Environmental and transgene expression effects on the barley seed proteome

Application of Mass Spectrometry-Based Proteomics to Barley Research

Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.

Proteome Analysis of Hordein-Null Barley Lines Reveals Storage Protein Synthesis and Compensation Mechanisms

Hordeins are the major barley seed storage proteins and are elicitors of celiac disease. Attempts to reduce the hordein level in barley have been made; however, the resultant pleiotropic effects are less understood. Here, data-independent acquisition mass spectrometry was used to measure proteome-wide abundance differences between wild-type and single hordein-null barley lines. Using comparative quantitative proteomics, we detected proteome-wide changes (∼59%) as a result of the specific reduction in hordein proteins. The comparative analysis and functional annotation revealed an increase in non-gluten storage proteins, such as globulins and lipid transfer proteins, and proteins rich in essential amino acids in the null lines. This study yields an informative molecular portrait of the hordein-null lines and the underlying mechanisms of storage protein biosynthesis. This study indicates the extent to which protein content can be manipulated without biological consequence, and we envision its wide-scale application for studying modified crops.

Shotgun proteomics of the barley seed proteome

Background

Barley seed proteins are of prime importance to the brewing industry, human and animal nutrition and in plant breeding for cultivar identification. To obtain comprehensive proteomic data from seeds, total protein from a two-rowed (Conrad) and a six-rowed (Lacey) barley cultivar were precipitated in acetone, digested in-solution, and the resulting peptides were analyzed by nano-liquid chromatography coupled with tandem mass spectrometry.

Results

The raw mass spectra data searched against Uniprot’s Barley database using in-house Mascot search engine identified 1168 unique proteins. Gene Ontology (GO) analysis indicated that the majority of the seed proteins were cytosolic, with catalytic activity and associated with carbohydrate metabolism. Spectral counting analysis showed that there are 20 differentially abundant seed proteins between the two-rowed Conrad and six-rowed Lacey cultivars.

Conclusion

This study paves the way for the use of a top-down gel-free proteomics strategy in barley for investigating more complex traits such as malting quality. Differential abundance of hordoindoline proteins impact the seed hardness trait of barley cultivars.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3408-5) contains supplementary material, which is available to authorized users.

Proteomic analysis of mature barley grains from C-hordein antisense lines

Hordeins are the major storage proteins in barley grains and are responsible for their low nutritional quality. Previously, antisense C-hordein barley lines were generated and were shown to contain a more balanced amino acid composition and an altered storage protein profile. In the present study, a proteomic approach that combined two-dimensional gel electrophoresis (2-DE) and mass spectrometry was used to (1) identify the changes in the protein profile of non-storage proteins (salt soluble fraction) in antisense C-hordein barley lines (L1, L2 and L3) and (2) map the differentially expressed proteins compared to the non-transgenic control line (Hordeum vulgare cv. Golden Promise). Moreover, the changes in the proteins were correlated with the more balanced amino acid composition of these lines, with special attention to the lysine content. The results showed that suppression of C-hordein expression does not exclusively affect hordein synthesis and accumulation. The more balanced amino acid composition observed in the transgenic lines L1, L2 and L3 was an indirect result of the profound alterations in the patterns of the non-storage proteins. The observed changes included up-regulated expression of the proteins involved in stress and detoxification (L1), defence (L2 and L3), and storage globulins (L1, L2 and L3). To a lesser extent, the proteins involved in grain metabolism were also changed. Thus, the increased essential amino acids content results from changes in distinct protein sources among the three antisense C-hordein lines analyzed, although the up-regulated expression of lysine-rich proteins was consistently observed in all lines.

Mass spectrometry in the proteome analysis of mature cereal kernels

In the last decade, the improved performance and versatility of the mass spectrometers together with the increasing availability of gene and genomic sequence database, led the mass spectrometry to become an indispensable tool for either protein and proteome analyses in cereals. Mass spectrometric works on prolamins have rapidly evolved from the determination of the molecular masses of proteins to the proteomic approaches aimed to a large-scale protein identification and study of functional and regulatory aspects of proteins. Mass spectrometry coupled with electrophoresis, chromatographic methods, and bioinformatics tools is currently making significant contributions to a better knowledge of the composition and structure of the cereal proteins and their structure-function relationships. Results obtained using mass spectrometry, including characterization of prolamins, investigation of the gluten toxicity for coeliac patients, identification of proteins responsible of cereal allergies, determination of the protein pattern and its modification under environmental or stress effects, investigation of genetically modified varieties by proteomic approaches, are summarized here, to illustrate current trends, analytical troubles and challenges, and suggest possible future perspectives.

Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium

Cereals are major crops worldwide, and improvement of their nitrogen use efficiency is a crucial challenge. In this study proteins responding to N supply in barley roots and shoots were analysed using a proteomics approach, to provide insight into mechanisms of N uptake and assimilation. Control plants grown hydroponically for 33 d with 5 mm nitrate, plants grown under N deficiency (0.5 mm nitrate, 33 d) or short-term N starvation (28 d with 5 mm nitrate followed by 5 d with no N source) were compared. N deficiency caused changes in C and N metabolism and ascorbate-glutathione cycle enzymes in shoots and roots. N starvation altered proteins of amino acid metabolism in roots. Both treatments caused proteome changes in roots that could affect growth. Shoots of plants grown with ammonium as N source (28 d with 5 mm nitrate followed by 5 d with 5 mm ammonium) showed responses similar to N deficient shoots, characterized by turnover of ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) and increases in proteins of the chloroplastic transcription and translation machinery. Identified proteins in 67 and 49 varying spots in roots and shoots respectively, corresponded to 62 functions and over 80 gene products, considerably advancing knowledge of N responses in barley.

Investigation of the effect of nitrogen on severity of Fusarium head blight in barley

The effect of nitrogen on Fusarium Head Blight (FHB) in a susceptible barley cultivar was investigated using gel-based proteomics. Barley grown with either 15 or 100kgha(-1)N fertilizer was inoculated with Fusarium graminearum (Fg). The storage protein fraction did not change significantly in response either to N level or Fg, whereas eighty protein spots in the water-soluble albumin fraction increased and 108 spots decreased more than two-fold in intensity in response to Fg. Spots with greater intensity in infected plants contained fungal proteins (9 spots) and proteolytic fragments of plant proteins (65 spots). Identified fungal proteins included two superoxide dismutases, L-xylulose reductase in two spots, peptidyl prolyl cis-trans isomerase and triosephosphate isomerase, and proteins of unknown function. Spots decreasing in intensity in response to Fg contained plant proteins possibly degraded by fungal proteases. Greater spot volume changes occurred in response to Fg in plants grown with low nitrogen, although proteomes of uninfected plants were similar for both treatments. Correlation of proteome changes with measurement of Fusarium-damaged kernels, fungal biomass and mycotoxin levels indicated that increased Fusarium infection occurred in barley with low N and suggests control of N fertilization as a possible way to minimise FHB in barley.

From proteomics to structural studies of cytosolic/mitochondrial-type thioredoxin systems in barley seeds

Thioredoxins (Trx) are ubiquitous proteins that participate in thiol disulfide reactions via two active site cysteine residues, allowing Trx to reduce disulfide bonds in target proteins. Recent progress in proteome analysis has resulted in identification of a wide range of potential target proteins for Trx, indicating that Trx plays a key role in several aspects of cell metabolism. In contrast to other organisms, plants contain multiple forms of Trx that are classified based on their primary structures and sub-cellular localization. The reduction of cytosolic and mitochondrial types of Trx is dependent on NADPH and catalyzed by NADPH-dependent thioredoxin reductase (NTR). In barley, two isoforms each of Trx and NTR have been identified and investigated using proteomics, gene expression, and structural studies. This review outlines the diverse roles suggested for cytosolic/mitochondrial-type Trx systems in cereal seeds and summarizes the current knowledge of the barley system including recent data on function, regulation, interactions, and structure. Directions for future research are discussed.

Serpins in plants and green algae

Control of proteolysis is important for plant growth, development, responses to stress, and defence against insects and pathogens. Members of the serpin protein family are likely to play a critical role in this control through irreversible inhibition of endogenous and exogenous target proteinases. Serpins have been found in diverse species of the plant kingdom and represent a distinct clade among serpins in multicellular organisms. Serpins are also found in green algae, but the evolutionary relationship between these serpins and those of plants remains unknown. Plant serpins are potent inhibitors of mammalian serine proteinases of the chymotrypsin family in vitro but, intriguingly, plants and green algae lack endogenous members of this proteinase family, the most common targets for animal serpins. An Arabidopsis serpin with a conserved reactive centre is now known to be capable of inhibiting an endogenous cysteine proteinase. Here, knowledge of plant serpins in terms of sequence diversity, inhibitory specificity, gene expression and function is reviewed. This was advanced through a phylogenetic analysis of amino acid sequences of expressed plant serpins, delineation of plant serpin gene structures and prediction of inhibitory specificities based on identification of reactive centres. The review is intended to encourage elucidation of plant serpin functions.

Spatio-temporal profiling and degradation of α-amylase isozymes during barley seed germination

Ten genes from two multigene families encode barley alpha-amylases. To gain insight into the occurrence and fate of individual isoforms during seed germination, the alpha-amylase repertoire was mapped by using a proteomics approach consisting of 2D gel electrophoresis, western blotting, and mass spectrometry. Mass spectrometric analysis confirmed that the 29 alpha-amylase positive 2D gel spots contained products of one (GenBank accession gi|113765) and two (gi|4699831 and gi|166985) genes encoding alpha-amylase 1 and 2, respectively, but lacked products from seven other genes. Eleven spots were identified only by immunostaining. Mass spectrometry identified 12 full-length forms and 12 fragments from the cultivar Barke. Products of both alpha-amylase 2 entries co-migrated in five full-length and one fragment spot. The alpha-amylase abundance and the number of fragments increased during germination. Assessing the fragment minimum chain length by peptide mass fingerprinting suggested that alpha-amylase 2 (gi|4699831) initially was cleaved just prior to domain B that protrudes from the (betaalpha)(8)-barrel between beta-strand 3 and alpha-helix 3, followed by cleavage on the C-terminal side of domain B and near the C-terminus. Only two shorter fragments were identified of the other alpha-amylase 2 (gi|166985). The 2D gels of dissected tissues showed alpha-amylase degradation to be confined to endosperm. In contrast, the aleurone layer contained essentially only full-length alpha-amylase forms. While only products of the above three genes appeared by germination also of 15 other barley cultivars, the cultivars had distinct repertoires of charge and molecular mass variant forms. These patterns appeared not to be correlated with malt quality.

Rice proteomics: a cornerstone for cereal food crop proteomes

Proteomics-a systematic study of proteins present in a cell, tissue, organ, or organism at a particular moment during the life cycle-that began with classical two-dimensional electrophoresis and its advancement during the 1990s, has been revolutionized by a series of tremendous technological developments in mass spectrometry (MS), a core technology. Proteomics is exerting its influence on biological function of genes and genomes in the era (21st century) of functional genomics, and for this reason yeast, bacterial, and mammalian systems are the best examples. Although plant proteomics is still in its infancy, evolving proteomic technologies and the availability of the genome sequences of Arabidopsis thaliana (L.) Heyhn, and rice (Oryza sativa L.), model dicotyledoneous and monocotyledoneous (monocot) species, respectively, are propelling it towards new heights, as evidenced by the rapid spurt in worldwide plant proteome research. Rice, with an immense socio-economic impact on human civilization, is a representative model of cereal food crops, and we consider it as a cornerstone for functional genomics of cereal plants. In this review, we look at the history and the current state of monocot proteomes, including barley, maize, and wheat, with a central focus on rice, which has the most extensive proteomic coverage to date. On one side, we highlight advances in technologies that have generated enormous amount of interest in plant proteomics, and the other side summarizes the achievements made towards establishing proteomes during plant growth & development and challenge to environmental factors, including disease, and for studying genetic relationships. In light of what we have learned from the proteomic journey in rice and other monocots, we finally reveal and assess their impact in our continuous strive towards completion of their full proteomes.