Plant Developmental Biology - Biotechnological Perspectives (eBook)

Chapter 1: Developmental Biology of Somatic Embryogenesis 22
Introduction 22
Basic Requirements for In Vitro SE 23
Explant and Stem Cell Biology 24
Genotype 24
Explant Cells 25
Earliest Event in Embryogenesis-Asymmetric Cell Division 27
Cell Wall in Establishment of Polarity, Division Asymmetry and Cell Fate 27
Division Asymmetry in the Initiation of SE 29
Asymmetric Division and the Suspensor in SE 29
Stress Component in the Initiation of SE 30
Reactive Oxygen Species 30
Stress-Related Hormone Signalling 31
Hormones and the Initiation of SE 32
Induction of SE by Over-Expression of Leafy Cotyledon Transcription Factors and Their Relationship to SE Induction and Repress 33
ABA, Stress and GA 35
Soluble Signals and Cell-Cell Interactions that Promote SE in Suspension Cultures 35
Secreted Proteins that Influence SE 35
AGP Signalling in SE: Mechanisms and Interactions Between Signalling Pathways 36
Cell-Cell Interaction and Relevance to SE in Suspension Cultures 37
Development Program After SE Induction 38
Concluding Remarks and a Model Based on Studies in Medicago truncatula 38
SE and Biotechnology 39
References 40
Chapter 2: Microspore Embryogenesis 46
Introduction 46
Discovery of the Production of Haploids by Anther Cultureanther culture 48
Strategies for the Induction of Microspore Embryogenesis 48
Influence of Different Factors in Microspore Embryogenesis 49
Genotype 49
Donor Plant Physiology 50
Stage of Pollen Development 50
Pre-treatments 51
Culture Conditions 51
Composition of the Medium 52
Cellular and Molecular Events Associated with Microspore Embryogenesis 53
Embryogenic Induction 53
Early Embryogenic Divisions 56
Development of Embryo Pattern 57
Plant Formation and Diploidization 58
Conclusions 58
References 59
Chapter 3: Stress and Somaclonal Variation 64
Introduction 64
Stress Responses in Plants 65
Short-Term Responses 65
Long-Term Responses 66
Modifications Induced by Stress Could be Inheritable 68
Tissue Culture Imposes a Stress to Cultivated In Vitro Cells 69
Cultured Cellscultured cells and Regenerated Plantsregenerated plants Show Variations 71
Heritable Changes Versus Non-Heritable Changes 73
Genetic Versus Epigenetic Changes 74
Variation Promoted by Tissue Culture is Not Randomly Distributed in the Genome 76
Are New Alleles Originated by In Vitro Stress Already Present in Other Plants of In Vivo Populations? 77
Concluding Remarks 77
References 77
Chapter 4: Photosynthate Partitioning 85
Introduction 85
Source and Sink 87
Sugars as Signalling Molecules 87
Key Metabolic Regulators 88
SNF1-Related Protein Kinase 1 (SnRK1) 88
Hexokinase 92
The Trehalose Pathway 92
Applications in Biotechnology 93
Concluding Remarks 97
References 98
Chapter 5: Molecular Physiology of Seed Maturation and Seed Storage ProteinSeed Storage Protein Biosynthesis 101
Introduction 101
Seed MaturationSeed maturation 102
SucroseSucrose as a Maturation Signal 103
Synthesis and Deposition of Storage Proteins in Crop Seedscrop seeds 104
Storage Proteins in Cereals 105
Storage Proteins in the Different Grain Parts 105
Transcriptional RegulationTranscriptional regulation of Arabidopsis Seed MaturationArabidopsis seed maturation 107
Transcriptional Regulation of Arabidopsis Seed Maturation-a Model Also for Cereal Seeds? 107
Unravelling Transcriptional Regulation by Co-Expression Analysisco-expression analysis 108
DNA MethylationDNA methylation and Storage Protein Gene Expression in the Barley Endosperm 110
Metabolic ControlMetabolic control of Seed Storage Protein Synthesis 111
Nitrogen Availability and Signalling 111
Nitrogen TransportNitrogen transport into Seeds 112
Overexpression of an Amino Acid Transporteramino acid transporter in Legume Seeds 112
Carbon Availability 114
Response to Increased Nitrogen to Carbon Statuscarbon status 114
Overexpression of Phosphoenolpyruvate Carboxylasephosphoenolpyruvate carboxylase in Narbon Beans 114
Repression of ADP-Glucose PyrophosphorylaseADP-glucose pyrophosphorylase in Narbon Beans 115
Repression of ADP-Glucose Pyrophosphorylase in Pea 116
Outlook 116
References 117
Chapter 6: Fatty Acid Biosynthesis and Regulation in Plants 123
Introduction 123
Fatty Acid Biosynthesis 124
De Novo Fatty Acid Biosynthesis 124
Regulation of ACCase 126
Fatty Acid Elongation 127
Fatty Acid Desaturation 128
Unusual Fatty Acids 128
Assembly of Fatty Acids 129
Conclusions 130
References 130
Chapter 7: Biosynthesis and Regulation of Carotenoids in Plants-Micronutrients, Vitamins and Health Benefits 134
Introduction: Carotenoid Biosynthesis in Higher Plants 134
Carotenoids and Plant Development 138
Health Benefits of Carotenoid-Derived Vitamins and Nutrients 140
Zeaxanthin, Lutein and Prevention of Macular Degeneration 142
beta-Carotene and the Biosynthesis of Vitamin A 143
Antioxidant Properties of Other Xanthophylls and Xanthophyll Derivatives 146
Conclusions and Future Prospects 147
References 147
Chapter 8: Biosynthesis and Regulation of Alkaloids 155
Introduction 155
Chemical Diversity and Biosynthesis 156
Biosynthesis of Monoterpene Indole Alkaloids (MIA) 156
Biosynthesis of Benzylisoquinoline Alkaloids (BIA) 163
Biosynthesis of Tropane and Nicotine Alkaloids (TNA) 163
Biosynthesis of Purine Alkaloids (PA) 164
Spatial Organisation of Alkaloid Biosynthesis 164
Crystallisation and Three-Dimensional Structure of Alkaloid Biosynthetic Enzymes 168
Transcription Factor Regulatory Networks of Alkaloid Biosynthesis 169
Metabolic Engineering of Alkaloid Biosynthesis 170
Conclusions 171
References 172
Chapter 9: Molecular Biology and Biotechnology of Flower Pigments 177
Introduction 177
Pigment Biosynthetic Pathways and Their Genetic Modification 178
Flavonoids 178
Core Biosynthetic Steps of the Flavonoid Pathway 180
Anthocyanin B-Ring Hydroxylation 181
Aurones and Chalcones 183
Carotenoids 183
Increasing Activity of Carotenoid Biosynthetic Enzymes 187
Inhibiting Activity of Carotenoid Biosynthetic Enzymes 187
Introducing Novel Carotenoid Biosynthetic Activities 188
Carotenoid Degradation 188
Sinks for Carotenoid Sequestration 189
Betalains 189
Regulation of Floral Pigmentation 191
Transcriptional Control 192
Developmental Signalling 194
Biotechnology Applications of TFs 195
Concluding Comments 196
References 197
Chapter 10: Biosynthesis and Regulation of Flower Scent 204
Introduction 204
Functions of Floral Scents 205
Floral Scents for Pollination 205
Floral Scents with Diverse Functions 205
Patterns of Floral Emission 206
Biosynthetic Pathways and Key Enzymes 208
Terpenoids 209
Benzenoids and Phenylpropanoids 209
Aliphatic Compounds 210
Regulation of Floral Volatile Biosynthesis 211
Regulation at the Molecular Level 211
Mechanisms of Regulation 212
Biotechnological Aspects 213
Conclusions 216
References 216
Chapter 11: Amino Compound-Containing Lipids: a Novel Class of Signals Regulating Plant Development 222
Introduction 222
Biosynthesis and Metabolism of Acylamides in Plants 223
Distribution of Acylamides 225
Role of NAEs and Alkamides in Plant Development 226
Seed Germination 227
Shoot Development 228
Root Development 230
Signals Interacting with NAEs and Alkamides 231
Auxins 231
Cytokinins 232
Nitric Oxide 232
Cellular Alterations Underlying Plant Responses to NAEs and Alkamides: Cell Cycle Progression and Microtubule Stability 233
Cell Cycle Progression 233
Microtubule Stability 234
AHLs: Inter-Kingdom Signals for Plant-Bacterial Interactions 234
Concluding Remarks 236
References 236
Chapter 12: The Roles of YUCCA Genes in Local Auxin Biosynthesis and Plant Development 240
Introduction 240
Identification of YUCCA Flavin Monooxygenases as Key Enzymes in Auxin Biosynthesis 240
YUC Genes Have Dynamic Expression Patterns 243
YUC Genes Are Conserved in the Plant Kingdom 244
Dissection of Auxin Action Mechanisms on the Basis of Auxin Biosynthesis 244
Conclusions 246
References 247
Chapter 13: Role of Cytokinin in the Regulation of Plant Development 249
Introduction 249
Cytokinin Biosynthesis and Metabolism 250
Chemical Structure and Activity of Cytokinins 250
De Novo Synthesis 250
Activation 251
Degradation 252
Cytokinin Signaling 252
HKs Act as Cytokinin Sensors 253
HPs Mediate the Cytokinin Signal 254
Type-B RRs Are Transcription Factors that Positively Regulate Cytokinin Responses 254
Type-A RRs Act as Negative Regulators of Cytokinin Signaling 255
Downstream Targets of His-Asp Phosphorelay 255
Molecular Mechanisms of Cytokinin Action in Plant Development 256
Maintenance of Vegetative Shoot Apical Meristems 256
Inflorescence Meristem Activity 258
Root Meristem Maintenance and Root Vascular Development 259
Nodule Organogenesis 261
Other Developmental Events 262
Perspectives 262
References 262
Chapter 14: Light Signalling in Plant Developmental Regulation 267
Introduction 267
Plant Photomorphogenesis: Various Responses to a Complex Stimulus 268
Sensing Changes in Light Conditions: Multiple Photoreceptors Continuously Monitor the Light Environment 268
Phytochromes 268
Cryptochromes 270
Phototropins, Other LOV Domain-Containing Proteins and UV-B Receptors 272
Physiological Responses During Photomorphogenesis: Roles of Photoreceptors in Plant Development 272
Germination 272
De-Etiolation 273
Phototropism 273
Chloroplast Movement 273
Shade Avoidance Syndrome 274
Photoperiodic Responses 274
Photoreceptor Signal Transduction 275
Genetic Analyses: Identification of Key Players 275
Phosphorylation/Dephosphorylation 277
Ubiquitination/Proteasome-Mediated Proteolysis 279
Light-Regulated Transcriptional Networks: Changes in Gene Expression 280
Light Interaction with Endogenous Networks 280
Hormone Connections 280
Light-Clock Signal Integration 283
Applied Aspects of Photomorphogenic Research 283
What Is Fit Under Natural Conditions Might Be Inadequate for Agriculture 283
Classical Breeding for the Development of Agronomical Varieties Has Selected Light-Regulated Traits 284
Plant Height 284
Branching 284
Flowering Time 285
Is There a General Strategy to Modulate Photomorphogenic Traits for Crop Improvement? 285
References 286
Chapter 15: RNA Silencing in Plants 288
Introduction 288
History of RNA Silencing in Plants 289
The Parallel Gene Silencing Pathways of Plants 292
The MicroRNA Pathway 293
The trans-Acting siRNA Pathway 295
The Natural-Antisense siRNA Pathway 296
The Repeat-Associated siRNA/RNA-Directed DNA Methylation Pathways 296
RNA Silencing as an Antiviral Defence Mechanism 298
Current Applications of RNA Silencing Strategies to Alter Plant Development 300
Concluding Remarks 301
References 302
Chapter 16: DNA Methylation: a Dynamic Regulator of Genome Organization and Gene Expression in Plants 306
Introduction 306
Mapping DNA Methylation 307
Technological Advances in Mapping Methylated Cytosine 307
High-Resolution Maps of DNA Methylation in the Arabidopsis Genome 309
Methylation Patterns Are the Balance Between Methyltransferase and Demethylase Activities 310
DNA Methyltransferases 310
Chromatin-Modifying Proteins Are Essential for DNA Methylation 313
DNA Demethylases 314
Targeting DNA Methylation 318
Interplay Between DNA Methylation and Chromatin Modifications 320
Heterochromatin Exists in a Self-Reinforcing Silencing Loop 320
A Putative Histone Demethylase Prevents the Spread of DNA Methylation 321
DNA Methyl-Binding Proteins Mediate the Interplay Between DNA Methylation and Chromatin Modification 321
Ubiquitination of Histone H2B Prevents DNA Methylation 322
Genome Stability Is Mediated by CpG Methylation 323
DNA Methylation Regulates Genes During Development and in Response to External Stimuli 324
Imprinting 324
Response to the Environment 325
Conclusions 326
References 327
Chapter 17: Molecular Mechanisms in Epigenetic Regulation of Plant Growth and Development 335
Introduction 335
Vernalization and Flowering Time 335
Histone Methylation in FLC Activation 336
Histone Methylation in FLC Repression 338
Regulation of Flowering by Histone Acetylation 339
ATP-Dependent Chromatin-Remodelling Complexes in Flowering Time Control 340
RNAi in Flowering Time Control 340
Parental Imprinting and Seed Development 341
The Maternally Expressed FWA, FIS2 and MEA Alleles 341
The Paternally Expressed PHE1 Allele 343
Genomic Imprinting in Maize 344
Chromatin in Stem Cell Maintenance 344
SAM 345
RAM 346
Chromatin in Plant Stress Responses 346
Histone Acetylation in Stress Responses 346
Chromatin-Remodelling Factors in Stress Responses 347
Perspectives 348
References 348
18: Activation Tagging for Gain-of-Function Mutants 355
Introduction 355
Importance of Mutants to Study Development 355
Phenotype Gap-the Lack of Mutant Phenotypes 356
Activation Tagging for Gain-of-Function Mutants 357
Genes that Modulate Development Discovered by Activation Tagging 360
Genes Involved in Hormonal Biosynthesis or Signaling that Affect Development 360
Identification of the First Component of Cytokinin Signaling 361
First Functional Demonstration of a Cytokinin Biosynthesis Gene in Plants 361
Discovery of a Rate-Limiting Enzyme in Auxin Biosynthesis 362
Unraveling the Brassinosteroid Perception Pathway 362
Cloning the First Regulatory Gene from Trees: the Gibberellin Catabolic Enzyme GA2ox 363
Integration of Environmental Cues Modulating Developmental Pathways 364
Cloning Key Integrators of Flowering Signals: the Floral Inducer FT 365
Meristem, Embryo, and Organ Development 366
Discovery of a miRNA that Targets a Family of Crucial Morphogenesis Regulators 366
Two Closely Linked Genes Involved in Leaf and Vasculature Development 367
Two Closely Related Genes with Functions in Meristem and Organ Development 367
Discovery of an Extra Embryonic Function of a Well-Known Meristem Gene 368
Other Examples of Genes Involved in Floral Organ Growth 368
Transcription Factors Regulating Secondary Metabolic Pathways 369
Activation Tagging Genes that Confer Resistance to Biotic and Abiotic Stresses 370
Genes Conferring Resistance to Pathogens 370
Genes Conferring Resistance to Drought 371
Activation Tagging of Genes Involved in Sensing Nutritional Status 372
Additional Considerations 372
Role of Enhancers 372
Instability and Nonviable Phenotypes 373
Conclusions 374
References 374
Chapter 19: Regulatory Mechanisms of Homologous Recombination in Higher Plants 381
Introduction 381
Molecular Mechanism of HR 383
Current Models of HR 384
The Double-Stranded DNA Break-Repair Model 385
The Synthesis-Dependent Strand Annealing Model 385
Single-Strand Annealing Model 386
HR Pathways in Plants 386
Meiotic Recombination in Plants 389
Meiotic Recombination Initiation 389
DSB Processing 389
Strand Invasion 390
Crossover Pathway (Resolution of Double Holliday Junction) 392
Signal Transduction from DSB to HR Repair 393
Conclusions 395
References 396
Chapter 20: Synthetic Promoter Engineering 402
Introduction 402
Promoters: Biotechnology Tools Combining Molecular `Switch´ and `Sensor´ Capabilities 403
The Promoter 403
Spatial and Temporal Control of Transgene Activity in Plants 404
Cauliflower Mosaic Virus 35S: the `Workhorse´ Promoter in Plant Biotechnology 405
Hurdles that Necessitate Promoter Modification 406
Synthetic Promoters: Refinement of cis-Regulatory Architecture Leads to Targeted Inducibility and High-Level Expression of Sin 407
cis-Motif Context Modified: the Centre for Synthetic Promoter Engineering 408
CaMV 35S cis-Motif Context Re-evaluated 408
Gaining Insight from Synthetic cis-Regulatory Complexity 410
Bidirectionalisation Improves Transcriptional Activity and Overall Versatility 411
Two-Component Transactivated Gene Switches: Promising Systems for Flexible Transgene Expression 413
Tight Control by Targeted cis-trans Interaction 414
Inducible Fine-Tuning by a Chemical Trigger 415
The Way Forward: Systematic Engineering and Integration Leads to Accurate Design 416
References 418
: Index 424