Annual Plant Reviews, Volume 46, Plant Nuclear Structure, Genome Architecture and Gene Regulation

List of Contributors xv

Preface xix

Acknowledgements xxiii

1 Introduction: Mysteries, Molecules and Mechanisms 1
John A. Bryant

1.1 Darwin and Margulis revisited 1

1.2 Nuclei - general features 3

1.3 The plant nuclear genome 5

1.3.1 General features 5

1.3.2 Replication of the nuclear genome 6

1.4 DNA inside, ribosomes outside 9

1.5 Concluding comments on the evolution of the nucleus 11

References 13

2 The Nuclear Envelope - Structure and Protein Interactions 19
Katja Graumann and David E. Evans

2.1 Introduction 19

2.2 Organization and structure of the plant nuclear envelope 20

2.3 Proteins of the plant nuclear envelope 21

2.3.1 Proteins involved in signalling 22

2.3.2 Proteins of the nuclear pore complex 22

2.3.3 Proteins of the INM 23

2.3.4 Proteins spanning the periplasm and linking the NE membranes 25

2.3.5 The plant lamina 28

2.4 The plant nuclear envelope and the nucleoskeleton; attachments at the INM 31

2.5 The plant nuclear envelope and the cytoskeleton; attachments at the ONM 35

2.6 Targeting of proteins to the plant NE 36

2.7 Nuclear envelope protein dynamics in mitosis 38

2.7.1 The role of NPC in regulating NE dynamics in cell division 38

2.7.2 NE protein dynamics in division 40

2.8 The phragmoplast and cell plate and their relationship to the NE 41

2.9 The plant NE in meiosis 42

2.10 Lipid composition of the plant NE and its homeostasis 43

2.10.1 Nuclear-vacuolar junctions and lipid homeostasis 43

2.10.2 NE phospholipid regulation by lipins 44

2.11 The role of plant NE components in stress responses 45

2.11.1 Nuclei repositioning in response to environmental stimuli 45

2.11.2 Functions of the plant NE during viral infection 47

2.12 Concluding remarks 48

References 48

3 The Plant Nuclear Pore Complex - The Nucleocytoplasmic Barrier and Beyond 57
Xiao Zhou, Joanna Boruc and Iris Meier

3.1 Nuclear pore complex structure 57

3.1.1 Structure of the NPC 58

3.1.2 Molecular composition of the NPC 59

3.1.3 Nucleocytoplasmic trafficking 62

3.2 Physiological and developmental roles of plant nuclear pore components 67

3.2.1 Plant-microbe interactions 67

3.2.2 Hormone responses 72

3.2.3 Abiotic stress responses 73

3.2.4 Growth and development 74

3.3 The Dynamics of the Nuclear Pore Complex 75

3.3.1 Types of mitosis 75

3.3.2 NPC disassembly and dynamics of animal NPC components 76

3.3.3 Dynamics of fungal NPC components 78

3.3.4 Dynamics of plant NPC components 79

3.4 Conclusions 81

References 81

4 Nucleoskeleton in Plants: The Functional Organization of Filaments in the Nucleus 93
Martin W. Goldberg

4.1 Introduction 94

4.2 Intermediate filaments and the nucleoskeleton 96

4.3 Plants do not have intermediate filaments but they may have functional equivalents 99

4.4 Plants can evolve different solutions to the same problem 100

4.5 Intermediate filaments first evolved in the nucleus 101

4.6 Plants require a rigid nuclear boundary 101

4.7 Is there a trans-nuclear envelope complex in plants that links the nucleoskeleton to the cytoskeleton? 102

4.8 Role of the nuclear lamina as part of the nucleoskeleton 102

4.9 Structural evidence for the nucleoskeleton 104

4.10 NuMA in plants 107

4.11 Matrix attachment regions (MARs) and the role of the nucleoskeleton in chromatin organization 108

4.12 Chromocentres and the plant nucleoskeleton 109

4.13 Long coiled-coil proteins in plants and their role in nuclear organization: candidates for plamins and nucleoskeletal proteins? 109

4.14 Actin and microtubules in the nucleus 112

4.15 Conclusions 113

Acknowledgements 113

References 114

5 Genomics and Chromatin Packaging 123
Eugenio Sanchez-Moran

5.1 Chromatin components and structure in higher eukaryotes 123

5.2 Histones and nucleosome fibre 126

5.2.1 Histone variants 131

5.2.2 Histone modifications 136

5.2.3 Nucleosome dynamics 137

5.3 Linker histone and the higher order chromatin-order fibre 138

5.3.1 The elusive higher order chromatin fibre 140

5.4 Chromatin loops and chromosome axis 141

5.5 Conclusions and future prospects 145

References 145

6 Heterochromatin Positioning and Nuclear Architecture 157
Emmanuel Vanrobays, M¿elanie Thomas and Christophe Tatout

6.1 Heterochromatin structure 158

6.1.1 Heterochromatic sequences 158

6.1.2 Epigenetic marks 161

6.1.3 Non-histone protein binding 164

6.1.4 Heterochromatin is an epigenetic state 165

6.2 Heterochromatin organization 166

6.2.1 Heterochromatin and nuclear architecture 166

6.2.2 Recruitment of heterochromatin at the nuclear periphery 171

6.2.3 Higher order of chromatin organization 173

6.3 Functional significance of heterochromatin positioning 176

6.3.1 Centric heterochromatin directs chromosome segregation 176

6.3.2 Spatial positioning of heterochromatin affects transcriptional activity 178

6.3.3 Heterochromatin positioning protects against genome instability 179

6.4 Perspectives 180

Acknowledgements 184

References 184

7 Telomeres in Plant Meiosis: Their Structure, Dynamics and Function 191
Nicola Y. Roberts, Kim Osman, F. Chris H. Franklin, Monica Pradillo, Javier Varas, Juan L. Santos and Susan J. Armstrong

7.1 Introduction 192

7.1.1 The meiotic pathway 192

7.1.2 Arabidopsis thaliana as a model for meiosis 193

7.2 The telomeres and associated proteins 194

7.2.1 Telomere binding proteins 196

7.2.2 Arabidopsis telomere binding proteins 197

7.2.3 DNA repair proteins 201

7.3 The behaviour of the telomeres in meiosis 203

7.3.1 The bouquet 203

7.3.2 A role for the bouquet 204

7.4 Telomere dynamics in Arabidopsis thaliana meiosis 206

7.4.1 Meiosis in A. thaliana telomere-deficient lines 206

7.5 How are the telomeres moved in meiotic prophase I? 208

7.5.1 Colchicine disrupts meiotic progression 208

7.5.2 The role of actin in telomere movement 210

7.6 Components of the nuclear envelope 213

7.7 Components of the plant nuclear envelope 216

7.8 Conclusions and future prospects 217

Acknowledgements 218

References 218

8 The Nuclear Pore Complex in Symbiosis and Pathogen Defence 229
Andreas Binder and Martin Parniske

8.1 Introduction 229

8.2 The nuclear pore and plant-microbe symbiosis 230

8.2.1 Common signalling in arbuscular mycorrhiza and root-nodule symbiosis 230

8.2.2 Symbiotic signalling at the nucleus 231

8.2.3 Symbiotic defects in ljnup85, ljnup133 and nena mutants 232

8.2.4 How do nucleoporins function in plant-microbe symbiosis? 233

8.3 The nuclear pore and plant defence 235

8.3.1 Plant immune responses can be triggered by pathogen-associated molecular patterns and
microbial effectors 235

8.3.2 AtNUP88 and AtNUP96 are required for basal and NB-LRR-mediated plant immunity 236

8.3.3 Mechanisms of nucleoporin-mediated plant
defence signalling 237

8.4 Specificity, redundancy and general functions of plant nucleoporins 239

8.4.1 The NUP107-160 sub-complex 239

8.4.2 Hormone signalling 242

8.4.3 Development, flowering time, stress tolerance and RNA transport 243

8.5 Challenges and conclusion 245

References 246

Index 255

Color plate (between pages 104 and 105)