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Barreiro C, Ibáñez AM. Bidimensional Analyses of the Intra- and Extracellular Proteomes of Steroid Producer Mycobacteria. Methods Mol Biol 2023; 2704:115-141. [PMID: 37642841 DOI: 10.1007/978-1-0716-3385-4_7] [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: 08/31/2023]
Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. However, those industrially relevant mycobacteria have received less attention, even though the steroid market sales in 2021 were estimated in $56.45 billion.The extracellular proteome, due to its relevance in the sterol processing and uptake, and the intracellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. Both, monodimensional gels, as preparatory analysis, and bidimensional gels as proteome analysis are described. As a proof of concept, the protein extraction methods for both sub-proteomes of Mycobacterium are described. Thus, procedures and relevant key points of these proteome analyses are fully detailed.
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Affiliation(s)
- Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain.
| | - Ana M Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, León, Spain
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, Valladolid, Spain
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Cho YS, Lee SE, Jang Y, Jung S, Kim JM. Identification of B cell antigenome in Mycobacterium bovis by immunoproteomic analysis. Acta Vet Hung 2020; 68:123-129. [PMID: 33055304 DOI: 10.1556/004.2020.00019] [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: 09/05/2019] [Accepted: 02/28/2020] [Indexed: 11/19/2022]
Abstract
Bovine tuberculosis (bTB) is a common zoonosis prevalent in many countries with grave economic consequences. Most developed and developing countries have implemented the test-and-slaughter policy to protect public health and reduce economic losses in the cattle industry. The official diagnosis of bTB is based on assays dependent on cell-mediated immunity (CMI). CMI-based diagnosis demonstrates diagnostic incapability at late stages of infection, which could be overcome by diagnosis based on humoral immunity (HI). Therefore, there is an urgent need to identify and define the B cell antigenome of Mycobacterium bovis. In this study, the B cell antigenome of culture filtrate proteins (CFP) was defined by mass spectrometry-based proteomics technology. Four spots were detected on 2-dimensional gel electrophoresis (2-DE) against M. bovis-positive serum in an immunoblotting experiment. Twenty-one proteins were identified in four spots by proteomic tools, such as Mb2900, Mb2898, Mb0448, Mb3834c, Mb1918c, Mb0134c, Mb0358 and Mb1868c, which are known B cell antigens, including 13 new proteins, i.e. Mb3751, Mb2006c, Mb3276c, Mb2244, Mb1164c, Mb2553c, Mb2946c, Mb1849c, Mb1511c, Mb1034c, Mb2616c, Mb0854c and Mb2267. These new proteins identified by 2-DE and immunoblotting were the B cell antigens used in developing serological diagnostic methods based on HI to bTB.
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Affiliation(s)
- Yun Sang Cho
- Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Sang Eun Lee
- Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Youngboo Jang
- Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Sukchan Jung
- Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Jong Man Kim
- Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
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Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development. Int J Mol Sci 2020; 21:ijms21196979. [PMID: 32977381 PMCID: PMC7582311 DOI: 10.3390/ijms21196979] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is a major public health concern for all ages. However, the disease presents a larger challenge in pediatric populations, partially owing to the lack of reliable diagnostic standards for the early identification of infection. Currently, there are no biomarkers that have been clinically validated for use in pediatric TB diagnosis. Identification and validation of biomarkers could provide critical information on prognosis of disease, and response to treatment. In this review, we discuss how the “omics” approach has influenced biomarker discovery and the advancement of a next generation rapid point-of-care diagnostic for TB, with special emphasis on pediatric disease. Limitations of current published studies and the barriers to their implementation into the field will be thoroughly reviewed within this article in hopes of highlighting future avenues and needs for combating the problem of pediatric tuberculosis.
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Song L, Wallstrom G, Yu X, Hopper M, Van Duine J, Steel J, Park J, Wiktor P, Kahn P, Brunner A, Wilson D, Jenny-Avital ER, Qiu J, Labaer J, Magee DM, Achkar JM. Identification of Antibody Targets for Tuberculosis Serology using High-Density Nucleic Acid Programmable Protein Arrays. Mol Cell Proteomics 2017; 16:S277-S289. [PMID: 28223349 DOI: 10.1074/mcp.m116.065953] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/17/2017] [Indexed: 12/11/2022] Open
Abstract
Better and more diverse biomarkers for the development of simple point-of-care tests for active tuberculosis (TB), a clinically heterogeneous disease, are urgently needed. We generated a proteomic Mycobacterium tuberculosis (Mtb) High-Density Nucleic Acid Programmable Protein Array (HD-NAPPA) that used a novel multiplexed strategy for expedited high-throughput screening for antibody responses to the Mtb proteome. We screened sera from HIV uninfected and coinfected TB patients and controls (n = 120) from the US and South Africa (SA) using the multiplex HD-NAPPA for discovery, followed by deconvolution and validation through single protein HD-NAPPA with biologically independent samples (n = 124). We verified the top proteins with enzyme-linked immunosorbent assays (ELISA) using the original screening and validation samples (n = 244) and heretofore untested samples (n = 41). We identified 8 proteins with TB biomarker value; four (Rv0054, Rv0831c, Rv2031c and Rv0222) of these were previously identified in serology studies, and four (Rv0948c, Rv2853, Rv3405c, Rv3544c) were not known to elicit antibody responses. Using ELISA data, we created classifiers that could discriminate patients' TB status according to geography (US or SA) and HIV (HIV- or HIV+) status. With ROC curve analysis under cross validation, the classifiers performed with an AUC for US/HIV- at 0.807; US/HIV+ at 0.782; SA/HIV- at 0.868; and SA/HIV+ at 0.723. With this study we demonstrate a new platform for biomarker/antibody screening and delineate its utility to identify previously unknown immunoreactive proteins.
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Affiliation(s)
- Lusheng Song
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Garrick Wallstrom
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Xiaobo Yu
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Marika Hopper
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Jennifer Van Duine
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Jason Steel
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Jin Park
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Peter Wiktor
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287.,¶Engineering Arts LLC, Tempe, Arizona 85287
| | - Peter Kahn
- ¶Engineering Arts LLC, Tempe, Arizona 85287
| | - Al Brunner
- ¶Engineering Arts LLC, Tempe, Arizona 85287
| | - Douglas Wilson
- ‖Department of Internal Medicine, Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Ji Qiu
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Joshua Labaer
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - D Mitchell Magee
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287;
| | - Jacqueline M Achkar
- **Departments of Medicine and .,‡‡Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
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Barreiro C, Morales A, Vázquez-Iglesias I, Sola-Landa A. Intra- and Extra-cellular Proteome Analyses of Steroid-Producer Mycobacteria. Methods Mol Biol 2017; 1645:73-92. [PMID: 28710622 DOI: 10.1007/978-1-4939-7183-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. In contrast, those industrially relevant mycobacteria have received less attention, even though the steroids market sales in 2011, in example, were estimated in $8 billion.The extra-cellular proteome, due to its relevance in the sterols processing and uptake; as well as the intra-cellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. As a proof of concept, the obtaining methods for both sub-proteomes of Mycobacterium neoaurum NRRL B-3805, a relevant industrial strain involved in steroids production, have been developed. Thus, procedures and relevant key points of these proteomes analyses are fully described.
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Affiliation(s)
- Carlos Barreiro
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain.
- Área de Microbiología, Departamento de Biología Molecular, Campus de Ponferrada, Universidad de León, Avda. Astorga, s/n, 24400, Ponferrada, Spain.
| | - Alejandro Morales
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
| | - Inés Vázquez-Iglesias
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
| | - Alberto Sola-Landa
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
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Genomic Changes Associated with the Loss of Nocardia brasiliensis Virulence in Mice after 200 In Vitro Passages. Infect Immun 2016; 84:2595-606. [PMID: 27354446 DOI: 10.1128/iai.00329-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/18/2016] [Indexed: 11/20/2022] Open
Abstract
Nocardia species, particularly Nocardia brasiliensis, are etiologic agents of mycetoma, a chronic subcutaneous infection. Until now, little has been known about the pathogenic mechanisms involved in nocardial infection. Traditionally, subculture in rich media has been a simple way to induce attenuation. In this work, we report the changes in virulence toward mice and in genomic constitution of N. brasiliensis produced after 200 continuous subcultures in brain heart infusion (BHI) medium (P-200 strain). The ability of the N. brasiliensis P-200 strain to produce experimental infection was tested using BALB/c mice. P-200 was also used to immunize mice to determine whether it could induce resistance against a challenge with a nonsubcultured isolate (P-0). Comparative proteomic analysis between N. brasiliensis P-0 and P-200 was performed by two-dimensional (2-D) electrophoresis, and the genome sequence was obtained through Roche 454 sequence analysis. Virulence in BALB/c mice was completely lost, and BALB/c mice immunized with P-200 bacterial cells were resistant to mycetoma production by the nonsubcultured strain. Whole-genome sequence analysis revealed that P-200 lost a total of 262,913 bp distributed in 19 deleted regions, involving a total of 213 open reading frames (ORFs). The deleted genes included those encoding bacterial virulence factors, e.g., catalase, nitrate reductase enzymes, and a group of mammalian cell entry (MCE) family proteins, which may explain the loss of virulence of the isolate. Thus, completely attenuated N. brasiliensis was obtained after 200 passages in BHI medium, and putative Nocardia virulence genes were identified for the first time.
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Imkamp F, Ziemski M, Weber-Ban E. Pupylation-dependent and -independent proteasomal degradation in mycobacteria. Biomol Concepts 2016; 6:285-301. [PMID: 26352358 DOI: 10.1515/bmc-2015-0017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/08/2015] [Indexed: 02/02/2023] Open
Abstract
Bacteria make use of compartmentalizing protease complexes, similar in architecture but not homologous to the eukaryotic proteasome, for the selective and processive removal of proteins. Mycobacteria as members of the actinobacteria harbor proteasomes in addition to the canonical bacterial degradation complexes. Mycobacterial proteasomal degradation, although not essential during normal growth, becomes critical for survival under particular environmental conditions, like, for example, during persistence of the pathogenic Mycobacterium tuberculosis in host macrophages or of environmental mycobacteria under starvation. Recruitment of protein substrates for proteasomal degradation is usually mediated by pupylation, the post-translational modification of lysine side chains with the prokaryotic ubiquitin-like protein Pup. This substrate recruitment strategy is functionally reminiscent of ubiquitination in eukaryotes, but is the result of convergent evolution, relying on chemically and structurally distinct enzymes. Pupylated substrates are recognized by the ATP-dependent proteasomal regulator Mpa that associates with the 20S proteasome core. A pupylation-independent proteasome degradation pathway has recently been discovered that is mediated by the ATP-independent bacterial proteasome activator Bpa (also referred to as PafE), and that appears to play a role under stress conditions. In this review, mechanistic principles of bacterial proteasomal degradation are discussed and compared with functionally related elements of the eukaryotic ubiquitin-proteasome system. Special attention is given to an understanding on the molecular level based on structural and biochemical analysis. Wherever available, discussion of in vivo studies is included to highlight the biological significance of this unusual bacterial degradation pathway.
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Abstract
The emerging field of proteomics has contributed greatly to improving our understanding of the human pathogen Mycobacterium tuberculosis over the last two decades. In this chapter we provide a comprehensive overview of mycobacterial proteome research and highlight key findings. First, studies employing a combination of two-dimensional gel electrophoresis and mass spectrometry (MS) provided insights into the proteomic composition, initially of the whole bacillus and subsequently of subfractions, such as the cell wall, cytosol, and secreted proteins. Comparison of results obtained under various culture conditions, i.e., acidic pH, nutrient starvation, and low oxygen tension, aiming to mimic facets of the intracellular lifestyle of M. tuberculosis, provided initial clues to proteins relevant for intracellular survival and manipulation of the host cell. Further attempts were aimed at identifying the biological functions of the hypothetical M. tuberculosis proteins, which still make up a quarter of the gene products of M. tuberculosis, and at characterizing posttranslational modifications. Recent technological advances in MS have given rise to new methods such as selected reaction monitoring (SRM) and data-independent acquisition (DIA). These targeted, cutting-edge techniques combined with a public database of specific MS assays covering the entire proteome of M. tuberculosis allow the simple and reliable detection of any mycobacterial protein. Most recent studies attempt not only to identify but also to quantify absolute amounts of single proteins in the complex background of host cells without prior sample fractionation or enrichment. Finally, we will discuss the potential of proteomics to advance vaccinology, drug discovery, and biomarker identification to improve intervention and prevention measures for tuberculosis.
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9
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A proteome reference map and virulence factors analysis of Yersinia pestis 91001. J Proteomics 2012; 75:894-907. [DOI: 10.1016/j.jprot.2011.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/27/2011] [Accepted: 10/08/2011] [Indexed: 01/06/2023]
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Wang XM, Lu C, Soetaert K, S'Heeren C, Peirs P, Lanéelle MA, Lefèvre P, Bifani P, Content J, Daffé M, Huygen K, De Bruyn J, Wattiez R. Biochemical and immunological characterization of a cpn60.1 knockout mutant of Mycobacterium bovis BCG. MICROBIOLOGY-SGM 2010; 157:1205-1219. [PMID: 21127129 DOI: 10.1099/mic.0.045120-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pathogenic mycobacteria possess two homologous chaperones encoded by cpn60.1 and cpn60.2. Cpn60.2 is essential for survival, providing the basic chaperone function, while Cpn60.1 is not. In the present study, we show that inactivation of the Mycobacterium bovis BCG cpn60.1 (Mb3451c) gene does not significantly affect bacterial growth in 7H9 broth, but that this knockout mutant (Δcpn60.1) forms smaller colonies on solid 7H11 medium than the parental and complemented strains. When growing on Sauton medium, the Δcpn60.1 mutant exhibits a thinner surface pellicle and is associated with higher culture filtrate protein content and, coincidentally, with less protein in its outermost cell envelope in comparison with the parental and complemented strains. Interestingly, in this culture condition, the Δcpn60.1 mutant is devoid of phthiocerol dimycocerosates, and its mycolates are two carbon atoms longer than those of the wild-type, a phenotype that is fully reversed by complementation. In addition, Δcpn60.1 bacteria are more sensitive to stress induced by H(2)O(2) but not by SDS, high temperature or acidic pH. Taken together, these data indicate that the cell wall of the Δcpn60.1 mutant is impaired. Analysis by 2D gel electrophoresis and MS reveals the upregulation of a few proteins such as FadA2 and isocitrate lyase in the cell extract of the mutant, whereas more profound differences are found in the composition of the mycobacterial culture filtrate, e.g. the well-known Hsp65 chaperonin Cpn60.2 is particularly abundant and increases about 200-fold in the filtrate of the Δcpn60.1 mutant. In mice, the Δcpn60.1 mutant is less persistent in lungs and, to a lesser extent, in spleen, but it induces a comparable mycobacteria-specific gamma interferon production and protection against Mycobacterium tuberculosis H37Rv challenge as do the parental and complemented BCG strains. Thus, by inactivating the cpn60.1 gene in M. bovis BCG we show that Cpn60.1 is necessary for the integrity of the bacterial cell wall, is involved in resistance to H(2)O(2)-induced stress but is not essential for its vaccine potential.
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Affiliation(s)
- Xiao-Ming Wang
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Changlong Lu
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Karine Soetaert
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Catherine S'Heeren
- Department of Proteomics and Microbiology, University of Mons, 20, place du Parc, B-7000 Mons, Belgium
| | - Priska Peirs
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Marie-Antoinette Lanéelle
- Department of Molecular Mechanisms of the Mycobacterial Infections, Institute of Pharmacology and Structural Biology of CNRS and the University Paul Sabatier (UMR 5089), 205 route de Narbonne, Toulouse 31077 cedex 04, France
| | - Philippe Lefèvre
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Pablo Bifani
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Jean Content
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Mamadou Daffé
- Department of Molecular Mechanisms of the Mycobacterial Infections, Institute of Pharmacology and Structural Biology of CNRS and the University Paul Sabatier (UMR 5089), 205 route de Narbonne, Toulouse 31077 cedex 04, France
| | - Kris Huygen
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Jacqueline De Bruyn
- Scientific Institute of Public Health, Operational Direction of Communicable and Infectious Diseases, Rue Engeland 642, B-1180 Brussels, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, 20, place du Parc, B-7000 Mons, Belgium
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Wolfe LM, Mahaffey SB, Kruh NA, Dobos KM. Proteomic definition of the cell wall of Mycobacterium tuberculosis. J Proteome Res 2010; 9:5816-26. [PMID: 20825248 PMCID: PMC2995261 DOI: 10.1021/pr1005873] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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The cell envelope of Mycobacterium tuberculosis (Mtb) is complex and diverse; composed of proteins intermingled in a matrix of peptidoglycan, mycolic acids, lipids, and carbohydrates. Proteomic studies of the Mtb cell wall have been limited; nonetheless, the characterization of resident and secreted proteins associated with the cell wall are critical to understanding bacterial survival and immune modulation in the host. In this study, the cell wall proteome was defined in order to better understand its unique biosynthetic and secretion processes. Mtb cell wall was subjected to extraction with organic solvents to remove noncovalently bound lipids and lipoglycans and remaining proteins were solubilized with either SDS, Guanidine-HCl, or TX-114. These extracts were analyzed by two-dimensional gel electrophoresis and mass-spectrometry and resulted in the identification of 234 total proteins. The lipoproteome of Mtb, enriched in the TX-114 extract, was further resolved by multidimensional chromatography and mass spectrometry to identify an additional 294 proteins. A query of the 528 total protein identifications against Neural Network or Hidden Markov model algorithms predicted secretion signals in 87 proteins. Classification of these 528 proteins also demonstrated that 35% are involved in small molecule metabolism and 25% are involved in macromolecule synthesis and degradation building upon evidence that the Mtb cell wall is actively engaged in mycobacterial survival and remodeling. The cell envelope of Mycobacterium tuberculosis (Mtb) is a unique structure comprised of proteins within a matrix of carbohydrates, lipids, and mycolylarabinogalactan linked to peptidoglycan. In this study, the Mtb cell wall (CW) proteome was further defined, revealing 528 proteins, with 105 novel identifications. Classification of CW proteins by signal sequence and predicted function identified 87 secreted proteins, and demonstrated 60% of the proteome engaged in small- and macromolecule metabolism.
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Affiliation(s)
- Lisa M Wolfe
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Rahman A, Srivastava SS, Sneh A, Ahmed N, Krishnasastry MV. Molecular characterization of tlyA gene product, Rv1694 of Mycobacterium tuberculosis: a non-conventional hemolysin and a ribosomal RNA methyl transferase. BMC BIOCHEMISTRY 2010; 11:35. [PMID: 20854656 PMCID: PMC2954847 DOI: 10.1186/1471-2091-11-35] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 09/20/2010] [Indexed: 11/10/2022]
Abstract
Background Mycobacterium tuberculosis is a virulent bacillus causing tuberculosis, a disease responsible for million deaths each year worldwide. In order to understand its mechanism of pathogenesis in humans and to help control tuberculosis, functions of numerous Mycobacterium tuberculosis genes are being characterized. In this study we report the dual functionality of tlyA gene product of Mycobacterium tuberculosis annotated as Rv1694, a 268 amino acid long basic protein. Results The recombinant purified Rv1694 protein was found to exhibit hemolytic activity in vitro. It showed concentration and time-dependent hemolysis of rabbit and human erythrocytes. Multiple oligomeric forms (dimers to heptamers) of this protein were seen on the membranes of the lysed erythrocytes. Like the oligomers of conventional, well-known, pore-forming toxins, the oligomers of Rv1694 were found to be resistant to heat and SDS, but were susceptible to reducing agents like β-mercaptoethanol as it had abolished the hemolytic activity of Rv1694 indicating the role of disulfide bond(s). The Rv1694 generated de novo by in vitro transcription and translation also exhibited unambiguous hemolysis confirming the self assembly and oligomerization properties of this protein. Limited proteolytic digestion of this protein has revealed that the amino terminus is susceptible while in solution but is protected in presence of membrane. Striking feature of Rv1694 is its presence on the cell wall of E. coli as visualized by confocal microscopy. The surface expression is consistent with the contact dependent haemolytic ability of E. coli expressing this protein. Also, immune serum specific to this protein inhibits the contact dependent hemolysis. Moreover, Rv1694 protein binds to and forms stable oligomers on the macrophage phagosomal membranes. In addition to all these properties, E. coli expressing Rv1694 was found to be susceptible to the antibiotic capreomycin as its growth was significantly slower than mock vector transformed E. coli. The S30 extract of E. coli expressing the Rv1694 had poor translational activity in presence of capreomycin, further confirming its methylation activity. Finally, incorporation of methyl group of [3H]-S-adenosylmethionine in isolated ribosomes also confirmed its methylation activity. Conclusions The Rv1694 has an unusual dual activity. It appears to contain two diverse functions such as haemolytic activity and ribosomal RNA methylation activity. It is possible that the haemolytic activity might be relevant to intra-cellular compartments such as phagosomes rather than cell lysis of erythrocytes and the self-assembly trait may have a potential role after successful entry into macrophages by Mycobacterium tuberculosis.
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Affiliation(s)
- Aejazur Rahman
- National Centre for Cell Science, Ganeshkhind Road, Pune - 411007, Maharashtra, India
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Mehaffy C, Hess A, Prenni JE, Mathema B, Kreiswirth B, Dobos KM. Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis. Proteomics 2010; 10:1966-84. [PMID: 20217870 DOI: 10.1002/pmic.200900836] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The use of isobaric tags such as iTRAQ allows the relative and absolute quantification of hundreds of proteins in a single experiment for up to eight different samples. More classical techniques such as 2-DE can offer a complimentary approach for the analysis of complex protein samples. In this study, the proteomes of secreted and cytosolic proteins of genetically closely related strains of Mycobacterium tuberculosis were analyzed. Analysis of 2-D gels afforded 28 spots with variations in protein abundance between strains. These were identified by MS/MS. Meanwhile, a rigorous statistical analysis of iTRAQ data allowed the identification and quantification of 101 and 137 proteins in the secreted and cytosolic fractions, respectively. Interestingly, several differences in protein levels were observed between the closely related strains BE, C28 and H6. Seven proteins related to cell wall and cell processes were more abundant in BE, while enzymes related to metabolic pathways (GltA2, SucC, Gnd1, Eno) presented lower levels in the BE strain. Proteins involved in iron and sulfur acquisition (BfrB, ViuB, TB15.3 and SseC2) were more abundant in C28 and H6. In general, iTRAQ afforded rapid identification of fine differences between protein levels such as those presented between closely related strains. This provides a platform from which the relevance of these differences can be assessed further using complimentary proteomic and biological modeling methods.
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Affiliation(s)
- Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
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Pleissner KP, Eifert T, Jungblut PR. A European pathogenic microorganism proteome database: construction and maintenance. Comp Funct Genomics 2010; 3:97-100. [PMID: 18628887 PMCID: PMC2447247 DOI: 10.1002/cfg.165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2002] [Accepted: 02/19/2005] [Indexed: 11/21/2022] Open
Abstract
A relational database structure based on MS-Access and MySQL to store and manage
proteomics data was established. This system may be used to publish two-dimensional
electrophoretic proteomics data, and also may be accessed by external users who want to
compare their own data with those in the databases. The maintenance of the database is
managed centrally. The producers of proteomics data do not need to construct a database
themselves. Users can introduce mass spectra into the database, which allows the searching
of peptide mass fingerprints against their own protein sequence databases. The first release
published in January 2002 contains data from Mycobacterium tuberculosis, Helicobacter
pylori, Borrelia garinii, Francisella tularensis, Chlamydia pneumoniae, Mycoplasma pneumoniae,
Jurkat T-cells and mouse mammary gland projects (http://www.mpiib-berlin.
mpg.de/2D-PAGE/).
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Affiliation(s)
- Klaus-Peter Pleissner
- Max Planck Institute for Infection Biology, Core Facility Bioinformatics, Berlin, Germany
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15
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Identification of novel Mycobacterium bovis antigens by dissection of crude protein fractions. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2009; 16:1352-9. [PMID: 19641100 DOI: 10.1128/cvi.00211-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Culture filtrate and cell extracts from Mycobacterium bovis cultures contain molecules which could promote protective immunity to tuberculosis in animals. Different protein fractions of M. bovis cultures were obtained by elution electrophoresis and were tested in experimentally infected cattle. The fractions that elicited gamma interferon (IFN-gamma) responses were resolved by two-dimensional gel electrophoresis, and individual proteins were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The open reading frames were cloned, expressed as their recombinant forms, and retested with naturally and experimentally infected animals. Eleven protein fractions were highly reactive, from which the Rv1636, HspX, Rv0138, Rv2524, EsxI, and Rv3740 recombinant proteins were obtained. EsxI and HspX were the antigens most recognized by the IFN-gamma release assay. In summary, a proteomic approach allowed the identification of novel antigens useful for the diagnosis of bovine tuberculosis.
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16
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17
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Sidders B, Withers M, Kendall SL, Bacon J, Waddell SJ, Hinds J, Golby P, Movahedzadeh F, Cox RA, Frita R, ten Bokum AMC, Wernisch L, Stoker NG. Quantification of global transcription patterns in prokaryotes using spotted microarrays. Genome Biol 2007; 8:R265. [PMID: 18078514 PMCID: PMC2246267 DOI: 10.1186/gb-2007-8-12-r265] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 11/01/2007] [Accepted: 12/13/2007] [Indexed: 11/18/2022] Open
Abstract
We describe an analysis, applicable to any spotted microarray dataset produced using genomic DNA as a reference, that quantifies prokaryotic levels of mRNA on a genome-wide scale. Applying this to Mycobacterium tuberculosis, we validate the technique, show a correlation between level of expression and biological importance, define the complement of invariant genes and analyze absolute levels of expression by functional class to develop ways of understanding an organism's biology without comparison to another growth condition.
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Affiliation(s)
- Ben Sidders
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Mike Withers
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Sharon L Kendall
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Joanna Bacon
- TB Research, CEPR, Health Protection Agency, Porton Down, Salisbury, SP4 0JG, UK
| | - Simon J Waddell
- Medical Microbiology, Division of Cellular and Molecular Medicine, St George's University of London, Cranmer Terrace, Tooting, London, SW17 0RE, UK
| | - Jason Hinds
- Medical Microbiology, Division of Cellular and Molecular Medicine, St George's University of London, Cranmer Terrace, Tooting, London, SW17 0RE, UK
| | - Paul Golby
- Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Farahnaz Movahedzadeh
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
- Institute for Tuberculosis Research College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60612-7231, USA
| | - Robert A Cox
- Division of Mycobacterial Research, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Rosangela Frita
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Annemieke MC ten Bokum
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Lorenz Wernisch
- School of Crystallography, Birkbeck College, London, WC1E 7HX, UK
| | - Neil G Stoker
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
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18
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Abstract
Like other actinomycetes Mycobacterium tuberculosis lacks glutathione and, consequently, the glutathione peroxidases that dominate the antioxidant defence of its mammalian hosts. The hydrogen peroxide metabolism of the pathogen has for long been recognised to depend on a heme-containing catalase/peroxidase. Clinical isolates lacking the catalase were virulent and proved to be resistant to the first line tuberculostatic isoniazid, because the enzyme is evidently required to activate this drug. The survival and virulence of such strains are attributed to the peroxiredoxin-type peroxidases alkyl hydroperoxide reductase (AhpC) and thioredoxin peroxidase (TPx). The most common AhpC reductant in bacteria, the disulfide reductase AhpF, is deleted in M. tuberculosis. Instead, AhpC can be reduced by AhpD, a CXXC-motif-containing protein, or by one of the mycobacterial thioredoxins, TrxC. TPx is reduced by thioredoxins B and C. Mycobacteria contain three more peroxiredoxins, the 1-Cys-Prx AhpE, Bcp and BcpB, whose function and reductants are still unknown.
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Affiliation(s)
- Timo Jaeger
- MOLISA GmbH, Molecular Links Sachsen-Anhalt, Magdeburg, Germany
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19
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Lin G, Hu G, Tsu C, Kunes YZ, Li H, Dick L, Parsons T, Li P, Chen Z, Zwickl P, Weich N, Nathan C. Mycobacterium tuberculosis prcBA genes encode a gated proteasome with broad oligopeptide specificity. Mol Microbiol 2006; 59:1405-16. [PMID: 16468985 DOI: 10.1111/j.1365-2958.2005.05035.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genes predicted to be associated with the putative proteasome of Mycobacterium tuberculosis (Mtb) play a critical role in defence of the bacillus against nitrosative stress. However, proteasomes are uncommon in eubacteria and it remains to be established whether Mtb's prcBA genes in fact encode a proteasome. We found that coexpression of recombinant PrcB and PrcA in Escherichia coli over a prolonged period at 37 degrees C allowed formation of an alpha(7)beta(7)beta(7)alpha(7), 750 kDa cylindrical stack of four rings in which all 14 beta-subunits were proteolytically processed to expose the active site threonine. In contrast to another Actinomycete, Rhodococcus erythropolis, Mtb's beta-chain propeptide was not required for particle assembly. Peptidolytic activity of the 750 kDa particle towards a hydrophobic oligopeptide was nearly two orders of magnitude less than that of the Rhodococcus 20S proteasome, and unlike eukaryotic and archaeal proteasomes, activity of the Mtb 750 kDa particle could not be stimulated by SDS, Mg(2+) or Ca(2+). Electron microscopy revealed what appeared to be obstructed alpha-rings in the Mtb 750 kDa particle. Deletion of the N-terminal octapeptide from Mtb's alpha-chain led to disappearance of the apparent obstruction and a marked increase of peptidolytic activity. Unlike proteasomes isolated from other Actinomycetes, the open-gate Mtb mutant 750 kDa particle cleaved oligopeptides not only after hydrophobic residues but also after basic, acidic and small, neutral amino acids. Thus, Mtb encodes a broadly active, gated proteasome that may work in concert with an endogenous activator.
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Affiliation(s)
- Gang Lin
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
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20
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ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis. Tuberculosis (Edinb) 2005; 86:445-60. [PMID: 16376151 DOI: 10.1016/j.tube.2005.10.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 09/19/2005] [Accepted: 10/13/2005] [Indexed: 11/15/2022]
Abstract
The non-replicating persistence (NRP) phenotype of Mycobacterium tuberculosis (NRP-TB) is assumed to be responsible for the maintenance of latent infection and the requirement of a long treatment duration for active tuberculosis. Isotope coded affinity tag-based proteomic analysis was used for the determination of the relative expression of large numbers of M. tuberculosis proteins during oxygen self-depletion under controlled conditions in a multi-chambered fermentor. Expression of the alpha-crystallin homolog protein, acr, was monitored and quantified to confirm entry into NRP. Relative expression of 586 and 628 proteins was determined in log phase vs. early stage NRP (NRP-1) and log phase vs. later stage NRP (NRP-2), respectively. Relative to expression in log phase and using an abundance ratio of +/-2.0 as a cutoff, 6.5% and 20.4% of proteins were found to be upregulated in NRP-1 and NRP-2, respectively while 20.3% and 13.4% were downregulated, respectively. Functional profiling revealed that 42.1%/39.8% of upregulated proteins and 41.2%/45.2% of downregulated proteins in NRP-1/NRP-2, respectively, were involved in small molecule metabolism. Among those proteins the highest proportions of 37.5% in NRP-1 were involved with degradation and of 45.1% in NRP-2 with energy metabolism. These results suggest distinct protein expression profiles in NRP-1 and NRP-2.
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21
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Mukherjee R, Chatterji D. Evaluation of the role of sigma B in Mycobacterium smegmatis. Biochem Biophys Res Commun 2005; 338:964-72. [PMID: 16248983 DOI: 10.1016/j.bbrc.2005.10.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2005] [Accepted: 10/07/2005] [Indexed: 11/24/2022]
Abstract
The alternate sigma factor, sigB, is known to play a crucial role in maintaining the stationary phase in mycobacteria. In this communication, we have studied the proteomics of Mycobacterium smegmatis mc(2)155 and its two derivatives, one of which has a disrupted sigB gene and the other, PMVSigB, which contains a multicopy plasmid containing sigB. We have identified by two-dimensional gel analyses, several proteins that are over-expressed in PMVSigB compared to mc(2)155. These proteins are either stress proteins or participate actively in different metabolic pathways of the organisms. On the other hand, when sigB deleted mycobacteria were grown until the stationary phase and its two-dimensional protein profile was compared to that of mc(2)155, few DNA binding proteins were found to be up-regulated. We have shown recently that upon over-expressing sigB, the cell surface glycopeptidolipids of M. smegmatis are hyperglycosylated, a situation similar to what was observed for nutritionally starved bacteria. Gene expression profile through quantitative PCR presented here identified a Rhamnosyltransferase responsible for this hyperglycosylation.
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Affiliation(s)
- Raju Mukherjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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22
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Ha MK, Chung KY, Bang D, Park YK, Lee KH. Proteomic analysis of the proteins expressed by hydrogen peroxide treated cultured human dermal microvascular endothelial cells. Proteomics 2005; 5:1507-19. [PMID: 15838903 DOI: 10.1002/pmic.200401043] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Reactive oxygen species (ROS) have been traditionally regarded as toxic by-products of aerobic metabolism. However, ROS also act as intracellular signaling molecules and can mediate phenotypes in vascular endothelial cells, which may be physiological or pathological in nature. To clarify the molecular mechanisms of ROS signaling, we examined hydrogen peroxide (H(2)O(2))-responsive proteins in cultured human dermal microvascular endothelial cells (HMVEC) using proteomic tools. Protein expression in HMVEC was studied after they had been exposed to low- and high-levels of H(2)O(2) for various times, and intracellular ROS production was examined by flow cytometer and UV spectrophotometer. Proteins obtained from dose- and time-dependent series were separated by two-dimensional gel electrophoresis and tentatively identified by matrix-assisted laser desorption-time of flight mass spectrometry, by matching the tryptic mass maps obtained with entries in the NCBI and Swiss-Prot protein sequence database. At least 163 proteins were changed by H(2)O(2), and 60 proteins were identified. Oxidative stress triggered dramatic change in the expression of proteins in primary microvessel endothelial cells, and their mapping to cellular process provided a view of the ubiquitous cellular changes elicited by H(2)O(2). These results could provide a framework for the understanding of the mechanisms of cellular redox homeostasis and H(2)O(2) metabolism in microendothelium environment in various biological processes as well as pathological conditions.
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Affiliation(s)
- Moon Kyung Ha
- Department of Dermatology and Cutaneous Biology Research Institute, Seoul, Korea
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23
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Gazdik MA, McDonough KA. Identification of cyclic AMP-regulated genes in Mycobacterium tuberculosis complex bacteria under low-oxygen conditions. J Bacteriol 2005; 187:2681-92. [PMID: 15805514 PMCID: PMC1070381 DOI: 10.1128/jb.187.8.2681-2692.2005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), which kills approximately 2 million people a year despite current treatment options. A greater understanding of the biology of this bacterium is needed to better combat TB disease. The M. tuberculosis genome encodes as many as 15 adenylate cyclases, suggesting that cyclic AMP (cAMP) has an important, yet overlooked, role in mycobacteria. This study examined the effect of exogenous cAMP on protein expression in Mycobacterium bovis BCG grown under hypoxic versus ambient conditions. Both shaking and shallow standing cultures were examined for each atmospheric condition. Different cAMP-dependent changes in protein expression were observed in each condition by two-dimensional gel electrophoresis. Shaking low-oxygen cultures produced the most changes (12), while standing ambient conditions showed the fewest (2). Five upregulated proteins, Rv1265, Rv2971, GroEL2, PE_PGRS6a, and malate dehydrogenase, were identified from BCG by mass spectrometry and were shown to also be regulated by cAMP at the mRNA level in both M. tuberculosis H37Rv and BCG. To our knowledge, these data provide the first direct evidence for cAMP-mediated gene regulation in TB complex mycobacteria.
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Affiliation(s)
- Michaela A Gazdik
- New York State Department of Health, University of Albany, 120 New Scotland Ave., Albany, NY 12208, USA
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24
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Mawuenyega KG, Forst CV, Dobos KM, Belisle JT, Chen J, Bradbury EM, Bradbury ARM, Chen X. Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. Mol Biol Cell 2005; 16:396-404. [PMID: 15525680 PMCID: PMC539182 DOI: 10.1091/mbc.e04-04-0329] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 09/13/2004] [Accepted: 10/17/2004] [Indexed: 11/11/2022] Open
Abstract
Trends in increased tuberculosis infection and a fatality rate of approximately 23% have necessitated the search for alternative biomarkers using newly developed postgenomic approaches. Here we provide a systematic analysis of Mycobacterium tuberculosis (Mtb) by directly profiling its gene products. This analysis combines high-throughput proteomics and computational approaches to elucidate the globally expressed complements of the three subcellular compartments (the cell wall, membrane, and cytosol) of Mtb. We report the identifications of 1044 proteins and their corresponding localizations in these compartments. Genome-based computational and metabolic pathways analyses were performed and integrated with proteomics data to reconstruct response networks. From the reconstructed response networks for fatty acid degradation and lipid biosynthesis pathways in Mtb, we identified proteins whose involvements in these pathways were not previously suspected. Furthermore, the subcellular localizations of these expressed proteins provide interesting insights into the compartmentalization of these pathways, which appear to traverse from cell wall to cytoplasm. Results of this large-scale subcellular proteome profile of Mtb have confirmed and validated the computational network hypothesis that functionally related proteins work together in larger organizational structures.
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Affiliation(s)
- Kwasi G Mawuenyega
- Cell Biology, Structural Biology, and Flow Cytometry, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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25
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Terwilliger TC, Park MS, Waldo GS, Berendzen J, Hung LW, Kim CY, Smith CV, Sacchettini JC, Bellinzoni M, Bossi R, De Rossi E, Mattevi A, Milano A, Riccardi G, Rizzi M, Roberts MM, Coker AR, Fossati G, Mascagni P, Coates ARM, Wood SP, Goulding CW, Apostol MI, Anderson DH, Gill HS, Eisenberg DS, Taneja B, Mande S, Pohl E, Lamzin V, Tucker P, Wilmanns M, Colovos C, Meyer-Klaucke W, Munro AW, McLean KJ, Marshall KR, Leys D, Yang JK, Yoon HJ, Lee BI, Lee MG, Kwak JE, Han BW, Lee JY, Baek SH, Suh SW, Komen MM, Arcus VL, Baker EN, Lott JS, Jacobs W, Alber T, Rupp B. The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb) 2004; 83:223-49. [PMID: 12906835 DOI: 10.1016/s1472-9792(03)00051-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.
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Affiliation(s)
- T C Terwilliger
- Los Alamos National Laboratory, Bioscience Division, Mail Stop M888, Los Alamos, NM 87545, USA.
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26
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Jaeger T, Budde H, Flohé L, Menge U, Singh M, Trujillo M, Radi R. Multiple thioredoxin-mediated routes to detoxify hydroperoxides in Mycobacterium tuberculosis. Arch Biochem Biophys 2004; 423:182-91. [PMID: 14871480 DOI: 10.1016/j.abb.2003.11.021] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Revised: 11/26/2003] [Indexed: 10/26/2022]
Abstract
Drug resistance and virulence of Mycobacterium tuberculosis are in part related to the pathogen's antioxidant defense systems. KatG(-) strains are resistant to the first line tuberculostatic isoniazid but need to compensate their catalase deficiency by alternative peroxidase systems to stay virulent. So far, only NADH-driven and AhpD-mediated hydroperoxide reduction by AhpC has been implicated as such virulence-determining mechanism. We here report on two novel pathways which underscore the importance of the thioredoxin system for antioxidant defense in M. tuberculosis: (i) NADPH-driven hydroperoxide reduction by AhpC that is mediated by thioredoxin reductase and thioredoxin C and (ii) hydroperoxide reduction by the atypical peroxiredoxin TPx that equally depends on thioredoxin reductase but can use both, thioredoxin B and C. Kinetic analyses with different hydroperoxides including peroxynitrite qualify the redox cascade comprising thioredoxin reductase, thioredoxin C, and TPx as the most efficient system to protect M. tuberculosis against oxidative and nitrosative stress in situ.
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Affiliation(s)
- Timo Jaeger
- Department of Biochemistry, Technical University of Braunschweig, Mascheroder Weg 1, 38124 Braunschweig, Germany
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27
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Abstract
Tuberculosis (TB) has afflicted humankind throughout history. Approximately one third of the world's population is currently infected with Mycobacterium tuberculosis and nearly two million people die of TB annually. Although much has been learned about the structure of the tubercle bacillus, the epidemiology of TB, the physiological and immunological responses of the host to infection, and the physiology of M. tuberculosis in laboratory broth cultures, much of the basic biology of M. tuberculosis in its natural setting (the infected human) remains to be elucidated. Within the past decade, there have been remarkable advances in the development of genetic and molecular biological tools with which to study M. tuberculosis. This review discusses the approaches that have been employed and the progress that has been made in discovering how M. tuberculosis has achieved its prowess as a successful pathogen.
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28
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Cash P. Proteomics of bacterial pathogens. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003; 83:93-115. [PMID: 12934927 DOI: 10.1007/3-540-36459-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The rapid growth of proteomics that has been built upon the available bacterial genome sequences has opened provided new approaches to the analysis of bacterial functional genomics. In the study of pathogenic bacteria the combined technologies of genomics, proteomics and bioinformatics has provided valuable tools for the study of complex phenomena determined by the action of multiple gene sets. The review considers some of the recent developments in the establishment of proteomic databases as well as attempts to define pathogenic determinants at the level of the proteome for some of the major human pathogens. Proteomics can also provide practical applications through the identification of immunogenic proteins that may be potential vaccine targets as well as in extending our understanding of antibiotic action. There is little doubt that proteomics has provided us with new and valuable information on bacterial pathogens and will continue to be an important source of information in the coming years.
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Affiliation(s)
- Phillip Cash
- Department of Medical Microbiology, University of Aberdeen, Foresterhill, Aberdeen AB32 6QX, Scotland.
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29
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Abstract
Tuberculosis (TB), one of the oldest known human diseases. is still is one of the major causes of mortality, since two million people die each year from this malady. TB has many manifestations, affecting bone, the central nervous system, and many other organ systems, but it is primarily a pulmonary disease that is initiated by the deposition of Mycobacterium tuberculosis, contained in aerosol droplets, onto lung alveolar surfaces. From this point, the progression of the disease can have several outcomes, determined largely by the response of the host immune system. The efficacy of this response is affected by intrinsic factors such as the genetics of the immune system as well as extrinsic factors, e.g., insults to the immune system and the nutritional and physiological state of the host. In addition, the pathogen may play a role in disease progression since some M. tuberculosis strains are reportedly more virulent than others, as defined by increased transmissibility as well as being associated with higher morbidity and mortality in infected individuals. Despite the widespread use of an attenuated live vaccine and several antibiotics, there is more TB than ever before, requiring new vaccines and drugs and more specific and rapid diagnostics. Researchers are utilizing information obtained from the complete sequence of the M. tuberculosis genome and from new genetic and physiological methods to identify targets in M. tuberculosis that will aid in the development of these sorely needed antitubercular agents.
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Affiliation(s)
- Issar Smith
- TB Center, Public Health Research Institute, International Center for Public Health, Newark, New Jersey 07103-3535, USA.
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30
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Hubálek M, Hernychová L, Havlasová J, Kasalová I, Neubauerová V, Stulík J, Macela A, Lundqvist M, Larsson P. Towards proteome database of Francisella tularensis. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 787:149-77. [PMID: 12659739 DOI: 10.1016/s1570-0232(02)00730-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The accessibility of the partial genome sequence of Francisella tularensis strain Schu 4 was the starting point for a comprehensive proteome analysis of the intracellular pathogen F. tularensis. The main goal of this study is identification of protein candidates of value for the development of diagnostics, therapeutics and vaccines. In this review, the current status of 2-DE F. tularensis database building, approaches used for identification of biologically important subsets of F. tularensis proteins, and functional and topological assignments of identified proteins using various prediction programs and database homology searches are presented.
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Affiliation(s)
- Martin Hubálek
- Proteome Center for the Study of Intracellular Parasitism of Bacteria, Purkyne Military Medical Academy, Trebesská 1575, 500 01 Hradec Králové, Czech Republic
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31
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Ge Y, El-Naggar M, Sze SK, Oh HB, Begley TP, McLafferty FW, Boshoff H, Barry CE. Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:253-261. [PMID: 12648932 DOI: 10.1016/s1044-0305(02)00913-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Secreted proteins of Mycobacterium tuberculosis are implicated in its disease pathogenesis and so are considered as potential diagnostic and vaccine candidates. The search for these has been slow, even though the entire genome sequence of M. tuberculosis is now available; of the 620 protein spots resolved by 2-D gel electrophoresis, 114 secreted proteins have been identified, but for only 13 has the primary structure been partly characterized. For comparison, in this top down mass spectrometry (MS) approach the secreted proteins were precipitated from cell culture filtrate, resuspended, and examined directly by electrospray ionization (ESI) Fourier transform MS. The ESI spectra of three precipitates showed 93, 535, and 369 molecular weight (M(r)) values, for a total of 689 different values. However, only approximately 10% of these values matched (+/-1 Da) the DNA predicted M(r) values, but these identifications were unreliable. Of nine molecular ions characterized by MS/MS, only one protein match was confirmed, and its isotopic molecular ions were overlapped by those of another protein. MS/MS identified a total of ten proteins by sequence tag search, of which three were unidentified previously. The low success of M(r) matching was due to unusually extensive posttranslational modifications, including loss of a signal sequence, loss of the N-terminal residue, proteolytic degradation, oxidation, and glycosylation. Although in eubacteria the latter is relatively rare, a 9 kDa protein showed 7 hexose attachments and two 20 kDa proteins each had 20 attachments. For MS/MS, electron capture dissociation was especially effective.
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Affiliation(s)
- Ying Ge
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA
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32
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Mollenkopf HJ, Mattow J, Schaible UE, Grode L, Kaufmann SHE, Jungblut PR. Mycobacterial proteomes. Methods Enzymol 2003; 358:242-56. [PMID: 12474391 DOI: 10.1016/s0076-6879(02)58093-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Affiliation(s)
- Hans-Joachim Mollenkopf
- Department of Immunology, Max Planck Institute for Infection Biology, D-10117 Berlin, Germany
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Probing the Molecular Physiology of the Microbial Organism, Escherichia coli Using Proteomics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003. [DOI: 10.1007/3-540-36459-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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34
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Camus JC, Pryor MJ, Médigue C, Cole ST. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. MICROBIOLOGY (READING, ENGLAND) 2002; 148:2967-2973. [PMID: 12368430 DOI: 10.1099/00221287-148-10-2967] [Citation(s) in RCA: 395] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Original genome annotations need to be regularly updated if the information they contain is to remain accurate and relevant. Here the complete re-annotation of the genome sequence of Mycobacterium tuberculosis strain H37Rv is presented almost 4 years after the first submission. Eighty-two new protein-coding sequences (CDS) have been included and 22 of these have a predicted function. The majority were identified by manual or automated re-analysis of the genome and most of them were shorter than the 100 codon cut-off used in the initial genome analysis. The functional classification of 643 CDS has been changed based principally on recent sequence comparisons and new experimental data from the literature. More than 300 gene names and over 1000 targeted citations have been added and the lengths of 60 genes have been modified. Presently, it is possible to assign a function to 2058 proteins (52% of the 3995 proteins predicted) and only 376 putative proteins share no homology with known proteins and thus could be unique to M. tuberculosis.
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Affiliation(s)
- Jean-Christophe Camus
- Annotation-Bases de Données (PT4), Génopole, Institut Pasteur, Paris, France2
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex, France1
| | - Melinda J Pryor
- Annotation-Bases de Données (PT4), Génopole, Institut Pasteur, Paris, France2
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex, France1
| | - Claudine Médigue
- Génoscope/UMR 8030, Atelier de Génomique Comparative, 2 rue Gaston Crémieux, 91006 Evry Cedex, France3
| | - Stewart T Cole
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex, France1
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35
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Abstract
The elucidation of genetic components of human diseases at the molecular level provides crucial information for developing future causal therapeutic intervention. High-throughput genome sequencing and systematic experimental approaches are fuelling strategic programs designed to investigate gene function at the biochemical, cellular and organism levels. Bioinformatics is one important tool in functional genomics, although showing clear limitations in predicting ab initio gene structures, gene function and protein folds from raw sequence data. Systematic large-scale data-set generation, using the same type of experiments that are used to decipher the function of single genes, are being applied on entire genomes. Comparative genomics, establishment of gene catalogues, and investigation of cellular and tissue molecular profiles are providing essential tools for understanding gene function in complex biological networks.
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Affiliation(s)
- M L Yaspo
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany.
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36
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Ong SE, Pandey A. An evaluation of the use of two-dimensional gel electrophoresis in proteomics. BIOMOLECULAR ENGINEERING 2001; 18:195-205. [PMID: 11911086 DOI: 10.1016/s1389-0344(01)00095-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With whole genomes being sequenced almost routinely, the next logical step towards a better understanding of cellular mechanisms lies in studying the functional units of gene expression-proteins. One of the fundamental approaches in proteomics is the use of two-dimensional gel electrophoresis as a mode of separation and visualization of complex protein mixtures. Despite several limitations of the method, its ability to separate large numbers of proteins, including their post-translationally modified forms, ensures that it will continue to be popular in several well-defined areas of proteomics. In this article, we discuss the merits and drawbacks of two-dimensional gels and compare them with alternative systems such as one-dimensional gels and liquid chromatography-based separation methods. In the wake of recent advances in mass spectrometry and related areas, we outline areas where two-dimensional gels can best be utilized as the preferred separation method in proteomic strategies.
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Affiliation(s)
- S E Ong
- Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Odense
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37
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Jungblut PR, Müller EC, Mattow J, Kaufmann SH. Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect Immun 2001; 69:5905-7. [PMID: 11500470 PMCID: PMC98710 DOI: 10.1128/iai.69.9.5905-5907.2001] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genomics revealed the sequence of 3924 genes of the H37Rv strain of Mycobacterium tuberculosis. Proteomics complements genomics in showing which genes are really expressed, and here we show the expression of six genes not predicted by genomics, as proved by two-dimensional electrophoresis and matrix-assisted laser desorption ionization and nano-electrospray mass spectrometry.
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Affiliation(s)
- P R Jungblut
- Core Facility for Protein Analysis, Max Planck Institute for Infection Biology, Berlin, Germany.
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38
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Mattow J, Jungblut PR, Schaible UE, Mollenkopf HJ, Lamer S, Zimny-Arndt U, Hagens K, Müller EC, Kaufmann SH. Identification of proteins from Mycobacterium tuberculosis missing in attenuated Mycobacterium bovis BCG strains. Electrophoresis 2001; 22:2936-46. [PMID: 11565788 DOI: 10.1002/1522-2683(200108)22:14<2936::aid-elps2936>3.0.co;2-s] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A proteome approach, combining high-resolution two-dimensional electrophoresis (2-DE) with mass spectrometry, was used to compare the cellular protein composition of two virulent strains of Mycobacterium tuberculosis with two attenuated strains of Mycobacterium bovis Bacillus Calmette-Guerin (BCG), in order to identify unique proteins of these strains. Emphasis was given to the identification of M. tuberculosis specific proteins, because we consider these proteins to represent putative virulence factors and interesting candidates for vaccination and diagnosis of tuberculosis. The genome of M. tuberculosis strain H37Rv comprises nearly 4000 predicted open reading frames. In contrast, the separation of proteins from whole mycobacterial cells by 2-DE resulted in silver-stained patterns comprising about 1800 distinct protein spots. Amongst these, 96 spots were exclusively detected either in the virulent (56 spots) or in the attenuated (40 spots) mycobacterial strains. Fifty-three of these spots were analyzed by mass spectrometry, of which 41 were identified, including 32 M. tuberculosis specific spots. Twelve M. tuberculosis specific spots were identified as proteins, encoded by genes previously reported to be deleted in M. bovis BCG. The remaining 20 spots unique for M. tuberculosis were identified as proteins encoded by genes that are not known to be missing in M. bovis BCG.
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Affiliation(s)
- J Mattow
- Max-Planck-Institute for Infection Biology, Berlin, Germany
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39
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Monahan IM, Betts J, Banerjee DK, Butcher PD. Differential expression of mycobacterial proteins following phagocytosis by macrophages. MICROBIOLOGY (READING, ENGLAND) 2001; 147:459-471. [PMID: 11158363 DOI: 10.1099/00221287-147-2-459] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis resides within the macrophages of the host, but the molecular and cellular mechanisms of survival are poorly understood. Recent evidence suggests that the attenuated vaccine strain Mycobacterium bovis BCG is both a deletion and regulatory mutant, yet retains both its immunoprotective and intra-macrophage survival potential. In an attempt to define M. bovis BCG genes expressed during interaction with macrophages, the patterns of protein synthesis were examined by both one- and two-dimensional gel electrophoresis of BCG while inside the human leukaemic macrophage cell line THP-1. This study demonstrated that BCG expresses proteins while resident inside macrophages that are not expressed during in vitro growth in culture media or under conditions of heat shock. Western blotting analysis revealed that some of the differentially expressed proteins are specifically recognized by human M. tuberculosis-infected sera. Proteome analysis by two-dimensional electrophoresis and MS identified six abundant proteins that showed increased expression inside macrophages: 16 kDa alpha-crystallin (HspX), GroEL-1 and GroEL-2, a 31.7 kDa hypothetical protein (Rv2623), InhA and elongation factor Tu (Tuf). Identification of proteins by such a strategy will help elucidate the molecular basis of the attenuation and the vaccine potential of BCG, and may provide antigens that distinguish infection with M. tuberculosis from vaccination with BCG.
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Affiliation(s)
- Irene M Monahan
- Department of Medical Microbiology, St George's Hospital Medical School, Cranmer Terrace, London SW17 ORE, UK1
| | - Joanna Betts
- Respiratory Systems, Glaxo Wellcome Research and Development, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK2
| | - Dilip K Banerjee
- Department of Medical Microbiology, St George's Hospital Medical School, Cranmer Terrace, London SW17 ORE, UK1
| | - Philip D Butcher
- Department of Medical Microbiology, St George's Hospital Medical School, Cranmer Terrace, London SW17 ORE, UK1
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40
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Affiliation(s)
- J Godovac-Zimmermann
- Center for Molecular Medicine, Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, United Kingdom.
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41
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Betts JC, Dodson P, Quan S, Lewis AP, Thomas PJ, Duncan K, McAdam RA. Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. MICROBIOLOGY (READING, ENGLAND) 2000; 146 Pt 12:3205-3216. [PMID: 11101678 DOI: 10.1099/00221287-146-12-3205] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genome sequences of two virulent strains of Mycobacterium tuberculosis (H37Rv and CDC 1551) are now available. CDC 1551 is a recent clinical isolate and H37Rv is a commonly used lab strain which has been subject to in vitro passage. The two strains have been shown to display differing phenotypes both in vivo and in vitro. The proteome of the two strains grown in liquid culture were examined over time to determine whether there are any major differences between them at the protein level and the differences were compared to the genome data. Total cell lysates of the two strains were analysed by two-dimensional electrophoresis. Approximately 1750 protein spots were visualized by silver staining and the protein profiles of the two strains were found to be highly similar. Out of a total of 17 protein spot differences, seven were unique to CDC 1551 and three to H37Rv. Two further spots showed increased intensity in H37Rv, one spot showed differing vertical mobility between the strains and four showed differing spot intensities with time. Twelve of the spot differences were identified using mass spectrometry; however, no obvious association with phenotype could be deduced. When genome differences were analysed and related to the proteome differences, a mobility shift identified in the MoxR protein could be explained by a point mutation at the gene level. This proteome analysis reveals that, despite having been maintained under vastly different conditions, namely in vitro passage and in vivo transmission, these two strains have remained highly similar.
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Affiliation(s)
- Joanna C Betts
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
| | - Paul Dodson
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
| | - Selwyn Quan
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
| | - Alan P Lewis
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
| | - Pam J Thomas
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
| | - Ken Duncan
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
| | - Ruth A McAdam
- Immunopathology Unit1 and Protein Science Unit2, Glaxo Wellcome Research and Development, Medicines Research Centre, Stevenage, Herts, SG1 2NY, UK
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42
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Abstract
Mass spectrometry (MS) has become the technique of choice to identify proteins. This has been largely accomplished by the combination of high-resolution two-dimensional (2-D) gel separation with robotic sample preparation, automated MS measurement, data analysis, and database query. Developments during the last five years in MS associated with protein gel separation are reviewed.
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Affiliation(s)
- H W Lahm
- F. Hoffmann-LaRoche Ltd., Pharmaceutical Research, Roche Genetics, Basel, Switzerland.
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43
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Abstract
Proteomics has begun to provide insight into the biology of microorganisms. The combination of proteomics with genetics, molecular biology, protein biochemistry and biophysics is particularly powerful, resulting in novel methods to analyse complex protein mixtures. Emerging proteomic technologies promise to increase the throughput of protein identifications from complex mixtures and allow for the quantification of protein expression levels.
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Affiliation(s)
- M P Washburn
- Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195, USA
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44
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Jungblut PR, Bumann D, Haas G, Zimny-Arndt U, Holland P, Lamer S, Siejak F, Aebischer A, Meyer TF. Comparative proteome analysis of Helicobacter pylori. Mol Microbiol 2000; 36:710-25. [PMID: 10844659 DOI: 10.1046/j.1365-2958.2000.01896.x] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Helicobacter pylori, the causative agent of gastritis, ulcer and stomach carcinoma, infects approximately half of the worlds population. After sequencing the complete genome of two strains, 26695 and J99, we have approached the demanding task of investigating the functional part of the genetic information containing macromolecules, the proteome. The proteins of three strains of H. pylori, 26695 and J99, and a prominent strain used in animal models SS1, were separated by a high-resolution two-dimensional electrophoresis technique with a resolution power of 5000 protein spots. Up to 1800 protein species were separated from H. pylori which had been cultivated for 5 days on agar plates. Using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) peptide mass fingerprinting we have identified 152 proteins, including nine known virulence factors and 28 antigens. The three strains investigated had only a few protein spots in common. We observe that proteins with an amino acid exchange resulting in a net change of only one charge are shifted in the two-dimensional electrophoresis (2-DE) pattern. The expression of 27 predicted conserved hypothetical open reading frames (ORFs) and six unknown ORFs were confirmed. The growth conditions of the bacteria were shown to have an effect on the presence of certain proteins. A preliminary immunoblotting study using human sera revealed that this approach is ideal for identifying proteins of diagnostic or therapeutic value. H. pylori 2-DE patterns with their identified protein species were added to the dynamic 2D-PAGE database (http://www.mpiib-berlin.mpg.de/2D-PAGE/). This basic knowledge of the proteome in the public domain will be an effective instrument for the identification of new virulence or pathogenic factors, and antigens of potentially diagnostic or curative value against H. pylori.
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Affiliation(s)
- P R Jungblut
- Max-Planck-Institute for Infection Biology, Central Support Unit Biochemistry, Berlin, Germany.
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45
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Abstract
The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.
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Affiliation(s)
- P Cash
- Department of Medical Microbiology, University of Aberdeen, Foresterhill, Scotland.
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46
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Drysdale R, Bayraktaroglu L. Current awareness. Yeast 2000; 17:159-66. [PMID: 10900461 PMCID: PMC2448328 DOI: 10.1155/2000/907141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on comparative and functional genomics. Each bibliography is divided into 16 sections. 1 Reviews & symposia; 2 General; 3 Large-scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large-scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted
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Affiliation(s)
- R Drysdale
- FlyBase-Cambridge, Department of Genetics, University of Cambridge, UK
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47
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Thiede B, Lamer S, Mattow J, Siejak F, Dimmler C, Rudel T, Jungblut PR. Analysis of missed cleavage sites, tryptophan oxidation and N-terminal pyroglutamylation after in-gel tryptic digestion. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:496-502. [PMID: 10717661 DOI: 10.1002/(sici)1097-0231(20000331)14:6<496::aid-rcm899>3.0.co;2-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Peptide mass fingerprinting is a powerful tool for the identification of proteins. Trypsin is the most widely used enzyme for this purpose. Therefore, 104 protein digests from human Jurkat T cells and Mycobacterium were analyzed considering missed cleavage sites, tryptophan oxidation and N-terminal pyroglutamylation. About 90% of the matched peptides with missed cleavage sites could be classified into three groups: (i) lysine and arginine with a neighbouring proline on the carboxy-terminal side, (ii) neighboring lysines/arginines, and (iii) lysines and arginines with an aspartic acid or glutamic acid residue on either the amino- or carboxy-terminal side. The first group is already accounted for by search programs. The number of missed cleavage sites can be increased without reducing the precision of the database search by taking the other two groups into consideration. Peptides with tryptophan were observed in non, singly (+16 Da) and doubly (+32 Da) oxidized forms. The higher oxidized form was only observed with lower intensity in the presence of the lower oxidized form. Peptides with N-terminal glutamine were found always as pyroglutamate (-17 Da), and in the majority of cases in pairs with unmodified glutamine. These data can be used for the refinement of protein searches by peptide mass fingerprinting.
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Affiliation(s)
- B Thiede
- Max-Planck-Institut für Infektionsbiologie, Monbijoustrasse 2, D-10117 Berlin, Germany.
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48
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49
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Jungblut PR, Grabher G, Stöffler G. Comprehensive detection of immunorelevant Borrelia garinii antigens by two-dimensional electrophoresis. Electrophoresis 1999; 20:3611-22. [PMID: 10612288 DOI: 10.1002/(sici)1522-2683(19991201)20:18<3611::aid-elps3611>3.0.co;2-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lyme disease is caused by spirochetes of the Borrelia burgdofferi complex and has been reported in many temperate parts of the Northern Hemisphere. The B. burgdorferi complex consists of at least five different species and five genotypes with different pathogenicity. Serodiagnosis was achieved by detection of antigens on one-dimensional (1-D) immunoblots. A systematic and comprehensive approach to elucidate antigens has been started here by the combination of two-dimensional electrophoresis (2-DE) immunoblotting with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Antigens in the proteome of B. garinii BITS were analyzed for their reactivity with sera from patients in early stage (erythema migrans) and late manifestations (neuroborreliosis late, arthritis and acrodermatitis chronica athrophicans) of borreliosis. A strategy to handle the enormous amount of data was developed and 65 antigens were detected, of which 20 were identified. These comprise the known antigens from 1-D immunoblots used routinely in serodiagnosis and additionally the two new antigens, GAPDH and the ABC transporter oligopeptide permease. Several disease-stage unique proteins were detected and some of them identified. The genetic variability between B. garinii strains BITS and 20047, B. afzelii, and B. burgdofferi, sensu stricto, seen on the 2-DE patterns underlines the necessity of the search for additional antigens to improve the serodiagnosis and development of vaccines to be used outside of Northern America. A 2-DE database of B. garinii was built up and is available on the World Wide Web (http://www.mpiib-berlin.mpg.de/2D-PAGE).
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Affiliation(s)
- P R Jungblut
- Institute of Microbiology, Medical Faculty, University Innsbruck, Austria.
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50
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Jungblut PR, Schaible UE, Mollenkopf HJ, Zimny-Arndt U, Raupach B, Mattow J, Halada P, Lamer S, Hagens K, Kaufmann SH. Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol Microbiol 1999; 33:1103-17. [PMID: 10510226 DOI: 10.1046/j.1365-2958.1999.01549.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 1993, the WHO declared tuberculosis a global emergency on the basis that there are 8 million new cases per year. The complete genome of the strain H37Rv of the causative microorganism, Mycobacterium tuberculosis, comprising 3924 genes has been sequenced. We compared the proteomes of two non-virulent vaccine strains of M. bovis BCG (Chicago and Copenhagen) with two virulent strains of M. tuberculosis (H37Rv and Erdman) to identify protein candidates of value for the development of vaccines, diagnostics and therapeutics. The mycobacterial strains were analysed by two-dimensional electrophoresis (2-DE) combining non-equilibrium pH gradient electrophoresis (NEPHGE) with SDS-PAGE. Distinct and characteristic proteins were identified by mass spectrometry and introduced into a dynamic 2-DE database (http://www.mpiib-berlin.mpg.de/2D-PAGE). Silver-stained 2-DE patterns of mycobacterial cell proteins or culture supernatants contained 1800 or 800 spots, respectively, from which 263 were identified. Of these, 54 belong to the culture supernatant. Sixteen and 25 proteins differing in intensity or position between M. tuberculosis H37Rv and Erdman, and H37Rv and M. bovis BCG Chicago, respectively, were identified and categorized into protein classes. It is to be hoped that the availability of the mycobacterial proteome will facilitate the design of novel measures for prevention and therapy of one of the great health threats, tuberculosis.
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Affiliation(s)
- P R Jungblut
- Protein Analysis Unit, Max-Planck-Institute for Infection Biology, Berlin, Germany.
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