Nutrients

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2 pages, 176 KiB

Open AccessEditorial

Protein Matters and Proteins Matter: Proteomics and Peptidomics in Nutrition and Health

by Martin Kussmann

Nutrients 2023, 15(12), 2762; https://doi.org/10.3390/nu15122762 - 15 Jun 2023

Cited by 1 | Viewed by 1548

Abstract

Protein matters and proteins matter in nutrition and health—why [...] Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

Research

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21 pages, 3460 KiB

Open AccessEditor’s ChoiceArticle

Exploring the Anti-Inflammatory Effect of Inulin by Integrating Transcriptomic and Proteomic Analyses in a Murine Macrophage Cell Model

by Federica Farabegoli, Francisco J. Santaclara, Daniel Costas, Mercedes Alonso, Ana G. Abril, Montserrat Espiñeira, Ignacio Ortea and Celina Costas

Nutrients 2023, 15(4), 859; https://doi.org/10.3390/nu15040859 - 8 Feb 2023

Cited by 10 | Viewed by 3830

Abstract

Inulin is a natural polysaccharide classified as a soluble fiber with demonstrated prebiotic activity. Prebiotics can reduce intestinal and systemic inflammation through modulation of the gut microflora and their metabolites. Additionally, extensive research is illuminating the role of macrophages in the interaction between [...] Read more.

Inulin is a natural polysaccharide classified as a soluble fiber with demonstrated prebiotic activity. Prebiotics can reduce intestinal and systemic inflammation through modulation of the gut microflora and their metabolites. Additionally, extensive research is illuminating the role of macrophages in the interaction between gut microbiota and many systemic inflammatory diseases. In this study, the anti-inflammatory properties of inulin were evaluated using a murine macrophage cell model (RAW 264.7) of inflammation, and the immunomodulatory mechanism was investigated using omics technologies. The cells underwent comprehensive transcriptomic and proteomic analyses to identify the mechanisms responsible for the observed anti-inflammatory phenotype. Functional analyses of these omics results revealed two potential mechanisms that may lead to an overall reduction in cytokine and chemokine transcription: the inhibition of the NF-κB signaling pathway, leading to the downregulation of proinflammatory factors such as COX2, and the promotion of the phase II defense protein Hmox1 via the Nrf2 pathway. This study provides promising targets for research on immune modulation by dietary fibers and offers new strategies for the design of functional ingredients, foods, and nutraceutical products, which could ultimately lead to personalized nutrition and improved consumer health. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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13 pages, 3284 KiB

Open AccessArticle

Getting Ready for Large-Scale Proteomics in Crop Plants

by Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer and Bernhard Kuster

Nutrients 2023, 15(3), 783; https://doi.org/10.3390/nu15030783 - 3 Feb 2023

Cited by 3 | Viewed by 4941

Abstract

Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In [...] Read more.

Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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14 pages, 3813 KiB

Open AccessArticle

The TriMet_DB: A Manually Curated Database of the Metabolic Proteins of Triticum aestivum

by Vincenzo Cunsolo, Antonella Di Francesco, Maria Gaetana Giovanna Pittalà, Rosaria Saletti and Salvatore Foti

Nutrients 2022, 14(24), 5377; https://doi.org/10.3390/nu14245377 - 18 Dec 2022

Cited by 1 | Viewed by 2337

Abstract

Mass-spectrometry-based wheat proteomics is challenging because the current interpretation of mass spectrometry data relies on public databases that are not exhaustive (UniProtKB/Swiss-Prot) or contain many redundant and poor or un-annotated entries (UniProtKB/TrEMBL). Here, we report the development of a manually curated database of [...] Read more.

Mass-spectrometry-based wheat proteomics is challenging because the current interpretation of mass spectrometry data relies on public databases that are not exhaustive (UniProtKB/Swiss-Prot) or contain many redundant and poor or un-annotated entries (UniProtKB/TrEMBL). Here, we report the development of a manually curated database of the metabolic proteins of Triticum aestivum (hexaploid wheat), named TriMet_DB (Triticum aestivum Metabolic Proteins DataBase). The manually curated TriMet_DB was generated in FASTA format so that it can be read directly by programs used to interpret the mass spectrometry data. Furthermore, the complete list of entries included in the TriMet_DB is reported in a freely available resource, which includes for each protein the description, the gene code, the protein family, and the allergen name (if any). To evaluate its performance, the TriMet_DB was used to interpret the MS data acquired on the metabolic protein fraction extracted from the cultivar MEC of Triticum aestivum. Data are available via ProteomeXchange with identifier PXD037709. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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13 pages, 2271 KiB

Open AccessArticle

Identification of Allergens in White- and Red-Fleshed Pitaya (Selenicereus undatus and Selenicereus costaricensis) Seeds Using Bottom-Up Proteomics Coupled with Immunoinformatics

by Mengzhen Hao, Xijiri, Ziyi Zhao and Huilian Che

Nutrients 2022, 14(9), 1962; https://doi.org/10.3390/nu14091962 - 7 May 2022

Cited by 7 | Viewed by 3134

Abstract

White-fleshed pitaya (Selenicereus undatus) and red-fleshed pitaya (Selenicereus costaricensis) are becoming increasingly popular because of their nutritional and medicinal benefits. However, in addition to their beneficial properties, allergy to pitaya fruits has occurred in daily life. In this study, [...] Read more.

White-fleshed pitaya (Selenicereus undatus) and red-fleshed pitaya (Selenicereus costaricensis) are becoming increasingly popular because of their nutritional and medicinal benefits. However, in addition to their beneficial properties, allergy to pitaya fruits has occurred in daily life. In this study, we investigated the protein profile of pitaya fruit seeds and focused on the most reactive proteins against immunoglobulin E (IgE) in sera from allergic patients by immunoblotting. A protein band of approximately 20 kDa displayed a clear reaction with the serum IgE. The protein bands of interest were excised, in-gel digested, and analyzed using liquid chromatography–tandem mass spectrometry (LC–MS/MS), followed by data searching against a restricted database (Caryophyllales in UniProtKB) for protein identification. Immunoinformatic tools were used to predict protein allergenicity. The potential allergens included cupin_1 and heat shock protein 70 (HSP70) in white-fleshed pitaya seeds, and cupin_1, heat shock protein 70, and heat shock protein sti1-like in red-fleshed pitaya seeds are potential allergens. The expression of potential allergens was further verified at the transcriptional level in the species of S. undatus and S. costaricensis. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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Review

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19 pages, 1892 KiB

Open AccessReview

Identifying and Analyzing Topic Clusters in a Nutri-, Food-, and Diet-Proteomic Corpus Using Machine Reading

by Jacqueline Pontes Monteiro, Melissa J. Morine, Fabio V. Ued and Jim Kaput

Nutrients 2023, 15(2), 270; https://doi.org/10.3390/nu15020270 - 5 Jan 2023

Viewed by 2666

Abstract

Nutrition affects the early stages of disease development, but the mechanisms remain poorly understood. High-throughput proteomic methods are being used to generate data and information on the effects of nutrients, foods, and diets on health and disease processes. In this report, a novel [...] Read more.

Nutrition affects the early stages of disease development, but the mechanisms remain poorly understood. High-throughput proteomic methods are being used to generate data and information on the effects of nutrients, foods, and diets on health and disease processes. In this report, a novel machine reading pipeline was used to identify all articles and abstracts on proteomics, diet, food, and nutrition in humans. The resulting proteomic corpus was further analyzed to produce seven clusters of “thematic” content defined as documents that have similar word content. Examples of publications from several of these clusters were then described in a similar way to a typical descriptive review. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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10 pages, 474 KiB

Open AccessReview

Prediction, Discovery, and Characterization of Plant- and Food-Derived Health-Beneficial Bioactive Peptides

by Martin Kussmann

Nutrients 2022, 14(22), 4810; https://doi.org/10.3390/nu14224810 - 14 Nov 2022

Cited by 8 | Viewed by 3219

Abstract

Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant and food sources, provide a plethora of molecular solutions to nutritionally actionable, chronic conditions. The spectrum of these conditions, [...] Read more.

Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant and food sources, provide a plethora of molecular solutions to nutritionally actionable, chronic conditions. The spectrum of these conditions, such as metabolic, immune, and gastrointestinal disorders, has changed with prolonged human life span, which should be matched with an appropriately extended health span, which would in turn favour more sustainable health care: “adding years to life and adding life to years”. To date, bioactive peptides have been undervalued and underexploited as food ingredients and drugs. The future of translational science on bioactive peptides—and natural bioactives in general—is being built on (a) systems-level rather than reductionist strategies for understanding their interdependent, and at times synergistic, functions; and (b) the leverage of artificial intelligence for prediction and discovery, thereby significantly reducing the time from idea and concept to finished solutions for consumers and patients. This new strategy follows the path from benefit definition via design to prediction and, eventually, validation and production. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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28 pages, 1637 KiB

Open AccessReview

Proteomics Characterization of Food-Derived Bioactive Peptides with Anti-Allergic and Anti-Inflammatory Properties

by Ana G. Abril, Manuel Pazos, Tomás G. Villa, Pilar Calo-Mata, Jorge Barros-Velázquez and Mónica Carrera

Nutrients 2022, 14(20), 4400; https://doi.org/10.3390/nu14204400 - 20 Oct 2022

Cited by 15 | Viewed by 4659

Abstract

Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial [...] Read more.

Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial action, mainly by the gastrointestinal microbiota from proteins present in food, originating from either vegetable or animal matter or by the action of different gastrointestinal proteases. Proteomics can play an important role in the identification of bioactive peptides. High-resolution mass spectrometry is the principal technique used to detect and identify different types of analytes present in complex mixtures, even when available at low concentrations. Moreover, proteomics may provide the characterization of epitopes to develop new food allergy vaccines and the use of immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. In addition, food-derived bioactive peptides have been investigated for their anti-inflammatory properties to provide safer alternatives to nonsteroidal anti-inflammatory drugs (NSAIDs). All these bioactive peptides can be a potential source of novel drugs and ingredients in food and pharmaceuticals. The following review is focused on food-derived bioactive peptides with antiallergic and anti-inflammatory properties and summarizes the new insights into the use of proteomics for their identification and quantification. Full article

(This article belongs to the Special Issue 'Protein Matters and Proteins Matter': Proteomics and Peptidomics in Nutrition and Health)

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