1
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Fuchs S, Engelmann S. Small proteins in bacteria - Big challenges in prediction and identification. Proteomics 2023; 23:e2200421. [PMID: 37609810 DOI: 10.1002/pmic.202200421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
Abstract
Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.
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Affiliation(s)
- Stephan Fuchs
- Genome Competence Center (MF1), Department MFI, Robert-Koch-Institut, Berlin, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung GmbH, Braunschweig, Germany
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2
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Sirichoat A, Kaewseekhao B, Nithichanon A, Roytrakul S, Faksri K. Proteomic Profiles and Protein Network Analysis of Primary Human Leukocytes Revealed Possible Clearance Biomarkers for Staphylococcus aureus Infection. Curr Microbiol 2023; 80:335. [PMID: 37665379 DOI: 10.1007/s00284-023-03450-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Staphylococcus aureus is a serious pathogen that can survive within host cells after a typical course of treatment completion, leading to chronic infection. Knowledge of host proteomic patterns after clearance of this pathogen from cells is limited. Here, we looked for S. aureus clearance biomarkers produced by in vitro-infected leukocytes. Extracellular proteins from primary human leukocytes infected with S. aureus ATCC 25923 were investigated as possible treatment-monitoring clearance biomarkers by applying a proteomics approach combining liquid chromatography with tandem mass spectrometry (LC-MS/MS) and protein interaction network analysis. It was found that the expression patterns of proteins secreted by S. aureus-infected leukocytes differed among stages of infection. Proteomic profiles showed that an ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2 (ATP8A2) was expressed in the clearance stage and was not detected at any earlier stage or in uninfected controls. Protein network analysis showed that TERF2 (telomeric repeat-binding factor 2), ZNF440 (zinc finger protein 440), and PPP1R14A (phosphatase 1 regulatory subunit 14A) were up-regulated, while GLE1, an essential RNA-export mediator, was suppressed in both infection and clearance stages, suggesting their potential roles in S. aureus infection and clearance. These findings are the first to report that the ATP8A2 has potential as a clearance biomarker for S. aureus infection.
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Affiliation(s)
- Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Arnone Nithichanon
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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3
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Raineri EJM, Maaß S, Wang M, Brushett S, Palma Medina LM, Sampol Escandell N, Altulea D, Raangs E, de Jong A, Vera Murguia E, Feil EJ, Friedrich AW, Buist G, Becher D, García-Cobos S, Couto N, van Dijl JM. Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity. MICROBIOME 2022; 10:239. [PMID: 36567349 PMCID: PMC9791742 DOI: 10.1186/s40168-022-01419-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus are the skin, nasopharynx, and gut. In particular, the mechanisms allowing S. aureus to pass the gut epithelial barrier and to invade the bloodstream were so far poorly understood. Therefore, the objective of our present study was to investigate the extent to which genetic differences between enteric S. aureus isolates and isolates that caused serious bloodstream infections contribute to the likelihood of invasive disease. RESULTS Here, we present genome-wide association studies (GWAS) that compare the genome sequences of 69 S. aureus isolates from enteric carriage by healthy volunteers and 95 isolates from bloodstream infections. We complement our GWAS results with a detailed characterization of the cellular and extracellular proteomes of the representative gut and bloodstream isolates, and by assaying the virulence of these isolates with infection models based on human gut epithelial cells, human blood cells, and a small animal infection model. Intriguingly, our results show that enteric and bloodstream isolates with the same sequence type (ST1 or ST5) are very similar to each other at the genomic and proteomic levels. Nonetheless, bloodstream isolates are not necessarily associated with an invasive profile. Furthermore, we show that the main decisive factor preventing infection of gut epithelial cells in vitro is the presence of a tight barrier. CONCLUSIONS Our data show that virulence is a highly variable trait, even within a single clone. Importantly, however, there is no evidence that blood stream isolates possess a higher virulence potential than those from the enteric carriage. In fact, some gut isolates from healthy carriers were more virulent than bloodstream isolates. Based on our present observations, we propose that the integrity of the gut epithelial layer, rather than the pathogenic potential of the investigated enteric S. aureus isolates, determines whether staphylococci from the gut microbiome will become invasive pathogens. Video Abstract.
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Affiliation(s)
- Elisa J. M. Raineri
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Siobhan Brushett
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Laura M. Palma Medina
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Present address: Department of Medicine Huddinge, Present Address: Center for Infectious Medicine, Karolinska Institute, Huddinge, Sweden
| | - Neus Sampol Escandell
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dania Altulea
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Present address: Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erwin Raangs
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Elias Vera Murguia
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Edward J. Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Alex W. Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Silvia García-Cobos
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Present address: Reference and Research Laboratory On Antimicrobial Resistance and Healthcare Associated Infections, Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Natacha Couto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Ahrens CH, Wade JT, Champion MM, Langer JD. A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry. J Bacteriol 2022; 204:e0035321. [PMID: 34748388 PMCID: PMC8765459 DOI: 10.1128/jb.00353-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
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Affiliation(s)
- Christian H. Ahrens
- Agroscope, Method Development and Analytics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Julian D. Langer
- Mass Spectrometry and Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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5
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Tu H, Xu F, Cheng Y, Pan Q, Cai X, Wang S, Ge S, Cao M, Su D, Li Y. Proteomic profiling of the endogenous peptides of MRSA and MSSA. PeerJ 2021; 9:e12508. [PMID: 34900427 PMCID: PMC8627652 DOI: 10.7717/peerj.12508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is a Gram-positive bacterium that can cause diverse skin and soft tissue infections. Methicillin-resistant Staphylococcus aureus (MRSA) can cause more severe infections than methicillin-susceptible Staphylococcus aureus (MSSA). Nevertheless, the physiological and metabolic regulation of MSSA and MRSA has not been well studied. In light of the increased interest in endogenous peptides and recognition of the important roles that they play, we studied the endogenous peptidome of MSSA and MRSA. We identified 1,065 endogenous peptides, among which 435 were differentially expressed (DE), with 292 MSSA-abundant endogenous peptides and 35 MRSA-abundant endogenous peptides. MSSA-abundant endogenous peptides have significantly enriched “VXXXK” motif of at the C-terminus. MSSA-abundant endogenous peptides are involved in penicillin-binding and immune responses, whereas MRSA-abundant endogenous peptides are associated with antibiotic resistance and increased toxicity. Our characterization of the peptidome of MSSA and MRSA provides a rich resource for future studies to explore the functional regulation of drug resistance in S. aureus and may also help elucidate the mechanisms of its pathogenicity and the development of treatments.
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Affiliation(s)
- Haixia Tu
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Fei Xu
- Blood Transfusion Department, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yiwei Cheng
- School of Basic Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Qianglong Pan
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiao Cai
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shouxing Wang
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shuting Ge
- School of Basic Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Min Cao
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Dongming Su
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yan Li
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
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6
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Kumar NG, Contaifer D, Wijesinghe DS, Jefferson KK. Staphylococcus aureus Lipase 3 (SAL3) is a surface-associated lipase that hydrolyzes short chain fatty acids. PLoS One 2021; 16:e0258106. [PMID: 34618844 PMCID: PMC8496776 DOI: 10.1371/journal.pone.0258106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial lipases play important roles during infection. The Staphylococcus aureus genome contains several genes that encode well-characterized lipases and several genes predicted to encode lipases or esterases for which the function has not yet been established. In this study, we sought to define the function of an uncharacterized S. aureus protein, and we propose the annotation S. aureus lipase 3 (SAL3) (SAUSA300_0641). We confirmed that SAL3 is a lipase and that it is surface associated and secreted through an unknown mechanism. We determined that SAL3 specifically hydrolyzes short chain (4-carbon and fewer) fatty acids and specifically binds negatively charged lipids including phosphatidic acid, phosphatidylinositol phosphate, and phosphatidylglycerol, which is the most abundant lipid in the staphylococcal cell membrane. Mutating the catalytic triad S66-A, D167-A, S168-A, and H301-A in the recombinant protein abolished lipase activity without altering binding to host lipid substrates. Taken together we report the discovery of a novel lipase from S. aureus specific to short chain fatty acids with yet to be determined roles in host pathogen interactions.
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Affiliation(s)
- Naren Gajenthra Kumar
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel Contaifer
- Department of Pharmacotherapy and Outcomes Sciences, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dayanjan S. Wijesinghe
- Department of Pharmacotherapy and Outcomes Sciences, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kimberly K. Jefferson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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7
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Pimentel-Filho NDJ, Fuchs S, Baracat-Pereira MC, Mantovani HC, Riedel K, Vanetti MCD. Protein expression profiling of Staphylococcus aureus in response to the bacteriocin bovicin HC5. Appl Microbiol Biotechnol 2021; 105:7857-7869. [PMID: 34554273 DOI: 10.1007/s00253-021-11594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Alternative strategies to antibiotic treatment are required to inhibit pathogens, including Staphylococcus aureus. Bacteriocins, such as the lantibiotic bovicin HC5, have shown potential to control pathogens. This study aims to evaluate the stress response of S. aureus to bovicin HC5 using a proteomic approach. Sublethal concentrations of the bacteriocin repressed the synthesis of 62 cytoplasmic proteins, whereas 42 proteins were induced in S. aureus COL. Specifically, synthesis of several proteins involved in amino acid biosynthesis, mainly products of ilv-leu operon, and DNA metabolism, such as DNA polymerase I, decreased following bovicin treatment while proteins involved in catabolism, mainly tricarboxylic acid cycle metabolism, and chaperones were over-expressed. The levels of CodY and CcpA, important regulators involved in the stationary phase adaptation and catabolite repression, respectively, also increased in the presence of the bacteriocin. These results indicate that stress caused by the sublethal concentration of bovicin HC5 in the cell membrane results in growth reduction, reduced protein synthesis, and, at the same time, enhanced the levels of chaperones and enzymes involved in energy-efficient catabolism in an attempt to restore energy and cell homeostasis. These results bring relevant information to amplify the knowledge concerning the bacterial physiological changes in response to the stress caused by the cell exposition to bovicin HC5. New potential targets for controlling this pathogen can also be determined from the new protein expression pattern presented. KEY POINTS: • Bovicin HC5 changed the synthesis of cytoplasmic proteins of S. aureus. • Bovicin HC5 interfered in the synthesis of proteins of amino acids biosynthesis. • Synthesis of chaperones enhanced in the presence of sublethal dosage of bovicin HC5.
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Affiliation(s)
- Natan de Jesus Pimentel-Filho
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-000, Brazil.,Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17489, Greifswald, Germany.,Centro de Ciências da Natureza, Universidade Federal de São Carlos, Rod. Lauri Simões de Barros, km 12 - SP 189, Buri, SP, 18290-000, Brazil
| | - Stephan Fuchs
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17489, Greifswald, Germany
| | - Maria Cristina Baracat-Pereira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-000, Brazil
| | - Hilário Cuquetto Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-000, Brazil
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17489, Greifswald, Germany
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8
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Graf AC, Striesow J, Pané-Farré J, Sura T, Wurster M, Lalk M, Pieper DH, Becher D, Kahl BC, Riedel K. An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum. Front Cell Infect Microbiol 2021; 11:724569. [PMID: 34513734 PMCID: PMC8432295 DOI: 10.3389/fcimb.2021.724569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.
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Affiliation(s)
- Alexander C Graf
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Johanna Striesow
- Research Group ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Thomas Sura
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Martina Wurster
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Dietmar H Pieper
- Research Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
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9
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Birk MS, Ahmed-Begrich R, Tran S, Elsholz AKW, Frese CK, Charpentier E. Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation. mSystems 2021; 6:e0021521. [PMID: 34342529 PMCID: PMC8407217 DOI: 10.1128/msystems.00215-21] [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: 02/24/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
The cellular proteome comprises all proteins expressed at a given time and defines an organism's phenotype under specific growth conditions. The proteome is shaped and remodeled by both protein synthesis and protein degradation. Here, we developed a new method which combines metabolic and chemical isobaric peptide labeling to simultaneously determine the time-resolved protein decay and de novo synthesis in an intracellular human pathogen. We showcase this method by investigating the Listeria monocytogenes proteome in the presence and absence of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L. monocytogenes remains elusive. Employing this new method, we observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlight the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. IMPORTANCE Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. Profiling the underlying changes on the bacterial proteome level during the infection process is important to gain a better understanding of the pathogenesis and the host-dependent adaptation processes. The cellular protein abundance is governed by the interplay between protein synthesis and decay. The direct readout of these events during infection can be accomplished using pulsed stable-isotope labeling by amino acids in cell culture (SILAC). Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. Here, we applied this integrated approach to investigate protein turnover during the temporal progression of adaptation of the human pathogen L. monocytogenes to its host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.
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Affiliation(s)
- Marlène S. Birk
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Stefan Tran
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
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10
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Dekio I, Sugiura Y, Hamada-Tsutsumi S, Murakami Y, Tamura H, Suematsu M. What Do We See in Spectra?: Assignment of High-Intensity Peaks of Cutibacterium and Staphylococcus Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics. Microorganisms 2021; 9:microorganisms9061243. [PMID: 34201063 PMCID: PMC8227259 DOI: 10.3390/microorganisms9061243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Matrix-assisted laser-desorption/ionization time-of-flight (MALDI–TOF) mass spectrometry is a widely used and reliable technology to identify microbial species and subspecies. The current methodology is based on spectral fingerprinting, analyzing protein peaks, most of which are yet to be characterized. In order to deepen the understanding of these peaks and to develop a more reasonable identification workflow, we applied proteogenomic approaches to assign the high-intensity peaks of MALDI–TOF spectra of two bacterial genera. First, the 3–22 kD proteomes of 5 Cutibacterium strains were profiled by UPLC–MS/MS, and the amino acid sequences were refined by referring to their genome in the public database. Then, the sequences were converted to m/z (x-axis) values based on their molecular masses. When the interspecies comparison of calculated m/z values was well-fitted to the observed peaks, the peak assignments for the five Cutibacterium species were confirmed. Second, the peak assignments for six Staphylococcus species were performed by using the above result for Cutibacterium and referring to ribosomal subunit proteins coded on the S10-spc-alpha operon (the S10-GERMS method), a previous proteomics report by Becher et al., and comprehensive genome analysis. We successfully assigned 13 out of 15 peaks for the Cutibacterium species and 11 out of 13 peaks for the Staphylococcus species. DNA-binding protein HU, the CsbD-like protein, and 50S ribosomal protein L7/L12 were observed in common. The commonality suggests they consist of high-intensity peaks in the MALDI spectra of other bacterial species. Our workflow may lead to the development of a more accurate species identification database of MALDI–TOF mass spectrometry based on genome data.
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Affiliation(s)
- Itaru Dekio
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.S.)
- Correspondence: ; Tel.: +81-3-3433-1111 (ext. 3341); Fax: +81-3-5401-0125
| | - Yuki Sugiura
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.S.)
| | - Susumu Hamada-Tsutsumi
- Department of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan; (S.H.-T.); (H.T.)
| | - Yoshiyuki Murakami
- Seikakai Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan;
| | - Hiroto Tamura
- Department of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan; (S.H.-T.); (H.T.)
| | - Makoto Suematsu
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.S.)
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11
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Fuchs S, Kucklick M, Lehmann E, Beckmann A, Wilkens M, Kolte B, Mustafayeva A, Ludwig T, Diwo M, Wissing J, Jänsch L, Ahrens CH, Ignatova Z, Engelmann S. Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach. PLoS Genet 2021; 17:e1009585. [PMID: 34061833 PMCID: PMC8195425 DOI: 10.1371/journal.pgen.1009585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 06/11/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023] Open
Abstract
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.
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Affiliation(s)
- Stephan Fuchs
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
| | - Martin Kucklick
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Erik Lehmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Alexander Beckmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maya Wilkens
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Baban Kolte
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Ayten Mustafayeva
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Tobias Ludwig
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maurice Diwo
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Josef Wissing
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Lothar Jänsch
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoya Ignatova
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Susanne Engelmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
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12
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Kandil A, Hanora A, Azab M, Enany S. Proteomic analysis of bacterial communities associated with atopic dermatitis. J Proteomics 2020; 229:103944. [DOI: 10.1016/j.jprot.2020.103944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022]
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13
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Martin DR, Witten JC, Tan CD, Rodriguez ER, Blackstone EH, Pettersson GB, Seifert DE, Willard BB, Apte SS. Proteomics identifies a convergent innate response to infective endocarditis and extensive proteolysis in vegetation components. JCI Insight 2020; 5:135317. [PMID: 32544089 DOI: 10.1172/jci.insight.135317] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Infective endocarditis is a life-threatening infection of heart valves and adjacent structures characterized by vegetations on valves and other endocardial surfaces, with tissue destruction and risk of embolization. We used high-resolution mass spectrometry to define the proteome of staphylococcal and non-staphylococcal vegetations and Terminal Amine Isotopic Labeling of Substrates (TAILS) to define their proteolytic landscapes. These approaches identified over 2000 human proteins in staphylococcal and non-staphylococcal vegetations. Individual vegetation proteomes demonstrated comparable profiles of quantitatively major constituents that overlapped with serum, platelet, and neutrophil proteomes. Staphylococcal vegetation proteomes resembled one another more than the proteomes of non-staphylococcal vegetations. TAILS demonstrated extensive proteolysis within vegetations, with numerous previously undescribed cleavages. Several proteases and pathogen-specific proteins, including virulence factors, were identified in most vegetations. Proteolytic peptides in fibronectin and complement C3 were identified as potential infective endocarditis biomarkers. Overlap of staphylococcal and non-staphylococcal vegetation proteomes suggests a convergent thrombotic and immune response to endocardial infection by diverse pathogens. However, the differences between staphylococcal and non-staphylococcal vegetations and internal variance within the non-staphylococcal group indicate that additional pathogen- or patient-specific effects exist. Pervasive proteolysis of vegetation components may arise from vegetation-intrinsic proteases and destabilize vegetations, contributing to embolism.
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Affiliation(s)
- Daniel R Martin
- Department of Biomedical Engineering, Lerner Research Institute
| | - James C Witten
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | - Carmela D Tan
- Department of Pathology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, and
| | - E Rene Rodriguez
- Department of Pathology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, and
| | - Eugene H Blackstone
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | - Gosta B Pettersson
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | | | - Belinda B Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Lerner Research Institute
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14
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Celis AI, Choby JE, Kentro J, Skaar EP, DuBois JL. Control of Metabolite Flux during the Final Steps of Heme b Biosynthesis in Gram-Positive Bacteria. Biochemistry 2019; 58:5259-5270. [PMID: 31241911 PMCID: PMC7160669 DOI: 10.1021/acs.biochem.9b00140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The pathway for assembling heme ends with a unique set of enzymes in Gram-positive bacteria. Substrates for these reactions include coproporphyrin III, Fe(II), and H2O2, which are highly reactive and toxic. Because these bacteria lack membranous compartments, we hypothesized that metabolite flux may occur via a transient protein-protein interaction between the final two pathway enzymes, coproporphyrin ferrochelatase (CpfC) and coproheme decarboxylase (ChdC). This hypothesis was tested using enzymes from the pathogen Staphylococcus aureus and a corresponding ΔchdC knockout strain. The ultraviolet-visible spectral features of coproporphyrin III served as an in vitro indicator of a protein-protein interaction. A CpfC-ChdC KD of 17 ± 7 μM was determined, consistent with transient complexation and supported by the observation that the catalytic competence of both enzymes was moderately suppressed in the stable complex. The ΔchdC S. aureus was transformed with plasmids containing single-amino acid mutants in the active site gate of ChdC. The porphyrin content and growth phenotypes of these mutants showed that K129 and Y133 promote the ChdC-CpfC interaction and revealed the importance of E120. Understanding the nature of interactions between these enzymes and those further upstream in the heme biosynthesis pathway could provide new means of specifically targeting pathogenic Gram-positive bacteria such as S. aureus.
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Affiliation(s)
- Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, United States
| | - Jacob E. Choby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2561, United States,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States,Graduate Program in Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - James Kentro
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2561, United States,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, United States,Corresponding Author Address: 221 Chemistry and Biochemistry Building, Bozeman, MT 59715. Phone: 406-994-2844.
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15
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Abdi RD, Dunlap JR, Gillespie BE, Ensermu DB, Almeida RA, Kerro Dego O. Comparison of Staphylococcus aureus surface protein extraction methods and immunogenicity. Heliyon 2019; 5:e02528. [PMID: 31687478 PMCID: PMC6820086 DOI: 10.1016/j.heliyon.2019.e02528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/05/2019] [Accepted: 09/24/2019] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus aureus is the major contagious bovine mastitis pathogen and has no effective vaccine. Strain variation and limited knowledge of common immunogenic antigen/s are among major constraints for developing effective vaccines. S. aureus cell surface proteins that are exposed to the host immune system constitute good vaccine candidates. The objective of this study was to compare two novel S. aureus surface protein extraction methods with biotinylation method and evaluate immune-reactivity of extracted proteins. Surface proteins were extracted from nine genetically distinct S. aureus strains from cases of bovine mastitis. After extraction, bacterial cell integrity was examined by Gram staining and electron microscopy to determine if extraction methods caused damage to cells that may release non-surface proteins. The extracted proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and evaluated for immune-reactivity using western blot. Results showed that all three extraction methods provided multiple protein bands on SDS-PAGE. Western blot result showed several immunoreactive surface proteins, in which some proteins strongly (well-resolved, thick, dark, and intense band) reacted across the nine strains tested. The three methods are valid for the extraction of surface proteins and hexadecane, and cholic acid methods are more feasible than biotinylation since both are easier, cheaper, and have minor effects on the bacterial cell. Strongly immune-reactive surface proteins may serve as potential candidates for a vaccine to control S. aureus mastitis in dairy cows.
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Affiliation(s)
- Reta Duguma Abdi
- Department of Animal Science, The University of Tennessee, Knoxville, TN37966, United States
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Greenvale, NY11548, United States
| | - John R. Dunlap
- Joint Institute for Advanced Materials (JIAM) Microscopy Center and Advanced Microscopy and Imaging Center, The University of Tennessee, Knoxville, TN, 37996, United States
| | - Barbara E. Gillespie
- Department of Animal Science, The University of Tennessee, Knoxville, TN37966, United States
| | - Desta Beyene Ensermu
- Department of Animal Science, The University of Tennessee, Knoxville, TN37966, United States
| | - Raul Antonio Almeida
- Department of Animal Science, The University of Tennessee, Knoxville, TN37966, United States
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee, Knoxville, TN37966, United States
- Corresponding author.
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16
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Graf AC, Leonard A, Schäuble M, Rieckmann LM, Hoyer J, Maass S, Lalk M, Becher D, Pané-Farré J, Riedel K. Virulence Factors Produced by Staphylococcus aureus Biofilms Have a Moonlighting Function Contributing to Biofilm Integrity. Mol Cell Proteomics 2019; 18:1036-1053. [PMID: 30850421 PMCID: PMC6553939 DOI: 10.1074/mcp.ra118.001120] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus is the causative agent of various biofilm-associated infections in humans causing major healthcare problems worldwide. This type of infection is inherently difficult to treat because of a reduced metabolic activity of biofilm-embedded cells and the protective nature of a surrounding extracellular matrix (ECM). However, little is known about S. aureus biofilm physiology and the proteinaceous composition of the ECM. Thus, we cultivated S. aureus biofilms in a flow system and comprehensively profiled intracellular and extracellular (ECM and flow-through (FT)) biofilm proteomes, as well as the extracellular metabolome compared with planktonic cultures. Our analyses revealed the expression of many pathogenicity factors within S. aureus biofilms as indicated by a high abundance of capsule biosynthesis proteins along with various secreted virulence factors, including hemolysins, leukotoxins, and lipases as a part of the ECM. The activity of ECM virulence factors was confirmed in a hemolysis assay and a Galleria mellonella pathogenicity model. In addition, we uncovered a so far unacknowledged moonlighting function of secreted virulence factors and ribosomal proteins trapped in the ECM: namely their contribution to biofilm integrity. Mechanistically, it was revealed that this stabilizing effect is mediated by the strong positive charge of alkaline virulence factors and ribosomal proteins in an acidic ECM environment, which is caused by the release of fermentation products like formate, lactate, and acetate because of oxygen limitation in biofilms. The strong positive charge of these proteins most likely mediates electrostatic interactions with anionic cell surface components, eDNA, and anionic metabolites. In consequence, this leads to strong cell aggregation and biofilm stabilization. Collectively, our study identified a new molecular mechanism during S. aureus biofilm formation and thus significantly widens the understanding of biofilm-associated S. aureus infections - an essential prerequisite for the development of novel antimicrobial therapies.
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Affiliation(s)
- Alexander C Graf
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Anne Leonard
- §Institute of Biochemistry, Department of Cellular Biochemistry and Metabolomics
| | - Manuel Schäuble
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Lisa M Rieckmann
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Juliane Hoyer
- ¶Institute of Microbiology, Department of Microbial Proteomics; University of Greifswald, Germany
| | - Sandra Maass
- ¶Institute of Microbiology, Department of Microbial Proteomics; University of Greifswald, Germany
| | - Michael Lalk
- §Institute of Biochemistry, Department of Cellular Biochemistry and Metabolomics
| | - Dörte Becher
- ¶Institute of Microbiology, Department of Microbial Proteomics; University of Greifswald, Germany
| | - Jan Pané-Farré
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Katharina Riedel
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology;
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17
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Maaß S, Moog G, Becher D. Subcellular Protein Fractionation in Legionella pneumophila and Preparation of the Derived Sub-proteomes for Analysis by Mass Spectrometry. Methods Mol Biol 2019; 1921:445-464. [PMID: 30694509 DOI: 10.1007/978-1-4939-9048-1_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Classical proteomic techniques are perfectly suited to reflect changes in the metabolism by detection of changed protein synthesis rates and protein abundances in a global protein-centered analysis. Although the proteome of microbes is considered as rather low complex, usually the subcellular fractionation of proteins leads to higher proteome coverage which might be important for the proteome quantification. Additionally, such fractionation provides the possibility to detect changes in the protein localization as well as the protein abundance in single sub-proteomes. Here, a workflow for subcellular fractionation of Legionella pneumophila into cytosolic, periplasmic, membrane, and extracellular proteins for global proteome analyses is provided. The methods included in this workflow can be used to analyze the adaptation of L. pneumophila to different environmental and nutritional situations during infection or during different life cycle stages including planktonic or biofilm phase.
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Affiliation(s)
- Sandra Maaß
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Gina Moog
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany.
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18
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Hofmann JD, Otto A, Berges M, Biedendieck R, Michel AM, Becher D, Jahn D, Neumann-Schaal M. Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production. Front Microbiol 2018; 9:1970. [PMID: 30186274 PMCID: PMC6110889 DOI: 10.3389/fmicb.2018.01970] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022] Open
Abstract
The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium difficile) causes nosocomial and community acquired diarrhea often associated with antibiotic therapy. Major virulence factors of the bacterium are the two large clostridial toxins TcdA and TcdB. The production of both toxins was found strongly connected to the metabolism and the nutritional status of the growth environment. Here, we systematically investigated the changes of the gene regulatory, proteomic and metabolic networks of C. difficile 630Δerm underlying the adaptation to the non-growing state in the stationary phase. Integrated data from time-resolved transcriptome, proteome and metabolome investigations performed under defined growth conditions uncovered multiple adaptation strategies. Overall changes in the cellular processes included the downregulation of ribosome production, lipid metabolism, cold shock proteins, spermine biosynthesis, and glycolysis and in the later stages of riboflavin and coenzyme A (CoA) biosynthesis. In contrast, different chaperones, several fermentation pathways, and cysteine, serine, and pantothenate biosynthesis were found upregulated. Focusing on the Stickland amino acid fermentation and the central carbon metabolism, we discovered the ability of C. difficile to replenish its favored amino acid cysteine by a pathway starting from the glycolytic 3-phosphoglycerate via L-serine as intermediate. Following the growth course, the reductive equivalent pathways used were sequentially shifted from proline via leucine/phenylalanine to the central carbon metabolism first to butanoate fermentation and then further to lactate fermentation. The toxin production was found correlated mainly to fluxes of the central carbon metabolism. Toxin formation in the supernatant was detected when the flux changed from butanoate to lactate synthesis in the late stationary phase. The holistic view derived from the combination of transcriptome, proteome and metabolome data allowed us to uncover the major metabolic strategies that are used by the clostridial cells to maintain its cellular homeostasis and ensure survival under starvation conditions.
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Affiliation(s)
- Julia D Hofmann
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Otto
- Department for Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika-Marisa Michel
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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19
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From the genome sequence via the proteome to cell physiology – Pathoproteomics and pathophysiology of Staphylococcus aureus. Int J Med Microbiol 2018; 308:545-557. [DOI: 10.1016/j.ijmm.2018.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 02/01/2023] Open
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20
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Monteiro R, Chafsey I, Leroy S, Chambon C, Hébraud M, Livrelli V, Pizza M, Pezzicoli A, Desvaux M. Differential biotin labelling of the cell envelope proteins in lipopolysaccharidic diderm bacteria: Exploring the proteosurfaceome of Escherichia coli using sulfo-NHS-SS-biotin and sulfo-NHS-PEG4-bismannose-SS-biotin. J Proteomics 2018; 181:16-23. [PMID: 29609094 DOI: 10.1016/j.jprot.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/15/2018] [Accepted: 03/23/2018] [Indexed: 12/28/2022]
Abstract
Surface proteins are the major factor for the interaction between bacteria and its environment, playing an important role in infection, colonisation, virulence and adaptation. However, the study of surface proteins has proven difficult mainly due to their hydrophobicity and/or relatively low abundance compared with cytoplasmic proteins. To overcome these issues new proteomic strategies have been developed, such as cell-surface protein labelling using biotinylation reagents. Sulfo-NHS-SS-biotin is the most commonly used reagent to investigate the proteins expressed at the cell surface of various organisms but its use in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria) remains limited to a handful of species. While generally pass over in silence, some periplasmic proteins, but also some inner membrane lipoproteins, integral membrane proteins and cytoplasmic proteins (cytoproteins) are systematically identified following this approach. To limit cell lysis and diffusion of the sulfo-NHS-SS-biotin through the outer membrane, biotin labelling was tested over short incubation times and proved to be as efficient for 1 min at room temperature. To further limit labelling of protein located below the outer membrane, the use of high-molecular weight sulfo-NHS-PEG4-bismannose-SS-biotin appeared to recover differentially cell-envelope proteins compared to low-molecular weight sulfo-NHS-SS-biotin. Actually, the sulfo-NHS-SS-biotin recovers at a higher extent the proteins completely or partly exposed in the periplasm than sulfo-NHS-PEG4-bismannose-SS-biotin, namely periplasmic and integral membrane proteins as well as inner membrane and outer membrane lipoproteins. These results highlight that protein labelling using biotinylation reagents of different sizes provides a sophisticated and accurate way to differentially explore the cell envelope proteome of lipopolysaccharidic diderm bacteria. SIGNIFICANCE While generally pass over in silence, some periplasmic proteins, inner membrane lipoproteins (IMLs), integral membrane proteins (IMPs) and cytoplasmic proteins (cytoproteins) are systematically identified following cell-surface biotin labelling in lipopolysaccharidic diderm bacteria (archetypal Gram-negative bacteria). The use of biotinylation molecules of different sizes, namely sulfo-NHS-SS-biotin and sulfo-NHS-PEG4-bismannose-SS-biotin, was demonstrated to provide a sophisticated and accurate way to differentially explore the cell envelope proteome of lipopolysaccharidic diderm bacteria.
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Affiliation(s)
- Ricardo Monteiro
- Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France; GSK, Via Fiorentina 1, 53100 Siena, Italy
| | - Ingrid Chafsey
- Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France
| | - Christophe Chambon
- INRA, Plate-Forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France
| | - Michel Hébraud
- Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France; INRA, Plate-Forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France
| | - Valérie Livrelli
- Centre de Recherche en Nutrition Humaine Auvergne, UMR UCA INSERM U1071, USC-INRA 2018, Clermont Université - Université d'Auvergne, Faculté de Pharmacie, CHU Clermont-Ferrand, Service Bactériologie Mycologie Parasitologie, Clermont-Ferrand, France
| | | | | | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France.
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21
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Junker S, Maaβ S, Otto A, Michalik S, Morgenroth F, Gerth U, Hecker M, Becher D. Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus. Mol Cell Proteomics 2018; 17:335-348. [PMID: 29183913 PMCID: PMC5795395 DOI: 10.1074/mcp.ra117.000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/19/2022] Open
Abstract
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.
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Affiliation(s)
- Sabryna Junker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Sandra Maaβ
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Andreas Otto
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Stephan Michalik
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | | | - Ulf Gerth
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Michael Hecker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, University of Greifswald, Germany
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22
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Abstract
Quantitative Proteomics based on stable isotope labeling by 15N is a versatile method in determination of changes in microbial protein expression profiles. Once set up, the workflow relies on defined chemical or commercially available complex media leading to universal heavy labeling by the stable isotope 15N. This chapter provides a detailed protocol for labeling of different bacteria and the strategy for evaluating the incorporation rate of the heavy stable isotopes in the sample is discussed.
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Affiliation(s)
- Andreas Otto
- Department of Microbial Proteomics, Institute for Microbiology, University Greifswald, Greifswald, Germany.
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23
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Fechter P. Mapping Changes in Cell Surface Protein Expression Through Selective Labeling of Live Cells. Methods Mol Biol 2018; 1737:119-127. [PMID: 29484591 DOI: 10.1007/978-1-4939-7634-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
ncRNAs are key players in the adaptation of bacteria to new environments, by modulating the composition of the membrane upon changes in the environment. Nevertheless, monitoring the changes in surface protein expression is still a challenge, since these proteins are present in low abundance, and are difficult to extract. Here is described a method to easily, reproducibly, and specifically enrich total protein extracts in surface proteins. This method comprises a direct labeling of surface proteins on living cells using fluorescent dyes, followed by total protein extraction and subsequent separation of these extracts by 2D gel electrophoresis.
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Affiliation(s)
- Pierre Fechter
- UMR7242 Biotechnologie et Signalisation Cellulaire, CNRS, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch-Graffenstaden, France.
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24
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Junker S, Maaβ S, Otto A, Michalik S, Morgenroth F, Gerth U, Hecker M, Becher D. Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus. MOLECULAR & CELLULAR PROTEOMICS : MCP 2017. [PMID: 29183913 DOI: 10.1074/mcp.ra117.000378.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.
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Affiliation(s)
- Sabryna Junker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Sandra Maaβ
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Andreas Otto
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Stephan Michalik
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | | | - Ulf Gerth
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Michael Hecker
- From the ‡Institute for Microbiology, University of Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, University of Greifswald, Germany
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25
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Fuchs S, Mehlan H, Bernhardt J, Hennig A, Michalik S, Surmann K, Pané-Farré J, Giese A, Weiss S, Backert L, Herbig A, Nieselt K, Hecker M, Völker U, Mäder U. AureoWiki ̵ The repository of the Staphylococcus aureus research and annotation community. Int J Med Microbiol 2017; 308:558-568. [PMID: 29198880 DOI: 10.1016/j.ijmm.2017.11.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 11/28/2022] Open
Abstract
In light of continuously accumulating data and knowledge on major human pathogens, comprehensive and up-to-date sources of easily accessible information are urgently required. The AureoWiki database (http://aureowiki.med.uni-greifswald.de) provides detailed information on the genes and proteins of clinically and experimentally relevant S. aureus strains, currently covering NCTC 8325, COL, Newman, USA300_FPR3757, and N315. By implementing a pan-genome approach, AureoWiki facilitates the transfer of knowledge gained in studies with different S. aureus strains, thus supporting functional annotation and better understanding of this organism. All data related to a given gene or gene product is compiled on a strain-specific gene page. The gene pages contain sequence-based information complemented by data on, for example, protein function and localization, transcriptional regulation, and gene expression. The information provided is connected via links to other databases and published literature. Importantly, orthologous genes of the individual strains, which are linked by a pan-genome gene identifier and a unified gene name, are presented side by side using strain-specific tabs. The respective pan-genome gene page contains an orthologue table for 32 S. aureus strains, a multiple-strain genome viewer, a protein sequence alignment as well as other comparative information. The data collected in AureoWiki is also accessible through various download options in order to support bioinformatics applications. In addition, based on two large-scale gene expression data sets, AureoWiki provides graphical representations of condition-dependent mRNA levels and protein profiles under various laboratory and infection-related conditions.
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Affiliation(s)
- Stephan Fuchs
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany; Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Henry Mehlan
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - André Hennig
- Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Anne Giese
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Linus Backert
- Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Alexander Herbig
- Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Kay Nieselt
- Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany; ZIK FunGene, Ernst-Moritz-Arndt-University Greifswald and University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; ZIK FunGene, Ernst-Moritz-Arndt-University Greifswald and University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
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26
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Stability of Proteins Out of Service: the GapB Case of Bacillus subtilis. J Bacteriol 2017; 199:JB.00148-17. [PMID: 28760849 DOI: 10.1128/jb.00148-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/22/2017] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis possesses two glyceraldehyde-3-phosphate dehydrogenases with opposite roles, the glycolytic NAD-dependent GapA and the NADP-dependent GapB enzyme, which is exclusively required during gluconeogenesis but not active under conditions promoting glycolysis. We propose that proteins that are no longer needed will be recognized and proteolyzed by Clp proteases and thereby recycled. To test this postulation, we analyzed the stability of the glycolytic enzyme GapA and the gluconeogenetic enzyme GapB in the presence and absence of glucose. It turned out that GapA remained rather stable under both glycolytic and gluconeogenetic conditions. In contrast, the gluconeogenetic enzyme GapB was degraded after a shift from malate to glucose (i.e., from gluconeogenesis to glycolysis), displaying an estimated half-life of approximately 3 h. Comparative in vivo pulse-chase labeling and immunoprecipitation experiments of the wild-type strain and isogenic mutants identified the ATP-dependent ClpCP protease as the enzyme responsible for the degradation of GapB. However, arginine protein phosphorylation, which was recently described as a general tagging mechanism for protein degradation, did not seem to play a role in GapB proteolysis, because GapB was also degraded in a mcsB mutant, lacking arginine kinase, in the same manner as in the wild type.IMPORTANCE GapB, the NADP-dependent glyceraldehyde-3-phosphosphate dehydrogenase, is essential for B. subtilis under gluconeogenetic conditions. However, after a shift to glycolytic conditions, GapB loses its physiological function within the cell and becomes susceptible to degradation, in contrast to GapA, the glycolytic NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, which remains stable under glycolytic and gluconeogenetic conditions. Subsequently, GapB is proteolyzed in a ClpCP-dependent manner. According to our data, the arginine kinase McsB is not involved as adaptor protein in this process. ClpCP appears to be in charge in the removal of inoperable enzymes in B. subtilis, which is a strictly regulated process in which the precise recognition mechanism(s) remains to be identified.
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27
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Kumari N, Götz F, Nguyen MT. Aspartate tightens the anchoring of staphylococcal lipoproteins to the cytoplasmic membrane. Microbiologyopen 2017; 6. [PMID: 28901671 PMCID: PMC5727369 DOI: 10.1002/mbo3.525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/22/2017] [Accepted: 07/03/2017] [Indexed: 12/16/2022] Open
Abstract
In gram-negative bacteria, the ABC transporter LolCDE complex translocates outer membrane-specific lipoproteins (Lpp) from the inner membrane to the outer membrane. Lpp possessing aspartate (Asp) at position +2 are not translocated because it functions as a LolCDE avoidance signal. In gram-positive bacteria, lacking an outer membrane and the Lol system, Lpp are only anchored at the outer leaflet of the cytoplasmic membrane. However, the release of Lpp particularly in pathogenic or commensal species is crucial for immune modulation. Here, we provide evidence that in Staphylococcus aureus Asp at position +2 plays a role in withholding Lpp to the cytoplasmic membrane. Screening of published exoproteomic data of S. aureus revealed that Lpp mainly with Gly or Ser at position +2 were found in exoproteome, but there was no Lpp with Asp+2. The occurrence of Lpp with Asp+2 is infrequent in gram-positive bacteria. In S. aureus USA300 only seven of the 67 Lpp possess Asp+2; among them five Lpp represented Lpl lipoproteins involved in host cell invasion. Our study demonstrated that replacing the Asp+2 present in Lpl8 with a Ser enhances its release into the supernatant. However, there is no different release of Asp+2 and Ser+2 in mprF mutant that lacks the positive charge of lysyl-phosphatidylglycerol (Lys-PG). Moreover, substitution of Ser+2 by Asp in SitC (MntC) did not lead to a decreased release indicating that in staphylococci positions +3 and +4 might also be important for a tighter anchoring of Lpp. Here, we show that Asp in position +2 and adjacent amino acids contribute in tightening the anchoring of Lpp by interaction of the negative charged Asp with the positive charged Lys-PG.
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Affiliation(s)
- Nimerta Kumari
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbial Genetics, University of Tübingen, Tübingen, Germany.,Institute of Microbiology, University of Sindh, Jamshoro, Pakistan
| | - Friedrich Götz
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbial Genetics, University of Tübingen, Tübingen, Germany
| | - Minh-Thu Nguyen
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbial Genetics, University of Tübingen, Tübingen, Germany.,School of Biological and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
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28
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A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions. Sci Rep 2017; 7:9718. [PMID: 28887440 PMCID: PMC5591248 DOI: 10.1038/s41598-017-10059-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/24/2017] [Indexed: 12/16/2022] Open
Abstract
Data-independent acquisition mass spectrometry promises higher performance in terms of quantification and reproducibility compared to data-dependent acquisition mass spectrometry methods. To enable high-accuracy quantification of Staphylococcus aureus proteins, we have developed a global ion library for data-independent acquisition approaches employing high-resolution time of flight or Orbitrap instruments for this human pathogen. We applied this ion library resource to investigate the time-resolved adaptation of S. aureus to the intracellular niche in human bronchial epithelial cells and in a murine pneumonia model. In epithelial cells, abundance changes for more than 400 S. aureus proteins were quantified, revealing, e.g., the precise temporal regulation of the SigB-dependent stress response and differential regulation of translation, fermentation, and amino acid biosynthesis. Using an in vivo murine pneumonia model, our data-independent acquisition quantification analysis revealed for the first time the in vivo proteome adaptation of S. aureus. From approximately 2.15 × 105 S. aureus cells, 578 proteins were identified. Increased abundance of proteins required for oxidative stress response, amino acid biosynthesis, and fermentation together with decreased abundance of ribosomal proteins and nucleotide reductase NrdEF was observed in post-infection samples compared to the pre-infection state.
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29
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Horvatić A, Kuleš J, Guillemin N, Galan A, Mrljak V, Bhide M. High-throughput proteomics and the fight against pathogens. MOLECULAR BIOSYSTEMS 2017; 12:2373-84. [PMID: 27227577 DOI: 10.1039/c6mb00223d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathogens pose a major threat to human and animal welfare. Understanding the interspecies host-pathogen protein-protein interactions could lead to the development of novel strategies to combat infectious diseases through the rapid development of new therapeutics. The first step in understanding the host-pathogen crosstalk is to identify interacting proteins in order to define crucial hot-spots in the host-pathogen interactome, such as the proposed pharmaceutical targets by means of high-throughput proteomic methodologies. In order to obtain holistic insight into the inter- and intra-species bimolecular interactions, apart from the proteomic approach, sophisticated in silico modeling is used to correlate the obtained large data sets with other omics data and clinical outcomes. Since the main focus in this area has been directed towards human medicine, it is time to extrapolate the existing expertise to a new emerging field: the 'systems veterinary medicine'. Therefore, this review addresses high-throughput mass spectrometry-based technology for monitoring protein-protein interactions in vitro and in vivo and discusses pathogen cultivation, model host cells and available bioinformatic tools employed in vaccine development.
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Affiliation(s)
- Anita Horvatić
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Josipa Kuleš
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Nicolas Guillemin
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Asier Galan
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Vladimir Mrljak
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Mangesh Bhide
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia. and Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia and Institute of Neuroimmunology, Slovakia Academy of Sciences, Bratislava, Slovakia
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30
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Yu Y, Bekele S, Pieper R. Quick 96FASP for high throughput quantitative proteome analysis. J Proteomics 2017; 166:1-7. [PMID: 28669814 DOI: 10.1016/j.jprot.2017.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/19/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3-5 times longer than single filter. To address this limitation, we now present a quick 96FASP (named q96FASP) approach that, relying on the use of filter membranes with a large MWCO size (~30kDa), significantly reduces centrifugal times. We show that q96FASP allows the generation of protein digests derived from whole cell lysates and body fluids in a quality similar to that of the single FASP method. Processing a sample in multiple wells in parallel, we observed excellent experimental repeatability by label-free quantitation approach. We conclude that the q96FASP approach promises to be a promising cost- and time-effective method for shotgun proteomics and will be particularly useful in large scale biomarker discovery studies. SIGNIFICANCE High throughput sample processing is of particular interests for quantitative proteomics. The previously developed 96FASP is high throughput and appealing, however it is time-consuming in the context of centrifugation-based liquid transfer (~1.5h per spin). This study presents a truly high throughput sample preparation method based on large cut-off 96-well filter plate, which shortens the spin time to ~20min. To our knowledge, this is the first multi-well method that is entirely comparable with conventional FASP. This study thoroughly examined two types of filter plates and performed side-by-side comparisons with single FASP. Two types of samples, whole cell lysate of a UTI (urinary tract infection)-associated Klebsiella pneumoniae cell and human urine, were tested which demonstrated its capability for quantitative proteomics. The q96FSAP approach makes the filter plate-based approach more appealing for protein biomarker discovery projects, and could be broadly applied to large scale proteomics analysis.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, United States.
| | - Shiferaw Bekele
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, United States
| | - Rembert Pieper
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, United States
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31
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An Intracellular Peptidyl-Prolyl cis/trans Isomerase Is Required for Folding and Activity of the Staphylococcus aureus Secreted Virulence Factor Nuclease. J Bacteriol 2016; 199:JB.00453-16. [PMID: 27795319 DOI: 10.1128/jb.00453-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that relies on a large repertoire of secreted and cell wall-associated proteins for pathogenesis. Consequently, the ability of the organism to cause disease is absolutely dependent on its ability to synthesize and successfully secrete these proteins. In this study, we investigate the role of peptidyl-prolyl cis/trans isomerases (PPIases) on the activity of the S. aureus secreted virulence factor nuclease (Nuc). We identify a staphylococcal cyclophilin-type PPIase (PpiB) that is required for optimal activity of Nuc. Disruption of ppiB results in decreased nuclease activity in culture supernatants; however, the levels of Nuc protein are not altered, suggesting that the decrease in activity results from misfolding of Nuc in the absence of PpiB. We go on to demonstrate that PpiB exhibits PPIase activity in vitro, is localized to the bacterial cytosol, and directly interacts with Nuc in vitro to accelerate the rate of Nuc refolding. Finally, we demonstrate an additional role for PpiB in S. aureus hemolysis and demonstrate that the S. aureus parvulin-type PPIase PrsA also plays a role in the activity of secreted virulence factors. The deletion of prsA leads to a decrease in secreted protease and phospholipase activity, similar to that observed in other Gram-positive pathogens. Together, these results demonstrate, for the first time to our knowledge, that PPIases play an important role in the secretion of virulence factors in S. aureus IMPORTANCE: Staphylococcus aureus is a highly dangerous bacterial pathogen capable of causing a variety of infections throughout the human body. The ability of S. aureus to cause disease is largely due to an extensive repertoire of secreted and cell wall-associated proteins, including adhesins, toxins, exoenzymes, and superantigens. These virulence factors, once produced, are typically transported across the cell membrane by the secretory (Sec) system in a denatured state. Consequently, once outside the cell, they must refold into their active form. This step often requires the assistance of bacterial folding proteins, such as PPIases. In this work, we investigate the role of PPIases in S. aureus and uncover a cyclophilin-type enzyme that assists in the folding/refolding of staphylococcal nuclease.
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32
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Shen J, Peng H, Zhang Y, Trinidad JC, Giedroc DP. Staphylococcus aureus sqr Encodes a Type II Sulfide:Quinone Oxidoreductase and Impacts Reactive Sulfur Speciation in Cells. Biochemistry 2016; 55:6524-6534. [PMID: 27806570 DOI: 10.1021/acs.biochem.6b00714] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent studies implicate hydrogen sulfide (H2S) oxidation as an important aspect of bacterial antibiotic resistance and sulfide homeostasis. The cst operon of the major human pathogen Staphylococcus aureus is induced by exogenous H2S stress and encodes enzymes involved in sulfide oxidation, including a group I flavoprotein disulfide oxidoreductase sulfide:quinone oxidoreductase (SQR). In this work, we show that S. aureus SQR catalyzes the two-electron oxidation of sodium sulfide (Na2S) into sulfane sulfur (S0) when provided flavin adenine dinucleotide and a water-soluble quinone acceptor. Cyanide, sulfite, and coenzyme A (CoA) are all capable of functioning as the S0 acceptor in vitro. This activity requires a C167-C344 disulfide bond in the resting enzyme, with the intermediacy of a C344 persulfide in the catalytic cycle, verified by mass spectrometry of sulfide-reacted SQR. Incubation of purified SQR and S. aureus CstB, a known FeII persulfide dioxygenase-sulfurtransferase also encoded by the cst operon, yields thiosulfate from sulfide, in a CoA-dependent manner, thus confirming the intermediacy of CoASSH as a product and substrate of SQR and CstB, respectively. Sulfur metabolite profiling of wild-type, Δsqr, and Δsqr::pSQR strains reveals a marked and specific elevation in endogenous levels of CoASSH and inorganic tetrasulfide in the Δsqr strain. We conclude that SQR impacts the cellular speciation of these reactive sulfur species but implicates other mechanisms not dependent on SQR in the formation of low-molecular weight thiol persulfides and inorganic polysulfides during misregulation of sulfide homeostasis.
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Affiliation(s)
- Jiangchuan Shen
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Biochemistry Graduate Program, Indiana University , Bloomington, Indiana 47405, United States
| | - Hui Peng
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Biochemistry Graduate Program, Indiana University , Bloomington, Indiana 47405, United States
| | - Yixiang Zhang
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Laboratory for Biological Mass Spectrometry, Indiana University , Bloomington, Indiana 47405, United States
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Laboratory for Biological Mass Spectrometry, Indiana University , Bloomington, Indiana 47405, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
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33
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Changes in the Expression of Biofilm-Associated Surface Proteins in Staphylococcus aureus Food-Environmental Isolates Subjected to Sublethal Concentrations of Disinfectants. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4034517. [PMID: 27868063 PMCID: PMC5102705 DOI: 10.1155/2016/4034517] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/05/2016] [Accepted: 09/21/2016] [Indexed: 12/15/2022]
Abstract
Sublethal concentrations (sub-MICs) of certain disinfectants are no longer effective in removing biofilms from abiotic surfaces and can even promote the formation of biofilms. Bacterial cells can probably adapt to these low concentrations of disinfectants and defend themselves by way of biofilm formation. In this paper, we report on three Staphylococcus aureus biofilm formers (strong B+++, moderate B++, and weak B+) that were cultivated with sub-MICs of commonly used disinfectants, ethanol or chloramine T, and quantified using Syto9 green fluorogenic nucleic acid stain. We demonstrate that 1.25–2.5% ethanol and 2500 μg/mL chloramine T significantly enhanced S. aureus biofilm formation. To visualize differences in biofilm compactness between S. aureus biofilms in control medium, 1.25% ethanol, or 2500 μg/mL chloramine T, scanning electron microscopy was used. To describe changes in abundance of surface-exposed proteins in ethanol- or chloramine T-treated biofilms, surface proteins were prepared using a novel trypsin shaving approach and quantified after dimethyl labeling by LC-LTQ/Orbitrap MS. Our data show that some proteins with adhesive functions and others with cell maintenance functions and virulence factor EsxA were significantly upregulated by both treatments. In contrast, immunoglobulin-binding protein A was significantly downregulated for both disinfectants. Significant differences were observed in the effect of the two disinfectants on the expression of surface proteins including some adhesins, foldase protein PrsA, and two virulence factors.
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Osbak KK, Houston S, Lithgow KV, Meehan CJ, Strouhal M, Šmajs D, Cameron CE, Van Ostade X, Kenyon CR, Van Raemdonck GA. Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry. PLoS Negl Trop Dis 2016; 10:e0004988. [PMID: 27606673 PMCID: PMC5015957 DOI: 10.1371/journal.pntd.0004988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/19/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. METHODOLOGY/PRINCIPAL FINDINGS To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. CONCLUSIONS This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.
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Affiliation(s)
- Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Karen V Lithgow
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
| | - Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
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Zühlke D, Dörries K, Bernhardt J, Maaß S, Muntel J, Liebscher V, Pané-Farré J, Riedel K, Lalk M, Völker U, Engelmann S, Becher D, Fuchs S, Hecker M. Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis. Sci Rep 2016; 6:28172. [PMID: 27344979 PMCID: PMC4921807 DOI: 10.1038/srep28172] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/31/2016] [Indexed: 01/19/2023] Open
Abstract
Absolute protein quantification was applied to follow the dynamics of the cytoplasmic proteome of Staphylococcus aureus in response to long-term oxygen starvation. For 1,168 proteins, the majority of all expressed proteins, molecule numbers per cell have been determined to monitor the cellular investments in single branches of bacterial life for the first time. In the presence of glucose the anaerobic protein pattern is characterized by increased amounts of glycolytic and fermentative enzymes such as Eno, GapA1, Ldh1, and PflB. Interestingly, the ferritin-like protein FtnA belongs to the most abundant proteins during anaerobic growth. Depletion of glucose finally leads to an accumulation of different enzymes such as ArcB1, ArcB2, and ArcC2 involved in arginine deiminase pathway. Concentrations of 29 exo- and 78 endometabolites were comparatively assessed and have been integrated to the metabolic networks. Here we provide an almost complete picture on the response to oxygen starvation, from signal transduction pathways to gene expression pattern, from metabolic reorganization after oxygen depletion to beginning cell death and lysis after glucose exhaustion. This experimental approach can be considered as a proof of principle how to combine cell physiology with quantitative proteomics for a new dimension in understanding simple life processes as an entity.
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Affiliation(s)
- Daniela Zühlke
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Kirsten Dörries
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Sandra Maaß
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Jan Muntel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Volkmar Liebscher
- Department of Mathematics and Informatics, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Strasse 47, D-17487 Greifswald, Germany
| | - Jan Pané-Farré
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15 a, D-17487 Greifswald, Germany
| | - Susanne Engelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Institute of Microbiology, Technical University Braunschweig, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.,Helmholtz Institute for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Burgstrasse 37, D-38855 Wernigerode, Germany
| | - Michael Hecker
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
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Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes 2016; 4:proteomes4010011. [PMID: 28248221 PMCID: PMC5217363 DOI: 10.3390/proteomes4010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.
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Smith DS, Siggins MK, Gierula M, Pichon B, Turner CE, Lynskey NN, Mosavie M, Kearns AM, Edwards RJ, Sriskandan S. Identification of commonly expressed exoproteins and proteolytic cleavage events by proteomic mining of clinically relevant UK isolates of Staphylococcus aureus. Microb Genom 2016; 2:e000049. [PMID: 28348843 PMCID: PMC5320583 DOI: 10.1099/mgen.0.000049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022] Open
Abstract
The range of exoproteins and core exoproteome of 14 Staphylococcus aureus isolates representing major lineages associated with asymptomatic carriage and clinical disease in the UK was identified by MS proteomics using a combined database incorporating sequences derived from 39 S. aureus genomes. In all, 632 different proteins were identified and, of these, only 52 (8 %) were found in all 14 isolates whereas 144 (23 %) were found in just a single isolate. Comparison of the observed mass of each protein (based on migration by SDS-PAGE) with its predicted mass (based on amino acid sequence) suggested that 95 % of the proteins identified were not subject to any major post-translational modification. Migration of 5 % of the proteins was not as expected: 1 % of the proteins migrated at a mass greater than predicted, while 4 % appeared to have undergone proteolytic cleavage; these included SsaA2, Aur, SspP, Ebh as well as BlaR1, MecR1, FsH, OatA and LtaS. Intriguingly, a truncated SasG was produced by a single CC8 USA300-like strain. The analysis provided evidence of the marked heterogeneity in protein expression by S. aureus in broth, while yielding a core but narrow common exoproteome.
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Affiliation(s)
- Debra S Smith
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Matthew K Siggins
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Magdalena Gierula
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Bruno Pichon
- 2Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom
| | - Claire E Turner
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Nicola N Lynskey
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Mia Mosavie
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Angela M Kearns
- 2Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom
| | - Robert J Edwards
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Shiranee Sriskandan
- 1Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
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Soufi Y, Soufi B. Mass Spectrometry-Based Bacterial Proteomics: Focus on Dermatologic Microbial Pathogens. Front Microbiol 2016; 7:181. [PMID: 26925048 PMCID: PMC4759281 DOI: 10.3389/fmicb.2016.00181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 02/02/2016] [Indexed: 12/14/2022] Open
Abstract
The composition of human skin acts as a natural habitat for various bacterial species that function in a commensal and symbiotic fashion. In a healthy individual, bacterial flora serves to protect the host. Under certain conditions such as minor trauma, impaired host immunity, or environmental factors, the risk of developing skin infections is increased. Although a large majority of bacterial associated skin infections are common, a portion can potentially manifest into clinically significant morbidity. For example, Gram-positive species that typically reside on the skin such as Staphylococcus and Streptococcus can cause numerous epidermal (impetigo, ecthyma) and dermal (cellulitis, necrotizing fasciitis, erysipelas) skin infections. Moreover, the increasing incidence of bacterial antibiotic resistance represents a serious challenge to modern medicine and threatens the health care system. Therefore, it is critical to develop tools and strategies that can allow us to better elucidate the nature and mechanism of bacterial virulence. To this end, mass spectrometry (MS)-based proteomics has been revolutionizing biomedical research, and has positively impacted the microbiology field. Advances in MS technologies have paved the way for numerous bacterial proteomes and their respective post translational modifications (PTMs) to be accurately identified and quantified in a high throughput and robust fashion. This technological platform offers critical information with regards to signal transduction, adherence, and microbial–host interactions associated with bacterial pathogenesis. This mini-review serves to highlight the current progress proteomics has contributed toward the understanding of bacteria that are associated with skin related diseases, infections, and antibiotic resistance.
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Affiliation(s)
- Youcef Soufi
- College of Medicine, University of Manitoba, Winnipeg MB, Canada
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Semanjski M, Macek B. Shotgun proteomics of bacterial pathogens: advances, challenges and clinical implications. Expert Rev Proteomics 2016; 13:139-56. [PMID: 26653908 DOI: 10.1586/14789450.2016.1132168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry-based proteomics is increasingly used in analysis of bacterial pathogens. Simple experimental set-ups based on high accuracy mass spectrometry and powerful biochemical and bioinformatics tools are capable of reliably quantifying levels of several thousand bacterial proteins in a single experiment, reaching the analytical capacity to completely map whole proteomes. Here the authors present the state-of-the-art in bacterial pathogen proteomics and discuss challenges that the field is facing, especially in analysis of low abundant, modified proteins from organisms that are difficult to culture. Constant improvements in speed and sensitivity of mass spectrometers, as well as in bioinformatic and biochemical workflows will soon allow for comprehensive analysis of regulatory mechanisms of pathogenicity and enable routine application of proteomics in the clinical setting.
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Affiliation(s)
- Maja Semanjski
- a Quantitative Proteomics and Proteome Center Tuebingen, Interfaculty Institute for Cell Biology , University of Tuebingen , Tuebingen , Germany
| | - Boris Macek
- a Quantitative Proteomics and Proteome Center Tuebingen, Interfaculty Institute for Cell Biology , University of Tuebingen , Tuebingen , Germany
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40
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comparative proteome analysis of Actinoplanes sp. SE50/110 grown with maltose or glucose shows minor differences for acarbose biosynthesis proteins but major differences for saccharide transporters. J Proteomics 2016; 131:140-148. [DOI: 10.1016/j.jprot.2015.10.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/13/2015] [Accepted: 10/20/2015] [Indexed: 01/08/2023]
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41
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Aurass P, Gerlach T, Becher D, Voigt B, Karste S, Bernhardt J, Riedel K, Hecker M, Flieger A. Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors. Mol Cell Proteomics 2015; 15:177-200. [PMID: 26545400 DOI: 10.1074/mcp.m115.053579] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 12/28/2022] Open
Abstract
Major differences in the transcriptional program underlying the phenotypic switch between exponential and post-exponential growth of Legionella pneumophila were formerly described characterizing important alterations in infection capacity. Additionally, a third state is known where the bacteria transform in a viable but nonculturable state under stress, such as starvation. We here describe phase-related proteomic changes in exponential phase (E), postexponential phase (PE) bacteria, and unculturable microcosms (UNC) containing viable but nonculturable state cells, and identify phase-specific proteins. We present data on different bacterial subproteomes of E and PE, such as soluble whole cell proteins, outer membrane-associated proteins, and extracellular proteins. In total, 1368 different proteins were identified, 922 were quantified and 397 showed differential abundance in E/PE. The quantified subproteomes of soluble whole cell proteins, outer membrane-associated proteins, and extracellular proteins; 841, 55, and 77 proteins, respectively, were visualized in Voronoi treemaps. 95 proteins were quantified exclusively in E, such as cell division proteins MreC, FtsN, FtsA, and ZipA; 33 exclusively in PE, such as motility-related proteins of flagellum biogenesis FlgE, FlgK, and FliA; and 9 exclusively in unculturable microcosms soluble whole cell proteins, such as hypothetical, as well as transport/binding-, and metabolism-related proteins. A high frequency of differentially abundant or phase-exclusive proteins was observed among the 91 quantified effectors of the major virulence-associated protein secretion system Dot/Icm (> 60%). 24 were E-exclusive, such as LepA/B, YlfA, MavG, Lpg2271, and 13 were PE-exclusive, such as RalF, VipD, Lem10. The growth phase-related specific abundance of a subset of Dot/Icm virulence effectors was confirmed by means of Western blotting. We therefore conclude that many effectors are predominantly abundant at either E or PE which suggests their phase specific function. The distinct temporal or spatial presence of such proteins might have important implications for functional assignments in the future or for use as life-stage specific markers for pathogen analysis.
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Affiliation(s)
- Philipp Aurass
- From the ‡Robert Koch-Institut, Wernigerode Branch, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Thomas Gerlach
- From the ‡Robert Koch-Institut, Wernigerode Branch, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Dörte Becher
- §Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Birgit Voigt
- §Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Susanne Karste
- From the ‡Robert Koch-Institut, Wernigerode Branch, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Jörg Bernhardt
- §Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Katharina Riedel
- §Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Michael Hecker
- §Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Antje Flieger
- From the ‡Robert Koch-Institut, Wernigerode Branch, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany;
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George SE, Nguyen T, Geiger T, Weidenmaier C, Lee JC, Liese J, Wolz C. Phenotypic heterogeneity and temporal expression of the capsular polysaccharide in Staphylococcus aureus. Mol Microbiol 2015; 98:1073-88. [PMID: 26303846 DOI: 10.1111/mmi.13174] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2015] [Indexed: 01/18/2023]
Abstract
Bacteria respond to ever-changing environments through several adaptive strategies. This includes mechanisms leading to a high degree of phenotypic variability within a genetically homogeneous population. In Staphylococcus aureus, the capsular polysaccharide (CP) protects against phagocytosis, but also impedes adherence to endothelial cells and/or matrix proteins. We analysed the regulation of core biosynthesis genes (capA-P) necessary for CP synthesis using single-cell assays (immunofluorescence and promoter-activity). In persistent human carriers, we found a distinct subpopulation of nasal S. aureus to be CP positive. In vitro, cap expression is also heterogeneous and strongly growth-phase dependent. We asked whether this peculiar expression pattern (earlyOff/lateHeterogen) is orchestrated by the quorum system Agr. We show that the Agr-driven effector molecule RNAIII promotes cap expression largely via inactivation of the repressor Rot. High NaCl, deletion of CodY or Sae also resulted in higher cap expression but did not change the earlyOFF/lateHeterogen expression pattern. Activity of the quorum system itself is largely homogenous and does not account for the observed heterogeneity of cap expression or the strictly growth phase dependent expression. Our findings are in contrast to the prevailing view that quorum sensing is the main driving force for virulence gene expression when bacterial cell densities increase.
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Affiliation(s)
- Shilpa E George
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Tran Nguyen
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Tobias Geiger
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christopher Weidenmaier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Jean C Lee
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jan Liese
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
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Depke M, Michalik S, Rabe A, Surmann K, Brinkmann L, Jehmlich N, Bernhardt J, Hecker M, Wollscheid B, Sun Z, Moritz RL, Völker U, Schmidt F. A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies. Proteomics 2015. [PMID: 26224020 DOI: 10.1002/pmic.201500091] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Staphylococcus aureus is an opportunistic human pathogen, which can cause life-threatening disease. Proteome analyses of the bacterium can provide new insights into its pathophysiology and important facets of metabolic adaptation and, thus, aid the recognition of targets for intervention. However, the value of such proteome studies increases with their comprehensiveness. We present an MS-driven, proteome-wide characterization of the strain S. aureus HG001. Combining 144 high precision proteomic data sets, we identified 19 109 peptides from 2088 distinct S. aureus HG001 proteins, which account for 72% of the predicted ORFs. Peptides were further characterized concerning pI, GRAVY, and detectability scores in order to understand the low peptide coverage of 8.7% (19 109 out of 220 245 theoretical peptides). The high quality peptide-centric spectra have been organized into a comprehensive peptide fragmentation library (SpectraST) and used for identification of S. aureus-typic peptides in highly complex host-pathogen interaction experiments, which significantly improved the number of identified S. aureus proteins compared to a MASCOT search. This effort now allows the elucidation of crucial pathophysiological questions in S. aureus-specific host-pathogen interaction studies through comprehensive proteome analysis. The S. aureus-specific spectra resource developed here also represents an important spectral repository for SRM or for data-independent acquisition MS approaches. All MS data have been deposited in the ProteomeXchange with identifier PXD000702 (http://proteomecentral.proteomexchange.org/dataset/PXD000702).
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Affiliation(s)
- Maren Depke
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Rabe
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Brinkmann
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Nico Jehmlich
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, WA, USA
| | | | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank Schmidt
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D. Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions. J Proteome Res 2015; 14:3804-22. [DOI: 10.1021/acs.jproteome.5b00148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Moche
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Kristina Plate
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Katharina Riedel
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
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Surmann K, Simon M, Hildebrandt P, Pförtner H, Michalik S, Stentzel S, Steil L, Dhople VM, Bernhardt J, Schlüter R, Depke M, Gierok P, Lalk M, Bröker BM, Schmidt F, Völker U. A proteomic perspective of the interplay of Staphylococcus aureus and human alveolar epithelial cells during infection. J Proteomics 2015; 128:203-17. [PMID: 26244908 DOI: 10.1016/j.jprot.2015.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022]
Abstract
Infectious diseases caused by pathogens such as Staphylococcus aureus are still a major threat for human health. Proteome analyses allow detailed monitoring of the molecular interplay between pathogen and host upon internalization. However, the investigation of the responses of both partners is complicated by the large excess of host cell proteins compared to bacterial proteins as well as by the fact that only a fraction of host cells are infected. In the present study we infected human alveolar epithelial A549 cells with S. aureus HG001 pMV158GFP and separated intact bacteria from host cell debris or infected from non-infected A549 cells by cell sorting to enable detailed proteome analysis. During the first 6.5h in the intracellular milieu S. aureus displayed reduced growth rate, induction of the stringent response, adaptation to microaerobic conditions as well as cell wall stress. Interestingly, both truly infected host cells and those not infected but exposed to secreted S. aureus proteins and host cell factors showed differences in the proteome pattern compared to A549 cells which had never been in contact with S. aureus. However, adaptation reactions were more pronounced in infected compared to non-infected A549 bystander cells.
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Affiliation(s)
- Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Marjolaine Simon
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Henrike Pförtner
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Sebastian Stentzel
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Sauerbruchstr. DZ7, 17475 Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Vishnu M Dhople
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Maren Depke
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Philipp Gierok
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Barbara M Bröker
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Sauerbruchstr. DZ7, 17475 Greifswald, Germany
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany.
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Theilacker C, Diederich AK, Otto A, Sava IG, Wobser D, Bao Y, Hese K, Broszat M, Henneke P, Becher D, Huebner J. Enterococcus faecalis Glycolipids Modulate Lipoprotein-Content of the Bacterial Cell Membrane and Host Immune Response. PLoS One 2015; 10:e0132949. [PMID: 26172831 PMCID: PMC4501811 DOI: 10.1371/journal.pone.0132949] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 06/21/2015] [Indexed: 12/25/2022] Open
Abstract
In this study, we investigated the impact of the cell membrane composition of E. faecalis on its recognition by the host immune system. To this end, we employed an E. faecalis deletion mutant (ΔbgsA) that does not synthesize the major cell membrane glycolipid diglycosyl-diacylglycerol (DGlcDAG). Proteomic analysis revealed that 13 of a total of 21 upregulated surface-associated proteins of E. faecalis ΔbgsA were lipoproteins. This led to a total lipoprotein content in the cell membrane of 35.8% in ΔbgsA compared to only 9.4% in wild-type bacteria. Increased lipoprotein content strongly affected the recognition of ΔbgsA by mouse macrophages in vitro with an increased stimulation of TNF-α production by heat-fixed bacteria and secreted antigens. Inactivation of the prolipoprotein diacylglycerol transferase (lgt) in ΔbgsA abrogated TNF-α induction by a ΔbgsA_lgt double mutant indicating that lipoproteins mediate increased activation of mouse macrophages by ΔbgsA. Heat-fixed ΔbgsA bacteria, culture supernatant, or cell membrane lipid extract activated transfected HEK cells in a TLR2-dependent fashion; the same was not true of wild-type bacteria. In mice infected intraperitoneally with a sublethal dose of E. faecalis we observed a 70% greater mortality in mice infected with ΔbgsA compared with wild-type-infected mice. Increased mortality due to ΔbgsA infection was associated with elevated plasma levels of the inflammatory cytokines TNF-α, IL-6 and MIP-2. In summary, our results provide evidence that an E. faecalis mutant lacking its major bilayer forming glycolipid DGlcDAG upregulates lipoprotein expression leading to increased activation of the host innate immune system and virulence in vivo.
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Affiliation(s)
- Christian Theilacker
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg, Freiburg, Germany
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany
- * E-mail:
| | - Ann-Kristin Diederich
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany
- Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Microbiology, Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Andreas Otto
- Institute for Microbiology, Department of Microbial Physiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Irina G. Sava
- Research Center for Nutrition and Food Science, Technical University Munich, Freising, Germany
| | - Dominique Wobser
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Yinyin Bao
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Katrin Hese
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg, Freiburg, Germany
| | - Melanie Broszat
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Philipp Henneke
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg, Freiburg, Germany
- Center for Paediatrics and Adolescent Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Dörte Becher
- Institute for Microbiology, Department of Microbial Physiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Johannes Huebner
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany
- Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
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47
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster. J Proteomics 2015; 125:1-16. [DOI: 10.1016/j.jprot.2015.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 01/05/2023]
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Voigt B, Albrecht D, Sievers S, Becher D, Bongaerts J, Evers S, Schweder T, Maurer KH, Hecker M. High-resolution proteome maps of Bacillus licheniformis
cells growing in minimal medium. Proteomics 2015; 15:2629-33. [DOI: 10.1002/pmic.201400504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/09/2015] [Accepted: 04/09/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Birgit Voigt
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dirk Albrecht
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Susanne Sievers
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dörte Becher
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology; Aachen University of Applied Sciences; Jülich Germany
| | | | - Thomas Schweder
- Institute of Pharmacy; Ernst-Moritz-Arndt-University; Greifswald Germany
| | | | - Michael Hecker
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
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49
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Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data. Int J Med Microbiol 2015; 305:339-47. [DOI: 10.1016/j.ijmm.2015.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 01/21/2015] [Accepted: 02/09/2015] [Indexed: 01/25/2023] Open
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50
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Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:135-54. [PMID: 26621466 DOI: 10.1007/978-3-319-23603-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
High-throughput genomic and proteomic methods provide a concise description of the molecular constituents of a cell, whereas systems biology strives to understand the way these components function as a whole. Recent developments, such as genome editing technologies and protein epitope-tagging coupled with high-sensitivity mass-spectrometry, allow systemic studies to be performed at an unprecedented scale. Available methods can be successfully applied to various goals, both expanding fundamental knowledge and solving applied problems. In this review, we discuss the present state and future of bacterial cell envelope interactomics, with a specific focus on host-pathogen interactions and drug target discovery. Both experimental and computational methods will be outlined together with examples of their practical implementation.
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