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Monteiro R, Chafsey I, Ageorges V, Leroy S, Chambon C, Hébraud M, Livrelli V, Pizza M, Pezzicoli A, Desvaux M. The Secretome landscape of Escherichia coli O157:H7: Deciphering the cell-surface, outer membrane vesicle and extracellular subproteomes. J Proteomics 2020; 232:104025. [PMID: 33160105 DOI: 10.1016/j.jprot.2020.104025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 12/14/2022]
Abstract
Among diarrheagenic E. coli (DEC), enterohaemorrhagic E. coli (EHEC) are the most virulent anthropozoonotic agents. The ability of bacterial cells to functionally interact with their surrounding essentially relies on the secretion of different protein effectors. To experimentally determine the repertoire of extracytoproteins in E. coli O157:H7, a subproteomic analysis was performed not only considering the extracellular milieu but the cell surface and outer membrane vesicles. Following a secretome-based approach, the proteins trafficking from the interior to the exterior of the cell were depicted considering cognate protein transport systems and subcellular localisation. Label-free quantitative analysis of the proteosurfaceome, proteovesiculome and exoproteome from E. coli O157:H7 grown in three different nutrient media revealed differential protein expression profiles and allowed defining the core and variant subproteomes. Network analysis further revealed the higher abundance of some protein clusters in chemically defined medium over rich complex medium, especially related to some outer membrane proteins, ABC transport and Type III secretion systems. This first comprehensive study of the EHEC secretome unravels the profound influence of environmental conditions on the extracytoplasmic proteome, provides new insight in the physiology of E. coli O157:H7 and identifies potentially important molecular targets for the development of preventive strategies against EHEC/STEC. SIGNIFICANCE: Escherichia coli O157:H7 is responsible for severe diarrhoea especially in young children. Despite years of investigations, the global view of the extracytoplasmic proteins expressed in this microorganism was eluded. To provide the first comprehensive view of the secretome landscape of E. coli O157:H7, the exoproteome, proteosurfaceome and proteovesiculome were profiled using growth conditions most likely to induce changes in bacterial protein secretion. The profound influence of growth conditions on the extracytoplasmic proteome was unravelled and allowed identifying the core and variant subproteomes. Besides new insight in the physiology of enterohaemorrhagic E. coli, these proteins potentially constitute important molecular targets for the development of preventive strategies.
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Affiliation(s)
- Ricardo Monteiro
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France; GSK, Siena, Italy
| | - Ingrid Chafsey
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Valentin Ageorges
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Christophe Chambon
- INRAE, Plate-Forme d'Exploration du Métabolisme, QuaPA, F-63122 Saint-Genès Champanelle, France
| | - Michel Hébraud
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France; INRAE, Plate-Forme d'Exploration du Métabolisme, QuaPA, F-63122 Saint-Genès Champanelle, France
| | - Valérie Livrelli
- Université Clermont-Auvergne, INSERM, INRAE, M2ISH, F-63000 Clermont-ferrand, France
| | | | | | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.
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Kailasa SK, Koduru JR, Park TJ, Wu HF, Lin YC. Progress of electrospray ionization and rapid evaporative ionization mass spectrometric techniques for the broad-range identification of microorganisms. Analyst 2019; 144:1073-1103. [DOI: 10.1039/c8an02034e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electrospray ionization and rapid evaporative ionization mass spectrometric techniques have attracted much attention in the identification of microorganisms, and in the diagnosis of bacterial infections from clinical samples.
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Affiliation(s)
- Suresh Kumar Kailasa
- Department of Applied Chemistry
- S. V. National Institute of Technology
- Surat – 395007
- India
- Department of Chemistry
| | | | - Tae Jung Park
- Department of Chemistry
- Institute of Interdisciplinary Convergence Research
- Research Institute of Halal Industrialization Technology
- Chung-Ang University
- Seoul 06974
| | - Hui-Fen Wu
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- Center for Nanoscience and Nanotechnology
| | - Ying-Chi Lin
- School of Pharmacy
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
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Nirujogi RS, Muthusamy B, Kim MS, Sathe GJ, Lakshmi PTV, Kovbasnjuk ON, Prasad TSK, Wade M, Jabbour RE. Secretome analysis of diarrhea-inducing strains of Escherichia coli. Proteomics 2017; 17. [PMID: 28070933 DOI: 10.1002/pmic.201600299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/19/2016] [Accepted: 01/05/2017] [Indexed: 01/05/2023]
Abstract
Secreted proteins constitute a major part of virulence factors that are responsible for pathogenesis caused by Gram-negative bacteria. Enterohemorrhagic Escherichia coli, O157:H7, is the major pathogen often causing outbreaks. However, studies have reported that the significant outbreaks caused by non-O157:H7 E. coli strains, also known as "Big-Six" serogroup strains, are increasing. There is no systematic study describing differential secreted proteins from these non-O157:H7 E. coli strains. In this study, we carried out MS-based differential secretome analysis using tandem mass tags labeling strategy of non-O157:H7 E. coli strains, O103, O111, O121, O145, O26, and O45. We identified 1241 proteins, of which 565 proteins were predicted to be secreted. We also found that 68 proteins were enriched in type III secretion system and several of them were differentially expressed across the strains. Additionally, we identified several strain-specific secreted proteins that could be used for developing potential markers for the identification and strain-level differentiation. To our knowledge, this study is the first comparative proteomic study on secretome of E. coli Big-Six serogroup and the several of these strain-specific secreted proteins can be further studied to develop potential markers for identification and strain-level differentiation. Moreover, the results of this study can be utilized in several applications, including food safety, diagnostics of E. coli outbreaks, and detection and identification of bio threats in biodefense.
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Bioinformatics, Pondicherry University, Puducherry, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal University, Madhav Nagar, Manipal, India
| | - P T V Lakshmi
- Centre for Bioinformatics, Pondicherry University, Puducherry, India
| | - Olga N Kovbasnjuk
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Bioinformatics, Pondicherry University, Puducherry, India.,Manipal University, Madhav Nagar, Manipal, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | - Mary Wade
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Rabih E Jabbour
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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