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Applied Proteomics in 'One Health'. Proteomes 2021; 9:proteomes9030031. [PMID: 34208880 PMCID: PMC8293331 DOI: 10.3390/proteomes9030031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, identification of pathogens and toxins, study of product traits and characterisation of proteins in food safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, shedding light on biomarker research and promoting the One Health concept.
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Du GF, Zheng YD, Chen J, He QY, Sun X. Novel Mechanistic Insights into Bacterial Fluoroquinolone Resistance. J Proteome Res 2019; 18:3955-3966. [DOI: 10.1021/acs.jproteome.9b00410] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Gao-Fei Du
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yun-Dan Zheng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Chen
- Department of Clinical Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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Correia S, Hébraud M, Chafsey I, Chambon C, Viala D, Torres C, Caniça M, Capelo JL, Poeta P, Igrejas G. Subproteomic signature comparison of in vitro selected fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B. Expert Rev Proteomics 2017; 14:941-961. [PMID: 28871888 DOI: 10.1080/14789450.2017.1375856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Fluoroquinolone resistance in nontyphoidal Salmonella is a situation of serious and international concern, particularly in S. Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. METHODS Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). CONCLUSION Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
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Affiliation(s)
- Susana Correia
- a Functional Genomics and Proteomics Unit , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,b Department of Genetics and Biotechnology , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Veterinary Science Department , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| | - Michel Hébraud
- e UR454 Microbiology , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France.,f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Ingrid Chafsey
- e UR454 Microbiology , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Christophe Chambon
- f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Didier Viala
- f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Carmen Torres
- g Área de Bioquímica y Biología Molecular , Universidad de La Rioja , Logroño , Spain
| | - Manuela Caniça
- h National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases , National Health Institute Doutor Ricardo Jorge (INSA) , Lisbon , Portugal
| | - José Luis Capelo
- d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal.,i Faculty of Sciences and Technology , ProteoMass Scientific Society , Caparica , Portugal
| | - Patrícia Poeta
- c Veterinary Science Department , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| | - Gilberto Igrejas
- a Functional Genomics and Proteomics Unit , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,b Department of Genetics and Biotechnology , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
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Das D, Rameshbabu AP, Patra P, Ghosh P, Dhara S, Pal S. Biocompatible amphiphilic microgel derived from dextrin and poly(methyl methacrylate) for dual drugs carrier. POLYMER 2016. [DOI: 10.1016/j.polymer.2016.11.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Proteomic Analyses of Chlorhexidine Tolerance Mechanisms in Delftia acidovorans Biofilms. mSphere 2016; 1:mSphere00017-15. [PMID: 27303691 PMCID: PMC4863599 DOI: 10.1128/msphere.00017-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/04/2015] [Indexed: 01/02/2023] Open
Abstract
Protein expression and fatty acid profiles of biofilm cells of chlorhexidine-tolerant Delftia acidovorans (MIC = 15 µg/ml) and its chlorhexidine-susceptible mutant (MIC = 1 µg/ml) were investigated. The chlorhexidine-susceptible mutant (MT51) was derived from the parental strain (WT15) using Tn5 transposon mutagenesis. The disrupted gene was identified as tolQ, a component of the tolQRAB gene cluster known to be involved in outer membrane stability. Proteomic responses of biofilm cells were compared by differential in-gel electrophoresis following exposure to chlorhexidine at sub-MIC (10 µg/ml) and above-MIC (30 µg/ml) concentrations. Numerous changes in protein abundance were observed in biofilm cells following chlorhexidine exposure, suggesting that molecular changes occurred during adaptation to chlorhexidine. Forty proteins showing significant differences (≥1.5-fold; P < 0.05) were identified by mass spectrometry and were associated with various functions, including amino acid and lipid biosynthesis, protein translation, energy metabolism, and stress-related functions (e.g., GroEL, aspartyl/glutamyl-tRNA amidotransferase, elongation factor Tu, Clp protease, and hydroxymyristoyl-ACP dehydratase). Several proteins involved in fatty acid synthesis were affected by chlorhexidine, in agreement with fatty acid analysis, wherein chlorhexidine-induced shifts in the fatty acid profile were observed in the chlorhexidine-tolerant cells, primarily the cyclic fatty acids. Transmission electron microscopy revealed more prominent changes in the cell envelope of chlorhexidine-susceptible MT51 cells. This study suggests that multiple mechanisms involving both the cell envelope (and likely TolQ) and panmetabolic regulation play roles in chlorhexidine tolerance in D. acidovorans. IMPORTANCE Delftia acidovorans has been associated with a number of serious infections, including bacteremia, empyema, bacterial endocarditis, and ocular and urinary tract infections. It has also been linked with a variety of surface-associated nosocomial infections. Biofilm-forming antimicrobial-resistant D. acidovorans strains have also been isolated, including ones displaying resistance to the common broad-spectrum agent chlorhexidine. The mechanisms of chlorhexidine resistance in D. acidovorans are not known; hence, a chlorhexidine-susceptible mutant of the tolerant wild-type strain was obtained using transposon mutagenesis, and the proteome and ultrastructural changes of both strains were compared under chlorhexidine challenge.
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Proteome studies of bacterial antibiotic resistance mechanisms. J Proteomics 2014; 97:88-99. [DOI: 10.1016/j.jprot.2013.10.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 10/12/2013] [Accepted: 10/19/2013] [Indexed: 01/10/2023]
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Lima TB, Pinto MFS, Ribeiro SM, de Lima LA, Viana JC, Gomes Júnior N, Cândido EDS, Dias SC, Franco OL. Bacterial resistance mechanism: what proteomics can elucidate. FASEB J 2013; 27:1291-303. [PMID: 23349550 DOI: 10.1096/fj.12-221127] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibiotics are important therapeutic agents commonly used for the control of bacterial infectious diseases; however, resistance to antibiotics has become a global public health problem. Therefore, effective therapy in the treatment of resistant bacteria is necessary and, to achieve this, a detailed understanding of mechanisms that underlie drug resistance must be sought. To fill the multiple gaps that remain in understanding bacterial resistance, proteomic tools have been used to study bacterial physiology in response to antibiotic stress. In general, the global analysis of changes in the protein composition of bacterial cells in response to treatment with antibiotic agents has made it possible to construct a database of proteins involved in the process of resistance to drugs with similar mechanisms of action. In the past few years, progress in using proteomic tools has provided the most realistic picture of the infective process, since these tools detect the end products of gene biosynthetic pathways, which may eventually determine a biological phenotype. In most bacterial species, alterations occur in energy and nitrogen metabolism regulation; glucan biosynthesis is up-regulated; amino acid, protein, and nucleotide synthesis is affected; and various proteins show a stress response after exposing these microorganisms to antibiotics. These issues have been useful in identifying targets for the development of novel antibiotics and also in understanding, at the molecular level, how bacteria resist antibiotics.
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Affiliation(s)
- Thais Bergamin Lima
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil
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Sá-Correia I, Teixeira MC. 2D electrophoresis-based expression proteomics: a microbiologist's perspective. Expert Rev Proteomics 2011; 7:943-53. [PMID: 21142894 DOI: 10.1586/epr.10.76] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist's perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of Pseudomonas strains to environmental toxicants are presented as case studies.
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Affiliation(s)
- Isabel Sá-Correia
- Institute for Biotechnology and Bioengineering, Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Technical University of Lisbon, Av. Rovisco Pais, Lisbon, Portugal.
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Varhimo E, Varmanen P, Fallarero A, Skogman M, Pyörälä S, Iivanainen A, Sukura A, Vuorela P, Savijoki K. Alpha- and β-casein components of host milk induce biofilm formation in the mastitis bacterium Streptococcus uberis. Vet Microbiol 2010; 149:381-9. [PMID: 21130586 DOI: 10.1016/j.vetmic.2010.11.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 10/15/2010] [Accepted: 11/08/2010] [Indexed: 12/01/2022]
Abstract
Streptococcus uberis is an environmental udder pathogen that infects cattle and can cause persistent intramammary infection (IMI), despite the fact that isolates are mainly susceptible to antibiotics. As biofilm growth can cause persistent infection, the ability of ten S. uberis isolates from clinical and subclinical IMIs to form biofilms on the polystyrene surface of a conventional 96-microplates model was examined. Biofilm formation was judged by different staining methods (crystal violet and resazurin) and by atomic force and fluorescence microscopy. These analyses revealed that two out of ten S. uberis strains tested were able to form biofilms. Upon treatment with Proteinase K, biofilms of S. uberis were completely disintegrated, which indicates that biofilm formation is protein-mediated in these strains. Addition of trace amounts of milk, the natural growth medium of S. uberis, significantly increased biofilm formation by most of the strains initially classified as non-biofilm producers. Alpha-casein and β-casein were the primary inducers of biofilm growth, and casein degradation by serine protease activity was required to achieve maximal biofilm production. These results suggest that the extracellular proteolytic activity of S. uberis contributes to an increased biofilm formation. Such a mode of growth induced by host proteins might help to explain the persistence of IMIs caused by this pathogen.
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Affiliation(s)
- Emilia Varhimo
- Department of Veterinary Biosciences, P.O. Box 66, University of Helsinki, FI-00014, Helsinki, Finland
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Lin XM, Yang JN, Peng XX, Li H. A Novel Negative Regulation Mechanism of Bacterial Outer Membrane Proteins in Response to Antibiotic Resistance. J Proteome Res 2010; 9:5952-9. [DOI: 10.1021/pr100740w] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xiang-Min Lin
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People’s Republic of China
| | - Jun-Ning Yang
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People’s Republic of China
| | - Xuan-Xian Peng
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People’s Republic of China
| | - Hui Li
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People’s Republic of China
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