Download 3 Molecular Biology of Parasitic Protozoa

3
Molecular Biology of
Parasitic Protozoa
EDITED BY
Deborah F. Smith
Department of Biochemistry
Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK
and
Marilyn Parsons
Seattle Biomedical Research Institute,
4 Nickerson Street, Seattle, WA 98109-1651 USA
and
Department ofPathobiology, School of Public Health and
Community Medicine, University of Washington, Seattle WA 98195 USA
Technfscfie Universitat Darmstadt
FACHBEREICH 10 — BIOLOGIE
— Bibliothek —
SchnittspahnstraGe 10
D-6 4 2 8 7 D a r m s t a d t
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OIRLatPRESS
OXFORD UNIVERSITY PRESS
Oxford New York Tokyo
Contents
List of contributors
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Abbreviations
xv
1 Introduction
1
DEBORAH F. SMITH and MARILYN PARSONS
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2 Trypanosomatid genetics
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JOHN SWINDLE and ANDREW TAIT
1 Introduction
2 Ploidy and genome size
3 Genetic analysis
3.1 Genetic exchange
3.2 Genetic exchange in natural populations
4 Molecular karyotype
4.1 Trypanosoma cruzi karyotype
4.2 Leishmania spp. karyotype
4.3 Trypanosoma brucei karyotype
5 Gene organization
6 Requirements for gene expression
7 DNA-mediated transformation systems
8 Transient transfection systems
8.1 Transient expression vectors
8.2 Reporter genes
8.3 Promoters and mRNA processing
8.4 Methods of transformation
8.5 Applications of transient transfection
9 Stable transformation
9.1 Selectable markers
9.2 Integrative transformation
9.3 Episomal transformation
9.4 Inducible gene expression
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10 Conclusion
References
3 The three genomes of Plasmodium
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JEAN E. FEAGIN and MICHAEL LANZER
1 Introduction
2 Nuclear genomic organization
2.1 Polymorphisms at chromosome ends
2.2 Repetitive elements in subtelomeric domains
2.3 Chromatin structure and breakage sites
3 Biological ramifications of chromosomal polymorphism
3.1 Chromosomal rearrangements and antigenic variation
3.2 Sexual recombination and genetic diversity
4 Subtelomeric organization and chromosome pairing
5 The extrachromosomal DNAs
5.1 The mitochondrial genome
5.2 Mitochondrial expression and function
5.3 The putative plastid genome
5.4 Expression and function of the 35kb DNA
5.5 Extrachromosomal DNA inheritance
6 Conclusions
References
4 Toxoplasma as a model genetic system
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L. DAVID SIBLEY, DAN K. HOWE, KIEW-LIAN WAN, SHAHID KHAN,
MARTIN A. ASLETT and JAMES W. AJIOKA
1 Introduction
1.1 Advantages of Toxoplasma as a model genetic system
1.2 Life cycle of Toxoplasma
1.3 Human infection and pathogenesis
2 Genomic organization
2.1 The genomes
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2.2 The genes
2.3 Repetitive DNAs
2.4 Gene expression
2.5 Stage-specific gene expression
3 Population genetic structure
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CONTENTS | vii
3.1 Strain-specific antigenic markers
3.2 Polymorphic isoenzyme and DNA markers
3.3 The clonal population structure of Toxoplasma
4 Classical genetic analyses
4.1 Tools for in vitro analysis
4.2 Use of drug resistance markers in genetic crosses
4.3 RFLP linkage studies
5 Genome mapping
5.1 Physical mapping, construction of contigs and mapping of cDNAs
5.2 Physical mapping of parasite genomes
5.3 Database development
6 Molecular genetics
6.1 DNA transfection
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6.2 Stable transformation
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6.3 Targeted gene disruption
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7 Future developments
References
5 Kinetoplast DNA: structure and replication
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PAUL T. ENGLUND, D. LYS GUILBRIDE, KUO-YUAN HWA, CATHARINE E. JOHNSON,
CONGJUN LI, LAURA J. ROCCO and AL F. TORRI
1 Introduction
2 Structure of a kDNA network
2.1 The isolated network
2.2 Organization of the network in vivo
2.3 Conditions required for network formation
3 Replication of the kDNA network
3.1 Free minicircles
3.2 Structure of a replicating network
3.3 Distribution of newly synthesized minicircles around the network
periphery
3.4 The spinning kinetoplast model
3.5 Changes in minicircle valence during replication
3.6 Final stages of network replication
4 A closer look at the replication of minicircles and maxicircles
4.1 Minicircle replication
4.2 Maxicircle replication
References
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CONTENTS
6 Developmental regulation of gene expression in
African trypanosomes
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ETIENNE PAYS and LUC VANHAMME
1 Introduction
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1.1 A model: Trypanosoma brucei
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1.2 Transcription units of the genes for the major stage-specific
antigens of T. brucei
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1.3 Possible levels of control for gene expression
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2 Promoters and the control of transcription initiation
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2.1 The few promoters known
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2.2 Regulation of promoter activity
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2.3 Influence of the chromosomal context
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3 Transcription elongation and processing of the primary transcripts
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3.1 RNA elongation
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3.2 Trans-splicing and polyadenylation
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3.3 The untranslated regions and RNA amounts
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4 RNA translation and protein stability
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4.1 Translational controls
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4.2 Protein stability
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5 Antigenic variation and novel mechanisms of gene regulation
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5.1 In situ (in)activation of VSG expression sites
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5.2 VSG gene rearrangements
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5.3 Programming of VSG expression
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5.4 Point mutations
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5.5 Evolution of VSGs
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6 Conclusions
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Acknowledgements
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References
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7 Trans-splicing in trypanosomatid protozoa
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ELISABETTATJLLU, CHRISTIAN TSCHUDI and ARTHUR GUNZL
1 Introduction
2 Mechanism of trans-splicing
2.1 Trans-spliceosomal U-snRNPs
2.2 U-snRNA interactions in trans-splicing.:
3 The substrates of trans-splicing
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CONTENTS | ix
3.1 The spliced leader RNA: structure and function
3.2 Structure of the pre-mRNA
4 Functional role and consequences of frans-splicing
5 The physiology and regulation of trans-splicing
6 Evolutionary considerations
References
8 RNA editing: post-transcriptional restructuring of
genetic information
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STEPHEN L. HAJDUK and ROBERT S. SABATINI
1 Introduction
1.1 RNA editing defined
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1.2 Mechanisms of RNA processing
1.3 Kinetoplastid RNA editing
2 General aspects of kinetoplastid RNA editing
2.1 The mitochondrial genome of trypanosomes ^
2.2 Guiding of RNA editing
3 Biochemical mechanisms of RNA editing
3.1 Cleavage-ligation mechanism
3.2 Transesterification mechanism
3.3 TUTase addition mechanism
4 Involvement of mitochondrial RNPs in RNA editing
5 Function and origin of RNA editing
5.1 Role of RNA editing in regulation of gene expression
5.2 RNA editing is developmentally regulated
5.3 Evolutionary origin of kinetoplastid-RNA editing
References
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9 Biogenesis of specialized organelles: glycosomes and
hydrogenosomes
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JURG M. SOMMER, PETER J. BRADLEY, C. C. WANG and PATRICIA J. JOHNSON
1 Introduction
2 The glycosome
2.1 Morphology
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CONTENTS
2.2 Function
2.3 Biogenesis
2.4 Glycosomal targeting signals
2.5 Glycosomal versus peroxisomal import
2.6 Mutational analysis of glycosome assembly
2.7 Glycosomal protein import as a potential target for chemotherapy
3 The hydrogenosome
3.1 Trichomonad hydrogenosomes
3.2 Morphology
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3.3 Function
3.4 Biogenesis
3.5 Hydrogenosome-like organelles in other organisms
4 Conclusions
Acknowledgements
References
10 Mechanisms of drug resistance in protozoan
parasites
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DYANN F. WIRTH and ALAN COWMAN
1 Emergence of drug resistance and its impact
2 Role of intrinsic genetic and biological components
3 Impact of drug resistance o n public health and disease
4 C o m m o n themes of resistance in protozoan parasites
5 Amplification and drug resistance
6 Mutations in target enzymes
7 Folate antagonists
8 Drug transport
9 Quinine-like antimalarials
10 Genetic characterization of chloroquine resistance
11 Drug resistance in Toxoplasma gondii
12 Metronidazole resistance
13 Conclusions and perspectives
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References
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CONTENTS
11 Glycosyl-phosphatidylinositols and the surface
architecture of parasitic protozoa
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MALCOLM J. McCONVILLE
1 Introduction
2 Structure of protozoan GPI protein anchors
3 Function of GPI protein anchors in the protozoa
3.1 Subcellular trafficking
3.2 Protein turnover
3.3 Lipase-mediated release
3.4 Maintenance of surface coats
3.5 Modulation of host signal transduction pathways
4 Protein-free GPI glycolipids in the trypanosomatids
4.1 Structure of the GIPLs and LPG in Leishmania parasites
4.2 Function of Leishmania LPG and GIPLs
4.3 Distribution of free GPIs in other protozoan parasites
5 Metabolism and biosynthesis of protozoan GPIs
5.1 Protein anchor biosynthesis
5.2 Biosynthesis of protein-free GPIs in Leishmania
6 Conclusion
References
Index
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