Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry

Screening of α-amylase/trypsin inhibitor activity in wheat, spelt and einkorn by high-performance thin-layer chromatography

α-Amylase/trypsin inhibitor proteins (ATI) are discussed as possible triggers for non-celiac gluten sensitivity. The potential of high-performance thin-layer chromatography (HPTLC) was studied for the first time to analyse the inhibitory properties of ATIs from flour of wheat, spelt, and einkorn. Inhibition by each flour of the digestive enzymes trypsin or α-amylase was determined by the reduction of released metabolisation products in comparison to non-digested flour, and positive (acarbose) and negative (water) controls. Firstly, amylolysis was carried out in miniaturized form on the HPTLC surface (HPTLC-nanoGIT) after in-vial pre-incubation of the amylase with the inhibitors from flour. α-Amylase inhibition was evident via the reduction of released saccharides, as analysed by normal phase HPTLC. A strong influence of the flour matrix on the assay results (individual saccharides) was evident, caused by an increased amylolysis of further polysaccharides present, making HPTLC analysis more reliable than currently used spectrophotometric sum value assays. The detection and visualization of such matrix influence helps to understand the problems associated with spectrophotometric assays. Only maltotriose was identified as a reliable marker of the amylolysis. The highest α-amylase inhibition and thus the lowest saccharide response was detected for maltotriose in refined spelt, whereas the lowest α-amylase inhibition and thus the highest saccharide response was detected for maltotriose in refined wheat. A comparison of refined and whole grain flours showed no clear trend in the responses. Secondly, trypsin inhibition and proteolysis were performed in-vial, and any inhibition was evident via the reduction of released peptides, analysed by reversed-phase HPTLC. Based on the product pattern of the proteolysis, einkorn and whole wheat showed the highest trypsin inhibition, whereas refined wheat and refined spelt showed the lowest inhibition. Advantageously, HPTLC analysis provided important information on changes in individual saccharides or peptides, which was more reliable and sustainable than spectrophotometric in-vial assays (only sum value) or liquid column chromatography analysis (targeting only the ATI proteins).

Rapid analysis of wheat gluten composition using a triple ELISA

BACKGROUND

Gluten composition is an important quality parameter of wheat flour. Reversed-phase high-performance liquid chromatography (RP-HPLC) is a state-of-the-art method for its analysis. As this is a very labour-intensive and time-consuming procedure, alternative faster methods are desirable. Enzyme-linked immunosorbent assay (ELISA) is a high-throughput method often used for the analysis of gluten traces in gluten-free products. In this proof-of-principle study, we introduce an experimental triple ELISA for the relative quantitation of gliadins, high-molecular-weight glutenin subunits (HMW-GS) and low-molecular-weight glutenin subunits (LMW-GS) of one wheat flour extract.

RESULTS

The results of 80 common wheat flour samples obtained from the triple ELISA and RP-HPLC were correlated. The results for gliadins (r = 0.69) and HMW-GS (r = 0.81) showed a medium and high correlation, respectively. Only a very weak correlation of ELISA and RP-HPLC results was observed for LMW-GS (r = 0.49). Results for glutenins (r = 0.69) and gluten (r = 0.72) had a medium correlation. The gliadin/glutenin ratio (r = 0.47) and LMW-GS/HMW-GS ratio (r = 0.40) showed a weak or no correlation. The gliadin, LMW-GS and gluten contents were lower and the HMW-GS content was higher in the ELISA measurement compared to RP-HPLC.

CONCLUSION

The quantitation of gliadins and HMW-GS by the experimental triple ELISA showed comparable results to RP-HPLC, whereas no strong correlation between the results from the two methods was found for LMW-GS. Overall, the experimental triple ELISA is suitable for relative gluten quantitation, especially for the analysis of large sample sets. Further work will focus on improving the experimental procedure of the ELISA. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Dietary wheat amylase trypsin inhibitors exacerbate CNS inflammation in experimental multiple sclerosis

OBJECTIVE

Wheat has become a main staple globally. We studied the effect of defined pro-inflammatory dietary proteins, wheat amylase trypsin inhibitors (ATI), activating intestinal myeloid cells via toll-like receptor 4, in experimental autoimmune encephalitis (EAE), a model of multiple sclerosis (MS).

DESIGN

EAE was induced in C57BL/6J mice on standardised dietary regimes with defined content of gluten/ATI. Mice received a gluten and ATI-free diet with defined carbohydrate and protein (casein/zein) content, supplemented with: (a) 25% of gluten and 0.75% ATI; (b) 25% gluten and 0.19% ATI or (c) 1.5% purified ATI. The effect of dietary ATI on clinical EAE severity, on intestinal, mesenteric lymph node, splenic and central nervous system (CNS) subsets of myeloid cells and lymphocytes was analysed. Activation of peripheral blood mononuclear cells from patients with MS and healthy controls was compared.

RESULTS

Dietary ATI dose-dependently caused significantly higher EAE clinical scores compared with mice on other dietary regimes, including on gluten alone. This was mediated by increased numbers and activation of pro-inflammatory intestinal, lymph node, splenic and CNS myeloid cells and of CNS-infiltrating encephalitogenic T-lymphocytes. Expectedly, ATI activated peripheral blood monocytes from both patients with MS and healthy controls.

CONCLUSIONS

Dietary wheat ATI activate murine and human myeloid cells. The amount of ATI present in an average human wheat-based diet caused mild intestinal inflammation, which was propagated to extraintestinal sites, leading to exacerbation of CNS inflammation and worsening of clinical symptoms in EAE. These results support the importance of the gut-brain axis in inflammatory CNS disease.

Breeding from 1891 to 2010 did not increase the content of amylase/trypsin-inhibitors in wheat (Triticum aestivum)

The prevalence of hypersensitivities towards wheat has increased in the last decades. Apart from celiac disease these include allergic and other inflammatory reactions summarized under the term non-celiac wheat sensitivity. One suspected trigger is the family of amylase/trypsin-inhibitors (ATIs), non-gluten proteins that are prominent wheat allergens and that activate the toll-like receptor 4 on intestinal immune cells to promote intestinal and extra-intestinal inflammation. We therefore quantified 13 ATIs in 60 German hexaploid winter wheat cultivars originating from 1891 to 2010 and harvested in three years by targeted liquid chromatography-tandem mass spectrometry combined with stable isotope dilution assay using specific marker peptides as internal standards. The total ATI content and that of the two major ATIs 0.19 and CM3 did not change from old cultivars (first registered from 1891 to 1950) to modern cultivars (1951-2010). There were also no significant changes in ATI distribution.

Transient drought during flowering modifies the grain proteome of bread winter wheat

Drought is among the most limiting factors for sustainable agricultural production. Water shortage at the onset of flowering severely affects the quality and quantity of grain yield of bread wheat (Triticum aestivum). Herein, we measured oxidative stress and photosynthesis-related parameters upon applying transient drought on contrasting wheat cultivars at the flowering stage of ontogenesis. The sensitive cultivar (Darunok Podillia) showed ineffective water management and a more severe decline in photosynthesis. Apparently, the tolerant genotype (Odeska 267) used photorespiration to dissipate excessive light energy. The tolerant cultivar sooner induced superoxide dismutase and showed less inhibited photosynthesis. Such a protective effect resulted in less affected yield and spectrum of seed proteome. The tolerant cultivar had a more stable gluten profile, which defines bread-making quality, upon drought. Water deficit caused the accumulation of medically relevant proteins: (i) components of gluten in the sensitive cultivar and (ii) metabolic proteins in the tolerant cultivar. We propose specific proteins for further exploration as potential markers of drought tolerance for guiding efficient breeding: thaumatin-like protein, 14-3-3 protein, peroxiredoxins, peroxidase, FBD domain protein, and Ap2/ERF plus B3 domain protein.

Attenuation of immune activation in patients with multiple sclerosis on a wheat-reduced diet: a pilot crossover trial

Background

Western lifestyle has been associated with an increase in relapsing-remitting multiple sclerosis (RRMS). In mice, dietary wheat amylase-trypsin inhibitors (ATIs) activate intestinal myeloid cells and augment T cell-mediated systemic inflammation.

Objective

The aim of this study was to assess whether a wheat- and thus ATI-reduced diet might exert beneficial effects in RRMS patients with modest disease activity.

Methods

In this 6-month, crossover, open-label, bicentric proof-of-concept trial, 16 RRMS patients with stable disease course were randomized to either 3 months of a standard wheat-containing diet with consecutive switch to a > 90% wheat-reduced diet, or vice versa.

Results

The primary endpoint was negative, as the frequency of circulating pro-inflammatory T cells did not decrease during the ATI-reduced diet. We did, however, observe decreased frequencies of CD14+ CD16++ monocytes and a concomitant increase in CD14++ CD16- monocytes during the wheat-reduced diet interval. This was accompanied by an improvement in pain-related quality of life in health-related quality of life assessed (SF-36).

Conclusion

Our results suggest that the wheat- and thus ATI-reduced diet was associated with changes in monocyte subsets and improved pain-related quality of life in RRMS patients. Thus, a wheat (ATI)-reduced diet might be a complementary approach accompanying immunotherapy for some patients.

Registration

German Clinical Trial Register (No. DRKS00027967).

Toward reducing the immunogenic potential of wheat flour: identification and characterization of wheat lines missing omega-5 gliadins encoded by the 1D chromosome

Eleven wheat lines that are missing genes for the 1D-encoded omega-5 gliadins will facilitate breeding efforts to reduce the immunogenic potential of wheat flour for patients susceptible to wheat allergy. Efforts to reduce the levels of allergens in wheat flour that cause wheat-dependent exercise-induced anaphylaxis are complicated by the presence of genes encoding omega-5 gliadins on both chromosomes 1B and 1D of hexaploid wheat. In this study, we screened 665 wheat germplasm samples using gene specific DNA markers for omega-5 gliadins encoded by the genes on 1D chromosome that were obtained from the reference wheat Chinese Spring. Eleven wheat lines missing the PCR product corresponding to 1D omega-5 gliadin gene sequences were identified. Two of the lines contained the 1BL·1RS translocation. Relative quantification of gene copy numbers by qPCR revealed that copy numbers of 1D omega-5 gliadins in the other nine lines were comparable to those in 1D null lines of Chinese Spring, while copy numbers of 1B omega-5 gliadins were like those of Chinese Spring. 2-D immunoblot analysis of total flour proteins from the selected lines using a specific monoclonal antibody against the N-terminal sequence of omega-5 gliadin showed no reactivity in regions of the blots containing previously identified 1D omega-5 gliadins. Interestingly, RP-UPLC analysis of the gliadin fractions of the selected lines indicated that the expression of omega-1,2 gliadins was also significantly reduced in seven of the lines, implying that 1D omega-5 gliadin and 1D omega-1,2 gliadin genes are tightly linked on the Gli-D1 loci of chromosome 1D. Wheat lines missing the omega-5 gliadins encoded by the genes on 1D chromosome should be useful in future breeding efforts to reduce the immunogenic potential of wheat flour.

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.

A chromatographic and immunoprofiling approach to optimising workflows for extraction of gluten proteins from flour

Ingestion of gluten proteins from wheat, and related prolamin proteins from barley, rye, and oats, can cause adverse reactions in individuals with coeliac disease and IgE-mediated allergies. As there is currently no cure for these conditions, patients must practice avoidance of gluten-containing foods. In order to support patients in making safe food choices, foods making a "gluten-free" claim must contain no more than 20 mg/Kg of gluten. Mass spectrometry methods have the potential to provide an alternative method for confirmatory analysis of gluten that is complementary to analysis currently undertaken by immunoassay. As part of the development of such methodology the effectiveness of two different extraction procedures was investigated using wholemeal wheat flour before and after defatting with water-saturated butan-1-ol. A single step extraction with 50 % (v/v) propan-2-ol containing 2 M urea and reducing agent (buffer 1) was compared with a two-step extraction using 60 % (v/v) aqueous ethanol (buffer 2) followed by re-extraction of the pellet using buffer 1, using either wheel mixing under ambient conditions (19 °C) or sonication at 60 °C. The procedures were compared based on total protein extraction efficiency and the composition of the extracts determined using a combination of HPLC, SDS-PAGE and immunoblotting with a panel of four gluten-specific monoclonal antibodies. Defatting generally had a detrimental effect on extraction efficiency and sonication at 60 °C only improved extraction efficiency with buffer 2. Although the single-step and two-step procedures were equally effective at extracting protein from the samples, analysis of extracts showed that the two-step method gave a more complete extraction of gluten proteins. Future studies will compare the effectiveness of these procedures when applied in the sample workflows for mass spectrometry based methods for determination of gluten in food.

Transcriptome and Proteome Analysis Revealed the Influence of High-Molecular-Weight Glutenin Subunits (HMW-GSs) Deficiency on Expression of Storage Substances and the Potential Regulatory Mechanism of HMW-GSs

The processing quality of wheat is affected by seed storage substances, such as protein and starch. High-molecular-weight glutenin subunits (HMW-GSs) are the major components of wheat seed storage proteins (SSPs); they are also key determinators of wheat end-use quality. However, the effects of HMW-GSs absence on the expression of other storage substances and the regulation mechanism of HMW-GSs are still limited. Previously, a wheat transgenic line LH-11 with complete deletions of HMW-GSs was obtained through introducing an exogenous gene Glu-1E^bx to the wild-type cultivar Bobwhite by transgenic approach. In this study, comparative seed transcriptomics and proteomics of transgenic and non-transgenic lines at different seed developmental stages were carried out to explore the changes in genes and proteins and the underlying regulatory mechanism. Results revealed that a number of genes, including genes related to SSPs, carbohydrates metabolism, amino acids metabolism, transcription, translation, and protein process were differentially enriched. Seed storage proteins displayed differential expression patterns between the transgenic and non-transgenic line, a major rise in the expression levels of gliadins were observed at 21 and 28 days post anthesis (DPA) in the transgenic line. Changes in expressions of low-molecular-weight glutenins (LMW-GSs), avenin-like proteins (ALPs), lipid transfer proteins (LTPs), and protease inhibitors (PIs) were also observed. In addition, genes related to carbohydrate metabolism were differentially expressed, which probably leads to a difference in starch component and deposition. A list of gene categories participating in the accumulation of SSPs was proposed according to the transcriptome and proteome data. Six genes from the MYB and eight genes from the NAC transcription families are likely important regulators of HMW-GSs accumulation. This study will provide data support for understanding the regulatory network of wheat storage substances. The screened candidate genes can lay a foundation for further research on the regulation mechanism of HMW-GSs.

Wheat grain proteins: Past, present, and future

Background and Objectives

Research on wheat grain proteins is reviewed, including achievements over the past century and priorities for future research. The focus is on three groups of proteins that have major impacts on wheat quality and utilization: the gluten proteins which determine dough viscoelasticity but also trigger celiac disease in susceptible individuals, the puroindolines which are major determinants of grain texture and the amylase/trypsin inhibitors which are food and respiratory allergens and are implicated in triggering celiac disease and nonceliac wheat sensitivity.

Findings

Although earlier work focused on protein structure and properties, the development of genomics and high-sensitivity proteomics has resulted in the availability of a vast amount of information on the amino acid sequences of individual wheat proteins, including allelic variants of gluten proteins which are associated with good processing quality and of puroindolines, which are associated with a hard or soft grain texture, and on protein expression and polymorphism.

Conclusions

However, our ability to exploit this knowledge is limited by a lack of detailed understanding of the structure:function relationships of wheat proteins. In particular, we need to understand how the three-dimensional structures of the individual proteins determine their interactions with other grain components (to determine functional properties) and with the immune systems of susceptible consumers (to trigger adverse responses), how these interactions are affected by allelic variation, and how they can be manipulated.

Significance and Novelty

The article, therefore, identifies priorities for future research which should enable the adoption of a more rational approach to improving the quality of wheat grain proteins.

Amylase Trypsin Inhibitors (ATIs) in a Selection of Ancient and Modern Wheat: Effect of Genotype and Growing Environment on Inhibitory Activities

Wheat amylase-trypsin inhibitors (ATIs) are a family of plant defense proteins with an important role in human health for their involvement in allergies, celiac disease and non-celiac wheat sensitivity. Information about the differences in ATI activities among wheat genotypes and the influence of the growing environment is scarce. Therefore, ten selected wheat accessions with different ploidy level and year of release, previously characterized for their ATI gene sequences, were grown during three consecutive crop years at two growing areas and used for in vitro ATI activities. The contributions of the genotype and the crop year were significant for both activities. The hexaploid wheat genotypes showed the highest inhibitory activities. Einkorn had a peculiar behavior showing the lowest alpha-amylase inhibitory activity, but the highest trypsin inhibitory activity. It was not possible to observe any trend in ATI activities as a function of the release year of the wheat samples. The two inhibitory activities were differently affected by the growing conditions and were negatively correlated with the protein content. This information can be important in understanding the extent of variation of ATI inhibitory properties in relation to the wheat genotype and the growing environment and the impact of ATIs, if any, on human health and nutrition.

Gut reactions: emerging mechanisms of abdominal pain from food intake

Abdominal pain, which is a form of visceral pain, is a highly prevalent symptom worldwide frequently occurring following food ingestion. Its pathophysiology is complex, and many factors, including intestinal environmental cues, the immune system, or the molecular composition of foods, can influence the development of postprandial abdominal pain. Because of the poor efficacy of drug treatments, current strategies are often limited to the exclusion of culprit food(s) from the diet. However, there are two important limitations to this approach. First, patients suffering from food-induced abdominal pain usually recognize several food items as the cause of their gastrointestinal symptoms. Second, not all offending foods can always be identified by these patients. Newly identified mechanisms involving neuroimmune interactions and their communication with the intestinal microbiota shed light on the development of new therapeutic strategies. In this Mini-Review, these novel mechanisms and relevance of such findings are highlighted.

Relating the protein composition and air-water interfacial properties of aqueous flour extracts from wheats grown at different nitrogen fertilization levels

Aqueous phase extractable proteins from wheat can play a functional role in foods requiring interfacial stabilization. We here investigated the (protein) composition of aqueous flour extracts from wheats grown at different nitrogen (N) fertilization levels and studied their air-water interfacial characteristics. An important finding was that α- and γ-gliadins were extracted from wheat flour with water, even to an extent that they in the present work comprised 62-71% of the extract proteins. Application of N fertilization during wheat cultivation led to flour extracts with higher foam stabilities and air-water interface dilatational moduli. In all cases, proteins were found to most likely be the dominant constituent at the air-water interface. Analysis of foam protein compositions revealed an enrichment of proteins with molecular weights matching those of α- and γ-gliadins. It thus seems that gliadins can to a large extent determine the foaming characteristics of aqueous wheat flour extracts.

Challenges and opportunities for proteomics and the improvement of bread wheat quality

Wheat remains a critical global food source, pressured by climate change and the need to maximize yield, improve processing and nutritional quality and ensure safety. An enormous amount of research has been conducted to understand gluten protein composition and structure in relation to end-use quality, yet progress has become stagnant. This is mainly due to the need and inability to biochemically characterize the intact functional glutenin polymer in order to correlate to quality, necessitating reduction to monomeric subunits and a loss of contextual information. While some individual gluten proteins might have a positive or negative influence on gluten quality, it is the sum total of these proteins, their relative and absolute expression, their sub-cellular trafficking, the amount and size of glutenin polymers, and ratios between gluten protein classes that define viscoelasticity of gluten. The sub-cellular trafficking of gluten proteins during seed maturation is still not completely clear and there is evidence of dual pathways and therefore different destinations for proteins, either constitutively or temporally. The trafficking of proteins is also unclear in endosperm cells as they undergo programmed cell death; Golgi disappear around 12 DPA but protein filling continues at least to 25 DPA. Modulation of the timing of cellular events will invariably affect protein deposition and therefore gluten strength and function. Existing and emerging proteomics technologies such as proteoform profiling and top-down proteomics offer new tools to study gluten protein composition as a whole system and identify compositional patterns that can modify gluten structure with improved functionality.

Consumption of Tritordeum Bread Reduces Immunogenic Gluten Intake without Altering the Gut Microbiota

Gluten proteins are responsible for the wheat breadmaking quality. However, gluten is also related to human pathologies for which the only treatment is a gluten-free diet (GFD). GFD has gained popularity among individuals who want to reduce their gluten intake. Tritordeum is a cereal species that originated after crossing durum wheat with wild barley and differs from bread wheat in its gluten composition. In this work, we have characterized the immunogenic epitopes of tritordeum bread and results from a four-phase study with healthy adults for preferences of bread and alterations in the gut microbiota after consuming wheat bread, gluten-free bread, and tritordeum bread are reported. Tritordeum presented fewer peptides related to gluten proteins, CD-epitopes, and IgE binding sites than bread wheat. Participants rated tritordeum bread higher than gluten-free bread. Gut microbiota analysis revealed that the adherence to a strict GFD involves some minor changes, especially altering the species producing short-chain fatty acids. However, the short-term consumption of tritordeum bread does not induce significant changes in the diversity or community composition of the intestinal microbiota in healthy individuals. Therefore, tritordeum bread could be an alternative for healthy individuals without wheat-related pathologies who want to reduce their gluten consumption without harming their gut health.

Chain Terminators and Glutathione Weaken Wheat Dough under Excess Nitrogen Input

An excessive nitrogen (N) supply may weaken dough due to an imbalance between N and sulfur (S) in the grains. However, the mechanism underlying the weakening effect of excessive N supply has yet to be fully elucidated. In this study, we evaluated the effect of the N rate × S rate interaction on the ratio of N to S (N/S ratio), grain protein concentration, amount and composition of protein fractions, and dough properties of a bread wheat cultivar. The concentrations of glutathione and modified gliadins with an odd number of cysteine residues (potential chain terminators for glutenins) were also examined. The results revealed that the weakening effect of excess N input is closely associated with an increased gliadin/glutenin ratio, reduced low-molecular-weight glutenin subunit concentrations, and the degree of polymerization of glutenin. More importantly, we found that the increased concentrations of glutathione and chain terminators in grains are involved in the modification of the polymerization degree in glutenins.

Basophil Activation to Gluten and Non-Gluten Proteins in Wheat-Dependent Exercise-Induced Anaphylaxis

Wheat-dependent exercise-induced anaphylaxis (WDEIA) is a cofactor-induced wheat allergy. Gluten proteins, especially ω5-gliadins, are known as major allergens, but partially hydrolyzed wheat proteins (HWPs) also play a role. Our study investigated the link between the molecular composition of gluten or HWP and allergenicity. Saline extracts of gluten (G), gluten with reduced content of ω5-gliadins (G-ω5), slightly treated HWPs (sHWPs), and extensively treated HWPs (eHWPs) were prepared as allergen test solutions and their allergenicity assessed using the skin prick test and basophil activation test (BAT) on twelve patients with WDEIA and ten controls. Complementary sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), high-performance liquid chromatography (HPLC), and mass spectrometry (MS) analyses revealed that non-gluten proteins, mainly α-amylase/trypsin inhibitors (ATIs), were predominant in the allergen test solutions of G, G-ω5, and sHWPs. Only eHWPs contained gliadins and glutenins as major fraction. All allergen test solutions induced significantly higher %CD63⁺ basophils/anti-FcεRI ratios in patients compared with controls. BAT using sHWPs yielded 100% sensitivity and 83% specificity at optimal cut-off and may be useful as another tool in WDEIA diagnosis. Our findings indicate that non-gluten proteins carrying yet unidentified allergenic epitopes appear to be relevant in WDEIA. Further research is needed to clarify the role of nutritional ATIs in WDEIA and identify specific mechanisms of immune activation.

Mining the Wheat Grain Proteome

Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).

The effect of nitrogen fertilization on the expression of protein in wheat and tritordeum varieties using a proteomic approach

Wheat, an essential ingredient for several bakery preparations, is also responsible for gluten-related diseases in sensitive subjects. The effect of the N fertilization rate (80 vs 160 kg N ha^-1) on gluten protein expression profile has been evaluated considering two soft wheats (landrace and modern) and one tritordeum cultivar (cv), grown in the same experimental field in North Italy. The proteins of refined flour were characterized through advanced proteomic approaches, including chromatography (RP-HPLC) and electrophoresis. A static model system was used to simulate in vitro digestion and the digestome peptides were examined by mass spectrometry and in silico approaches, to investigate the celiac and allergenic sequences. The CD-toxic epitopes in the digested samples were quantified by means of a R5 ELISA assay. The N fertilization rate increased the grain protein content, but it did not lead to any difference in gluten composition, with exception of glu/glia ratio in the modern wheat cv. Moreover, the gluten composition and the occurrence of toxic/allergenic epitopes varied to a great extent, according mostly to the genotype. A lower immunoreactivity, determined using R5 ELISA, was detected for the digested tritordeum flours than for the landrace (-51%) or modern (-58%) cvs, while no significant difference was observed for the N rates between each genotype. In silico analysis showed that tritordeum has fewer CD epitopes belonging to the ω-gliadins and a lower LMW-GS than the landrace or modern cv. Tritordeum presented fewer α-gliadin allergenic epitopes than the modern wheat cv. The lower frequency of celiac epitopes in tritordeum, compared to the old and the modern wheat, is probably due to the absence of a D genome.

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.

Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process

Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.

Changes in Hydrophobic Interactions among Gluten Proteins during Dough Formation

In this study, changes in hydrophobic interactions among gluten proteins were analyzed during dough mixing. Size-exclusion high-performance chromatography and two-dimensional fluorescence difference gel electrophoresis were performed on proteins extracted with 1-propanol by weakening the hydrophobic interaction. The amount of proteins extracted with 30% 1-propanol increased from the start of mixing to peak consistency, suggesting that the hydrophobic interactions among the strongly aggregated proteins weakened and resulted in disaggregation. The amount of proteins extracted with 10% 1-propanol decreased during hydration, indicating that these proteins aggregated through relatively weak hydrophobic interactions. The proteins that extractability decreased were mainly low molecular weight glutenin, α-gliadin, and γ-gliadin. The amount of monomeric proteins extracted with 30% 1-propanol decreased after peak consistency. The decreased protein was mainly ω-gliadin, indicating that ω-gliadin aggregated with other proteins through hydrophobic interactions. A front-face fluorescence analysis was performed on the dough with the addition of 8-anilino-1-naphthalenesulfonic acid or thioflavin T. The fluorescence intensity increased as a result of exposure to the hydrophobic groups of the gluten proteins and the formation of protein aggregates during dough mixing. These results indicate the importance of hydrophobic interactions in dough formation.

Comprehensive proteome analysis of bread deciphering the allergenic potential of bread wheat, spelt and rye

BACKGROUND/OBJECTIVES

Cereal products like flour and bread are known to trigger diseases such as wheat allergy, celiac disease and non-celiac wheat sensitivity (NCWS). Some of these diseases are caused by allergenic proteins, the expression of which might vary depending on the grain type and manufacturing processes. Therefore, we examined the protein composition and abundance of potentially allergenic proteins in flours from bread wheat, spelt and rye, and corresponding breads.

MATERIALS AND METHODS

Using Nano-LC-ESI-MS/MS and label free quantification (LFQ) we analyzed the proteome of six different bread flours (wholegrain and superfine flours from rye, spelt and bread wheat) and 14 bread types (yeast and sourdough fermented breads from all flours and wheat breads plus/minus bread improver). Potentially allergenic proteins in flours and breads were functionally categorized using the Pfam database and relatively quantified by LFQ.

RESULTS

We could show that almost equal numbers of proteins can be identified in rye- and spelt samples compared to wheat samples using the Uniprot bread wheat protein database, indicating high sequence conservation between cereals. In total, 4424 proteins were identified in the 20 flour and bread samples. The average number of identified proteins in flour (2719 ± 243) was slightly higher than in bread (2283 ± 232; P < 0.001). In wheat- and spelt wholegrain flour higher protein numbers (wheat: 2891 ± 90; spelt: 2743 ± 140) were identified on average than in superfine flour (wheat: 2562 ± 79; P = 0.009; spelt: 2431 ± 140; P = 0.004). Neither the absolute number nor the abundance distribution of potentially allergenic proteins were dependent on the flour type or the fermentation process, but known allergenic proteins like gliadins showed higher relative abundance in spelt- and wheat samples, compared to rye samples.

CONCLUSION

We provide comprehensive proteome data for six flour types and related breads showing that the grain species have greater influence on proteome composition than milling and fermentation processes. Our data indicate that allergenic proteins are not selectively degraded during bread production and are more abundant in bread wheat and spelt compared to rye.

SIGNIFICANCE

Our proteomics study revealed that bread contains a number of potentially and proven allergenic proteins. Most likely allergenicity is not dependent on milling or conventional fermentation processes, but on the grain type. Relative abundance of allergenic proteins was higher in spelt- and wheat samples than in rye samples. Considering rye bread as better suited to atopic individuals predisposed to react to cereal allergens, clinical trials are warranted to verify this assumption.

Expression analysis of α-gliadin isoforms in wheat grains

Gliadin is a major wheat seed storage protein that affects the extensibility of flour dough. Multiple genes encode gliadin, and there are numerous isoforms encoded by these genes, some of which might be related to flour quality. In this study, gliadin isoforms encoded by 30 α-gliadin genes from the wheat cultivar "Chinese Spring" (CS) were identified using 2-DE and MS/MS. The chromosomes where these isoform genes are located were determined using Gli-2 locus-deficient lines. A quantitative analysis by 2-DE revealed differences in expression levels among α-gliadin isoforms. We also separated the polymer and monomer fractions of the total protein by SEC. We found that an α-gliadin isoform with 7 cysteine residues was present at relatively higher levels in the polymer fraction than an α-gliadin isoform with 6 cysteine residues. The present study results can help in understanding the relationship between the properties of α-gliadin isoforms and the physical properties of dough in the future. SIGNIFICANCE: For investigating the relationship between isoforms and dough extensibility, we identified α-gliadin isoforms encoded by 30 genes among the 50 genes cloned until date. Moreover, the polymer and monomer fractions of the total protein were separated by SEC. We found that an α-gliadin isoform with 7 cysteine residues was present at relatively higher levels in the polymer fraction than an α-gliadin isoform with 6 cysteine residues. This study provided useful information for elucidating the relationship between the properties of α-gliadin isoforms and the physical properties of dough.

Fermentation of Gluten by Lactococcus lactis LLGKC18 Reduces its Antigenicity and Allergenicity

Wheat is a worldwide staple food, yet some people suffer from strong immunological reactions after ingesting wheat-based products. Lactic acid bacteria (LAB) constitute a promising approach to reduce wheat allergenicity because of their proteolytic system. In this study, 172 LAB strains were screened for their proteolytic activity on gluten proteins and α-amylase inhibitors (ATIs) by SDS-PAGE and RP-HPLC. Gliadins, glutenins, and ATI antigenicity and allergenicity were assessed by Western blot/Dot blot and by degranulation assay using RBL-SX38 cells. The screening resulted in selecting 9 high gluten proteolytic strains belonging to two species: Enterococcus faecalis and Lactococcus lactis. Proteomic analysis showed that one of selected strains, Lc. lactis LLGKC18, caused degradation of the main gluten allergenic proteins. A significant decrease of the gliadins, glutenins, and ATI antigenicity was observed after fermentation of gluten by Lc. lactis LLGKC18, regardless the antibody used in the tests. Also, the allergenicity as measured by the RBL-SX38 cell degranulation test was significantly reduced. These results indicate that Lc. lactis LLGKC18 gluten fermentation can be deeply explored for its capability to hydrolyze the epitopes responsible for wheat allergy.

Wheat ATIs: Characteristics and Role in Human Disease

Amylase/trypsin-inhibitors (ATIs) comprise about 2–4% of the total wheat grain proteins and may contribute to natural defense against pests and pathogens. However, they are currently among the most widely studied wheat components because of their proposed role in adverse reactions to wheat consumption in humans. ATIs have long been known to contribute to IgE-mediated allergy (notably Bakers' asthma), but interest has increased since 2012 when they were shown to be able to trigger the innate immune system, with attention focused on their role in coeliac disease which affects about 1% of the population and, more recently, in non-coeliac wheat sensitivity which may affect up to 10% of the population. This has led to studies of their structure, inhibitory properties, genetics, control of expression, behavior during processing, effects on human adverse reactions to wheat and, most recently, strategies to modify their expression in the plant using gene editing. We therefore present an integrated account of this range of research, identifying inconsistencies, and gaps in our knowledge and identifying future research needs.

Note 

This paper is the outcome of an invited international ATI expert meeting held in Amsterdam, February 3-5 2020

Cellular and molecular bases of refractory celiac disease

Refractory celiac disease (RCD) encompasses biologically heterogeneous disorders that develop in a small proportion (0.3%) of individuals with celiac disease that are associated with high morbidity. Two broad categories are currently recognized, type I (RCD I) and type II (RCD II), based on immunophenotypic and molecular features of the intraepithelial lymphocytes (IELs). RCD I is characterized by a polyclonal expansion of IELs displaying a normal immunophenotype, while RCD II represents a clonal proliferation of immunophenotypically "aberrant" IELs, and is considered a low-grade lymphoproliferative disorder. The pathogenesis of RCD I has not been clarified, but limited studies suggest multifactorial etiology. On the other hand, recent immunologic, molecular and immunophenotypic analyses have proposed lineage-negative innate IELs to be the cell of origin of a proportion of RCD II cases. Furthermore, sequencing studies have identified frequent, recurrent, activating mutations in members of the JAK-STAT pathway in RCD II. This finding, in conjunction with prior in vitro experimental observations, suggests roles of deregulated cytokine signaling in disease pathogenesis. In this review, we describe current understanding of environmental, immune and genetic factors associated with the development of RCD and briefly discuss diagnostic and therapeutic considerations.

Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts

Wheat amylase/trypsin inhibitors (ATIs) have gained significant relevance as inducers of intestinal and extra-intestinal inflammation. In this study, we present a novel hybrid data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS) approach, combining QconCAT technology with short microflow LC gradients and DIA and apply the method toward the quantitative proteome analysis of ATI extracts. The presented method is fast, robust, and reproducible and provides precise QconCAT-based absolute quantification of major ATI proteins while simultaneously quantifying the proteome by label-free quantification (LFQ). We analyzed extracts of 60 varieties of common wheat grown in replication and evaluated the reproducibility and precision of the workflow for the quantification of ATIs. Applying the method to analyze different wheat species (i.e., common wheat, spelt, durum wheat, emmer, and einkorn) and comparing the results to published data, we validated inter-laboratory and cross-methodology reproducibility of ATI quantification, which is essential in the context of large-scale breeding projects. Additionally, we applied our workflow to assess environmental effects on ATI expression, analyzing ATI content and proteome of same varieties grown at different locations. Finally, we explored the potential of combining QconCAT-based absolute quantification with DIA-based LFQ proteome analysis for the generation of new hypotheses or assay development.

Purification and Functional Characterization of the Chloroform/Methanol-Soluble Protein 3 (CM3) From Triticum aestivum in Drosophila melanogaster

Non-celiac wheat sensitivity (NCWS) has been proposed to be an independent disease entity that is characterized by intestinal (e.g., abdominal pain, flatulence) and extra-intestinal symptoms (e.g., headache, fatigue), which are propagated following the ingestion of wheat products. Increased activity of amylase trypsin inhibitors (ATIs) in modern wheat is suggested to be major trigger of NCWS, while underlying mechanisms still remain elusive. Here, we aimed to generate and functionally characterize the most abundant ATI in modern wheat, chloroform/methanol-soluble protein 3 (CM3), in vitro and in Drosophila melanogaster. We demonstrate that CM3 displays α-glucosidase but not α-amylase or trypsin inhibitory activity in vitro. Moreover, fruit flies fed a sucrose-containing diet together with CM3 displayed significant overgrowth of intestinal bacteria in a sucrose-dependent manner while the consumption of α-amylase and α-glucosidase inhibitors was sufficient to limit bacterial quantities in the intestine. Notably, both CM3 and acarbose-treated flies showed a reduced lifespan. However, this effect was absent in amylase inhibitor (AI) treated flies. Together, given α-glucosidase is a crucial requirement for disaccharide digestion, we suggest that inhibition of α-glucosidase by CM3 enhances disaccharide load in the distal gastrointestinal tract, thereby promoting intestinal bacteria overgrowth. However, it remains speculative if this here described former unknown function of CM3 might contribute to the development of gastrointestinal symptoms observed in NCWS patients which are very similar to symptoms of patients with small intestinal bacterial overgrowth.

Non-celiac wheat sensitivity: rationality and irrationality of a gluten-free diet in individuals affected with non-celiac disease: a review

Non-celiac gluten or wheat sensitivity (NCWS) is a “clinical entity induced by the ingestion of wheat leading to intestinal and/or extraintestinal symptoms that improve once the wheat-containing foodstuff is removed from the diet, and celiac disease and wheat allergy have been excluded”. This mostly accepted definition raises several points that remain controversial on this condition. In the present review, the authors summarize the most recent advances in the clinic and research on NCWS through an accurate analysis of different studies. We screened PubMed, Medline, Embase, and Scopus using the keywords “non-celiac gluten sensitivity”, “non-celiac wheat sensitivity”, and “diagnosis”. We would like to emphasize two main points, including (A) the controversial clinical and etiological aspects in different trials and experiences with particular attention to the Salerno criteria for the diagnosis of NCWS and (B) the histological aspects. The etiology of NCWS remains controversial, and the relationship with irritable bowel syndrome is obscure. Histologically, the duodenal mucosa may show a variable pattern from unremarkable to a slight increase in the number of T lymphocytes in the superficial epithelium of villi. The endorsement of this disease is based on a positive response to a gluten-free diet for a limited period, followed by the reappearance of symptoms after gluten challenge. The Salerno expert criteria may help to diagnose NCWS accurately. Social media and inaccurate interpretation of websites may jeopardize the diagnostic process if individuals self-label as gluten intolerant.

Relative Abundance of Alpha-Amylase/Trypsin Inhibitors in Selected Sorghum Cultivars

Sorghum is of growing interest and considered as a safe food for wheat related disorders. Besides the gluten, α-amylase/trypsin-inhibitors (ATIs) have been identified as probable candidates for these disorders. Several studies focused on wheat-ATIs although there is still a lack of data referring to the relative abundance of sorghum-ATIs. The objective of this work was therefore to contribute to the characterization of sorghum ATI profiles by targeted proteomics tools. Fifteen sorghum cultivars from different regions were investigated with raw proteins ranging from 7.9 to 17.0 g/100 g. Ammonium bicarbonate buffer in combination with urea was applied for protein extraction, with concentration from 0.588 ± 0.047 to 4.140 ± 0.066 mg/mL. Corresponding electrophoresis data showed different protein profiles. UniProtKB data base research reveals two sorghum ATIs, P81367 and P81368; both reviewed and a targeted LC–MS/MS method was developed to analyze these. Quantifier peptides ELAAVPSR (P81367) and TYMVR (P81368) were identified and retained as biomarkers for relative quantification. Different reducing and alkylating agents were assessed and combination of tris (2 carboxyethyl) phosphine/iodoacetamide gave the best response. Linearity was demonstrated for the quantifier peptides with standard recovery between 92.2 and 107.6%. Nine sorghum cultivars presented up to 60 times lower ATI contents as compared to wheat samples. This data suggests that sorghum can effectively be considered as a good alternative to wheat.

Is Gluten the Only Culprit for Non-Celiac Gluten/Wheat Sensitivity?

The gluten-free diet (GFD) has gained increasing popularity in recent years, supported by marketing campaigns, media messages and social networks. Nevertheless, real knowledge of gluten and GF-related implications for health is still poor among the general population. The GFD has also been suggested for non-celiac gluten/wheat sensitivity (NCG/WS), a clinical entity characterized by intestinal and extraintestinal symptoms induced by gluten ingestion in the absence of celiac disease (CD) or wheat allergy (WA). NCG/WS should be regarded as an "umbrella term" including a variety of different conditions where gluten is likely not the only factor responsible for triggering symptoms. Other compounds aside from gluten may be involved in the pathogenesis of NCG/WS. These include fructans, which are part of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs), amylase trypsin inhibitors (ATIs), wheat germ agglutinin (WGA) and glyphosate. The GFD might be an appropriate dietary approach for patients with self-reported gluten/wheat-dependent symptoms. A low-FODMAP diet (LFD) should be the first dietary option for patients referring symptoms more related to FODMAPs than gluten/wheat and the second-line treatment for those with self-reported gluten/wheat-related symptoms not responding to the GFD. A personalized approach, regular follow-up and the help of a skilled dietician are mandatory.

Non-Celiac Gluten Sensitivity and Irritable Bowel Disease: Looking for the Culprits

During the last 30 y, a gluten-free diet has been classified among the most popular fad diets mainly due to the ambiguous notion that gluten avoidance promotes health. Gluten intolerance has been implicated in non-celiac gluten sensitivity (NCGS) and irritable bowel syndrome (IBS), 2 disorders with overlapping symptoms and increasing trend. Together with gluten, other wheat components; fermentable oligo-, di-, monosaccharide, and polyols (FODMAPs); and amylase trypsin inhibitors (ATIs), are implicated in the pathogenesis of both disorders. Gut microflora alterations in IBS and NCGS have been described, while microbiota manipulations have been shown to be promising in some IBS cases. This literature review summarizes our current knowledge on the impact of wheat ingredients (gluten, FODMAPs, and ATIs) in IBS and NCGS. In both disorders, FODMAPs and ATIs trigger gut dysbiosis, suggesting that gluten may not be the culprit, and microbiota manipulations can be applied in diagnostic and intervention approaches.

Changes in Protein Non-Covalent Bonds and Aggregate Size during Dough Formation

This research investigated changes in the amounts and sizes of monomeric proteins and protein aggregates during dough mixing, with a focus on the contribution of non-covalent bonds in the aggregation of gluten proteins. High protein flour (HF) and low protein flour (LF) were used in this study. As dough mixing progressed from flour to overmixed dough, the total amount of protein aggregates increased while the amount of monomeric protein decreased. Omega-gliadin was the major monomeric protein that decreased in quantity. Interestingly, the amount of larger-sized protein aggregates decreased and that of smaller-sized protein aggregates increased. The amount of gluten protein macro-polymer aggregated through strong non-covalent bonds decreased whereas aggregates formed with weaker non-covalent bonds increased. LF dough behaved similar to HF dough. Large-sized gluten protein aggregates disaggregated due to the weakening of non-covalent bonds and became smaller. Omega-gliadin was incorporated into gluten protein aggregates during dough mixing.

The Two Faces of Wheat

Wheat-based foods have been staple foods since about 10,000 years and constitute a major source of energy, dietary fiber, and micronutrients for the world population. The role of wheat in our diet, however, has recently been scrutinized by pseudoscientific books and media reports promoting the overall impression that wheat consumption makes people sick, stupid, fat, and addicted. Consequently, numerous consumers in Western countries have started to question their dietary habits related to wheat consumption and voluntarily decided to adopt a wheat-free diet without a medical diagnosis of any wheat-related disorder (WRD), such as celiac disease, wheat allergy, or non-celiac gluten sensitivity. The aim of this review is to achieve an objective judgment of the positive aspects of wheat consumption as well as adverse effects for individuals suffering from WRDs. The first part presents wheat constituents and their positive nutritional value, in particular, the consumption of products from whole-grain flours. The second part is focused on WRDs that affect predisposed individuals and can be treated with a gluten-free or -reduced diet. Based on all available scientific knowledge, wheat consumption is safe and healthy for the vast majority of people. There is no scientific evidence to support that the general population would benefit from a wheat-free diet.

Comprehensive Characterization and Relative Quantification of α-Amylase/Trypsin Inhibitors from Wheat Cultivars by Targeted HPLC-MS/MS

The α-amylase/trypsin inhibitors (ATIs) are discussed as being responsible for non-celiac wheat sensitivity (NCWS), besides being known as allergenic components for baker’s asthma. Different approaches for characterization and quantification including proteomics-based methods for wheat ATIs have been documented. In these studies generally the major ATIs have been addressed. The challenge of current study was then to develop a more comprehensive workflow encompassing all reviewed wheat-ATI entries in UniProt database. To substantially test proof of concept, 46 German and Turkish wheat samples were used. Two extractions systems based on chloroform/methanol mixture (CM) and under buffered denaturing conditions were evaluated. Three aspects were optimized, tryptic digestion, chromatographic separation, and targeted tandem mass spectrometric analysis (HPLC-MS/MS). Preliminary characterization with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) documented the purity of the extracted ATIs with CM mixture and the amylase (60–80%)/trypsin (10–20%) inhibition demonstrated the bifunctional activity of ATIs. Thirteen (individual/common) biomarkers were established. Major ATIs (7–34%) were differently represented in samples. Finally, to our knowledge, the proposed HPLC-MS/MS method allowed for the first time so far the analysis of all 14 reviewed wheat ATI entries reported.

Comparative quantitative LC-MS/MS analysis of 13 amylase/trypsin inhibitors in ancient and modern Triticum species

Amylase/trypsin inhibitors (ATIs) are major wheat allergens and they are also implicated in causing non-celiac gluten sensitivity and worsening other inflammatory conditions. With only few studies on ATI contents in different Triticum species available so far, we developed a targeted liquid chromatography-tandem mass spectrometry (LC–MS/MS) method based on stable isotope dilution assays to quantitate the 13 most important ATIs in a well-defined sample set of eight cultivars of common wheat and durum wheat (modern species), as well as spelt, emmer and einkorn (ancient species) grown at three locations in Germany, respectively. Only few ATIs with low contents were detected in einkorn. In contrast, spelt had the highest total ATI contents. Emmer and common wheat had similar total ATI contents, with durum wheat having lower contents than common wheat. Due to the lack of correlation, it was not possible to estimate ATI contents based on crude protein contents. The wheat species had a higher influence on ATI contents than the growing location and the heritability of this trait was high. Despite comparatively low intra-species variability, some cultivars were identified that may be promising candidates for breeding for naturally low ATI contents.

Deciphering the immunogenic potential of wheat flour: a reference map of the salt-soluble proteome from the U.S. wheat Butte 86

Background

Within the complex wheat flour proteome, the gluten proteins have attracted most of the attention because of their importance in determining the functional properties of wheat flour doughs and their roles in human health conditions such as celiac disease and food allergies. However, certain non-gluten proteins also trigger immunological responses but may be present in flour in low amounts or obscured by the more abundant gluten proteins in two-dimensional gels of total protein preparations.

Methods

Non-gluten proteins were preferentially extracted from the flour with a dilute salt solution and separated by two-dimensional gel electrophoresis. Proteins in 173 gel spots were identified by tandem mass spectrometry after cleavage with trypsin or chymotrypsin. Transgenic wheat lines in which specific groups of gluten proteins were suppressed by RNA interference were used to estimate the amount of carry-over of gluten proteins in the salt-soluble protein fraction.

Results

Fifty-seven different types of non-gluten proteins were identified, including 14 types that are known or suspected immunogenic proteins. The predominant proteins in 18 gel spots were gluten proteins. Some of these also contained non-gluten proteins. Analysis of the salt-soluble proteins from a transgenic line in which omega-1,2 gliadins were eliminated by RNA interference indicated that certain omega-1,2 gliadins were present in large amounts in the salt-soluble fraction and obscured relatively small amounts of beta-amylase and protein disulfide isomerase. In comparison, analysis of a transgenic line in which alpha gliadins were absent revealed that glyceraldehyde-3 phosphate dehydrogenase was a moderately abundant protein that co-migrated with several alpha gliadins.

Conclusions

In this study, we constructed a proteomic map of the non-gluten protein fraction of wheat flour from the US wheat Butte 86 that complements a proteomic map of the total flour proteins developed previously for the same cultivar. Knowing the identities of low abundance proteins in the flour as well as proteins that are hidden by some of the major gluten proteins on two-dimensional gels is critical for studies aimed at assessing the immunogenic potential of wheat flour and determining which wheat proteins that should be targeted in future gene editing experiments to reduce the immunogenic potential of wheat flour.

Mapping Coeliac Toxic Motifs in the Prolamin Seed Storage Proteins of Barley, Rye, and Oats Using a Curated Sequence Database

Wheat gluten, and related prolamin proteins in rye, barley and oats cause the immune-mediated gluten intolerance syndrome, coeliac disease. Foods labelled as gluten-free which can be safely consumed by coeliac patients, must not contain gluten above a level of 20 mg/Kg. Current immunoassay methods for detection of gluten can give conflicting results and may underestimate levels of gluten in foods. Mass spectrometry methods have great potential as an orthogonal method, but require curated protein sequence databases to support method development. The GluPro database has been updated to include avenin-like sequences from bread wheat (n = 685; GluPro v1.1) and genes from the sequenced wheat genome (n = 699; GluPro v 1.2) and Triticum turgidum ssp durum (n = 210; GluPro v 2.1). Companion databases have been developed for prolamin sequences from barley (n = 64; GluPro v 3.0), rye (n = 41; GluPro v 4.0), and oats (n = 27; GluPro v 5.0) and combined to provide a complete cereal prolamin database, GluPro v 6.1 comprising 1,041 sequences. Analysis of the coeliac toxic motifs in the curated sequences showed that they were absent from the minor avenin-like proteins in bread and durum wheat and barley, unlike the related avenin proteins from oats. A comparison of prolamin proteins from the different cereal species also showed α- and γ-gliadins in bread and durum wheat, and the sulphur poor prolamins in all cereals had the highest density of coeliac toxic motifs. Analysis of ion-mobility mass spectrometry data for bread wheat (cvs Chinese Spring and Hereward) showed an increased number of identifications when using the GluPro v1.0, 1.1 and 1.2 databases compared to the limited number of verified sequences bread wheat sequences in reviewed UniProt. This family of databases will provide a basis for proteomic profiling of gluten proteins from all the gluten containing cereals and support identification of specific peptide markers for use in development of new methods for gluten quantitation based on coeliac toxic motifs found in all relevant cereal species.

Comprehensive Comparison of Clinically Relevant Grain Proteins in Modern and Traditional Bread Wheat Cultivars

Bread wheat (Triticum aestivum L.) is one of the most valuable cereal crops for human consumption. Its grain storage proteins define bread quality, though they may cause food intolerances or allergies in susceptible individuals. Herein, we discovered a diversity of grain proteins in three Ukrainian wheat cultivars: Sotnytsia, Panna (both modern selection), and Ukrainka (landrace). Firstly, proteins were isolated with a detergent-containing buffer that allowed extraction of various groups of storage proteins (glutenins, gliadins, globulins, and albumins); secondly, the proteome was profiled by the two-dimensional gel electrophoresis. Using multi-enzymatic digestion, we identified 49 differentially accumulated proteins. Parallel ultrahigh-performance liquid chromatography separation followed by direct mass spectrometry quantification complemented the results. Principal component analysis confirmed that differences among genotypes were a major source of variation. Non-gluten fraction better discriminated bread wheat cultivars. Various accumulation of clinically relevant plant proteins highlighted one of the modern genotypes as a promising donor for the breeding of hypoallergenic cereals.

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.

Identification and Quantitation of Amylase Trypsin Inhibitors Across Cultivars Representing the Diversity of Bread Wheat

α-Amylase/trypsin inhibitors (ATIs) may have a role in nonceliac wheat sensitivity (NCWS) and celiac disease (CD), but the ATI content and diversity across a range of wheat cultivars are not well characterized. Discovery proteomics was used to detect ATIs across two wheat cultivars: Chara and Magenta. Comprehensive mapping of detected ATIs with the ATIs from the recently published wheat genome RefSeq v1.0 shows the presence of three major subclasses: monomeric (9%), dimeric (61%), and chloroform-methanol (CM) type (30%). Subsequently, the level of 18 ATI isoforms (63 peptides) grouped into four subtypes was monitored across 15 commercial wheat cultivars and the eight parental lines from a multiparent advanced-generation intercross (MAGIC) population using liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS). The ATI content of wheat cultivars Janz, Sunvale, Diamond Bird, and Longreach Scout was significantly lower than that of other wheat cultivars. The MAGIC parental cultivars Baxter and Xiaoyan 54 contain higher levels (∼115% relative to the average wheat ATI content), whereas cultivar Pastor contained the lowest levels (∼87%). Comprehensive sequence analysis, annotation, chromosomal locations, and epitope mapping enabled us to build an LC-MRM-MS method to monitor and quantify the immunostimulatory ATI proteins potentially related to NCWS, autoimmune diseases, and metabolic disorders. This provides an opportunity to select wheat cultivars with significantly lower levels of ATIs.

Mass spectrometry of in-gel digests reveals differences in amino acid sequences of high-molecular-weight glutenin subunits in spelt and emmer compared to common wheat

High-molecular-weight glutenin subunits (HMW-GS) play an important role for the baking quality of wheat. The ancient wheats emmer and spelt differ in their HMW-GS pattern compared to modern common wheat and this might be one reason for their comparatively poor baking quality. The aim of this study was to elucidate similarities and differences in the amino acid sequences of two 1Bx HMW-GS of common wheat, spelt and emmer. First, the sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE) system was optimized to separate common wheat, spelt and emmer Bx6 and Bx7 from other HMW-GS (e.g., 1Ax and 1By) in high concentrations. The in-gel digests of the Bx6 and Bx7 bands were analyzed by untargeted LC-MS/MS experiments revealing different UniProtKB accessions in spelt and emmer compared to common wheat. The HMW-GS Bx6 and Bx7, respectively, of emmer and spelt showed differences in the amino acid sequences compared to those of common wheat. The identities of the peptide variations were confirmed by targeted LC-MS/MS. These peptides can be used to differentiate between Bx6 and Bx7 of spelt and emmer and Bx6 and Bx7 of common wheat. The findings should help to increase the reliability and curation status of wheat protein databases and to understand the effects of protein structure on the functional properties. Graphical abstract.