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Food Safety - Transcriptomics and Proteomics

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 13346

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Dr. Mónica Carrera

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Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
Interests: proteomics; mass spectrometry; tandem mass spectrometry; proteins; food science and technology; molecular biology; food safety; confocal microscopy; food quality; food and nutrition
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Dear Colleagues,

Food safety refers to routines in the preparation, handling and storage of food meant to prevent foodborne illness and injury. From farm to fork, food products may encounter any number of health hazards through the supply chain. In this sense, foodborne diseases caused by bacteria, viruses and parasites cause considerable disease burden worldwide. Moreover, food allergy prevalence has also been increasing over the last few decades.

Recent successes of Transcriptomics and Proteomics methodologies make them favorable strategies for food safety studies, where research institutions, agencies, industries and regulatory laboratories are combining efforts to acquire the needed knowledge and to guarantee the food safety to the consumers. The power of these methodologies allows the food authenticity, detection of food parasites, food microorganisms detection, detection of food allergens, food processing analysis, bioinformatics analysis of food components, by-products safety and systems biology studies, among others.

In this special issue we would like to invite all of you, experts, and beginners in the field of Transcriptomics and Proteomics, to contribute to this Special Issue with your ideas for accelerating the implementation of omics procedures in Food Safety from a research point of view and clinical practice.

Dr. Mónica Carrera
Guest Editor

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

transcriptome
proteome
food safety
foodborne
food allergy
food microbiota
mass spectrometry

Related Special Issue

Marine Omics in International Journal of Molecular Sciences

Published Papers (7 papers)

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Editorial

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5 pages, 233 KiB

Open AccessEditorial

Food Safety—Transcriptomics and Proteomics

by Mónica Carrera

Int. J. Mol. Sci. 2023, 24(24), 17127; https://doi.org/10.3390/ijms242417127 - 05 Dec 2023

Viewed by 826

Abstract

Food safety is a critical aspect of public health and involves the handling, preparation, and storage of food to avoid contamination and foodborne illnesses [...] Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

Research

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17 pages, 3333 KiB

Open AccessArticle

Quantitative Proteomic Analysis on the Slightly Acidic Electrolyzed Water Triggered Viable but Non-Culturable Listeria monocytogenes

by Hsin-Yi Chang, Chin-Ying Gui, Tsui-Chin Huang, Yen-Con Hung and Tai-Yuan Chen

Int. J. Mol. Sci. 2023, 24(13), 10616; https://doi.org/10.3390/ijms241310616 - 25 Jun 2023

Cited by 1 | Viewed by 1766

Abstract

This study undertakes a comprehensive exploration of the impact of slightly acidic electrolyzed water (SAEW) on Listeria monocytogenes, a common foodborne pathogen, with a particular focus on understanding the molecular mechanisms leading to the viable but nonculturable (VBNC) state. Given the widespread application of SAEW as an effective disinfectant in the food industry, uncovering these molecular pathways is crucial for improving food safety measures. We employed tandem mass tags (TMT), labeling proteomic techniques and LC-MS/MS to identify differentially expressed proteins under two doses of SAEW conditions. We indicated 203 differential expressed proteins (DEPs), including 78 up-regulated and 125 down-regulated DEPs. The functional enrichment analysis of these proteins indicated that ribosomes, biosynthesis of secondary metabolites, and aminoacyl-tRNA biosynthesis were enriched functions affected by SAEW. Further, we delved into the role of protein chlorination, a potential consequence of reactive chlorine species generated during the SAEW production process, by identifying 31 chlorinated peptides from 22 proteins, with a dominant sequence motif of Rxxxxx[cY] and functionally enriched in translation. Our findings suggest that SAEW might prompt alterations in the protein translation process and trigger compensatory ribosome biosynthesis. However, an imbalance in the levels of elongation factors and AARSs could hinder recovery, leading to the VBNC state. This research carries substantial implications for food safety and sanitation, as it adds to our understanding of the SAEW-induced VBNC state in L. monocytogenes and offers potential strategies for its control. Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

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23 pages, 4097 KiB

Open AccessArticle

Comparative Anatomical and Transcriptomics Reveal the Larger Cell Size as a Major Contributor to Larger Fruit Size in Apricot

by Mengzhen Huang, Xuchun Zhu, Haikun Bai, Chu Wang, Ningning Gou, Yujing Zhang, Chen Chen, Mingyu Yin, Lin Wang and Tana Wuyun

Int. J. Mol. Sci. 2023, 24(10), 8748; https://doi.org/10.3390/ijms24108748 - 14 May 2023

Cited by 4 | Viewed by 1681

Abstract

Fruit size is one of the essential quality traits and influences the economic value of apricots. To explore the underlying mechanisms of the formation of differences in fruit size in apricots, we performed a comparative analysis of anatomical and transcriptomics dynamics during fruit growth and development in two apricot cultivars with contrasting fruit sizes (large-fruit Prunus armeniaca ‘Sungold’ and small-fruit P. sibirica ‘F43’). Our analysis identified that the difference in fruit size was mainly caused by the difference in cell size between the two apricot cultivars. Compared with ‘F43’, the transcriptional programs exhibited significant differences in ‘Sungold’, mainly in the cell expansion period. After analysis, key differentially expressed genes (DEGs) most likely to influence cell size were screened out, including genes involved in auxin signal transduction and cell wall loosening mechanisms. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that PRE6/bHLH was identified as a hub gene, which interacted with 1 TIR1, 3 AUX/IAAs, 4 SAURs, 3 EXPs, and 1 CEL. Hence, a total of 13 key candidate genes were identified as positive regulators of fruit size in apricots. The results provide new insights into the molecular basis of fruit size control and lay a foundation for future breeding and cultivation of larger fruits in apricot. Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

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23 pages, 2479 KiB

Open AccessArticle

Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria

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

Int. J. Mol. Sci. 2023, 24(9), 7704; https://doi.org/10.3390/ijms24097704 - 22 Apr 2023

Cited by 4 | Viewed by 1637

Abstract

Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs. Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

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19 pages, 3928 KiB

Open AccessArticle

Identifying Natural Bioactive Peptides from the Common Octopus (Octopus vulgaris Cuvier, 1797) Skin Mucus By-Products Using Proteogenomic Analysis

by Sara Pérez-Polo, Md Abdus Shukur Imran, Sonia Dios, Jaime Pérez, Lorena Barros, Mónica Carrera and Camino Gestal

Int. J. Mol. Sci. 2023, 24(8), 7145; https://doi.org/10.3390/ijms24087145 - 12 Apr 2023

Cited by 4 | Viewed by 1901

Abstract

The common octopus is a cephalopod species subject to active fisheries, with great potential in the aquaculture and food industry, and which serves as a model species for biomedical and behavioral studies. The analysis of the skin mucus allows us to study their health in a non-invasive way, by using a hardly exploited discard of octopus in the fishing sector. A shotgun proteomics approach combined with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using an Orbitrap-Elite instrument was used to create a reference dataset from octopus skin mucus. The final proteome compilation was investigated by integrated in-silico studies, including Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, network studies, and prediction and characterization analysis of potential bioactive peptides. This work presents the first proteomic analysis of the common octopus skin mucus proteome. This library was created by merging 5937 identified spectra of 2038 different peptides. A total of 510 non-redundant proteins were identified. Obtained results show proteins closely related to the defense, which highlight the role of skin mucus as the first barrier of defense and the interaction with the environment. Finally, the potential of the bioactive peptides with antimicrobial properties, and their possible application in biomedicine, pharmaceutical, and nutraceutical industry was addressed. Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

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12 pages, 1173 KiB

Open AccessArticle

Rapid Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from Foodstuffs

by Marcos Quintela-Baluja, Kelly Jobling, David W. Graham, Shamas Tabraiz, Burhan Shamurad, Mohamed Alnakip, Karola Böhme, Jorge Barros-Velázquez, Mónica Carrera and Pilar Calo-Mata

Int. J. Mol. Sci. 2022, 23(22), 13830; https://doi.org/10.3390/ijms232213830 - 10 Nov 2022

Cited by 3 | Viewed by 2093

Abstract

Enterococcus belongs to a group of microorganisms known as lactic acid bacteria (LAB), which constitute a broad heterogeneous group of generally food-grade microorganisms historically used in food preservation. Enterococci live as commensals of the gastrointestinal tract of warm-blooded animals, although they also are present in food of animal origin (milk, cheese, fermented sausages), vegetables, and plant materials because of their ability to survive heat treatments and adverse environmental conditions. The biotechnological traits of enterococci can be applied in the food industry; however, the emergence of enterococci as a cause of nosocomial infections makes their food status uncertain. Recent advances in high-throughput sequencing allow the subtyping of bacterial pathogens, but it cannot reflect the temporal dynamics and functional activities of microbiomes or bacterial isolates. Moreover, genetic analysis is based on sequence homologies, inferring functions from databases. Here, we used an end-to-end proteomic workflow to rapidly characterize two bacteriocin-producing Enterococcus faecium (Efm) strains. The proteome analysis was performed with liquid chromatography coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) for high-throughput and high-resolution characterization of bacterial proteins. Thus, we identified almost half of the proteins predicted in the bacterial genomes (>1100 unique proteins per isolate), including quantifying proteins conferring resistance to antibiotics, heavy metals, virulence factors, and bacteriocins. The obtained proteomes were annotated according to function, resulting in 22 complete KEGG metabolic pathway modules for both strains. The workflow used here successfully characterized these bacterial isolates and showed great promise for determining and optimizing the bioengineering and biotechnology properties of other LAB strains in the food industry. Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

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24 pages, 974 KiB

Open AccessArticle

Proteomic Characterization of Virulence Factors and Related Proteins in Enterococcus Strains from Dairy and Fermented Food Products

by Ana G. Abril, Marcos Quintela-Baluja, Tomás G. Villa, Pilar Calo-Mata, Jorge Barros-Velázquez and Mónica Carrera

Int. J. Mol. Sci. 2022, 23(18), 10971; https://doi.org/10.3390/ijms231810971 - 19 Sep 2022

Cited by 9 | Viewed by 2708

Abstract

Enterococcus species are Gram-positive bacteria that are normal gastrointestinal tract inhabitants that play a beneficial role in the dairy and meat industry. However, Enterococcus species are also the causative agents of health care-associated infections that can be found in dairy and fermented food products. Enterococcal infections are led by strains of Enterococcus faecalis and Enterococcus faecium, which are often resistant to antibiotics and biofilm formation. Enterococci virulence factors attach to host cells and are also involved in immune evasion. LC-MS/MS-based methods offer several advantages compared with other approaches because one can directly identify microbial peptides without the necessity of inferring conclusions based on other approaches such as genomics tools. The present study describes the use of liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to perform a global shotgun proteomics characterization for opportunistic pathogenic Enterococcus from different dairy and fermented food products. This method allowed the identification of a total of 1403 nonredundant peptides, representing 1327 proteins. Furthermore, 310 of those peptides corresponded to proteins playing a direct role as virulence factors for Enterococcus pathogenicity. Virulence factors, antibiotic sensitivity, and proper identification of the enterococcal strain are required to propose an effective therapy. Data are available via ProteomeXchange with identifier PXD036435. Label-free quantification (LFQ) demonstrated that the majority of the high-abundance proteins corresponded to E. faecalis species. Therefore, the global proteomic repository obtained here can be the basis for further research into pathogenic Enterococcus species, thus facilitating the development of novel therapeutics. Full article

(This article belongs to the Special Issue Food Safety - Transcriptomics and Proteomics)

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