BRIEF CONTENTS COPYRIGHTED MATERIAL III METABOLIC AND DEVELOPMENTAL INTEGRATION COMPARTMENTS CELL REPRODUCTION PLANT ENVIRONMENT AND AGRICULTURE

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1 BRIEF CONTENTS I COMPARTMENTS 1 Membrane Structure and Membranous Organelles 2 2 The Cell Wall 45 3 Membrane Transport Protein Sorting and Vesicle Traffic The Cytoskeleton 191 II CELL REPRODUCTION 6 Nucleic Acids Amino Acids Lipids Genome Structure and Organization Protein Synthesis, Folding, and Degradation Cell Division 476 III ENERGY FLOW 12 Photosynthesis Carbohydrate Metabolism Respiration and Photorespiration 610 IV METABOLIC AND DEVELOPMENTAL INTEGRATION 15 Long Distance Transport Nitrogen and Sulfur Biosynthesis of Hormones Signal Transduction Molecular Regulation of Reproductive Development Senescence and Cell Death 925 V PLANT ENVIRONMENT AND AGRICULTURE 21 Responses to Plant Pathogens Responses to Abiotic Stress Mineral Nutrient Acquisition, Transport, and Utilization 1101 COPYRIGHTED MATERIAL 24 Natural Products 1132 v

2 CONTENTS The Editors xi List of Contributors xii Preface xv About the Companion Website xvi I COMPARTMENTS 1 Membrane Structure and Membranous Organelles 2 Introduction Common properties and inheritance of cell membranes The fluid mosaic membrane model Plasma membrane Endoplasmic reticulum Golgi apparatus Exocytosis and endocytosis Vacuoles The nucleus Peroxisomes Plastids Mitochondria 39 Summary 44 2 The Cell Wall 45 Introduction Sugars are building blocks of the cell wall Macromolecules of the cell wall Cell wall architecture Cell wall biosynthesis and assembly Growth and cell walls Cell differentiation Cell walls as sources of food, feed, fiber, and fuel, and their genetic improvement 108 Summary Membrane Transport 111 Introduction Overview of plant membrane transport systems Pumps Ion channels Cotransporters Water transport through aquaporins 146 Summary Protein Sorting and Vesicle Traffic 151 Introduction The cellular machinery of protein sorting Targeting proteins to the plastids Targeting proteins to mitochondria Targeting proteins to peroxisomes Transport in and out of the nucleus ER is the secretory pathway port of entry and a protein nursery Protein traffic and sorting in the secretory pathway: the ER Protein traffic and sorting in the secretory pathway: the Golgi apparatus and beyond Endocytosis and endosomal compartments 188 Summary The Cytoskeleton 191 Introduction Introduction to the cytoskeleton Actin and tubulin gene families Characteristics of actin filaments and microtubules Cytoskeletal accessory proteins Observing the cytoskeleton: Statics and dynamics Role of actin filaments in directed intracellular movement Cortical microtubules and expansion The cytoskeleton and signal transduction Mitosis and cytokinesis 222 Summary 238 vi

3 CONTENTS vii II CELL REPRODUCTION 6 Nucleic Acids 240 Introduction Composition of nucleic acids and synthesis of nucleotides Replication of nuclear DNA DNA repair DNA recombination Organellar DNA DNA transcription Characteristics and functions of RNA RNA processing 278 Summary Amino Acids 289 Introduction Amino acid biosynthesis in plants: research and prospects Assimilation of inorganic nitrogen into N transport amino acids Aromatic amino acids Aspartate derived amino acids Branched chain amino acids Glutamate derived amino acids Histidine 333 Summary Lipids 337 Introduction Structure and function of lipids Fatty acid biosynthesis Acetyl CoA carboxylase Fatty acid synthase Desaturation and elongation of C 16 and C 18 fatty acids Synthesis of unusual fatty acids Synthesis of membrane lipids Function of membrane lipids Synthesis and function of extracellular lipids Synthesis and catabolism of storage lipids Genetic engineering of lipids 395 Summary Genome Structure and Organization 401 Introduction Genome structure: a 21st century perspective Genome organization Transposable elements Gene expression Chromatin and the epigenetic regulation of gene expression 430 Summary Protein Synthesis, Folding, and Degradation 438 Introduction Organellar compartmentalization of protein synthesis From RNA to protein Mechanisms of plant viral translation Protein synthesis in plastids Post translational modification of proteins Protein degradation 463 Summary Cell Division 476 Introduction Animal and plant cell cycles Historical perspective on cell cycle research Mechanisms of cell cycle control The cell cycle in action Cell cycle control during development 497 Summary 506 III ENERGY FLOW 12 Photosynthesis 508 Introduction Overview of photosynthesis Light absorption and energy conversion Photosystem structure and function Electron transport pathways in chloroplast membranes ATP synthesis in chloroplasts Organization and regulation of photosynthetic complexes Carbon reactions: the Calvin Benson cycle 542

4 viii CONTENTS 12.8 Rubisco Regulation of the Calvin Benson cycle by light Variations in mechanisms of CO 2 fixation 557 Summary Carbohydrate Metabolism 567 Introduction The concept of metabolite pools The hexose phosphate pool: a major crossroads in plant metabolism Sucrose biosynthesis Sucrose metabolism Starch biosynthesis Partitioning of photoassimilates between sucrose and starch Starch degradation The pentose phosphate/triose phosphate pool Energy and reducing power for biosynthesis Sugar regulated gene expression 606 Summary Respiration and Photorespiration 610 Introduction Overview of respiration Citric acid cycle Plant mitochondrial electron transport Plant mitochondrial ATP synthesis Regulation of the citric acid cycle and the cytochrome pathway Integration of the cytochrome pathway and nonphosphorylating pathways Interactions between mitochondria and other cellular compartments Biochemical basis of photorespiration The photorespiratory pathway Role of photorespiration in plants 652 Summary 655 IV METABOLIC AND DEVELOPMENTAL INTEGRATION 15 Long Distance Transport 658 Introduction Selection pressures and long distance transport systems Cell biology of transport modules Short-distance transport events between xylem and nonvascular cells Short distance transport events between phloem and nonvascular cells Whole plant organization of xylem transport Whole plant organization of phloem transport Communication and regulation controlling phloem transport events 705 Summary Nitrogen and Sulfur 711 Introduction Overview of nitrogen in the biosphere and in plants Overview of biological nitrogen fixation Enzymology of nitrogen fixation Symbiotic nitrogen fixation Ammonia uptake and transport Nitrate uptake and transport Nitrate reduction Nitrite reduction Nitrate signaling Interaction between nitrate assimilation and carbon metabolism Overview of sulfur in the biosphere and plants Sulfur chemistry and function Sulfate uptake and transport The reductive sulfate assimilation pathway Cysteine synthesis Synthesis and function of glutathione and its derivatives Sulfated compounds Regulation of sulfate assimilation and interaction with nitrogen and carbon metabolism 764 Summary Biosynthesis of Hormones 769 Introduction Gibberellins Abscisic acid Cytokinins Auxins Ethylene Brassinosteroids Polyamines Jasmonic acid Salicylic acid 826

5 CONTENTS ix Strigolactones 830 Summary Signal Transduction 834 Introduction Characteristics of signal perception, transduction, and integration in plants Overview of signal perception at the plasma membrane Intracellular signal transduction, amplification, and integration via second messengers and MAPK cascades Ethylene signal transduction Cytokinin signal transduction Integration of auxin signaling and transport Signal transduction from phytochromes Gibberellin signal transduction and its integration with phytochrome signaling during seedling development Integration of light, ABA, and CO 2 signals in the regulation of stomatal aperture Prospects 870 Summary Molecular Regulation of Reproductive Development 872 Introduction The transition from vegetative to reproductive development The molecular basis of flower development The formation of male gametes The formation of female gametes Pollination and fertilization The molecular basis of self incompatibility Seed development 913 Summary Senescence and Cell Death 925 Introduction Types of cell death PCD during seed development and germination Cell death during the development of secretory bodies, defensive structures and organ shapes PCD during reproductive development Senescence and PCD in the terminal development of leaves and other lateral organs Pigment metabolism in senescence Macromolecule breakdown and salvage of nutrients in senescence Energy and oxidative metabolism during senescence Environmental influences on senescence and cell death I: Abiotic interactions Environmental influences on senescence and cell death II: PCD responses to pathogen attack Plant hormones in senescence and defense related PCD 974 Summary 982 V PLANT ENVIRONMENT AND AGRICULTURE 21 Responses to Plant Pathogens 984 Introduction Pathogens, pests, and disease An overview of immunity and defense How pathogens and pests cause disease Preformed defenses Induced defense Effector triggered immunity, a second level of induced defense Other sources of genetic variation for resistance Local and systemic defense signaling Plant gene silencing confers virus resistance, tolerance, and attenuation Control of plant pathogens by genetic engineering 1044 Summary Responses to Abiotic Stress 1051 Introduction Plant responses to abiotic stress Physiological and cellular responses to water deficit Gene expression and signal transduction in response to dehydration Freezing and chilling stress Flooding and oxygen deficit Oxidative stress Heat stress Crosstalk in stress responses 1097 Summary 1099

6 x CONTENTS 23 Mineral Nutrient Acquisition, Transport, and Utilization 1101 Introduction Overview of essential mineral elements Mechanisms and regulation of plant K + transport Phosphorus nutrition and transport The molecular physiology of micronutrient acquisition Plant responses to mineral toxicity 1127 Summary Natural Products 1132 Introduction Terpenoids Biosynthesis of the basic five carbon unit Repetitive additions of C 5 units Formation of parent carbon skeletons Modification of terpenoid skeletons Metabolic engineering of terpenoid production Cyanogenic glycosides Cyanogenic glycoside biosynthesis Functions of cyanogenic glycosides Glucosinolates Alkaloids Alkaloid biosynthesis Biotechnological application of alkaloid biosynthesis research Phenolic compounds Phenolic biosynthesis The phenylpropanoid acetate pathway The phenylpropanoid pathway Universal features of phenolic biosynthesis Evolution of secondary pathways 1205 Summary 1206 Further reading 1207 Index 1222