Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions

Flour Treatments Affect Gluten Protein Extractability, Secondary Structure, and Antibody Reactivity

Commercial Brazilian wheat flour was subjected to extrusion, oven, and microwave treatments. The solubility, monomeric and polymeric proteins, and the glutenin and gliadin profiles of the gluten were analyzed. In addition, in vitro digestibility and response against potential celiac disease immune-stimulatory epitopes were investigated. All treatments resulted in low solubility of the polymeric and monomeric proteins. The amounts of insoluble proteins increased from 5.6% in control flour to approximately 10% for all (treatments), whereas soluble proteins decreased from 6.5% to less than 0.5% post treatment. In addition, the treatments affected glutenin and gliadin profiles. The amount of α/β-gliadin extracted decreased after all treatments, while that of γ-gliadin was unaffected. Finally, the potential celiac disease immune stimulatory epitopes decreased in oven and microwave treatment using the G12 ELISA, but no change was observed using the R5 antibody. However, the alteration of the gluten structure and complexity was not sufficient to render a product safe for consumption for individuals with celiac disease; the number of potential celiac disease immune-stimulatory epitopes remained high.

Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses

Tobacco (Nicotiana tabacum L.) is an important industrial crop, which is sensitive to chilling stress. Tobacco seedlings that have been subjected to chilling stress readily flower early, which seriously affects the yield and quality of their leaves. Currently, there has been progress in elucidating the molecular mechanisms by which tobacco responds to chilling stress. However, little is known about the phosphorylation that is mediated by chilling. In this study, the transcriptome, proteome and phosphoproteome were analyzed to elucidate the mechanisms of the responses of tobacco shoot and root to chilling stress (4 °C for 24 h). A total of 6,113 differentially expressed genes (DEGs), 153 differentially expressed proteins (DEPs) and 345 differential phosphopeptides were identified in the shoot, and the corresponding numbers in the root were 6,394, 212 and 404, respectively. This study showed that the tobacco seedlings to 24 h of chilling stress primarily responded to this phenomenon by altering their levels of phosphopeptide abundance. Kyoto Encyclopedia of Genes and Genomes analyses revealed that starch and sucrose metabolism and endocytosis were the common pathways in the shoot and root at these levels. In addition, the differential phosphopeptide corresponding proteins were also significantly enriched in the pathways of photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms in the shoot and arginine and proline metabolism, peroxisome and RNA transport in the root. These results suggest that phosphoproteins in these pathways play important roles in the response to chilling stress. Moreover, kinases and transcription factors (TFs) that respond to chilling at the levels of phosphorylation are also crucial for resistance to chilling in tobacco seedlings. The phosphorylation or dephosphorylation of kinases, such as CDPKs and RLKs; and TFs, including VIP1-like, ABI5-like protein 2, TCP7-like, WRKY 6-like, MYC2-like and CAMTA7 among others, may play essential roles in the transduction of tobacco chilling signal and the transcriptional regulation of the genes that respond to chilling stress. Taken together, these findings provide new insights into the molecular mechanisms and regulatory networks of the responses of tobacco to chilling stress.

Multilayer omics landscape analyses reveal the regulatory responses of tea plants to drought stress

Adverse environments, especially drought conditions, deeply influence plant development and growth in all aspects, and the yield and quality of tea plants are largely dependent on favorable growth conditions. Although tea plant responses to drought stress (DS) have been studied, a comprehensive multilayer epigenetic, transcriptomic, and proteomic investigation of how tea responds to DS is lacking. In this study, we generated DNA methylome, transcriptome, proteome, and phosphoproteome data to explore multiple regulatory landscapes in the tea plant response to DS. An integrated multiomics analysis revealed the response of tea plants to DS at multiple regulatory levels. Furthermore, a set of DS-responsive genes involved in photosynthesis, transmembrane transportation, phytohormone metabolism and signaling, secondary metabolite pathways, transcription factors, protein kinases, posttranslational and epigenetic modification, and other key stress-responsive genes were identified for further functional investigation. These results reveal the multilayer regulatory landscape of the tea plant response to DS and provide insight into the mechanisms of these DS responses.

When drought meets heat - a plant omics perspective

Changes in weather patterns with emerging drought risks and rising global temperature are widespread and negatively affect crop growth and productivity. In nature, plants are simultaneously exposed to multiple biotic and abiotic stresses, but most studies focus on individual stress conditions. However, the simultaneous occurrence of different stresses impacts plant growth and development differently than a single stress. Plants sense the different stress combinations in the same or in different tissues, which could induce specific systemic signalling and acclimation responses; impacting different stress-responsive transcripts, protein abundance and modifications, and metabolites. This mini-review focuses on the combination of drought and heat, two abiotic stress conditions that often occur together. Recent omics studies indicate common or independent regulators involved in heat or drought stress responses. Here, we summarize the current research results, highlight gaps in our knowledge, and flag potential future focus areas.

Integration of Phosphoproteomics and Transcriptome Studies Reveals ABA Signaling Pathways Regulate UV-B Tolerance in Rhododendron chrysanthum Leaves

The influence of UV-B stress on the growth, development, and metabolism of alpine plants, such as the damage to DNA macromolecules, the decline in photosynthetic rate, and changes in growth, development, and morphology cannot be ignored. As an endogenous signal molecule, ABA demonstrates a wide range of responses to UV-B radiation, low temperature, drought, and other stresses. The typical effect of ABA on leaves is to reduce the loss of transpiration by closing the stomata, which helps plants resist abiotic and biological stress. The Changbai Mountains have a harsh environment, with low temperatures and thin air, so Rhododendron chrysanthum (R. chrysanthum) seedlings growing in the Changbai Mountains can be an important research object. In this study, a combination of physiological, phosphorylated proteomic, and transcriptomic approaches was used to investigate the molecular mechanisms by which abiotic stress leads to the phosphorylation of proteins in the ABA signaling pathway, and thereby mitigates UV-B radiation to R. chrysanthum. The experimental results show that a total of 12,289 differentially expressed genes and 109 differentially phosphorylated proteins were detected after UV-B stress in R. chrysanthum, mainly concentrated in plant hormone signaling pathways. Plants were treated with ABA prior to exposure to UV-B stress, and the results showed that ABA mitigated stomatal changes in plants, thus confirming the key role of endogenous ABA in plant adaptation to UV-B. We present a model that suggests a multifaceted R. chrysanthum response to UV-B stress, providing a theoretical basis for further elaboration of the mechanism of ABA signal transduction regulating stomata to resist UV-B radiation.

Sucrose nonfermenting-1-related protein kinase 1 regulates sheath-to-panicle transport of nonstructural carbohydrates during rice grain filling

The remobilization of nonstructural carbohydrates (NSCs) reserved in rice (Oryza sativa) sheaths is essential for grain filling. This assimilate distribution between plant tissues and organs is determined by sucrose non-fermenting-1-related protein kinase 1 (SnRK1). However, the SnRK1-mediated mechanism regulating the sheath-to-panicle transport of NSCs in rice remains unknown. In this study, leaf cutting treatment was used to accelerate NSC transport in the rice sheaths. Accelerated NSC transport was accompanied by increased levels of OsSnRK1a mRNA expression, SnRK1a protein expression, catalytic subunit phosphorylation of SnRK1, and SnRK1 activity, indicating that SnRK1 activity plays an important role in sheath NSC transport. We also discovered that trehalose-6-phosphate, a signal of sucrose availability, slightly reduced SnRK1 activity in vitro. Since SnRK1 activity is mostly regulated by OsSnRK1a transcription in response to low sucrose content, we constructed an snrk1a mutant to verify the function of SnRK1 in NSC transport. NSCs accumulated in the sheaths of snrk1a mutant plants and resulted in a low seed setting rate and grain weight, verifying that SnRK1 activity is essential for NSC remobilization. Using phosphoproteomics and parallel reaction monitoring, we identified 20 SnRK1-dependent phosphosites that are involved in NSC transport. In addition, the SnRK1-mediated phosphorylation of the phosphosites directly affected starch degradation, sucrose metabolism, phloem transport, sugar transport across the tonoplast, and glycolysis in rice sheaths to promote NSC transport. Therefore, our findings reveal the importance, function, and possible regulatory mechanism of SnRK1 in the sheath-to-panicle transport of NSCs in rice.

Wheat Quality Formation and Its Regulatory Mechanism

Elucidation of the composition, functional characteristics, and formation mechanism of wheat quality is critical for the sustainable development of wheat industry. It is well documented that wheat processing quality is largely determined by its seed storage proteins including glutenins and gliadins, which confer wheat dough with unique rheological properties, making it possible to produce a series of foods for human consumption. The proportion of different gluten components has become an important target for wheat quality improvement. In many cases, the processing quality of wheat is closely associated with the nutritional value and healthy effect of the end-products. The components of wheat seed storage proteins can greatly influence wheat quality and some can even cause intestinal inflammatory diseases or allergy in humans. Genetic and environmental factors have great impacts on seed storage protein synthesis and accumulation, and fertilization and irrigation strategies also greatly affect the seed storage protein content and composition, which together determine the final end-use quality of wheat. This review summarizes the recent progress in research on the composition, function, biosynthesis, and regulatory mechanism of wheat storage proteins and their impacts on wheat end-product quality.

Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

Label-Free Quantitative Proteome Analysis Reveals the Underlying Mechanisms of Grain Nuclear Proteins Involved in Wheat Water-Deficit Response

In this study, we performed the first nuclear proteome analysis of wheat developing grains under water deficit by using a label-free based quantitative proteomic approach. In total, we identified 625 unique proteins as differentially accumulated proteins (DAPs), of which 398 DAPs were predicted to be localized in nucleus. Under water deficit, 146 DAPs were up-regulated and mainly involved in the stress response and oxidation-reduction process, while 252 were down-regulated and mainly participated in translation, the cellular amino metabolic process, and the oxidation-reduction process. The cis-acting elements analysis of the key nuclear DAPs encoding genes demonstrated that most of these genes contained the same cis-acting elements in the promoter region, mainly including ABRE involved in abscisic acid response, antioxidant response element, MYB responsive to drought regulation and MYC responsive to early drought. The cis-acting elements related to environmental stress and hormones response were relatively abundant. The transcription expression profiling of the nuclear up-regulated DAPs encoding genes under different organs, developmental stages and abiotic stresses was further detected by RNA-seq and Real-time quantitative polymerase chain reaction, and more than 50% of these genes showed consistency between transcription and translation expression. Finally, we proposed a putative synergistic responsive network of wheat nuclear proteome to water deficit, revealing the underlying mechanisms of wheat grain nuclear proteome in response to water deficit.

Fulvic acid enhances drought resistance in tea plants by regulating the starch and sucrose metabolism and certain secondary metabolism

The aim of this work was to gain insight into the molecular mechanisms underlying the effect of fulvic acid on drought-exposed tea plants. We performed proteomic analysis of fulvic acid-treated tea leaves from the target plants using tandem mass tag quantitative labeling technology and compared the results with those of a previous transcriptomic analysis. We identified 48 and 611 differentially abundant proteins in the leaves of tea plants treated with fulvic acid compared with the control under mild and severe drought, respectively. Comparative analysis showed that, under severe drought, 55 genes had similar expression patterns at the transcriptome and proteome levels, such as PAL, GBE, GBSS and bAS. Bioinformatic analysis revealed that those genes were mainly related to the starch and sucrose metabolism, phenylpropanoid biosynthesis and triterpenoid biosynthesis. SIGNIFICANCE: This study broadens the understanding of the molecular mechanisms underlying the improved drought resistance seen in tea plants in the presence of fulvic acid and provides a basis for further research on the genomics of drought tolerance in these plants. In addition, these findings could be used to develop new guidance strategies for improved drought management systems in tea plantation.

N-linked glycoproteome analysis reveals central glycosylated proteins involved in wheat early seedling growth

Glycosylation is an important protein post-translational modification in eukaryotic organisms. It is involved in many important life processes, such as cell recognition, differentiation, development, signal transduction and immune response. This study carried out the first N-linked glycosylation proteome analysis of wheat seedling leaves using HILIC glycosylation enrichment, chemical deglycosylation, HPLC separation and tandem mass spectrometric identification. In total, we detected 308 glycosylated peptides and 316 glycosylated sites corresponding to 248 unique glycoproteins. The identified glycoproteins were mainly concentrated in plasma membranes (25.6%), cell wall (16.8%) and extracellular area (16%). In terms of molecular function, 65% glycoproteins belonged to various enzymes with catalytic activity such as kinase, carboxypeptidase, peroxidase and phosphatase, and, particularly, 25% of glycoproteins were related to binding functions. These glycoproteins are involved in cell wall reconstruction, biomacromolecular metabolism, signal transduction, endoplasmic reticulum quality control and stress response. Analysis indicated that 57.66% of glycoproteins were highly conserved in other plant species while 42.34% of glycoproteins went unidentified among the conserved glycosylated homologous proteins in other plant species; these may be the new N-linked glycosylated proteins first identified in wheat. The glycosylation sites generally occurred on the random coil, which could play roles in maintaining the structural stability of proteins. PNGase F digestion and glycosylation site mutations further verified the glycosylation modification and glycosylation sites of LRR receptor-like serine/threonine-protein kinase (LRR-RLK) and Beta-D-glucan exohydrolase (β-D-GEH). Our results indicated that N-linked glycosylated proteins could play important roles in the early seedling growth of wheat.

Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice

Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.

Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops

Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.

Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply

Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.

Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes' brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

Dynamic proteome changes of wheat developing grains in response to water deficit and high-nitrogen fertilizer conditions

This study investigated grain proteomic profiles in response to water deficit, high nitrogen (N) fertilizer, and their combined treatments in elite Chinese bread wheat cultivar Jingdong 17, using a two-dimensional difference gel electrophoresis (2D-DIGE)-based approach. Water deficit negatively affected the main agronomic traits of wheat and grain yield, while high-N fertilizer had the opposite effects. The application of a high-N fertilizer under water deficit conditions moderately improved kernel development and grain yield. 2D-DIGE led to the identification of 124 differentially accumulated protein (DAP) spots during five different grain developmental stages, corresponding to 97 unique proteins. The more significant changes of DAPs occurred at 10-20 days after flowering. DAPs were involved in carbohydrate metabolism, protein turnover, protein folding, cell cycle control, stress response, nitrogen metabolism, photosynthesis, and energy metabolism. In particular, water deficit caused a significant downregulation of proteins involved in starch biosynthesis, whereas high-N fertilizer led to a significant upregulation of proteins involved in nitrogen metabolism, carbohydrate metabolism, and starch biosynthesis. The combined treatment resulted in a moderate upregulation of DAPs related to carbohydrate metabolism, starch biosynthesis, and nitrogen metabolism. Our results indicated that high-N fertilization could alleviate yield loss caused by water deficit by promoting the accumulation of proteins involved in nitrogen and carbohydrate metabolism.

Genomic and functional genomics analyses of gluten proteins and prospect for simultaneous improvement of end-use and health-related traits in wheat

KEY MESSAGE

Recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins, which are important determinants of wheat grain quality traits. The new insights obtained and the availability of precise, versatile and high-throughput genome editing technologies will accelerate simultaneous improvement of wheat end-use and health-related traits. Being a major staple food crop in the world, wheat provides an indispensable source of dietary energy and nutrients to the human population. As worldwide population grows and living standards rise in both developed and developing countries, the demand for wheat with high quality attributes increases globally. However, efficient breeding of high-quality wheat depends on critically the knowledge on gluten proteins, which mainly include several families of prolamin proteins specifically accumulated in the endospermic tissues of grains. Although gluten proteins have been studied for many decades, efficient manipulation of these proteins for simultaneous enhancement of end-use and health-related traits has been difficult because of high complexities in their expression, function and genetic variation. However, recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins. Therefore, the main objective of this review is to summarize the genomic and functional genomics information obtained in the last 10 years on gluten protein chromosome loci and genes and the cis- and trans-factors regulating their expression in the grains, as well as the efforts in elucidating the involvement of gluten proteins in several wheat sensitivities affecting genetically susceptible human individuals. The new insights gathered, plus the availability of precise, versatile and high-throughput genome editing technologies, promise to speed up the concurrent improvement of wheat end-use and health-related traits and the development of high-quality cultivars for different consumption needs.

Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq

Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.

Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Jatropha Curcas Seedling under Chilling Stress

As a promising energy plant for biodiesel, Jatropha curcas is a tropical and subtropical shrub and its growth is affected by one of major abiotic stress, chilling. Therefore, we adopt the phosphoproteomic analysis, physiological measurement and ultrastructure observation to illustrate the responsive mechanism of J. curcas seedling under chilling (4 °C) stress. After chilling for 6 h, 308 significantly changed phosphoproteins were detected. Prolonged the chilling treatment for 24 h, obvious physiological injury can be observed and a total of 332 phosphoproteins were examined to be significantly changed. After recovery (28 °C) for 24 h, 291 phosphoproteins were varied at the phosphorylation level. GO analysis showed that significantly changed phosphoproteins were mainly responsible for cellular protein modification process, transport, cellular component organization and signal transduction at the chilling and recovery periods. On the basis of protein-protein interaction network analysis, phosphorylation of several protein kinases, such as SnRK2, MEKK1, EDR1, CDPK, EIN2, EIN4, PI4K and 14-3-3 were possibly responsible for cross-talk between ABA, Ca²⁺, ethylene and phosphoinositide mediated signaling pathways. We also highlighted the phosphorylation of HOS1, APX and PIP2 might be associated with response to chilling stress in J. curcas seedling. These results will be valuable for further study from the molecular breeding perspective.

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.

Identification of phosphorylation proteins in response to water deficit during wheat flag leaf and grain development

BACKGROUND

Wheat (Triticum aestivum L.) serves as important grain crop widely cultivated in the world, which is often suffered by drought stress in natural conditions. As one of the most important post translation modifications, protein phosphorylation widely participates in plant abiotic stress regulation. In this study, we performed the first comparative analysis of phosphorylated protein characterization in flag leaves and developing grains of elite Chinese bread wheat cultivar Zhongmai 175 under water deficit by combining with proteomic approach and Pro-Q Diamond gel staining.

RESULTS

Field experiment showed that water deficit caused significant reduction of plant height, tiller number, ear length and grain yield. 2-DE and Pro-Q Diamond gel staining analysis showed that 58 proteins were phosphorylated among 112 differentially accumulated proteins in response to water deficit, including 20 in the flag leaves and 38 in the developing grains. The phosphorylated proteins from flag leaves mainly involved in photosynthesis, carbohydrate and energy metabolism, while those from developing grains were closely related with detoxification and defense, protein, carbohydrate and energy metabolism. Particularly, water deficit resulted in significant downregulation of phosphorylated modification level in the flag leaves, which could affect photosynthesis and grain yield. However, some important phosphorylated proteins involved in stress defense, energy metabolism and starch biosynthesis were upregulated under water deficit, which could benefit drought tolerance, accelerate grain filling and shorten grain developing time.

CONCLUSIONS

The modification level of those identified proteins from flag leaves and grains had great changes when wheat was suffered from water deficit, indicating that phosphoproteins played a key role in response to drought stress. Our results provide new insights into the molecular mechanisms how phosphoproteins respond to drought stress and thus reduce production.

Crop resistant starch and genetic improvement: a review of recent advances

Resistant starch (RS), as a healthy dietary fiber, meets with great human favor along with the rapid development and improvement of global living standards. RS shows direct effects in reducing postprandial blood glucose levels, serum cholesterol levels and glycemic index. Therefore, RS plays an important role in preventing and improving non-communicable diseases, such as obesity, diabetes, colon cancer, cardiovascular diseases and chronic kidney disease. In addition, RS leads to its potential applied value in the development of high-quality foodstuffs, such as bread, noodles and dumplings. This paper reviews the recent advances in RS research, focusing mainly on RS classification and measurement, formation, quantitative trait locus mapping, genome-wide association studies, molecular marker development and genetic improvement through induced mutations, plant breeding combined with marker-assisted selection and genetic transformation. Challenges and perspectives on further RS research are also discussed.

Nitric Oxide Enhancing Resistance to PEG-Induced Water Deficiency is Associated with the Primary Photosynthesis Reaction in Triticum aestivum L

Photosynthesis is affected by water-deficiency (WD) stress, and nitric oxide (NO) is a free radical that participates in the photosynthesis process. Previous studies have suggested that NO regulates excitation-energy distribution of photosynthesis under WD stress. Here, quantitative phosphoproteomic profiling was conducted using iTRAQ. Differentially phosphorylated protein species (DEPs) were identified in leaves of NO- or polyethylene glycol (PEG)-treated wheat seedlings (D), and in control seedlings. From 1396 unique phosphoproteins, 2257 unique phosphorylated peptides and 2416 phosphorylation sites were identified. Of these, 96 DEPs displayed significant changes (≥1.50-fold, p < 0.01). These DEPs are involved in photosynthesis, signal transduction, etc. Furthermore, phosphorylation of several DEPs was upregulated by both D and NO treatments, but downregulated only in NO treatment. These differences affected the chlorophyll A–B binding protein, chloroplast post-illumination chlorophyll-fluorescence-increase protein, and SNT7, implying that NO indirectly regulated the absorption and transport of light energy in photosynthesis in response to WD stress. The significant difference of chlorophyll (Chl) content, Chl a fluorescence-transient, photosynthesis index, and trapping and transport of light energy further indicated that exogenous NO under D stress enhanced the primary photosynthesis reaction compared to D treatment. A putative pathway is proposed to elucidate NO regulation of the primary reaction of photosynthesis under WD.

Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.

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.

Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality

Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.

Genome-wide analysis of the Brachypodium distachyon (L.) P. Beauv. Hsp90 gene family reveals molecular evolution and expression profiling under drought and salt stresses

The structure, evolution, and function of heat shock proteins 90 (Hsp90s) have been investigated in great detail in fungi and animals. However, studies on the Hsp90 genes in plants are generally limited. Brachypodium distachyon (L.) P. Beauv., as a model plant for cereal crops, has become a potential biofuel grass. During its long evolution, the Hsp90 gene family in Brachypodium has developed some strategies to cope with adverse environments. How the Hsp90 gene family in Brachypodium evolved in different plant lineages and what its role is in plant responses to drought and salt stresses remains to be elucidated. We used a set of different bioinformatics tools to identify 94 Hsp90 genes from 10 species representing four plant lineages and classified into three subgroups. Eight BdHsp90 genes were detected from B. distachyon. The number of exon-intron structures differed in each subgroup, and the motif analysis revealed that these genes were relatively conservative in each group. The fragments duplication and tandem duplication, which are the prime powers for functional diversity, generally occurred during the duplication of the whole plant genome. Transcriptional analysis of the BdHsp90 genes under salt and drought stress conditions indicated that the expression of these genes was delayed or increased at different stress time points; The expression was more affected in that of Bradi3g39630, Bradi4g06370, and Bradi1g30130. Our findings suggest the involvement of BdHsp90s in plant abiotic stress response, and further consolidate our views on the stress response mechanism of Hsp90 in general.

In vivo phosphoproteome characterization reveals key starch granule-binding phosphoproteins involved in wheat water-deficit response

BACKGROUND

Drought stress during grain development causes significant yield loss in cereal production. The phosphorylated modification of starch granule-binding proteins (SGBPs) is an important mechanism regulating wheat starch biosynthesis. In this study, we performed the first proteomics and phosphoproteomics analyses of SGBPs in elite Chinese bread wheat (Triticum aestivum L.) cultivar Jingdong 17 under well-watered and water-stress conditions.

RESULTS

Water stress treatment caused significant reductions in spike grain numbers and weight, total starch and amylopectin content, and grain yield. Two-dimensional gel electrophoresis revealed that the quantity of SGBPs was reduced significantly by water-deficit treatment. Phosphoproteome characterization of SGBPs under water-deficit treatment demonstrated a reduced level of phosphorylation of main starch synthesis enzymes, particularly for granule-bound starch synthase (GBSS I), starch synthase II-a (SS II-a), and starch synthase III (SS III). Specifically, the Ser34 site of the GBSSI protein, the Tyr358 site of SS II-a, and the Ser837 site of SS III-a exhibited significant less phosphorylation under water-deficit treatment than well-watered treatment. Furthermore, the expression levels of several key genes related with starch biosynthesis detected by qRT-PCR were decreased significantly at 15 days post-anthesis under water-deficit treatment. Immunolocalization showed a clear movement of GBSS I from the periphery to the interior of starch granules during grain development, under both water-deficit and well-watered conditions.

CONCLUSIONS

Our results demonstrated that the reduction in gene expression or transcription level, protein expression and phosphorylation levels of starch biosynthesis related enzymes under water-deficit conditions is responsible for the significant decrease in total starch content and grain yield.

Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots

Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs). Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.

Integrated physiological and proteomic analysis reveals underlying response and defense mechanisms of Brachypodium distachyon seedling leaves under osmotic stress, cadmium and their combined stresses

Drought stress, a major abiotic stress, commonly occurs in metal-contaminated environments and affects crop growth and yield. In this study, we performed the first integrated phenotypic, physiological, and proteomic analysis of Brachypodium distachyon L. seedling leaves under polyethylene glycol (PEG) mock osmotic stress, cadmium (Cd²⁺), and their combined stresses. Combined osmotic and Cd²⁺ stress had more significant effects than each individual stress on seedling growth, and the physiological traits and ultrastructures of leaves. Totally 117 differentially accumulated protein (DAP) spots detected by two-dimensional difference gel electrophoresis (2D-DIGE) were identified, and representing 89 unique proteins under individual and combined stresses. These DAPs were involved in photosynthesis/respiration (34%), energy and carbon metabolism (21%), stress/defense/detoxification (13%), protein folding and degradation (12%), and amino acid metabolism (7%). Principal component analysis (PCA) revealed that DAPs from the Cd²⁺ and combined stresses grouped much closer than those from osmotic stress, indicating Cd²⁺ and combined stresses resulted in more changes to the leaf proteome than osmotic stress alone. Protein-protein interaction analyses showed that a 14-3-3 centered sub-network could play important roles in responses to abiotic stresses. An overview pathway of proteome metabolic changes in Bd21 seedling leaves under combined stresses is proposed, representing a synergistic responsive network and underlying response and defense mechanisms.

SIGNIFICANCE

Drought stress is one of the major abiotic stresses, which commonly occurs in metal-contaminated environments, and affects crop growth and yield performance. We performed the first integrated phenotypic, physiological and proteomic analysis of Brachypodium distachyon L. seedling leaves under drought (PEG), cadmium (Cd²⁺) and their combined stresses.

The Phosphoproteomic Response of Rice Seedlings to Cadmium Stress

The environmental damage caused by cadmium (Cd) pollution is of increasing concern in China. While the overall plant response to Cd has been investigated in some depth, the contribution (if any) of protein phosphorylation to the detoxification of Cd and the expression of tolerance is uncertain. Here, the molecular basis of the plant response has been explored in hydroponically raised rice seedlings exposed to 10 μΜ and 100 μΜ Cd²⁺ stress. An analysis of the seedlings’ quantitative phosphoproteome identified 2454 phosphosites, associated with 1244 proteins. A total of 482 of these proteins became differentially phosphorylated as a result of exposure to Cd stress; the number of proteins affected in this way was six times greater in the 100 μΜ Cd²⁺ treatment than in the 10 μΜ treatment. A functional analysis of the differentially phosphorylated proteins implied that a significant number was involved in signaling, in stress tolerance and in the neutralization of reactive oxygen species, while there was also a marked representation of transcription factors.

Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress

Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites, and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Five and thirty-five phosphoproteins with the phosphorylation levels significantly changed (PLSC) were identified in M26 and MBB, respectively. Among these, four PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlap of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins represent a unique combination of metabolism, transcription, translation, and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new and unique homeostasis of major cellular processes. The basic trend was an increase in protein and organic molecules abundance related to drought. These increases were higher in MBB than in M26. Our study is the first to address the phosphoproteome of apple rootstocks in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.

Effect of irrigation and nitrogen application on grain amino acid composition and protein quality in winter wheat

Water management and nitrogen application are critical factors in wheat grain yield and protein quality. This study aimed to evaluate the effect of irrigation and nitrogen application on the grain yield, protein content and amino acid composition of winter wheat. Field experiments were conducted in a split-plot design with three replications in high-yielding land on the North China Plain in 2012/2013, 2013/2014 and 2014/2015. Three irrigation treatments were examined in main plots: no irrigation, irrigation at jointing, and irrigation at jointing plus anthesis, while subplots were assigned to nitrogen treatment at four different rates: 0, 180, 240, 300 kg N ha^-1, respectively. The results indicated that irrigation at jointing and at jointing plus anthesis improved grain yield by an average of 12.79 and 18.65% across three cropping seasons, respectively, compared with no irrigation. However, different irrigation treatments had no significant effect on grain protein content in any cropping season. Compared with no N treatment, 180, 240, and 300 kg N ha^-1 N application significantly increased grain yield, by 58.66, 61.26 and 63.42% respectively, averaged over three cropping seasons. Grain protein and the total, essential and non-essential amino acid content significantly increased with increasing nitrogen application. Irrigation significantly improved the essential amino acid index (EAAI) and protein-digestibility-corrected amino acid score (PDCAAS) compared with no irrigation; however, N application decreased them by an average of 7.68 and 11.18% across three cropping seasons, respectively. EAAI and PDCAAS were positively correlated, however, they were highly negatively correlated with yield and grain protein content.

Phosphoproteomic Analysis of Paper Mulberry Reveals Phosphorylation Functions in Chilling Tolerance

Paper mulberry is a valuable woody species with a good chilling tolerance. In this study, phosphoproteomic analysis, physiological measurement, and mRNA quantification were employed to explore the molecular mechanism of chilling (4 °C) tolerance in paper mulberry. After chilling for 6 h, 427 significantly changed phosphoproteins were detected in paper mulberry seedlings without obvious physiological injury. When obvious physiological injury occurred after chilling for 48 h, a total of 611 phosphoproteins were found to be significantly changed at the phosphorylation level. Several protein kinases, especially CKII, were possibly responsible for these changes according to conserved sequence analysis. The results of Gene Ontology analysis showed that phosphoproteins were mainly responsible for signal transduction, protein modification, and translation during chilling. Additionally, transport and cellular component organization were enriched after chilling for 6 and 48 h, respectively. On the basis of the protein-protein interaction network analysis, a protein kinase and phosphatases hub protein (P1959) were found to be involved in cross-talk between Ca²⁺, BR, ABA, and ethylene-mediated signaling pathways. We also highlighted the phosphorylation of BpSIZ1 and BpICE1 possibly impacted on the CBF/DREB-responsive pathway. From these results, we developed a schematic for the chilling tolerance mechanism at phosphorylation level.

Physiological and proteomic analyses of the drought stress response in Amygdalus Mira (Koehne) Yü et Lu roots

BACKGROUND

Plants are oftentimes exposed to many types of abiotic stresses. Drought is one of the main environmental stresses which limits plant growth, distribution and crop yield worldwide. Amygdalus mira (Koehne) Yü et Lu is an important wild peach, and it is considered an ideal wild peach germplasm for improving cultivated peach plants. Because of the loss of genetic variation, cultivated peach plants are sensitive to biotic and abiotic stresses. Wild peach germplasm can offer many useful genes for peach improvement. Responses to drought by withholding water have been studied in Amygdalus mira (Koehne) Yü et Lu roots. In this study, plants were divided into well-watered (control) and water-stressed (treatment) groups, and the treatment group did not receive water until the recovery period (day 16).

RESULTS

Several physiological parameters, including root water content and root length, were reduced by drought stress and recovered after rewatering. In addition, the relative conductivity, the levels of proline, MDA and H₂O₂, and the activities of ROS scavenging enzymes (POD, APX and CAT) were increased, and none of these factors, except the level of proline, recovered after rewatering. In total, 95 differentially expressed proteins were revealed after drought. The identified proteins refer to a extensive range of biological processes, molecular functions and cellular components, including cytoskeleton dynamics (3.16% of the total 95 proteins), carbohydrate and nitrogen metabolism (6.33% of the total 95 proteins), energy metabolism (7.37% of the total 95 proteins), transcription and translation (18.95% of the total 95 proteins), transport (4.21% of the total 95 proteins), inducers (3.16% of the total 95 proteins), stress and defense (26.31% of the total 95 proteins), molecular chaperones (9.47% of the total 95 proteins), protein degradation (3.16% of the total 95 proteins), signal transduction (7.37% of the total 95 proteins), other materials metabolism (5.26% of the total 95 proteins) and unknown functions (5.26% of the total 95 proteins). Proteins related to defense, stress, transcription and translation play an important role in drought response. In addition, we also examined the correlation between protein and transcript levels.

CONCLUSIONS

The interaction between enzymatic and non-enzymatic antioxidants, the levels of proline, MDA, H₂O₂ and the relative conductivity, and the expression level of proteins in drought-treated plants all contribute to drought resistance in Amygdalus mira (Koehne) Yü et Lu.

Proteome Profiling of Wheat Shoots from Different Cultivars

Wheat is a cereal grain and one of the world's major food crops. Recent advances in wheat genome sequencing are by now facilitating its genomic and proteomic analyses. However, little is known about possible differences in total protein levels of hexaploid versus tetraploid wheat cultivars, and also knowledge of phosphorylated wheat proteins is still limited. Here, we performed a detailed analysis of the proteome of seedling leaves from two hexaploid wheat cultivars (Triticum aestivum L. Pavon 76 and USU-Apogee) and one tetraploid wheat (T. turgidum ssp. durum cv. Senatore Cappelli). Our shotgun proteomics data revealed that, whereas we observed some significant differences, overall a high similarity between hexaploid and tetraploid varieties with respect to protein abundance was observed. In addition, already at the seedling stage, a small set of proteins was differential between the small (USU-Apogee) and larger hexaploid wheat cultivars (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first searchable repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.

Comparative Phosphoproteomic Analysis under High-Nitrogen Fertilizer Reveals Central Phosphoproteins Promoting Wheat Grain Starch and Protein Synthesis

Nitrogen (N) is a macronutrient important for plant growth and development. It also strongly influences starch and protein synthesis, closely related to grain yield and quality. We performed the first comparative phosphoproteomic analysis of developing wheat grains in response to high-N fertilizer. Physiological and biochemical analyses showed that application of high-N fertilizer resulted in significant increases in leaf length and area, chlorophyll content, the activity of key enzymes in leaves such as nitrate reductase (NR), and in grains such as sucrose phosphate synthase (SPS), sucrose synthase (SuSy), and ADP glucose pyrophosphorylase (AGPase). This enhanced enzyme activity led to significant improvements in starch content, grain yield, and ultimately, bread making quality. Comparative phosphoproteomic analysis of developing grains under the application of high-N fertilizer performed 15 and 25 days post-anthesis identified 2470 phosphosites among 1372 phosphoproteins, of which 411 unique proteins displayed significant changes in phosphorylation level (>2-fold or <0.5-fold). These phosphoproteins are involved mainly in signaling transduction, starch synthesis, energy metabolism. Pro-Q diamond staining and Western blotting confirmed our phosphoproteomic results. We propose a putative pathway to elucidate the important roles of the central phosphoproteins regulating grain starch and protein synthesis. Our results provide new insights into the molecular mechanisms of protein phosphorylation modifications involved in grain development, yield and quality formation.

Global Scale Transcriptional Profiling of Two Contrasting Barley Genotypes Exposed to Moderate Drought Conditions: Contribution of Leaves and Crowns to Water Shortage Coping Strategies

Drought is a serious threat for sustainable agriculture. Barley represents a species well adapted to environmental stresses including drought. To elucidate the adaptive mechanism of barley on transcriptional level we evaluated transcriptomic changes of two contrasting barley cultivars upon drought using the microarray technique on the level of leaves and crowns. Using bioinformatic tools, differentially expressed genes in treated vs. non-treated plants were identified. Both genotypes revealed tissue dehydration under drought conditions as shown at water saturation deficit and osmotic potential data; however, dehydration was more severe in Amulet than in drought-resistant Tadmor under the same ambient conditions. Performed analysis showed that Amulet enhanced expression of genes related to active plant growth and development, while Tadmor regarding the stimulated genes revealed conservative, water saving strategy. Common reactions of both genotypes and tissues included an induction of genes encoding several stress-responsive signaling proteins, transcription factors as well as effector genes encoding proteins directly involved in stress acclimation. In leaf, tolerant cultivar effectively stimulated mainly the expression of genes encoding proteins and enzymes involved in protein folding, sulfur metabolism, ROS detoxification or lipid biosynthesis and transport. The crown specific reaction of tolerant cultivar was an enhanced expression of genes encoding proteins and enzymes involved in cell wall lignification, ABRE-dependent abscisic acid (ABA) signaling, nucleosome remodeling, along with genes for numerous jasmonate induced proteins.

Dynamic Phosphoproteome Analysis of Seedling Leaves in Brachypodium distachyon L. Reveals Central Phosphorylated Proteins Involved in the Drought Stress Response

Drought stress is a major abiotic stress affecting plant growth and development. In this study, we performed the first dynamic phosphoproteome analysis of Brachypodium distachyon L. seedling leaves under drought stress for different times. A total of 4924 phosphopeptides, contained 6362 phosphosites belonging to 2748 phosphoproteins. Rigorous standards were imposed to screen 484 phosphorylation sites, representing 442 unique phosphoproteins. Comparative analyses revealed significant changes in phosphorylation levels at 0, 6, and 24 h under drought stress. The most phosphorylated proteins and the highest phosphorylation level occurred at 6 h. Venn analysis showed that the up-regulated phosphopeptides at 6 h were almost two-fold those at 24 h. Motif-X analysis identified the six motifs: [sP], [Rxxs], [LxRxxs], [sxD], [sF], and [TP], among which [LxRxxs] was also previously identified in B. distachyon. Results from molecular function and protein-protein interaction analyses suggested that phosphoproteins mainly participate in signal transduction, gene expression, drought response and defense, photosynthesis and energy metabolism, and material transmembrane transport. These phosphoproteins, which showed significant changes in phosphorylation levels, play important roles in signal transduction and material transmembrane transport in response to drought conditions. Our results provide new insights into the molecular mechanism of this plant’s abiotic stress response through phosphorylation modification.

Plant Organellar Proteomics in Response to Dehydration: Turning Protein Repertoire into Insights

Stress adaptation or tolerance in plants is a complex phenomenon involving changes in physiological and metabolic processes. Plants must develop elaborate networks of defense mechanisms, and adapt to and survive for sustainable agriculture. Water-deficit or dehydration is the most critical environmental factor that plants are exposed to during their life cycle, which influences geographical distribution and productivity of many crop species. The cellular responses to dehydration are orchestrated by a series of multidirectional relays of biochemical events at organelle level. The new challenge is to dissect the underlying mechanisms controlling the perception of stress signals and their transmission to cellular machinery for activation of adaptive responses. The completeness of current descriptions of spatial distribution of proteins, the relevance of subcellular locations in diverse functional processes, and the changes of protein abundance in response to dehydration hold the key to understanding how plants cope with such stress conditions. During past decades, organellar proteomics has proved to be useful not only for deciphering reprograming of plant responses to dehydration, but also to dissect stress-responsive pathways. This review summarizes a range of organellar proteomics investigations under dehydration to gain a holistic view of plant responses to water-deficit conditions, which may facilitate future efforts to develop genetically engineered crops for better adaptation.

Advances in crop proteomics: PTMs of proteins under abiotic stress

Under natural conditions, crop plants are frequently subjected to various abiotic environmental stresses such as drought and heat wave, which may become more prevalent in the coming decades. Plant acclimation and tolerance to an abiotic stress are always associated with significant changes in PTMs of specific proteins. PTMs are important for regulating protein function, subcellular localization and protein activity and stability. Studies of plant responses to abiotic stress at the PTMs level are essential to the process of plant phenotyping for crop improvement. The ability to identify and quantify PTMs on a large-scale will contribute to a detailed protein functional characterization that will improve our understanding of the processes of crop plant stress acclimation and stress tolerance acquisition. Hundreds of PTMs have been reported, but it is impossible to review all of the possible protein modifications. In this review, we briefly summarize several main types of PTMs regarding their characteristics and detection methods, review the advances in PTMs research of crop proteomics, and highlight the importance of specific PTMs in crop response to abiotic stress.

Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress

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

A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight

BACKGROUND

Rice is a major crop worldwide. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice. It has been clear that phosphorylation plays essential roles in plant disease resistance. However, the role of phosphorylation is poorly understood in rice-Xoo system. Here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after Xoo infection.

RESULTS

We have successfully identified 2367 and 2223 phosphosites on 1334 and 1297 representative proteins in 0 h and 24 h after Xoo infection, respectively. A total of 762 differentially phosphorylated proteins, including transcription factors, kinases, epi-genetic controlling factors and many well-known disease resistant proteins, are identified after Xoo infection suggesting that they may be functionally relevant to Xoo resistance. In particular, we found that phosphorylation/dephosphorylation might be a key switch turning on/off many epi-genetic controlling factors, including HDT701, in response to Xoo infection, suggesting that phosphorylation switch overriding the epi-genetic regulation may be a very universal model in the plant disease resistance pathway.

CONCLUSIONS

The phosphosites identified in this study would be a big complementation to our current knowledge in the phosphorylation status and sites of rice proteins. This research represents a substantial advance in understanding the rice phosphoproteome as well as the mechanism of rice bacterial blight resistance.

Recent advances and challenges in plant phosphoproteomics

Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.