Fifthifth EditiEditionditi

Lincoln Taiz Professor Emeritus University of California, Santa Cruz Eduardo Zeiger Professor Emeritus University of California, Los Angeles

Sinauer Associates Inc., Publishers Sunderland, Massachusetts U.S.A.

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CHAPTER 1 Plant Cells 1

Plant Life: Unifying Principles 2 Independently Dividing, Semiautonomous Organelles 18 Overview of Plant Structure 2 Proplastids mature into specialized plastids in Plant cells are surrounded by rigid cell walls 2 different plant tissues 21 New cells are produced by dividing Chloroplast and mitochondrial division are tissues called meristems 2 independent of nuclear division 21 Three major tissue systems make up the plant body 4 The Plant Cytoskeleton 22 The plant cytoskeleton consists of microtubules Plant Cell Organelles 4 and microfi laments 22 Biological membranes are phospholipid Microtubules and microfi laments can assemble bilayers that contain proteins 4 and disassemble 23 The Endomembrane System 8 Cortical microtubules can move around the cell by The nucleus contains the majority of the “treadmilling” 24 genetic material 8 Cytoskeletal motor proteins mediate cytoplasmic Gene expression involves both transcription streaming and organelle traffi c 24 and translation 10 Cell Cycle Regulation 25 The endoplasmic reticulum is a network Each phase of the cell cycle has a specifi c set of of internal membranes 10 biochemical and cellular activities 26 Secretion of proteins from cells begins with the The cell cycle is regulated by cyclins and rough ER (RER) 13 cyclin-dependent kinases 26 Glycoproteins and polysaccharides destined Mitosis and cytokinesis involve both microtubules for secretion are processed in the Golgi and the endomembrane system 27 apparatus 14 The plasma membrane has specialized regions Plasmodesmata 29 involved in membrane recycling 16 Primary and secondary plasmodesmata help to Vacuoles have diverse functions in plant cells 16 maintain tissue developmental gradients 29 Independently Dividing Organelles Derived SUMMARY 31 from the Endomembrane System 17 Oil bodies are lipid-storing organelles 17 Microbodies play specialized metabolic roles in leaves and seeds 17

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©2012 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured TAIZ_FM_JD.indd XVI or disseminated in any form without express written permission from the publisher. 5/19/10 4:09:15 PM CHAPTER 2 Genome Organization and Gene Expression 35

Nuclear Genome Organization 35 Epigenetic modifi cations help determine gene The nuclear genome is packaged into activity 48 chromatin 36 Posttranscriptional Regulation of Centromeres, telomeres, and nucleolar organizers Nuclear Gene Expression 50 contain repetitive sequences 36 RNA stability can be infl uenced by Transposons are mobile sequences within cis-elements 50 the genome 37 Noncoding RNAs regulate mRNA activity via Polyploids contain multiple copies of the entire the RNA interference (RNAi) pathway 50 genome 38 Posttranslational regulation determines Phenotypic and physiological responses to the life span of proteins 54 polyploidy are unpredictable 41 Tools for Studying Gene Function 55 Plant Cytoplasmic Genomes: Mitochondria Mutant analysis can help to elucidate and Chloroplasts 42 gene function 55 The endosymbiotic theory describes the origin Molecular techniques can measure the of cytoplasmic genomes 42 activity of genes 55 Organellar genomes consist mostly of linear Gene fusions can introduce reporter genes 56 chromosomes 43 Organellar genetics do not obey Genetic Modifi cation of Crop Plants 59 Mendelian laws 44 Transgenes can confer resistance to herbicides or plant pests 59 Transcriptional Regulation of Nuclear Gene Expression 45 Genetically modifi ed organisms are controversial 60 RNA polymerase II binds to the promoter region of most protein-coding genes 45 SUMMARY 61

UNIT I Transport and Translocation of Water and Solutes 65 CHAPTER 3 Water and Plant Cells 67

Water in Plant Life 67 Water Potential 73 The Structure and Properties of Water 68 The chemical potential of water represents the free-energy status of water 74 Water is a polar molecule that forms hydrogen bonds 68 Three major factors contribute to cell water potential 74 Water is an excellent solvent 69 Water potentials can be measured 75 Water has distinctive thermal properties relative to its size 69 Water Potential of Plant Cells 75 Water molecules are highly cohesive 69 Water enters the cell along a water potential Water has a high tensile strength 70 gradient 75 Water can also leave the cell in response to a water Diffusion and Osmosis 71 potential gradient 77 Diffusion is the net movement of molecules by Water potential and its components vary with random thermal agitation 71 growth conditions and location within the Diffusion is most effective over short distances 72 plant 77 Osmosis describes the net movement of water Cell Wall and Membrane Properties 78 across a selectively permeable barrier 73

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Small changes in plant cell volume cause large Plant Water Status 80 changes in turgor pressure 78 Physiological processes are affected by plant water The rate at which cells gain or lose water is status 80 infl uenced by cell membrane hydraulic Solute accumulation helps cells maintain turgor conductivity 79 and volume 80 Aquaporins facilitate the movement of water across cell membranes 79 SUMMARY 81

CHAPTER 4 Water Balance of Plants 85

Water in the Soil 85 Xylem transport of water in trees faces physical A negative hydrostatic pressure in soil water challenges 94 lowers soil water potential 86 Plants minimize the consequences of Water moves through the soil by bulk fl ow 87 xylem cavitation 96 Water Absorption by Roots 87 Water Movement from the Leaf to the Water moves in the root via the apoplast, Atmosphere 96 symplast, and transmembrane pathways 88 Leaves have a large hydraulic resistance 96 Solute accumulation in the xylem can generate The driving force for transpiration is the “root pressure” 89 difference in water vapor concentration 96 Water loss is also regulated by the pathway Water Transport through the Xylem 90 resistances 98 The xylem consists of two types of tracheary Stomatal control couples leaf transpiration to elements 90 leaf photosynthesis 98 Water moves through the xylem by The cell walls of guard cells have specialized pressure-driven bulk fl ow 92 features 99 Water movement through the xylem requires An increase in guard cell turgor pressure a smaller pressure gradient than movement opens the stomata 101 through living cells 93 The transpiration ratio measures the relationship What pressure difference is needed to lift water between water loss and carbon gain 101 100 meters to a treetop? 93 The cohesion–tension theory explains water trans- Overview: The Soil–Plant–Atmosphere port in the xylem 93 Continuum 102 SUMMARY 102 CHAPTER 5 Mineral Nutrition 107

Essential Nutrients, Defi ciencies, Some mineral nutrients can be absorbed by and Plant Disorders 108 leaves 118 Special techniques are used in nutritional Soil, Roots, and Microbes 119 studies 110 Negatively charged soil particles affect the adsorp- Nutrient solutions can sustain rapid tion of mineral nutrients 119 plant growth 110 Soil pH affects nutrient availability, soil microbes, Mineral defi ciencies disrupt plant metabolism and root growth 120 and function 113 Excess mineral ions in the soil limit plant Analysis of plant tissues reveals mineral growth 120 defi ciencies 117 Plants develop extensive root systems 121 Treating Nutritional Defi ciencies 117 Root systems differ in form but are based on Crop yields can be improved by addition of common structures 121 fertilizers 118

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Different areas of the root absorb different Nutrients move from mycorrhizal fungi to mineral ions 123 root cells 126 Nutrient availability infl uences root growth 124 SUMMARY 126 Mycorrhizal fungi facilitate nutrient uptake by roots 125

CHAPTER 6 Solute Transport 131

Passive and Active Transport 132 The genes for many transporters have been identifi ed 144 Transport of Ions across Membrane Transporters exist for diverse Barriers 133 nitrogen-containing compounds 146 Different diffusion rates for cations and anions Cation transporters are diverse 147 produce diffusion potentials 134 Anion transporters have been identifi ed 148 How does membrane potential relate to ion distribution? 134 Metal transporters transport essential micronutrients 149 The Nernst equation distinguishes between active and passive transport 136 Aquaporins have diverse functions 149 + Proton transport is a major determinant of Plasma membrane H -ATPases are highly the membrane potential 137 regulated P-type ATPases 150 The tonoplast H+-ATPase drives solute Membrane Transport Processes 137 accumulation in vacuoles 151 Channels enhance diffusion across H+-pyrophosphatases also pump protons at membranes 139 the tonoplast 153 Carriers bind and transport specifi c substances 140 Ion Transport in Roots 153 Primary active transport requires energy 140 Solutes move through both apoplast and Secondary active transport uses stored symplast 153 energy 142 Ions cross both symplast and apoplast 153 Kinetic analyses can elucidate transport mechanisms 143 Xylem parenchyma cells participate in xylem loading 154 Membrane Transport Proteins 144 SUMMARY 156

UNIT II Biochemistry and Metabolism 161 CHAPTER 7 Photosynthesis: The Light Reactions 163

Photosynthesis in Higher Plants 164 Photosynthesis takes place in complexes containing light-harvesting antennas and General Concepts 164 photochemical reaction centers 169 Light has characteristics of both a particle The chemical reaction of photosynthesis is and a wave 164 driven by light 170 When molecules absorb or emit light, Light drives the reduction of NADP and the they change their electronic state 165 formation of ATP 171 Photosynthetic pigments absorb the light that Oxygen-evolving organisms have two powers photosynthesis 166 photosystems that operate in series 171 Key Experiments in Understanding Organization of the Photosynthetic Photosynthesis 167 Apparatus 172 Action spectra relate light absorption to The chloroplast is the site of photosynthesis 172 photosynthetic activity 168

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Thylakoids contain integral membrane proteins 173 The photosystem I reaction center + Photosystems I and II are spatially separated reduces NADP 185 in the thylakoid membrane 174 Cyclic electron fl ow generates ATP but no Anoxygenic photosynthetic bacteria have a NADPH 185 single reaction center 174 Some herbicides block photosynthetic electron fl ow 186 Organization of Light-Absorbing Antenna Systems 176 Proton Transport and ATP Synthesis Antenna systems contain chlorophyll and in the Chloroplast 187 are membrane associated 176 Repair and Regulation of the The antenna funnels energy to the Photosynthetic Machinery 189 reaction center 176 Carotenoids serve as photoprotective agents 190 Many antenna pigment–protein complexes Some xanthophylls also participate in energy have a common structural motif 176 dissipation 190 Mechanisms of Electron Transport 178 The photosystem II reaction center is easily Electrons from chlorophyll travel through damaged 191 the carriers organized in the “Z scheme” 178 Photosystem I is protected from active oxygen Energy is captured when an excited chlorophyll species 191 reduces an electron acceptor molecule 179 Thylakoid stacking permits energy partitioning The reaction center chlorophylls of the two between the photosystems 191 photosystems absorb at different Genetics, Assembly, and Evolution of wavelengths 180 Photosynthetic Systems 192 The photosystem II reaction center is a multisubunit pigment–protein complex 181 Chloroplast genes exhibit non-Mendelian patterns of inheritance 192 Water is oxidized to oxygen by photosystem II 181 Most chloroplast proteins are imported from the cytoplasm 192 Pheophytin and two quinones accept electrons from photosystem II 183 The biosynthesis and breakdown of chlorophyll are complex pathways 192 Electron fl ow through the cytochrome b6f complex also transports protons 183 Complex photosynthetic organisms have evolved from simpler forms 193 Plastoquinone and plastocyanin carry electrons between photosystems II and I 184 SUMMARY 194

CHAPTER 8 Photosynthesis: The Carbon Reactions 199

The Calvin–Benson Cycle 200 Light-dependent ion movements modulate en- The Calvin–Benson cycle has three stages: zymes of the Calvin–Benson cycle 208 carboxylation, reduction, and regeneration 200 Light controls the assembly of chloroplast enzymes The carboxylation of ribulose 1,5-bisphosphate fi xes into supramolecular complexes 208 CO2 for the synthesis of triose phosphates 201 The C2 Oxidative Photosynthetic Carbon Ribulose 1,5-bisphosphate is regenerated for Cycle 208 the continuous assimilation of CO 201 2 The carboxylation and the oxygenation of ribulose An induction period precedes the steady state 1,5-bisphosphate are competing reactions 210 of photosynthetic CO assimilation 204 2 Photorespiration depends on the photosynthetic Regulation of the Calvin–Benson Cycle 205 electron transport system 213 The activity of rubisco increases in the light 206 Photorespiration protects the photosynthetic ap- Light regulates the Calvin–Benson cycle via the paratus under stress conditions 214 ferredoxin–thioredoxin system 207 Photorespiration may be engineered to increase the production of biomass 214

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Inorganic Carbon–Concentrating Formation and Mobilization of Mechanisms 216 Chloroplast Starch 225 Starch is synthesized in the chloroplast Inorganic Carbon–Concentrating Mechanisms: during the day 225 The C Carbon Cycle 216 4 Starch degradation at night requires the Malate and aspartate are carboxylation products of phosphorylation of amylopectin 228 the C cycle 217 4 The export of maltose prevails in the nocturnal Two different types of cells participate in the C4 breakdown of transitory starch 230 cycle 218 Sucrose Biosynthesis and Signaling 231 The C4 cycle concentrates CO2 in the chloroplasts of bundle sheath cells 220 Triose phosphates supply the cytosolic pool of three important hexose phosphates in the The C4 cycle also concentrates CO2 in single cells 221 light 231 Light regulates the activity of key C enzymes 221 Fructose 2,6-bisphosphate regulates the hexose 4 phosphate pool in the light 235 In hot, dry climates, the C4 cycle reduces photo- respiration and water loss 221 The cytosolic interconversion of hexose phos- phates governs the allocation of assimilated Inorganic Carbon–Concentrating Mechanisms: carbon 235 Crassulacean Acid Metabolism (CAM) 221 Sucrose is continuously synthesized in the CAM is a versatile mechanism sensitive to environ- cytosol 235 mental stimuli 223 SUMMARY 237 Accumulation and Partitioning of Photosynthates—Starch and Sucrose 224

Photosynthesis: Physiological and Ecological CHAPTER 9 Considerations 243

Photosynthesis Is the Primary Function of There is an optimal temperature for Leaves 244 photosynthesis 256 Leaf anatomy maximizes light absorption 245 Photosynthetic Responses to Carbon Plants compete for sunlight 246 Dioxide 256 Leaf angle and leaf movement can control light Atmospheric CO2 concentration keeps rising 257 absorption 247 CO2 diffusion to the chloroplast is essential to Plants acclimate and adapt to sun and shade photosynthesis 258 environments 248 Patterns of light absorption generate gradients of Photosynthetic Responses to Light by the CO2 fi xation 259 Intact Leaf 249 CO2 imposes limitations on photosynthesis 260 Light-response curves reveal photosynthetic How will photosynthesis and respiration change in properties 249 the future under elevated CO2 conditions? 261 Leaves must dissipate excess light energy 251 Identifying Different Photosynthetic Absorption of too much light can lead to Pathways 263 photoinhibition 253 How do we measure the stable carbon isotopes of Photosynthetic Responses to plants? 263 Temperature 254 Why are there carbon isotope ratio variations in Leaves must dissipate vast quantities of heat 254 plants? 264 Photosynthesis is temperature sensitive 255 SUMMARY 266

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CHAPTER 10 Translocation in the Phloem 271

Pathways of Translocation 272 Phloem loading in the apoplastic pathway + Sugar is translocated in phloem sieve involves a sucrose–H symporter 287 elements 273 Phloem loading is symplastic in some Mature sieve elements are living cells specialized species 288 for translocation 273 The polymer-trapping model explains Large pores in cell walls are the prominent feature symplastic loading in plants with intermediary of sieve elements 274 cells 288 Damaged sieve elements are sealed off 274 Phloem loading is passive in a number of tree species 289 Companion cells aid the highly specialized sieve elements 276 The type of phloem loading is correlated with a number of signifi cant characteristics 290 Patterns of Translocation: Source to Sink 276 Phloem Unloading and Sink-to-Source Materials Translocated in the Phloem 277 Transition 291 Phloem sap can be collected and analyzed 278 Phloem unloading and short-distance transport Sugars are translocated in nonreducing form 279 can occur via symplastic or apoplastic Other solutes are translocated in the phloem 280 pathways 291 Transport into sink tissues requires metabolic Rates of Movement 280 energy 292 The Pressure-Flow Model, a Passive The transition of a leaf from sink to source is Mechanism for Phloem Transport 281 gradual 292 An osmotically-generated pressure gradient drives Photosynthate Distribution: Allocation and translocation in the pressure-fl ow model 281 Partitioning 294 The predictions of mass fl ow have been Allocation includes storage, utilization, and confi rmed 282 transport 294 Sieve plate pores are open channels 283 Various sinks partition transport sugars 295 There is no bidirectional transport in single sieve Source leaves regulate allocation 295 elements 284 Sink tissues compete for available translocated The energy requirement for transport through the photosynthate 296 phloem pathway is small 284 Sink strength depends on sink size and Positive pressure gradients exist in the phloem activity 296 sieve elements 284 The source adjusts over the long term to changes Does translocation in gymnosperms involve a in the source-to-sink ratio 297 different mechanism? 285 The Transport of Signaling Molecules 297 Phloem Loading 285 Turgor pressure and chemical signals coordinate Phloem loading can occur via the apoplast or source and sink activities 297 symplast 285 Proteins and RNAs function as signal molecules Abundant data support the existence of in the phloem to regulate growth and apoplastic loading in some species 286 development 298 Sucrose uptake in the apoplastic pathway requires metabolic energy 286 SUMMARY 299

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CHAPTER 11 Respiration and Lipid Metabolism 305 Overview of Plant Respiration 305 Aerobic respiration yields about 60 molecules of ATP per molecule of sucrose 322 Glycolysis 309 Several subunits of respiratory complexes Glycolysis metabolizes carbohydrates from are encoded by the mitochondrial genome 324 several sources 309 Plants have several mechanisms that lower The energy-conserving phase of glycolysis the ATP yield 324 extracts usable energy 310 Short-term control of mitochondrial Plants have alternative glycolytic reactions 310 respiration occurs at different levels 326 In the absence of oxygen, fermentation + Respiration is tightly coupled to other regenerates the NAD needed for pathways 327 glycolysis 311 Plant glycolysis is controlled by its products 312 Respiration in Intact Plants and Tissues 327 Plants respire roughly half of the daily The Oxidative Pentose Phosphate photosynthetic yield 328 Pathway 312 Respiration operates during photosynthesis 329 The oxidative pentose phosphate pathway Different tissues and organs respire at different produces NADPH and biosynthetic rates 329 intermediates 314 Environmental factors alter respiration rates 329 The oxidative pentose phosphate pathway is redox-regulated 314 Lipid Metabolism 330 The Citric Acid Cycle 315 Fats and oils store large amounts of energy 331 Mitochondria are semiautonomous Triacylglycerols are stored in oil bodies 331 organelles 315 Polar glycerolipids are the main structural lipids in Pyruvate enters the mitochondrion and is membranes 332 oxidized via the citric acid cycle 316 Fatty acid biosynthesis consists of cycles of two- The citric acid cycle of plants has unique carbon addition 334 features 317 Glycerolipids are synthesized in the plastids and the ER 335 Mitochondrial Electron Transport and Lipid composition infl uences membrane ATP Synthesis 317 function 336 The electron transport chain catalyzes a fl ow of Membrane lipids are precursors of important electrons from NADH to O 318 2 signaling compounds 336 The electron transport chain has supplementary Storage lipids are converted into carbohydrates branches 320 in germinating seeds 336 ATP synthesis in the mitochondrion is coupled to electron transport 320 SUMMARY 338 Transporters exchange substrates and products 322

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CHAPTER 12 Assimilation of Mineral Nutrients 343

Nitrogen in the Environment 344 Establishing symbiosis requires an exchange of Nitrogen passes through several forms in a biogeo- signals 354 chemical cycle 344 Nod factors produced by bacteria act as signals Unassimilated ammonium or nitrate may be dan- for symbiosis 354 gerous 346 Nodule formation involves phytohormones 355

Nitrate Assimilation 346 The nitrogenase enzyme complex fi xes N2 357 Many factors regulate nitrate reductase 347 Amides and ureides are the transported forms of nitrogen 358 Nitrite reductase converts nitrite to ammonium 347 Sulfur Assimilation 358 Both roots and shoots assimilate nitrate 348 Sulfate is the absorbed form of sulfur in plants 358 Ammonium Assimilation 348 Sulfate assimilation requires the reduction of Converting ammonium to amino acids requires sulfate to cysteine 359 two enzymes 348 Sulfate assimilation occurs mostly in leaves 360 Ammonium can be assimilated via an alternative pathway 350 Methionine is synthesized from cysteine 360 Transamination reactions transfer nitrogen 350 Phosphate Assimilation 360 Asparagine and glutamine link carbon and Cation Assimilation 361 nitrogen metabolism 350 Cations form noncovalent bonds with carbon Amino Acid Biosynthesis 351 compounds 361 Biological Nitrogen Fixation 351 Roots modify the rhizosphere to acquire iron 362 Free-living and symbiotic bacteria fi x Iron forms complexes with carbon nitrogen 351 and phosphate 363 Nitrogen fi xation requires anaerobic Oxygen Assimilation 363 conditions 352 The Energetics of Nutrient Assimilation 364 Symbiotic nitrogen fi xation occurs in specialized structures 354 SUMMARY 365

CHAPTER 13 Secondary Metabolites and Plant Defense 369

Secondary Metabolites 370 Some terpenes have roles in growth and Secondary metabolites defend plants against her- development 373 bivores and pathogens 370 Terpenes defend many plants against Secondary metabolites are divided into three ma- herbivores 373 jor groups 370 Phenolic Compounds 374 Terpenes 370 Phenylalanine is an intermediate in the Terpenes are formed by the fusion of fi ve-carbon biosynthesis of most plant phenolics 375 isoprene units 370 Ultraviolet light activates some simple There are two pathways for terpene phenolics 377 biosynthesis 370 The release of phenolics into the soil may IPP and its isomer combine to form larger limit the growth of other plants 377 terpenes 371 Lignin is a highly complex phenolic macromolecule 377

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There are four major groups of fl avonoids 378 Damage by insect herbivores induces Anthocyanins are colored fl avonoids that attract systemic defenses 389 animals 378 Herbivore-induced volatiles have complex Flavones and fl avonols may protect against dam- ecological functions 389 age by ultraviolet light 379 Insects have developed strategies to cope Isofl avonoids have widespread pharmacological with plant defenses 391 activity 379 Plant Defenses against Pathogens 391 Tannins deter feeding by herbivores 380 Pathogens have developed various strategies to Nitrogen-Containing Compounds 381 invade host plants 391 Alkaloids have dramatic physiological effects on Some antimicrobial compounds are synthesized animals 381 before pathogen attack 392 Cyanogenic glycosides release the poison Infection induces additional antipathogen hydrogen cyanide 384 defenses 392 Glucosinolates release volatile toxins 385 Phytoalexins often increase after pathogen attack 393 Nonprotein amino acids are toxic to herbivores 385 Some plants recognize specifi c pathogen-derived substances 393 Induced Plant Defenses against Insect Exposure to elicitors induces a signal transduction Herbivores 386 cascade 394 Plants can recognize specifi c components of A single encounter with a pathogen may increase insect saliva 386 resistance to future attacks 394 Jasmonic acid activates many defensive Interactions of plants with nonpathogenic bacteria responses 387 can trigger induced systemic resistance 395 Some plant proteins inhibit herbivore digestion 389 SUMMARY 396

UNIT III Growth and Development 401 CHAPTER 14 Signal Transduction 403

Signal Transduction in Plant and Several plant hormone receptors encode Animal Cells 404 components of the ubiquitination machinery 413 Plants and animals have similar transduction Inactivation of repressor proteins results in a components 404 gene expression response 414 Receptor kinases can initiate a signal Plants have evolved mechanisms for switching transduction cascade 406 off or attenuating signaling responses 414 Plants signal transduction components have Cross-regulation allows signal transduction evolved from both prokaryotic and eukaryotic pathways to be integrated 416 ancestors 406 Signal Transduction in Space and Time 418 Signals are perceived at many locations within plant cells 408 Plant signal transduction occurs over a wide range of distances 418 Plant signal transduction often involves inactivation of repressor proteins 409 The timescale of plant signal transduction ranges from seconds to years 419 Protein degradation is a common feature in plant signaling pathways 411 SUMMARY 421

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Cell Walls: Structure, Biogenesis, CHAPTER 15 and Expansion 425

The Structure and Synthesis of Secondary walls form in some cells after Plant Cell Walls 426 expansion ceases 438 Plant cell walls have varied architecture 426 Patterns of Cell Expansion 441 The primary cell wall is composed of Microfi bril orientation infl uences growth cellulose microfi brils embedded in a directionality of cells with diffuse growth 441 polysaccharide matrix 428 Cortical microtubules infl uence the orientation Cellulose microfi brils are synthesized at of newly deposited microfi brils 443 the plasma membrane 430 Matrix polymers are synthesized in the The Rate of Cell Elongation 443 Golgi apparatus and secreted via vesicles 433 Stress relaxation of the cell wall drives water Hemicelluloses are matrix polysaccharides uptake and cell elongation 445 that bind to cellulose 433 Acid-induced growth and wall stress relaxation Pectins are hydrophilic gel-forming components are mediated by expansins 446 of the matrix 434 Many structural changes accompany the Structural proteins become cross-linked in cessation of wall expansion 448 the wall 437 New primary walls are assembled during SUMMARY 448 cytokinesis 437

CHAPTER 16 Growth and Development 453

Overview of Plant Growth and The differentiation of cortical and endodermal Development 454 cells involves the intercellular movement of a Sporophytic development can be divided transcription factor 465 into three major stages 455 Many developmental processes involve the intercellular movement of macromolecules 467 Embryogenesis: The Origins of Polarity 456 Embryogenesis differs between dicots and Meristematic Tissues: Foundations for monocots, but also features common Indeterminate Growth 468 fundamental processes 456 The root and shoot apical meristems use similar Apical–basal polarity is established early strategies to enable indeterminate growth 469 in embryogenesis 457 The Root Apical Meristem 469 Position-dependent signaling guides The root tip has four developmental zones 469 embryogenesis 458 The origin of different root tissues can be Auxin may function as a mobile chemical traced to specifi c initial cells 470 signal during embryogenesis 460 Cell ablation experiments implicate directional Mutant analysis has helped identify genes signaling processes in determination of cell essential for embryo organization 461 identity 471 The GNOM protein establishes a Auxin contributes to the formation and polar distribution of auxin effl ux proteins 463 maintenance of the RAM 471 MONOPTEROS encodes a transcription factor Responses to auxin depend on specifi c that is activated by auxin 463 transcription factors 472 Radial patterning guides formation of tissue Cytokinin activity in the RAM is required for root layers 464 development 473

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The Shoot Apical Meristem 474 Localized zones of auxin accumulation promote The shoot apical meristem has distinct zones leaf initiation 480 and layers 474 Spatially regulated gene expression determines Shoot tissues are derived from several discrete the planar form of the leaf 481 sets of apical initials 475 Distinct mechanisms initiate roots and shoots 483 The locations of PIN proteins infl uence SAM Senescence and Programmed Cell Death 484 formation 476 Leaf senescence is adaptive and strictly Embryonic SAM formation requires the regulated 484 coordinated expression of transcription factors 477 Plants exhibit various types of senescence 485 Negative feedback limits apical meristem size 478 Senescence involves the ordered degradation of potentially phototoxic chlorophyll 487 Similar mechanisms maintain initials in the RAM and in the SAM 479 Programmed cell death is a specialized type of senescence 487 Vegetative Organogenesis 480 SUMMARY 488

Phytochrome and Light Control of Plant CHAPTER 17 Development 493

The Photochemical and Biochemical Properties Genetic Analysis of Phytochrome of Phytochrome 494 Function 503 Phytochrome can interconvert between Pr Phytochrome A mediates responses to and Pfr forms 496 continuous far-red light 504 Pfr is the physiologically active form of Phytochrome B mediates responses phytochrome 496 to continuous red or white light 504 Characteristics of Phytochrome-Induced Roles for phytochromes C, D, and E are emerging 504 Responses 497 Phy gene family interactions are complex 504 Phytochrome responses vary in lag time and escape time 497 PHY gene functions have diversifi ed during evolution 505 Phytochrome responses can be distinguished by the amount of light required 497 Phytochrome Signaling Pathways 505 Very low–fl uence responses are Phytochrome regulates membrane nonphotoreversible 497 potentials and ion fl uxes 506 Low-fl uence responses are photoreversible 498 Phytochrome regulates gene expression 506 High-irradiance responses are proportional to Phytochrome interacting factors (PIFs) act the irradiance and the duration 499 early in phy signaling 507 Structure and Function of Phytochrome Phytochrome associates with protein kinases Proteins 499 and phosphatases 507 Phytochrome has several important functional Phytochrome-induced gene expression domains 500 involves protein degradation 508 Phytochrome is a light-regulated protein Circadian Rhythms 509 kinase 501 The circadian oscillator involves a Pfr is partitioned between the cytosol and transcriptional negative feedback loop 510 the nucleus 501 Ecological Functions 512 Phytochromes are encoded by a multigene family 502 Phytochrome enables plant adaptation to changes in light quality 512

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Decreasing the R:FR ratio causes elongation in Phytochrome responses show ecotypic sun plants 512 variation 515 Small seeds typically require a high R:FR ratio Phytochrome action can be modulated 515 for germination 513 Reducing shade avoidance responses can SUMMARY 516 improve crop yields 514

Blue-Light Responses: Morphogenesis and CHAPTER 18 Stomatal Movements 521

The Photophysiology of Blue-Light The Regulation of Blue Light–Stimulated Responses 522 Responses 531 Blue light stimulates asymmetric growth and Blue-Light Photoreceptors 532 bending 523 Cryptochromes regulate plant development 532 Blue light rapidly inhibits stem elongation 523 Phototropins mediate blue light–dependent Blue light stimulates stomatal opening 524 phototropism and chloroplast movements 533 Blue light activates a proton pump at the Zeaxanthin mediates blue-light photoreception guard cell plasma membrane 527 in guard cells 534 Blue-light responses have characteristic Green light reverses blue light–stimulated kinetics and lag times 528 opening 536 Blue light regulates the osmotic balance of guard cells 528 SUMMARY 539 Sucrose is an osmotically active solute in guard cells 530

Auxin: The First Discovered Plant Growth CHAPTER 19 Hormone 545

The Emergence of the Auxin Concept 546 Auxin Signal Transduction Pathways 560 The Principal Auxin: Indole-3-Acetic Acid 546 The principal auxin receptors are soluble protein heterodimers 561 IAA is synthesized in meristems and young dividing tissues 549 Auxin-induced genes are negatively regulated by AUX/IAA proteins 561 Multiple pathways exist for the biosynthesis of IAA 549 Auxin binding to a TIR1/AFB-AUX/IAA heterodimer stimulates AUX/IAA Seeds and storage organs contain covalently destruction 562 bound auxin 550 Auxin-induced genes fall into two classes: IAA is degraded by multiple pathways 550 early and late 562 Auxin Transport 551 Rapid, nontranscriptional auxin responses Polar transport requires energy and is gravity appear to involve a different receptor independent 552 protein 562 Chemiosmotic potential drives polar transport 553 Actions of Auxin: Cell Elongation 562 PIN and ABCB transporters regulate cellular auxin Auxins promote growth in stems and coleoptiles, homeostasis 555 while inhibiting growth in roots 563 Auxin infl ux and effl ux can be chemically The outer tissues of dicot stems are the targets inhibited 556 of auxin action 563 Auxin transport is regulated by multiple The minimum lag time for auxin-induced mechanisms 558 elongation is ten minutes 565

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Auxin rapidly increases the extensibility of Auxin is redistributed laterally in the root cap 572 the cell wall 565 Developmental Effects of Auxin 573 Auxin-induced proton extrusion increases cell extension 565 Auxin regulates apical dominance 574 Auxin-induced proton extrusion involves activation Auxin transport regulates fl oral bud development and protein mobilization 566 and phyllotaxy 576 Auxin promotes the formation of lateral and Actions of Auxin: Plant Tropisms 566 adventitious roots 576 Phototropism is mediated by the lateral redistribu- Auxin induces vascular differentiation 576 tion of auxin 566 Auxin delays the onset of leaf abscission 577 Gravitropism involves lateral redistribution of Auxin promotes fruit development 577 auxin 568 Synthetic auxins have a variety of commercial Dense plastids serve as gravity sensors 569 uses 578 Gravity sensing may involve pH and calcium ions (Ca2+) as second messengers 571 SUMMARY 578

Gibberellins: Regulators of Plant Height and CHAPTER 20 Seed Germination 583

Gibberellins: Their Discovery and Chemical Some enzymes in the GA pathway are Structure 584 highly regulated 591 Gibberellins were discovered by studying Gibberellin regulates its own metabolism 592 a disease of rice 584 GA biosynthesis occurs at multiple plant organs Gibberellic acid was fi rst purifi ed from Gibberella and cellular sites 592 culture fi ltrates 584 Environmental conditions can infl uence All gibberellins are based on an ent-gibberellane GA biosynthesis 593 skeleton 585 GA1 and GA4 have intrinsic bioactivity for stem growth 594 Effects of Gibberellins on Growth and Development 586 Plant height can be genetically engineered 595 Gibberellins promote seed germination 586 Dwarf mutants often show other phenotypic defects 595 Gibberellins can stimulate stem and root growth 586 Auxins can regulate GA biosynthesis 595 Gibberellins regulate the transition from juvenile Gibberellin Signaling: Signifi cance of to adult phases 587 Response Mutants 596 Gibberellins infl uence fl oral initiation and sex GID1 encodes a soluble GA receptor 596 determination 588 DELLA-domain proteins are negative Gibberellins promote pollen development regulators of GA response 600 and tube growth 588 Mutation of negative regulators of GA may Gibberellins promote fruit set and produce slender or dwarf phenotypes 600 parthenocarpy 588 Gibberellins signal the degradation of negative Gibberellins promote early seed regulators of GA response 601 development 588 F-box proteins target DELLA domain proteins Commercial uses of gibberellins and for degradation 601 GA biosynthesis inhibitors 588 Negative regulators with DELLA domains have Biosynthesis and Deactivation of agricultural importance 602 Gibberellins 589 Gibberellin Responses: Early Targets Gibberellins are synthesized via the terpenoid of DELLA Proteins 602 pathway 589

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DELLA proteins can activate or suppress gene Gibberellin Responses: Anther Development expression 603 and Male Fertility 607 DELLA proteins regulate transcription by interact- GAMYB regulates male fertility 609 ing with other proteins such as phytochrome- Events downstream of GAMYB in rice aleurone interacting factors 603 and anthers are quite different 611 Gibberellin Responses: The Cereal Aleurone MicroRNAs regulate MYBs after transcription Layer 605 in anthers but not in aleurone 611 GA is synthesized in the embryo 605 Gibberellin Responses: Stem Growth 612 Aleurone cells may have two types of GA recep- Gibberellins stimulate cell elongation and tors 605 cell division 612 Gibberellins enhance the transcription of GAs regulate the transcription of cell cycle α-amylase mRNA 605 kinases 613 GAMYB is a positive regulator of α-amylase Reducing GA sensitivity may prevent crop transcription 607 losses 613 DELLA-domain proteins are rapidly degraded 607 SUMMARY 614

CHAPTER 21 Cytokinins: Regulators of Cell Division 621

Cell Division and Plant Development 622 Cellular and Molecular Modes of Cytokinin Differentiated plant cells can resume division 622 Action 629 Diffusible factors control cell division 622 A cytokinin receptor related to bacterial Plant tissues and organs can be cultured 622 two-component receptors has been identifi ed 629 The Discovery, Identifi cation, and Properties Cytokinins increase expression of the type-A of Cytokinins 623 response regulator genes via activation of the Kinetin was discovered as a breakdown type-B ARR genes 630 product of DNA 623 Histidine phosphotransfer proteins are also Zeatin was the fi rst natural cytokinin involved in cytokinin signaling 632 discovered 623 The Biological Roles of Cytokinins 632 Some synthetic compounds can mimic Cytokinins promote shoot growth by increasing cytokinin action 624 cell proliferation in the shoot apical Cytokinins occur in both free and bound meristem 632 forms 625 Cytokinins interact with other hormones and with Some plant pathogenic bacteria, fungi, insects, several key transcription factors 634 and nematodes secrete free cytokinins 625 Cytokinins inhibit root growth by promoting the Biosynthesis, Metabolism, and Transport exit of cells from the root apical meristem 635 of Cytokinins 625 Cytokinins regulate specifi c components of Crown gall cells have acquired a gene for the cell cycle 636 cytokinin synthesis 626 The auxin:cytokinin ratio regulates morphogenesis IPT catalyzes the fi rst step in cytokinin in cultured tissues 637 biosynthesis 628 Cytokinins modify apical dominance and promote Cytokinins can act both as long distance and lateral bud growth 638 local signals 628 Cytokinins delay leaf senescence 638 Cytokinins are rapidly metabolized by Cytokinins promote movement of nutrients 639 plant tissues 628

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Cytokinins affect light signaling via Cytokinins are involved in the formation of phytochrome 640 nitrogen-fi xing nodules in legumes 641 Cytokinins regulate vascular development 641 SUMMARY 643 Manipulation of cytokinins to alter agriculturally important traits 641

CHAPTER 22 Ethylene: The Gaseous Hormone 649

Structure, Biosynthesis, and Measurement Ethylene promotes the ripening of some of Ethylene 650 fruits 659 Regulated biosynthesis determines the Fruits that respond to ethylene exhibit a physiological activity of ethylene 650 climacteric 659 Ethylene biosynthesis is promoted by several The receptors of never-ripe mutants of tomato factors 652 fail to bind ethylene 660 Ethylene biosynthesis can be elevated through a Leaf epinasty results when ACC from the root is stabilization of ACC synthase protein 652 transported to the shoot 660 Various inhibitors can block ethylene Ethylene induces lateral cell expansion 661 biosynthesis 653 There are two distinct phases to growth inhibition by ethylene 662 Ethylene Signal Transduction Pathways 653 The hooks of dark-grown seedlings are Ethylene receptors are related to bacterial two- maintained by ethylene production 662 component system histidine kinases 654 Ethylene breaks seed and bud dormancy in High-affi nity binding of ethylene to its receptor some species 663 requires a copper cofactor 655 Ethylene promotes the elongation growth of Unbound ethylene receptors are negative submerged aquatic species 663 regulators of the response pathway 655 Ethylene induces the formation of roots and A serine/threonine protein kinase is also involved root hairs 664 in ethylene signaling 657 Ethylene regulates fl owering and sex determination encodes a transmembrane protein 657 EIN2 in some species 664 Ethylene Regulation of Gene Expression 657 Ethylene enhances the rate of leaf Specifi c transcription factors are involved in senescence 664 ethylene-regulated gene expression 657 Ethylene mediates some defense responses 665 Genetic epistasis reveals the order of the Ethylene acts on the abscission layer 665 ethylene signaling components 658 Ethylene has important commercial uses 667 Developmental and Physiological SUMMARY 668 Effects of Ethylene 659

Abscisic Acid: A Seed Maturation and CHAPTER 23 Stress-Response Hormone 673

Occurrence, Chemical Structure, and Biosynthesis, Metabolism, and Measurement of ABA 674 Transport of ABA 674 The chemical structure of ABA determines its ABA is synthesized from a carotenoid physiological activity 674 intermediate 674 ABA is assayed by biological, physical, and ABA concentrations in tissues are chemical methods 674 highly variable 676 ABA is translocated in vascular tissue 677

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ABA Signal Transduction Pathways 678 ABA regulates seed maturation 684 Receptor candidates include diverse classes of ABA inhibits precocious germination and proteins 678 vivipary 685 Secondary messengers function in ABA ABA promotes seed storage reserve accumulation signaling 680 and desiccation tolerance 686 Ca2+-dependent and Ca2+-independent pathways Seed dormancy can be regulated by ABA and mediate ABA signaling 680 environmental factors 686 ABA-induced lipid metabolism generates second Seed dormancy is controlled by the ratio of ABA messengers 681 to GA 687 Protein kinases and phosphatases regulate ABA inhibits GA-induced enzyme production 688 important steps in ABA signaling 682 ABA promotes root growth and inhibits shoot PP2Cs interact directly with the PYR/PYL/RCAR growth at low water potentials 688 family of ABA receptors 683 ABA promotes leaf senescence independently ABA shares signaling intermediates with other of ethylene 689 hormonal pathways 683 ABA accumulates in dormant buds 689 ABA Regulation of Gene Expression 683 ABA closes stomata in response to water Gene activation by ABA is mediated by stress 690 transcription factors 684 ABA regulates ion channels and the plasma membrane ATPase in guard cells 690 Developmental and Physiological Effects of ABA 684 SUMMARY 693

Brassinosteroids: Regulators of Cell Expansion CHAPTER 24 and Development 699

Brassinosteroid Structure, Occurrence, Brassinosteroids act locally near their sites of and Genetic Analysis 700 synthesis 710 BR-defi cient mutants are impaired in Brassinosteroids: Effects on Growth and photomorphogenesis 701 Development 710 The Brassinosteroid Signaling Pathway 703 BRs promote both cell expansion and cell division BR-insensitive mutants identifi ed the BR cell in shoots 711 surface receptor 703 BRs both promote and inhibit root growth 712 Phosphorylation activates the BRI1 receptor 704 BRs promote xylem differentiation during vascular BIN2 is a repressor of BR-induced gene development 713 expression 704 BRs are required for the growth of pollen BES1/BZR1 regulate gene expression 706 tubes 714 BRs promote seed germination 714 Biosynthesis, Metabolism, and Transport of Brassinosteroids 706 Prospective Uses of Brassinosteroids in Brassinolide is synthesized from campesterol 707 Agriculture 714 Catabolism and negative feedback contribute to SUMMARY 715 BR homeostasis 708

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CHAPTER 25 The Control of Flowering 719

Floral Meristems and Floral Organ The circadian clock and photoperiodic Development 720 timekeeping 736 The shoot apical meristem in Arabidopsis changes The coincidence model is based on oscillating with development 721 light sensitivity 737 The four different types of fl oral organs are The coincidence of CONSTANS expression initiated as separate whorls 721 and light promotes fl owering in LDPs 737 Two major types of genes regulate fl oral SDPs use a coincidence mechanism to inhibit development 722 fl owering in long days 739 Meristem identity genes regulate meristem Phytochrome is the primary photoreceptor in function 722 photoperiodism 739 Homeotic mutations led to the identifi cation of A blue-light photoreceptor regulates fl owering fl oral organ identity genes 723 in some LDPs 740 Three types of homeotic genes control fl oral organ Vernalization: Promoting Flowering with identity 723 Cold 741 The ABC model explains the determination of Vernalization results in competence to fl ower fl oral organ identity 724 at the shoot apical meristem 742 Floral Evocation: Integrating Environmental Vernalization can involve epigenetic changes in Cues 725 gene expression 742 A range of vernalization pathways may have The Shoot Apex and Phase Changes 726 evolved 743 Plant development has three phases 726 Juvenile tissues are produced fi rst and are located Long-Distance Signaling Involved in at the base of the shoot 727 Flowering 744 Phase changes can be infl uenced by nutrients, The fl oral stimulus is transported in the gibberellins, and other signals 728 phloem 744 Competence and determination are two stages in Grafting studies have provided evidence for a fl oral evocation 728 transmissible fl oral stimulus 744 Circadian Rhythms: The Clock Within 730 The Discovery of Florigen 745 Circadian rhythms exhibit characteristic The Arabidopsis protein FLOWERING LOCUS T features 730 is fl origen 746 Phase shifting adjusts circadian rhythms to Gibberellins and ethylene can induce different day–night cycles 732 fl owering 747 Phytochromes and cryptochromes entrain Climate change has already caused measurable the clock 732 changes in fl owering time of wild plants 748 The transition to fl owering involves multiple Photoperiodism: Monitoring Day Length 732 factors and pathways 748 Plants can be classifi ed according to their photoperiodic responses 732 SUMMARY 749 The leaf is the site of perception of the photoperiodic signal 734 Plants monitor day length by measuring the length of the night 734 Night breaks can cancel the effect of the dark period 735

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CHAPTER 26 Responses and Adaptations to Abiotic Stress 755

Adaptation and Phenotypic Plasticity 756 High Light Stress 764 Adaptations involve genetic modifi cation 756 Photoinhibition by high light leads to the Phenotypic plasticity allows plants to respond to production of destructive forms of oxygen 764 environmental fl uctuations 756 Developmental and Physiological Mechanisms The Abiotic Environment and its Biological that Protect Plants against Environmental Impact on Plants 756 Extremes 765 Climate and soil infl uence plant fi tness 757 Plants can modify their life cycles to avoid Imbalances in abiotic factors have primary and abiotic stress 765 secondary effects on plants 757 Phenotypic changes in leaf structure and behavior are important stress responses 765 Water Defi cit and Flooding 757 The ratio of root-to-shoot growth increases in Soil water content and the relative humidity of the response to water defi cit 769 atmosphere determine the water status of the Plants can regulate stomatal aperture in response plant 758 to dehydration stress 769 Water defi cits cause cell dehydration and Plants adjust osmotically to drying soil by an inhibition of cell expansion 759 accumulating solutes 769 Flooding, soil compaction, and O2 defi ciency are Submerged organs develop aerenchyma tissue in related stresses 759 response to hypoxia 770 Imbalances in Soil Minerals 760 Plants have evolved two different strategies to Soil mineral content can result in plant stress protect themselves from toxic ions: exclusion and in various ways 760 internal tolerance 772 Soil salinity occurs naturally and as the result of Chelation and active transport contribute to improper water management practices 761 internal tolerance 773 The toxicity of high Na+ and Cl– in the cytosol is Many plants have the capacity to acclimate to cold due to their specifi c ion effects 761 temperatures 773 Plants survive freezing temperatures by limiting ice Temperature Stress 762 formation 774 High temperatures are most damaging to The lipid composition of membranes affects their growing, hydrated tissues 762 response to temperature 775 Temperature stress can result in damaged Plant cells have mechanisms that maintain protein membranes and enzymes 762 structure during temperature stress 776 Temperature stress can inhibit photosynthesis 763 Scavenging mechanisms detoxify reactive oxygen Low temperatures above freezing can species 776 cause chilling injury 764 Metabolic shifts enable plants to cope with Freezing temperatures cause ice crystal formation a variety of abiotic stresses 777 and dehydration 764 SUMMARY 778

APPENDIX ONE A1–1 GLOSSARY G–1 APPENDIX TWO A2–1 AUTHOR INDEX AI–1 APPENDIX THREE A3–1 SUBJECT INDEX SI–1

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