Molecular Biology and Pathogenicity of Mycoplasmas (eBook)

Preface 9
Contents 12
Chapter 1 Taxonomy of Mollicutes 15
1. INTRODUCTION 15
2. TAXONOMY 16
2.1 General concepts 16
2.2 The species concept 17
2.3 The Candidatus concept 19
3. PHYLOGENY 19
3.1 Some basic definitions 20
3.2 The 16S rRNA gene as a phylogenetic tool 20
3.3 Construction of phylogenetic trees 22
3.4 Taxonomy and phylogeny based on genes other than 16S rRNA 23
4. TAXONOMY AND PHYLOGENY OF THE 23
4.1 Taxonomy and phylogeny of the genus 26
4.2 Taxonomy and phylogeny of the genera Entomoplasma and Mesoplasma 31
4.3 Taxonomy and phylogeny of the genus 31
4.4 Taxonomy and phylogeny of the genera Acholeplasma, Anaeroplasma and Asteroleplasma 32
4.5 Taxonomy and phylogeny of the phytoplasmas 33
4.6 Taxonomy and phylogeny of the genus 33
5. THE USE OF 16S rRNA SEQUENCE DATA FOR DESCRIPTION OF NEW SPECIES 34
5.1 The relationship between 16S rRNA sequence data and DNA-DNA reassociation values 35
6. THE IMPACT OF WHOLE GENOME SEQUENCING ON TAXONOMY AND PHYLOGENY 36
7. CONCLUSIONS 37
ACKNOWLEDGMENTS 37
Chapter 2 Phylogeny and Evolution 44
1. INTRODUCTION 44
2. ANALYSIS OF 16S rRNA PHYLOGENETIC TREES 45
3. ORIGIN AND EVOLUTION OF THE MOLLICUTES 45
4. THE AAP PHYLOGENETIC BRANCH 49
5. THE SEM PHYLOGENETIC BRANCH 49
6. EVOLUTION OF MOLLICUTES GENOME SIZE 55
ACKNOWLEDGMENTS 55
REFERENCES 56
Chapter 3 Mycoplasmas of Humans 57
1. INTRODUCTION 57
2. CLINICAL SIGNIFICANCE 58
2.1 Many species are commensals 58
2.2 Respiratory diseases 59
2.3 Urogenital diseases 60
2.4 Neonatal infections 62
2.5 Arthritis and systemic infections in the immunocompromised patient 63
3. BIOLOGICAL FEATURES OF HUMAN MYCOPLASMAS RELEVANT TO PATHOGENICITY 66
3.1 Ureaplasma species 66
3.2 Mycoplasma hominis 69
3.3 Mycoplasma genitalium 70
3.4 Other mycoplasmas 71
REFERENCES 74
Chapter 4 Mycoplasmas of Animals 84
1. INTRODUCTION 84
2. MYCOPLASMAS OF RUMINANTS 86
2.1 Bovine mycoplasmas 86
2.2 Mycoplasmas of sheep, goats and wild caprinae 88
3. MYCOPLASMAS OF POULTRY 90
4. PORCINE MYCOPLASMAS 91
5. EQUINE MYCOPLASMAS 92
6. MYCOPLASMAS OF DOGS AND CATS 92
7. MYCOPLASMAS OF SMALL RODENTS 93
8. CONCLUSIONS 93
ACKNOWLEDGMENTS 94
REFERENCES 94
Chapter 5 Mycoplasmas of Plants and Insects 102
1. INTRODUCTION 102
2. PHYLOGENETIC DIVERSITY OF PLANT AND INSECT MYCOPLASMAS 103
3. DIVERSITY OF PHYTOPLASMAS AND SPIROPLASMAS 105
3.1 Biological and pathological diversity 105
3.2 Molecular diversity of phytoplasmas 109
3.3 Taxonomic and molecular diversity of spiroplasmas 116
4. CONCLUDING REMARKS 118
ACKNOWLEDGMENTS 119
REFERENCES 119
Chapter 6 Cell Division 127
1. INTRODUCTION 127
2. DIVISION MODE 127
3. DNA REPLICATION 128
4. SEGREGATION OF THE REPLICATED CHROMOSOME 130
5. DUPLICATION OF THE ATTACHMENT ORGANELLE 131
5.1 Scheme for migration of the attachment organelle 131
5.2 Formation of nascent organelle 133
6. CYTOSKELETAL STRUCTURES 134
7. CYTOKINESIS 134
7.1 Constriction 134
7.2 Gliding motility 135
7.3 Branch formation 136
8. PERSPECTIVES 136
ACKNOWLEDGMENTS 137
REFERENCES 137
Chapter 7 The Cell Membrane and Transport 141
1. INTRODUCTION 141
2. STRUCTURE AND FUNCTION OF MEMBRANE PROTEINS 142
2.1 General properties 142
2.2 Types and numbers of Mollicute proteins 143
2.3 Major membrane protein functions 145
3. MEMBRANE LIPID BILAYERS 154
3.1 Biosynthetic pathways: lipids, enzymes and genes 154
3.2 Regulation of lipid bilayer packing properties 159
4. CONCLUSIONS 164
ACKNOWLEDGEMENTS 164
REFERENCES 165
Chapter 8 Central Carbohydrate Pathways: Metabolic Flexibility and the Extra Role of Some “Housekeeping” Enzymes 172
1. INTRODUCTION 172
2. THE MOST ANCIENT WAY 172
3. BUT WHY GLUCOSE? 173
4. CARBOHYDRATE CATABOLISM 173
5. FUELS, THEIR PRIMING AND THEIR ENTRY INTO THE CELL 175
6. PRIMING ENTRY OF CARBOHYDRATE (GLUCOSE) 176
7. GLUCOSE INSIDE THE CELL: ATP FORMATION AND THE INVOLVED PATHS TO OXYGEN AND PYRUVATE 177
8. THE INVOLVEMENT OF OXYGEN 178
9. THE CONTRIBUTORY ROLE OF THE THIOREDOXIN REDUCTASE SYSTEM 179
10. THE DIRECT ROUTE TO PYRUVATE 180
11. THE REVERSIBLE PPI-6PFK 180
12. THE ROLES OF PYROPHOSPHATE IN MOLLICUTES 181
13. NON-FERMENTATIVE MOLLICUTES: THEIR GLYCOLYTIC DEFICITS AND ROLE OF THE PENTOSE PHOSPHATE PATHWAY 182
14. BEYOND PHOSPHOFRUCTOKINASE TO PYRUVATE AND THE PYRUVATE “ROUNDHOUSE” 183
15. PHOSPHOGLYCERATE KINASE (PGK) AND PYRUVATE KINASE (PK) 183
16. THE PYRUVATE “ROUNDHOUSE” 184
17. THE TCA CYCLE IS ABSENT IN MOLLICUTES BUT FOR MALATE DEHYDROGENASE 186
18. LINKAGE OF THE PPP AND EMP 187
19. THE ROLE OF THE PPP AND DEOYXRIBOSE-5-PHOSPHATE ALDOLASE IN MOLLICUTES 188
20. OTHER CARBOHYDRATE PATHS IN MOLLICUTES 189
21. METABOLIC TAXONOMY 190
22. PHYLOGENY, BUT NOT WITH rRNA 192
23. EPILOGUE: MYCOPLASMATALES? 196
ACKNOWLEDGMENTS 198
REFERENCES 198
Chapter 9 Database Systems for the Analysis of Biochemical Pathways 209
1. INTRODUCTION 209
2. BIOCHEMICAL DATABASES 210
2.1 General resources 211
2.2 Existing biochemical pathway specific resources 213
3. QUERYING AND EXTRACTING THE INFORMATION 215
3.1 Querying the data 215
3.2 Extracting the information for its use in your own project 216
4. PRINCIPLES FOR BUILDING YOUR OWN PATHWAY DATABASE 217
5. CONCLUSIONS 223
ACKNOWLEDGMENTS 224
REFERENCES 224
APPENDIX 226
Chapter 10 Mycoplasmas and the Minimal Genome Concept 229
1. MYCOPLASMAS AS SIMPLE MODEL CELLS 229
2. THE RANGE OF GENOME COMPLEXITY 230
3. WHAT IS A MINIMAL GENOME AND CAN IT BE DEFINED? 230
4. COMPARATIVE GENOMICS AND THE MINIMAL GENOME 232
5. EXPERIMENTAL APPROACHES TO DEFINING A MINIMAL GENOME 234
6. IMPLICATIONS OF THE PROPOSED MINIMAL GENE SETS 236
7. POTENTIAL APPLICATIONS OF MINIMAL GENOMES 237
ACKNOWLEDGMENTS 238
REFERENCES 238
APPENDIX 240
Chapter 11 Comparative Genome Analysis of the Mollicutes 262
1. OVERVIEW 262
2. EVOLVING MOLLICUTE ANNOTATION: THE EXAMPLE 266
3. EVOLVING METHODS FOR MOLLICUTE GENOME ANALYSIS: THE EXAMPLE 270
4. COMPARATIVE GENOME ANALYSIS TO DETECT FEATURES OF SPECIFIC MOLLICUTES 273
5. COMPARATIVE ANALYSIS TO REVEAL COMMON FEATURES OF MOLLICUTES 278
6. COMBINING GENOMIC FEATURES WITH BIOCHEMICAL KNOWLEDGE 281
REFERENCES 282
Chapter 12 Transcriptome and Proteome Analyses of Mollicutes 286
1. INTRODUCTION 286
1.1 Transcriptome analysis 287
1.2 Proteome analysis 289
1.3 Transcriptome versus proteome 291
2. THE TRANSCRIPTOME OF M. PNEUMONIAE 295
3. THE PROTEOME OF SPIROPLASMA MELLIFERUM 297
4. THE PROTEOME OF M. GENITALIUM 298
5. THE PROTEOME OF M. PNEUMONIAE 299
6. COMPARISON OF THE PROTEOMES OF M. GENITALIUM AND M. PNEUMONIAE 302
7. CONCLUSION 303
ACKNOWLEDGEMENTS 303
REFERENCES 304
Chapter 13 DNA Replication, Repair and Stress Response 310
1. INTRODUCTION 310
2. REPLICATION INITIATION 310
2.1 DnaA protein 311
2.2 Replication origin (oriC) 311
3. REPLICATION FORKS 313
3.1 DNA polymerase III holoenzyme 314
3.2 Primosomal proteins 316
3.3 Proteins involved in sealing Okazaki fragments 316
3.4 Replication fork arrest and termination of DNA replication 317
4. OTHER PROTEINS INVOLVED IN DNA REPLICATION 318
4.1 Single-stranded DNA binding protein (SSB) 318
4.2 Topoisomerases 318
5. DNA REPAIR AND STRESS RESPONSE 319
5.1 SOS stress response 319
5.2 Base excision repair 320
5.3 Nucleotide excision repair 321
5.4 Recombinational repair system 322
6. CONCLUSIONS 324
ACKNOWLEDGMENTS 324
REFERENCES 324
Chapter 14 Transcription and Translation 329
1. INTRODUCTION 329
2. GENERAL FEATURES OF MYCOPLASMA GENOMES AND GENES 330
3. TRANSCRIPTION 332
3.1 RNA polymerase 332
3.2 Promoters and transcription initiation 332
3.3 Termination and attenuation 333
3.4 Processing of RNA gene transcripts 334
3.5 Regulation 335
4. TRANSLATION 336
4.1 Ribosomes, translation factors and aminoacyl tRNA synthetases 336
4.2 Shine-Dalgarno sequence and translational initiation 337
4.3 Codon usage 338
4.4 tRNA anticodons and codon-recognition 340
4.5 UGA as a tryptophan codon 344
4.6 Translation in vivo and in vitro 345
4.7 tmRNA and trans-translation 345
REFERENCES 346
Chapter 15 Extrachromosomal Elements and Gene Transfer 352
1. INTRODUCTION 352
2. EXTRACHROSOMAL ELEMENTS 353
2.1 Plasmids 353
2.2 Viruses 354
3. GENE TRANSFER 357
3.1 Transformation 357
3.2 Selectable markers 359
3.3 Cloning and expression vectors 360
3.4 Transposon mutagenesis 363
3.5 Gene disruption through homologous recombination 365
3.6 Mycoplasma mating 367
4. CONCLUSIONS 368
ACKNOWLEDGMENTS 368
REFERENCES 368
Chapter 16 Restriction-Modification Systems and Chromosomal Rearrangements in Mycoplasmas 376
1. TYPES OF RESTRICTION-MODIFICATION 376
2. RESTRICTION-MODIFICATION SYSTEMS IN MYCOPLASMAS 378
2.1 Mycoplasma arthritidis 378
2.2 Mycoplasma pulmonis 379
3. RESTRICTION-MODIFICATION VIS-A-VIS MYCOPLASMA GENETICS 380
4. CHROMOSOMAL REARRANGEMENTS IN MYCOPLASMAS 381
4.1 Mycoplasmal speciation and chromosomal rearrangements 382
4.2 Recombination 383
4.3 Illegitimate recombination 387
4.4 Other instances of chromosomal rearrangements in mycoplasmas 389
REFERENCES 390
Chapter 17 Invasion of Mycoplasmas into and Fusion with Host Cells 396
1. INVASION INTO HOST CELLS 396
1.1 Experimental systems 396
1.2 Invasins and receptors 397
1.3 Changes in the host cell cytoskeleton 398
1.4 Signal transduction 399
1.5 Survival and multiplication within host cells 400
1.6 Cytopathic effects 400
2. FUSION WITH HOST CELLS 401
2.1 Factors mediating fusion 401
2.2 Molecules implicated in fusion 401
2.3 Role in virulence 403
3. CONCLUSIONS 403
REFERENCES 404
Chapter 18 Apoptotic, Antiapoptotic, Clastogenic and Oncogenic Effects 407
1. INTRODUCTION 407
2. THE NATURE OF CANCERS 407
3. APOPTOTIC AND ANTIAPOPTOTIC EFFECTS OF MYCOPLASMAS 408
3.1 Apoptotic effects 408
3.2 Mitogenic effects and antiapoptotic effects 410
4. CLASTOGENIC EFFECTS 411
5. ONCOGENIC EFFECTS 413
5.1 Acute form of induction 413
5.2 Chronic form of induction 414
6. MYCOPLASMAS AS A MODEL SYSTEM FOR CANCER RESEARCH 415
7. CONCLUSION 416
REFERENCES 417
Chapter 19 Genetic Mechanisms of Surface Variation 421
1. INTRODUCTION 421
2. FREQUENT MUTATIONS AS GENETIC SWITCHES 423
2.1 Mutations in regulatory elements 423
2.2 Mutations within coding regions 425
3. SITE-SPECIFIC DNA INVERSIONS AND PHENOTYPIC SWITCHING 427
3.1 The vsa gene system of Mycoplasma pulmonis 428
3.2 The vsp gene system of Mycoplasma bovis 429
3.3 Catalysis by site-specific recombinases 432
4. EXTENDED REPERTOIRES OF HOMOLOGOUS GENES ENCODING VARIABLE SURFACE ANTIGENS 433
4.1 vlp gene repertoire of M. hyorhinis 433
4.2 vsp gene repertoire of M. bovis 434
5. OTHER MECHANISMS OF SURFACE VARIATION 434
5.1 Generation of chimeric vsp genes by intragenic recombination in M. bovis 434
5.2 Generation of chimeric genes by multiple gene conversions: the vlhA system of Mycoplasma synoviae 435
5.3 Transcriptional effects determine variable P35 expression in Mycoplasma penetrans 437
5.4 Repetitive DNA and antigenic variation in Mycoplasma genitalium and Mycoplasma pneumoniae 437
6. EFFECTS OF VARIABLE PRODUCTS: SURFACE ARCHITECTURE AND EXOPROTEIN MODIFICATION 438
6.1 Surface phenotypes affected by phase-variable masking 438
6.2 Size variation 439
6.3 Posttranslational modification and variable release of exoproteins 440
ACKNOWLEDGMENTS 441
REFERENCES 441
Chapter 20 Immunomodulation by Mycoplasmas: Artifacts, Facts and Active Molecules 448
1. MISHAPS AND MISINTERPRETATIONS 448
1.1 Mycoplasmas and malaria 449
1.2 Mycoplasmas and natural killer (NK) cells 450
1.3 Mycoplasmas and T cell glycolipids 450
1.4 Mycoplasmas and “lymphokines” which activate B cells to proliferate and produce immunoglobulins 450
1.5 Mycoplasmas and a differentiation-inducing cytokine 450
1.6 Mycoplasmas and nonself discrimination of malignant cells 452
1.7 Mycoplasmas and a cytotoxicity inducing activity 452
2. CAUSE AND EFFECTS 453
2.1 Earlier reports on immunomodulation by mycoplasmas 454
3. MYCOPLASMAL LIPOPROTEINS AND LIPOPEPTIDES AS IMMUNOMODULATORY COMPONENTS 455
3.1 Pioneer work 455
3.2 Mycoplasmal lipoproteins 455
3.3 MALP-2, the molecule 456
3.4 Structural details that determine the biological activity of MALP-2 458
3.5 Structural similarities between macrophageactivating lipopeptides and LPS endotoxins 459
3.6 Biological activities of MALP-2 and other mycoplasmal lipoproteins 460
3.7 Receptors and signal transduction 463
4. IMMUNOMODULATION BY MYCOPLASMAL PRODUCTS NOT DUE TO MACROPHAGE ACTIVATION 465
4.1 Activation of complement 465
4.2 Interaction of mycoplasmal compounds with bone organ cultures 465
4.3 Interaction of mycoplasmal compounds with cells of the nervous system 466
4.4 Effects of MALP-2 and other mycoplasmal compounds on fibroblasts and alveolar type II lung epithelial cells 466
5. SUMMARY AND CONCLUSIONS 466
ACKNOWLEDGMENTS 467
REFERENCES 468
Chapter 21 Mycoplasma arthritidis Pathogenicity: Membranes, MAM, and MAV1 476
1. INTRODUCTION 476
2. DISEASE 477
2.1 Rats 477
2.2 Mice 478
2.3 Rabbits 479
3. PATHOGENIC MECHANISMS IN MURINE ARTHRITIS 480
3.1 Membranes 480
3.2 MAM 482
3.3 MAV1 485
4. MODEL OF PATHOGENESIS FOR RATS 486
REFERENCES 487
Chapter 22 Cytadherence and the Cytoskeleton 493
1. INTRODUCTION 493
1.1 The attachment organelle 493
1.2 The cytoskeleton 493
2. THE ATTACHMENT ORGANELLE AND CELL DIVISION 495
3. ATTACHMENT ORGANELLE PROTEINS 495
3.1 Introduction 495
3.2 The P1 adhesin 496
3.3 ORF6 gene products 498
3.4 Protein P65 499
3.5 Protein P30 501
3.6 HMW3 503
3.7 HMW1 504
3.8 HMW2 and P28 506
3.9 Protein P200 as a candidate attachment organelle protein 509
3.10 Order of attachment organelle assembly 509
4. OTHER COMPONENTS OF THE MYCOPLASMA CYTOSKELETON 510
4.1 TX partitioning of Mycoplasma proteins 510
4.2 Identification of Mycoplasma cytoskeletal proteins 511
5. THE NATURE OF THE MYCOPLASM A CYTOSKELETON 512
5.1 Biochemical definition of the cytoskeleton 512
5.2 Physiological definition of the cytoskeleton 513
5.3 Defining the Mycoplasma cytoskeleton 513
6. CONCLUSION 514
ACKNOWLEDGMENTS 514
REFERENCES 515
Chapter 23 Mycoplasma pneumoniae Disease Manifestations and Epidemiology 521
1. INTRODUCTION 521
2. THE AGENT’S HISTORY AND ITS RESERVOIR 522
3. EPIDEMIOLOGY 524
4. MANIFESTATIONS OF DISEASES 527
REFERENCES 529
Diagnosis of Mycoplasmal Infections 533
1. INTRODUCTION 533
2. CULTURAL PROPERTIES AND BIOCHEMICAL TESTS 533
3. SEROLOGICAL TESTS 535
4. MOLECULAR GENETIC METHODS 537
4.1 Restriction endonuclease analysis (REA) 537
4.2 PCR-based diagnostic procedures 538
Chapter 25 Antimycoplasmal Agents 547
1. INTRODUCTION 547
2. ANTIMICROBIAL SUSCEPTIBILITY TESTING 547
2.1 Broth dilution methods 548
2.2 Agar dilution and gradient diffusion methods 549
2.3 Minimal bactericidal concentration (MBC) tests 550
2.4 Interpretation of results 550
3. INNATE ANTIBIOTIC RESISTANCE OF MYCOPLASMAS 551
3.1 Resistance related to the class 551
3.2 Resistance related to the species 551
4. ANTIBIOTICS USED FOR TREATMENT OF MYCOPLASMAL INFECTIONS 553
4.1 Tetracyclines 554
4.2 Macrolide-Lincosamide-Streptogramin (MLS) group 555
4.3 Fluoroquinolones 556
4.4 Miscellaneous 557
5. ACQUIRED RESISTANCE OF MYCOPLASMAS 557
5.1 Tetracyclines 558
5.2 MLS group 559
5.3 Fluoroquinolones 560
5.4 Aminoglycosides 561
5.5 Chloramphenicol 562
6. CONCLUSION 562
REFERENCES 562
Index 569

Chapter 9
Database Systems for the Analysis of Biochemical Pathways (p. 201-202)

ISABEL ROJAS-MUJICA* and ERICH BORNBERG-BAUER#
*European Media Laboratory, Heidelberg, Germany,
#UMBER - Bioinformatics Group, School of Biological Sciences, University of Manchester, UK

1. INTRODUCTION

The mycoplasmas were amongst the first organisms for which the complete genome sequence was obtained and made available to the public domain (13, 10, 6). Complementary information, such as the proteome of mycoplasma pneumoniae (26) and reconstructed pathways, has also been made available and can be queried or downloaded from various locations on the web. However, database systems that allow scientists to work with these data in an integrated manner, together with other relevant information, are still not common. This is a wide-spread problem that not only applies to mycoplasma. Current biological research uses a wide range of interacting software which in turn uses a large number of disparate data source. These problems have arisen for several reasons which are, amongst others, the specialisation of biological disciplines, the lack of unified interfaces and the variations in the interpretation of the data, Bioinformatic tools need to overcome these difficulties. For biochemical pathways this implies the development of a system which is based on the functional roles of molecular objects such as reactions and pathways.

From a data modelling point of view the modelling of biochemical processes is a complex problem. Fuzziness of the definitions, exceptions and complex relations, are some of the common characteristics that are found when attempting to model these processes. Models for storage and representation of pathways and data on expression and the genome, must reflect the logics of the cellular machinery. At the same time they must be designed to offer a platform for optimal storage, retrieval and analysis of such data for the biological researcher. In this chapter, we provide an overview of available data resources and relevant tools for extracting pathway-related information from the most widely used databases and briefly explain their usage. We will also discuss some of the systems and methods, both established and new, to support the process of examination and understanding of the data. We will revise several of the methods and problems related to the integration, handling and interpretation of biochemical data. As an introduction to data modelling, we present a small example related to the modelling of enzymatic reactions. This is meant to raise awareness of the importance of structuring data. It should give researchers, who have no experience in creating databases, a rough idea of what they could gain from putting their data into an integrated system.

2. BIOCHEMICAL DATABASES

The genomes of Mycoplasma pneumoniae (M.pn.) and Mycoplasma genitalium (M.gen.) are widely viewed as a blueprint for a cell with a minimal metabolism. The availability of data generated from the sequencing of their genomes and results from both comparative genome analysis and experiments, such as global transposon mutagenesis (14), make them a sensible choice to study methods for pathway analysis and data integration. There are several databases – accessible through the World Wide Web (WWW) – that contain information about biochemical pathways, to different extends and with different focuses (see Appendix). With the growing amount of information related to biochemical reactions and thus with the growing interest towards the study of biochemical networks, the number of projects and databases (or data collections)i dealing with biochemical pathways is rapidly expanding. This means that, like any other study, this short description of some of the existing biochemical pathway databases can only be a snapshot of the current stand. We will mention a few of these databases, not all of which contain explicit information about mycoplasmas.