Introduction of the Disulfide Proteome: Application of a Technique for the Analysis of Plant Storage Proteins as Well as Allergens

Cross-linking reactions in food proteins and proteomic approaches for their detection

Various protein cross-linking reactions leading to molecular polymerization and covalent aggregates have been described in processed foods. They are an undesired side effect of processes designed to reduce bacterial load, extend shelf life, and modify technological properties, as well as being an expected result of treatments designed to modify raw material texture and function. Although the formation of these products is known to affect the sensory and technological properties of foods, the corresponding cross-linking reactions and resulting protein polymers have not yet undergone detailed molecular characterization. This is essential for describing how their generation can be related to food processing conditions and quality parameters. Due to the complex structure of cross-linked species, bottom-up proteomic procedures developed to characterize various amino acid modifications associated with food processing conditions currently offer a limited molecular description of bridged peptide structures. Recent progress in cross-linking mass spectrometry for the topological characterization of protein complexes has facilitated the development of various proteomic methods and bioinformatic tools for unveiling bridged species, which can now also be used for the detailed molecular characterization of polymeric cross-linked products in processed foods. We here examine their benefits and limitations in terms of evaluating cross-linked food proteins and propose future scenarios for application in foodomics. They offer potential for understanding the protein cross-linking formation mechanisms in processed foods, and how the inherent beneficial properties of treated foodstuffs can be preserved or enhanced.

Proteomic analysis and candidate allergenic proteins in Populus deltoides CL. "2KEN8" mature pollen

Proteomic analysis was used to generate a map of Populus deltoides CL. "2KEN8" mature pollen proteins. By applying 2-D electrophoresis, we resolved 403 protein spots from mature pollen. Using the matrix-assisted laser desorption/ionization time time-of-flight/time-of-flight tandem mass spectrometry method, we identified 178 distinct proteins from 218 protein spots expressed in mature pollen. Moreover, out of these, 28 proteins were identified as putative allergens. The expression patterns of these putative allergen genes indicate that several of these genes are highly expressed in pollen. In addition, the members of profilin allergen family were analyzed and their expression patterns were compared with their homologous genes in Arabidopsis and rice. Knowledge of these identified allergens has the potential to improve specific diagnosis and allergen immunotherapy treatment for patients with poplar pollen allergy.

Proteomics-based allergen analysis in plants

Plants may trigger hypersensitivity reactions when individuals with allergies consume foods derived from plant materials or inhale plant pollen. As each plant food or pollen contains multiple allergens, proteomics is a powerful tool to detect the allergens present. Allergen-targeted proteomics, termed allergenomics, has been used for comprehensive identification and/or quantification of plant allergens, because it is a simple and inexpensive tool for rapid detection of proteins that bind to IgE. There are increasing numbers of reports on the applications of allergenomics. In this review, we outline some of the applications of proteomics, including: (i) identification of novel allergens, (ii) allergic diagnoses, (iii) quantification of allergens, and (iv) natural diversity of allergens, and finally discuss (v) the use of allergenomics for safety assessment of genetically modified (GM) plants.

BIOLOGICAL SIGNIFICANCE

Recently, the number of allergic patients is increasing. Therefore, a comprehensive analysis of allergens (allergenomics) in plants is highly important for not only risk assessment of food plants but also diagnosis of allergic symptoms. In this manuscript, we reviewed the recent progress of allergenomics for identification, quantification and profiling of allergens. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Mobilization of seed protein reserves

The mobilization of seed storage proteins upon seed imbibition and germination is a crucial process in the establishment of the seedling. Storage proteins fold compactly, presenting only a few vulnerable regions for initial proteolytic digestion. Evolutionarily related storage proteins have similar three-dimensional structure, and thus tend to be initially cleaved at similar sites. The initial cleavage makes possible subsequent rapid and extensive breakdown catalyzed by endo- and exopeptidases. The proteolytic enzymes that degrade the storage proteins during mobilization identified so far are mostly cysteine proteases, but also include serine, aspartic and metalloproteases. Plants often ensure early initiation of storage protein mobilization by depositing active proteases during seed maturation, in the very compartments where storage proteins are sequestered. Various means are used in such cases to prevent proteolytic attack until after imbibition of the seed with water. This constraint, however, is not always enforced as the dry seeds of some plant species contain proteolytic intermediates as a result of limited proteolysis of some storage proteins. Besides addressing fundamental questions in plant protein metabolism, studies of the mobilization of storage proteins will point out proteolytic events to avoid in large-scale production of cloned products in seeds. Conversely, proteolytic enzymes may be applied toward reduction of food allergens, many of which are seed storage proteins.

The disulfide proteome and other reactive cysteine proteomes: analysis and functional significance

Ten years ago, proteomics techniques designed for large-scale investigations of redox-sensitive proteins started to emerge. The proteomes, defined as sets of proteins containing reactive cysteines that undergo oxidative post-translational modifications, have had a particular impact on research concerning the redox regulation of cellular processes. These proteomes, which are hereafter termed "disulfide proteomes," have been studied in nearly all kingdoms of life, including animals, plants, fungi, and bacteria. Disulfide proteomics has been applied to the identification of proteins modified by reactive oxygen and nitrogen species under stress conditions. Other studies involving disulfide proteomics have addressed the functions of thioredoxins and glutaredoxins. Hence, there is a steadily growing number of proteins containing reactive cysteines, which are probable targets for redox regulation. The disulfide proteomes have provided evidence that entire pathways, such as glycolysis, the tricarboxylic acid cycle, and the Calvin-Benson cycle, are controlled by mechanisms involving changes in the cysteine redox state of each enzyme implicated. Synthesis and degradation of proteins are processes highly represented in disulfide proteomes and additional biochemical data have established some mechanisms for their redox regulation. Thus, combined with biochemistry and genetics, disulfide proteomics has a significant potential to contribute to new discoveries on redox regulation and signaling.

A DIGE-based quantitative proteomic analysis of grape berry flesh development and ripening reveals key events in sugar and organic acid metabolism

Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components, such as sugars, acids, flavours, anthocyanins, tannins, etc., are accumulated during the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance the understanding of the berry development and ripening processes. Here, the developmental analysis of V. vinifera cv. Muscat Hamburg berries is reported at protein level, from fruit set to full ripening. A top-down proteomic approach based on differential in-gel electrophoresis (DIGE) followed by tandem mass spectrometry led to identification and quantification of 156 and 61 differentially expressed proteins in green and ripening phases, respectively. Two key points in development, with respect to changes in protein level, were detected: end of green development and beginning of ripening. The profiles of carbohydrate metabolism enzymes were consistent with a net conversion of sucrose to malate during green development. Pyrophosphate-dependent phosphofructokinase is likely to play a key role to allow an unrestricted carbon flow. The well-known change of imported sucrose fate at the beginning of ripening from accumulation of organic acid (malate) to hexoses (glucose and fructose) was well correlated with a switch in abundance between sucrose synthase and soluble acid invertase. The role of the identified proteins is discussed in relation to their biological function, grape berry development, and to quality traits. Another DIGE experiment comparing fully ripe berries from two vintages showed very few spots changing, thus indicating that protein changes detected throughout development are specific.

Two-dimensional electrophoresis and IgE-mediated food allergy

Food allergy is recognized as one of the major health concerns. It is estimated that ca. 4% of the population is affected by food allergenic disorders. Food allergies are defined as IgE-mediated hypersensitivity reactions. Foods such as peanuts, tree nuts, wheat, soy, cow's milk, egg, fish and shellfish are regarded as responsible for the majority of reactions. The ubiquitous presence of allergens in the human foods coupled with an increased awareness of food allergies warrants to undertake appropriate preventive measures for protecting sensitive consumers from unwanted exposure to offending food allergens. 2-DE followed by immunoblotting and identification of IgE-reactive proteins, as a proteomic approach to identify new allergens in foods, are reviewed. Specific examples of identification of allergens in foods and beverages by using 2-DE and IgE are described. Protein profiling using 2-DE and allergens detection by IgE has become a powerful method for analyzing changes of allergens content in complex matrix during food processing.

Introduction to omics

Exploiting the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes has currently been receiving a lot of attention. In recent years, most of the effort has been put into demonstrating the possible clinical applications of the various omics fields. The cost-effectiveness analysis has been, so far, rather neglected. The cost of omics-derived applications is still very high, but future technological improvements are likely to overcome this problem. In this chapter, we will give a general background of the main omics fields and try to provide some examples of the most successful applications of omics that might be used in clinical diagnosis and in a therapeutic context.