Plant Physiology and Development

Cover
Half Title
Title Page
Copyright Page
Brief Contents
Editors
Reviewers
Preface
Media and Supplements
Table of Contents
Chapter 1 Plant and Cell Architecture
Plant Classification and Life Cycles
Plant Life Processes: Unifying Principles
Plant life cycles alternate between diploid and haploid generations
Overview of Plant Structure
Plant cells are surrounded by rigid cell walls
Plasmodesmata allow the free movement of molecules between cells
New cells originate in dividing tissues called meristems
Biological membranes are phospholipid bilayers that contain proteins
Plant Cell Organelles
The Endomembrane System
The nucleus contains the majority of the genetic material
Gene expression involves both transcription and translation
The endoplasmic reticulum is a network of internal membranes
Secretion of proteins from cells begins with the rough ER
Glycoproteins and polysaccharides destined for secretion are processed in the Golgi apparatus
The plasma membrane has specialized regions involved in membrane recycling
Vacuoles have diverse functions in plant cells
Independently Dividing or Fusing Organelles Derived from the Endomembrane System
Oil bodies are lipid-storing organelles
Microbodies play specialized metabolic roles in leaves and seeds
Independently Dividing, Semiautonomous Organelles
Proplastids mature into specialized plastids in different plant tissues
Chloroplast and mitochondrial division are independent of nuclear division
The plant cytoskeleton consists of microtubules and microfilaments
The Plant Cytoskeleton
Actin, tubulin, and their polymers are in constant flux in the living cell
Cortical microtubules move around the cell by treadmilling
Cytoskeletal motor proteins mediate cytoplasmic streaming and directed organelle movement
Cell Cycle Regulation
Each phase of the cell cycle has a specific set of biochemical and cellular activities
The cell cycle is regulated by cyclins and cyclin-dependent kinases
Mitosis and cytokinesis involve both microtubules and the endomembrane system
Plant Cell Types
Dermal tissues cover the surfaces of plants
Ground tissues form the bodies of plants
Vascular tissues form transport networks between different parts of the plant
Summary
Web Material
Suggested Reading
Chapter 2 Genome Structure and Gene Expression
Nuclear Genome Organization
The nuclear genome is packaged into chromatin
Centromeres, telomeres, and nucleolar organizer regions contain repetitive sequences
Transposons are mobile sequences within the genome
Meiosis halves the number of chromosomes and allows for the recombination of alleles
Chromosome organization is not random in the interphase nucleus
Polyploids contain multiple copies of the entire genome
Phenotypic and physiological responses to polyploidy are unpredictable
The role of polyploidy in evolution is still unclear
Plant Cytoplasmic Genomes: Mitochondria and Plastids
The endosymbiotic theory describes the origin of cytoplasmic genomes
Organellar genetics do not obey Mendelian principles
Organellar genomes vary in size
RNA polymerase II binds to the promoter region of most protein-coding genes
Transcriptional Regulation of Nuclear Gene Expression
Conserved nucleotide sequences signal transcriptional termination and polyadenylation
Epigenetic modifications help determine gene activity
Noncoding RNAs regulate mRNA activity via the RNA interference (RNAi) pathway
Posttranscriptional Regulation of Nuclear Gene Expression
All RNA molecules are subject to decay
Posttranslational regulation determines the life span of proteins
Tools for Studying Gene Function
Mutant analysis can help elucidate gene function
Molecular techniques can measure the activity of genes
Gene fusions can introduce reporter genes
Genetic Modification of Crop Plants
Transgenes can confer resistance to herbicides or plant pests
Genetically modified organisms are controversial
Plant Cytoplasmic Genomes: Mitochondria and Plastids
Summary
Web Material
Suggested Reading
Chapter 3 Water and Plant Cells
Water in Plant Life
The Structure and Properties of Water
Water is a polar molecule that forms hydrogen bonds
Water molecules are highly cohesive
Water is an excellent solvent
Water has distinctive thermal properties relative to its size
Water has a high tensile strength
Diffusion and Osmosis
Diffusion is the net movement of molecules by random thermal agitation
Diffusion is most effective over short distances
Osmosis describes the net movement of water across a selectively permeable barrier
Water Potential
The chemical potential of water represents the free-energy status of water
Three major factors contribute to cell water potential
Water potentials can be measured
Water Potential of Plant Cells
Water enters the cell along a water potential gradient
Water can also leave the cell in response to a water potential gradient
Cell Wall and Membrane Properties
Small changes in plant cell volume cause large changes in turgor pressure
Water potential and its components vary with growth conditions and location within the plant
The rate at which cells gain or lose water is influenced by plasma membrane hydraulic conductivity
Aquaporins facilitate the movement of water across plasma membranes
Plant Water Status
Solute accumulation helps cells maintain turgor and volume
Physiological processes are affected by plant water status
Summary
Web Material
Suggested Reading
Chapter 4 Water Balance of Plants
Water in the Soil
A negative hydrostatic pressure in soil water lowers soil water potential
Water moves through the soil by bulk flow
Water Absorption by Roots
Water moves in the root via the apoplast, symplast, and transmembrane pathways
Solute accumulation in the xylem can generate “root pressure”
The xylem consists of two types of transport cells
Water Transport through the Xylem
Water moves through the xylem by pressure-driven bulk flow
Water movement through the xylem requires a smaller pressure gradient than movement through living cells
What pressure difference is needed to lift water 100 meters to a treetop?
The cohesion–tension theory explains water transport in the xylem
Xylem transport of water in trees faces physical challenges
Water Movement from the Leaf to the Atmosphere
Plants minimize the consequences of xylem cavitation
Leaves have a large hydraulic resistance
The driving force for transpiration is the difference in water vapor concentration
Water loss is also regulated by the pathway resistances
Stomatal control couples leaf transpiration to leaf photosynthesis
The cell walls of guard cells have specialized features
An increase in guard cell turgor pressure opens the stomata
Overview: The Soil–Plant– Atmosphere Continuum
The transpiration ratio measures the relationship between water loss and carbon gain
Summary
Web Material
Suggested Reading
Chapter 5 Mineral Nutrition
Essential Nutrients, Deficiencies, and Plant Disorders
Special techniques are used in nutritional studies
Nutrient solutions can sustain rapid plant growth
Mineral deficiencies disrupt plant metabolism and function
Analysis of plant tissues reveals mineral deficiencies
Treating Nutritional Deficiencies
Crop yields can be improved by the addition of fertilizers
Some mineral nutrients can be absorbed by leaves
Negatively charged soil particles affect the adsorption of mineral nutrients
Soil, Roots, and Microbes
Soil pH affects nutrient availability, soil microbes, and root growth
Some plants develop extensive root systems
Excess mineral ions in the soil limit plant growth
Root systems differ in form but are based on common structures
Different areas of the root absorb different mineral ions
Nutrient availability influences root growth
Mycorrhizal symbioses facilitate nutrient uptake by roots
Nutrients move between mycorrhizal fungi and root cells
Summary
Web Material
Suggested Reading
Chapter 6 Solute Transport
Passive and Active Transport
Transport of Ions across Membrane Barriers
Different diffusion rates for cations and anions produce diffusion potentials
How does membrane potential relate to ion distribution?
The Nernst equation distinguishes between active and passive transport
Proton transport is a major determinant of the membrane potential
Membrane Transport Processes
Channels enhance diffusion across membranes
Carriers bind and transport specific substances
Primary active transport requires energy
Secondary active transport uses stored energy
Kinetic analyses can elucidate transport mechanisms
Membrane Transport Proteins
The genes for many transporters have been identified
Transporters exist for diverse nitrogen-containing compounds
Cation transporters are diverse
Anion transporters have been identified
Aquaporins have diverse functions
Transporters for metal and metalloid ions transport essential micronutrients
Plasma membrane H+-ATPases are highly regulated P-type ATPases
The tonoplast H+-ATPase drives solute accumulation in vacuoles
H+-pyrophosphatases also pump protons at the tonoplast
Ion Transport in Roots
Solutes move through both apoplast and symplast
Ions cross both symplast and apoplast
Xylem parenchyma cells participate in xylem loading
Summary
Web Material
Suggested Reading
Chapter 7 Photosynthesis: The Light Reactions
Photosynthesis in Higher Plants
General Concepts
Light has characteristics of both a particle and a wave
When molecules absorb or emit light, they change their electronic state
Photosynthetic pigments absorb the light that powers photosynthesis
Key Experiments in Understanding Photosynthesis
Photosynthesis takes place in complexes containing light-harvesting antennas and photochemical reaction centers
Action spectra relate light absorption to photosynthetic activity
Light drives the reduction of NADP+ and the formation of ATP
The chemical reaction of photosynthesis is driven by light
Oxygen-evolving organisms have two photosystems that operate in series
Organization of the Photosynthetic Apparatus
The chloroplast is the site of photosynthesis
Thylakoids contain integral membrane proteins
Photosystems I and II are spatially separated in the thylakoid membrane
Anoxygenic photosynthetic bacteria have a single reaction center
The antenna funnels energy to the reaction center
Organization of Light-Absorbing Antenna Systems
Antenna systems contain chlorophyll and are membrane-associated
Many antenna pigment–protein complexes have a common structural motif
Electrons from chlorophyll travel through the carriers organized in the Z scheme
Mechanisms of Electron Transport
Energy is captured when an excited chlorophyll reduces an electron acceptor molecule
The reaction center chlorophylls of the two photosystems absorb at different wavelengths
Water is oxidized to oxygen by PSII
The PSII reaction center is a multi-subunit pigment–protein complex
Pheophytin and two quinones accept electrons from PSII
Electron flow through the cytochrome
complex also transports protons
Plastoquinone and plastocyanin carry electrons between photosystems II and I
The PSI reaction center reduces NADP+
Cyclic electron flow generates ATP but no NADPH
Proton Transport and ATP Synthesis in the Chloroplast
Some herbicides block photosynthetic electron flow
Repair and Regulation of the Photosynthetic Machinery
Carotenoids serve as photoprotective agents
Some xanthophylls also participate in energy dissipation
The PSII reaction center is easily damaged
PSI is protected from active oxygen species
Genetics, Assembly, and Evolution of Photosynthetic Systems
Thylakoid stacking permits energy partitioning between the photosystems
Chloroplast genes exhibit non-Mendelian patterns of inheritance
Most chloroplast proteins are imported from the cytoplasm
Complex photosynthetic organisms have evolved from simpler forms
The biosynthesis and breakdown of chlorophyll are complex pathways
Mechanisms of Electron Transport
Summary
Web Material
Suggested Reading
Chapter 8 Photosynthesis: The Carbon Reactions
The Calvin–Benson Cycle
The Calvin–Benson cycle has three phases: carboxylation, reduction, and regeneration
The fixation of CO2 via carboxylation of ribulose 1,5-bisphosphate and the reduction of the product 3-phosphoglycerate yield triose phosphates
The regeneration of ribulose 1,5-bisphosphate ensures the continuous assimilation of CO2
An induction period precedes the steady state of photosynthetic CO2 assimilation
Many mechanisms regulate the Calvin–Benson cycle
Rubisco-activase regulates the catalytic activity of rubisco
Light regulates the Calvin–Benson cycle via the ferredoxin–thioredoxin system
Light-dependent ion movements modulate enzymes of the Calvin–Benson cycle
Light controls the assembly of chloroplast enzymes into supramolecular complexes
The C2 Oxidative Photosynthetic Carbon Cycle
The oxygenation of ribulose 1,5-bisphosphate sets in motion the C2 oxidative photosynthetic carbon cycle
Enzymes of the plant C2 oxidative photosynthetic carbon cycle derive from different ancestors
Photorespiration is linked to the photosynthetic electron transport system
Cyanobacteria use a proteobacterial pathway for bringing carbon atoms of 2-phosphoglycolate back to the Calvin–Benson cycle
The C2 oxidative photosynthetic carbon cycle interacts with many metabolic pathways
Production of biomass may be enhanced by engineering photorespiration
Inorganic Carbon–Concentrating Mechanisms
Inorganic Carbon–Concentrating Mechanisms: The C4 Carbon Cycle
Malate and aspartate are the primary carboxylation products of the C4 cycle
The C4 cycle assimilates CO2 by the concerted action of two different types of cells
The C4 cycle uses different mechanisms for decarboxylation of four-carbon acids transported to bundle sheath cells
Bundle sheath cells and mesophyll cells exhibit anatomical and biochemical differences
The C4 cycle also concentrates CO2 in single cells
Light regulates the activity of key C4 enzymes
Photosynthetic assimilation of CO2 in C4 plants demands more transport processes than in C3 plants
In hot, dry climates, the C4 cycle reduces photorespiration
Inorganic Carbon–Concentrating Mechanisms: Crassulacean Acid Metabolism (CAM)
Different mechanisms regulate C4 PEPCase and CAM PEPCase
CAM is a versatile mechanism sensitive to environmental stimuli
Accumulation and Partitioning of Photosynthates—Starch and Sucrose
Formation and Mobilization of Chloroplast Starch
Chloroplast stroma accumulates starch as insoluble granules during the day
Starch degradation at night requires the phosphorylation of amylopectin
The export of maltose prevails in the nocturnal breakdown of transitory starch
The synthesis and degradation of the starch granule are regulated by multiple mechanisms
Sucrose Biosynthesis and Signaling
Triose phosphates from the Calvin–Benson cycle build up the cytosolic pool of three important hexose phosphates in the light
Sucrose is continuously synthesized in the cytosol
Fructose 2,6-bisphosphate regulates the hexose phosphate pool in the light
Summary
Web Material
Suggested Reading
Chapter 9 Photosynthesis: Physiological and Ecological Considerations
Photosynthesis Is Influenced by Leaf Properties
Leaf anatomy and canopy structure maximize light absorption
Leaf angle and leaf movement can control light absorption
Leaves acclimate to sun and shade environments
Effects of Light on Photosynthesis in the Intact Leaf
Light-response curves reveal photosynthetic properties
Leaves must dissipate excess light energy
Absorption of too much light can lead to photoinhibition
Effects of Temperature on Photosynthesis in the Intact Leaf
Leaves must dissipate vast quantities of heat
There is an optimal temperature for photosynthesis
Photosynthesis is sensitive to both high and low temperatures
Photosynthetic efficiency is temperature-sensitive
Effects of Carbon Dioxide on Photosynthesis in the Intact Leaf
Atmospheric CO2 concentration keeps rising
CO2 diffusion to the chloroplast is essential to photosynthesis
CO2 imposes limitations on photosynthesis
How will photosynthesis and respiration change in the future under elevated CO2 conditions?
Stable Isotopes Record Photosynthetic Properties
How do we measure the stable carbon isotopes of plants?
Why are there carbon isotope ratio variations in plants?
Summary
Web Material
Suggested Reading
Chapter 10 Stomatal Biology
Light-dependent Stomatal Opening
Guard cells respond to blue light
Blue light activates a proton pump at the guard cell plasma membrane
Blue light regulates the osmotic balance of guard cells
Blue-light responses have characteristic kinetics and lag times
Sucrose is an osmotically active solute in guard cells
Mediation of Blue-light Photoreception in Guard Cells by Zeaxanthin
Reversal of Blue Light–Stimulated Opening by Green Light
A carotenoid–protein complex senses light intensity
The Resolving Power of Photophysiology
Mediation of Blue-light Photoreception in Guard Cells by Zeaxanthin
Summary
Web Material
Suggested Reading
Chapter 11 Translocation in the Phloem
Pathways of Translocation
Sugar is translocated in phloem sieve elements
Mature sieve elements are living cells specialized for translocation
Large pores in cell walls are the prominent feature of sieve elements
Damaged sieve elements are sealed off
Companion cells aid the highly specialized sieve elements
Patterns of Translocation: Source to Sink
Phloem sap can be collected and analyzed
Materials Translocated in the Phloem
Sugars are translocated in a nonreducing form
Other solutes are translocated in the phloem
Rates of Movement
An osmotically generated pressure gradient drives translocation in the pressure-flow model
The Pressure-Flow Model, a Passive Mechanism for Phloem Transport
Some predictions of pressure flow have been confirmed, while others require further experimentation
The energy requirement for transport through the phloem pathway is small in herbaceous plants
There is no bidirectional transport in single sieve elements, and solutes and water move at the same velocity
Sieve plate pores appear to be open channels
Pressure gradients in the sieve elements may be modest; pressures in herbaceous plants and trees appear to be similar
Alternative models for translocation by mass flow have been suggested
Does translocation in gymnosperms involve a different mechanism?
Phloem Loading
Phloem loading can occur via the apoplast or symplast
Abundant data support the existence of apoplastic loading in some species
Sucrose uptake in the apoplastic pathway requires metabolic energy
Phloem loading is symplastic in some species
Phloem loading in the apoplastic pathway involves a sucrose–H+ symporter
The polymer-trapping model explains symplastic loading in plants with intermediary-type companion cells
The type of phloem loading is correlated with several significant characteristics
Phloem loading is passive in several tree species
Phloem Unloading and Sink-to-Source Transition
Phloem unloading and short-distance transport can occur via symplastic or apoplastic pathways
Transport into sink tissues requires metabolic energy
The transition of a leaf from sink to source is gradual
Photosynthate Distribution: Allocation and Partitioning
Various sinks partition transport sugars
Allocation includes storage, utilization, and transport
Source leaves regulate allocation
Sink tissues compete for available translocated photosynthate
The source adjusts over the long term to changes in the source-to-sink ratio
Sink strength depends on sink size and activity
Transport of Signaling Molecules
Turgor pressure and chemical signals coordinate source and sink activities
Proteins and RNAs function as signal molecules in the phloem to regulate growth and development
Plasmodesmata function in phloem signaling
Summary
Web Material
Suggested Reading
Chapter 12 Respiration and Lipid Metabolism
Overview of Plant Respiration
Glycolysis
Glycolysis metabolizes carbohydrates from several sources
Plants have alternative glycolytic reactions
The energy-conserving phase of glycolysis extracts usable energy
In the absence of oxygen, fermentation regenerates the NAD+ needed for glycolysis
Plant glycolysis is controlled by its products
The Oxidative Pentose Phosphate Pathway
The oxidative pentose phosphate pathway is redox-regulated
The oxidative pentose phosphate pathway produces NADPH and biosynthetic intermediates
The Citric Acid Cycle
Mitochondria are semiautonomous organelles
Pyruvate enters the mitochondrion and is oxidized via the citric acid cycle
Mitochondrial Electron Transport and ATP Synthesis
The citric acid cycle of plants has unique features
The electron transport chain catalyzes a flow of electrons from NADH to O2
The electron transport chain has supplementary branches
ATP synthesis in the mitochondrion is coupled to electron transport
Aerobic respiration yields about 60 molecules of ATP per molecule of sucrose
Transporters exchange substrates and products
Several subunits of respiratory complexes are encoded by the mitochondrial genome
Plants have several mechanisms that lower the ATP yield
Short-term control of mitochondrial respiration occurs at different levels
Respiration is tightly coupled to other pathways
Plants respire roughly half of the daily photosynthetic yield
Respiration in Intact Plants and Tissues
Different tissues and organs respire at different rates
Respiration operates during photosynthesis
Environmental factors alter respiration rates
Triacylglycerols are stored in oil bodies
Lipid Metabolism
Fats and oils store large amounts of energy
Polar glycerolipids are the main structural lipids in membranes
Fatty acid biosynthesis consists of cycles of two-carbon addition
Glycerolipids are synthesized in the plastids and the ER
Membrane lipids are precursors of important signaling compounds
Lipid composition influences membrane function
Storage lipids are converted into carbohydrates in germinating seeds
Summary
Web Material
Suggested Reading
Chapter 13 Assimilation of Inorganic Nutrients
Nitrogen in the Environment
Nitrogen passes through several forms in a biogeochemical cycle
Unassimilated ammonium or nitrate may be dangerous
Nitrate Assimilation
Many factors regulate nitrate reductase
Nitrite reductase converts nitrite to ammonium
Both roots and shoots assimilate nitrate
Converting ammonium to amino acids requires two enzymes
Ammonium Assimilation
Ammonium can be assimilated via an alternative pathway
Transamination reactions transfer nitrogen
Amino Acid Biosynthesis
Asparagine and glutamine link carbon and nitrogen metabolism
Biological Nitrogen Fixation
Free-living and symbiotic bacteria fix nitrogen
Nitrogen fixation requires microanaerobic or anaerobic conditions
Symbiotic nitrogen fixation occurs in specialized structures
Establishing symbiosis requires an exchange of signals
Nod factors produced by bacteria act as signals for symbiosis
Nodule formation involves phytohormones
The nitrogenase enzyme complex fixes N2
Amides and ureides are the transported forms of nitrogen
Sulfur Assimilation
Sulfate assimilation requires the reduction of sulfate to cysteine
Sulfate is the form of sulfur transported into plants
Methionine is synthesized from cysteine
Phosphate Assimilation
Sulfate assimilation occurs mostly in leaves
Cations form noncovalent bonds with carbon compounds
Cation Assimilation
Roots modify the rhizosphere to acquire iron
Oxygen Assimilation
Iron cations form complexes with carbon and phosphate
The Energetics of Nutrient Assimilation
Summary
Web Material
Suggested Reading
Chapter 14 Cell Walls: Structure, Formation, and Expansion
Overview of Plant Cell Wall Functions and Structures
Plant cell walls vary in structure and function
Components differ for primary and secondary cell walls
Cellulose microfibrils have an ordered structure and are synthesized at the plasma membrane
Matrix polymers are synthesized in the Golgi apparatus and secreted via vesicles
Pectins are hydrophilic gel-forming components of the primary cell wall
Hemicelluloses are matrix polysaccharides that bind to cellulose
New primary cell walls are assembled during cytokinesis and continue to be assembled during growth
Primary Cell Wall Structure and Function
The primary cell wall is composed of cellulose microfibrils embedded in a matrix of pectins and hemicelluloses
Mechanisms of Cell Expansion
Microfibril orientation influences growth directionality of cells with diffuse growth
Cortical microtubules influence the orientation of newly deposited microfibrils
The Extent and Rate of Cell Growth
Stress relaxation of the cell wall drives water uptake and cell expansion
Acid-induced growth and wall stress relaxation are mediated by expansins
Cell wall models are hypotheses about how molecular components fit together to make a functional wall
Secondary Cell Wall Structure and Function
Many structural changes accompany the cessation of wall expansion
Secondary cell walls are rich in cellulose and hemicellulose and often have a hierarchical organization
Lignification transforms the SCW into a hydrophobic structure resistant to deconstruction
Summary
Web Material
Suggested Reading
Chapter 15 Signals and Signal Transduction
Temporal and Spatial Aspects of Signaling
Signal Perception and Amplification
Receptors are located throughout the cell and are conserved across kingdoms
Signals must be amplified intracellularly to regulate their target molecules
The MAP kinase signal amplification cascade is present in all eukaryotes
Ca2+ is the most ubiquitous second messenger in plants and other eukaryotes
Changes in the cytosolic or cell wall pH can serve as second messengers for hormonal and stress responses
Reactive oxygen species act as second messengers mediating both environmental and developmental signals
Hormones and Plant Development
Lipid signaling molecules act as second messengers that regulate a variety of cellular processes
Gibberellins promote stem growth and were discovered in relation to the “foolish seedling disease” of rice
Auxin was discovered in early studies of coleoptile bending during phototropism
Cytokinins were discovered as cell division– promoting factors in tissue culture experiments
Ethylene is a gaseous hormone that promotes fruit ripening and other developmental processes
Abscisic acid regulates seed maturation and stomatal closure in response to water stress
Brassinosteroids regulate photomorphogenesis, germination, and other developmental processes
Strigolactones suppress branching and promote rhizosphere interactions
Phytohormone Metabolism and Homeostasis
Indole-3-pyruvate is the primary intermediate in auxin biosynthesis
Gibberellins are synthesized by oxidation of the diterpene ent-kaurene
Cytokinins are adenine derivatives with isoprene side chains
Abscisic acid is synthesized from a carotenoid intermediate
Ethylene is synthesized from methionine via the intermediate ACC
Brassinosteroids are derived from the sterol campesterol
Signal Transmission and Cell–Cell Communication
Strigolactones are synthesized from beta-carotene
The cytokinin and ethylene signal transduction pathways are derived from the bacterial two-component regulatory system
Hormonal Signaling Pathways
Receptor-like kinases mediate brassinosteroid and certain auxin signaling pathways
The core ABA signaling components include phosphatases and kinases
Plant hormone signaling pathways generally employ negative regulation
Several plant hormone receptors encode components of the ubiquitination machinery and mediate signaling via protein degradation
Plants have evolved mechanisms for switching off or attenuating signaling responses
The cellular response output to a signal is often tissue-specific
Cross-regulation allows signal transduction pathways to be integrated
Summary
Suggested Reading
Chapter 16 Signals from Sunlight
Plant Photoreceptors
Photoresponses are driven by light quality or spectral properties of the energy absorbed
Plants responses to light can be distinguished by the amount of light required
Phytochrome is the primary photoreceptor for red and far-red light
Phytochromes
Phytochrome can interconvert between Pr and Pfr forms
The phytochrome chromophore and protein both undergo conformational changes in response to red light
Pfr is the physiologically active form of phytochrome
Pfr is partitioned between the cytosol and the nucleus
Phytochrome Responses
Phytochrome responses fall into three main categories based on the amount of light required
Phytochrome responses vary in lag time and escape time
Phytochrome A mediates responses to continuous far-red light
Roles for phytochromes C, D, and E are emerging
Phytochrome Signaling Pathways
Phytochrome B mediates responses to continuous red or white light
Phytochrome regulates membrane potentials and ion fluxes
Phytochrome interacting factors (PIFs) act early in signaling
Phytochrome regulates gene expression
Phytochrome signaling involves protein phosphorylation and dephosphorylation
Phytochrome-induced photomorphogenesis involves protein degradation
Blue-Light Responses and Photoreceptors
Blue-light responses have characteristic kinetics and lag times
Cryptochromes
The activated FAD chromophore of cryptochrome causes a conformational change in the protein
Nuclear cryptochromes inhibit COP1-induced protein degradation
cry1 and cry2 have different developmental effects
Cryptochrome can also bind to transcriptional regulators directly
The Coaction of Cryptochrome, Phytochrome, and Phototropins
Stem elongation is inhibited by both red and blue photoreceptors
The circadian clock is regulated by multiple aspects of light
Phototropins
Phytochrome interacts with cryptochrome to regulate flowering
Blue light induces changes in FMN absorption maxima associated with conformation changes
The LOV2 domain is primarily responsible for kinase activation in response to blue light
Blue light induces a conformational change that “uncages” the kinase domain of phototropin and leads to autophosphorylation
Phototropism requires changes in auxin mobilization
Phototropins regulate chloroplast movements via F-actin filament assembly
Stomatal opening is regulated by blue light, which activates the plasma membrane H+-ATPase
The main signal transduction events of phototropin-mediated stomatal opening have been identified
Responses to Ultraviolet Radiation
Summary
Web Material
Suggested Reading
Chapter 17 Embryogenesis
Overview of Plant Growth and Development
Sporophytic development can be divided into three major stages
Embryogenesis differs between eudicots and monocots, but also features common fundamental processes
Embryogenesis: The Origins of Polarity
Apical–basal polarity is established early in embryogenesis
Position-dependent mechanisms guide embryogenesis
Intercellular signaling processes play key roles in guiding position-dependent development
Embryo development features regulated communication between cells
The analysis of mutants identifies genes for signaling processes that are essential for embryo organization
Auxin functions as a mobile chemical signal during embryogenesis
Plant polarity is maintained by polar auxin streams
Auxin transport is regulated by multiple mechanisms
The GNOM protein establishes a polar distribution of PIN auxin efflux proteins
Radial patterning guides formation of tissue layers
MONOPTEROS encodes a transcription factor that is activated by auxin
The origin of epidermis: a boundary and interface at the edge of the radial axis
Procambial precusors for the vascular stele lie at the center of the radial axis
The differentiation of cortical and endodermal cells involves the intercellular movement of a transcription factor
Meristematic Tissues: Foundations for Indeterminate Growth
The root and shoot apical meristems use similar strategies to enable indeterminate growth
The Root Apical Meristem
The origin of different root tissues can be traced to specific initial cells
The root tip has four developmental zones
Responses to auxin are mediated by several distinct families of transcription factors
Cell ablation experiments implicate directional signaling processes in determination of cell identity
Auxin contributes to the formation and maintenance of the RAM
Cytokinin is required for normal root development
The Shoot Apical Meristem
The shoot apical meristem has distinct zones and layers
Shoot tissues are derived from several discrete sets of apical initials
Factors involved in auxin movement and responses influence SAM formation
Embryonic SAM formation requires the coordinated expression of transcription factors
A combination of positive and negative interactions determines apical meristem size
class homeodomain genes help maintain the proliferative ability of the SAM through regulation of cytokinin and GA levels
Localized zones of auxin accumulation promote leaf initiation
The Vascular Cambium
The maintenance of undetermined initials in various meristem types depends on similar mechanisms
Summary
Web Material
Suggested Reading
Chapter 18 Seed Dormancy, Germination, and Seedling Establishment
Seed Structure
Seed anatomy varies widely among different plant groups
Seed Dormancy
Dormancy can be imposed on the embryo by the surrounding tissues
Embryo dormancy may be caused by physiological or morphological factors
Non-dormant seeds can exhibit vivipary and precocious germination
The ABA:GA ratio is the primary determinant of seed dormancy
Release from Dormancy
Some seeds require either chilling or after-ripening to break dormancy
Light is an important signal that breaks dormancy in small seeds
Seed Germination
Germination can be divided into three phases corresponding to the phases of water uptake
Seed dormancy can by broken by various chemical compounds
The cereal aleurone layer is a specialized digestive tissue surrounding the starchy endosperm
Mobilization of Stored Reserves
Gibberellins enhance the transcription of
mRNA
The gibberellin receptor, GID1, promotes the degradation of negative regulators of the gibberellin response
DELLA repressor proteins are rapidly degraded
GA-MYB is a positive regulator of
amylase transcription
ABA inhibits gibberellin-induced enzyme production
Seedling Growth and Establishment
The outer tissues of eudicot stems are the targets of auxin action
The minimum lag time for auxin-induced elongation is 10 minutes
Auxin promotes growth in stems and coleoptiles, while inhibiting growth in roots
Auxin-induced proton extrusion induces cell wall creep and cell elongation
Gravitropism involves the lateral redistribution of auxin
Tropisms: Growth in Response to Directional Stimuli
Polar auxin transport requires energy and is gravity independent
According to the starch–statolith hypothesis, specialized amyloplasts serve as gravity sensors in root caps
Auxin movements in the root are regulated by specific transporters
The gravitropic stimulus perturbs the symmetric movement of auxin from the root tip
Gravity perception in eudicot stems and stemlike organs occurs in the starch sheath
Gravity sensing may involve pH and calcium ions (Ca2+) as second messengers
Phototropism
Phototropism is mediated by the lateral redistribution of auxin
Phototropism occurs in a series of posttranslational events
Photomorphogenesis
Gibberellins and brassinosteroids both suppress photomorphogenesis in the dark
Hook opening is regulated by phytochrome and auxin
Ethylene induces lateral cell expansion
Shade Avoidance
Decreasing the R:FR ratio causes elongation in sun plants
Phytochrome enables plants to adapt to changes in light quality
Reducing shade avoidance responses can improve crop yields
Vascular Tissue Differentiation
Auxin and cytokinin are required for normal vascular development
Zinnia suspension-cultured cells can be induced to undergo xylogenesis
Xylogenesis involves chemical signaling between neighboring cells
Root Growth and Differentiation
Root epidermal development follows three basic patterns
Auxin and other hormones regulate root hair development
Lateral root formation and emergence depend on endogenous and exogenous signals
Regions of lateral root emergence correspond with regions of auxin maxima
Lateral roots and shoots have gravitropic setpoint angles
Summary
Web Material
Suggested Reading
Chapter 19 Vegetative Growth and Organogenesis
Leaf Development
The Establishment of Leaf Polarity
Hormonal signals play key roles in regulating leaf primordia emergence
A signal from the SAM initiates adaxial–abaxial polarity
Adaxial leaf development requires HD-ZIP III transcription factors
ARP genes promote adaxial identity and repress the KNOX1 gene
The expression of HD-ZIP III genes is antagonized by miR166 in abaxial regions of the leaf
Interactions between adaxial and abaxial tissues are required for blade outgrowth
Antagonism between KANADI and HD-ZIP III is a key determinant of adaxial–abaxial leaf polarity
Blade outgrowth is auxin dependent and regulated by the YABBY and WOX genes
Leaf proximal–distal polarity also depends on specific gene expression
In compound leaves, de-repression of the KNOX1 gene promotes leaflet formation
Differentiation of Epidermal Cell Types
Guard cell fate is ultimately determined by a specialized epidermal lineage
Two groups of bHLH transcription factors govern stomatal cell fate transitions
Peptide signals regulate stomatal patterning by interacting with cell surface receptors
Genetic screens have led to the identification of positive and negative regulators of trichome initiation
GLABRA2 acts downstream of the GL1–GL3–TTG1 complex to promote trichome formation
Venation Patterns in Leaves
Jasmonic acid regulates Arabidopsis leaf trichome development
Auxin canalization initiates development of the leaf trace
The primary leaf vein is initiated discontinuously from the preexisting vascular system
Basipetal auxin transport from the L1 layer of the leaf primordium initiates development of the leaf trace procambium
The existing vasculature guides the growth of the leaf trace
Higher-order leaf veins differentiate in a predictable hierarchical order
Auxin canalization regulates higher-order vein formation
Localized auxin biosynthesis is critical for higher-order venation patterns
Shoot Branching and Architecture
Axillary meristem initiation involves many of the same genes as leaf initiation and lamina outgrowth
Auxin, cytokinins, and strigolactones regulate axillary bud outgrowth
Strigolactones act locally to repress axillary bud growth
Auxin from the shoot tip maintains apical dominance
Cytokinins antagonize the effects of strigolactones
The initial signal for axillary bud growth may be an increase in sucrose availability to the bud
Integration of environmental and hormonal branching signals is required for plant fitness
Axillary bud dormancy in woody plants is affected by season, position, and age factors
Plants can modify their root system architecture to optimize water and nutrient uptake
Root System Architecture
Monocots and eudicots differ in their root system architecture
Root system architecture changes in response to phosphorous deficiencies
Root system architecture responses to phosphorus deficiency involve both local and systemic regulatory networks
Mycorrhizal networks augment root system architecture in all major terrestrial ecosystems
Secondary Growth
The vascular cambium and cork cambium are the secondary meristems where secondary growth originates
Phytohormones have important roles in regulating vascular cambium activity and differentiation of secondary xylem and phloem
Secondary growth evolved early in the evolution of land plants
Secondary growth from the vascular cambium gives rise to secondary xylem and phloem
Genes involved in stem cell maintenance, proliferation, and differentiation regulate secondary growth
Environmental factors influence vascular cambium activity and wood properties
Summary
Web Material
Suggested Reading
Chapter 20 The Control of Flowering and Floral Development
Floral Evocation: Integrating Environmental Cues
The Shoot Apex and Phase Changes
Plant development has three phases
Juvenile tissues are produced first and are located at the base of the shoot
Phase changes can be influenced by nutrients, gibberellins, and other signals
Circadian Rhythms: The Clock Within
Circadian rhythms exhibit characteristic features
Phytochromes and cryptochromes entrain the clock
Phase shifting adjusts circadian rhythms to different day–night cycles
Photoperiodism: Monitoring Day Length
Plants can be classified according to their photoperiodic responses
Night breaks can cancel the effect of the dark period
The leaf is the site of perception of the photoperiodic signal
Photoperiodic timekeeping during the night depends on a circadian clock
Plants monitor day length by measuring the length of the night
The coincidence model is based on oscillating light sensitivity
The coincidence of CONSTANS expression and light promotes flowering in LDPs
Phytochrome is the primary photoreceptor in photoperiodism
SDPs use a coincidence mechanism to inhibit flowering in long days
A blue-light photoreceptor regulates flowering in some LDPs
Vernalization: Promoting Flowering with Cold
Vernalization results in competence to flower at the shoot apical meristem
Vernalization can involve epigenetic changes in gene expression
A range of vernalization pathways may have evolved
Long-distance Signaling Involved in Flowering
Grafting studies provided the first evidence for a transmissible floral stimulus
Florigen is translocated in the phloem
The Identification of Florigen
The Arabidopsis protein FLOWERING LOCUS T (FT) is florigen
Gibberellins and ethylene can induce flowering
The transition to flowering involves multiple factors and pathways
Floral Meristems and Floral Organ Development
The four different types of floral organs are initiated as separate whorls
The shoot apical meristem in Arabidopsis changes with development
Two major categories of genes regulate floral development
Floral meristem identity genes regulate meristem function
Homeotic mutations led to the identification of floral organ identity genes
The ABC model partially explains the determination of floral organ identity
Arabidopsis Class E genes are required for the activities of the A, B, and C genes
According to the Quartet Model, floral organ identity is regulated by tetrameric complexes of the ABCE proteins
Class D genes are required for ovule formation
Floral asymmetry in flowers is regulated by gene expression
Summary
Web Material
Suggested Reading
Chapter 21 Gametophytes, Pollination, Seeds, and Fruits
Development of the Male and Female Gametophyte Generations
Formation of Male Gametophytes in the Stamen
Pollen grain formation occurs in two successive stages
The multilayered pollen cell wall is surprisingly complex
Female Gametophyte Development in the Ovule
The Arabidopsis gynoecium is an important model system for studying ovule development
The vast majority of angiosperms exhibit Polygonum-type embryo sac development
Functional megaspores undergo a series of free nuclear mitotic divisions followed by cellularization
Embryo sac development involves hormonal signaling between sporophytic and gametophytic generations
Pollination and Fertilization in Flowering Plants
Delivery of sperm cells to the female gametophyte by the pollen tube occurs in six phases
Adhesion and hydration of a pollen grain on a compatible flower depend on recognition between pollen and stigma surfaces
Ca2+-triggered polarization of the pollen grain precedes tube formation
Pollen tubes grow by tip growth
Receptor-like kinases are thought to regulate the ROP1 GTPase switch, a master regulator of tip growth
Style tissue conditions the pollen tube to respond to attractants produced by the synergids of the embryo sac
Pollen tube tip growth in the pistil is directed by both physical and chemical cues
Double fertilization occurs in three distinct stages
Selfing versus Outcrossing
Hermaphroditic and monoecious species have evolved floral features to ensure outcrossing
Self-incompatibility (SI) is the primary mechanism that enforces outcrossing in angiosperms
Cytoplasmic male sterility (CMS) occurs in the wild and is of great utility in agriculture
The Brassicaceae sporophytic SI system requires two S-locus genes
Gametophytic self-incompatibility (GSI) is mediated by cytotoxic S-RNases and F-box proteins
Apomixis: Asexual Reproduction by Seed
Apomixis is not an evolutionary dead end
Endosperm Development
Cellularization of coenocytic endosperm in Arabidopsis progresses from the micropylar to the chalazal region
Endosperm development and embryogenesis can occur autonomously
Cellularization of the coenocytic endosperm of cereals progresses centripetally
Many of the genes that control endosperm development are maternally expressed genes
The FIS proteins are members of a Polycomb repressive complex (PRC2) that represses endosperm development
Two genes, DEK1 and CR4, have been implicated in aleurone layer differentiation
Cells of the starchy endosperm and aleurone layer follow divergent developmental pathways
Seed Coat Development
Seed coat development appears to be regulated by the endosperm
Seed Maturation and Desiccation Tolerance
Seed filling and desiccation tolerance phases overlap in most species
LEA proteins and nonreducing sugars have been implicated in seed desiccation tolerance
The acquisition of desiccation tolerance involves many metabolic pathways
During the acquisition of desiccation tolerance, the cells of the embryo acquire a glassy state
Specific LEA proteins have been implicated in desiccation tolerance in
Coat-imposed dormancy is correlated with longterm seed-viability
Abscisic acid plays a key role in seed maturation
Fruit Development and Ripening
Arabidopsis and tomato are model systems for the study of fruit development
Fleshy fruits undergo ripening
Ripening involves changes in the color of fruit
The causal link between ethylene and ripening was demonstrated in transgenic and mutant tomatoes
Fruit softening involves the coordinated action of many cell wall–degrading enzymes
Taste and flavor reflect changes in acids, sugars, and aroma compounds
Climacteric and non-climacteric fruit differ in their ethylene responses
Angiosperms share a range of common molecular mechanisms controlling fruit development and ripening
The ripening process is transcriptionally regulated
Fruit ripening is under epigenetic control
A mechanistic understanding of the ripening process has commercial applications
Summary
Web Material
Suggested Reading
Chapter 22 Plant Senescence and Cell Death
Programmed Cell Death and Autolysis
PCD during normal development differs from that of the hypersensitive response
The autophagy pathway captures and degrades cellular constituents within lytic compartments
A subset of the autophagy-related genes controls the formation of the autophagosome
The autophagy pathway plays a dual role in plant development
The Leaf Senescence Syndrome
The developmental age of a leaf may differ from its chronological age
Leaf senescence may be sequential, seasonal, or stress-induced
Developmental leaf senescence consists of three distinct phases
The earliest cellular changes during leaf senescence occur in the chloroplast
The autolysis of chloroplast proteins occurs in multiple compartments
The STAY-GREEN (SGR) protein is required for both LHCP II protein recycling and chlorophyll catabolism
Leaf senescence is preceded by a massive reprogramming of gene expression
The NAC and WRKY gene families are the most abundant transcription factors regulating leaf senescence
Leaf Senescence: The Regulatory Network
ROS serve as internal signaling agents in leaf senescence
Sugars accumulate during leaf senescence and may serve as a signal
Plant hormones interact in the regulation of leaf senescence
Leaf Abscission
The timing of leaf abscission is regulated by the interaction of ethylene and auxin
Whole Plant Senescence
Angiosperm life cycles may be annual, biennial, or perennial
Whole plant senescence differs from aging in animals
The determinacy of shoot apical meristems is developmentally regulated
Nutrient or hormonal redistribution may trigger senescence in monocarpic plants
The rate of carbon accumulation in trees increases continuously with tree size
Summary
Web Material
Suggested Reading
Chapter 23 Biotic Interactions
Beneficial Interactions between Plants and Microorganisms
Arbuscular mycorrhizal associations and nitrogen-fixing symbioses involve related signaling pathways
Nod factors are recognized by the Nod factor receptor (NFR) in legumes
Rhizobacteria can increase nutrient availability, stimulate root branching, and protect against pathogens
Harmful Interactions between Plants, Pathogens, and Herbivores
Mechanical barriers provide a first line of defense against insect pests and pathogens
Plant secondary metabolites can deter insect herbivores
Plants store constitutive toxic compounds in specialized structures
Plants often store defensive chemicals as nontoxic water-soluble sugar conjugates in the vacuole
Inducible Defense Responses to Insect Herbivores
Constitutive levels of secondary compounds are higher in young developing leaves than in older tissues
Modified fatty acids secreted by grasshoppers act as elicitors of jasmonic acid accumulation and ethylene emission
Plants can recognize specific components of insect saliva
Phloem feeders activate defense signaling pathways similar to those activated by pathogen infections
Calcium signaling and activation of the MAP kinase pathway are early events associated with insect herbivory
Jasmonic acid activates defense responses against insect herbivores
Jasmonic acid acts through a conserved ubiquitin ligase signaling mechanism
Hormonal interactions contribute to plant–insect herbivore interactions
JA initiates the production of defense proteins that inhibit herbivore digestion
Herbivore damage induces systemic defenses
Glutamate receptor-like (GLR) genes are required for long-distance electrical signaling during herbivory
Herbivore-induced volatiles can repel herbivores and attract natural enemies
Herbivore-induced volatiles can serve as longdistance signals between plants
Defense responses to herbivores and pathogens are regulated by circadian rhythms
Herbivore-induced volatiles can also act as systemic signals within a plant
Plant Defenses against Pathogens
Insects have evolved mechanisms to defeat plant defenses
Microbial pathogens have evolved various strategies to invade host plants
Pathogens produce effector molecules that aid in the colonization of their plant host cells
Pathogen infection can give rise to molecular “danger signals” that are perceived by cell surface pattern recognition receptors
R genes provide resistance to individual pathogens by recognizing strain-specific effectors
Effectors released by phloem-feeding insects also activate NBS–LRR receptors
Exposure to elicitors induces a signal transduction cascade
The hypersensitive response is a common defense against pathogens
Phytoalexins with antimicrobial activity accumulate after pathogen attack
A single encounter with a pathogen may increase resistance to future attacks
The main components of the salicylic acid signaling pathway for SAR have been identified
Interactions of plants with nonpathogenic bacteria can trigger systemic resistance through a process called induced systemic res
Plant Defenses against Other Organisms
Some plant parasitic nematodes form specific associations through the formation of distinct feeding structures
Plants compete with other plants by secreting allelopathic secondary metabolites into the soil
Some plants are biotrophic pathogens of other plants
Summary
Web Material
Suggested Reading
Chapter 24 Abiotic Stress
Defining Plant Stress
Physiological adjustment to abiotic stress involves trade-offs between vegetative and reproductive development
Adaptation to stress involves genetic modification over many generations
Acclimation allows plants to respond to environmental fluctuations
Acclimation and Adaptation
Environmental Factors and Their Biological Impacts on Plants
Water deficit decreases turgor pressure, increases ion toxicity, and inhibits photosynthesis
Light stress can occur when shade-adapted or shade-acclimated plants are subjected to full sunlight
Salinity stress has both osmotic and cytotoxic effects
Temperature stress affects a broad spectrum of physiological processes
Heavy metals can both mimic essential mineral nutrients and generate ROS
Flooding results in anaerobic stress to the root
Mineral nutrient deficiencies are a cause of stress
During freezing stress, extracellular ice crystal formation causes cell dehydration
Ozone and ultraviolet light generate ROS that cause lesions and induce PCD
Combinations of abiotic stresses can induce unique signaling and metabolic pathways
Stress-Sensing Mechanisms in Plants
Sequential exposure to different abiotic stresses sometimes confers cross-protection
Signaling Pathways Activated in Response to Abiotic Stress
Early-acting stress sensors provide the initial signal for the stress response
The signaling intermediates of many stress-response pathways can interact
Acclimation to stress involves transcriptional regulatory networks called
Chloroplast genes respond to high-intensity light by sending stress signals to the nucleus
A self-propagating wave of ROS mediates systemic acquired acclimation
Hormonal interactions regulate normal development and abiotic stress responses
Epigenetic mechanisms and small RNAs provide additional protection against stress
Developmental and Physiological Mechanisms That Protect Plants against Abiotic Stress
Plants adjust osmotically to drying soil by accumulating solutes
Submerged organs develop aerenchyma tissue in response to hypoxia
Antioxidants and ROS-scavenging pathways protect cells from oxidative stress
Molecular chaperones and molecular shields protect proteins and membranes during abiotic stress
Plants can alter their membrane lipids in response to temperature and other abiotic stresses
Exclusion and internal tolerance mechanisms allow plants to cope with toxic ions
Phytochelatins and other chelators contribute to internal tolerance of toxic metal ions
Plants use cryoprotectant molecules and antifreeze proteins to prevent ice crystal formation
ABA signaling during water stress causes the massive efflux of K+ and anions from guard cells
Plants can alter their morphology in response to abiotic stress
Metabolic shifts enable plants to cope with a variety of abiotic stresses
Developing crops with enhanced tolerance to abiotic stress conditions is a major goal of agricultural research
The process of recovery from stress can be dangerous to the plant and requires a coordinated adjustment of plant metabolism and
Summary
Web Material
Suggested Reading
Glossary
Illustration Credits
Photo Credits
Subject Index
Blank Page