Shotgun Proteomics and Protein-Based Bioinformatics for the Characterization of Food-Derived Bioactive Peptides.

A workflow for the characterization of food-derived bioactive peptides is described in this chapter. The workflow integrates two consecutive steps: a discovery phase and a protein-based bioinformatic phase. In the first step (discovery phase), a shotgun bottom-up proteomics approach is used to create a reference data set for a selected food proteome. Afterward, in a second step (bioinformatic phase), the reference proteome is subjected to several in silico protein-based bioinformatic analyses to predict and characterize potential bioactive peptides after an in silico human gastrointestinal digestion. Using this workflow, bioactive collagen peptides, antihypertensive, antimicrobial, and antitumor peptides were predicted as potential valuable bioactive peptides from seafood and marine by-products. It is concluded that the combination of the global shotgun proteomic analysis and the analysis by protein-based bioinformatics can provide a rapid strategy for the characterization of new potential food-derived bioactive peptides.

Molecular characterization of B-cell epitopes for the major fish allergen, parvalbumin, by shotgun proteomics, protein-based bioinformatics and IgE-reactive approaches.

Parvalbumins beta (ß-PRVBs) are the main fish allergens. The only proven and effective treatment for this type of hypersensitivity is to consume a diet free of fish. We present the molecular characterization of B-cell epitopes by shotgun proteomics of different ß-PRVBs combined with protein-based bioinformatics and IgE-reactive approaches. The final goal of this work is to identify potential peptide vaccine candidates for fish allergy. Purified ß-PRVBs from the main fifteen different fish species that cause allergy were analyzed by shotgun proteomics. Identified ß-PRVBs peptide sequences and ninety-eight ß-PRVB protein sequences from UniProtKB were combined, aligned and analyzed to determine B-cell epitopes using the Kolaskar and Tongaonkar algorithm. The highest rated predicted B-cell peptide epitopes were evaluated by ELISA using the corresponding synthetic peptides and sera from healthy and fish allergic patients. A total of 35 peptides were identified as B-cell epitopes. The top B-cell peptide epitopes (LKLFLQV, ACAHLCK, FAVLVKQ and LFLQNFV) that may induce protective immune responses were selected as potential peptide vaccine candidates. The 3D model of these peptides were located in the surface of the protein. This study provides the global characterization of B-cell epitopes for all ß-PRVBs sequences that will facilitate the design of new potential immunotherapies. SIGNIFICANCE: This work provides the global characterization of B-cell epitopes for all ß-PRVBs sequences by Shotgun Proteomics combined with Protein-based Bioinformatics and IgE-reactive approaches. This study will increase our understanding of the molecular mechanisms whereby fish allergens elicit allergic reactions and will facilitate the design of new potential peptide vaccine candidates.

A lipidomic study on the regulation of inflammation and oxidative stress targeted by marine ω-3 PUFA and polyphenols in high-fat high-sucrose diets.

The ability of polyphenols to ameliorate potential oxidative damage of ω-3 PUFAs when they are consumed together and then, to enhance their potentially individual effects on metabolic health is discussed through the modulation of fatty acids profiling and the production of lipid mediators. For that, the effects of the combined consumption of fish oils and grape seed procyanidins on the inflammatory response and redox unbalance triggered by high-fat high-sucrose (HFHS) diets were studied in an animal model of Wistar rats. A standard diet was used as control. Results suggested that fish oils produced a replacement of ω-6 by ω-3 PUFAs in membranes and tissues, and consequently they improved inflammatory and oxidative stress parameters: favored the activity of 12/15-lipoxygenases on ω-3 PUFAs, enhanced glutathione peroxidases activity, modulated proinflammatory lipid mediators synthesis through the cyclooxygenase (COX) pathways and down-regulated the synthesis de novo of ARA leaded by Δ5 desaturase. Although polyphenols exerted an antioxidative and antiinflammatory effect in the standard diet, they were less effective to reduce inflammation in the HFHS dietary model. Contrary to the effect observed in the standard diet, polyphenols up-regulated COX pathways toward ω-6 proinflammatory eicosanoids as PGE2 and 11-HETE and decreased the detoxification of ω-3 hydroperoxides in the HFHS diet. As a result, additive effects between fish oils and polyphenols were found in the standard diet in terms of reducing inflammation and oxidative stress. However, in the HFHS diets, fish oils seem to be the one responsible for the positive effects found in the combined group.

Changes in liver proteins of rats fed standard and high-fat and sucrose diets induced by fish omega-3 PUFAs and their combination with grape polyphenols according to quantitative proteomics.

This study considered the physiological modulation of liver proteins due to the supplementation with fish oils under two dietary backgrounds: standard or high in fat and sucrose (HFHS), and their combination with grape polyphenols. By using a quantitative proteomics approach, we showed that the capacity of the supplements for regulating proteins depended on the diet; namely, 10 different proteins changed into standard diets, while 45 changed into the HFHS diets and only scarcely proteins were found altered in common. However, in both contexts, fish oils were the main regulatory force, although the addition of polyphenols was able to modulate some fish oils' effects. Moreover, we demonstrated the ability of fish oils and their combination with grape polyphenols in improving biochemical parameters and reducing lipogenesis and glycolysis enzymes, enhancing fatty acid beta-oxidation and insulin signaling and ameliorating endoplasmic reticulum stress and protein oxidation when they are included in an unhealthy diet.

Characterization of Foodborne Strains of Staphylococcus aureus by Shotgun Proteomics: Functional Networks, Virulence Factors and Species-Specific Peptide Biomarkers.

In the present work, we applied a shotgun proteomics approach for the fast and easy characterization of 20 different foodborne strains of Staphylococcus aureus (S. aureus), one of the most recognized foodborne pathogenic bacteria. A total of 644 non-redundant proteins were identified and analyzed via an easy and rapid protein sample preparation procedure. The results allowed the differentiation of several proteome datasets from the different strains (common, accessory, and unique datasets), which were used to determine relevant functional pathways and differentiate the strains into different Euclidean hierarchical clusters. Moreover, a predicted protein-protein interaction network of the foodborne S. aureus strains was created. The whole confidence network contains 77 nodes and 769 interactions. Most of the identified proteins were surface-associated proteins that were related to pathways and networks of energy, lipid metabolism and virulence. Twenty-seven virulence factors were identified, and most of them corresponded to autolysins, N-acetylmuramoyl-L-alanine amidases, phenol-soluble modulins, extracellular fibrinogen-binding proteins and virulence factor EsxA. Potential species-specific peptide biomarkers were screened. Twenty-one species-specific peptide biomarkers, belonging to eight different proteins (nickel-ABC transporter, N-acetylmuramoyl-L-alanine amidase, autolysin, clumping factor A, gram-positive signal peptide YSIRK, cysteine protease/staphopain, transcriptional regulator MarR, and transcriptional regulator Sar-A), were proposed to identify S. aureus. These results constitute the first major dataset of peptides and proteins of foodborne S. aureus strains. This repository may be useful for further studies, for the development of new therapeutic treatments for S. aureus food intoxications and for microbial source-tracking in foodstuffs.

Protein carbonylation associated to high-fat, high-sucrose diet and its metabolic effects.

The present research draws a map of the characteristic carbonylation of proteins in rats fed high-caloric diets with the aim of providing a new insight of the pathogenesis of metabolic diseases derived from the high consumption of fat and refined carbohydrates. Protein carbonylation was analyzed in plasma, liver and skeletal muscle of Sprague-Dawley rats fed a high-fat, high-sucrose (HFHS) diet by a proteomics approach based on carbonyl-specific fluorescence-labeling, gel electrophoresis and mass spectrometry. Oxidized proteins along with specific sites of oxidative damage were identified and discussed to illustrate the consequences of protein oxidation. The results indicated that long-term HFHS consumption increased protein oxidation in plasma and liver; meanwhile, protein carbonyls from skeletal muscle did not change. The increment of carbonylation by HFHS diet was singularly selective on specific target proteins: albumin from plasma and liver, and hepatic proteins such as mitochondrial carbamoyl-phosphate synthase (ammonia), mitochondrial aldehyde dehydrogenase, argininosuccinate synthetase, regucalcin, mitochondrial adenosine triphosphate synthase subunit beta, actin cytoplasmic 1 and mitochondrial glutamate dehydrogenase 1. The possible consequences that these specific protein carbonylations have on the excessive weight gain, insulin resistance and nonalcoholic fatty liver disease resulting from HFHS diet consumption are discussed.

Fast monitoring of species-specific peptide biomarkers using high-intensity-focused-ultrasound-assisted tryptic digestion and selected MS/MS ion monitoring.

A new strategy for the fast monitoring of peptide biomarkers is described. It is based on the use of accelerated in-solution trypsin digestions under an ultrasonic field provided by high-intensity focused ultrasound (HIFU) and the monitoring of several peptides by selected MS/MS ion monitoring in a linear ion trap mass spectrometer. The performance of the method was established for the unequivocal identification of all commercial fish species belonging to the Merlucciidae family. Using a particular combination of only 11 peptides, resulting from the HIFU-assisted tryptic digestion of the thermostable proteins parvalbumins, the workflow allowed the unequivocal identification of these closely related fish species in any seafood product, including processed and precooked products, in less than 2 h. The present strategy constitutes the fastest method for peptide biomarker monitoring. Its application for food quality control provides to the authorities an effective and rapid method of food authentication and traceability to guarantee the quality and safety to the consumers.

A strong genetic association between the tumor necrosis factor locus and proliferative vitreoretinopathy: the retina 4 project.

OBJECTIVE: To assess the genetic contribution to proliferative vitreoretinopathy (PVR) and report the strong association observed in the tumor necrosis factor (TNF) locus. DESIGN: As a component of The Retina 4 Project, a case-controlled, candidate gene association study in the TNF locus was conducted. PARTICIPANTS AND CONTROLS: Blood from 450 patients with (138 cases) and without (312 controls) post-rhegmatogenous retinal detachment (RD) PVR was genotyped to determine polymorphisms located in the TNFα gene. METHODS: Single nucleotide polymorphisms (SNPs) with correlation coefficients of ≥ 0.8 and a minor allelic frequency of ≥ 10% were studied. Functional SNPs or SNPs previously described in association with other inflammatory diseases were also added for analysis. The SNPlex Genotyping System (Applied Biosystems, Foster City, CA) was used for genotyping. Single nucleotide polymorphism and haplotype analyses were performed. Bioinformatic tools were used to evaluate those SNPs that were significantly associated. MAIN OUTCOME MEASURES: Single and haplotypic significant associations with PVR. RESULTS: A total of 11 common tag SNPs in the following genes were analyzed: lymphotoxin alpha (LTA), TNFα, leukocyte-specific transcript 1 (LST1), and the activating natural killer receptor p30 (NCR3). After permutation, there was a significant association in the non-synonymous polymorphism rs2229094(T→C) in the LTA gene (P = 0.0283), which encodes a cysteine to arginine change in the signal peptide. This marker was also present in all significant haplotypic associations and was not observed in any nonsignificant associations. When this SNP was analyzed using bioinformatic tools, the hydropathy profile changed, as well as the transmembrane region and the splicing site predictions. CONCLUSIONS: The strong association found in the rs2229094(T→C) of the LTA gene may indicate an important role of this polymorphism in the development of PVR. If supported in extended studies, the rs2229094(T→C) may have significant implications regarding the genetic risk of the retinal repairing process.

Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species.

The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyses, is proposed for the identification of shrimp species with commercial interest. MALDI-TOF peptide mass fingerprint from arginine kinase tryptic digests were used for the identification of seven commercial, closely related species of Decapoda shrimps. Further identification and characterization of these peptides was performed by CID on an ESI-IT instrument, database search and de novo sequence interpretation, paying special attention to differential, species-specific peptides. Fisheries and manufacturers may take advantage of this methodology as a tool for a rapid and effective seafood product identification and authentication, providing and guaranteeing the quality and safety of the foodstuffs to consumers.