Plant Genes, Genomes and Genetics

Dr Erich Grotewold is currently a professor in the Department of Molecular Genetics (College of Arts & Sciences) as well as in the Department of Horticulture & Crop Sciences (College of Food, Agriculture & Environmental Sciences) at The Ohio State University. His research focuses on plant systems biology. Dr Joseph Chappell joined the faculty at the University of Kentucky in 1985, where he has developed an internationally recognized research program pioneering the molecular genetics and biochemistry of natural products in plants. Dr Elizabeth A. Kellogg was formerly the E. Desmond Lee and Family Professor of Botanical Studies at the University of Missouri–St. Louis, and is currently a Member of the Donald Danforth Plant Science Center in St. Louis. Her work focuses on the evolution of plant genes, genomes and development, particularly in the cereal crops and their wild relatives.

Acknowledgements xi

Introduction xiii

About the Companion Website xix

PART I: PLANT GENOMES AND GENES

Chapter 1 Plant genetic material 3

1.1 DNA is the genetic material of all living organisms, including plants 3

1.2 The plant cell contains three independent genomes 8

1.3 A gene is a complete set of instructions for building an RNA molecule 10

1.4 Genes include coding sequences and regulatory sequences 11

1.5 Nuclear genome size in plants is variable but the numbers of protein-coding, non-transposable element genes are roughly the same 12

1.6 Genomic DNA is packaged in chromosomes 15

1.7 Summary 15

1.8 Problems 15

References 16

Chapter 2 The shifting genomic landscape 17

2.1 The genomes of individual plants can differ in many ways 17

2.2 Differences in sequences between plants provide clues about gene function 20

2.3 SNPs and lengthmutations in simple sequence repeats are useful tools for genome mapping and marker assisted selection 22

2.4 Genome size and chromosome number are variable 28

2.5 Segments of DNA are often duplicated and can recombine 30

2.6 Some genes are copied nearby in the genome 31

2.7 Whole genome duplications are common in plants 34

2.8 Whole genome duplication has many effects on the genome and on gene function 37

2.9 Summary 41

2.10 Problems 42

Further reading 42

References 42

Chapter 3 Transposable elements 45

3.1 Transposable elements are common in genomes of all organisms 45

3.2 Retrotransposons are mainly responsible for increases in genome size 46

3.3 DNA transposons create small mutations when they insert and excise 52

3.4 Transposable elements move genes and change their regulation 57

3.5 How are transposable elements controlled? 60

3.6 Summary 60

3.7 Problems 61

References 61

Chapter 4 Chromatin, centromeres and telomeres 63

4.1 Chromosomes are made up of chromatin, a complex of DNA and protein 63

4.2 Telomeres make up the ends of chromosomes 66

4.3 The chromosome middles–centromeres 71

4.4 Summary 77

4.5 Problems 77

Further reading 77

References 77

Chapter 5 Genomes of organelles 79

5.1 Plastids and mitochondria are descendants of free-living bacteria 79

5.2 Organellar genes have been transferred to the nuclear genome 80

5.3 Organellar genes sometimes include introns 82

5.4 Organellar mRNA is often edited 82

5.5 Mitochondrial genomes contain fewer genes than chloroplasts 84

5.6 Plant mitochondrial genomes are large and undergo frequent recombination 87

5.7 All plastid genomes in a cell are identical 91

5.8 Plastid genomes are similar among land plants but contain some structural rearrangements 93

5.9 Summary 95

5.10 Problems 95

Further reading 95

References 95

PART II: TRANSCRIBING PLANT GENES

Chapter 6 RNA 99

6.1 RNA links components of the Central Dogma 99

6.2 Structure provides RNA with unique properties 102

6.3 RNA has multiple regulatory activities 105

6.4 Summary 108

6.5 Problems 108

References 109

Chapter 7 The plant RNA polymerases 111

7.1 Transcription makes RNA from DNA 111

7.2 Varying numbers of RNA polymerases in the different kingdoms 112

7.3 RNA polymerase I transcribes rRNAs 114

7.4 RNA polymerase III recruitment to upstream and internal promoters 116

7.5 Plant-specific RNP-IV and RNP-V participate in transcriptional gene silencing 117

7.6 Organelles have their own set of RNA polymerases 117

7.7 Summary 118

7.8 Problems 118

References 118

Chapter 8 Making mRNAs – Control of transcription by RNA polymerase II 121

8.1 RNA polymerase II transcribes protein-coding genes 121

8.2 The structure of RNA polymerase II reveals how it functions 121

8.3 The core promoter 123

8.4 Initiation of transcription 125

8.5 The mediator complex 127

8.6 Transcription elongation: the role of RNP-II phosphorylation 128

8.7 RNP-II pausing and termination 129

8.8 Transcription re-initiation 130

8.9 Summary 130

8.10 Problems 130

References 130

Chapter 9 Transcription factors interpret cis-regulatory information 133

9.1 Information on when, where and how much a gene is expressed is codified by the gene’s regulatory regions 133

9.2 Identifying regulatory regions requires the use of reporter genes 134

9.3 Gene regulatory regions have a modular structure 135

9.4 Enhancers: Cis-regulatory elements or modules that function at a distance 137

9.5 Transcription factors interpret the gene regulatory code 138

9.6 Transcription factors can be classified in families 138

9.7 How transcription factors bind DNA 139

9.8 Modular structure of transcription factors 143

9.9 Organization of transcription factors into gene regulatory grids and networks 146

9.10 Summary 146

9.11 Problems 146

More challenging problems 147

References 147

Chapter 10 Control of transcription factor activity 149

10.1 Transcription factor phosphorylation 149

10.2 Protein–protein interactions 151

10.3 Preventing transcription factors from access to the nucleus 155

10.4 Movement of transcription factors between cells 156

10.5 Summary 158

10.6 Problems 158

References 158

Chapter 11 Small RNAs 161

11.1 The phenomenon of cosuppression or gene silencing 161

11.2 Discovery of small RNAs 162

11.3 Pathways for miRNA formation and function 163

11.4 Plant siRNAs originate from different types of double-stranded RNAs 166

11.5 Intercellular and systemic movement of small RNAs 168

11.6 Role of miRNAs in plant physiology and development 170

11.7 Summary 171

11.8 Problems 171

References 172

Chapter 12 Chromatin and gene expression 173

12.1 Packing long DNA molecules in a small space: the function of chromatin 173

12.2 Heterochromatin and euchromatin 173

12.3 Histone modifications 174

12.4 Histone modifications affect gene expression 175

12.5 Introducing and removing histone marks: writers and erasers 175

12.6 ‘Readers’ recognize histone modifications 177

12.7 Nucleosome positioning 177

12.8 DNA methylation 178

12.9 RNA-directed DNA methylation 179

12.10 Control of flowering by histone modifications 180

12.11 Summary 181

12.12 Problems 181

References 181

PART III: FROM RNA TO PROTEINS

Chapter 13 RNA processing and transport 185

13.1 RNA processing can be thought of as steps 185

13.2 RNA capping provides a distinctive 5’ end to mRNAs 185

13.3 Transcription termination consists of mRNA 3’-end formation and polyadenylation 189

13.4 RNA splicing is another major source of genetic variation 192

13.5 Export of mRNA from the nucleus is a gateway for regulating which mRNAs actually get translated 194

13.6 Summary 196

13.7 Problems 196

References 196

Chapter 14 Fate of RNA 199

14.1 Regulation of RNA continues upon export from nucleus 199

14.2 Mechanisms for RNA turnover 199

14.3 RNA surveillance mechanisms 201

14.4 RNA sorting 202

14.5 RNA movement 203

14.6 Summary 204

14.7 Problems 204

Further reading 205

References 205

Chapter 15 Translation of RNA 207

15.1 Translation: a key aspect of gene expression 207

15.2 Initiation 209

15.3 Elongation 209

15.4 Termination 210

15.5 Tools for studying the regulation of translation 211

15.6 Specific translational control mechanisms 211

15.7 Summary 213

15.8 Problems 214

Further reading 214

References 214

Chapter 16 Protein folding and transport 215

16.1 The pathway to a protein’s function is a complicated matter 215

16.2 Protein folding and assembly 215

16.3 Protein targeting 218

16.4 Co-translational targeting 218

16.5 Post-translational targeting 219

16.6 Post-translational modifications regulating function 220

16.7 Summary 222

16.8 Problems 223

Further reading 223

References 224

Chapter 17 Protein degradation 225

17.1 Two sides of gene expression–synthesis and degradation 225

17.2 Autophagy, senescence and programmed cell death 225

17.3 Protein-tagging mechanisms 226

17.4 The ubiquitin proteasome system rivals gene transcription 228

17.5 Summary 231

17.6 Problems 231

Further reading 231

Reference 231

Index 233