Comparative proteomic analysis of salt response proteins in seedling roots of two wheat varieties

Grafting enhances drought tolerance by regulating and mobilizing proteome, transcriptome and molecular physiology in okra genotypes

Drought stress poses a serious concern to the growth, development, and quality of the okra crop due to factors including decreased yield, inadequate development of dietary fibre, increased mite infestation, and decreased seed viability. Grafting is one of the strategies that have been developed to increase the drought stress tolerance of crops. We conducted proteomics, transcriptomics and integrated it with molecular physiology to assess the response of sensitive okra genotypes; NS7772 (G1), Green gold (G2) and OH3312 (G3) (scion) grafted to NS7774 (rootstock). In our studies we observed that sensitive okra genotypes grafted to tolerant genotypes mitigated the deleterious effects of drought stress through an increase in physiochemical parameters, and lowered reactive oxygen species. A comparative proteomic analysis showed a stress responsive proteins related to Photosynthesis, energy and metabolism, defence response, protein and nucleic acid biosynthesis. A proteomic investigation demonstrated that scions grafted onto okra rootstocks increased more photosynthesis-related proteins during drought stress, indicating an increase in photosynthetic activity when plants were subjected to drought stress. Furthermore, transcriptome of RD2, PP2C, HAT22, WRKY and DREB increased significantly, specifically for grafted NS7772 genotype. Furthermore, our study also indicated that grafting improved the yield components such as number of pods and seeds per plant, maximum fruit diameter, and maximum plant height in all genotypes which directly contributed towards their high resistance towards drought stress.

Wheat Omics: Advancements and Opportunities

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.

Physiological and Proteomic Analysis Responsive Mechanisms for Salt Stress in Oat

Oat is considered as a moderately salt-tolerant crop that can be used to improve saline and alkaline soils. Previous studies have focused on short-term salt stress exposure, and the molecular mechanisms of salt tolerance in oat have not yet been elucidated. In this study, the salt-tolerant oat cultivar Vao-9 and the salt-sensitive oat cultivar Bai5 were treated with 6 days of 0 and 150 mmol L^-1 salt stress (nNaCl:nNa₂SO₄ = 1:1). Label-Free technology was then used to analyze the differentially expressed proteins in leaves under 0 and 150 mmol L^-1 salt stress. The obtained results indicated that total of 2,631 proteins were identified by mass spectrometry in the four samples. The salt-tolerant cultivar Vao-9 mainly enhances its carbohydrate and energy metabolism through the pentose and glucuronate interconversions, and carbon fixation pathways in prokaryotes, thereby reducing the damage caused by salt stress. In addition, the down-regulation of ribosomes expression and the up-regulated expression of HSPs and CRT are all through the regulation of protein synthesis in response to salt stress. However, GABA metabolism presents a different synthesis pattern in Bai5 and Vao-9. The main KEGG function of differential expressed protein (DEP) in Bai5 is classified into protein processing in the endoplasmic reticulum, estrogen signaling pathway, antigen processing and presentation, longevity regulating pathway-multiple species, arginine and proline metabolism, beta-alanine metabolism, vitamin B6 metabolism, salmonella infection, chloroalkane and chloroalkene degradation, and limonene and pinene degradation. Moreover, the main KEGG functions of DEP in Vao-9 are classified as ribosome and carbon fixation pathways in prokaryotes, pentose and glucuronate interconversions, GABA ergic synapse, and taurine and hypotaurine metabolism. The results obtained in this study provide an important basis for further research on the underlying mechanisms of salt response and tolerance in oat and other plant species.

Proteomic, biochemical, and anatomical influences of nanographene oxide on soybean (Glycine max)

Nano-graphene oxide (NGO) is an engineered nanostructure that is used in various fields including biology, chemistry, medicine, and environmental protection. This kind of highly used nanomaterial (NM) is being released and accumulated gradually in nature and can have some adverse influences on living organisms including plants. Soybean as a cultivated plant with a high importance in food industry, but sensitive to stresses, was chosen in the present study to be examined in terms of proteomic, biochemical, and anatomical properties under the NGO stress. Accordingly, a 2-dimensional gel electrophoresis (2-DE) approach was adopted for proteomic analysis of the NGO treated soybean roots, where significant changes were observed in the abundance of 48 proteins. MALDI TOF/TOF analysis revealed the upregulation of the proteins involved in the redox regulation in plants. Furthermore, anatomical examination of soybean roots under light microscopy showed that the NGO could enter into the root epidermis through the apoplastic pathway and accumulated in some parts of the root. With increasing NGO concentration, the diameter of the vascular apertures increased and then decreased at higher concentrations. To evaluate the toxicity of NGO, some of the growth parameters including fresh and dry weight, and height of the shoots, as well as some stress-related biochemical properties such as H2O2 production, antioxidant enzymes activity, and phenolics and flavonoids contents were measured. The results indicated that NGO could cause an oxidative stress, which can be considered a toxic effect evoking antioxidative and detoxification mechanisms in soybean.

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

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

Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance

Background

Soil salinity is a major environmental stress that restricts crop growth and yield.

Methods

Here, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum ‘Y1805’ using the data-independent acquisition proteomics techniques to explore its salt-tolerance mechanism.

Results

In total, 44 and 102 differentially expressed proteins (DEPs) were identified in ‘Y1805’ under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. ‘Response to stimulus’, ‘antioxidant activity’, ‘carbohydrate metabolism’, ‘amino acid metabolism’, ‘signal transduction’, ‘transport and catabolism’ and ‘biosynthesis of other secondary metabolites’ were present under both conditions in ‘Y1805’. In addition, ‘energy metabolism’ and ‘lipid metabolism’ were recovery-specific pathways, while ‘antioxidant activity’, and ‘molecular function regulator’ under salt-stress conditions, and ‘virion’ and ‘virion part’ during recovery, were ‘Y1805’-specific compared with the salt-sensitive wheat ‘Chinese Spring’. ‘Y1805’ contained eight specific DEPs related to salt-stress responses. The strong salt tolerance of ‘Y1805’ could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat.

Comparative Analysis of Physiological, Enzymatic, and Transcriptomic Responses Revealed Mechanisms of Salt Tolerance and Recovery in Tritipyrum

Salt stress results in the severe decline of yield and quality in wheat. In the present study, salt-tolerant Tritipyrum ("Y1805") and salt-sensitive wheat "Chinese Spring" ("CS") were selected from 121 wheat germplasms to test their physiological, antioxidant enzyme, and transcriptomic responses and mechanisms against salt stress and recovery. 56 chromosomes were identified in "Y1805" that comprised A, B, and D chromosomes from wheat parent and E chromosomes from Thinopyrum elongatum, adding to salt-tolerant trait. Salt stress had a greater inhibitory effect on roots than on shoots, and "Y1805" demonstrated stronger salt tolerance than "CS." Compared with "CS," the activities of superoxide dismutase and catalase in "Y1805" significantly increased under salt stress. "Y1805" could synthesize more proline and soluble sugars than "CS." Both the net photosynthetic rate and chlorophyll a/b were affected by salt stress, though the level of damage in "Y1805" was significantly less than in "CS." Transcriptome analysis showed that the differences in the transcriptional regulatory networks of "Y1805" were not only in response to salt stress but also in recovery. The functions of many salt-responsive differentially expressed genes were correlated closely with the pathways "peroxisome," "arginine and proline metabolism," "starch and sucrose metabolism," "chlorophyll and porphyrin metabolism," and "photosynthesis."

Tandem mass tag-based (TMT) quantitative proteomics analysis reveals the response of fine roots to drought stress in cotton (Gossypium hirsutum L.)

BACKGROUND

Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Fine roots are the central part of the root system that contributes to plant water and nutrient uptake. However, the mechanisms underlying the response of cotton fine roots to soil drought remains unclear. To elucidate the proteomic changes in fine roots of cotton plants under drought stress, 70-75% and 40-45% soil relative water content treatments were imposed on control (CK) and drought stress (DS) groups, respectively. Then, tandem mass tags (TMT) technology was used to determine the proteome profiles of fine root tissue samples.

RESULTS

Drought significantly decreased the value of average root diameter of cotton seedlings, whereas the total root length and the activities of antioxidases were increased. To study the molecular mechanisms underlying drought response further, the proteome differences between tissues under CK and DS treatments were compared pairwise at 0, 30, and 45 DAD (days after drought stress). In total, 118 differentially expressed proteins (DEPs) were up-regulated and 105 were down-regulated in the 'DS30 versus CK30' comparison; 662 DEPs were up-regulated, and 611 were down-regulated in the 'DS45 versus CK45' comparison. The functions of these DEPs were classified according to their pathways. Under early stage drought (30 DAD), some DEPs involved in the 'Cutin, suberin, and wax synthesis' pathway were up-regulated, while the down-regulated DEPs were mainly enriched within the 'Monoterpenoid biosynthesis' pathway. Forty-five days of soil drought had a greater impact on DEPs involved in metabolism. Many proteins involving 'Carbohydrate metabolism,' 'Energy metabolism,' 'Fatty acid metabolism,' 'Amino acid metabolism,' and 'Secondary metabolite biosynthesis' were identified as DEPs. Additionally, proteins related to ion transport, stress/defense, and phytohormones were also shown to play roles in determining the fine root growth of cotton plants under drought stress.

CONCLUSIONS

Our study identified potential biological pathways and drought-responsive proteins related to stress/defense responses and plant hormone metabolism under drought stress. Collectively, our results provide new insights for further improving drought tolerance in cotton and other crops.

Proteomic dissection of the similar and different responses of wheat to drought, salinity and submergence during seed germination

Wheat (Triticum aestivum L.) is one of the major crops worldwide and its production is inevitably subjected to various biotic/abiotic stresses during the life cycle. Drought, salinity and flooding are among the most severe abiotic stresses restricting wheat yields and could occur at very early stages such as seed germination. How wheat seed germination responds to these different stresses remains incomplete. To fill the information gap, a label-free proteomic analysis was applied to decipher the proteomic profiling of the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 4295 proteins were detected, of which 465, 397 and 732 showed significant alterations in abundance under those stresses when compared with control. A common denominator found in the response observed to all three stresses are changes related to small molecule metabolic processes, and particularly in pathways associated with phenylpropanoid biosynthesis and fatty acid degradation. It was also noticeable that pathways like cysteine and methionine metabolism in the PEG or submergence treatment and starch and sucrose metabolism in the submergence treatment are specifically pronounced. Functional analysis of putative proteins participating in these pathways revealed distinct responsive patterns across different stresses. SIGNIFICANCE: Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, but its growth and productivity are frequently restrained by stresses such as drought, salinity and flooding. To date, many resources have been documented to investigate how wheat responds and adapts to these individual stresses during plant development and yield formation, but little attention was paid to the understandings of the internal link between different conditions, especially during the germination process, a critical stage that determines the optimal growth of wheat. In this study, we carried out the proteome profiling of the germinating seeds of a common wheat cultivar, Chinese Spring, subjected to PEG, NaCl and submergence stresses. We found that the phenylpropanoid biosynthesis and fatty acid degradation pathways were enriched as the ubiquitous stress responses, while some pathways were stress-specific, for instance, starch and sucrose metabolism against submergence. The changes in some of the altered processes were further validated by physiological and molecular approaches. Our results suggest that the overall pathway profiles concerned with the three stresses were similar, but the specific procedures and components in each process varied greatly. The altered proteins and processes can be taken as effective candidates in future breeding and agronomic modification researches.

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

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

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Comparative Physiological and Proteomic Analysis of Two Sugar Beet Genotypes with Contrasting Salt Tolerance

Soil salinity is one of the major constraints affecting agricultural production and crop yield. A detailed understanding of the underlying physiological and molecular mechanisms of the different genotypic salt tolerance response in crops under salinity is therefore a prerequisite for enhancing this tolerance. In this study, we explored the changes in physiological and proteome profiles of salt-sensitive (S210) and salt-tolerant (T510) sugar beet cultivars in response to salt stress. T510 showed better growth status, higher antioxidant enzymes activities and proline level, less Na accumulation, and lower P levels after salt-stress treatments. With iTRAQ-based comparative proteomics method, 47 and 56 differentially expressed proteins were identified in the roots and leaves of S210, respectively. In T510, 56 and 50 proteins changed significantly in the roots and leaves of T510, respectively. These proteins were found to be involved in multiple aspects of functions such as photosynthesis, metabolism, stress and defense, protein synthesis, and signal transduction. Our proteome results indicated that sensitive and tolerant sugar beet cultivars respond differently to salt stress. The proteins that were mapped to the protein modification, amino acid metabolism, tricarboxylic acid cycle, cell wall synthesis, and reactive oxygen species scavenging changed differently between the sensitive and tolerant cultivars, suggesting that these pathways may promote salt tolerance in the latter. This work leads to a better understanding of the salinity mechanism in sugar beet and provides a list of potential markers for the further engineering of salt tolerance in crops.

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

Background

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

Results

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

Conclusions

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

Electronic supplementary material

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

Salt-adaptive strategies in oil seed crop Ricinus communis early seedlings (cotyledon vs. true leaf) revealed from proteomics analysis

Soil salinity is a major abiotic stress affecting crop growth and productivity. Ricinus communis has good salt tolerance and is also an important oilseed crop throughout the world. Early seedling stage (such as cotyledon expansion stage) is the most vulnerable period for plant under stresses. However, little information exist concerning the physiological and molecular mechanisms of Ricinus communis seedlings and the role play by cotyledons and true leaf under salt stress. In the present study, biomass, photosynthesis, chlorophyll fluorescence, inorganic ions and organic solutes contents were measured, and two dimensional gel electrophoresis-based proteomic technology was employed to identify the differentially abundant proteins in the salt-treated Ricinus communis cotyledons and true leaves. The results showed that salt stress reduced growth and photosynthesis in the seedlings. With increasing salinity, the Na⁺ content increased and K⁺ content decreased in both cotyledons and leaves, but the true leaves had lower Na⁺ and higher K⁺ contents. Soluble sugars and proline are the primary organic solutes to cope with osmotic stress. In addition, proteomic analysis revealed 30 and 42 differentially accumulated protein spots in castor cotyledon and true leaf under salt stress, respectively. Most of the identified proteins were involved in carbohydrate and energy metabolism, photosynthesis, genetic information process, reactive oxygen species metabolism, amino acid metabolism and cell structure. The physiological and proteomic results highlighted that cotyledons accumulated a large number of Na⁺ and provided more energy to help true leaves cope with salt stress. The true leaves saved carbon structures to synthesize osmotic substances, and the enhancement of chlorophyll synthesis and electron transfer in true leaves could also maintain photosynthesis under salt stress. These findings provide new insights into different physiological mechanisms in cotyledon and true leaf of Ricinus communis response to salt stress during early seedling stage.

Metabolic Adjustment of Arabidopsis Root Suspension Cells During Adaptation to Salt Stress and Mitotic Stress Memory

Sessile plants reprogram their metabolic and developmental processes during adaptation to prolonged environmental stresses. To understand the molecular mechanisms underlying adaptation of plant cells to saline stress, we established callus suspension cell cultures from Arabidopsis roots adapted to high salt for an extended period of time. Adapted cells exhibit enhanced salt tolerance compared with control cells. Moreover, acquired salt tolerance is maintained even after the stress is relieved, indicating the existence of a memory of acquired salt tolerance during mitotic cell divisions, known as mitotic stress memory. Metabolite profiling using 1H-nuclear magnetic resonance (NMR) spectroscopy revealed metabolic discrimination between control, salt-adapted and stress-memory cells. Compared with control cells, salt-adapted cells accumulated higher levels of sugars, amino acids and intermediary metabolites in the shikimate pathway, such as coniferin. Moreover, adapted cells acquired thicker cell walls with higher lignin contents, suggesting the importance of adjustments of physical properties during adaptation to elevated saline conditions. When stress-memory cells were reverted to normal growth conditions, the levels of metabolites again readjusted. Whereas most of the metabolic changes reverted to levels intermediate between salt-adapted and control cells, the amounts of sugars, alanine, γ-aminobutyric acid and acetate further increased in stress-memory cells, supporting a view of their roles in mitotic stress memory. Our results provide insights into the metabolic adjustment of plant root cells during adaptation to saline conditions as well as pointing to the function of mitotic memory in acquired salt tolerance.

iTRAQ-Based Protein Profiling and Biochemical Analysis of Two Contrasting Rice Genotypes Revealed Their Differential Responses to Salt Stress

Salt stress is one of the key abiotic stresses causing huge productivity losses in rice. In addition, the differential sensitivity to salinity of different rice genotypes during different growth stages is a major issue in mitigating salt stress in rice. Further, information on quantitative proteomics in rice addressing such an issue is scarce. In the present study, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative protein quantification was carried out to investigate the salinity-responsive proteins and related biochemical features of two contrasting rice genotypes—Nipponbare (NPBA, japonica) and Liangyoupeijiu (LYP9, indica), at the maximum tillering stage. The rice genotypes were exposed to four levels of salinity: 0 (control; CK), 1.5 (low salt stress; LS), 4.5 (moderate salt stress; MS), and 7.5 g of NaCl/kg dry soil (high salt stress, HS). The iTRAQ protein profiling under different salinity conditions identified a total of 5340 proteins with 1% FDR in both rice genotypes. In LYP9, comparisons of LS, MS, and HS compared with CK revealed the up-regulation of 28, 368, and 491 proteins, respectively. On the other hand, in NPBA, 239 and 337 proteins were differentially upregulated in LS and MS compared with CK, respectively. Functional characterization by KEGG and COG, along with the GO enrichment results, suggests that the differentially expressed proteins are mainly involved in regulation of salt stress responses, oxidation-reduction responses, photosynthesis, and carbohydrate metabolism. Biochemical analysis of the rice genotypes revealed that the Na⁺ and Cl⁻ uptake from soil to the leaves via the roots was increased with increasing salt stress levels in both rice genotypes. Further, increasing the salinity levels resulted in increased cell membrane injury in both rice cultivars, however more severely in NPBA. Moreover, the rice root activity was found to be higher in LYP9 roots compared with NPBA under salt stress conditions, suggesting the positive role of rice root activity in mitigating salinity. Overall, the results from the study add further insights into the differential proteome dynamics in two contrasting rice genotypes with respect to salt tolerance, and imply the candidature of LYP9 to be a greater salt tolerant genotype over NPBA.

Integrated proteome analyses of wheat glume and awn reveal central drought response proteins under water deficit conditions

Integrated proteome analyses revealed differentially accumulated proteins in the non-leaf green organs in wheat glume and awn that play important roles in photosynthesis and drought resistance. Two non-leaf green organs in wheat, glume and awn, have photosynthetic potential, contribute to grain yield, and also play roles in resistance to adverse conditions. We performed the first integrated proteome analysis of wheat glume and awn in response to water deficit. Water deficit caused a significant decrease in important agronomic traits and grain yield. A total of 120 and 77 differentially accumulated protein (DAP) spots, representing 100 and 67 unique proteins responsive to water deficit, were identified by two-dimensional difference gel electrophoresis (2D-DIGE) in glumes and awns, respectively, of the elite Chinese bread wheat cultivar Zhongmai 175. The DAPs of both organs showed similar functional classification and proportion and were mainly involved in photosynthesis, detoxification/defense, carbon/energy metabolism, and proteometabolism. Comparative proteome analyses revealed many more drought-responsive DAP spots in glumes than in awns, which indicate that glumes underwent more proteome changes in response to water deficit. The main DAPs involved in photosynthesis and carbon metabolism were significantly downregulated, whereas those related to detoxification/defense and energy metabolism were markedly upregulated under water deficit. The potential functions of the identified DAPs revealed an intricate interaction network that responds synergistically to drought stress during grain development. Our results from the proteome perspective illustrate the potential roles of wheat non-leaf green organs glume and awn in photosynthetic and defensive responses under drought stress.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Comparative Proteome Analysis of Wheat Flag Leaves and Developing Grains Under Water Deficit

In this study, we performed the first comparative proteomic analysis of wheat flag leaves and developing grains in response to drought stress. Drought stress caused a significant decrease in several important physiological and biochemical parameters and grain yield traits, particularly those related to photosynthesis and starch biosynthesis. In contrast, some key indicators related to drought stress were significantly increased, including malondialdehyde, soluble sugar, proline, glycine betaine, abscisic acid content, and peroxidase activity. Two-dimensional difference gel electrophoresis (2D-DIGE) identified 87 and 132 differentially accumulated protein (DAP) spots representing 66 and 105 unique proteins following exposure to drought stress in flag leaves and developing grains, respectively. The proteomes of the two organs varied markedly, and most DAPS were related to the oxidative stress response, photosynthesis and energy metabolism, and starch biosynthesis. In particular, DAPs in flag leaves mainly participated in photosynthesis while those in developing grains were primarily involved in carbon metabolism and the drought stress response. Western blotting and quantitative real-time polymerase chain reaction (qRT-PCR) further validated some key DAPs such as rubisco large subunit (RBSCL), ADP glucose pyrophosphorylase (AGPase), chaperonin 60 subunit alpha (CPN-60 alpha) and oxalate oxidase 2 (OxO 2). The potential functions of the identified DAPs revealed that a complex network synergistically regulates drought resistance during grain development. Our results from proteome perspective provide new insight into the molecular regulatory mechanisms used by different wheat organs to respond to drought stress.

Evaluation of DNA methylation and mRNA expression of heat shock proteins in thermal manipulated chicken

Thermal manipulation during embryogenesis has been demonstrated to enhance the thermotolerance capacity of broilers through epigenetic modifications. Heat shock proteins (HSPs) are induced in response to stress for guarding cells against damage. The present study investigates the effect of thermal conditioning during embryogenesis and thermal challenge at 42 days of age on HSP gene and protein expression, DNA methylation and in vitro luciferase assay in brain tissue of Naked Neck (NN) and Punjab Broiler-2 (PB-2) chicken. On the 15th day of incubation, fertile eggs from two breeds, NN and PB-2, were randomly divided in to two groups: control (C)-eggs were incubated under standard incubation conditions, and thermal conditioning (TC)-eggs were exposed to higher incubation temperature (40.5°C) for 3 h on the 15th, 16th, and 17th days of incubation. The chicks obtained from each group were further subdivided and reared under different environmental conditions from the 15th to the 42nd day as normal [N; 25 ± 1 °C, 70% relative humidity (RH)] and heat exposed (HE; 35 ± 1 °C, 50% RH) resulting in four treatment groups (CN, CHE, TCN, and TCHE). The results revealed that HSP promoter activity was stronger in CHE, which had lesser methylation and higher gene expression. The activity of promoter region was lesser in TCHE birds that were thermally manipulated at the embryonic stage, thus reflecting their stress-free condition. This was confirmed by the lower level of mRNA expression of all the HSP genes. In conclusion, thermal conditioning during embryogenesis has a positive impact and improves chicken thermotolerance capacity in postnatal life.

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

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

Chemical hybridizing agent SQ-1-induced male sterility in Triticum aestivum L.: a comparative analysis of the anther proteome

BACKGROUND

Heterosis is widely used to increase the yield of many crops. However, as wheat is a self-pollinating crop, hybrid breeding is not so successful in this organism. Even though male sterility induced by chemical hybridizing agents is an important aspect of crossbreeding, the mechanisms by which these agents induce male sterility in wheat is not well understood.

RESULTS

We performed proteomic analyses using the wheat Triticum aestivum L.to identify those proteins involved in physiological male sterility (PHYMS) induced by the chemical hybridizing agent CHA SQ-1. A total of 103 differentially expressed proteins were found by 2D-PAGE and subsequently identified by MALDI-TOF/TOF MS/MS. In general, these proteins had obvious functional tendencies implicated in carbohydrate metabolism, oxidative stress and resistance, protein metabolism, photosynthesis, and cytoskeleton and cell structure. In combination with phenotypic, tissue section, and bioinformatics analyses, the identified differentially expressed proteins revealed a complex network behind the regulation of PHYMS and pollen development. Accordingly, we constructed a protein network of male sterility in wheat, drawing relationships between the 103 differentially expressed proteins and their annotated biological pathways. To further validate our proposed protein network, we determined relevant physiological values and performed real-time PCR assays.

CONCLUSIONS

Our proteomics based approach has enabled us to identify certain tendencies in PHYMS anthers. Anomalies in carbohydrate metabolism and oxidative stress, together with premature tapetum degradation, may be the cause behind carbohydrate starvation and male sterility in CHA SQ-1 treated plants. Here, we provide important insight into the mechanisms underlying CHA SQ-1-induced male sterility. Our findings have practical implications for the application of hybrid breeding in wheat.

Comparative proteomic analysis of rats subjected to water immersion and restraint stress as an insight into gastric ulcers

In the present study, comparative proteomic analysis was performed in rats subjected to water immersion-restraint stress (WRS). A total of 26 proteins were differentially expressed and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Among the 26 differentially expressed protein spots identified, 13 proteins were significantly upregulated under WRS, including pyruvate kinase and calreticulin, which may be closely associated with energy metabolism. In addition, 12 proteins were downregulated under WRS, including hemoglobin subunit β-2 and keratin type II cytoskeletal 8, which may be important in protein metabolism and cell death. Gene Ontology analysis revealed the cellular distribution, molecular function and biological processes of the identified proteins. The mRNA levels of certain differentially expressed proteins were analyzed using fluorescence quantitative polymerase chain reaction analysis. The results of the present study aimed to offer insights into proteins, which are differentially expressed in gastric ulcers in stress, and provide theoretical evidence of a radical cure for gastric ulcers in humans.

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

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

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

Integrated proteomic analysis of Brachypodium distachyon roots and leaves reveals a synergistic network in the response to drought stress and recovery

In this study, we performed the first integrated physiological and proteomic analysis of the response to drought and recovery from drought, using Brachypodium distachyon L. Roots and leaves. Drought stress resulted in leaves curling, root tips becoming darker in color and significant changes in some physiological parameters. Two-dimensional difference gel electrophoresis (2D-DIGE) identified 78 and 98 differentially accumulated protein (DAP) spots representing 68 and 73 unique proteins responding to drought stress and/or recovery in roots and leaves, respectively. Differences between the root and leaf proteome were most marked for photosynthesis, energy metabolism, and protein metabolism. In particular, some DAPs involved in energy and protein metabolism had contrasting accumulation patterns in roots and leaves. Protein-protein interaction (PPI) analysis of roots and leaves revealed complex protein interaction networks that can generate synergistic responses to drought stress and during recovery from drought. Transcript analysis using quantitative real-time polymerase chain reaction (qRT-PCR) validated the differential expression of key proteins involved in the PPI network. Our integrated physiological and proteomic analysis provides evidence for a synergistic network involved in responses to drought and active during recovery from drought, in Brachypodium roots and leaves.

iTRAQ-based quantitative proteomic analysis of wheat roots in response to salt stress

Salinity is a major abiotic stress that affects plant growth and development. Plant roots are the sites of salt uptake. Here, an isobaric tag for a relative and absolute quantitation based proteomic technique was employed to identify the differentially expressed proteins (DEPs) from seedling roots of the salt-tolerant genotype Han 12 and the salt-sensitive genotype Jimai 19 in response to salt treatment. A total of 121 NaCl-responsive DEPs were observed in Han 12 and Jimai 19. The main DEPs were ubiquitination-related proteins, transcription factors, pathogen-related proteins, membrane intrinsic protein transporters and antioxidant enzymes, which may work together to obtain cellular homeostasis in roots and to determine the overall salt tolerance of different wheat varieties in response to salt stress. Functional analysis of three salt-responsive proteins was performed in transgenic plants as a case study to confirm the salt-related functions of the detected proteins. Taken together, the results of this study may be helpful in further elucidating salt tolerance mechanisms in wheat.

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

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

Na2CO3-responsive mechanisms in halophyte Puccinellia tenuiflora roots revealed by physiological and proteomic analyses

Soil alkalization severely affects crop growth and agricultural productivity. Alkali salts impose ionic, osmotic, and high pH stresses on plants. The alkali tolerance molecular mechanism in roots from halophyte Puccinellia tenuiflora is still unclear. Here, the changes associated with Na₂CO₃ tolerance in P. tenuiflora roots were assessed using physiological and iTRAQ-based quantitative proteomic analyses. We set up the first protein dataset in P. tenuiflora roots containing 2,671 non-redundant proteins. Our results showed that Na₂CO₃ slightly inhibited root growth, caused ROS accumulation, cell membrane damage, and ion imbalance, as well as reduction of transport and protein synthesis/turnover. The Na₂CO₃-responsive patterns of 72 proteins highlighted specific signaling and metabolic pathways in roots. Ca²⁺ signaling was activated to transmit alkali stress signals as inferred by the accumulation of calcium-binding proteins. Additionally, the activities of peroxidase and glutathione peroxidase, and the peroxiredoxin abundance were increased for ROS scavenging. Furthermore, ion toxicity was relieved through Na⁺ influx restriction and compartmentalization, and osmotic homeostasis reestablishment due to glycine betaine accumulation. Importantly, two transcription factors were increased for regulating specific alkali-responsive gene expression. Carbohydrate metabolism-related enzymes were increased for providing energy and carbon skeletons for cellular metabolism. All these provide new insights into alkali-tolerant mechanisms in roots.

Proteomic and phosphoproteomic analysis reveals the response and defense mechanism in leaves of diploid wheat T. monococcum under salt stress and recovery

Salinity is a major abiotic stress factor affecting crops production and productivity. Triticum monococcum is closely related to Triticum urartu (A(U)A(U)), which is used as a model plant of wheat A genome study. Here, salt stress induced dynamic proteome and phosphoproteome profiling was focused. The T. monococcum seedlings were initially treated with different concentrations of NaCl ranging from 80 to 320mM for 48h followed by a recovery process for 48h prior to proteomic and phosphoproteomic analysis. As a result, a total of 81 spots corresponding to salt stress and recovery were identified by MALDI-TOF/TOF-MS from 2-DE gels. These proteins were mainly involved in regulatory, stress defense, protein folding/assembly/degradation, photosynthesis, carbohydrate metabolism, energy production and transportation, protein metabolism, and cell structure. Pro-Q Diamond staining was used to detect the phosphoproteins. Finally, 20 spots with different phosphorylation levels during salt treatment or recovery compared with controls were identified. A set of potential salt stress response and defense biomarkers was identified, such as cp31BHv, betaine-aldehyde dehydrogenase, leucine aminopeptidase 2, Cu/Zn superoxide dismutase, and 2-Cys peroxiredoxin BAS1, which could lead to a better understanding of the molecular basis of salt response and defense in food crops.

BIOLOGICAL SIGNIFICANCE

Soil salinity reduces the yield of the major crops, which is one of the severest problems in irrigated agriculture worldwide. However, how crops response and defense during different levels of salt treatment and recovery processes is still unclear, especially at the post-translational modification level. T. monococcum is a useful model for common wheat. Thus, proteomic and phosphoproteomic analyses of T. monococcum leaves were performed in our study, which provided novel insights into the underlying salt response and defense mechanisms in wheat and other crops.

RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.)

The dwarfing mechanism of Rht-dp in dwarf Polish wheat (DPW) is unknown. Each internode of DPW was significantly shorter than it in high Polish wheat (HPW), and the dwarfism was insensitive to photoperiod, abscisic acid (ABA), gibberellin (GA), cytokinin (CK), auxin and brassinolide (BR). To understand the mechanism, three sets of transcripts, DPW, HPW, and a chimeric set (a combination of DPW and HPW), were constructed using RNA sequencing (RNA-Seq). Based on the chimeric transcripts, 2,446 proteins were identified using isobaric tags for relative and absolute quantification (iTRAQ). A total of 108 unigenes and 12 proteins were considered as dwarfism-related differentially expressed genes (DEGs) and differentially expressed proteins (DEPs), respectively. Among of these DEGs and DEPs, 6 DEGs and 6 DEPs were found to be involved in flavonoid and S-adenosyl-methionine (SAM) metabolisms; 5 DEGs and 3 DEPs were involved in cellulose metabolism, cell wall plasticity and cell expansion; 2 DEGs were auxin transporters; 2 DEPs were histones; 1 DEP was a peroxidase. These DEGs and DEPs reduced lignin and cellulose contents, increased flavonoid content, possibly decreased S-adenosyl-methionine (SAM) and polyamine contents and increased S-adenosyl-L-homocysteine hydrolase (SAHH) content in DPW stems, which could limit auxin transport and reduce extensibility of the cell wall, finally limited cell expansion (the cell size of DPW was significantly smaller than HPW cells) and caused dwarfism in DPW.

Comparative proteomic analysis of β-aminobutyric acid-mediated alleviation of salt stress in barley

The non-protein amino acid β-aminobutyric acid (BABA) is known to induce plant resistance to a broad spectrum of biotic and abiotic stresses. This is the first study describing the effect of BABA seed priming on physiological and proteomic changes under salt stress conditions in barley (Hordeum vulgare). The aim of our study was to investigate the changes of fresh weight, dry weight and relative water content (RWC) as well as root proteome changes of two barley lines contrasting in salt tolerance (DH14, DH 187) in response to salt stress after seed priming in water or in 800 μM BABA. Seed priming with BABA significantly increased (p ≤ 0.05) RWC in both barley lines, which indicates considerably lower water loss in BABA-primed plants than in the non-primed control plants. Dry and fresh matter increased significantly in line DH 187, whereas no changes were detected in line DH14. BABA-primed plants of both lines showed different proteomic patterns than the non-primed control plants. The root proteins exhibiting significant abundance changes (1.75-fold change, p ≤ 0.05) were separated by two-dimensional polyacrylamide gel electrophoresis (2D- PAGE). Thirty-one spots, representing 24 proteins, were successfully identified by MALDI TOF/TOF mass spectrometry. The most prominent differences include the up-regulation of antioxidant enzymes (catalase, peroxidase and superoxide dismutase), PR proteins (chitinase, endo-1,3-β-glucosidase), and chaperones (cyclophilin, HSC 70). Our results indicate that BABA induces defence and detoxification processes which may enable faster and more effective responses to salt stress, increasing the chances of survival under adverse environmental conditions.

Heat Priming Induces Trans-generational Tolerance to High Temperature Stress in Wheat

Wheat plants are very sensitive to high temperature stress during grain filling. Effects of heat priming applied to the first generation on tolerance of the successive generation to post-anthesis high temperature stress were investigated. Compared with the progeny of non-heat primed plants (NH), the progeny of heat-primed plants (PH) possessed higher grain yield, leaf photosynthesis and activities of antioxidant enzymes and lower cell membrane damage under high temperature stress. In the transcriptome profile, 1430 probes showed obvious difference in expression between PH and NH. These genes were related to signal transduction, transcription, energy, defense, and protein destination and storage, respectively. The gene encoding the lysine-specific histone demethylase 1 (LSD1) which was involved in histone demethylation related to epigenetic modification was up-regulated in the PH compared with NH. The proteome analysis indicated that the proteins involved in photosynthesis, energy production and protein destination and storage were up-regulated in the PH compared with NH. In short, thermos-tolerance was induced through heritable epigenetic alternation and signaling transduction, both processes further triggered prompt modifications of defense related responses in anti-oxidation, transcription, energy production, and protein destination and storage in the progeny of the primed plants under high temperature stress. It was concluded that trans-generation thermo-tolerance was induced by heat priming in the first generation, and this might be an effective measure to cope with severe high-temperature stresses during key growth stages in wheat production.

Integrated Proteome Analysis of the Wheat Embryo and Endosperm Reveals Central Metabolic Changes Involved in the Water Deficit Response during Grain Development

The embryo and endosperm of wheat have different physiological functions and large differences in protein level. In this study, we performed the first integrated proteome analysis of wheat embryo and endosperm in response to the water deficit during grain development. In total, 155 and 130 differentially expressed protein (DEP) spots in the embryo and endosperm, respectively, were identified by nonlinear two-dimensional electrophoresis and tandem mass spectrometry. These DEPs in the embryo were mainly involved in stress/defense responses such as heat shock-related proteins (HSP) and peroxidase, whereas those in endosperm were mainly related to starch and storage protein synthesis such as α-amylase inhibitor and the globulin-1 S allele. In particular, some storage proteins such as avenin-like proteins and high-molecular weight glutenin subunit Dy12 displayed higher expression levels in the mature endosperm under a water deficit, which might contribute to the improvement in the quality of breadmaking.

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

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

Comparative proteomic analysis of drought tolerance in the two contrasting Tibetan wild genotypes and cultivated genotype

BACKGROUND

Drought is one of major abiotic stresses constraining crop productivity worldwide. To adapt to drought stress, plants have evolved sophisticated defence mechanisms. Wild barley germplasm is a treasure trove of useful genes and offers rich sources of genetic variation for crop improvement. In this study, a proteome analysis was performed to identify the genetic resources and to understand the mechanisms of drought tolerance in plants that could result in high levels of tolerance to drought stress.

RESULTS

A greenhouse pot experiment was performed to compare proteomic characteristics of two contrasting Tibetan wild barley genotypes (drought-tolerant XZ5 and drought-sensitive XZ54) and cv. ZAU3, in response to drought stress at soil moisture content 10% (SMC10) and 4% (SMC4) and subsequently 2 days (R1) and 5 days (R2) of recovery. More than 1700 protein spots were identified that are involved in each gel, wherein 132, 92, 86, 242 spots in XZ5 and 261, 137, 156, 187 in XZ54 from SMC10, SMC4, R1 and R2 samples were differentially expressed by drought over the control, respectively. Thirty-eight drought-tolerance-associated proteins were identified using mass spectrometry and data bank analysis. These proteins were categorized mainly into photosynthesis, stress response, metabolic process, energy and amino-acid biosynthesis. Among them, 6 protein spots were exclusively expressed or up-regulated under drought stress in XZ5 but not in XZ54, including melanoma-associated antigen p97, type I chlorophyll a/b-binding protein b, glutathione S-transferase 1, ribulosebisphosphate carboxylase large chain. Moreover, type I chlorophyll a/b-binding protein b was specifically expressed in XZ5 (Spots A4, B1 and C3) but not in both of XZ54 and ZAU3. These proteins may play crucial roles in drought-tolerance in XZ5. Coding Sequences (CDS) of rbcL and Trx-M genes from XZ5, XZ54 and ZAU3 were cloned and sequenced. CDS length of rbcL and Trx-M was 1401 bp (the partial-length CDS region) and 528 bp (full-length CDS region), respectively, encoding 467 and 176 amino acids. Comparison of gene sequences among XZ5, XZ54 and ZAU3 revealed 5 and 2 SNPs for rbcL and Trx-M, respectively, with two 2 SNPs of missense mutation in the both genes.

CONCLUSIONS

Our findings highlight the significance of specific-proteins associated with drought tolerance, and verified the potential value of Tibetan wild barley in improving drought tolerance of barley as well as other cereal crops.

Screening for salt-responsive proteins in two contrasting alfalfa cultivars using a comparative proteome approach

A comparative proteomic approach was carried out between two contrasting alfalfa cultivars, nonomu (NM-801; salt tolerant) and vernal (VN; salt intolerant) in terms of salt tolerance. Seedlings were subjected to salt stress (50 and 100 mM NaCl) for three days. Several physiological parameters (leaf water, chlorophyll, root Na(+), K(+), and Ca(2+)) and root proteome profile were analyzed. Comparison of physiological status revealed that NM-801 is more tolerant to salt than VN. Eighty three differentially expressed proteins were found on 2-DE maps, of which 50 were identified by MALDI-TOF or MALDI-TOF/TOF mass spectrometry. These proteins were involved in ion homeostasis, protein turnover and signaling, protein folding, cell wall components, carbohydrate and energy metabolism, reactive oxygen species regulation and detoxification, and purine and fatty acid metabolism. The comparative proteome analysis showed that 33 salt-responsive proteins were significantly changed in both cultivars, while 17 (14 in VN and 3 in NM-801) were cultivar-specific. Peroxidase, protein disulfide-isomerase, NAD synthetase, and isoflavone reductase were up-regulated significantly only in NM-801 in all salt concentrations. In addition, we identified novel proteins including NAD synthetase and biotin carboxylase-3 that were not reported previously as salt-responsive. Taken together, these results provide new insights of salt stress tolerance in alfalfa.

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.

Deciphering the protective role of spermidine against saline-alkaline stress at physiological and proteomic levels in tomato

In this research, the protective effect of spermidine (Spd) in mitigating saline-alkaline stress in tomato (Solanum lycopersicum L.) at physiological and proteomic levels were examined. The results showed that saline-alkaline stress induced accumulation of H2O2 and O2(-*), and increased the activities of antioxidase (SOD, CAT, and POD). Spermidine efficiently alleviated the inhibitory role of saline-alkaline on plant growth and inhibited saline-alkaline stress-induced H2O2 and O2(-*) accumulation. Proteomics investigations of the leaves of tomato seedlings, responding to a 75 mM saline-alkaline solution and 0.25 mM Spd, were performed. Maps of the proteome of leaf extracts were obtained by two-dimensional gel electrophoresis. An average of 49, 47 and 34 spots, which appeared repeatedly and that significantly altered the relative amounts of polypeptides by more than twofold, were detected for seedlings treated with saline-alkaline solution (S) compared to normal solution (CK), saline-alkaline plus spermidine (MS) compared to CK, or S versus MS, respectively. Thirty-nine of these proteins were identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and were classified into five functional categories, including energy and metabolism, signal transduction, amino acid metabolism, protein metabolism, and stress-defense response. Proteomics analysis coupled with bioinformatics indicated that Spd treatment helps tomato seedlings combat saline-alkaline stress by modulating the defense mechanism of plants and activating cellular detoxification, which protect plants from oxidative damage induced by saline-alkaline stress.

Alterations in root proteome of salt-sensitive and tolerant barley lines under salt stress conditions

Salinity is one of the most important abiotic stresses causing a significant reduction of crop plants yield. To gain a better understanding of salinity tolerance mechanisms in barley (Hordeum vulgare), we investigated the changes in root proteome of salt-sensitive (DH14) and tolerant (DH187) lines in response to salt-stress. The seeds of both barley lines were germinating in water or in 100mM NaCl for 6 days. The root proteins were separated by two-dimensional gel electrophoresis. To identify proteins regulated in response to salt stress, MALDI-TOF/TOF mass spectrometry was applied. It was demonstrated that the sensitive and tolerant barley lines respond differently to salt stress. Some of the identified proteins are well-documented as markers of salinity resistance, but several proteins have not been detected in response to salt stress earlier, although they are known to be associated with other abiotic stresses. The most significant differences concerned the proteins that are involved in signal transduction (annexin, translationally-controlled tumor protein homolog, lipoxygenases), detoxification (osmotin, vacuolar ATP-ase), protein folding processes (protein disulfide isomerase) and cell wall metabolism (UDP-glucuronic acid decarboxylase, β-d-glucan exohydrolase, UDP-glucose pyrophosphorylase). The results suggest that the enhanced salinity tolerance of DH187 line results mainly from an increased activity of signal transduction mechanisms eventually leading to the accumulation of stress protective proteins and cell wall structure changes.

Advances in plant proteomics toward improvement of crop productivity and stress resistancex

Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.

Identification of early salt stress responsive proteins in seedling roots of upland cotton (Gossypium hirsutum L.) employing iTRAQ-based proteomic technique

Soil salinity is a major abiotic stress that limits plant growth and agricultural productivity. Upland cotton (Gossypium hirsutum L.) is highly tolerant to salinity; however, large-scale proteomic data of cotton in response to salt stress are still scant. Here, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic technique was employed to identify the early differentially expressed proteins (DEPs) from salt-treated cotton roots. One hundred and twenty-eight DEPs were identified, 76 of which displayed increased abundance and 52 decreased under salt stress conditions. The majority of the proteins have functions related to carbohydrate and energy metabolism, transcription, protein metabolism, cell wall and cytoskeleton metabolism, membrane and transport, signal transduction, in addition to stress and defense. It is worth emphasizing that some novel salt-responsive proteins were identified, which are involved in cell cytoskeleton metabolism (actin-related protein2, ARP2, and fasciclin-like arabinogalactan proteins, FLAs), membrane transport (tonoplast intrinsic proteins, TIPs, and plasma membrane intrinsic proteins, PIPs), signal transduction (leucine-rich repeat receptor-like kinase encoding genes, LRR-RLKs) and stress responses (thaumatin-like protein, TLP, universal stress protein, USP, dirigent-like protein, DIR, desiccation-related protein PCC13-62). High positive correlation between the abundance of some altered proteins (superoxide dismutase, SOD, peroxidase, POD, glutathione S-transferase, GST, monodehydroascorbate reductase, MDAR, and malate dehydrogenase, MDH) and their enzyme activity was evaluated. The results demonstrate that the iTRAQ-based proteomic technique is reliable for identifying and quantifying a large number of cotton root proteins. qRT-PCR was used to study the gene expression levels of the five above-mentioned proteins; four patterns are consistent with those of induced protein. These results showed that the proteome of cotton roots under NaCl stress is complex. The comparative protein profiles of roots under salinity vs control improves the understanding of the molecular mechanisms involved in the tolerance of plants to salt stress. This work provides a good basis for further functional elucidation of these DEPs using genetic and/or other approaches, and, consequently, candidate genes for genetic engineering to improve crop salt tolerance.

iTRAQ-based quantitative proteome and phosphoprotein characterization reveals the central metabolism changes involved in wheat grain development

BACKGROUND

Wheat (Triticum aestivum L.) is an economically important grain crop. Two-dimensional gel-based approaches are limited by the low identification rate of proteins and lack of accurate protein quantitation. The recently developed isobaric tag for relative and absolute quantitation (iTRAQ) method allows sensitive and accurate protein quantification. Here, we performed the first iTRAQ-based quantitative proteome and phosphorylated proteins analyses during wheat grain development.

RESULTS

The proteome profiles and phosphoprotein characterization of the metabolic proteins during grain development of the elite Chinese bread wheat cultivar Yanyou 361 were studied using the iTRAQ-based quantitative proteome approach, TiO2 microcolumns, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Among 1,146 non-redundant proteins identified, 421 showed at least 2-fold differences in abundance, and they were identified as differentially expressed proteins (DEPs), including 256 upregulated and 165 downregulated proteins. Of the 421 DEPs, six protein expression patterns were identified, most of which were up, down, and up-down expression patterns. The 421 DEPs were classified into nine functional categories mainly involved in different metabolic processes and located in the membrane and cytoplasm. Hierarchical clustering analysis indicated that the DEPs involved in starch biosynthesis, storage proteins, and defense/stress-related proteins significantly accumulated at the late grain development stages, while those related to protein synthesis/assembly/degradation and photosynthesis showed an opposite expression model during grain development. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 12 representative genes encoding different metabolic proteins showed certain transcriptional and translational expression differences during grain development. Phosphorylated proteins analyses demonstrated that 23 DEPs such as AGPase, sucrose synthase, Hsp90, and serpins were phosphorylated in the developing grains and were mainly involved in starch biosynthesis and stress/defense.

CONCLUSIONS

Our results revealed a complex quantitative proteome and phosphorylation profile during wheat grain development. Numerous DEPs are involved in grain starch and protein syntheses as well as adverse defense, which set an important basis for wheat yield and quality. Particularly, some key DEPs involved in starch biosynthesis and stress/defense were phosphorylated, suggesting their roles in wheat grain development.

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.