1
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Du Y, May RC, Cooper HJ. Native ambient mass spectrometry of intact protein assemblies directly from Escherichia coli colonies. Chem Commun (Camb) 2022; 58:6857-6860. [PMID: 35617055 PMCID: PMC9196203 DOI: 10.1039/d2cc02085h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Here, we demonstrate that by combining electroporation with native ambient mass spectrometry, it is possible to detect intact non-covalent protein complexes directly from bacterial colonies growing on agar. Homodimers HdeA and HdeB were identified, together with the 50 kDa Mn-bound superoxide dismutase homodimer, in addition to some previously undetected monomeric proteins.
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Affiliation(s)
- Yuying Du
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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2
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Sun Y, Wang X, Li J, Xue F, Tang F, Dai J. Extraintestinal pathogenic Escherichia coli utilizes the surface-expressed elongation factor Tu to bind and acquire iron from holo-transferrin. Virulence 2022; 13:698-713. [PMID: 35443872 PMCID: PMC9037478 DOI: 10.1080/21505594.2022.2066274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is a common anthropozoonotic pathogen that causes systemic infections. To establish infection, ExPEC must utilize essential nutrients including iron from the host. Transferrin is an important iron source for multiple bacteria. However, the mechanism by which ExPEC utilizes transferrin remains unclear. In this study, we found that iron-saturated holo-transferrin rather than iron-free apo-transferrin promoted the vitality of ExPEC in heat-inactivated human serum. The multifunctional protein Elongation factor Tu (EFTu) worked as a holo-transferrin binding protein. EFTu not only bound holo-transferrin rather than apo-transferrin but also released transferrin-related iron, with all domains of EFTu involved in holo-transferrin binding and iron release events. We also identified the surface location of EFTu on ExPEC. Overexpression of EFTu on the surface of nonpathogenic E. coli not only promoted the binding of bacteria to holo-transferrin but also facilitated the uptake of transferrin-related iron. More importantly, it significantly enhanced the survival of E. coli in heat-inactivated human serum, which was positively correlated with holo-transferrin but not apo-transferrin. Our research revealed a novel function of EFTu in binding holo-transferrin to promote iron uptake by bacteria, suggesting that EFTu was a potential virulence factor of ExPEC. In addition, our study provided research avenues into the iron acquisition and pathogenicity mechanisms of ExPEC.
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Affiliation(s)
- Yu Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xuhang Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jin Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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3
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Fagerquist CK, Zaragoza WJ. Proteolytic Surface-Shaving and Serotype-Dependent Expression of SPI-1 Invasion Proteins in Salmonella enterica Subspecies enterica. Front Nutr 2018; 5:124. [PMID: 30619870 PMCID: PMC6295468 DOI: 10.3389/fnut.2018.00124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022] Open
Abstract
We performed proteolytic surface-shaving with trypsin on three strains/sevovars of Salmonella enterica enterica (SEE): Newport, Kentucky, and Thompson. Surfaced-exposed proteins of live bacterial cells were digested for 15 min. A separate 20 h re-digestion was also performed on the supernatant of each shaving experiment to more completely digest protein fragments into detectable peptides for proteomic analysis by nano-liquid chromatography-electrospray ionization-Orbitrap mass spectrometry. Control samples (i.e., no trypsin during surface-shaving step) were also performed in parallel. We detected peptides of flagella proteins: FliC (filament), FliD (cap), and FlgL (hook-filament junction) as well as peptides of FlgM (anti-σ28 factor), i.e., the negative regulator of flagella synthesis. For SEE Newport and Thompson, we detected Salmonella pathogenicity island 1 (SPI-1) secreted effector/invasion proteins: SipA, SipB, SipC, and SipD, whereas no Sip proteins were detected in control samples. No Sip proteins were detected for SEE Kentucky (or its control) although sip genes were confirmed to be present. Our results may suggest a biological response (<15 min) to proteolysis of live cells for these SEE strains and, in the case of Newport and Thompson, a possible invasion response.
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Affiliation(s)
- Clifton K Fagerquist
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, United States
| | - William J Zaragoza
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, United States
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Papanastasiou M, Orfanoudaki G, Kountourakis N, Koukaki M, Sardis MF, Aivaliotis M, Tsolis KC, Karamanou S, Economou A. Rapid label-free quantitative analysis of the E. coli
BL21(DE3) inner membrane proteome. Proteomics 2015; 16:85-97. [DOI: 10.1002/pmic.201500304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/05/2015] [Accepted: 10/12/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Malvina Papanastasiou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department Pathology & Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania; Philadelphia USA
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marina Koukaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marios Frantzeskos Sardis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
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5
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Alfonso-Garrido J, Garcia-Calvo E, Luque-Garcia JL. Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry. Anal Bioanal Chem 2015; 407:4893-905. [PMID: 25967148 DOI: 10.1007/s00216-015-8732-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.
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Affiliation(s)
- Javier Alfonso-Garrido
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28004, Madrid, Spain
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Olaya-Abril A, Jiménez-Munguía I, Gómez-Gascón L, Rodríguez-Ortega MJ. Surfomics: shaving live organisms for a fast proteomic identification of surface proteins. J Proteomics 2013; 97:164-76. [PMID: 23624344 DOI: 10.1016/j.jprot.2013.03.035] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/25/2013] [Accepted: 03/24/2013] [Indexed: 12/11/2022]
Abstract
Surface proteins play a critical role in the interaction between cells and their environment, as they take part in processes like signaling, adhesion, transport, etc. In pathogenic microorganisms, they can also participate in virulence or cytotoxicity. As these proteins have the highest chances to be recognized by the immune system, they are often the targets for the discovery of new vaccines. In addition, they can serve for the development of serological-based tools to diagnose infectious diseases. First-generation proteomic strategies for the identification of surface proteins rely on the biochemical fractionation and/or enrichment of this group of molecules or organelles containing them. However, in the last years, a novel second-generation approach has been developed, consisting of the digestion of live, intact cells with proteases, so that surface-exposed moieties (i.e. the "surfome" of a cell) are "shaved" and analyzed by LC/MS/MS. Here we review such a strategy, firstly set up and developed in Gram-positive bacteria, and further applied to Gram-negative bacteria, unicellular fungi, and also pluricellular organisms. We also discuss the advantages and inconvenients of the approach, and the still unresolved question about the intriguing presence of proteins predicted as cytoplasmic in the surfomes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Irene Jiménez-Munguía
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Lidia Gómez-Gascón
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Departamento de Sanidad Animal, Universidad de Córdoba, Córdoba, Spain
| | - Manuel J Rodríguez-Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional CeiA3, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.
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7
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After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli? J Proteomics 2012; 75:2773-89. [PMID: 22245553 DOI: 10.1016/j.jprot.2011.12.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 12/30/2022]
Abstract
Proteomic approaches have been considerably improved during the past decade and have been used to investigate the differences in protein expression profiles of cells grown under a broad spectrum of growth conditions and with different stress factors including antibiotics. In Europe, the most significant disease threat remains the presence of microorganisms that have become resistant to antimicrobials and so it is important that different scientific tools are combined to achieve the largest amount of knowledge in this area of expertise. The emergence and spread of the antibiotic-resistant Gram-negative pathogens, such as Escherichia coli, can lead to serious problem public health in humans. E. coli, a very well described prokaryote, has served as a model organism for several biological and biotechnological studies increasingly so since the completion of the E. coli genome-sequencing project. The purpose of this review is to present an overview of the different proteomic approaches to antimicrobial-resistant E. coli that will be helpful to obtain a better knowledge of the antibiotic-resistant mechanism(s). This can also aid to understand the molecular determinants involved with pathogenesis, which is essential for the development of effective strategies to combat infection and to reveal new therapeutic targets. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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8
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Chiappetta G, Ndiaye S, Demey E, Haddad I, Marino G, Amoresano A, Vinh J. Dansyl-peptides matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) and tandem mass spectrometric (MS/MS) features improve the liquid chromatography/MALDI-MS/MS analysis of the proteome. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3021-3032. [PMID: 20872635 DOI: 10.1002/rcm.4734] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Peptide tagging is a useful tool to improve matrix-assisted laser desorption/ionization tandem mass spectrometric (MALDI-MS/MS) analysis. We present a new application of the use of the dansyl chloride (DNS-Cl). DNS-Cl is a specific primary amine reagent widely used in protein biochemistry. It adds a fluorescent dimethylaminonaphthalene moiety to the molecule. The evaluation of MALDI-MS and MS/MS analyses of dansylated peptides shows that dansylation raises the ionization efficiency of the most hydrophilic species compared with the most hydrophobic ones. Consequently, higher Mascot scores and protein sequence coverage are obtained by combining MS and MS/MS data of native and tagged samples. The N-terminal DNS-Cl sulfonation improves the peptide fragmentation and promotes the generation of b-fragments allowing better peptide sequencing. In addition, we set up a labeling protocol based on the microwave chemistry. Peptide dansylation proved to be a rapid and cheap method to improve the performance of liquid chromatography (LC)/MALDI-MS/MS analysis at the proteomic scale in terms of peptide detection and sequence coverage.
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Affiliation(s)
- Giovanni Chiappetta
- USR 3149 CNRS/ESPCI ParisTech, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, Paris, France.
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9
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Thein M, Sauer G, Paramasivam N, Grin I, Linke D. Efficient Subfractionation of Gram-Negative Bacteria for Proteomics Studies. J Proteome Res 2010; 9:6135-47. [DOI: 10.1021/pr1002438] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marcus Thein
- Department I, Protein Evolution and Department II, Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Guido Sauer
- Department I, Protein Evolution and Department II, Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Nagarajan Paramasivam
- Department I, Protein Evolution and Department II, Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Iwan Grin
- Department I, Protein Evolution and Department II, Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Dirk Linke
- Department I, Protein Evolution and Department II, Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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10
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Bendz M, Möller MC, Arrigoni G, Wåhlander Å, Stella R, Cappadona S, Levander F, Hederstedt L, James P. Quantification of Membrane Proteins Using Nonspecific Protease Digestions. J Proteome Res 2009; 8:5666-73. [DOI: 10.1021/pr900741t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Maria Bendz
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Mirja Carlsson Möller
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Giorgio Arrigoni
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Åsa Wåhlander
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Roberto Stella
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Salvatore Cappadona
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Fredrik Levander
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Lars Hederstedt
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Peter James
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
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11
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Exploring the inner membrane proteome of Escherichia coli: which proteins are eluding detection and why? Trends Microbiol 2009; 17:444-9. [PMID: 19766000 DOI: 10.1016/j.tim.2009.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 07/13/2009] [Accepted: 07/17/2009] [Indexed: 11/22/2022]
Abstract
Proteins embedded in membranes are important for helping the cell adapt to changes in the extracellular milieu and often play key roles in the life cycles of pathogenic microbes. Bioinformatic predictions can provide an estimate of membrane proteins, but experimental approaches of detection are required for a deeper understanding of their functions. To determine the effectiveness of experimental detection approaches, here we collate and discuss data from available proteomic analyses on the inner (or cytoplasmic) membrane of Escherichia coli. We compile a list of proteins that have been experimentally detected and by comparing this to a predicted proteome we identify membrane proteins that have eluded us experimentally. Limitations of current proteomic analyses together with possible solutions are discussed. We also provide a list of proteins for benchmarking the performance of future proteomic studies.
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12
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Amoresano A, Carpentieri A, Giangrande C, Palmese A, Chiappetta G, Marino G, Pucci P. Technical advances in proteomics mass spectrometry: identification of post-translational modifications. Clin Chem Lab Med 2009; 47:647-65. [DOI: 10.1515/cclm.2009.154] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Díaz-Mejía JJ, Babu M, Emili A. Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. FEMS Microbiol Rev 2008; 33:66-97. [PMID: 19054114 PMCID: PMC2704936 DOI: 10.1111/j.1574-6976.2008.00141.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The bacterial cell-envelope consists of a complex arrangement of lipids, proteins and carbohydrates that serves as the interface between a microorganism and its environment or, with pathogens, a human host. Escherichia coli has long been investigated as a leading model system to elucidate the fundamental mechanisms underlying microbial cell-envelope biology. This includes extensive descriptions of the molecular identities, biochemical activities and evolutionary trajectories of integral transmembrane proteins, many of which play critical roles in infectious disease and antibiotic resistance. Strikingly, however, only half of the c. 1200 putative cell-envelope-related proteins of E. coli currently have experimentally attributed functions, indicating an opportunity for discovery. In this review, we summarize the state of the art of computational and proteomic approaches for determining the components of the E. coli cell-envelope proteome, as well as exploring the physical and functional interactions that underlie its biogenesis and functionality. We also provide a comprehensive comparative benchmarking analysis on the performance of different bioinformatic and proteomic methods commonly used to determine the subcellular localization of bacterial proteins.
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Affiliation(s)
- Juan Javier Díaz-Mejía
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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14
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A rapid and selective mass spectrometric method for the identification of nitrated proteins. Methods Mol Biol 2008; 477:15-29. [PMID: 19082935 DOI: 10.1007/978-1-60327-517-0_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The nitration of protein tyrosine residues represents an important posttranslational modification during development, oxidative stress, and biological aging. The major challenge in the proteomic analysis of nitroproteins is the need to discriminate modified proteins, usually occurring at substoichiometric levels, from the large amount of nonmodified proteins. Moreover, precise localization of the nitration site is often required to fully describe the biological process. Identification of the specific targets of protein oxidation was previously accomplished using immunoprecipitation techniques followed by immunochemical detection. Here, we report a totally new approach involving dansyl chloride labeling of the nitration sites which relies on the enormous potential of MS(n) analysis. The tryptic digest from the entire protein mixture is directly analyzed by MS on a linear ion trap mass spectrometer. Discrimination between nitro- and unmodified peptide is based on two selectivity criteria obtained by combining a precursor ion scan and a MS3 analysis. The novel labeling procedure was successfully applied to the identification of 3-nitrotyrosine residues in complex protein mixtures.
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