Salt stress-induced modulations in the shoot proteome of Brassica juncea genotypes

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.

Plant growth regulators mediated mitigation of salt-induced toxicities in mustard (Brassica juncea L.) by modifying the inherent defense system

Salt stress is one of the common environmental threats to crop growth, development, and productivity. Plant growth regulators (PGRs) are natural messengers and are known to play pivotal roles at different stages of the growth and development of plants under various environmental conditions. Keeping in mind the importance of PGRs in stress management, a factorial randomized pot experiment was conducted to evaluate the efficiency of three selected PGRs, namely gibberellic acid (GA₃), salicylic acid (SA) and triacontanol (Tria) for the amelioration of NaCl stress in mustard. Plants were subjected to four concentrations of NaCl (0, 50, 100 and 150 mM). Two foliar sprays of PGRs (GA₃, SA and Tria), each at 5 μM were applied to the foliage of plants using a hand sprayer. The increasing levels of NaCl decreased growth, physio-biochemical, histochemical and yield parameters in a dose-dependent manner while increasing activities of antioxidant enzymes, contents of osmolytes and oxidative stress biomarkers linearly with increasing levels of NaCl. The spray of GA₃, SA and Tria under stressed-free and stressed conditions improved the aforesaid attributes while decreasing the generation of stress biomarkers. Of sprayed PGRs, SA proved to be the best for alleviating the adverse effect of NaCl stress. Furthermore, it provides experimental data for its possible biotechnological applications in mustard crops exposed to high concentrations of salinity and possibly to other environmental stresses which have associated oxidative stress.

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.

Transcriptional regulation-mediating ROS homeostasis and physio-biochemical changes in wild tomato (Solanum chilense) and cultivated tomato (Solanum lycopersicum) under high salinity

Salinity intrusion is one of the biggest problems in the context of sustainable agricultural practices. The major concern and challenge in developing salt-resistance in cultivated crops is the genetic complexity of the trait and lack of natural variability for stress-responsive traits. In this context, tomato wild relatives are important and have provided novel alleles for breeding abiotic stress tolerance including salt tolerance. We provide here a case study, involving tomato wild relative Solanum chilense and cultivated variety Solanum lycopersicum, carried out under high salt stress to investigate comparative transcriptional regulation mediating ROS homeostasis and other physiological attributes. Salt dependent oxidative stress in S. lycopersicum was characterized by a relatively higher H₂O₂ content, generation of O₂^•−, electrolytic leakage and lipid peroxidation whereas reduced content of both ascorbate and glutathione. On the contrary, the robust anti-oxidative system in the S. chilense particularly counteracted the salt-induced oxidative damages by a higher fold change in expression profile of defense-related salt-responsive genes along with the increased activities of anti-oxidative enzymes. We conclude that S. chilense harbours novel genes or alleles for salt stress-related traits that could be identified, characterized, and mapped for its possible introgression into cultivated tomato lines.

Comparative Proteomics Unravels the Differences in Salt Stress Response of Own-Rooted and 110R-Grafted Thompson Seedless Grapevines

Thompson Seedless, a commonly grown table grape variety, is sensitive to salinity when grown on its own roots, and therefore, it is frequently grafted onto salinity-tolerant wild grapevine rootstocks. Rising soil salinity is a growing concern in irrigated agricultural systems. The accumulation of salts near the root zone severely hampers plant growth, leading to a decrease in the productive lifespan of grapevine and causing heavy yield losses to the farmer. In the present study, we investigated the differences in response to salinity between own-rooted Thompson Seedless (TSOR) and 110R-grafted Thompson Seedless (TS110R) grapevines, wherein 110R is reported to be a salt-tolerant rootstock. The grapevines were subjected to salt stress by treating them with a 150 mM NaCl solution. The stress-induced changes in protein abundance were investigated using a label-free shotgun proteomics approach at three time-points viz. 6 h, 48 h, and 7 days of salt treatment. A total of 2793 proteins were identified, of which 246 were differentially abundant at various time-points in TSOR and TS110R vines. The abundance of proteins involved in several biological processes such as photosynthesis, amino acid metabolism, translation, chlorophyll biosynthesis, and generation of precursor metabolites was significantly affected by salt stress in both the vines but at different stages of stress. The results revealed that TSOR vines responded fervently to salt stress, while TS110R vines adopted a preventive approach. The findings of this study add to the knowledge of salinity response in woody and grafted plants and hence open the scope for further studies on salt stress-specific differences induced by grafting.

Proteome Profiling of the Mutagen-Induced Morphological and Yield Macro-Mutant Lines of Nigella sativa L

In the present investigation, the leaf proteome profile of the macro-mutant lines of Nigella sativa L. was analyzed to identify the key proteins involved in the expression of traits associated with the morphology, seed yield, and content of thymoquinone. In our earlier study, the macro-mutants were generated with contrasting morphological traits and seed yields through induced mutagenesis, using ethyl methyl sulfonate, gamma rays, and combinations of both. Analysis of the leaf proteome of the control and macro-mutant lines of N. sativa showed that twenty-three proteins were differentially expressed. These differentially expressed proteins were sequenced through mass spectrometry and identified using the MASCOT software. On the basis of their function, these proteins were categorized into several groups. Most proteins were found in the categories of signal transduction (18%) and carbon metabolism (18%). A total of 13% of proteins belonged to the categories of energy and metabolism. Proteins in the categories of secondary plant metabolism, stress defense, cytoskeleton, and protein synthesis were also found. The polycomb group protein (FIE1), transcription factor (PRE1), and geranyl diphosphate synthase were notable proteins, in addition to some proteins of signal transduction and carbon metabolism. Expression patterns of the differentially expressed proteins were also studied at the transcript level by using qRT-PCR. Transcriptomics analysis was consistent with the proteomics data. This study shows the changes that take place at the proteomic level through induced mutagenesis, as well as the involvement of some proteins in the expression traits associated with plant height, seed yield, and the thymoquinone content of N. sativa. The identified proteins might help elucidate the metabolic pathways involved in the expression of traits, including seed yield, and the active compounds of medicinal plants.

Effects of cerium oxide on rice seedlings as affected by co-exposure of cadmium and salt

Effects of CeO₂ NPs (200 mg.L^-1) on rice (Oryza sativa L.) alone or co-exposure with cadmium (Cd) and salt (sodium chloride, NaCl) were investigated in hydroponic systems for two weeks. Physiological results show that rice biomass was significantly inhibited when NaCl or CdCl₂ added alone or in co-exposure treatment. CeO₂ NPs significantly relieve the chlorophyll damage under CdCl₂ environmental stress. The presence of CeO₂ NPs alleviated both stressors induced damages to rice as indicated by the reduced proline level. Additionally, CeO₂ NPs triggered the antioxidant defense systems to counteract the oxidative stress caused by NaCl and CdCl₂. The level of 8-OHdG, one of the most important indicators for genotoxicity, in rice suggest that the presence of CeO₂ NPs reduced the DNA damage in NaCl treated rice. Elemental analysis indicated that co-exposure to NaCl and CdCl₂ slightly decreased the Cd content as compared to the one in the CdCl₂ alone treatment, and this co-exposure also significantly reduced the Na content when comparing with the NaCl alone treatment. Taken together, our findings suggest that CeO₂ NPs could alleviate the CdCl₂ and NaCl stresses, but could not completely change the phenotype of both contaminants treated rice.

Tackling Salinity in Sustainable Agriculture—What Developing Countries May Learn from Approaches of the Developed World

Soil salinity is a common problem of the developing world as well as the developed world. However, the pace to reduce salinity is much slower in the developing world. The application of short-term approaches with an unsustainable supply of funds are the major reasons of low success. In contrast, the developed world has focused on long-term and sustainable techniques, and considerable funds per unit area have been allocated to reduce soil salinity. Here, we review the existing approaches in both worlds. Approaches like engineering and nutrient use were proven to be unsustainable, while limited breeding and biosaline approaches had little success in the developing countries. In contrast, advanced breeding and genetics tools were implemented in the developed countries to improve the salinity tolerance of different crops with more success. Resultantly, developed countries not only reduced the area for soil salinity at a higher rate, but more sustainable and cheaper ways to resolve the issue were implemented at the farmers’ field. Similarly, plant microbial approaches and the application of fertigation through drip irrigation have great potential for both worlds, and farmer participatory approaches are required to obtain fruitful outcomes. In this regard, a challenging issue is the transition of sustainable approaches from developed countries to developing ones, and possible methods for this are discussed.

Responsive Proteins in Wheat Cultivars with Contrasting Nitrogen Efficiencies under the Combined Stress of High Temperature and Low Nitrogen

Productivity of wheat (Triticumaestivum) is markedly affected by high temperature and nitrogen deficiency. Identifying the functional proteins produced in response to these multiple stresses acting in a coordinated manner can help in developing tolerance in the crop. In this study, two wheat cultivars with contrasting nitrogen efficiencies (N-efficient VL616 and N-inefficient UP2382) were grown in control conditions, and under a combined stress of high temperature (32 °C) and low nitrogen (4 mM), and their leaf proteins were analysed in order to identify the responsive proteins. Two-dimensional electrophoresis unravelled sixty-one proteins, which varied in their expression in wheat, and were homologous to known functional proteins involved in biosynthesis, carbohydrate metabolism, energy metabolism, photosynthesis, protein folding, transcription, signalling, oxidative stress, water stress, lipid metabolism, heat stress tolerance, nitrogen metabolism, and protein synthesis. When exposed to high temperature in combination with low nitrogen, wheat plants altered their protein expression as an adaptive means to maintain growth. This response varied with cultivars. Nitrogen-efficient cultivars showed a higher potential of redox homeostasis, protein stability, osmoprotection, and regulation of nitrogen levels. The identified stress-responsive proteins can pave the way for enhancing the multiple-stress tolerance in wheat and developing a better understanding of its mechanism.

Cerium oxide nanoparticles alter the salt stress tolerance of Brassica napus L. by modifying the formation of root apoplastic barriers

Rapidly growing global population adds significant strains on the fresh water resources. Consequently, saline water is increasingly tapped for crop irrigation. Meanwhile, rapid advancement of nanotechnology is introducing more and more engineered nanoparticles into the environment and in agricultural soils. While some negative effects of ENPs on plant health at very high concentrations have been reported, more beneficial effects of ENPs at relatively low concentrations are increasingly noticed, opening doors for potential applications of nanotechnology in agriculture. In particular, we found that cerium oxide nanoparticles (CeO₂NPs) improved plant photosynthesis in salt stressed plants. Due to the close connections between salt stress tolerance and the root anatomical structures, we postulated that CeO₂NPs could modify plant root anatomy and improve plant salt stress tolerance. This study aimed at testing the hypothesis with Brassica napus in the presence of CeO₂NPs (0, 500 mg kg^-1 dry sand) and/or NaCl (0, 50 mM) in a growth chamber. Free hand sections of fresh roots were taken every seven days for three weeks and the suberin lamellae development was examined under a fluorescence microscope. The results confirmed the hypothesis that CeO₂NPs modified the formation of the apoplastic barriers in Brassica roots. In salt stressed plants, CeO₂NPs shortened the root apoplastic barriers which allowed more Na⁺ transport to shoots and less accumulation of Na⁺ in plant roots. The altered Na⁺ fluxes and transport led to better physiological performance of Brassica and may lead to new applications of nanotechnology in agriculture.

OsNucleolin1-L Expression in Arabidopsis Enhances Photosynthesis via Transcriptome Modification under Salt Stress Conditions

OsNUC1 encodes rice nucleolin, which has been shown to be involved in salt stress responses. Expression of the full-length OsNUC1 gene in Arabidopsis resulted in hypersensitivity to ABA during germination. Transcriptome analysis of the transgenic lines, in comparison with the wild type, revealed that the RNA abundance of >1,900 genes was significantly changed under normal growth conditions, while under salt stress conditions the RNAs of 999 genes were found to be significantly regulated. Gene enrichment analysis showed that under normal conditions OsNUC1 resulted in repression of genes involved in photosynthesis, while in salt stress conditions OsNUC1 increased expression of the genes involved in the light-harvesting complex. Correspondingly, the net rate of photosynthesis of the transgenic lines was increased under salt stress. Transgenic rice lines with overexpression of the OsNUC1-L gene were generated and tested for photosynthetic performance under salt stress conditions. The transgenic rice lines treated with salt stress at the booting stage had a higher photosynthetic rate and stomatal conductance in flag leaves and second leaves than the wild type. Moreover, higher contents of Chl a and carotenoids were found in flag leaves of the transgenic rice. These results suggest a role for OsNUC1 in the modification of the transcriptome, especially the gene transcripts responsible for photosynthesis, leading to stabilization of photosynthesis under salt stress conditions.

The impact of cerium oxide nanoparticles on the salt stress responses of Brassica napus L

Dwindling high quality water resources and growing population are forcing growers to irrigate crops with water of high salinity. It is well recognized that salinity negatively affects plant physiology and biochemistry, and represents one of the most serious threats to crop production and food security. Meanwhile, engineered nanoparticles (ENPs) are increasingly detected in irrigation water and agricultural soils due to the rapid advancement of nanotechnology. Previous research has demonstrated that ENPs such as cerium oxide nanoparticles (CeO₂-NPs) exert significant impact on plant growth and production. However, almost all previous studies were conducted in well controlled environment. Knowledge on how ENPs affect plant development in a stressed condition is almost empty. The goal of the present study was to understand the physiological and biochemical changes in Brassica napus L. (canola) cv. 'Dwarf Essex' under synergistic salt stress and CeO₂-NPs effects. Two salinity levels: 0 (control) and 100 mM NaCl, and three CeO₂-NPs concentrations: 0 (control), 200 and 1000 mg kg^-1 dry sand and clay mixture, were employed. As expected, 100 mM of NaCl significantly hindered plant growth and negatively affected the physiological processes of canola. Plants treated with CeO₂-NPs had higher plant biomass, exhibited higher efficiency of the photosynthetic apparatus and less stress in both fresh water and saline water irrigation conditions Overall, our results demonstrated that CeO₂-NPs led to changes in canola growth and physiology which improved the plant salt stress response but did not completely alleviate the salt stress of canola.

Differential gene expression of salt-stressed Peganum harmala L

The response of Peganum harmala L. seedlings subjected to salinity was investigated through the observation of germination at the 4th, 6th and 8th days under normal and two salinity levels (150 and 200 mM NaCl). Genetic response of P. harmala was examined by quantitative estimation and electrophoretic separation of catalase and salt-soluble proteins. The gene expression of catalase and osmotin were investigated using RT-PCR. Final percentage of germination at the eighth day of germination was reduced from 85% in the control to 70 and 30% under the concentration of 150 and 200 mM. The catalase activity and protein content increased as the salinity increased compared to control seedlings. The electrophoretic separation of catalase and salt-soluble proteins exhibited stress-related isozymes and protein bands. RT-PCR of cat1, cat2-3 and cat3 and osmotin genes exhibited up-regulation and down-regulation of genes subsequent to salinity. The reduced germination percentage of salt stressed seedlings was attributed to oxidative damage and osmotic imbalance. The increased catalase activity and protein content were concluded as protective response of P. harmala seedlings to salinity induced oxidative stress and osmoregulation. The additional isozyme bands in the salt-stressed seedlings indicated modulation of CAT gene expression in response to elevated H2O2 subsequent to salinity. The stress specific gene expression was interpreted as molecular mechanism by which plants can tolerate salinity stress. The up-regulation of cat2-3 gene in relation to stress suggests it crucial role in salinity tolerance in P. harmala and further studies are needed for its sequence identification.

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.

Nitrogen-Efficient and Nitrogen-Inefficient Indian Mustard Showed Differential Expression Pattern of Proteins in Response to Elevated CO2 and Low Nitrogen

Carbon (C) and nitrogen (N) are two essential elements that influence plant growth and development. The C and N metabolic pathways influence each other to affect gene expression, but little is known about which genes are regulated by interaction between C and N or the mechanisms by which the pathways interact. In the present investigation, proteome analysis of N-efficient and N-inefficient Indian mustard, grown under varied combinations of low-N, sufficient-N, ambient [CO2], and elevated [CO2] was carried out to identify proteins and the encoding genes of the interactions between C and N. Two-dimensional gel electrophoresis (2-DE) revealed 158 candidate protein spots. Among these, 72 spots were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins are related to various molecular processes including photosynthesis, energy metabolism, protein synthesis, transport and degradation, signal transduction, nitrogen metabolism and defense to oxidative, water and heat stresses. Identification of proteins like PII-like protein, cyclophilin, elongation factor-TU, oxygen-evolving enhancer protein and rubisco activase offers a peculiar overview of changes elicited by elevated [CO2], providing clues about how N-efficient cultivar of Indian mustard adapt to low N supply under elevated [CO2] conditions. This study provides new insights and novel information for a better understanding of adaptive responses to elevated [CO2] under N deficiency in Indian mustard.