Wheat quality related differential expressions of albumins and globulins revealed by two-dimensional difference gel electrophoresis (2-D DIGE)

Molecular prospective on the wheat grain development

Wheat grain development is an important biological process to determine grain yield and quality, which is controlled by the interplay of genetic, epigenetic, and environmental factors. Wheat grain development has been extensively characterized at the phenotypic and genetic levels. The advent of innovative molecular technologies allows us to characterize genes, proteins, and regulatory factors involved in wheat grain development, which have enhanced our understanding of the wheat seed development process. However, wheat is an allohexaploid with a large genome size, the molecular mechanisms underlying the wheat grain development have not been well understood as those in diploids. Understanding grain development, and how it is regulated, is of fundamental importance for improving grain yield and quality through conventional breeding or genetic engineering. Herein, we review the current discoveries on the molecular mechanisms underlying wheat grain development. Notably, only a handful of genes that control wheat grain development have, thus far, been well characterized, their interplay underlying the grain development remains elusive. The synergistic network-integrated genomics and epigenetics underlying wheat grain development and how the subgenome divergence dynamically and precisely regulates wheat grain development are unknown.

Investigating phenotypic relationships in persimmon accessions through integrated proteomic and metabolomic analysis of corresponding fruits

Together with phenological and genomic approaches, gel-based and label-free proteomic as well metabolomic procedures were separately applied to plants to highlight differences between ecotypes, to estimate genetic variability within/between organism populations, or to characterize specific mutants/genetically modified lines at metabolic level. To investigate the possible use of tandem mass tag (TMT)-based quantitative proteomics in the above-mentioned contexts and based on the absence of combined proteo-metabolomic studies on Diospyros kaki cultivars, we here applied integrated proteomic and metabolomic approaches to fruits from Italian persimmon ecotypes with the aim to characterize plant phenotypic diversity at molecular level. We identified 2255 proteins in fruits, assigning 102 differentially represented components between cultivars, including some related to pomological, nutritional and allergenic characteristics. Thirty-three polyphenols were also identified and quantified, which belong to hydroxybenzoic acid, flavanol, hydroxycinnamic acid, flavonol, flavanone and dihydrochalcone sub-classes. Heat-map representation of quantitative proteomic and metabolomic results highlighted compound representation differences in various accessions, whose elaboration through Euclidean distance functions and other linkage methods defined dendrograms establishing phenotypic relationships between cultivars. Principal component analysis of proteomic and metabolomic data provided clear information on phenotypic differences/similarities between persimmon accessions. Coherent cultivar association results were observed between proteomic and metabolomic data, emphasizing the utility of integrating combined omic approaches to identify and validate phenotypic relationships between ecotypes, and to estimate corresponding variability and distance. Accordingly, this study describes an original, combined approach to outline phenotypic signatures in persimmon cultivars, which may be used for a further characterization of other ecotypes of the same species and an improved description of nutritional characteristics of corresponding fruits.

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.

The 10,000-Year Success Story of Wheat!

Wheat is one of the most important cereal crops in the world as it is used in the production of a diverse range of traditional and modern processed foods. The ancient varieties einkorn, emmer, and spelt not only played an important role as a source of food but became the ancestors of the modern varieties currently grown worldwide. Hexaploid wheat (Triticum aestivum L.) and tetraploid wheat (Triticum durum Desf.) now account for around 95% and 5% of the world production, respectively. The success of this cereal is inextricably associated with the capacity of its grain proteins, the gluten, to form a viscoelastic dough that allows the transformation of wheat flour into a wide variety of staple forms of food in the human diet. This review aims to give a holistic view of the temporal and proteogenomic evolution of wheat from its domestication to the massively produced high-yield crop of our day.

How Foliar Fungal Diseases Affect Nitrogen Dynamics, Milling, and End-Use Quality of Wheat

Foliar fungal diseases may cause important losses on yield and quality of wheat (Triticum aestivum L.). They may impact crop growth rate differently, modifying nitrogen (N) dynamics and carbohydrate accumulation in the grain. The relationship between N and carbohydrates accumulation determines the grain protein concentration, which impacts the gluten concentration and rheological properties of the wheat flour. In addition, types of fungicides and N fertilization can influence the intensity of foliar diseases and have an effect on the milling and end-use quality, depending on the bread-making aptitude of the genotypes, the nutritional habit of the pathogen involved, the amount and time of infection, environmental factors, and interactions between these factors. In that way, N fertilization may modify the severity of the diseases according to the nutritional habit of the pathogen involved. Some fungicides, such as strobilurins and carboxamides, produce high levels of disease control and prolong the healthy leaf area duration, which translates into important yield responses, potentially compromising the grain protein concentration by additional carbohydrate production, with consequences in the bread-making quality. Furthermore, infections caused by biotrophic pathogens can be more damaging to N deposition than to dry matter accumulation, whereas the reverse has been generally true for diseases caused by necrotrophic pathogens. The time of infection could also affect yield components and N dynamics differentially. Early epidemics may reduce the number of grains per area and the N remobilization, whereas late epidemics may affect the thousand kernel weight and mainly the N absorption post-flowering. A review updating findings of the effects of infections caused by foliar fungal pathogens of different nutritional habits and the incidence of several factors modifying these effects on the above-ground biomass generation, N dynamics, protein and gluten concentration, milling, rheological properties, loaf volume, and other quality-related traits is summarized. Three main pathogens in particular, for which recent information is available, were taken as representative of biotrophic (Puccinia triticina), necrotrophic (Pyrenophora tritici-repentis), and hemibiotrophic (Zymoseptoria tritici) nutritional habit, and some general models of their effects are proposed. New challenges for researchers to minimize the impact of foliar diseases on end-use quality are also discussed.

Seed Proteomic Profiles of Three Paeonia Varieties and Evaluation of Peony Seed Protein as a Food Product

Peony (Paeonia) has high ornamental, edible, and medicinal values. In order to distinguish seeds varieties, describe the proteomic profiles correlated with stress tolerance, and evaluate peony seed protein (PSP) as a functional food product, we characterized the seed protein profiles of these three species and their glucosidase inhibition activities. Results showed that the intensity of protein bands in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and specific protein ID (especially for specifically expressed proteins (SEPs)) was effective to distinguish these peony seed varieties. Proteomic analysis of the three species showed that P. ostii "Fengdan" has heat and pathogen tolerance-related proteins, while P. rockii has higher content of proteins related to cold resistance, which were all highly consistent with their adaptation of heat or cold habitat. Moreover, stress-related proteins were also accumulated in P. lactiflora Pall "Hangshao" seeds, showing its potential for stress resistance. Further protein analysis showed that the primary composition of PSP was albumin and globulin. And the solubility of PSP was good. Furthermore, PSP also showed high glucosidase inhibition activity, indicating that PSP might have some potential function for the remission of hyperglycemia. And P. ostii "Fengdan" seeds may be a better source for protein production than seeds of the other two species in terms of protein solubility and the content of total protein, albumin, and globulin. In addition, an optimal protocol of microwave-assisted alkali extraction was developed to produce PSP. In conclusion, the evaluated stress-related proteins in three peony seed species by proteomic analysis quite agreed with their adaptation of heat or cold stress; proteomics could also be a very useful tool for distinguishing species in the production; and peony seeds may be a good source for protein production.

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.

Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors

Wheat grain development after anthesis is an important biological process, in which major components of seeds are synthesised, and these components are further required for germination and seed vigour. We have made a comparative RNA-Seq analysis between hexaploid wheat and its individual diploid progenitors to know the major differentially expressed genes (DEGs) involved during grain development. Two libraries from each species were generated with an average of 55.63, 55.23, 68.13, and 103.81 million reads, resulting in 79.3K, 113.7K, 90.6K, and 121.3K numbers of transcripts in AA, BB, DD, and AABBDD genome species respectively. Number of expressed genes in hexaploid wheat was not proportional to its genome size, but marginally higher than that of its diploid progenitors. However, to capture all the transcripts in hexaploid wheat, sufficiently higher number of reads was required. Functional analysis of DEGs, in all the three comparisons, showed their predominance in three major classes of genes during grain development, i.e., nutrient reservoirs, carbohydrate metabolism, and defence proteins; some of them were subsequently validated through real time quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Further, developmental stage-specific gene expression showed most of the defence protein genes expressed during initial developmental stages in hexaploid contrary to the diploids at later stages. Genes related to carbohydrates anabolism expressed during early stages, whereas catabolism genes expressed at later stages in all the species. However, no trend was observed in case of different nutrient reservoirs gene expression. This data could be used to study the comparative gene expression among the three diploid species and homeologue-specific expression in hexaploid.

Introgression of an expressed HMW 1Ay glutenin subunit allele into bread wheat cv. Lincoln increases grain protein content and breadmaking quality without yield penalty

An expressed HMW glutenin subunit Glu-Ay showed positive impacts on a range of wheat processing quality and yield traits. The grain protein compositions are significantly optimised for baking, resulting in a better breadmaking quality. The unique breadmaking properties of wheat flour are related to the quality and quantity of high-molecular weight glutenin subunits (HMW-GSs) present in the grain. In the current study, the silent 1Ay HMW-GS allele, present in most bread wheat cultivars, was replaced by the expressed 1Ay21* allele, which was introgressed into Australian bread wheat cultivar Lincoln by a backcrossing and selfing scheme. Stability of gene expression and the effect of the introgressed 1Ay21* subunit on protein composition, agronomic traits, flour functionality, and breadmaking quality were studied using BC4F5 grain grown in glasshouse and field. Field phenotyping and grain quality testing showed that the 1Ay21* gene conferred significant improvements to a range of traits, including an increase in grain protein content by up to 9%, UPP% by up to 24%, bread volume by up to 28%. The glasshouse experiment and one of the field trials showed positive 1Ay21* effects on yield, while one field trial showed one significant effects. This indicates that expression of the 1Ay21* gene has the potential of simultaneously increasing protein content and grain yield under certain environment. The qualitative improvements of the grain also led to a reduction of the energy required during the baking process in addition to the significant positive effects on bread quality.

A Comprehensive Peptidomic Approach to Characterize the Protein Profile of Selected Durum Wheat Genotypes: Implication for Coeliac Disease and Wheat Allergy

The wheat varietal selection undertaken by breeders in recent decades has been tailored mainly to improve technological and productivity-related traits; however, the latter has resulted in a considerable impoverishment of the genetic diversity of wheat-based products available on the market. This pitfall has encouraged researchers to revalue the natural diversity of cultivated and non-cultivated wheat genotypes in light of their different toxic/immunogenic potential for celiac disease and wheat-allergic patients. In the present investigation, an advanced proteomic approach was designed for the global characterization of the protein profile of selected tetraploid wheat genotypes (Triticum turgidum). The approach combined proteins/peptides sequence information retrieved by specific enzymatic digestions (single and dual proteolytic enzymes) with protein digestibility information disclosed by means of in-vitro simulated human gastroduodenal digestion experiments. In both cases, the peptide pools were characterized by discovery analysis with liquid chromatography high-resolution tandem mass spectrometry, and specific amino acid sequences were identified via commercial software. The peptide list was screened for in silico toxicity/immunogenicity risk assessment, with the aid of various open-source bioinformatics tools for epitopes matching. Given the global information provided by the designed proteomic approach, the in silico risk assessment not only tackled toxicity implication for celiac disease patients, but also scouted for immunogenic sequences relevant for wheat allergic patients, achieving a comprehensive characterization of the protein profile of the selected genotypes. These latter were assessed to encrypt a variable number of toxic/immunogenic epitopes for celiac disease and wheat allergy, and as such they could represent convenient bases for breeding practices and for the development of new detoxification strategies.

Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition

Albumins and globulins (AGs) of wheat endosperm represent about 20% of total grain proteins. Some of these physiologically active proteins can influence the synthesis of storage proteins (SPs) (gliadins and glutenins) and consequently, rheological properties of wheat flour and processing. To identify such AGs, data, (published by Bonnot et al., 2017) concerning abundance in 352 AGs and in the different seed SPs during grain filling and in response to different nitrogen (N) and sulfur (S) supply, were integrated with mixOmics R package. Relationships between AGs and SPs were first unraveled using the unsupervised method sparse Partial Least Square, also known as Projection to Latent Structure (sPLS). Then, data were integrated using a supervised approach taking into account the nutrition and the grain developmental stage. We used the block.splda procedure also referred to as DIABLO (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies). These approaches led to the identification of discriminant and highly correlated features from the two datasets (AGs and SPs) which are not necessarily differentially expressed during seed development or in response to N or S supply. Eighteen AGs were correlated with the quantity of SPs per grain. A statistical validation of these proteins by genetic association analysis confirmed that 5 out of this AG set were robust candidate proteins able to modulate the seed SP synthesis. In conclusion, this latter result confirmed that the integrative strategy is an adequate way to reduce the number of potentially relevant AGs for further functional validation.

Topological features of the intermolecular contacts in gluten-forming proteins: Exploring a novel methodological approach based on gold nanoparticles

This work introduces a novel methodological approach to study both the geometry of complex protein networks and the nature of the interacting proteins. This approach is based on the high reactivity of Au⁺ ions on the surface of gold nanoparticles (AuNPs) towards thiols, that allows fast formation of a covalent bond between accessible protein thiols and AuNPs. In the case of the durum wheat semolina used in the exploratory studies reported here, the nature of proteins covalently bound to AuNPs is expected to be affected by both the compactness of the protein network and by the AuNPs size. Simple centrifugation procedures allowed recovery of the protein-loaded AuNPs that remained soluble, and the protein(s) covalently bound on the surface of soluble AuNP were identified by MS analysis of their proteolytic fragments. Gluten-forming proteins were found to be bound to soluble AuNPs only when detergents or chaotropes were added to the semolina/AuNPs suspension at room temperature. AuNPs-bound proteins also included gluten-forming proteins with no reported free thiols, suggesting that they are piggybacked on other thiol-containing gluten-forming proteins via disulfide bonds already present in the otherwise untreated semolina. The potential of this approach is discussed in terms of the possibility of developing a methodology suitable for further clarification of the geometrical features of protein networks, of the nature of the involved proteins, and of the type of interaction they establish, as well as any modifications of these features upon processing.

Technological Quality and Nutritional Value of Two Durum Wheat Varieties Depend on Both Genetic and Environmental Factors

Durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husn) is a major food source in Mediterranean countries since it is utilized for the production of pasta, leavened and unleavened breads, couscous, and other traditional foods. The technological and nutritional properties of durum wheat semolina depend mainly on the type of gluten proteins and on their amount, which is a genotype- and environment-dependent trait. Gluten proteins are also responsible for celiac disease (CD), an autoimmune enteropathy with a prevalence of about 0.7-2% in the human population. At this purpose, two Italian durum wheat cultivars, Saragolla and Cappelli, currently used for monovarietal pasta, were chosen to compare (i) the reserve and embryo proteome, (ii) the free and bound phenolics, antioxidant activity, and amino acid composition, and (iii) the content of immunogenic peptides produced after a simulated gastrointestinal digestion. The results obtained from 2 years of field cultivation on average showed a higher amount of gluten proteins, amino acids, and immunogenic peptides in Cappelli. Saragolla showed a higher abundance in bound phenolics, antioxidant enzymes, and stress response proteins in line with its higher antioxidant activity. However, the impact of the year of cultivation, largely depending on varying rainfall regimes through the wheat growth cycle, was significant for most of the parameters investigated. Differences in technological and nutritional characteristics observed between the two cultivars are discussed in relation to the influence of genetic and environmental factors.

Integrated physiological and proteomic analysis of embryo and endosperm reveals central salt stress response proteins during seed germination of winter wheat cultivar Zhengmai 366

BACKGROUND

Salinity is a major abiotic stressor that affects seed germination, plant growth, and crop production. Seed germination represents the beginning of plant growth and is closely linked with subsequent crop development and ultimate yield formation. This study attempted to extend findings regarding the potential proteomic dynamics during wheat seed germination under salt stress and to explore the mechanism of crop salt response.

RESULTS

Salt stress significantly affected seed physiological activities during the germination process, resulting in significant decreases in phytohormone and α-amylase activity and significant increases in soluble sugar, starch, and ADP glucose pyrophosphorylase activity. A comparative proteomics approach was applied to analyze the dynamic proteome changes of embryo and endosperm during seed germination in Chinese winter wheat cultivar Zhengmai 366 under salt stress. Two-dimensional electrophoresis identified 92 and 61 differentially accumulated proteins (DAPs) in response to salt stress in embryo and endosperm, respectively. Both organs contained a high proportion of DAPs involved in stress defense, energy metabolism, and protein/amino acid metabolism. The endosperm had more DAPs related to storage proteins and starch metabolism than the embryo, and 2% of DAPs participating in lipid and sterol metabolism were specifically detected in the embryo.

CONCLUSIONS

Seed physiological activities were significantly affected during the germination process when subjected to salt stress. The DAPs involved in stress defense and energy metabolism were upregulated whereas those related to reserve substance degradation and protein/amino acid metabolism were significantly downregulated, leading to delayed seed germination under salt stress. Our proteomic results revealed synergistic regulation of the response to salt stress during seed germination.

Wheat grain protein accumulation and polymerization mechanisms driven by nitrogen fertilization

In wheat (Triticum aestivum) grain yield and grain protein content are negatively correlated, making the simultaneous increase of the two traits challenging. Apart from genetic approaches, modification of nitrogen fertilization offers a feasible option to achieve this aim. In this study, a range of traits related to nitrogen-use efficiency in six Australian bread wheat varieties were investigated under different nitrogen treatments using 3-year multisite field trials. Changes in the individual storage protein composition were detected by high-performance liquid chromatography. Our results indicated that wheat grain yield and grain protein content reacted similarly to nitrogen availability, with grain yield being slightly more sensitive than grain protein content, and that genotype is a vital determinant of grain protein yield. Measurement of the glutamine synthetase activity of flag leaves and developing grains revealed that high nitrogen availability prompted the participation of glutamine in biological processes. In addition, a more significant accumulation of gluten macropolymer was observed under the high-nitrogen treatment from 21 days post-anthesis, and the underlying mechanism was elucidated by a comparative proteomics study. A yeast two-hybrid experiment confirmed this mechanism. The results of this study revealed that peptidyl-prolyl cis-trans isomerase (PPIase) was SUMOylated with the assistance of small ubiquitin-related modifier 1 and that high nitrogen availability facilitated this connection for the subsequent protein polymerization. Additionally, luminal-binding protein 2 in the endoplasmic reticulum played a similar role to PPIase in the aggregation of protein under high-nitrogen conditions.

Biosynthesis and Regulation of Wheat Amylose and Amylopectin from Proteomic and Phosphoproteomic Characterization of Granule-binding Proteins

Waxy starch has an important influence on the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and grain yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Our results revealed the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.

Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D-DIGE-based integrative proteome analysis

Two Chinese bread wheat cultivars, Jinghua 9 and Zhongmai 175, distinct in grain weight and dough quality, were used to study proteome changes in the embryo and endosperm during grain development using a two-dimensional difference gel electrophoresis (2D-DIGE)-based proteomics approach. In total, 138 and 127 differentially expressed protein (DEP) spots representing 116 and 113 unique DEPs were identified in the embryo and endosperm, respectively. Among them, 54 (31%) DEPs were commonly present in both organs while 62 (35%) and 59 (34%) DEPs occurred only in the embryo and endosperm, respectively. Embryonic DEPs are primarily stress-related proteins and involved in carbohydrate and lipid metabolism, while those from the endosperm are related primarily to carbohydrate metabolism and storage. Principal component analysis (PCA) indicated that the proteome differences in the endosperm caused by different cultivars were greater than those by development stages, while the differences in the embryo showed the opposite pattern. Protein-protein interaction (PPI) analysis revealed a complex network centered primarily on enzymes involved in carbohydrate and protein metabolism. The transcriptional levels of fourteen important DEPs encoding genes showed high similarity between organs and cultivars. In particular, some key DEPs of the endosperm, such as phosphoglucomutase, ADP-glucose pyrophosphorylase (AGPase), and sucrose synthase (SUS), showed significantly upregulated expression, indicating their key roles in starch biosynthesis and grain yield. Moreover, upregulated expression of some storage proteins in the endosperm could improve wheat bread-making quality.

Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) is one of the oldest cultivated crops and the second most important food crop in the world. Seed germination is the key developmental process in plant growth and development, and poor germination directly affects plant growth and subsequent grain yield. In this study, we performed the first dynamic proteome analysis of wheat seed germination using a two-dimensional differential gel electrophoresis (2D-DIGE)-based proteomic approach. A total of 166 differentially expressed protein (DEP) spots representing 73 unique proteins were identified, which are mainly involved in storage, stress/defense/detoxification, carbohydrate metabolism, photosynthesis, cell metabolism, and transcription/translation/transposition. The identified DEPs and their dynamic expression profiles generally correspond to three distinct seed germination phases after imbibition: storage degradation, physiological processes/morphogenesis, and photosynthesis. Some key DEPs involved in storage substance degradation and plant defense mechanisms, such as globulin 3, sucrose synthase type I, serpin, beta-amylase, and plastid ADP-glucose pyrophosphorylase (AGPase) small subunit, were found to be phosphorylated during seed germination. Particularly, the phosphorylation site Ser(355) was found to be located in the enzyme active region of beta-amylase, which promotes substrate binding. Phosphorylated modification of several proteins could promote storage substance degradation and environmental stress defense during seed germination. The central metabolic pathways involved in wheat seed germination are proposed herein, providing new insights into the molecular mechanisms of cereal seed germination.

Identification of Differently Regulated Proteins after Fusarium graminearum Infection of Emmer (Triticum dicoccum) at Several Grain Ripening Stages

This study was conducted to improve the knowledge of molecular processes involved in the interaction between Fusarium graminearum and emmer in the course of grain ripening. Emmer plants were artificially inoculated with a F. graminearum spore suspension at anthesis. In the course of grain ripening from milk ripe to plant death stage, grains at four phenological growth stages were collected for analysis. The infection degree was evaluated based on the F. graminearum DNA content in emmer grain infolding tissues (glumes and rachis). For proteome analysis the albumin and globulin fractions of emmer grains, consisting of proteins with various functions related to the development and stress response, were analysed regarding the changes due to Fusarium infection by two-dimensional gel electrophoresis. Altogether, forty-three proteins affected by infection were identified by mass spectrometry. Enzymes detoxifying reactive oxygen species were regulated at all developmental stages. In the early stage of grain development, the abundance of proteins related to stress response, such as 2-Cys peroxiredoxin, a chitinase, a xylanase inhibitor and a spermidine synthase was increased. During later stage of grain development, the abundance of stress-related proteins, such as chitinases, heat shock proteins and an α-amylase inhibitor-like protein, decreased. During all ripening stages, but especially during medium milk stage (BBCH 75) and soft dough stage (BBCH 85), the abundance of proteins related to carbon metabolism, starch and protein biosynthesis as well as photosynthesis increased due to F. graminearum infection. At the plant death stage (BBCH 97) the abundance of only two proteins related to metabolism decreased.

Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination

BACKGROUND

Wheat seeds provide a staple food and an important protein source for the world's population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination.

RESULTS

The proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes.

CONCLUSION

Wheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and proteomic changes. The first process is a rapid water uptake, in which the seed coat becomes softer and the physical state of storage materials change gradually. Then the germinated seed enters the second process (a plateau phase) and the third process (the embryonic axes elongation). Seed embryo and endosperm display distinct differentially expressed proteins, and their synergistic expression mechanisms provide a basis for the normal germination of wheat seeds.

Proteomic analysis of middle and late stages of bread wheat (Triticum aestivum L.) grain development

Proteomic approaches were applied in four grain developmental stages of the Chinese bread wheat Yunong 201 and its ethyl methanesulfonate (EMS) mutant line Yunong 3114. 2-DE and tandem MALDI-TOF/TOF-MS analyzed proteome characteristics during middle and late grain development of the Chinese bread wheat Yunong 201 and its EMS mutant line Yunong 3114 with larger grain sizes. We identified 130 differentially accumulated protein spots representing 88 unique proteins, and four main expression patterns displayed a dynamic description of middle and late grain formation. Those identified protein species participated in eight biochemical processes: stress/defense, carbohydrate metabolism, protein synthesis/assembly/degradation, storage proteins, energy production and transportation, photosynthesis, transcription/translation, signal transduction. Comparative proteomic characterization demonstrated 12 protein spots that co-accumulated in the two wheat cultivars with different expression patterns, and six cultivar-specific protein spots including serpin, small heat shock protein, β-amylase, α-amylase inhibitor, dimeric α-amylase inhibitor precursor, and cold regulated protein. These cultivar-specific protein spots possibly resulted in differential yield-related traits of the two wheat cultivars. Our results provide valuable information for dissection of molecular and genetics basis of yield-related traits in bread wheat and the proteomic characterization in this study could also provide insights in the biology of middle and late grain development.

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.

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

Wheat (Triticum aestivum), one of the most important cereal crops, is often threatened by drought. In this study, water deficit significantly reduced the height of plants and yield of grains. To explore further the effect of drought stress on the development and yield of grains, we first performed a large scale phosphoproteome analysis of developing grains in wheat. A total of 590 unique phosphopeptides, representing 471 phosphoproteins, were identified under well-watered conditions. Motif-X analysis showed that four motifs were enriched, including [sP], [Rxxs], [sDxE], and [sxD]. Through comparative phosphoproteome analysis between well-watered and water-deficit conditions, we found that 63 unique phosphopeptides, corresponding to 61 phosphoproteins, showed significant changes in phosphorylation level (≥2-fold intensities). Functional analysis suggested that some of these proteins may be involved in signal transduction, embryo and endosperm development of grains, and drought response and defense under water-deficit conditions. Moreover, we also found that some chaperones may play important roles in protein refolding or degradation when the plant is subjected to water stress. These results provide a detailed insight into the stress response and defense mechanisms of developmental grains at the phosphoproteome level. They also suggested some potential candidates for further study of transgenosis and drought stress as well as incorporation into molecular breeding for drought resistance.

Stress-related genes distinctly expressed in unfertilized wheat ovaries under both normal and water deficit conditions whereas differed in fertilized ovaries

In this study, a proteomic approach was utilized to identify differentially accumulated proteins in developing wheat ovaries before and after fertilization and in response to water deficit. Proteins were extracted, quantified, and resolved by 2-DE at pH4-7. Statistical analysis of spot intensity was performed by using principal component analysis and samples were clustered by using Euclidean distance. In total, 136 differentially accumulated protein spots representing 88 unique proteins were successfully identified by MALDI-TOF/TOF MS. Under normal conditions, stress-related proteins were abundant in unfertilized ovaries while proteins involved in the metabolism of energy and matter were enriched in fertilized ovaries just 48h after fertilization. Similar trends were observed in unfertilized and fertilized wheat ovaries under water deficit conditions, except for increased accumulation of stress-related proteins in fertilized ovaries. Some proteins required for normal development were not present in ovaries subjected to water deficit. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit.

BIOLOGICAL SIGNIFICANCE

Fertilization initiates the most dramatic changes that occur in the life cycle of higher plants; research into differences in gene expression before and after ovary pollination can make a substantial contribution to understanding the physiological and biochemical processes associated with fertilization. To date, a small number of studies have examined changes in transcriptional activity of the developing plant embryo sac before and after fertilization. However, comparative proteomic analysis of wheat ovary development before and after fertilization, and in response to water deficit, has not yet been reported. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit.

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).

Role of non-prolamin proteins and low molecular weight redox agents in protein folding and polymerization in wheat grains and influence on baking quality parameters

The various enzyme systems and low molecular weight (LMW) redox agents are related to the folding and polymerization of prolamins in the ripening wheat grains and the formation of baking quality. Protein disulfide isomerases (PDIs) and cyclophylins accelerate "correct" folding of prolamins, which is most likely necessary for the subsequent formation of the macromolecular structure of the gluten protein matrix. PDIs are also involved in the polymerization of prolamins, catalyzing the oxidation of protein sulfhydryl groups. Molecular chaperone binding BiP protein facilitates folding of prolamins, with its role increasing in the stressful conditions. Reducing systems of thioredoxin and glutaredoxin, LMW redox pairs GSH/GSSG and Asc/DHAsc, thiol oxidases, and lipoxygenases (LOXs) regulate redox balance and the rate of polymerization of prolamins at the different stages of grain ripening. Additionally, LOX is probably involved in the protein-starch-lipid interactions between the starch granule and the protein matrix, mediated by puroindolines, determining the formation of grain texture. It is assumed that the high variability of baking quality in different environmental conditions is due to the interaction of labile enzyme systems with the storage proteins in the developing wheat caryopsis.

Wheat drought-responsive grain proteome analysis by linear and nonlinear 2-DE and MALDI-TOF mass spectrometry

A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the nonlinear 2-DE had much higher resolution than the linear 2-DE. A total of 153 differentially expressed protein spots were detected by both 2-DE maps, of which 122 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified differential proteins were mainly involved in carbohydrate metabolism (26%), detoxification and defense (23%), and storage proteins (17%). Some key proteins demonstrated significantly different expression patterns between the two varieties. In particular, catalase isozyme 1, WD40 repeat protein, LEA and alpha-amylase inhibitors displayed an upregulated expression pattern in Kauz, whereas they were downregulated or unchanged in Janz. Small and large subunit ADP glucose pyrophosphorylase, ascorbate peroxidase and G beta-like protein were all downregulated under drought stress in Janz, but had no expression changes in Kauz. Sucrose synthase and triticin precursor showed an upregulated expression pattern under water deficits in both varieties, but their upregulation levels were much higher in Kauz than in Janz. These differentially expressed proteins could be related to the biochemical pathways for stronger drought resistance of Kauz.

Molecular characterization of LMW-GS genes in Brachypodium distachyon L. reveals highly conserved Glu-3 loci in Triticum and related species

BACKGROUND

Brachypodium distachyon L. is a newly emerging model plant system for temperate cereal crop species. However, its grain protein compositions are still not clear. In the current study, we carried out a detailed proteomics and molecular genetics study on grain glutenin proteins in B. distachyon.

RESULTS

SDS-PAGE and RP-HPLC analysis of grain proteins showed that Brachypodium has few gliadins and high molecular weight glutenin subunits. In contrast the electrophoretic patterns for the albumin, globulin and low molecular weight glutenin subunit (LMW-GS) fractions of the grain protein were similar to those in wheat. In particular, the LMW-C type subunits in Brachypodium were more abundant than the equivalent proteins in common wheat. Southern blotting analysis confirmed that Brachypodium has 4-5 copies of LMW-GS genes. A total of 18 LMW-GS genes were cloned from Brachypodium by allele specific PCR. LMW-GS and 4 deduced amino acid sequences were further confirmed by using Western-blotting and MALDI-TOF-MS. Phylogenetic analysis indicated that Brachypodium was closer to Ae. markgrafii and Ae. umbellulata than to T. aestivum.

CONCLUSIONS

Brachypodium possessed a highly conserved Glu-3 locus that is closely related to Triticum and related species. The presence of LMW-GS in B. distachyon grains indicates that B. distachyon may be used as a model system for studying wheat quality attributes.

Molecular characterization and dynamic expression patterns of two types of γ-gliadin genes from Aegilops and Triticum species

Gliadins were the major components of wheat storage proteins and determine the extensibility properties of gluten dough. In this work, 19 new full-length γ-gliadin genes were isolated from various Aegilops and Triticum species. Sequence characterization showed that a specific octapeptide and celiac disease (CD)-toxic epitope Gliγ-3 (VQGQGIIQPQQPAQL) were present in the rich glutamine domain and C-terminal non-repetitive domain, respectively. Based on the sequence features of both peptides, a new classification system for γ-gliadin gene family was established, in which γ-gliadins were classified into two types (types I and II) with each consisting of two groups. An uneven distribution of different types and groups of γ-gliadin genes was exhibited among 11 Aegilops and Triticum genomes. Phylogenetic analysis revealed that types I and II genes diverged at about 14 MYA while the divergence of 4 γ-gliadin group genes occurred at around 10 MYA almost simultaneously. The γ-gliadin genes from S(l) and B genomes displayed a different transcriptional expression pattern during grain development, and rapid increasing of gliadin mRNA and proteins occurred at 15-20 DPA. In addition, genome-specific variations of CD-toxic epitopes among Aegilops and Triticum genomes were found. The A genome and its related progenitor genomes A(u) and A(m) had fewer CD epitopes than other genomes, suggesting that these genomes might be valuable gene resources to remove CD toxic peptides for wheat quality improvement.

Proteomic analysis of albumins and globulins from wheat variety Chinese Spring and its fine deletion line 3BS-8

The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance variation (p < 0.05) in matured wheat grains and 21 spots were identified by tandem MALDI-TOF/TOF-MS. Among the identified spots, four were cultivar-specific, including three (spots B15, B16, and B21) in Chinese Spring and one in 3BS-8 (spot B10). Among variety-different DEPs between Chinese Spring and 3BS-8, most spots showed a higher express profile in CS; only four spots showed up-regulated expression tendency in 3BS-8. An interesting observation was that more than half of the identified protein spots were involved in storage proteins, of which 11 spots were identified as globulins. According to these results, we can presume that the encoded genes of protein spots B15, B16, and B21 were located on the chromosome segment deleted in 3BS-8.

Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.)

BACKGROUND

The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins.

RESULTS

Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different.

CONCLUSIONS

Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.

Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.)

BACKGROUND

The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins.

RESULTS

Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different.

CONCLUSIONS

Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.