Molecular Biology and Pathogenicity of Mycoplasmas
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Shmuel Razin, Richard Herrmann (Eds.)
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Molecular Biology and Pathogenicity of Mycoplasmas
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Kluwer Academic Publishers
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9780306476068
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CHF 134.90
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Naturwissenschaft
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The recent sequencing of mycoplasma genomes has marked a turning point in the molecular genetic analysis of these microorganisms. Transcriptome and proteome analyses promise to provide the first definition of the total protein complement of a cell. The mycoplasma group includes the smallest known self-replicating organisms carrying the smallest number of genes. No wonder, therefore, that mycoplasmas have a special appeal to those interested in deciphering the minimal set of genes essential for life. Mycoplasma genomics facilitated better understanding of mycoplasma pathogenesis.
Most impressive are the findings concerning the interaction of mycoplasmas with the immune system, macrophage activation, cytokine induction, mycoplasma cell components acting as superantigens, and autoimmune manifestations. The molecular definition of mycoplasmal adhesins responsible for mycoplasma attachment to host cells and evasion of the host immune system by antigenic variation of mycoplasmal surface components are other `hot' subjects of research. Demonstration of the ability of mycoplasmas to enter host cells, cause fusogenic, apoptotic and oncogenic effects, as well as the possible association of mycoplasmas with arthritis, had their share in intensifying research on mycoplasma pathogenesis, bringing more researchers into the circle of those interested in this group of organisms. The present book is a comprehensive, up-to-date, multi-authored treatise.
Writ en for:
Mycoplasmologists, molecular biologists, geneticists, bioinformatics researchers
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.
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
105
