Proteomics of Microbial Pathogens

✍ Scribed by Peter R. Jungblut, Michael Hecker

• Publisher: Wiley-VCH
• Year: 2007
• Tongue: English
• Leaves: 346
• Edition: 1
• Category: Library

✦ Synopsis

High-quality research articles on proteomic analyses of microbial pathogens, made available in a handy form.Containing proven, high-quality research articles selected from the popular Proteomics journal, this is a current overview of the latest research into the proteomics analysis of microbial pathogens as well as several review articles.

✦ Table of Contents

Proteomics of Microbial Pathogens......Page 4
Table of Contents......Page 8
Preface Proteomics of microbial pathogens......Page 18
1.1 Introduction......Page 20
1.1.1.1 Diseases......Page 21
1.1.1.2 The developmental cycle......Page 22
1.2.1 Sequenced Chlamydia genomes......Page 24
1.2.2 Chlamydial genes......Page 25
1.2.3 Genome comparison......Page 26
1.3 Proteome analysis of Chlamydia......Page 28
1.3.2 C. trachomatis proteome studies......Page 29
1.3.3 C. pneumoniae proteome studies......Page 30
1.3.4 Identification of secreted proteins by comparative proteomics......Page 32
1.3.6 Proteome comparison of S. trachomatis serovars......Page 34
1.3.8 Considerations in proteomics......Page 35
1.4 Concluding remarks......Page 36
2.1 Introduction......Page 40
2.3 Subunit Helicobacter vaccines: Conventional antigen selection......Page 41
2.4.1 Proteomics as a tool for antigen characterization......Page 42
2.4.2 The Helicobacter proteome......Page 43
2.4.3 Criteria for promising antigen candidates......Page 44
2.4.4 Identification of protective antigens based on multiple criteria......Page 46
2.5 Concluding remarks......Page 47
3 Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics......Page 50
3.1 Introduction......Page 51
3.2 Subproteomes vs. the total theoretical proteome......Page 52
3.3 The vegetative proteome of growing cells......Page 53
3.4 Proteomes of nongrowing cells – the adaptational network......Page 58
3.5 Proteomic signatures – tools for microbial physiology and their practical application......Page 67
3.6 Transcriptomics vs. proteomics – towards a second generation of proteomics......Page 69
3.7 The interactome......Page 71
3.9 Post-translational modifications......Page 72
3.10 Protein quality control/protein degradation at a proteomic scale......Page 74
3.11 Gene expression network – horizontal and vertical approach......Page 75
3.12 Concluding remarks......Page 77
4 Web-accessible proteome databases for microbial research......Page 82
4.2.1 Data generation and data storage......Page 83
4.3.1 Data management, analysis and presentation......Page 84
4.3.2 2D-PAGE database......Page 85
4.3.4 FUNC_CLASS database......Page 87
4.3.5 Data analysis and visualization......Page 88
4.4 Concluding remarks......Page 92
5.1 Introduction......Page 94
5.2.1 Chemicals......Page 95
5.2.4 MALDI-TOF MS and unimolecular decomposition product ion analysis......Page 96
5.2.5 Database searches and identification of Bacillus species......Page 97
5.3.1.2 Bacillus globigii and sphaericus 14577......Page 98
5.3.1.3 Bacillus cereus Tand anthracis Sterne......Page 100
5.3.2.1 Unimolecular decomposition product ion analysis (UDPIA)......Page 102
5.3.3.1 Flagellin and surface layer protein precursor......Page 104
5.3.3.2 Cold shock and cold shock-like proteins......Page 106
5.3.3.4 DNA-binding proteins......Page 109
5.3.3.5 Heat shock proteins......Page 110
5.3.4 Analysis of a 1:1 mixture of B. globigii and B. sphaericus 14577......Page 111
5.4 Concluding remarks......Page 113
6 Protein identification and tracking in two-dimensional electrophoretic gels by minimal protein identifiers......Page 116
6.1 Introduction......Page 117
6.2.1 Materials......Page 118
6.2.4 Compilation of a theoretical dataset comprising all tryptic peptides of M. tuberculosis H37Rv......Page 119
6.2.6 Determination of exogenous contaminant masses......Page 120
6.3.2 Determination of exogenous contaminant masses by MS-Screener......Page 121
6.3.3 The MPI approach revealed HspX-specific peptide masses in multiple spectra......Page 125
6.3.4 The MS-Screener analysis revealed truncated variants of Tuf previously not identified by PMF......Page 130
6.3.5 Frequency of tryptic peptides with similar m/z ratios in M. tuberculosis H37Rv......Page 132
6.3.6 In mass spectrometry it is important to consider detection probabilities of proteins and peptides......Page 133
6.4 Concluding remarks......Page 136
7.1 Introduction......Page 140
7.2.1 Preparation and separation of M. leprae proteins......Page 144
7.2.2 MS......Page 145
7.3 Results and discussion......Page 146
7.4 Concluding remarks......Page 157
8.1 Introduction......Page 160
8.2.1 Protein samples......Page 161
8.2.3 Mass spectrometry......Page 162
8.3.2 Mass analysis of ESAT-6 spots......Page 163
8.3.3 Interaction of recombinant CFP10 with ESAT-6 spots......Page 168
8.4 Discussion......Page 169
9.1 Introduction......Page 172
9.2.1 Bacterial strain and growth conditions......Page 173
9.2.5 2-D-PAGE......Page 174
9.2.7.1 Postembedding labeling studies......Page 175
9.2.8 Overlay blot......Page 176
9.2.10 Cloning and purification of proteins......Page 177
9.2.12 Bioinformatic analysis......Page 178
9.3.1.2 Validation of the cell wall subproteome......Page 179
9.3.2 Analysis of protein processing and localization......Page 186
9.3.3 Analysis of plasminogen-binding proteins......Page 187
9.4.1 Analysis of proteins identified from surface extracts......Page 192
9.4.2 Analysis of protein processing and localization in surface extracts......Page 193
9.4.3 Possible function of plasminogen binding in virulence......Page 194
9.5 Concluding remarks......Page 196
10 Low virulent strains of Candida albicans: Unravelling the antigens for a future vaccine......Page 200
10.1 Introduction......Page 201
10.2.3 Systemic infection conditions and generation of immune sera......Page 202
10.2.5.1 Protoplast lysate preparation......Page 203
10.2.6 Immunoblot analyses......Page 204
10.2.7 MALDI-TOF and MALDI-TOF MS analyses of spots......Page 205
10.3.1 Vaccination assays with different mutant strains and generation of immune sera......Page 206
10.3.2.1 Role of Th1/Th2 cytokines in CNC13 immune response......Page 207
10.3.2.2 Protection induced by passive transfer of sensitized CNC13 lymphocytes......Page 208
10.3.3.1 Detection and identification of the immunoreactive proteins......Page 209
10.4.1 Low virulent C. albicans strains as a tool to study the host immune response......Page 213
10.4.2 C. albicans hog1 mutant induces protection in a vaccination assay......Page 215
10.4.4 Antibody profile linked to successful vaccination against systemic candidiasis......Page 216
10.5 Concluding remarks......Page 217
11.1 Introduction......Page 222
11.2.3 Protease exposure......Page 224
11.2.6 2-D NEPHGE......Page 225
11.2.7 MALDI-TOF-MS......Page 226
11.3.1 Enrichment of B. henselae OMPs......Page 227
11.3.2 1-D SDS-PAGE of B. henselae OMPs and protein assignment by PMF......Page 228
11.3.3 2-D NEPHGE of B. henselae OMPs and protein assignment by PMF......Page 230
11.4 Discussion......Page 234
12.1 Introduction......Page 244
12.2.3 Analytical and preparative PAGE......Page 246
12.3.1 Growth phase dependent regulation of extracellular proteins......Page 247
12.3.2 The influence of agr and σ(B) on the extracellular proteome......Page 255
12.4 Discussion......Page 258
12.5 Concluding remarks......Page 264
13 Comparative proteome analysis of cellular proteins extracted from highly virulent Francisella tularensis ssp. tularensis and less virulent F. tularensis ssp. holarctica and F. tularensis ssp. mediaasiatica......Page 268
13.1 Introduction......Page 269
13.2.1 Bacterial cultures and sample preparation for 2-DE......Page 270
13.2.3 Statistical analysis......Page 271
13.2.5 Mass spectrometric identification......Page 272
13.3 Results and discussion......Page 273
13.4 Concluding remarks......Page 284
14.1 Introduction......Page 286
14.2.3 2-DE......Page 288
14.3 Results and discussion......Page 289
14.3.1 Identified protein species more abundant in aerobic culture......Page 293
14.3.2 Identified protein species which are more abundant in anaerobic culture......Page 294
14.4 Concluding remarks......Page 295
15 Induction of Mycobacterium avium proteins upon infection of human macrophages......Page 298
16 Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies......Page 308
16.1 Introduction......Page 309
16.2.1 Human serum samples......Page 310
16.2.3 Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE)......Page 311
16.2.5.2 Desalting......Page 313
16.2.6.2 Peptide fragmentation and sequencing by nanoESI-IT-MS......Page 314
16.3.1.1 Overall 2-D C. albicans antigen recognition pattern......Page 315
16.3.1.2 Identification of C. albicans immunoreactive proteins by peptide mass fingerprinting (PMF)......Page 316
16.3.1.3 Peptide sequencing of C. albicans immunoreactive proteins......Page 317
16.3.1.4 Reference 2-DE C. albicans antigen pattern display on the Net......Page 324
16.3.2 Comparison of 2-D C. albicans antigen recognition patterns obtained with serum samples from patients with and without systemic candidiasis......Page 328
16.3.3 Differences in the 2-D C. albicans antigen recognition profile associated with infection progression......Page 330
16.4 Discussion......Page 331
16.4.1 C. albicans housekeeping enzymes can stimulate the human immune system during systemic candidiasis......Page 335
16.4.1.1 Heat shock proteins (Hsps)......Page 336
16.4.1.3 Elongation factors and ribosomal proteins......Page 337
16.4.2 Natural anti-Candida antibodies might be correlated with differentiation of the human immune response......Page 338
16.4.3 Serum levels of specific anti-Candida antibodies could be useful for the clinical follow-up of systemic candidiasis......Page 339
Index......Page 344