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Contents

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

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