in melon seedling roots by salt stress; the other gene was down regulated by salt stress. The expression of CmNAC14 continually increased in 12 h under salt stress, and was selected for transformation into Arabidopsis for functional verification. Overexpression of CmNAC14 increased the sensitivity of transgenic Arabidopsis lines to salt stress, which were simultaneously demonstrated by reduced expression of abiotic stress-response genes and variation in several physiological indices. This study increases our knowledge and may enable further characterization of the roles of CmNAC family in the response to salt stress.

Comparative proteomics illustrates the complexity of drought resistance mechanisms in two wheat (Triticum aestivum L.) cultivars under dehydration and rehydration

BACKGROUND

Drought stress is one of the most adverse environmental constraints to plant growth and productivity. Comparative proteomics of drought-tolerant and sensitive wheat genotypes is a strategy to understand the complexity of molecular mechanism of wheat in response to drought. This study attempted to extend findings regarding the potential proteomic dynamics in wheat under drought stress and to enrich the research content of drought tolerance mechanism.

RESULTS

A comparative proteomics approach was applied to analyze proteome change of Xihan No. 2 (a drought-tolerant cultivar) and Longchun 23 (a drought-sensitive cultivar) subjected to a range of dehydration treatments (18 h, 24 h and 48 h) and rehydration treatment (R24 h) using 2-DE, respectively. Quantitative image analysis showed a total of 172 protein spots in Xihan No. 2 and 215 spots from Longchun 23 with their abundance significantly altered (p < 0.05) more than 2.5-fold. Out of these spots, a total of 84 and 64 differentially abundant proteins were identified by MALDI-TOF/TOF MS in Xihan No. 2 and Longchun 23, respectively. Most of these identified proteins were involved in metabolism, photosynthesis, defence and protein translation/processing/degradation in both two cultivars. In addition, the proteins involved in redox homeostasis, energy, transcription, cellular structure, signalling and transport were also identified. Furthermore, the comparative analysis of drought-responsive proteome allowed for the general elucidation of the major mechanisms associated with differential responses to drought of both two cultivars. These cellular processes work more cooperatively to re-establish homeostasis in Xihan No. 2 than Longchun 23. The resistance mechanisms of Xihan No. 2 mainly included changes in the metabolism of carbohydrates and amino acids as well as in the activation of more antioxidation and defense systems and in the levels of proteins involved in ATP synthesis and protein degradation/refolding.

CONCLUSIONS

This study revealed that the levels of a number of proteins involved in various cellular processes were affected by drought stress in two wheat cultivars with different drought tolerance. The results showed that there exist specific responses to drought in Xihan No. 2 and Longchun 23. The proposed hypothetical model would explain the interaction of these identified proteins that are associated with drought-responses in two cultivars, and help in developing strategies to improve drought tolerance in wheat.