Biochemistry and Molecular Biology of Plants

Prof. em. Bob B. Buchanan, Department of Plant & Microbial Biology, University of California, Berkeley.

Prof. Dr. Wilhelm Gruissem, Professor of Plant Biotechnology, ETH Zurich, Switzerland.

Prof. em. Russell L. Jones, Department of Plant & Microbial Biology, University of California, Berkeley.

The Editors xi

List of Contributors xii

Preface xv

About the Companion Website xvi

COMPARTMENTS

1 Membrane Structure and Membranous Organelles 2

Introduction 2

1.1 Common properties and inheritance of cell membranes 2

1.2 The fluid mosaic membrane model 4

1.3 Plasma membrane 10

1.4 Endoplasmic reticulum 13

1.5 Golgi apparatus 18

1.6 Exocytosis and endocytosis 23

1.7 Vacuoles 27

1.8 The nucleus 28

1.9 Peroxisomes 31

1.10 Plastids 32

1.11 Mitochondria 39

Summary 44

2 The Cell Wall 45

Introduction 45

2.1 Sugars are building blocks of the cell wall 45

2.2 Macromolecules of the cell wall 51

2.3 Cell wall architecture 73

2.4 Cell wall biosynthesis and assembly 80

2.5 Growth and cell walls 90

2.6 Cell differentiation 99

2.7 Cell walls as sources of food, feed, fiber, and fuel, and their genetic improvement 108

Summary 110

3 Membrane Transport 111

Introduction 111

3.1 Overview of plant membrane transport systems 111

3.2 Pumps 120

3.3 Ion channels 128

3.4 Cotransporters 142

3.5 Water transport through aquaporins 146

Summary 148

4 Protein Sorting and Vesicle Traffic 151

Introduction 151

4.1 The cellular machinery of protein sorting 151

4.2 Targeting proteins to the plastids 153

4.3 Targeting proteins to mitochondria 157

4.4 Targeting proteins to peroxisomes 159

4.5 Transport in and out of the nucleus 160

4.6 ER is the secretory pathway port of entry and a protein nursery 161

4.7 Protein traffic and sorting in the secretory pathway: the ER 175

4.8 Protein traffic and sorting in the secretory pathway: the Golgi apparatus and beyond 182

4.9 Endocytosis and endosomal compartments 188

Summary 189

5 The Cytoskeleton 191

Introduction 191

5.1 Introduction to the cytoskeleton 191

5.2 Actin and tubulin gene families 194

5.3 Characteristics of actin filaments and microtubules 196

5.4 Cytoskeletal accessory proteins 202

5.5 Observing the cytoskeleton: Statics and dynamics 207

5.6 Role of actin filaments in directed intracellular movement 210

5.7 Cortical microtubules and expansion 216

5.8 The cytoskeleton and signal transduction 219

5.9 Mitosis and cytokinesis 222

Summary 238

CELL REPRODUCTION

6 Nucleic Acids 240

Introduction 240

6.1 Composition of nucleic acids and synthesis of nucleotides 240

6.2 Replication of nuclear DNA 245

6.3 DNA repair 250

6.4 DNA recombination 255

6.5 Organellar DNA 260

6.6 DNA transcription 268

6.7 Characteristics and functions of RNA 270

6.8 RNA processing 278

Summary 288

7 Amino Acids 289

Introduction 289

7.1 Amino acid biosynthesis in plants: research and prospects 289

7.2 Assimilation of inorganic nitrogen into N transport amino acids 292

7.3 Aromatic amino acids 302

7.4 Aspartate derived amino acids 318

7.5 Branched chain amino acids 326

7.6 Glutamate derived amino acids 330

7.7 Histidine 333

Summary 336

8 Lipids 336

Introduction 337

8.1 Structure and function of lipids 337

8.2 Fatty acid biosynthesis 344

8.3 Acetyl CoA carboxylase 348

8.4 Fatty acid synthase 350

8.5 Desaturation and elongation of C16 and C18 fatty acids 352

8.6 Synthesis of unusual fatty acids 360

8.7 Synthesis of membrane lipids 365

8.8 Function of membrane lipids 373

8.9 Synthesis and function of extracellular lipids 382

8.10 Synthesis and catabolism of storage lipids 389

8.11 Genetic engineering of lipids 395

Summary 400

9 Genome Structure and Organization 401

Introduction 401

9.1 Genome structure: a 21st century perspective 401

9.2 Genome organization 404

9.3 Transposable elements 416

9.4 Gene expression 422

9.5 Chromatin and the epigenetic regulation of gene expression 430

Summary 436

10 Protein Synthesis, Folding, and Degradation 438

Introduction 438

10.1 Organellar compartmentalization of protein synthesis 438

10.2 From RNA to protein 439

10.3 Mechanisms of plant viral translation 447

10.4 Protein synthesis in plastids 450

10.5 Post translational modification of proteins 457

10.6 Protein degradation 463

Summary 475

11 Cell Division 476

Introduction 476

11.1 Animal and plant cell cycles 476

11.2 Historical perspective on cell cycle research 477

11.3 Mechanisms of cell cycle control 482

11.4 The cell cycle in action 488

11.5 Cell cycle control during development 497

Summary 506

ENERGY FLOW

12 Photosynthesis 508

Introduction 508

12.1 Overview of photosynthesis 508

12.2 Light absorption and energy conversion 511

12.3 Photosystem structure and function 519

12.4 Electron transport pathways in chloroplast membranes 529

12.5 ATP synthesis in chloroplasts 537

12.6 Organization and regulation of photosynthetic complexes 540

12.7 Carbon reactions: the Calvin–Benson cycle 542

12.8 Rubisco 548

12.9 Regulation of the Calvin–Benson cycle by light 551

12.10 Variations in mechanisms of CO 2 fixation 557

Summary 565

13 Carbohydrate Metabolism 567

Introduction 567

13.1 The concept of metabolite pools 570

13.2 The hexose phosphate pool: a major crossroads in plant metabolism 571

13.3 Sucrose biosynthesis 573

13.4 Sucrose metabolism 577

13.5 Starch biosynthesis 580

13.6 Partitioning of photoassimilates between sucrose and starch 587

13.7 Starch degradation 593

13.8 The pentose phosphate/triose phosphate pool 597

13.9 Energy and reducing power for biosynthesis 601

13.10 Sugar regulated gene expression 606

Summary 608

14 Respiration and Photorespiration 610

Introduction 610

14.1 Overview of respiration 610

14.2 Citric acid cycle 613

14.3 Plant mitochondrial electron transport 620

14.4 Plant mitochondrial ATP synthesis 632

14.5 Regulation of the citric acid cycle and the cytochrome pathway 634

14.6 Integration of the cytochrome pathway and nonphosphorylating pathways 635

14.7 Interactions between mitochondria and other cellular compartments 639

14.8 Biochemical basis of photorespiration 646

14.9 The photorespiratory pathway 648

14.10 Role of photorespiration in plants 652

Summary 655

METABOLIC AND DEVELOPMENTAL INTEGRATION

15 Long Distance Transport 658

Introduction 658

15.1 Selection pressures and long distance transport systems 658

15.2 Cell biology of transport modules 664

15.3 Short-distance transport events between xylem and nonvascular cells 668

15.4 Short distance transport events between phloem and nonvascular cells 673

15.5 Whole plant organization of xylem transport 691

15.6 Whole plant organization of phloem transport 696

15.7 Communication and regulation controlling phloem transport events 705

Summary 710

16 Nitrogen and Sulfur 711

Introduction 711

16.1 Overview of nitrogen in the biosphere and in plants 711

16.2 Overview of biological nitrogen fixation 715

16.3 Enzymology of nitrogen fixation 715

16.4 Symbiotic nitrogen fixation 718

16.5 Ammonia uptake and transport 735

16.6 Nitrate uptake and transport 735

16.7 Nitrate reduction 739

16.8 Nitrite reduction 744

16.9 Nitrate signaling 745

16.10 Interaction between nitrate assimilation and carbon metabolism 745

16.11 Overview of sulfur in the biosphere and plants 746

16.12 Sulfur chemistry and function 747

16.13 Sulfate uptake and transport 750

16.14 The reductive sulfate assimilation pathway 752

16.15 Cysteine synthesis 755

16.16 Synthesis and function of glutathione and its derivatives 758

16.17 Sulfated compounds 763

16.18 Regulation of sulfate assimilation and interaction with nitrogen and carbon metabolism 764

Summary 767

17 Biosynthesis of Hormones 769

Introduction 769

17.1 Gibberellins 769

17.2 Abscisic acid 777

17.3 Cytokinins 785

17.4 Auxins 795

17.5 Ethylene 806

17.6 Brassinosteroids 810

17.7 Polyamines 818

17.8 Jasmonic acid 821

17.9 Salicylic acid 826

17.10 Strigolactones 830

Summary 833

18 Signal Transduction 834

Introduction 834

18.1 Characteristics of signal perception, transduction, and integration in plants 834

18.2 Overview of signal perception at the plasma membrane 838

18.3 Intracellular signal transduction, amplification, and integration via second messengers and MAPK cascades 843

18.4 Ethylene signal transduction 847

18.5 Cytokinin signal transduction 850

18.6 Integration of auxin signaling and transport 852

18.7 Signal transduction from phytochromes 857

18.8 Gibberellin signal transduction and its integration with phytochrome signaling during seedling development 861

18.9 Integration of light, ABA, and CO2 signals in the regulation of stomatal aperture 866

18.10 Prospects 870

Summary 870

19 Molecular Regulation of Reproductive Development 872

Introduction 872

19.1 The transition from vegetative to reproductive development 872

19.2 The molecular basis of flower development 881

19.3 The formation of male gametes 889

19.4 The formation of female gametes 897

19.5 Pollination and fertilization 902

19.6 The molecular basis of self incompatibility 908

19.7 Seed development 913

Summary 923

20 Senescence and Cell Death 925

Introduction 925

20.1 Types of cell death 925

20.2 PCD during seed development and germination 930

20.3 Cell death during the development of secretory bodies, defensive structures and organ shapes 932

20.4 PCD during reproductive development 937

20.5 Senescence and PCD in the terminal development of leaves and other lateral organs 940

20.6 Pigment metabolism in senescence 948

20.7 Macromolecule breakdown and salvage of nutrients in senescence 951

20.8 Energy and oxidative metabolism during senescence 957

20.9 Environmental influences on senescence and cell death I: Abiotic interactions 961

20.10 Environmental influences on senescence and cell death II: PCD responses to pathogen attack 964

20.11 Plant hormones in senescence and defense related PCD 974

Summary 982

PLANT ENVIRONMENT AND AGRICULTURE

21 Responses to Plant Pathogens 984

Introduction 984

21.1 Pathogens, pests, and disease 984

21.2 An overview of immunity and defense 985

21.3 How pathogens and pests cause disease 989

21.4 Preformed defenses 1009

21.5 Induced defense 1012

21.6 Effector triggered immunity, a second level of induced defense 1022

21.7 Other sources of genetic variation for resistance 1032

21.8 Local and systemic defense signaling 1033

21.9 Plant gene silencing confers virus resistance, tolerance, and attenuation 1042

21.10 Control of plant pathogens by genetic engineering 1044

Summary 1050

22 Responses to Abiotic Stress 1051

Introduction 1051

22.1 Plant responses to abiotic stress 1051

22.2 Physiological and cellular responses to water deficit 1054

22.3 Gene expression and signal transduction in response to dehydration 1061

22.4 Freezing and chilling stress 1068

22.5 Flooding and oxygen deficit 1076

22.6 Oxidative stress 1085

22.7 Heat stress 1094

22.8 Crosstalk in stress responses 1097

Summary 1099

23 Mineral Nutrient Acquisition, Transport, and Utilization 1101

Introduction 1101

23.1 Overview of essential mineral elements 1102

23.2 Mechanisms and regulation of plant K+ transport 1103

23.3 Phosphorus nutrition and transport 1113

23.4 The molecular physiology of micronutrient acquisition 1118

23.5 Plant responses to mineral toxicity 1127

Summary 1131

24 Natural Products 1132

Introduction 1132

24.1 Terpenoids 1133

24.2 Biosynthesis of the basic five carbon unit 1135

24.3 Repetitive additions of C5 units 1138

24.4 Formation of parent carbon skeletons 1141

24.5 Modification of terpenoid skeletons 1143

24.6 Metabolic engineering of terpenoid production 1145

24.7 Cyanogenic glycosides 1146

24.8 Cyanogenic glycoside biosynthesis 1152

24.9 Functions of cyanogenic glycosides 1157

24.10 Glucosinolates 1158

24.11 Alkaloids 1159

24.12 Alkaloid biosynthesis 1164

24.13 Biotechnological application of alkaloid biosynthesis research 1171

24.14 Phenolic compounds 1178

24.15 Phenolic biosynthesis 1185

24.16 The phenylpropanoid ]acetate pathway 1188

24.17 The phenylpropanoid pathway 1195

24.18 Universal features of phenolic biosynthesis 1202

24.19 Evolution of secondary pathways 1205

Summary 1206

Further reading 1207

Index 1222