Advances in Functional Proteomics and Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 8624

Special Issue Editor

Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
Interests: proteomics; metabolomics; fluxomics; PTM dynamics

Special Issue Information

Dear Colleagues,

The interplay between metabolism, metabolites, proteins and posttranslational modification is well known to regulate cellular processes and can lead to disease development. Metabolomics and proteomics have become powerful and indispensable technologies in the life sciences. To understand molecular mechanisms and gain functional insights into biological systems, analytical approaches must be developed and applied to quantify the metabolome and proteome—ideally simultaneously, dynamically and spatially resolved, though this is not always possible. To achieve this ideal, strategies need to be developed at the level of sample preparation, mass spectrometric acquisition, bioinformatics analysis and computational modeling, especially data integration.

This Special Issue collects papers reporting on the recent development and application of innovative approaches in the fields of (simultaneous) metabolomics, proteomics, and fluxomics, including computational omics, to provide new insights into the molecular aspects of pathophysiology and biochemistry in health and disease.

Dr. Marcel Kwiatkowski
Guest Editor

Manuscript Submission Information

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolomics
  • proteomics
  • fluxomics
  • spatial proteomics and metabolomics
  • computational omics
  • multi-omics data integration
  • analytical methods
  • statistical methods
  • biomarkers

Published Papers (5 papers)

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Research

16 pages, 1317 KiB  
Article
Changes in a Protein Profile Can Account for the Altered Phenotype of the Yeast Saccharomyces cerevisiae Mutant Lacking the Copper-Zinc Superoxide Dismutase
by Magdalena Kwolek-Mirek, Aleksandra Dubicka-Lisowska, Sabina Bednarska, Renata Zadrag-Tecza and Pawel Kaszycki
Metabolites 2023, 13(3), 459; https://doi.org/10.3390/metabo13030459 - 22 Mar 2023
Cited by 1 | Viewed by 1330
Abstract
Copper-zinc superoxide dismutase (SOD1) is an antioxidant enzyme that catalyzes the disproportionation of superoxide anion to hydrogen peroxide and molecular oxygen (dioxygen). The yeast Saccharomyces cerevisiae lacking SOD1sod1) is hypersensitive to the superoxide anion and displays a number of oxidative [...] Read more.
Copper-zinc superoxide dismutase (SOD1) is an antioxidant enzyme that catalyzes the disproportionation of superoxide anion to hydrogen peroxide and molecular oxygen (dioxygen). The yeast Saccharomyces cerevisiae lacking SOD1sod1) is hypersensitive to the superoxide anion and displays a number of oxidative stress-related alterations in its phenotype. We compared proteomes of the wild-type strain and the Δsod1 mutant employing two-dimensional gel electrophoresis and detected eighteen spots representing differentially expressed proteins, of which fourteen were downregulated and four upregulated. Mass spectrometry-based identification enabled the division of these proteins into functional classes related to carbon metabolism, amino acid and protein biosynthesis, nucleotide biosynthesis, and metabolism, as well as antioxidant processes. Detailed analysis of the proteomic data made it possible to account for several important morphological, biochemical, and physiological changes earlier observed for the SOD1 mutation. An example may be the proposed additional explanation for methionine auxotrophy. It is concluded that protein comparative profiling of the Δsod1 yeast may serve as an efficient tool in the elucidation of the mutation-based systemic alterations in the resultant S. cerevisiae phenotype. Full article
(This article belongs to the Special Issue Advances in Functional Proteomics and Metabolomics)
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18 pages, 1599 KiB  
Article
Bioactive Metabolite Survey of Actinobacteria Showing Plant Growth Promoting Traits to Develop Novel Biofertilizers
by Teresa Faddetta, Giulia Polito, Loredana Abbate, Pasquale Alibrandi, Marcello Zerbo, Ciro Caldiero, Chiara Reina, Guglielmo Puccio, Edoardo Vaccaro, Maria Rosa Abenavoli, Vincenzo Cavalieri, Francesco Mercati, Antonio Palumbo Piccionello and Giuseppe Gallo
Metabolites 2023, 13(3), 374; https://doi.org/10.3390/metabo13030374 - 02 Mar 2023
Cited by 6 | Viewed by 2139
Abstract
The use of chemical fertilizers and pesticides has caused harmful impacts on the environment with the increase in economic burden. Biofertilizers are biological products containing living microorganisms capable of improving plant growth through eco-friendly mechanisms. In this work, three actinobacterial strains Streptomyces violaceoruber [...] Read more.
The use of chemical fertilizers and pesticides has caused harmful impacts on the environment with the increase in economic burden. Biofertilizers are biological products containing living microorganisms capable of improving plant growth through eco-friendly mechanisms. In this work, three actinobacterial strains Streptomyces violaceoruber, Streptomyces coelicolor, and Kocuria rhizophila were characterized for multiple plant growth promoting (PGP) traits such as indole acetic acid production, phosphate solubilization, N2-fixation, and drought and salt tolerance. Then, these strains were investigated for their secreted and cellular metabolome, revealing a rich arsenal of bioactive molecules, including antibiotics and siderophores, with S. violaceoruber being the most prolific strain. Furthermore, the in vivo assays, performed on tomato (Solanum lycopersicum L.), resulted in an improved germination index and the growth of seedlings from seeds treated with PGP actinobacteria, with a particular focus on S. violaceoruber cultures. In particular, this last strain, producing volatile organic compounds having antimicrobial activity, was able to modulate volatilome and exert control on the global DNA methylation of tomato seedlings. Thus, these results, confirming the efficacy of the selected actinobacteria strains in promoting plant growth and development by producing volatile and non-volatile bioactive molecules, can promote eco-friendly alternatives in sustainable agriculture. Full article
(This article belongs to the Special Issue Advances in Functional Proteomics and Metabolomics)
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15 pages, 2194 KiB  
Article
Data Independent Acquisition Reveals In-Depth Serum Proteome Changes in Canine Leishmaniosis
by Franjo Martinković, Marin Popović, Ozren Smolec, Vladimir Mrljak, Peter David Eckersall and Anita Horvatić
Metabolites 2023, 13(3), 365; https://doi.org/10.3390/metabo13030365 - 28 Feb 2023
Viewed by 1145
Abstract
Comprehensive profiling of serum proteome provides valuable clues of health status and pathophysiological processes, making it the main strategy in biomarker discovery. However, the high dynamic range significantly decreases the number of detectable proteins, obstructing the insights into the underlying biological processes. To [...] Read more.
Comprehensive profiling of serum proteome provides valuable clues of health status and pathophysiological processes, making it the main strategy in biomarker discovery. However, the high dynamic range significantly decreases the number of detectable proteins, obstructing the insights into the underlying biological processes. To circumvent various serum enrichment methods, obtain high-quality proteome wide information using the next-generation proteomic, and study host response in canine leishmaniosis, we applied data-independent acquisition mass spectrometry (DIA-MS) for deep proteomic profiling of clinical samples. The non-depleted serum samples of healthy and naturally Leishmania-infected dogs were analyzed using the label-free 60-min gradient sequential window acquisition of all theoretical mass spectra (SWATH-MS) method. As a result, we identified 554 proteins, 140 of which differed significantly in abundance. Those were included in lipid metabolism, hematological abnormalities, immune response, and oxidative stress, providing valuable information about the complex molecular basis of the clinical and pathological landscape in canine leishmaniosis. Our results show that DIA-MS is a method of choice for understanding complex pathophysiological processes in serum and serum biomarker development. Full article
(This article belongs to the Special Issue Advances in Functional Proteomics and Metabolomics)
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14 pages, 2719 KiB  
Article
Assessing the Potential of Untargeted SWATH Mass Spectrometry-Based Metabolomics to Differentiate Closely Related Exposures in Observational Studies
by Frank Klont, Piotr Sosnowski, Daan Kremer, Tim J. Knobbe, Ron Bonner, Hans Blokzijl, Rinse K. Weersma, Stephan J. L. Bakker, TransplantLines Investigators, Eelko Hak, Daan J. Touw and Gérard Hopfgartner
Metabolites 2022, 12(10), 942; https://doi.org/10.3390/metabo12100942 - 04 Oct 2022
Cited by 2 | Viewed by 1459
Abstract
Mass spectrometry (MS) is increasingly used in clinical studies to obtain molecular evidence of chemical exposures, such as tobacco smoke, alcohol, and drugs. This evidence can help verify clinical data retrieved through anamnesis or questionnaires and may provide insights into unreported exposures, for [...] Read more.
Mass spectrometry (MS) is increasingly used in clinical studies to obtain molecular evidence of chemical exposures, such as tobacco smoke, alcohol, and drugs. This evidence can help verify clinical data retrieved through anamnesis or questionnaires and may provide insights into unreported exposures, for example those classified as the same despite small but possibly relevant chemical differences or due to contaminants in reported exposure compounds. Here, we aimed to explore the potential of untargeted SWATH metabolomics to differentiate such closely related exposures. This data-independent acquisition MS-based profiling technique was applied to urine samples of 316 liver and 570 kidney transplant recipients from the TransplantLines Biobank and Cohort Study (NCT03272841), where we focused on the immunosuppressive drug mycophenolate, which is either supplied as a morpholino-ester prodrug or as an enteric-coated product, the illicit drug cocaine, which is usually supplied as an adulterated product, and the proton pump inhibitors omeprazole and esomeprazole. Based on these examples, we found that untargeted SWATH metabolomics has considerable potential to identify different (unreported) exposure or co-exposure metabolites and may determine variations in their abundances. We also found that these signals alone may sometimes be unable to distinguish closely related exposures, and enhancement of differentiation, for example by integration with pharmacogenomics data, is needed. Full article
(This article belongs to the Special Issue Advances in Functional Proteomics and Metabolomics)
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15 pages, 2432 KiB  
Article
Proteomics and Metabolomics Profiling of Pork Exudate Reveals Meat Spoilage during Storage
by Fan Zhao, Zhenqian Wei, Yun Bai, Chunbao Li, Guanghong Zhou, Karsten Kristiansen and Chong Wang
Metabolites 2022, 12(7), 570; https://doi.org/10.3390/metabo12070570 - 21 Jun 2022
Cited by 6 | Viewed by 1938
Abstract
Previous studies have evaluated pork quality by omics methods. However, proteomics coupled with metabolomics to investigate pork freshness by using pork exudates has not been reported. This study determined the changes in the profiles of peptides and metabolites in exudates from pork stored [...] Read more.
Previous studies have evaluated pork quality by omics methods. However, proteomics coupled with metabolomics to investigate pork freshness by using pork exudates has not been reported. This study determined the changes in the profiles of peptides and metabolites in exudates from pork stored at different temperatures (25, 10, 4, and −2 °C). Multivariate statistical analysis revealed similar changes in profiles in exudates collected from pork stored at −2 and 4 °C, and additional changes following storage at higher temperatures. We identified peptides from 7 proteins and 30 metabolites differing in abundance between fresh and spoiled pork. Significant correlations between pork quality and most of the peptides from these 7 proteins and 30 metabolites were found. The present study provides insight into changes in the peptide and metabolite profiles of exudates from pork during storage at different temperatures, and our analysis suggests that such changes can be used as markers of pork spoilage. Full article
(This article belongs to the Special Issue Advances in Functional Proteomics and Metabolomics)
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