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Karuppusamy S, Mutharia L, Kelton D, Karrow N, Kirby G. Identification of antigenic proteins from Mycobacterium avium subspecies paratuberculosis cell envelope by comparative proteomic analysis. MICROBIOLOGY-SGM 2018; 164:322-337. [PMID: 29458660 DOI: 10.1099/mic.0.000606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Johne's disease (JD) is a contagious, chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). The aim of this study was to identify antigenic proteins from the MAP cell envelope (i.e. cell wall and cytoplasmic membranes) by comparing MAP, M. avium subsp. hominissuis (MAH) and M. smegmatis (MS) cell envelope protein profiles using a proteomic approach. Composite two-dimensional (2D) difference gel electrophoresis images revealed 13 spots present only in the image of the MAP cell envelope proteins. Using serum from MAP-infected cattle, immunoblot analysis of 2D gels revealed that proteins in the 13 spots were antigenic. These proteins were identified by liquid chromatography tandem mass spectrometry as products of the following genes: sdhA, fadE25_2, mkl, citA, gapdh, fadE3_2, moxR1, mmp, purC, mdh, atpG, fbpB and desA2 as well as two proteins without gene names identified as transcriptional regulator (MAP0035) protein and hypothetical protein (MAP1233). Protein functions ranged from energy generation, cell wall biosynthesis, protein maturation, bacterial replication and invasion of epithelial cells, functions considered essential to MAP virulence and intracellular survival. Five MAP cell envelope proteins, i.e. SdhA, FadE25_2, FadE3_2, MAP0035 and DesA2 were recombinantly expressed, three of which, i.e. SdhA, FadE25_2 and DesA2, were of sufficient purity and yield to generate polyclonal antibodies. Immunoblot analysis revealed antibodies reacted specifically to the respective MAP cell envelope proteins with minimal cross-reactivity with MAH and MS cell envelope proteins. Identification and characterization of MAP-specific proteins and antibodies to those proteins may be useful in developing new diagnostic tests for JD diagnosis.
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Affiliation(s)
| | - Lucy Mutharia
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - David Kelton
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Niel Karrow
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Gordon Kirby
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota. Appl Environ Microbiol 2013; 80:478-85. [PMID: 24212578 DOI: 10.1128/aem.02472-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.
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Flow cytometric detection of Mycobacterium avium subsp. paratuberculosis-specific antibodies in experimentally infected and naturally exposed calves. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:1457-65. [PMID: 23885032 DOI: 10.1128/cvi.00295-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A desirable test to diagnose infections with Mycobacterium avium subsp. paratuberculosis facilitates identification of infected cattle prior to the state of M. avium subsp. paratuberculosis shedding. This study aimed at adjusting a flow cytometry (FC)-based assay, using intact M. avium subsp. paratuberculosis bacteria as the antigen, for diagnosis of M. avium subsp. paratuberculosis infections in calves. Serum samples were collected from experimentally infected (n = 12) and naturally exposed (n = 32) calves. Samples from five calves from positive dams were analyzed to determine the dynamics of maternal antibodies. Samples from adult cattle with defined infection status served as the standard (18 M. avium subsp. paratuberculosis shedders, 22 M. avium subsp. paratuberculosis free). After preadsorption with Mycobacterium phlei, sera were incubated with M. avium subsp. paratuberculosis and M. avium subsp. avium bacterial suspensions, respectively, followed by the separate detection of bovine IgG, IgG1, IgG2, and IgM attached to the bacterial surface. M. avium subsp. paratuberculosis-specific sample/positive (S/P) ratios were compared to enzyme-linked immunosorbent assay (ELISA) S/P ratios. In adult cattle, the FC assay for IgG1 had a sensitivity of 78% at a specificity of 100%. Maternally acquired antibodies could be detected in calves up to 121 days of life. While all but two sera taken at day 100 ± 10 postnatum from naturally exposed calves tested negative, elevated S/P ratios (IgG and IgG1) became detectable from 44 and 46 weeks postinoculation onwards in two calves infected experimentally. Even with the optimized FC assay, M. avium subsp. paratuberculosis-specific antibodies can only occasionally be detected in infected calves less than 12 months of age. The failure to detect such antibodies apparently reflects the distinct immunobiology of M. avium subsp. paratuberculosis infections rather than methodological constraints.
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Weigoldt M, Meens J, Bange FC, Pich A, Gerlach GF, Goethe R. Metabolic adaptation of Mycobacterium avium subsp. paratuberculosis to the gut environment. Microbiology (Reading) 2013; 159:380-391. [DOI: 10.1099/mic.0.062737-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mathias Weigoldt
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Franz-Christoph Bange
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Medical School Hannover, Hannover, Germany
| | - Gerald F. Gerlach
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
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Pinel C, Arlotto M, Issartel JP, Berger F, Pelloux H, Grillot R, Symoens F. Comparative proteomic profiles of Aspergillus fumigatus and Aspergillus lentulus strains by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS). BMC Microbiol 2011; 11:172. [PMID: 21798007 PMCID: PMC3162871 DOI: 10.1186/1471-2180-11-172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 07/28/2011] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) was applied to analyze the protein profiles in both somatic and metabolic extracts of Aspergillus species. The study was carried out on some Aspergillus species within the Fumigati section (Aspergillus fumigatus wild-types and natural abnormally pigmented mutants, and Aspergillus lentulus). The aim was to validate whether mass spectrometry protein profiles can be used as specific signatures to discriminate different Aspergillus species or even mutants within the same species. RESULTS The growth conditions and the SELDI-TOF parameters were determined to generate characteristic protein profiles of somatic and metabolic extracts of Aspergillus fumigatus strains using five different ProteinChips®, eight growth conditions combining two temperatures, two media and two oxygenation conditions. Nine strains were investigated: three wild-types and four natural abnormally pigmented mutant strains of A. fumigatus and two strains of A. lentulus. A total of 242 fungal extracts were prepared. The spectra obtained are protein signatures linked to the physiological states of fungal strains depending on culture conditions. The best resolutions were obtained using the chromatographic surfaces CM10, NP20 and H50 with fractions of fungi grown on modified Sabouraud medium at 37 °C in static condition. Under these conditions, the SELDI-TOF analysis allowed A. fumigatus and A. lentulus strains to be grouped into distinct clusters. CONCLUSIONS SELDI-TOF analysis distinguishes A. fumigatus from A. lentulus strains and moreover, permits separate clusters of natural abnormally pigmented A. fumigatus strains to be obtained. In addition, this methodology allowed us to point out fungal components specifically produced by a wild-type strain or natural mutants. It offers attractive potential for further studies of the Aspergillus biology or pathogenesis.
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Affiliation(s)
- Claudine Pinel
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie et Pathologie (IBP), Centre Hospitalier Universitaire Albert Michallon, BP 217, Grenoble, 38043, France
| | - Marie Arlotto
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
| | - Jean-Paul Issartel
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
| | - François Berger
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
| | - Hervé Pelloux
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie et Pathologie (IBP), Centre Hospitalier Universitaire Albert Michallon, BP 217, Grenoble, 38043, France
| | - Renée Grillot
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie et Pathologie (IBP), Centre Hospitalier Universitaire Albert Michallon, BP 217, Grenoble, 38043, France
| | - Françoise Symoens
- Mycology & Aerobiology Section, Scientific Institute of Public Health, 14 rue Juliette Wytsmanstreet, Brussels, 1050, Belgium
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Wynne JW, Bull TJ, Seemann T, Bulach DM, Wagner J, Kirkwood CD, Michalski WP. Exploring the zoonotic potential of Mycobacterium avium subspecies paratuberculosis through comparative genomics. PLoS One 2011; 6:e22171. [PMID: 21799786 PMCID: PMC3142125 DOI: 10.1371/journal.pone.0022171] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/16/2011] [Indexed: 12/19/2022] Open
Abstract
A comparative genomics approach was utilised to compare the genomes of Mycobacterium avium subspecies paratuberculosis (MAP) isolated from early onset paediatric Crohn's disease (CD) patients as well as Johne's diseased animals. Draft genome sequences were produced for MAP isolates derived from four CD patients, one ulcerative colitis (UC) patient, and two non-inflammatory bowel disease (IBD) control individuals using Illumina sequencing, complemented by comparative genome hybridisation (CGH). MAP isolates derived from two bovine and one ovine host were also subjected to whole genome sequencing and CGH. All seven human derived MAP isolates were highly genetically similar and clustered together with one bovine type isolate following phylogenetic analysis. Three other sequenced isolates (including the reference bovine derived isolate K10) were genetically distinct. The human isolates contained two large tandem duplications, the organisations of which were confirmed by PCR. Designated vGI-17 and vGI-18 these duplications spanned 63 and 109 open reading frames, respectively. PCR screening of over 30 additional MAP isolates (3 human derived, 27 animal derived and one environmental isolate) confirmed that vGI-17 and vGI-18 are common across many isolates. Quantitative real-time PCR of vGI-17 demonstrated that the proportion of cells containing the vGI-17 duplication varied between 0.01 to 15% amongst isolates with human isolates containing a higher proportion of vGI-17 compared to most animal isolates. These findings suggest these duplications are transient genomic rearrangements. We hypothesise that the over-representation of vGI-17 in human derived MAP strains may enhance their ability to infect or persist within a human host by increasing genome redundancy and conferring crude regulation of protein expression across biologically important regions.
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Affiliation(s)
- James W Wynne
- Australian Animal Health Laboratory, CSIRO Livestock Industries, Geelong, Victoria, Australia.
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Weigoldt M, Meens J, Doll K, Fritsch I, Möbius P, Goethe R, Gerlach GF. Differential proteome analysis of Mycobacterium avium subsp. paratuberculosis grown in vitro and isolated from cases of clinical Johne's disease. Microbiology (Reading) 2011; 157:557-565. [DOI: 10.1099/mic.0.044859-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bovine Johne's disease (paratuberculosis), caused by Mycobacterium avium subspecies paratuberculosis, poses a significant economic problem to the beef and dairy industry worldwide. Despite its relevance, however, pathogenesis of Johne's disease is still only partially resolved. Since mycobacterial membrane proteins expressed during infection are likely to play an important role in pathogenesis, membrane-enriched fractions, namely mucosa-derived membranes (MDM) and culture-derived membranes (CDM), of M. avium subsp. paratuberculosis from three cows with clinical paratuberculosis were investigated. An initial analysis by 2D difference gel electrophoresis (2D DIGE) and MALDI-TOF-MS analysis revealed four differentially expressed proteins with only one predicted membrane protein. Due to this limited outcome, membrane preparations were subjected to a tube–gel trypsin digestion and investigated by using nanoflow-liquid-chromatography-coupled tandem MS. Based on this approach a total of 212 proteins were detected in MDM including 32 proteins of bovine origin; 275 proteins were detected in CDM; 59 % of MDM and CDM proteins were predicted to be membrane-associated. A total of 130 of the proteins were detected in both MDM and CDM and 48 predicted membrane proteins were detected in MDM from at least two cows. Four of these proteins were not detected in CDM, implying differential expression in the host. All membrane-associated proteins, especially the four identified as being differentially expressed, might be relevant targets for further analyses into the pathogenesis of bovine paratuberculosis.
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Affiliation(s)
- Mathias Weigoldt
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Klaus Doll
- Clinic for Ruminants and Swine (Internal Medicine and Surgery), Justus-Liebig-University, Giessen, Germany
| | - Isabel Fritsch
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
| | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gerald. F. Gerlach
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
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Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155. BMC Microbiol 2010; 10:121. [PMID: 20412585 PMCID: PMC2867950 DOI: 10.1186/1471-2180-10-121] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Accepted: 04/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background The usually non-pathogenic soil bacterium Mycobacterium smegmatis is commonly used as a model mycobacterial organism because it is fast growing and shares many features with pathogenic mycobacteria. Proteomic studies of M. smegmatis can shed light on mechanisms of mycobacterial growth, complex lipid metabolism, interactions with the bacterial environment and provide a tractable system for antimycobacterial drug development. The cell wall proteins are particularly interesting in this respect. The aim of this study was to construct a reference protein map for these proteins in M. smegmatis. Results A proteomic analysis approach, based on one dimensional polyacrylamide gel electrophoresis and LC-MS/MS, was used to identify and characterize the cell wall associated proteins of M. smegmatis. An enzymatic cell surface shaving method was used to determine the surface-exposed proteins. As a result, a total of 390 cell wall proteins and 63 surface-exposed proteins were identified. Further analysis of the 390 cell wall proteins provided the theoretical molecular mass and pI distributions and determined that 26 proteins are shared with the surface-exposed proteome. Detailed information about functional classification, signal peptides and number of transmembrane domains are given next to discussing the identified transcriptional regulators, transport proteins and the proteins involved in lipid metabolism and cell division. Conclusion In short, a comprehensive profile of the M. smegmatis cell wall subproteome is reported. The current research may help the identification of some valuable vaccine and drug target candidates and provide foundation for the future design of preventive, diagnostic, and therapeutic strategies against mycobacterial diseases.
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Windle HJ, Brown PA, Kelleher DP. Proteomics of bacterial pathogenicity: therapeutic implications. Proteomics Clin Appl 2010; 4:215-27. [PMID: 21137045 DOI: 10.1002/prca.200900145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 10/13/2009] [Accepted: 10/19/2009] [Indexed: 01/04/2023]
Abstract
Identification of the molecular mechanisms of host-pathogen interaction is becoming a key focus of proteomics. Analysis of these interactions holds promise for significant developments in the identification of new therapeutic strategies to combat infectious diseases, a process that will also benefit parallel improvements in molecular diagnostics, biomarker identification and drug discovery. This review highlights recent advances in functional proteomics initiatives in infectious disease with emphasis on studies undertaken within physiologically relevant parameters that enable identification of the infectious proteome rather than that of the vegetative state. Deciphering the molecular details of what constitutes physiologically relevant host-pathogen interactions remains an underdeveloped aspect of research into infectious disease. The magnitude of this deficit will be largely influenced by the ease with which model systems can be established to investigate such interactions. As the selective pressures exerted by the host on an infecting pathogen are numerous, the adequacy of certain model systems should be considered carefully.
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Affiliation(s)
- Henry J Windle
- Institute of Molecular Medicine, Trinity College, University of Dublin, Dublin, Ireland.
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Kirkwood CD, Wagner J, Boniface K, Vaughan J, Michalski WP, Catto-Smith AG, Cameron DJS, Bishop RF. Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease. Inflamm Bowel Dis 2009; 15:1643-55. [PMID: 19462429 DOI: 10.1002/ibd.20967] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Mycobacterium avium subspecies paratuberculosis (MAP) is the most enduring infectious candidate that may be associated with inflammatory bowel disease (IBD). It is possible that the inconsistencies in the prevalence studies of MAP in adults reflect clinical differences in adult patients studied, including duration of disease and treatment regimens, and also in lack of specificity of some of the assays used. The aim was to determine the presence of MAP in children with symptoms of Crohn's disease (CD) and ulcerative colitis (UC), using gut biopsy tissue and peripheral blood mononuclear cells (PBMC) collected at initial endoscopic examination prior to clinical treatment. METHODS Mucosal biopsies and/or PBMC specimens were collected from a total of 142 children, comprising 62 with CD, 26 with UC, and 54 with non-IBD. MAP-specific IS900 polymerase chain reaction (PCR) analysis was performed on all biopsies and PBMC specimens. Conventional MAP culture technique was performed on a subset of 10 CD, 2 UC, and 4 non-IBD patients to isolate MAP. RESULTS MAP was identified by IS900 PCR significantly more often in mucosal biopsies from CD 39% (22/56) than from non-IBD 15% (6/39) patients (P < 0.05), and in PBMC from CD 16% (8/50) than from non-IBD 0% (0/31) patients (P < 0.05). Viable MAP were cultured from mucosal biopsies from 4/10 CD, 0/2 UC, and 0/4 non-IBD patients, but were not cultured from PBMC specimens. CONCLUSIONS This unique study on the occurrence of MAP in gut tissue and blood from pediatric IBD patients suggests the possible involvement of MAP in the early stages of development of CD in children.
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Affiliation(s)
- Carl D Kirkwood
- Enteric Virus Group, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.
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