Molecular Biology of Plant Viruses

Viral Genomic RNA as a Single Translation Unit 100 Initiation Codon Choice and Translation in Plants 100 Conventional Scanning and Initiation 100 Non-AUG Initiation Codons in Plant Virus RNAs 101 Role of5'- and 3'- Noncoding Regions in Initiation of Translation 101 Access to Internal Genes 103 Divided versus Monopartite Genomes 104 Transcriptional Control: Subgenomic RNAs 104 Non-Orthodox Mechanisms of Initiation 107 Leaky Scanning 107 Internal Ribosome Entry Sites (IRES Elements) 107 Non-Orthodox Mechanisms of Elongation and Termination 108 Readthrough of Leaky Stop Codons 108 Ribosomal Frameshifiting 109 Proteolytic Processing 110 Chymotrypsin-like Serine or Cysteine Proteinases 112 Papain-like Cysteine Proteinases 112 Conclusions 113 References 114 5. Molecular Basis of Genetic Variability in RNA Viruses 121-141 Jozef J. Bujarski Introduction 121 Genetic Mechanisms of Variability 121 Mutation 121 Point Mutations 122 Insertions and Deletions 123 Frameshift Mutations 123 Mutant Stability 124 Effects of Mutations on Host-Virus Interactions 124 RNA Recombination 125 Natural Sequence Rearrangement 126 Recombination between Viral and Host RNAs 126 Role of RNA Structure 127 Role of Replicase Proteins 130 Pseudorecombination 131 Defective Interfering RNAs 132 Conclusions 134 Acknowledgements 136 References 136 viii 6. Genetic Variability and Evolution 143-159 F. Garcia-Arenal, A. Fraile, and J. M. Malpica Introduction 143 Variability under Experimental Conditions 143 Variability under Natural Conditions 145 Factors Determining Genetic Structure of Virus Populations 149 Founder Effects 149 Selection 150 Complementation 152 Conclusions 153 Acknowledgements 155 References 155 7. Molecular Basis of Virus Transport in Plants 161-182 Scott M.

Viral Genomic RNA as a Single Translation Unit 100 Initiation Codon Choice and Translation in Plants 100 Conventional Scanning and Initiation 100 Non-AUG Initiation Codons in Plant Virus RNAs 101 Role of5''- and 3''- Noncoding Regions in Initiation of Translation 101 Access to Internal Genes 103 Divided versus Monopartite Genomes 104 Transcriptional Control: Subgenomic RNAs 104 Non-Orthodox Mechanisms of Initiation 107 Leaky Scanning 107 Internal Ribosome Entry Sites (IRES Elements) 107 Non-Orthodox Mechanisms of Elongation and Termination 108 Readthrough of Leaky Stop Codons 108 Ribosomal Frameshifiting 109 Proteolytic Processing 110 Chymotrypsin-like Serine or Cysteine Proteinases 112 Papain-like Cysteine Proteinases 112 Conclusions 113 References 114 5. Molecular Basis of Genetic Variability in RNA Viruses 121-141 Jozef J. Bujarski Introduction 121 Genetic Mechanisms of Variability 121 Mutation 121 Point Mutations 122 Insertions and Deletions 123 Frameshift Mutations 123 Mutant Stability 124 Effects of Mutations on Host-Virus Interactions 124 RNA Recombination 125 Natural Sequence Rearrangement 126 Recombination between Viral and Host RNAs 126 Role of RNA Structure 127 Role of Replicase Proteins 130 Pseudorecombination 131 Defective Interfering RNAs 132 Conclusions 134 Acknowledgements 136 References 136 viii 6. Genetic Variability and Evolution 143-159 F. Garcia-Arenal, A. Fraile, and J. M. Malpica Introduction 143 Variability under Experimental Conditions 143 Variability under Natural Conditions 145 Factors Determining Genetic Structure of Virus Populations 149 Founder Effects 149 Selection 150 Complementation 152 Conclusions 153 Acknowledgements 155 References 155 7. Molecular Basis of Virus Transport in Plants 161-182 Scott M.