Plant Physiology: Comparing Animal and Plant Development, Cell Walls and Hormones - Prof. , Study notes of Biology

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Plant Physiology Lecture 17  Animal vs. Plant Development  Time of establishment of the body plan  Animal: Embryo  Plant: Adult  Organization of body plan  Animal: Different organs  Plant: One functional unit (phytomer: leaf stem) which is repeated  Adaptation to changes of the environment  Animal: Limited to no adaptation  Plant: Ability to change their development to respond to the environment  Determination of growth  Animal: Determined growth; growth stops  Plants: Undetermined growth; growth continues until death  Stem Cells – cells that can renew themselves through mitotic cell division and differentiate into a diverse range of specialized cell types  Animal: Stem cells are limited  Plants: Stem cells are very active and give rise to all organs; located in meristem at the top of the shoot and the tip of the root  Determination of cell fate – what the cell is and what it is doing  Cell lineage vs. cell position  Totipotency – Ability of a single cell to divide and produce all the differentiated cells in an organism (Ex. zygote)  Presence of cell wall  Animals: no cell wall  Plants: presence of cell wall  The Cell Wall  Structure is not uniform  Cellulose is principle component  Linear chains of 1,4 linked beta-d-glucose  Microfibrils – H-bonds between linear chains  Macrofibrils-link of sever microfibrils; embedded in a matrix of non-cellulosic molecules  20-30% dry weight of primary wall  40-60% dry weight of secondary wall  Synthesized at plasma membrane  Hemicelluloses  Heterogeneous groups  One type dominates  Synthesized in Golgi and secreted via vesicles  Form H-bonds with each other and with cellulose macrofibrils  Different types in primary and secondary cell wall  Primary Wall  Xyloglucans (type I primary) – linear chains of glucose with short side chain; Main hemicellulose of the dicots and half of the monocots  Glucoronoarabinoxylans (type II primary)- linear chains of xylose; present in monocots  Pectins  Hydrophilic  Form hydrated gel phase in which cellulose and hemicellulose are embedded  Form large and complex molecules made of sugar and sugar acids  Most heterogeneous components of the cell wall  Two main components: polygalacturonic and rhamnogalacturonan  Dicots: 30-50% dry weight of primary wall

 Monocots: 2-3% dry weight of primary wall  May be absent from secondary  Proteins – role not known  Three types  Structural prtoeins  Non-structural proteins (Ex. Arabinogalactans – signaling) (Ex. Expansins – wall loosening-expansion)  Enzymes  During cell maturation, proteins become cross-linked to the cell wall and therefore less soluble  Lignins  Phenolic polymers  Covalently linked to cell wall (irreversible)  In cell wall from vascular tissues and damaged tissues  Other components  Callose: linear 1,3-linked glucose between plasma membrane and cell wall  Cutin: waxy polymers and convers all aerial surfaces of plants  Suberin: waxy polymers present in cork cells and Casparian strips  Cell wall layers – formed interior to the previous one  Middle lamella: junction between cell walls of two neighboring cells (high in pectin and specific proteins)  Primary cell wall: allows cell expansion  Secondary cell wall: after end cell expansion  Primary Cell Wall  Cellulose, macrofibrils, and hemicelluloses are embedded in a highly hydrated matrix made of proteins  Chemical bonds between H-bonds provides strength and flexibility  Structural proteins – role not known, may add mechanical strength  Secondary Cell Wall  After cell wall expansion ends, cells can synthesis a secondary cell wall  Usually thick  Ex. secondary cell wall of xylem  Same structure as primary, but different components and often includes lignin  Increase mechanical strength  Hydrophobicity of cell wall (prevent enzyme from pathogen)  No cell expansion Lecture 18  Pits – region where the secondary cell wall is absent, but the primary cell wall and plasma membrane are present; facilitate movement of molecules cell to cell  Phragmoplast – the cell wall formed between to developing daughter cells in plants  Synthesis of new cell wall  Formation of primary wall during last stages of cell division  Secretion of components in the intercellular space, need to be assembled correctly  Synthesis → secretion → assembly → expansion → cross-linking and secondary wall formation  Cell Expansion  Location of Growth  Tip growth – localized expansion  Diffuse growth – expansion evenly distributed  Direction of Growth  Determined by the structure of the cell wall (orientation of cellulose microfibrils)  Orientation is isotropic (random; cells in meristems)  Orientation is anisotropic (most plant cells)  Cell Wall Loosening  Loosened during expansion (irreversible)  Stress relaxation of cell wall drives water uptake and cell elongation  Expands 10-100 fold in volume

 Acid growth: growing cell wall will extend much faster at acidic pH than at neutral pH  Expansions: belong to large superfamily of proteins; allow pH dependent extension and stress relaxation  Cessation of Expansion  Cell maturation: cell reaches final size; growth stops  Irreversible; cell wall more rigid  Reduction in wall-loosening process  Increase in cell wall cross-linking  Composition of cell wall  Synthesis of secondary cell wall  Functions of Cell Wall  Determine and maintain cell shape (protoplasts are always round)  Control rate and direction of cell growth and regulates cell volume  Support and mechanical strength  Prevents cell membrane from bursting in a hypotonic medium  Carbohydrate storage  Physical barrier to pathogens  Signaling – legumes and nitrogen-fixing bacteria  Economic products  Use of model organism  Model organism:  Simple organism  Has several advantages  Extensively studied to understand biological processes  Examples  Drosophila melanogaster (fruit fly)  Saccharomyces cerevisiae (budding yeast)  Caenorgabditis elegans (round worms)  Danio rerio (Zebra dano fish)  Plant model system  Arabidopsis thaliana (weed from Brassicacea)  Dicot and monocotyledon  Oryza sativa (rice)  Monocotyledon  Different approaches to understanding the mechanisms regulating plant development  Genetics (forward and reverse)  Forward  Goal is to understand a process  Identify genes involved in process  Identify mutant that are altered in the process  Identify mutated gene in mutant  Study gene  Reverse  Requirements:  Sequence of genome (we know all the genes)  Collection of mutants  Goal:  to understand the function of a specific gene  Identify a mutant in this gene  Compare wild type and mutant: look for phenotype  Deduce function of gene  Genomics  Biochemical

Lecture 19 – Signal Transduction  Signals: elements that modify the development of an organism  Nature of signals:  Endogenous (from organism) usually small molecules  From another organism: ex. from pathogen  Form environment: light, temperature  Hormone:  Usually effective at very low concentration  Produced in one cell or tissue, then transported to its site of action (target)  Usually small molecule  Plant hormones:  Auxin  Gibberellin  Cytokinin  Ethylene  Brassinolide  Systemin  Jasmonic acid  Abscisic acid (ABA)  How does a signal work?  Perceived by specific receptor from the cell  Initiate a cascade of events leading to specific response  From signal to response: multistep process  Signaling transduction pathway or signaling cascade  different steps between signal response  multistep process  Generation of signal  Perception of signal: receptor  Transmission of signal: phosphorylation  Secondary messenger  Final step: response  Receptors  Ligand: a signal that binds to a receptor  Binding of ligand modifies the properties of the receptor  Activation or inhibition of receptor  Cellular location of receptor  Stability or degradation of receptor  Receptor forms new function  Two types of receptors  Cell-surface: ligand does not penetrate the cell  Receptor-Like Kinase (RLK): serine and threonine kinase (ex. Leucine-rich repeats RLK)  Bacterial two components systems: histidine kinase (ex. cytokinin receptor, ethylene receptor)  Sensor protein: detect the signal and then modify the response regulator protein  Response regulator protein: transmit the signal to the next protein  Intracellular: ligand penetrates the cell  Common for animal/human cell  Uncommon for plant cells  Ex. auxin receptor  Phosphorylation as a mean to transduce a signal  Change protein functions  Enzyme activity  Cellular location  Stability/degradation

 Interacting partners  Kinase in signaling  High number of protein kinases in plants  Kinases are arranged in families  Examples of kinase  Receptor-like kinase  Histidine kinase  Glycogen synthase kinase-3 (GSK-3)  Calcium dependent kinase  MAP kinase  MAP Kinase cascade  Series of three kinases  MAP kinase kinase kinase (MAPKKK)  MAP kinase kinase (MAPKK)  MAP kinase (MAPK)  Secondary Messenger  Signal transduction pathways often involve the generation of second messengers  Transient secondary signals inside cell  Greatly amplify original signal  Ex. Ca2+^ and cAMP  Ca2+^ levels are released from internal stores when Ca2+^ channels are open  cAMP is produced by the enzyme adenylate cyclase  Ca2+^ and cAMP are co-factors of kinases and/or phosphatases: required for proteins to work  Response  Modification of gene expression by transcription factors  Modification of enzyme activity  Accumulation of new proteins and new chemicals  Degradation of proteins and chemicals  Modulation of signal cascade: feedback control  Stop of signal cascade when signal is gone: ex. reduction of hormone level Lecture 20 : Auxin part I  Dose Response – change in effects on an organism caused by different levels of exposure of a chemical  Change in plant development in response to increased level of a hormone  Example: cytokinin and root growth (effects depend on concentration of hormone)  Charles and Francis Darwin (1880) determined the site of light perception  Signal perceived at tip of seedlings  Phototropism response: the bending of plants towards light  Auxin (means to increase or grow)  Biosynthesis  Mid 1930’s structure identified as indole-3-acetic acid (IAA)  Synthesized in the shoot apical meristem (top of plant), young leaves, and developing fruit  Multiple pathways  Tryptophan-dependent: use tryptophan for synthesis (three different pathways)  Tryptophan-independent  Inactivation  IAA can be conjugated to other compounds  Conjugation is reversible  Conjugation is inactive: used for storage and transport  Transport  Polar transport from shoot apex down to root  Polar auxin alone is not sufficient  Secondary active transport located at apical side of cell: symporter H+ and IAA-

 Symporter is called AUX1 in Arabidopsis  AUX1 is only expressed in few cells in root  Asymmetic location in cell: presence in apical (top) part of cell  Auxin efflux carriers: PIN proteins  Asymmetric location: presence in basal (bottom) part of cell  Different PIN proteins are expressed in different tissues  Transport Inhibitors  Ex. NPA and TIBA  Inhibit auxin efflux (not auxin uptake)  Auxin in no more transported from top to bottom  Cell localization of auxin efflux is changed (evenly distributed)  Roles of Auxin in growth and development  Involved in apical dominance  Embryogenesis (establishment of polarity)  Promotes fruit growth  Promotes the formation of lateral root  Delays leaf abscission  Promotes vascular differentiation  Synthetic auxin are powerful herbicides  Cell elongation  Phototropism and gravitropism  Acid growth hypothesis  Addition of auxin induces the acidification of the extracellular space and cell wall  Acidification of cell wall increases the activity of the expansins  Expansins increases the loosening of the cell wall  Cell can grow more  Growth or elongation of stem  Auxin induces acidification by:  Increasing the expression of the H+-ATPase (more protein)  Increasing the protein trafficking (more protein to plasma membrane)  Increasing the stabilization of the H+-ATPase (protein stays longer within the plasma membrane)  More active H+-ATPase at the plasma membrane: acidification of the cell wall  Tropism  Phototropism: growth in response to light  Positive phototropism: towards light  Negative phototropism: away from light  Lateral redistribution of auxin  Normal light: light comes from every direction  Auxin is present everywhere in stem  Unilateral light source  Redistribution of auxin on the side away from light  Acidification of cell wall and expansion where auxin is present  Gravitropism: growth in response to gravity  Positive gravitropism: towards gravity (ex. roots grown down)  Negative gravitropism: away from gravity (ex. shoot grows up)  Lateral redistribution of auxin  Root gravitropism:  Cell growth in region of low auxin  Cell growth inhibition in region of high auxin (too much auxin) Lecture 21 : Auxin part II  Auxin receptor (TIR1)  Identified in 2005

 Intracellular receptor in the cytoplasm  Soluble  TIR1 is a subunit of a specific Ubiquitin E3 ligase called SCF complex  SCF complex catalyzes the addition of ubiquitin molecules to proteins for proteolytic degradation  Can tag AUX/IAA with U for degradation  Does not work if no auxin is present: no degradation  Ubiquitin: small protein added to proteins to signal their degradation by the protein complex 26S proteasome  Addition of U made by a group of three enzymes (E1, E2, E3)  E3 will transfer U to the protein to be degraded  Auxin transcription factors  Two types  Activator: auxin response factors (ARF) → transcription factors that regulate the expression genes in response to auxin by binding to their promoters and activating transcription  Repressor: AUX/IAA → repress transcriptioin  Can bind to ARF and inhibit ARF activity  Binding of auxin to its receptor induces the degradation of transcriptional repressors Lecture 22 : (Ethylene and Gibberellin)  Ethylene (C 2 H 4 )  Discovery  19 th^ century: coal gas used in street lights, trees nearby displayed premature leaf drop and senescence  1901: dark growth pea seedling exhibit the triple response  1910: ethylene produced by plants; emanations from orange caused premature ripening of bananas  Structure  Simple gas lighter than air  Can diffuse through air spaces of a plant  Acts locally  Biosynthesis  Can be produced by all parts of plants, but rate of production varies  Regulation of biosynthesis  Stress induced ethylene production  Fruit ripening  Auxin induces ethylene production by enhancing ACC synthase activity.  Regulation of biosynthesis by ethylene itself  Gene for ACC synthase is induced by ethylene. Once induced, the ethylene that it produces freeds back and further induces ACC synthase gene expression (pos feedback loop)  Ethylene produced by one plant can diffuse to another plant at a different developmental stage and prematurely induce the expression of ACC synthase – leading to ethylene production  As ACC increases, ethylene increases  Ethylene produces as plants rot  Inactivation  Conjugation: the ethylene precursor ACC can be conjugated → irreversible  Inactivation of ACC, which cannot be converted into ethylene  Ethylene degradation happens in plants but appears not to be important for the regulation of ethylene level  Roles in growth and development  Promotion of ripening of the fruits  Ripening: changes in fruit that makes it ready to eat  Softening of fruit due to enzymatic breakdown of cell wall  Two types of fruit  Climacteric: ethylene can induce ripening (apple, avocado, banana)  Non climacteric: no ripening response (citrus, grape, pineapple)  Induction lateral cell expansion

 Reduces rate of cell elongation and increases lateral expansion by changing orientation of microtubules of cell wall.  Results: triple response  Inhibition of shoot growth and swelling of shoot  Inhibition of root elongation  Exaggeration of curvature of apical hook  Enhancement of leaf senescence  Regulation of leaf abscission  Ethylene promotes abscission process  Auxin suppresses abscission process  Induction formation of roots and root hairs  Induction flowering in the pineapple family  Important commercial uses  Most used plant hormone in agriculture  Hastens fruit ripening of apple and tomato  Degreening of citrus fruits  Inducing fruit thinning or drop in cotton, cherry  Synchronizing flowering and fruit set in pineapple  Stores inhibit ethylene to preserve food  Ethylene Receptor  Five receptors in Arabidopsis  Related to bacterial two-components receptors (like cytokinin receptor)  Identified in a screen for insensitive mutants (no response to ethylene)  White: triple response in presence of ethylene  Mutant: no triple response  Receptors active in absence of ethylene (signal); binding of ethylene leads to inactivation (no signal)  Gibberellic  Discovery  1930’s-50’s: identification of the active compound produced by the fungus Gibberella fujikuroi  This fungus causes disease on rice that makes the plants grow very tall call “foolish seedling disease”  1958: first gibberellin identified  Defined by their chemical structure  Have been numbered as they have been purified and characterized  More than 136 compounds identified, but not all have biological activity  Ex. GA 1 and GA 3 are actives  GA 20 , GA 29 , GA 8 are not actives  Structure  19 or 20 carbon-containing compounds  Four rings  Structural modifications (insertion of additional functional groups and stereochemistry)  Structure is important for their bioactivity: GA are active only if structure allows the binding to receptor  Biosynthesis  Synthesized in seeds, shoots, and in growing vegetative tissues  Regulation of biosynthesis: several levels  GA biosynthesis enzymes (ex. GA 20-oxidase)  GA itself: GA inhibits GA biosynthesis & promote GA degradation (neg feedback)  Environment (ex. temperature and photoperiod): GA mediate the effects of environment signals  Inactivation  GA can be inactivated by conjugation to sugars: reversible  Active GA can be converted to inactive GA (reversible)  GA can be degraded (irreversible)  Roles of GA in growth and development  GA can stimulate stem growth

 GA influence floral initiation  GA promotes pollen development  GA promotes fruit set  GA promotes seed development and germination  Stem growth  GA promotes cell elongation (cell expansion like auxin)  GA increases both the extensibility and the stress relaxation of the cell wall  GA does not increase acidification of cell wall (like auxin does)  It is not clearly known how GA stimulates cell elongation but it appears that GA influences expansins  Cereal Aleurone Layer  Grain from cereal:  Embryo  Endosperm (starchy, aleurone layer)  Seed coat (fruit wall)  Starchy endosperm: cells with thin wall filled with starch (embryo can’t use starch)  Aleurone layer: cells with thick primary wall and contains large number of proteins-storing vacuoles; functions to synthesize and release hydrolytic enzymes into starchy endosperm during germination  Alpha and beta-amylases: degrade starch into glucose, used by embryo to grow  Synthesis and release of alpha and beta-amylases are under control of GA  Embryo synthesizes GA  GA moves into aleurone layer and induces the expression of alpha and beta-amylases  Hydrolytic enzymes are released in starchy endosperm and convert starch into glucose  Glucose is used by embryo to germinate and grow  GA receptor  Receptor was identified in rice in 2005: GID  Soluble cytoplasmic and intracellular  Responses to GA is based on degradation of repressors  Increased GA concentration = no starch degradation Lecture 23 : Flowering  Flowering  Propagation of species (seeds)  Agriculture: fruits, seeds  Goal: to understand the mechanism regulating flowering to improve plant development/yield  Vegetative and reproductive organs  Vegetative: root, stem, leaf  Reproductive: flower made of modified leaves  Shoot apical meristem: transition from producing leaf to flower depends on :  Endogenous regulation (circadian rhythms and hormones)  Environmental factors (cold treatment and day length)  Flower Initiation  Floral evocation: Events leading to commitment of shoot apical meristem to produce flowers  Flowers: initiated from the shoot apical meristem  Both flower and leaf are lateral organs but…  leaf primordial is an organ that will grow (cell division and elongation)  Floral primordial is a meristem (floral meristem)  Same organization as shoot apical meristem (zonation organization)  Formation of lateral organs: continuous  Determinate meristem: make a fixed number of lateral organs=floral organs  Floral meristem: determinate meristem  Floral: stem cells are used to form lateral organ and then they die (not resued)  Shoot apical: reused  Arabidopsis flower:

 4 sepals  4 petals  6 stamens  2 fused carpels  Floral organs  May have a spiral phyllotaxy but usually occur in whorls (when 3+ lateral organs are attached at same level)  ABC Model of floral development (1991)  Floral organ identity is controlled by homeotic or organ identity genes  Organ identity in each whorl is determined by unique combination of the activities of three organ identity genes  Activity A alone → sepal  Activity A and B → petal  Activity B and C → stamen  Activity C alone → carpel  Floral evocation  Events leading to the commitment of shoot apical meristem to produce flowers  Time to flowering varies among species  Some annual species may flower within weeks of germination  Some perennials species (trees) may grow for 20 years before flowering  Different responses from plant species  Regulated by internal and external clues  Depending of the importance of these clues on the regulation of flowering  Autonomous regulation: flowering only depends on internal clues  Obligate response to environment: flowering depends on environmental clues  Facultative response to environment: flowering is promoted by environmental clues but will occur still w/o  Tight control of flowering time:  Flowering at the optimum time for reproductive success  Synchrony of flowering for crossbreeding  Phase changes  Juvenile vegetative phase → adult vegetative phase → adult reproductive phase → flowering  Associated with the phase change is different organ morphology (ex. leaf)  Transition from different phases:  Nutriments: carbohydrate supply reduction of the amount of light (reduction of photosynthesis and sugar produced) can lead to reversion to juvenile phase  Gibberellic acid: treatment with GA promotes phase transition (conifer family)  Two stages of floral evocation  Shoot apical meristem that produces vegetative organs  Competence: plant is able to flower when given the right signal; the shoot apical meristem still produces vegetative organs  Determination: the shoot apical is set to flower even if you removed it from the plant  External Clues regulating flowering  Photoperiod (day length)  Cold (vernalization)  Photoperiodism  Ability of an organism to detect day length  Allows a seasonal response  Two types of flowering plants  Short-day: flowering only in short day(obligatory short day) or short day accelerate flowering (facultative short day)

 Long-day: flower only in long day (obligate long day) or long day accelerate flowering (facultative long day)  Critical day length  Long day: flowering promotes when day length exceeds the critical day length  Short day plants: flowering promotes when day length is shorter the critical day length  Plants measure the length of night: night breaks  Leaves are the site of perception of the photoperiodic signal  Production and transmission of a floral signal or floral stimulus or florigen to the shoot apical meristem resulting  Florigen is transported by phloem  After more than 70 years of research, the florigen was identified the mRNA of the gene FT (kinase inhibitor)  Vernalization  Process leading to the promotion of flowering by a cold treatment of either hydrated seeds or growing plants  Effective temperature and length (depends on plant species) 2⁰C to 10⁰C for several weeks  Results in the competence of the shoot apical meristem to flower  Plants, which require vernalization to flower, display delayed flowering or only production of leaves without this treatment