Biochemistry and Molecular Biology of Plants

EDITED BYBob B. Buchanan, University of California, Berkeley, USAWilhelm Gruissem, ETH Zurich, SwitzerlandRussell L. Jones, University of California, Berkeley, USA

“Biochemistry and Molecular Biology of Plants, 2nd edition is a beast, but it’s a user-friendly one that should be welcomed into one’s life to provide much-appreciated companionship to further one’s plant biology studies. (AoB Blog, 1 November 2015)

• The Editors xi List of Contributors xiiPreface xvAbout the Companion Website xviCOMPARTMENTS1 Membrane Structure and Membranous Organelles 2Introduction 21.1 Common properties and inheritance of cell membranes 21.2 The fluid-mosaic membrane model 41.3 Plasma membrane 101.4 Endoplasmic reticulum 131.5 Golgi apparatus 181.6 Exocytosis and endocytosis 231.7 Vacuoles 271.8 The nucleus 281.9 Peroxisomes 311.10 Plastids 321.11 Mitochondria 39Summary 442 The Cell Wall 45Introduction 452.1 Sugars are building blocks of the cell wall 452.2 Macromolecules of the cell wall 512.3 Cell wall architecture 732.4 Cell wall biosynthesis and assembly 802.5 Growth and cell walls 902.6 Cell differentiation 992.7 Cell walls as sources of food, feed, fiber, and fuel, and their genetic improvement 108Summary 1103 Membrane Transport 111Introduction 1113.1 Overview of plant membrane transport systems 1113.2 Pumps 1203.3 Ion channels 1283.4 Cotransporters 1423.5 Water transport through aquaporins 146Summary 1484 Protein Sorting and Vesicle Traffic 151Introduction 1514.1 The cellular machinery of protein sorting 1514.2 Targeting proteins to the plastids 1534.3 Targeting proteins to mitochondria 1574.4 Targeting proteins to peroxisomes 1594.5 Transport in and out of the nucleus 1604.6 ER is the secretory pathway port of entry and a protein nursery 1614.7 Protein traffic and sorting in the secretory pathway: the ER 1754.8 Protein traffic and sorting in the secretory pathway: the Golgi apparatus and beyond 1824.9 Endocytosis and endosomal compartments 188Summary 1895 The Cytoskeleton 191Introduction 1915.1 Introduction to the cytoskeleton 1915.2 Actin and tubulin gene families 1945.3 Characteristics of actin filaments and microtubules 1965.4 Cytoskeletal accessory proteins 2025.5 Observing the cytoskeleton: Statics and dynamics 2075.6 Role of actin filaments in directed intracellular movement 2105.7 Cortical microtubules and expansion 2165.8 The cytoskeleton and signal transduction 2195.9 Mitosis and cytokinesis 222Summary 238CELL REPRODUCTION6 Nucleic Acids 240Introduction 2406.1 Composition of nucleic acids and synthesis of nucleotides 2406.2 Replication of nuclear DNA 2456.3 DNA repair 2506.4 DNA recombination 2556.5 Organellar DNA 2606.6 DNA transcription 2686.7 Characteristics and functions of RNA 2706.8 RNA processing 278Summary 2887 Amino Acids 289Introduction 2897.1 Amino acid biosynthesis in plants: research and prospects 2897.2 Assimilation of inorganic nitrogen into N-transport amino acids 2927.3 Aromatic amino acids 3027.4 Aspartate-derived amino acids 3187.5 Branched-chain amino acids 3267.6 Glutamate-derived amino acids 3307.7 Histidine 333Summary 3368 Lipids 336Introduction 3378.1 Structure and function of lipids 3378.2 Fatty acid biosynthesis 3448.3 Acetyl-CoA carboxylase 3488.4 Fatty acid synthase 3508.5 Desaturation and elongation of C16 and C18 fatty acids 3528.6 Synthesis of unusual fatty acids 3608.7 Synthesis of membrane lipids 3658.8 Function of membrane lipids 3738.9 Synthesis and function of extracellular lipids 3828.10 Synthesis and catabolism of storage lipids 3898.11 Genetic engineering of lipids 395Summary 4009 Genome Structure and Organization 401Introduction 4019.1 Genome structure: a 21st]century perspective 4019.2 Genome organization 4049.3 Transposable elements 4169.4 Gene expression 4229.5 Chromatin and the epigenetic regulation of gene expression 430Summary 43610 Protein Synthesis, Folding, and Degradation 438Introduction 43810.1 Organellar compartmentalization of protein synthesis 43810.2 From RNA to protein 43910.3 Mechanisms of plant viral translation 44710.4 Protein synthesis in plastids 45010.5 Post-translational modification of proteins 45710.6 Protein degradation 463Summary 47511 Cell Division 476Introduction 47611.1 Animal and plant cell cycles 47611.2 Historical perspective on cell cycle research 47711.3 Mechanisms of cell cycle control 48211.4 The cell cycle in action 48811.5 Cell cycle control during development 497Summary 506ENERGY FLOW12 Photosynthesis 508Introduction 50812.1 Overview of photosynthesis 50812.2 Light absorption and energy conversion 51112.3 Photosystem structure and function 51912.4 Electron transport pathways in chloroplast membranes 52912.5 ATP synthesis in chloroplasts 53712.6 Organization and regulation of photosynthetic complexes 54012.7 Carbon reactions: the Calvin-Benson cycle 54212.8 Rubisco 54812.9 Regulation of the Calvin-Benson cycle by light 55112.10 Variations in mechanisms of CO 2 fixation 557Summary 56513 Carbohydrate Metabolism 567Introduction 56713.1 The concept of metabolite pools 57013.2 The hexose phosphate pool: a major crossroads in plant metabolism 57113.3 Sucrose biosynthesis 57313.4 Sucrose metabolism 57713.5 Starch biosynthesis 58013.6 Partitioning of photoassimilates between sucrose and starch 58713.7 Starch degradation 59313.8 The pentose phosphate/triose phosphate pool 59713.9 Energy and reducing power for biosynthesis 60113.10 Sugar-regulated gene expression 606Summary 60814 Respiration and Photorespiration 610Introduction 61014.1 Overview of respiration 61014.2 Citric acid cycle 61314.3 Plant mitochondrial electron transport 62014.4 Plant mitochondrial ATP synthesis 63214.5 Regulation of the citric acid cycle and the cytochrome pathway 63414.6 Integration of the cytochrome pathway and nonphosphorylating pathways 63514.7 Interactions between mitochondria and other cellular compartments 63914.8 Biochemical basis of photorespiration 64614.9 The photorespiratory pathway 64814.10 Role of photorespiration in plants 652Summary 655METABOLIC AND DEVELOPMENTAL INTEGRATION15 Long]Distance Transport 658Introduction 65815.1 Selection pressures and long-distance transport systems 65815.2 Cell biology of transport modules 66415.3 Short-distance transport events between xylem and nonvascular cells 66815.4 Short-]distance transport events between phloem and nonvascular cells 67315.5 Whole-plant organization of xylem transport 69115.6 Whole-plant organization of phloem transport 69615.7 Communication and regulation controlling phloem transport events 705Summary 71016 Nitrogen and Sulfur 711Introduction 71116.1 Overview of nitrogen in the biosphere and in plants 71116.2 Overview of biological nitrogen fixation 71516.3 Enzymology of nitrogen fixation 71516.4 Symbiotic nitrogen fixation 71816.5 Ammonia uptake and transport 73516.6 Nitrate uptake and transport 73516.7 Nitrate reduction 73916.8 Nitrite reduction 74416.9 Nitrate signaling 74516.10 Interaction between nitrate assimilation and carbon metabolism 74516.11 Overview of sulfur in the biosphere and plants 74616.12 Sulfur chemistry and function 74716.13 Sulfate uptake and transport 75016.14 The reductive sulfate assimilation pathway 75216.15 Cysteine synthesis 75516.16 Synthesis and function of glutathione and its derivatives 75816.17 Sulfated compounds 76316.18 Regulation of sulfate assimilation and interaction with nitrogen and carbon metabolism 764Summary 76717 Biosynthesis of Hormones 769Introduction 76917.1 Gibberellins 76917.2 Abscisic acid 77717.3 Cytokinins 78517.4 Auxins 79517.5 Ethylene 80617.6 Brassinosteroids 81017.7 Polyamines 81817.8 Jasmonic acid 82117.9 Salicylic acid 82617.10 Strigolactones 830Summary 83318 Signal Transduction 834Introduction 83418.1 Characteristics of signal perception, transduction, and integration in plants 83418.2 Overview of signal perception at the plasma membrane 83818.3 Intracellular signal transduction, amplification, and integration via second messengers and MAPK cascades 84318.4 Ethylene signal transduction 84718.5 Cytokinin signal transduction 85018.6 Integration of auxin signaling and transport 85218.7 Signal transduction from phytochromes 85718.8 Gibberellin signal transduction and its integration with phytochrome signaling during seedling development 86118.9 Integration of light, ABA, and CO2 signals in the regulation of stomatal aperture 86618.10 Prospects 870Summary 87019 Molecular Regulation of Reproductive Development 872Introduction 87219.1 The transition from vegetative to reproductive development 87219.2 The molecular basis of flower development 88119.3 The formation of male gametes 88919.4 The formation of female gametes 89719.5 Pollination and fertilization 90219.6 The molecular basis of self]incompatibility 90819.7 Seed development 913Summary 92320 Senescence and Cell Death 925Introduction 92520.1 Types of cell death 92520.2 PCD during seed development and germination 93020.3 Cell death during the development of secretory bodies, defensive structures and organ shapes 93220.4 PCD during reproductive development 93720.5 Senescence and PCD in the terminal development of leaves and other lateral organs 94020.6 Pigment metabolism in senescence 94820.7 Macromolecule breakdown and salvage of nutrients in senescence 95120.8 Energy and oxidative metabolism during senescence 95720.9 Environmental influences on senescence and cell death I: Abiotic interactions 96120.10 Environmental influences on senescence and cell death II: PCD responses to pathogen attack 96420.11 Plant hormones in senescence and defense-related PCD 974Summary 982PLANT ENVIRONMENT AND AGRICULTURE21 Responses to Plant Pathogens 984Introduction 98421.1 Pathogens, pests, and disease 98421.2 An overview of immunity and defense 98521.3 How pathogens and pests cause disease 98921.4 Preformed defenses 100921.5 Induced defense 101221.6 Effector-triggered immunity, a second level of induced defense 102221.7 Other sources of genetic variation for resistance 103221.8 Local and systemic defense signaling 103321.9 Plant gene silencing confers virus resistance, tolerance, and attenuation 104221.10 Control of plant pathogens by genetic engineering 1044Summary 105022 Responses to Abiotic Stress 1051Introduction 105122.1 Plant responses to abiotic stress 105122.2 Physiological and cellular responses to water deficit 105422.3 Gene expression and signal transduction in response to dehydration 106122.4 Freezing and chilling stress 106822.5 Flooding and oxygen deficit 107622.6 Oxidative stress 108522.7 Heat stress 109422.8 Crosstalk in stress responses 1097Summary 109923 Mineral Nutrient Acquisition, Transport, and Utilization 1101Introduction 110123.1 Overview of essential mineral elements 110223.2 Mechanisms and regulation of plant K+ transport 110323.3 Phosphorus nutrition and transport 111323.4 The molecular physiology of micronutrient acquisition 111823.5 Plant responses to mineral toxicity 1127Summary 113124 Natural Products 1132Introduction 113224.1 Terpenoids 113324.2 Biosynthesis of the basic five-carbon unit 113524.3 Repetitive additions of C5 units 113824.4 Formation of parent carbon skeletons 114124.5 Modification of terpenoid skeletons 114324.6 Metabolic engineering of terpenoid production 114524.7 Cyanogenic glycosides 114624.8 Cyanogenic glycoside biosynthesis 115224.9 Functions of cyanogenic glycosides 115724.10 Glucosinolates 115824.11 Alkaloids 115924.12 Alkaloid biosynthesis 116424.13 Biotechnological application of alkaloid biosynthesis research 117124.14 Phenolic compounds 117824.15 Phenolic biosynthesis 118524.16 The phenylpropanoid-acetate pathway 118824.17 The phenylpropanoid pathway 119524.18 Universal features of phenolic biosynthesis 120224.19 Evolution of secondary pathways 1205Summary 1206Further reading 1207Index 1222