Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
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 lnv,Nr. OIRLatPRESS OXFORD UNIVERSITY PRESS Oxford New York Tokyo Contents List of contributors xii Abbreviations xv 1 Introduction 1 DEBORAH F. SMITH and MARILYN PARSONS f 2 Trypanosomatid genetics 6 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 . 6 7 8 8 10 11 12 12 14 14 16 18 19 19 19 20 21 21 22 22 22 24 24 vi CONTENTS 10 Conclusion References 3 The three genomes of Plasmodium 25 26 35 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 35 36 37 38 39 41 41 42 42 43 43 44 45 47 48 48 48 55 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 " 2.2 The genes 2.3 Repetitive DNAs 2.4 Gene expression 2.5 Stage-specific gene expression 3 Population genetic structure 55 55 55 56 57 57 57 58 58 59 59 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 ' 6.2 Stable transformation / 6.3 Targeted gene disruption ' 7 Future developments References 5 Kinetoplast DNA: structure and replication ' 59 59 60 60 60 61 61 62 63 64 64 65 66 66 67 68 68 75 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 75 76 76 77 78 78 78 79 81 81 83 83 85 85 85 86 viii CONTENTS 6 Developmental regulation of gene expression in African trypanosomes 88 ETIENNE PAYS and LUC VANHAMME 1 Introduction 88 1.1 A model: Trypanosoma brucei 88 1.2 Transcription units of the genes for the major stage-specific antigens of T. brucei 90 1.3 Possible levels of control for gene expression * 92 2 Promoters and the control of transcription initiation 93 2.1 The few promoters known 94 2.2 Regulation of promoter activity 95 2.3 Influence of the chromosomal context , 97 3 Transcription elongation and processing of the primary transcripts 98 3.1 RNA elongation 98 e 3.2 Trans-splicing and polyadenylation 98 3.3 The untranslated regions and RNA amounts 100 4 RNA translation and protein stability 100 4.1 Translational controls 100 4.2 Protein stability . 100 5 Antigenic variation and novel mechanisms of gene regulation 101 5.1 In situ (in)activation of VSG expression sites 103 5.2 VSG gene rearrangements 103 5.3 Programming of VSG expression 104 5.4 Point mutations 105 5.5 Evolution of VSGs 106 6 Conclusions 107 Acknowledgements 107 References " 107 7 Trans-splicing in trypanosomatid protozoa 115 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 115 115 116 118 119 r 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 119 121 124 125 128 129 134 STEPHEN L. HAJDUK and ROBERT S. SABATINI 1 Introduction 1.1 RNA editing defined / 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 134 135 135 136 140 140 143 144 144 145 147 148 150 150 152 152 153 9 Biogenesis of specialized organelles: glycosomes and hydrogenosomes 159 JURG M. SOMMER, PETER J. BRADLEY, C. C. WANG and PATRICIA J. JOHNSON 1 Introduction 2 The glycosome 2.1 Morphology 159 160 160 x 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 * 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 160 161 161 167 167 168 168 168 169 170 171 174 174 175 175 i8i 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 • References 181 182 182 183 183 185 185 187 191 192 194 195 196 196 CONTENTS 11 Glycosyl-phosphatidylinositols and the surface architecture of parasitic protozoa xi 205 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 205 205 207 208 209 210 210 211 212 212 213 217 218 218 220 222 222 229