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Kovalyova Y, Hatzios SK. Activity-Based Protein Profiling at the Host-Pathogen Interface. Curr Top Microbiol Immunol 2018; 420:73-91. [PMID: 30203396 DOI: 10.1007/82_2018_129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activity-based protein profiling (ABPP) is a technique for selectively detecting reactive amino acids in complex proteomes with the aid of chemical probes. Using probes that target catalytically active enzymes, ABPP can rapidly define the functional proteome of a biological system. In recent years, this approach has been increasingly applied to globally profile enzymes active at the host-pathogen interface of microbial infections. From in vitro co-culture systems to animal models of infection, these studies have revealed enzyme-mediated mechanisms of microbial pathogenicity, host immunity, and metabolic adaptation that dynamically shape pathogen interactions with the host.
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Affiliation(s)
- Yekaterina Kovalyova
- Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.,Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Stavroula K Hatzios
- Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, New Haven, CT, 06511, USA.
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52
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Proteomics and the human microbiome: where we are today and where we would like to be. Emerg Top Life Sci 2017; 1:401-409. [DOI: 10.1042/etls20170051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022]
Abstract
What are all these hundreds of different bacterial species doing in and on us? What interactions occur between the host and the microbes, and between the microbes themselves? By studying proteins, metaproteomics tries to find preliminary answers to these questions. There is daunting complexity around this; in fact, many of these proteins have never been studied before. This article is an introduction to the field of metaproteomics in the context of the human microbiome. It summarizes where we are and what we have learnt so far. The focus will be on faecal proteomics as most metaproteomics research has been conducted on that sample type. Metaproteomics has made major advances in the past decade, but new sample preparation strategies, improved mass spectrometric analysis and, most importantly, data analysis and interpretation have the potential to pave the way for large-cohort metaproteomics.
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Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang CK, Mack D, Stintzi A, Figeys D. Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach. J Proteome Res 2017; 17:154-163. [PMID: 29130306 DOI: 10.1021/acs.jproteome.7b00461] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.
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Affiliation(s)
- Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - David Mack
- Department of Paediatrics, CHEO Inflammatory Bowel Disease Centre and Research Institute, University of Ottawa , Ottawa, Ontario K1H 8L1, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada.,Canadian Institute for Advanced Research , Toronto, Ontario M5G 1Z8, Canada
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54
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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