Comparative proteomic analysis of early salt stress-responsive proteins in roots of SnRK2 transgenic rice

Genome-wide identification, phylogenetic, structural and functional evolution of the core components of ABA signaling in plant species: a focus on rice

MAIN CONCLUSION

A genome-wide analysis had identified 642 ABA core component genes from 20 plant species, which were further categorized into three distinct subfamilies. The gene structures and evolutionary relationships of these genes had been characterized. PP2C_1, PP2C_2, and SnRK2_1 had emerged as key players in mediating the ABA signaling transduction pathway, specifically in rice, in response to abiotic stresses. The plant hormone abscisic acid (ABA) is essential for growth, development, and stress response, relying on its core components, pyrabactin resistance, pyrabactin resistance-like, and the regulatory component of ABA receptor (PYR/PYL/RCAR), 2C protein phosphatase (PP2C), sucrose non-fermenting-1-related protein kinase 2 (SnRK2). However, there's a lack of research on their structural evolution and functional differentiation across plants. Our study analyzed the phylogenetic, gene structure, homology, and duplication evolution of this complex in 20 plant species. We found conserved patterns in copy number and homology across subfamilies. Segmental and tandem duplications drove the evolution of these genes, while whole-genome duplication (WGD) expanded PYR/PYL/RCAR and PP2C subfamilies, enhancing environmental adaptation. In rice and Arabidopsis, the PYR/PYL/RCAR, PP2C, and SnRK2 genes showed distinct tissue-specific expression and responded to various stresses. Notably, PP2C_1 and PP2C_2 interacted with SnRK2_1 and were crucial for ABA signaling in rice. These findings offered new insights into ABA signaling evolution, interactions, and integration in green plants, benefiting future research in agriculture, evolutionary biology, ecology, and environmental science.

Bacillus altitudinis AD13-4 Enhances Saline-Alkali Stress Tolerance of Alfalfa and Affects Composition of Rhizosphere Soil Microbial Community

Saline and alkaline stresses limit plant growth and reduce crop yield. Soil salinization and alkalization seriously threaten the sustainable development of agriculture and the virtuous cycle of ecology. Biofertilizers made from plant growth-promoting rhizobacteria (PGPR) not only enhance plant growth and stress tolerance, but also are environmentally friendly and cost-effective. There have been many studies on the mechanisms underlying PGPRs enhancing plant salt resistance. However, there is limited knowledge about the interaction between PGPR and plants under alkaline-sodic stress. To clarify the mechanisms underlying PGPR's improvement of plants' tolerance to alkaline-sodic stress, we screened PGPR from the rhizosphere microorganisms of local plants growing in alkaline-sodic land and selected an efficient strain, Bacillus altitudinis AD13-4, as the research object. Our results indicate that the strain AD13-4 can produce various growth-promoting substances to regulate plant endogenous hormone levels, cell division and differentiation, photosynthesis, antioxidant capacity, etc. Transcriptome analysis revealed that the strain AD13-4 significantly affected metabolism and secondary metabolism, signal transduction, photosynthesis, redox processes, and plant-pathogen interactions. Under alkaline-sodic conditions, inoculation of the strain AD13-4 significantly improved plant biomass and the contents of metabolites (e.g., soluble proteins and sugars) as well as secondary metabolites (e.g., phenols, flavonoids, and terpenoids). The 16S rRNA gene sequencing results indicated that the strain AD13-4 significantly affected the abundance and composition of the rhizospheric microbiota and improved soil activities and physiochemical properties. Our study provides theoretical support for the optimization of saline-alkali-tolerant PGPR and valuable information for elucidating the mechanism of plant alkaline-sodic tolerance.

Role of methylglyoxal and glyoxalase in the regulation of plant response to heavy metal stress

KEY MESSAGE

Methylglyoxal and glyoxalase function a significant role in plant response to heavy metal stress. We update and discuss the most recent developments of methylglyoxal and glyoxalase in regulating plant response to heavy metal stress. Methylglyoxal (MG), a by-product of several metabolic processes, is created by both enzymatic and non-enzymatic mechanisms. It plays an important role in plant growth and development, signal transduction, and response to heavy metal stress (HMS). Changes in MG content and glyoxalase (GLY) activity under HMS imply that they may be potential biomarkers of plant stress resistance. In this review, we summarize recent advances in research on the mechanisms of MG and GLY in the regulation of plant responses to HMS. It has been discovered that appropriate concentrations of MG assist plants in maintaining a balance between growth and development and survival defense, therefore shielding them from heavy metal harm. MG and GLY regulate plant physiological processes by remodeling cellular redox homeostasis, regulating stomatal movement, and crosstalking with other signaling molecules (including abscisic acid, gibberellic acid, jasmonic acid, cytokinin, salicylic acid, melatonin, ethylene, hydrogen sulfide, and nitric oxide). We also discuss the involvement of MG and GLY in the regulation of plant responses to HMS at the transcriptional, translational, and metabolic levels. Lastly, considering the current state of research, we present a perspective on the future direction of MG research to elucidate the MG anti-stress mechanism and offer a theoretical foundation and useful advice for the remediation of heavy metal-contaminated environments in the future.

Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat

BACKGROUND

The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat.

RESULTS

To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance.

CONCLUSION

Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.

Comprehensive analysis of the aldehyde dehydrogenase gene family in Phaseolus vulgaris L. and their response to saline-alkali stress

Background

Aldehyde dehydrogenase (ALDH) scavenges toxic aldehyde molecules by catalyzing the oxidation of aldehydes to carboxylic acids. Although ALDH gene family members in various plants have been extensively studied and were found to regulate plant response to abiotic stress, reports on ALDH genes in the common bean (Phaseolus vulgaris L.) are limited. In this study, we aimed to investigate the effects of neutral (NS) and basic alkaline (AS) stresses on growth, physiological and biochemical indices, and ALDH activity, ALDH gene expression of common bean. In addition, We used bioinformatics techniques to analyze the physical and chemical properties, phylogenetic relationships, gene replication, collinearity, cis-acting elements, gene structure, motifs, and protein structural characteristics of PvALDH family members.

Results

We found that both NS and AS stresses weakened the photosynthetic performance of the leaves, induced oxidative stress, inhibited common bean growth, and enhanced the antioxidative system to scavenge reactive oxygen species. Furthermore, we our findings revealed that ALDH in the common bean actively responds to NS or AS stress by inducing the expression of PvALDH genes. In addition, using the established classification criteria and phylogenetic analysis, 27 PvALDHs were identified in the common bean genome, belonging to 10 ALDH families. The primary expansion mode of PvALDH genes was segmental duplication. Cis-acting elemental analysis showed that PvALDHs were associated with abiotic stress and phytohormonal responses. Gene expression analysis revealed that the PvALDH gene expression was tissue-specific. For instance, PvALDH3F1 and PvALDH3H1 were highly expressed in flower buds and flowers, respectively, whereas PvALDH3H2 and PvALDH2B4 were highly expressed in green mature pods and young pods, respectively. PvALDH22A1 and PvALDH11A2 were highly expressed in leaves and young trifoliates, respectively; PvALDH18B2 and PvALDH18B3 were highly expressed in stems and nodules, respectively; and PvALDH2C2 and PvALDH2C3 were highly expressed in the roots. PvALDHs expression in the roots responded positively to NS-AS stress, and PvALDH2C3, PvALDH5F1, and PvALDH10A1 were significantly (P < 0.05) upregulated in the roots.

Conclusion

These results indicate that AS stress causes higher levels of oxidative damage than NS stress, resulting in weaker photosynthetic performance and more significant inhibition of common bean growth. The influence of PvALDHs potentially modulates abiotic stress response, particularly in the context of saline-alkali stress. These findings establish a basis for future research into the potential roles of ALDHs in the common bean.

Physiological and Transcriptome Analysis of the Effects of Exogenous Strigolactones on Drought Responses of Pepper Seedlings

Drought stress significantly restricts the growth, yield, and quality of peppers. Strigolactone (SL), a relatively new plant hormone, has shown promise in alleviating drought-related symptoms in pepper plants. However, there is limited knowledge on how SL affects the gene expression in peppers when exposed to drought stress (DS) after the foliar application of SL. To explore this, we conducted a thorough physiological and transcriptome analysis investigation to uncover the mechanisms through which SL mitigates the effects of DS on pepper seedlings. DS inhibited the growth of pepper seedlings, altered antioxidant enzyme activity, reduced relative water content (RWC), and caused oxidative damage. On the contrary, the application of SL significantly enhanced RWC, promoted root morphology, and increased leaf pigment content. SL also protected pepper seedlings from drought-induced oxidative damage by reducing MDA and H2O2 levels and maintaining POD, CAT, and SOD activity. Moreover, transcriptomic analysis revealed that differentially expressed genes were enriched in ribosomes, ABC transporters, phenylpropanoid biosynthesis, and Auxin/MAPK signaling pathways in DS and DS + SL treatment. Furthermore, the results of qRT-PCR showed the up-regulation of AGR7, ABI5, BRI1, and PDR4 and down-regulation of SAPK6, NTF4, PYL6, and GPX4 in SL treatment compared with drought-only treatment. In particular, the key gene for SL signal transduction, SMXL6, was down-regulated under drought. These results elucidate the molecular aspects underlying SL-mediated plant DS tolerance, and provide pivotal strategies for effectively achieving pepper drought resilience.

Genome-Wide Identification and Analysis of Stress Response of Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase Genes in Quinoa

Saline-alkali stress seriously affects the yield and quality of crops, threatening food security and ecological security. Improving saline-alkali land and increasing effective cultivated land are conducive to sustainable agricultural development. Trehalose, a nonreducing disaccharide, is closely related to plant growth and development and stress response. Trehalose 6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) are key enzymes catalyzing trehalose biosynthesis. To elucidate the effects of long-term saline-alkali stress on trehalose synthesis and metabolism, we conducted an integrated transcriptome and metabolome analysis. As a result, 13 TPS and 11 TPP genes were identified in quinoa (Chenopodium quinoa Willd.) and were named CqTPS1-13 and CqTPP1-11 according to the order of their Gene IDs. Through phylogenetic analysis, the CqTPS family is divided into two classes, and the CqTPP family is divided into three classes. Analyses of physicochemical properties, gene structures, conservative domains and motifs in the proteins, and cis-regulatory elements, as well as evolutionary relationships, indicate that the TPS and TPP family characteristics are highly conserved in quinoa. Transcriptome and metabolome analyses of the sucrose and starch metabolism pathway in leaves undergoing saline-alkali stress indicate that CqTPP and Class II CqTPS genes are involved in the stress response. Moreover, the accumulation of some metabolites and the expression of many regulatory genes in the trehalose biosynthesis pathway changed significantly, suggesting the metabolic process is important for the saline-alkali stress response in quinoa.

Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress

Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.

Identification and expression pattern analysis of the OsSnRK2 gene family in rice

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a class of plant-specific serine/threonine (Ser/Thr) protein kinase that plays an important role in rice stress tolerance, growth and development. However, systematic bioinformatics and expression pattern analysis have not been reported. In the current study, ten OsSnRK2 genes were identified in the rice genome and located on 7 chromosomes, which can be classified into three subfamilies (I, II, and III). Many cis-regulatory elements were identified in the promoter region of OsSnRK2 genes, including hormone response elements, defense and stress responsive elements, indicating that the OsSnRK2 family may play a crucial role in response to hormonal and abiotic stress. Quantitative tissue analysis showed that OsSnRK2 genes expressed in all tissues of rice, but the expression abundance varied from different tissues and showed varietal variability. In addition, expression pattern of OsSnRK2 were analyzed under abiotic stress (salt, drought, salt and drought) and showed obvious difference in diverse abiotic stress. In general, these results provide useful information for understanding the OsSnRK2 gene family and analyzing its functions in rice in response to ABA, salt and drought stress, especially salt-drought combined stress.

Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L^-1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet's response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet's response to salt stress.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

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.

Salt stress proteins in plants: An overview

Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.

iTRAQ-based proteomic analysis provides insights into the molecular mechanisms of rice formyl tetrahydrofolate deformylase in salt response

A new molecular mechanism of tetrahydrofolate deformylase involved in the salt response presumably affects mitochondrial and chloroplast function by regulating energy metabolism and accumulation of reactive oxygen species. High salinity severely restrains plant growth and development, consequently leading to a reduction in grain yield. It is therefore critical to identify the components involved in plant salt resistance. In our previous study, we identified a rice leaf early-senescence mutant hpa1, which encodes a formyl tetrahydrofolate deformylase (Xiong et al. in Sci China Life Sci 64(5):720-738, 2021). Here, we report that HPA1 also plays a role in the salt response. To explore the molecular mechanism of HPA1 in salt resistance, we attempted to identify the differentially expressed proteins between wild type and hpa1 mutant for salinity treatment using an iTRAQ-based comparative protein quantification approach. A total of 4598 proteins were identified, of which 279 were significantly altered, including 177 up- and 102 down-regulated proteins. A functional analysis suggested that the 279 differentially expressed proteins are involved mainly in the regulation of oxidative phosphorylation, phenylpropanoid biosynthesis, photosynthesis, posttranslational modifications, protein turnover and energy metabolism. Moreover, a deficiency in HPA1 impaired chlorophyll metabolism and photosynthesis in chloroplasts and affected the electron flow of the electron transport chain in mitochondria. These changes led to abnormal energy metabolism and accumulation of reactive oxygen species, which may affect the permeability and integrity of cell membranes, leading to cell death. In addition, the results were verified by transcriptional or physiological experiments. Our results provide an insight into a new molecular mechanism of the tetrahydrofolate cycle protein formyl tetrahydrofolate deformylase, which is involved in the salt response, presumably by affecting mitochondrial and chloroplast function regulating energy metabolism and accumulation of reactive oxygen species under salt stress.

CCCH protein-PvCCCH69 acted as a repressor for leaf senescence through suppressing ABA-signaling pathway

CCCH is a subfamily of zinc finger proteins involved in plant growth, development, and stresses response. The function of CCCH in regulating leaf senescence, especially its roles in abscisic acid (ABA)-mediated leaf senescence is largely unknown. The objective of this study was to determine functions and mechanisms of CCCH gene in regulating leaf senescence in switchgrass (Panicum virgatum). A CCCH gene, PvCCCH69 (PvC3H69), was cloned from switchgrass. Overexpressing PvC3H69 in rice suppressed both natural senescence with leaf aging and dark-induced leaf senescence. Endogenous ABA content, ABA biosynthesis genes (NCED3, NCED5, and AAO3), and ABA signaling-related genes (SnRKs, ABI5, and ABF2/3/4) exhibited significantly lower levels in senescencing leaves of PvC3H69-OE plants than those in WT plants. PvC3H69-suppression of leaf senescence was associated with transcriptional upregulation of genes mainly involved in the light-dependent process of photosynthesis, including light-harvesting complex proteins, PSI proteins, and PSII proteins and downregulation of ABA biosynthesis and signaling genes and senescence-associated genes. PvC3H69 could act as a repressor for leaf senescence via upregulating photosynthetic proteins and repressing ABA synthesis and ABA signaling pathways.

Nitric Oxide Is Associated With Heterosis of Salinity Tolerance in Brassica napus L

Heterosis is most frequently manifested as the superior performance of a hybrid than either of the parents, especially under stress conditions. Nitric oxide (NO) is a well-known gaseous signaling molecule that acts as a functional component during plant growth, development, and defense responses. In this study, the Brassica napus L. hybrid (F1, NJ4375 × MB1942) showed significant heterosis under salt stress, during both germination and post-germination periods. These phenotypes in the hybrid were in parallel with the better performance in redox homeostasis, including alleviation of reactive oxygen species accumulation and lipid peroxidation, and ion homeostasis, evaluated as a lower Na/K ratio in the leaves than parental lines. Meanwhile, stimulation of endogenous NO was more pronounced in hybrid plants, compared with parental lines, which might be mediated by nitrate reductase. Proteomic and biochemical analyses further revealed that protein abundance related to several metabolic processes, including chlorophyll biosynthesis, proline metabolism, and tricarboxylic acid cycle metabolism pathway, was greatly suppressed by salt stress in the two parental lines than in the hybrid. The above responses in hybrid plants were intensified by a NO-releasing compound, but abolished by a NO scavenger, both of which were matched with the changes in chlorophyll and proline contents. It was deduced that the above metabolic processes might play important roles in heterosis upon salt stress. Taken together, we proposed that heterosis derived from F1 hybridization in salt stress tolerance might be mediated by NO-dependent activation of defense responses and metabolic processes.

Sulfur nanoparticles mediated improvement of salt tolerance in wheat relates to decreasing oxidative stress and regulating metabolic activity

Salinity is a critical issue impairing the growth and productivity of most crop species through the mediated ionic and osmotic imbalances. As a way forward, the current study was tailored to elucidate the capacity of sulfur nanoparticles (SNPs) to amend salinity consequences on growth and physio-biochemical attributes of wheat. In a controlled experiment, wheat seeds were primed for 12 h with either 100 μM SNPs or deionized water then sown in plastic pots containing 5 kg clay-sand mixture (2:1 w/w). A week later, pots received NaCl (100 or 200 mM) as a sole treatment or in combination with SNPs and after three weeks the data of morph-bio-physiological traits were recorded. Salinity decreased growth rate, pigmentation, protein, amino acids, cysteine, ascorbate, flavonoids and phenolics content in wheat leaves. Plants pre-treated with 100 μM SNPs showed improved growth rate, pigmentation, nitrogen metabolism as well as non-enzymatic antioxidant contents as compared with salinized treatments. Neither salt nor SNP treatments affected photosynthetic performance rate (Fv/fm), however both treatments induced glutathione content. SNP treatment retrieved the undue excessive activities of catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), superoxide dismutase (SOD) and polyphenol oxidase (PPO) besides the increased level of proline caused by salt stress. Likewise, 100 μM SNPs rebalanced the declined nitrogen, phosphorus and potassium contents and decreased sodium uptake caused by salinity. On the whole, priming with 100 μM SNPs improved photosynthetic pigments, nitrogen metabolism, antioxidant status and ionic relations contributing to the enhancement of growth attributes in wheat under salinity.

CCOAOMT1, a candidate cargo secreted via VAMP721/722 secretory vesicles in Arabidopsis

We previously found that VAMP721/722 SNARE proteins guide secretory vesicles to pathogen-attacking sites during immune responses in Arabidopsis, which suggests that these vesicles should deliver immune molecules. However, the lethality of vamp721 vamp722 double null mutant makes it difficult to understand the nature of cargo transported via VAMP721/722 vesicles. Since VAMP721/722-depleted (VAMP721^+/-VAMP722^-/- and VAMP721^-/-VAMP722^+/-) plants show compromised resistance to extracellular pathogens, we assume that an immune protein secreted through the VAMP721/722-engaged exocytosis would be remained more in VAMP721/722-depleted plants than WT. By comparing intracellular proteins between WT and VAMP721/722-depleted plants, we found caffeoyl-CoA O-methyltransferase 1 (CCOAOMT1) involved in the lignin biosynthesis was more abundantly detected in both VAMP721/722-depleted lines than WT. Plants are well-known to deposit secondary cell walls as physical barriers at pathogen-attempting sites. Therefore, extracellular detection of CCOAOMT1 and impaired resistance to Pseudomonas syringae DC3000 in ccoaomt1 plants suggest that plants secrete cell wall-modifying enzymes at least including CCOAOMT1 to reinforce the secondary cell walls for immunity.

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

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

Salt-Treated Roots of Oryza australiensis Seedlings are Enriched with Proteins Involved in Energetics and Transport

Salinity is a major constraint on rice productivity worldwide. However, mechanisms of salt tolerance in wild rice relatives are unknown. Root microsomal proteins are extracted from two Oryza australiensis accessions contrasting in salt tolerance. Whole roots of 2-week-old seedlings are treated with 80 mM NaCl for 30 days to induce salt stress. Proteins are quantified by tandem mass tags (TMT) and triple-stage Mass Spectrometry. More than 200 differentially expressed proteins between the salt-treated and control samples in the two accessions (p-value <0.05) are found. Gene Ontology (GO) analysis shows that proteins categorized as "metabolic process," "transport," and "transmembrane transporter" are highly responsive to salt treatment. In particular, mitochondrial ATPases and SNARE proteins are more abundant in roots of the salt-tolerant accession and responded strongly when roots are exposed to salinity. mRNA quantification validated the elevated protein abundances of a monosaccharide transporter and an antiporter observed in the salt-tolerant genotype. The importance of the upregulated monosaccharide transporter and a VAMP-like protein by measuring salinity responses of two yeast knockout mutants for genes homologous to those encoding these proteins in rice are confirmed. Potential new mechanisms of salt tolerance in rice, with implications for breeding of elite cultivars are also discussed.

Comparative proteomic analysis of two sesame genotypes with contrasting salinity tolerance in response to salt stress

Sesame is one of the most important oilseed crops and has high nutritional value. The yield and quality of sesame are severely affected by high salinity in coastal and semi-arid/arid regions. In this study, the phenotypic, physiological, and proteomic changes induced by salt treatment were analyzed in salt-tolerant (G441) and salt-sensitive (G358) seedlings. Phenotypic and physiological results indicated that G441 had an enhanced capacity to withstand salinity stress compared to G358. Proteomic analysis revealed a strong induction of salt-responsive protein species in sesame, mainly related to catalytic, hydrolase, oxidoreductase, and binding activities. Pathway enrichment analysis showed that more salt-responsive proteins in G441 were involved in tyrosine metabolism, carbon fixation in photosynthetic organisms, carbon metabolism, alpha-linolenic acid metabolism, biosynthesis of amino acids, photosynthesis, and glutathione metabolism. Furthermore, G441 displayed unique differentially accumulated proteins in seedlings functioning as heat shock proteins, abscisic acid receptor PYL2-like, calcium-dependent protein kinases, serine/threonine-protein phosphatases, nucleoredoxin, and antioxidant enzymes. Quantitative real-time PCR analysis revealed that some of the proteins were also regulated by salinity stress at the transcript level. Our findings provide important information on salinity responses in plants and may constitute useful resources for enhancing salinity tolerance in sesame. SIGNIFICANCE: Our study identified potential biological pathways and salt-responsive protein species related to transducing stress signals and scavenging reactive oxygen species under salt stress. These findings will provide possible participants/pathways/proteins that contribute to salt tolerance and may serve as the basis for improving salinity tolerance in sesame and other plants.

Advances in understanding salt tolerance in rice

This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.

Advances in understanding salt tolerance in rice

This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.

Identification of Early Salinity Stress-Responsive Proteins in Dunaliella salina by isobaric tags for relative and absolute quantitation (iTRAQ)-Based Quantitative Proteomic Analysis

Salt stress is one of the most serious abiotic factors that inhibit plant growth. Dunaliella salina has been recognized as a model organism for stress response research due to its high capacity to tolerate extreme salt stress. A proteomic approach based on isobaric tags for relative and absolute quantitation (iTRAQ) was used to analyze the proteome of D. salina during early response to salt stress and identify the differentially abundant proteins (DAPs). A total of 141 DAPs were identified in salt-treated samples, including 75 upregulated and 66 downregulated DAPs after 3 and 24 h of salt stress. DAPs were annotated and classified into gene ontology functional groups. The Kyoto Encyclopedia of Genes and Genomes pathway analysis linked DAPs to tricarboxylic acid cycle, photosynthesis and oxidative phosphorylation. Using search tool for the retrieval of interacting genes (STRING) software, regulatory protein⁻protein interaction (PPI) networks of the DAPs containing 33 and 52 nodes were built at each time point, which showed that photosynthesis and ATP synthesis were crucial for the modulation of early salinity-responsive pathways. The corresponding transcript levels of five DAPs were quantified by quantitative real-time polymerase chain reaction (qRT-PCR). These results presented an overview of the systematic molecular response to salt stress. This study revealed a complex regulatory mechanism of early salt tolerance in D. salina and potentially contributes to developing strategies to improve stress resilience.

The sucrose non-fermenting-1-related protein kinases SAPK1 and SAPK2 function collaboratively as positive regulators of salt stress tolerance in rice

BACKGROUND

The sucrose non-fermenting-1-related protein kinase 2 family (SnRK2s) unifies different abiotic stress signals in plants. To date, the functions of two rice SnRK2s, osmotic stress/ABA-activated protein kinase 1 (SAPK1) and SAPK2, have been unknown. We investigated their roles in response to salt stress by generating loss-of-function lines using the CRISPR/Cas9 system and by overexpressing these proteins in transgenic rice plants.

RESULTS

Expression profiling revealed that SAPK1 and SAPK2 expression were strongly induced by drought, NaCl, and PEG treatment, but not by ABA. SAPK2 expression was highest in the leaves, followed by the roots, whereas SAPK1 was highest expressed in roots followed by leaves. Both proteins were localized to the nucleus and the cytoplasm. Under salt stress, sapk1, sapk2 and, in particular, sapk1/2 mutants, exhibited reduced germination rates, more severe growth inhibition, more distinct chlorosis, reduced chlorophyll contents, and reduced survival rates in comparison with the wild-type plants. In contrast, SAPK1- and SAPK2-overexpression lines had increased germination rates and reduced sensitivities to salt; including mild reductions in growth inhibition, reduced chlorosis, increased chlorophyll contents and improved survival rates in comparison with the wild-type plants. These results suggest that SAPK1 and SAPK2 may function collaboratively as positive regulators of salt stress tolerance at the germination and seedling stages. We also found that SAPK1 and SAPK2 affected the osmotic potential following salt stress by promoting the generation of osmotically active metabolites such as proline. SAPK1 and SAPK2 also improved reactive oxygen species (ROS) detoxification following salt stress by promoting the generation of ROS scavengers such as ascorbic acid, and by increasing the expression levels of proteins such as superoxide dismutase (SOD) and catalase (CAT). SAPK1 and SAPK2 may function collaboratively in reducing Na⁺ toxicity by affecting the Na⁺ distribution between roots and shoots, Na⁺ exclusion from the cytoplasm, and Na⁺ sequestration into the vacuoles. These effects may be facilitated through the expression of Na⁺-and K⁺-homeostasis-related genes.

CONCLUSION

SAPK1 and SAPK2 may function collaboratively as positive regulators of salt stress tolerance at the germination and seedling stages in rice. SAPK1 and SAPK2 may be useful to improve salt tolerance in crop plants.

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

Background

DNA methylation has a potential role in controlling gene expression and may, therefore, contribute to salinity adaptation in plants. Caliph medic (Medicago truncatula) is a model legume of moderate salinity tolerance capacity; however, a base-resolution DNA methylome map is not yet available for this plant.

Results

In this report, a differential whole-genome bisulfite sequencing (WGBS) was carried out using DNA samples extracted from root tissues exposed to either control or saline conditions. Around 50 million differentially methylated sites (DMSs) were recognized, 7% of which were significantly (p < 0.05, FDR < 0.05) altered in response to salinity. This analysis showed that 77.0% of the contexts of DMSs were mCHH, while only 9.1% and 13.9% were mCHG and mCG, respectively. The average change in methylation level was increased in all sequence contexts, ranging from 3.8 to 10.2% due to salinity stress. However, collectively, the level of the DNA methylation in the gene body slightly decreased in response to salinity treatment. The global increase in DNA methylation due to salinity was confirmed by mass spectrometry analysis. Gene expression analysis using qPCR did not reveal a constant relationship between the level of mCG methylation and the transcription abundance of some genes of potential importance in salinity tolerance, such as the potassium channel KAT3, the vacuolar H⁺-pyrophosphatase (V-PPase), and the AP2/ERF and bZIP transcription factors, implying the involvement of other epigenetic gene expression controllers. Computational functional prediction of the annotated genes that embrace DMSs revealed the presence of enzymes with potential cellular functions in biological processes associated with salinity tolerance mechanisms.

Conclusions

The information obtained from this study illustrates the effect of salinity on DNA methylation and shows how plants can remodel the landscape of 5-methylcytosine nucleotide (5-mC) in the DNA across gene structures, in response to salinity. This remodeling varies between gene regions and between 5-mC sequence contexts. The mCG has a vague impact on the expression levels of a few selected potentially important genes in salt tolerant mechanisms.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4484-5) contains supplementary material, which is available to authorized users.

Proteomic analysis of early salt stress responsive proteins in alfalfa roots and shoots

Background

Alfalfa (Medicago sativa) is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue variations in response to salt stress, comparative physiological and proteomic analyses were made of salt responses in the roots and shoots of the alfalfa.

Method

A two-dimensional gel electrophoresis (2-DE)-based proteomic technique was employed to identify the differentially abundant proteins (DAPs) from salt-treated alfalfa roots and shoots of the salt tolerance cultivars Zhongmu No 1 cultivar, which was subjected to a range of salt stress concentrations for 9 days. In parallel, REL, MAD and H₂O₂ contents, and the activities of antioxidant enzymes of shoots and roots were determinand.

Result

Twenty-seven spots in the shoots and 36 spots in the roots that exhibited showed significant abundance variations were identified by MALDI-TOF-TOF MS. These DAPs are mainly involved in the biological processes of photosynthesis, stress and defense, carbohydrate and energy metabolism, second metabolism, protein metabolism, transcriptional regulation, cell wall and cytoskeleton metabolism, ion transpor, signal transduction. In parallel, physiological data were correlated well with our proteomic results. It is worth emphasizing that some novel salt-responsive proteins were identified, such as CP12, pathogenesis-related protein 2, harvest-induced protein, isoliquiritigenin 2′-O-methyltransferase. qRT-PCR was used to study the gene expression levels of the four above-mentioned proteins; four patterns are consistent with those of induced protein.

Conclusion

The primary mechanisms underlying the ability of alfalfa seedlings to tolerate salt stress were photosynthesis, detoxifying and antioxidant, secondary metabolism, and ion transport. And it also suggests that the different tissues responded to salt-stress in different ways.

Methylmalonate-semialdehyde dehydrogenase mediated metabolite homeostasis essentially regulate conidiation, polarized germination and pathogenesis in Magnaporthe oryzae

Plants generate multitude of aldehydes under abiotic and biotic stress conditions. Ample demonstrations have shown that rice-derived aldehydes enhance the resistance of rice against the rice-blast fungus Magnaporthe oryzae. However, how the fungal pathogen nullifies the inhibitory effects of host aldehydes to establish compatible interaction remains unknown. Here we identified and evaluated the in vivo transcriptional activities of M. oryzae aldehyde dehydrogenase (ALDH) genes. Transcriptional analysis of M. oryzae ALDH genes revealed that the acetylating enzyme Methylmalonate-Semialdehyde Dehydrogenase (MoMsdh/MoMmsdh) elevated activities during host invasion and colonization of the fungus. We further examined the pathophysiological importance of MoMSDH by deploying integrated functional genetics, and biochemical approaches. MoMSDH deletion mutant ΔMomsdh exhibited germination defect, hyper-branching of germ tube and failed to form appressoria on hydrophobic and hydrophilic surface. The MoMSDH disruption caused accumulation of small branch-chain amino acids, pyridoxine and AMP/cAMP in the ΔMomsdh mutant and altered Spitzenkörper organization in the conidia. We concluded that MoMSDH contribute significantly to the pathogenesis of M. oryzae by regulating the mobilization of Spitzenkörper during germ tube morphogenesis, appressoria formation by acting as metabolic switch regulating small branch-chain amino acids, inositol, pyridoxine and AMP/cAMP homeostasis.

OsSAPK2 Confers Abscisic Acid Sensitivity and Tolerance to Drought Stress in Rice

SNF 1-RELATED PROTEIN KINASE 2 (SnRK2) is a family of plant-specific protein kinases which is the key regulator of hyper-osmotic stress signaling and abscisic acid (ABA)-dependent development in various plants. Among the rice subclass-I and -II SnRK2s, osmotic stress/ABA-activated protein kinase 2 (SAPK2) may be the primary mediator of ABA signaling. However, SAPK2 has not been comprehensively characterized. In this study, we elucidated the functional properties of SAPK2 using loss-of-function mutants produced with the CRISPR/Cas9 system. The SAPK2 expression level was strongly upregulated by drought, high-salinity, and polyethylene glycol (PEG) treatments. The sapk2 mutants exhibited an ABA-insensitive phenotype during the germination and post-germination stages, suggesting that SAPK2 had a pivotal role related to ABA-mediated seed dormancy. The sapk2 mutants were more sensitive to drought stress and reactive oxygen species (ROS) than the wild-type plants, indicating that SAPK2 was important for responses to drought conditions in rice. An additional investigation revealed that SAPK2 increased drought tolerance in the following two ways: (i) by reducing water loss via the accumulation of compatible solutes, promoting stomatal closure, and upregulating the expression levels of stress-response genes such as OsRab16b, OsRab21, OsbZIP23, OsLEA3, OsOREB1 and slow anion channel (SLAC)-associated genes such as OsSLAC1 and OsSLAC7; (ii) by inducing the expression of antioxidant enzyme genes to promote ROS-scavenging abilities that will ultimately decrease ROS damages. Moreover, we also observed that SAPK2 significantly increased the tolerance of rice plants to salt and PEG stresses. These findings imply that SAPK2 is a potential candidate gene for future crop improvement studies.

Proteomic Analysis Reveals the Positive Roles of the Plant-Growth-Promoting Rhizobacterium NSY50 in the Response of Cucumber Roots to Fusarium oxysporum f. sp. cucumerinum Inoculation

Plant-growth-promoting rhizobacteria (PGPR) can both improve plant growth and enhance plant resistance against a variety of environmental stresses. To investigate the mechanisms that PGPR use to protect plants under pathogenic attack, transmission electron microscopy analysis and a proteomic approach were designed to test the effects of the new potential PGPR strain Paenibacillus polymyxa NSY50 on cucumber seedling roots after they were inoculated with the destructive phytopathogen Fusarium oxysporum f. sp. cucumerinum (FOC). NSY50 could apparently mitigate the injury caused by the FOC infection and maintain the stability of cell structures. The two-dimensional electrophoresis (2-DE) approach in conjunction with MALDI-TOF/TOF analysis revealed a total of 56 proteins that were differentially expressed in response to NSY50 and/or FOC. The application of NSY50 up-regulated most of the identified proteins that were involved in carbohydrate metabolism and amino acid metabolism under normal conditions, which implied that both energy generation and the production of amino acids were enhanced, thereby ensuring an adequate supply of amino acids for the synthesis of new proteins in cucumber seedlings to promote plant growth. Inoculation with FOC inhibited most of the proteins related to carbohydrate and energy metabolism and to protein metabolism. The combined inoculation treatment (NSY50+FOC) accumulated abundant proteins involved in defense mechanisms against oxidation and detoxification as well as carbohydrate metabolism, which might play important roles in preventing pathogens from attacking. Meanwhile, western blotting was used to analyze the accumulation of enolase (ENO) and S-adenosylmethionine synthase (SAMs). NSY50 further increased the expression of ENO and SAMs under FOC stress. In addition, NSY50 adjusted the transcription levels of genes related to those proteins. Taken together, these results suggest that P. polymyxa NSY50 may promote plant growth and alleviate FOC-induced damage by improving the metabolism and activation of defense-related proteins in cucumber roots.

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress

Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance.

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.

Ectopic over-expression of BoHO1, a cabbage heme oxygenase gene, improved salt tolerance in Arabidopsis: A case study on proteomic analysis

Plant heme oxygenase (HO) catalyzes the oxygenation of heme to biliverdin, carbon monoxide, and free iron, and is regarded as a stress-responsive protein. Here, a cabbage HO1 gene (named as BoHO1) was isolated and characterized. BoHO1 shares a high degree homology with Arabidopsis AtHO1, and could locate in Arabidopsis chloroplast. BoHO1 mRNA was ubiquitously expressed in cabbage tissues, and was responsive to several stimuli and chemicals. Genetic evidence illustrated that over-expression of BoHO1 in transgenic Arabidopsis plants (35S:BoHO1-1 and 35S:BoHO1-2) significantly alleviated salinity stress-inhibited seedling growth, which were accompanied with the re-establishment of reactive oxygen species and ion homeostasis. Comparative proteomic analysis was subsequently performed. Results revealed that protein abundance related to light reactions was greatly suppressed by NaCl stress in wild-type, whereas was partially recovered in 35S:BoHO1-1. Salinity stress also strongly activated stress-related metabolic processes in wild-type, i.e. carbon and energy metabolism, ammonium detoxification, and protein turnover, and these induced tendencies were more intensive in 35S:BoHO1-1. Particularly, proteins related to glutathione metabolism and ion homeostasis were specifically enriched in NaCl-stressed 35S:BoHO1-1. On the basis of above results, we propose that BoHO1 could activate multiple stress-responsive pathways to help Arabidopsis regain cellular homeostasis, thus presenting enhanced adaptation to salinity stress.

Rootstock-scion interaction affecting citrus response to CTV infection: a proteomic view

Citrus tristeza virus (CTV) is the causal agent of various diseases with dramatic effects on citrus crops worldwide. Most Citrus species, grown on their own roots, are symptomless hosts for many CTV isolates. However, depending on different scion-rootstock combination, CTV infection should result in distinct syndromes, being 'tristeza' the more severe one, leading to a complete decline of the susceptible plants in a few weeks. Transcriptomic analyses revealed several genes involved either in defense response, or systemic acquired resistance, as well as transcription factors and components of the phosphorylation cascades, to be differentially regulated during CTV infection in Citrus aurantifolia species. To date little is known about the molecular mechanism of this host-pathogen interaction, and about the rootstock effect on citrus response to CTV infection. In this work, the response to CTV infection has been investigated in tolerant and susceptible scion-rootstock combinations by two-dimensional gel electrophoresis (2DE). A total of 125 protein spots have been found to be differently accumulated and/or phosphorylated between the two rootstock combinations. Downregulation in tolerant plants upon CTV infection was detected for proteins involved in reactive oxygen species (ROS) scavenging and defense response, suggesting a probable acclimation response able to minimize the systemic effects of virus infection. Some of these proteins resulted to be modulated also in absence of virus infection, revealing a rootstock effect on scion proteome modulation. Moreover, the phospho-modulation of proteins involved in ROS scavenging and defense response, further supports their involvement either in scion-rootstock crosstalk or in the establishment of tolerance/susceptibility to CTV infection.

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

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

Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics

Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.

Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress

Salinity is a limiting factor affecting crop growth. We evaluated the responses of a salt-tolerant recombinant inbred rice (Oryza sativa L.) line, FL478, and the salt-sensitive IR29. Seedlings were exposed to salt stress and the growth rate was monitored to decipher the effect of long-term stress. At Day 16, IR29 produced lower shoot biomass than FL478. Significant differences for Na+ and K+ concentrations and Na+ : K+ ratios in roots and shoots were observed between genotypes. Changes in the proteomes of control and salt-stressed plants were analysed, identifying 59 and 39 salt-responsive proteins in roots and leaves, respectively. Proteomic analysis showed greater downregulation of proteins in IR29. In IR29, proteins related to pathways involved in salt tolerance (e.g. oxidative stress response, amino acid biosynthesis, polyamine biosynthesis, the actin cytoskeleton and ion compartmentalisation) changed to combat salinity. We found significant downregulation of proteins related to photosynthetic electron transport in IR29, indicating that photosynthesis was influenced, probably increasing the risk of reactive oxygen species formation. The sensitivity of IR29 might be related to its inability to exclude salt from its transpiration stream, to compartmentalise excess ions and to maintain a healthy photosynthetic apparatus during salt stress, or might be because of the leakiness of its roots, allowing excess salt to enter apoplastically. In FL478, superoxide dismutase, ferredoxin thioredoxin reductase, fibre protein and inorganic pyrophosphatase, which may participate in salt tolerance, increased in abundance. Our analyses provide novel insights into the mechanisms behind salt tolerance and sensitivity in genotypes with close genetic backgrounds.

High Throughput Sequencing of Small RNAs in the Two Cucurbita Germplasm with Different Sodium Accumulation Patterns Identifies Novel MicroRNAs Involved in Salt Stress Response

MicroRNAs (miRNAs), a class of small non-coding RNAs, recognize their mRNA targets based on perfect sequence complementarity. MiRNAs lead to broader changes in gene expression after plants are exposed to stress. High-throughput sequencing is an effective method to identify and profile small RNA populations in non-model plants under salt stresses, significantly improving our knowledge regarding miRNA functions in salt tolerance. Cucurbits are sensitive to soil salinity, and the Cucurbita genus is used as the rootstock of other cucurbits to enhance salt tolerance. Several cucurbit crops have been used for miRNA sequencing but salt stress-related miRNAs in cucurbit species have not been reported. In this study, we subjected two Cucurbita germplasm, namely, N12 (Cucurbita. maxima Duch.) and N15 (Cucurbita. moschata Duch.), with different sodium accumulation patterns, to Illumina sequencing to determine small RNA populations in root tissues after 4 h of salt treatment and control. A total of 21,548,326 and 19,394,108 reads were generated from the control and salt-treated N12 root tissues, respectively. By contrast, 19,108,240 and 20,546,052 reads were obtained from the control and salt-treated N15 root tissues, respectively. Fifty-eight conserved miRNA families and 33 novel miRNAs were identified in the two Cucurbita germplasm. Seven miRNAs (six conserved miRNAs and one novel miRNAs) were up-regulated in salt-treated N12 and N15 samples. Most target genes of differentially expressed novel miRNAs were transcription factors and salt stress-responsive proteins, including dehydration-induced protein, cation/H⁺ antiporter 18, and CBL-interacting serine/threonine-protein kinase. The differential expression of miRNAs between the two Cucurbita germplasm under salt stress conditions and their target genes demonstrated that novel miRNAs play an important role in the response of the two Cucurbita germplasm to salt stress. The present study initially explored small RNAs in the response of pumpkin to salt stress, and provided valuable information on novel miRNAs and their target genes in Cucurbita.

Identification of Leaf Proteins Differentially Accumulated between Wheat Cultivars Distinct in Their Levels of Drought Tolerance

The drought-tolerant ‘Ningchun 47’ (NC47) and drought-sensitive ‘Chinese Spring’ (CS) wheat (Triticum aestivum L.) cultivars were treated with different PEG6000 concentrations at the three-leaf stage. An analysis on the physiological and proteomic changes of wheat seedling in response to drought stress was performed. In total, 146 differentially accumulated protein (DAP) spots were separated and recognised using two-dimensional gel electrophoresis. In total, 101 DAP spots representing 77 unique proteins were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. These proteins were allocated to 10 groups according to putative functions, which were mainly involved in carbon metabolism (23.4%), photosynthesis/respiration (22.1%) and stress/defence/detoxification (18.2%). Some drought stress-related proteins in NC47, such as enolase, 6-phosphogluconate dehydrogenase, Oxygen-evolving enhancer protein 2, fibrillin-like protein, 2-Cys peroxiredoxin BAS1 and 70-kDa heat shock protein, were more upregulated than those in CS. Multivariate principal components analysis revealed obvious differences between the control and treatments in both NC47 and CS, while cluster analysis showed that the DAPs displayed five and six accumulation patterns in NC47 and CS, respectively. Protein–protein interaction network analysis showed that some key DAPs, such as 2-Cys peroxiredoxin BAS1, RuBisCO large subunit-binding protein, 50S ribosomal protein L1, 6-phosphogluconate dehydrogenase, glyceraldehyde 3-phosphate dehydrogenase isoenzyme and 70-kDa heat shock protein, with upregulated accumulation in NC47, had complex interactions with other proteins related to amino acid metabolism, carbon metabolism, energy pathway, signal transduction, stress/defence/detoxification, protein folding and nucleotide metabolism. These proteins could play important roles in drought-stress tolerance and contribute to the relatively stronger drought tolerance of NC47.

Proteomic study related to vascular connections in watermelon scions grafted onto bottle-gourd rootstock under different light intensities

Although grafting is broadly used in the production of crops, no information is available about the proteins involved in vascular connections between rootstock and scion. Similarly, proteome changes under the light intensities widely used for grafted seedlings are of practical use. The objective of this study was to determine the proteome of vascular connections using watermelon (Citrullus vulgaris Schrad.) ‘Sambok Honey’ and ‘Speed’ as the scion and bottle gourd (Lagenaria siceraria Stanld.) ‘RS Dongjanggun’ as the rootstock grown under different light intensities (25, 50, 75 and 100 μmol m⁻² s⁻¹). Our proteomic analysis revealed 24 and 27 differentially expressed proteins in ‘Sambok Honey’ and ‘Speed’, respectively, under different light intensities. The identified proteins were largely involved in ion binding, amino acid metabolism, transcriptional regulation and defense response. The enhancement of ion-binding, transcriptional regulation, amino acid metabolism, and defense response proteins suggests a strengthening of the connection between the rootstock and scion under high light intensity. Indeed, the accumulation of key enzymes in the biological processes described above appears to play an important role in the vascular connections of grafted seedlings. Moreover, it appears that 100 μmol m⁻² s⁻¹ results in better protein expression responses in grafted seedlings.

Salinity affects the proteomics of rice roots and leaves

While insights into the molecular mechanisms underlying salinity tolerance have been obtained from transcriptome and genome analysis, the molecules affected directly by salt and linking the extracellular stimulus to intracellular responses remain largely unknown. Protein alterations upon exogenous stimulus are vital in outlining differences that cannot otherwise be measured quantitatively. So proteomic analysis may reveal novel aspects of the plant protection mechanism from salinity. The pioneering work of Liu et al. (Proteomics 2014, 14, 1759-1775) found the differentially expressed proteins in rice roots and leaves after salt treatment, and these proteins may serve as marker group of rice resistant to salt stress. Metabolic pathways maintain cellular homeostasis and are very important for imparting stress tolerance in rice.

Comparative proteomic analysis of cauliflower under high temperature and flooding stresses

High-temperature and waterlogging are major abiotic stresses that affect the yield and quality of cauliflower. Cauliflower cultivars 'H41' and 'H69' are tolerant to high temperature and flooding, respectively; however, 'H71' is sensitive to both stresses. The objectives of this study were to identify the proteins that were differentially regulated and the physiological changes that occurred during different time periods in 'H41', 'H69', and 'H71' when responding to treatments of flooding, 40 °C, and both stresses combined. Changes in the leaf proteome were analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) and identified by Mascot peptide mass fingerprint (PMF) and database searching. Stress treatments caused significant reductions in electrolyte leakage, chlorophyll fluorescence Fv/Fm, chlorophyll content, and water potential as stress times were prolonged. By the comparative proteomic analysis, 85 protein peaks that were differentially expressed in response to combination treatments at 0, 6, and 24 h, 69 (33 in 'H41', 29 in 'H69', and 9 in 'H71') were identified, of which were cultivar specific. Differentially regulated proteins predominantly functioned in photosynthesis and to a lesser extent in energy metabolism, cellular homeostasis, transcription and translation, signal transduction, and protein biosynthesis. This is the first report that utilizes proteomics to discover changes in the protein expression profile of cauliflower in response to heat and flooding.

NADPH oxidase-dependent H2O2 production is required for salt-induced antioxidant defense in Arabidopsis thaliana

The involvement of hydrogen peroxide (H2O2) generated by nicotinamide adenine dinucleotide phosphate-oxidase (NADPH oxidase) in the antioxidant defense system was assessed in salt-challenged Arabidopsis thaliana seedlings. In the wild-type, short-term salt exposure led to a transient and significant increase of H2O2 concentration, followed by a marked increase in catalase (CAT, EC 1.11.16), ascorbate peroxidase (APX, EC 1.11.1.11) and glutathione reductase (GR, EC 1.6.4.2) activities. Pre-treatment with either a chemical trap for H2O2 (dimethylthiourea) or two widely used NADPH oxidase inhibitors (imidazol and diphenylene iodonium) significantly decreased the above-mentioned enzyme activities under salinity. Double mutant atrbohd/f plants failed to induce the antioxidant response under the culture conditions. Under long-term salinity, the wild-type was more salt-tolerant than the mutant based on the plant biomass production. The better performance of the wild-type was related to a significantly higher photosynthetic activity, a more efficient K(+) selective uptake, and to the plants' ability to deal with the salt-induced oxidative stress as compared to atrbohd/f. Altogether, these data suggest that the early H2O2 generation by NADPH oxidase under salt stress could be the beginning of a reaction cascade that triggers the antioxidant response in A. thaliana in order to overcome the subsequent reactive oxygen species (ROS) production, thereby mitigating the salt stress-derived injuries.

Proteomic analysis of salt stress and recovery in leaves of Vigna unguiculata cultivars differing in salt tolerance

Cowpea cultivars differing in salt tolerance reveal differences in protein profiles and adopt different strategies to overcome salt stress. Salt-tolerant cultivar shows induction of proteins related to photosynthesis and energy metabolism. Salinity is a major abiotic stress affecting plant cultivation and productivity. The objective of this study was to examine differential proteomic responses to salt stress in leaves of the cowpea cultivars Pitiúba (salt tolerant) and TVu 2331 (salt sensitive). Plants of both cultivars were subjected to salt stress (75 mM NaCl) followed by a recovery period of 5 days. Proteins extracted from leaves of both cultivars were analyzed by two-dimensional electrophoresis (2-DE) under salt stress and after recovery. In total, 22 proteins differentially regulated by both salt and recovery were identified by LC-ESI-MS/MS. Our current proteome data revealed that cowpea cultivars adopted different strategies to overcome salt stress. For the salt-tolerant cultivar (Pitiúba), increase in abundance of proteins involved in photosynthesis and energy metabolism, such as rubisco activase, ribulose-5-phosphate kinase (Ru5PK) (EC 2.7.1.19), glycine decarboxylase (EC 1.4.4.2) and oxygen-evolving enhancer (OEE) protein 2, was observed. However, these vital metabolic processes were more profoundly affected in salt-sensitive cultivar (TVu), as indicated by the down-regulation of OEE protein 1, Mn-stabilizing protein-II, carbonic anhydrase (EC 4.2.1.1) and Rubisco (EC 4.1.1.39), leading to energy reduction and a decline in plant growth. Other proteins differentially regulated in both cultivars corresponded to different physiological responses. Overall, our results provide information that could lead to a better understanding of the molecular basis of salt tolerance and sensitivity in cowpea plants.

Comparative proteomic analysis of early salt stress responsive proteins in roots and leaves of rice

Growth and productivity of rice (Oryza sativa L.) are severely affected by salinity. Understanding the mechanisms that protect rice and other important cereal crops from salt stress will help in the development of salt-stress-tolerant strains. In this study, rice seedlings of the same genetic species with various salt tolerances were studied. We first used 2DE to resolve the expressed proteome in rice roots and leaves and then used nanospray liquid chromatography/tandem mass spectrometry to identify the differentially expressed proteins in rice seedlings after salt treatment. The 2DE assays revealed that there were 104 differentially expressed protein spots in rice roots and 59 in leaves. Then, we identified 83 proteins in rice roots and 61 proteins in rice leaves by MS analysis. Functional classification analysis revealed that the differentially expressed proteins from roots could be classified into 18 functional categories while those from leaves could be classified into 11 functional categories. The proteins from rice seedlings that most significantly contributed to a protective effect against increased salinity were cysteine synthase, adenosine triphosphate synthase, quercetin 3-O-methyltransferase 1, and lipoxygenase 2. Further analysis demonstrated that the primary mechanisms underlying the ability of rice seedlings to tolerate salt stress were glycolysis, purine metabolism, and photosynthesis. Thus, we suggest that differentially expressed proteins may serve as marker group for the salt tolerance of rice.

Abiotic stress responses in plant roots: a proteomics perspective

Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abundance that can be best explored through proteomics. This review summarizes comparative proteomic studies conducted with roots of various plant species subjected to different abiotic stresses especially drought, salinity, flood, and cold. The main purpose of this article is to highlight and classify the protein level changes in abiotic stress response pathways specifically in plant roots. Shared as well as stressor-specific proteome signatures and adaptive mechanism(s) are simultaneously described. Such a comprehensive account will facilitate the design of genetic engineering strategies that enable the development of broad-spectrum abiotic stress-tolerant crops.

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

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