• Stomatal Biology

• Guard cells change their size and

shape in response to internal and
external stimuli
– Results in alteration of stomatal
aperture
– Pore size is regulated by uptake and
release of water to change turgor
pressure
• Aerial leaves typically have most
stomates interspersed on lower
(abaxial) surface, but often on
upper (adaxial) surface as well
• Floating leaves lack stomates on
abaxial side
• Figure 10.1 Light-stimulated
stomatal opening in detached
epidermis of Vicia faba
• Stomatal aperture follows
photosynthetically active
radiation at the leaf surface

• Light mediates stomatal aperture

• Photosynthetic component
– Can be opened partially by red light
– inhibited by DCMU’s competition
in the e- transport chain
– CO2-depletion effect can be
eliminated by using epidermal peels
• Specific blue light component
– Co-irradiation after saturating
photosynthetic response allows
separation of the two effects
 – Reversible
– Guard cell-specific irradiation
• Figure 10.3 Response of stomata
to blue light under a red-light
background
• Figure 10.4 Action spectrum for
blue light–stimulated stomatal
opening (under a red-light
background)

• Isolated guard cell protoplasts

swell in blue light, which allows
study of mechanism
– Water uptake driven by ion uptake
and the resulting lower Ψs
– Sensitive to poisoning of PM H+-
ATPase by orthovanadate
• Figure 10.5 Blue light–stimulated
swelling of guard cell protoplasts
• Figure 10.6 Acidification of a
suspension medium of guard cell
protoplasts of V. faba stimulated
by a 30-s pulse of blue light
• Figure 10.7 Activation of the H+-
ATPase at the plasma membrane
of guard cell protoplasts by
fusicoccin and blue light can be
measured as electric current in
patch clamp experiments
• At least three separable
osmoregulatory pathways in
guard cells
 – Proton pumping drives uptake of K+
and Cl- ions, and malate2- produced
from starch metabolites
– Sucrose accumulation from starch
metabolism
– Sucrose production from
photosynthetic carbon fixation
• Figure 10.8 Three distinct
osmoregulatory pathways in
guard cells (Part 1)
• Figure 10.8 Three distinct
osmoregulatory pathways in
guard cells (Part 2)
• Figure 10.8 Three distinct
osmoregulatory pathways in
guard cells (Part 3)
• Sucrose and K+ (and counterions
Cl-/malate2-) act together to
provide the more negative Ψs for
water uptake
– Circadian change in major
component:
– K+ is primarily responsible for
opening, while decrease in sucrose
is responsible for closing
• Figure 10.9 Daily course of
changes in stomatal aperture, and
in potassium and sucrose content,
of guard cells from intact leaves
of broad bean (V. faba)
• Multiple Blue-light receptors
• One of the receptors regulating Blue-
specific opening is the carotenoid
zeaxanthin
 – npq1 mutants lack low intensity
component of closing in some plants
– Reducing agent dithiothreitol (DTT)
enhances accumulation of zeaxanthin and
sensitivity to blue light
– phot1/2 mutants also have reduced
opening
• Action spectra consistent with both
carotenoid and flavin receptors
• Zeaxanthin accumulation tracks
sensitivity to blue light

• Figure 10.10 Blue-light

sensitivity of the zeaxanthinless
mutant npq1 and of the
phototropin-less double mutant
phot1/phot2
• Figure 10.11 Zeaxanthin content
of guard cells correlates with
 photosynthetically active
radiation and stomatal apertures
• Figure 10.12 Absorption
spectrum of zeaxanthin in ethanol
• Figure 10.13 Role of zeaxanthin
in blue-light sensing in guard
cells

• Blue light pulse-induced opening

is reversed/suppressed by a
subsequent green light pulse
• phot1/phot2 have a significant
effect on regulating the decreased
aperture response to green
• Figure 10.14 Blue/green
reversibility of stomatal
movements
• Figure 10.15 Green light
regulates stomatal apertures in the
intact leaf
• Figure 10.16 Action spectrum for
blue light–stimulated stomatal
opening and for its reversal by
green light

• Photobiology/Photophysiology
are powerful tools for
understanding light receptors,
signaling pathways, and responses
 – Action spectra, reversibility,
lag/escape times, fluence
responsiveness
– Genetic experiments (e.g. mutants,
transgenics)
– Pharmacological agents (DCMU,
DTT, CCCP, orthovanadate, CN-)

• However…
– Confounding factors (e.g. screening
pigments, alternative explanations)
– Pleiotropic effects of gene
mutations (zeaxanthins also act in
photoprotection and as antennae
pigments, and hormone ABA
derived from violaxanthin)
– Reagents often have multiple effects
(e.g. reducing agents like DTT;
Altering H+-ATPase will affect
 many transport pathways, pH
responses, etc.)

LECTURE 11
Phloem loading and transport
How do the products of photosynthesis travel from sites of carbon fixation
to sites of carbon and energy utilization and storage?

Phloem
Phloem anatomy
Phloem
Phloem sieve elements conduct material
• Sieve tube elements (angiosperms)
• Sieve cells (gymnosperms)
Companion cells (support sieve element functions)
Parenchyma (uptake, storage, release of food)
Sclereids/sclerenchyma (strength, support, protection)
Laticifers (latex conduits)
Bundle sheath surrounding vascular tissue (not just in C4 plants)
1º and 2º phloem
10.1 Transverse section of a vascular bundle of trefoil, a clover ( Trifolium)

10.2 Transverse section of a 3-year-old stem of an ash (Fraxinus excelsior)

tree

Phloem anatomy
Phloem sieve tube elements are living at maturity
Relatively few organelles (lack nuclei, vacuoles)
Few ribosomes, cytoskeletal elements
Thickened primary cell wall, but no lignified secondary cell wall
Sieve plate (angiosperms) and lateral sieve areas
10.3 Schematic drawings of mature sieve elements (sieve tube elements)
Transverse section of ordinary companion cells and
mature sieve tube elements
10.5 Sieve elements and open sieve plate pores
Sieve plate pores between sieve tube elements can be
very large
(1-15 μm)
10.6 Electron micrograph of a sieve area (sa) linking two sieve cells of a
conifer (Pinus resinosa)
Gymnosperm sieve areas have much smaller pores; no
sieve plates

Pores are not open, but occluded and traversed by

smooth ER

No P-proteins
Phloem protection
Angiosperm P-proteins are diverse proteins that clog pores when turgor
released rapidly
Wound callose (β-1,3-glucan) is produced to seal pores of functional sieve
tube elements from damaged cells

Companion cells
Tightly linked through numerous complex plasmodesmata to adjacent sieve
tube element
Perform many of the metabolic functions of the organelle-deficient sieve
tube elements
Three basic types:
Ordinary companion cells
 • Plasmodesmata almost
exclusively to sieve tube
elements
• Chloroplasts
10.7 Electron micrographs of companion cells in minor veins of mature
leaves (Part 1)

Companion cells

Transfer cells
• Similar to ordinary companion
cells
• Cell wall invaginations yielding
increased PM surface area
• Transfer from apoplast (cell wall
space) to symplast/phloem
10.7 Electron micrographs of companion cells in minor veins of mature
leaves (Part 2)

Companion cells

Intermediary cells
 • Abundant plasmodesmata
connections to bundle sheath
cells
• Poorly developed chloroplasts

The companion cell types may be emphasized differently in different

tissues or species
10.7 Electron micrographs of companion cells in minor veins of mature
leaves (Part 3)

Phloem links sources to sinks

Photosynthate sources

Sites of net export

• Mature leaves
• Storage tissues during some
phases of development
Photosynthate sinks

Sites of import
• Rapidly growing regions
(meristems, young leaves)
• Non-photosynthetic tissues
(roots, floral organs, fruits)
 • Storage tissues during some
phases of development
10.8 Source-to-sink patterns of phloem translocation
--Proximity may determine which sources feed which
sinks
--Development may shift source-sink relationships
--Source-sink connections may follow direct
connections along the plant body
--Vascular interconnections (anastomoses) can
circumvent blockages or wounds
Phloem sap
Collected through aphid stylets and analyzed:
Sugars (especially sucrose and non-reducing di-, tri- and small oligo-
saccharides)
Amino acids (especially Glu, Gln, Asp, Asn) and other nitrogenous
compounds
Organic acids, mineral nutrients and ions
Hormones
Proteins & RNA (regulatory, defense, stress responses)

10.9 Structures of compounds both not normally and commonly

translocated in the phloem (Part 1)

10.9 Structures of compounds both not normally and commonly

translocated in the phloem (Part 2)

10.9 Structures of compounds both not normally and commonly

translocated in the phloem (Part 3)

Phloem movement
Much too fast for diffusion—bulk flow required
Pressure flow model
 Driven by differences in osmotic pressure between sources and sinks
Phloem loading and accompanying water uptake at source
Phloem unloading and reduced osmotic potential at sink
10.10 Pressure-flow model of translocation in the phloem

10.11 Translocation in living, functional sieve elements of a leaf (Part 1)

10.11 Translocation in living, functional sieve elements of a leaf (Part 2)

Leaf vein architecture

Phloem loading
Transport of photosynthates from mesophyll to sieve tube elements:
Chloroplasts to cytosol as triose phosphates
Conversion to hexose phosphates and then to sucrose (fructose +
glucose) in the cytosol
Short-distance transport of sucrose to small veins
Concentration in the companion cells and sieve elements
Export and long-distance transport to sinks
Symplastic vs. Apoplastic loading is species-specific
10.14 Schematic diagram of pathways of phloem loading in source leaves
(Part 1)

10.14 Schematic diagram of pathways of phloem loading in source leaves

(Part 2)

10.15 Labeled sugar moves from the apoplast into sieve elements and
companion cells
Sucrose is actively transported into the phloem
Phloem loading is product specific

10.16 ATP-dependent sucrose transport in sieve element loading

Active sucrose transport involves a H - +

ATPase and a H+-sucrose symporter

 (AtSUC2) for uptake from the apoplast to
the symplast
Phloem loading
In species utilizing the symplast pathway, the polymer-trapping model
explains net movement into the phloem
Sucrose from mesophyll diffuses into intermediate cells
Addition of galactoses (e.g. raffinose, stachyose) prevent them from
diffusing back
These larger sugars (as well as sucrose) can diffuse into the phloem
and move by bulk flow down the sieve tubes
10.17 Polymer-trapping model of phloem loading

Phloem unloading
Sugars move from phloem to sink tissues
Short-distance transport into and through local cells may be symplastic or
apoplastic
Storage/metabolism in the sink tissue cells
Requires energy
10.18 Pathways for phloem unloading and short-distance transport

Source-sink
relationships change
Sinks may gradually transition to sources
Young leaves to mature leaves
Storage organs
10.19 Autoradiographs of a leaf of summer squash ( Cucurbita pepo)
Developmental transition from sink to
source
10.20 Division of labor in the veins of a tobacco leaf
Different sets of veins are used for unloading (as a
sink) versus loading (as a source)
Immature (sink) minor veins not used for
unloading
Minor veins mature (source) and can be used for
export.
Figure 10.21 Export from source tissue depends on active sucrose
transporters
Sugar allocation

In sources, fixed carbon may be

allocated for
Storage
Metabolism
Export
Sources regulate allocation to storage
or export via triose phosphate/Pi
chloroplast antiporter and
regulation of starch- and sucrose-
synthesizing enzymes
In sinks, imported sugars may be
allocated for metabolism or storage
Determination of which sink tissues
receive photosynthates is
partitioning
10.21 A simplified scheme for starch and sucrose synthesis during the day

Photosynthate partitioning
Regulated dynamically via complex mechanisms
Sink strength (size and activity)
Turgor
Overall sucrose levels
Hormones
Gene expression (sucrose metabolism, transporters, etc.)
Other molecules move in the phloem stream
Proteins (e.g. pathogenesis-related proteins)
RNAs (mRNAs, small gene-silencing miRNAs, pathogen RNA,
ribonuclear proteins)
Hormones, remobilized minerals, etc.
10.22 GFP fluorescence in source and sink leaves from transgenic
Arabidopsis plants
SUC2 promoter-driven expression of GFP in source
and sink leaves shows plasmodesmatal
movement of protein from source to sink tissues

LECTURE 12
Respiration and Fatty Acid Metabolism
What do plants do when light is not available for photosynthesis?
Respiration [glycolysis, Oxidative Pentose phosphate shunt,
Citric Acid (Krebs) Cycle]
Products for Calvin cycle
 NADH, FADH2, and ATP
Lipid metabolism
Respiration
Glucose equivalents (sucrose, triose phosphates, fructans, lipids,
etc.) oxidized to form CO2 and H2O
Glycolysis oxidizes sugars, via hexose phosphates and
triose phosphates, to organic acids (e.g. pyruvate) and yields
NADH and ATP
Oxidative pentose phosphate pathway uses glucose
phosphate to yield ribulose 5-phosphate and NADPH, then
various interconvertible sugars
Citric Acid (Krebs) Cycle breaks pyruvate down to CO2 and
yields NADH and FADH2
Electron transport chain and oxidative phosphorylation
reduces O2 to water, producing ATP and NAD+
12.1 Overview of respiration
12.2 Structures and reactions of major electron-carrying
cofactors (Part 1)

12.2 Structures and reactions of major electron-carrying

cofactors (Part 2)

Reactions of plant glycolysis and fermentation (1)

12.3 Reactions of plant glycolysis and fermentation (Part 2)

12.3 Reactions of plant glycolysis and fermentation (Part 3)

12.4 Reactions of the oxidative pentose phosphate pathway in

higher plants
The Oxidative Pentose phosphate shunt occurs in
the cytosol and especially plastids
-alternative to glycolysis
 -Supplies NADPH for redox and respiration
reactions
-produces substrates for biosynthetic pathways
and Calvin cycle
-Primarily occurs in the dark

-Many of the same enzymatic carbon-shuffling

processes and intermediates involved in the
Regeneration phase of the Calvin Cycle
12.5 Structure of plant mitochondria
The Citric acid (TCA) cycle occurs in mitochondria
-pyruvate transported into mitochondrial matrix
12.6 Reactions and enzymes of the plant citric acid cycle
12.7 Malic enzyme and PEP carboxylase provide plants with
metabolic flexibility (Part 1)

12.7 Malic enzyme and PEP carboxylase provide plants with

metabolic flexibility (Part 2)

12.7 Malic enzyme and PEP carboxylase provide plants with

metabolic flexibility (Part 3)

Electron transport
Complex I, NAD(P)H
dehydrogenases, and Complex II
feed electrons to a pool of
ubiquinones
 Complex I pumps 4 H+ out of the matrix
for each e- transferred
Ubiquinone passes e- to Complex III
and, via Cytochrome c, on to
Complex IV
Both complexes pump H+ out of the
matrix
Complex IV uses O2 as the e- acceptor
to produce H2O. Poisoned by cyanide.
The alternative oxidase can also accept
e- from ubiquinone to reduce O2 to H2O,
but does not have the accompanying H+
transport. Inhibited by SHAM
ATP synthase (complex V) functions
like the chloroplast ATP synthase,
but is driven more by charge
difference (ΔE) than H+ gradient.
NADH and NADPH are oxidized as the source of e- .
NAD(P)+ reduced by Glycolysis, Krebs cycle, PSI
Figure 12.10 Transmembrane transport in plant mitochondria
Aerobic respiration
Yields approximately 60 ATP per sucrose
 52 from oxidative phosphorylation via 20 molecules
NAD(P)H and 4 FADH2 molecules
8 from substrate-level phosphorylation
Represents 52% energy efficiency (vs. 4% from
glycolysis/fermentation)
Plant mitochondria
Genome is much larger than in animals and fungi
RNA splicing occurs on a limited basis
RNA editing occurs (~ C  U)
RNA stability signals differ
Use the universal genetic code (unlike other organisms’
mitochondrial genomes)
Plants can decrease efficiency
Why?
Energy may not be limiting
Plasticity for use of metabolites may be
more important
Alternative oxygenase reduces O2 to
water, siphoning off excess electrons
and producing heat
Stresses that increase Reactive Oxygen
Species (ROS) activate alternative
oxygenase to prevent overreduction
Uncoupling protein relieves the H+
gradient without producing ATP
Non-proton-pumping NADH
dehydrogenases when ADP is
limiting
ADP and Pi are major regulators of
respiration
Figure 12.11 Metabolic interactions between mitochondria and
cytosol
11.11 Metabolic regulation of pyruvate dehydrogenase (PDH)
activity
Regulatory kinases and phosphatases control
Pyruvate dehydrogenase, coupling energy status
and metabolites to activity

Thioredoxins alter S—S bridges to regulate

enzymes according to redox status

11.12 Concept of bottom-up regulation of plant respiration

Allosteric “bottom up” regulation of
pathways by ADP and by metabolic
products allows for fine control of
respiration and use of metabolites for
biosynthetic pathways
Figure 12.14 Glycolysis, the oxidative pentose phosphate shunt,
and the citric acid cycle contribute precursors to many
biosynthetic pathways in plants
Plants respire even during photosynthesis
Metabolism of photorespiratory products (e.g. glycine to serine
conversion, N recovery)
Non-photosynthetic/sink tissues
Provide substrates for numerous biochemical reactions, e.g.
2-oxoglutarate for nitrogen assimilation
NADH production

Lipids in plants
Triacylglycerols
Storage fats and oils
High metabolic energy content
Polar glycerolipids
Membrane components

11.14 Structural features of triacylglycerols and polar

glycerolipids in higher plants
Oils and Fats
Oils often contain unsaturated fatty acid chains
Remain liquid at room temp
Stored in oleosomes with a half lipid bilayer
Fats generally have saturated straight-chain fatty acids
Produced in the ER and accumulate between the bilayer layers
until an oleosome (oil body) buds off
Abundant in seed cotyledons and endosperm

Fatty acid chains

Polar glycerolipids
Primary membrane structural lipids
Glyceroglycolipids
Sugar head group
Abundant in chloroplast membranes
Glycerophospholipids
Phosphate on head group
 Sphingolipids, sterols, and other lipids are also membrane
components
Plastoquinones, chlorophylls, carotenoids, tocopherols
involved in photosynthesis and other functions
Very abundant in photosynthetic tissues

11.15 Major polar lipids of plant membranes (Part 1)

11.15 Major polar lipids of plant membranes (Part 2)

Fatty acid metabolism

Sequential addition of 2C acetyl in plastids
Condensation reaction with Malonyl-ACP (acyl-carrier
protein) results in decarboxylation and addition of 2C at each
sequential step
Major products are 16:0- or 18:0-ACP and, after modification by a
desaturase, 18:1-ACP
May be further desaturated to 16:3 and 18:3 fatty acids in
chloroplasts and ER
Fatty acid metabolism
Lipid components alter membrane characteristics
Desaturation maintains fluidity at lower temperatures
Different lipids affect other membrane functions
Lipids and metabolites serve as signals
PIP2 (phosphatidyl inositol 4,5-bisphosphate) breaks down to
IP3 and DAG (diacylglycerol)
11.16 Cycle of fatty acid synthesis in plastids of plant cells
Figure 11.17 The two pathways for glycerolipid synthesis

Fatty acid metabolism

Breakdown of fatty acids yields numerous metabolites including
sugars
Triacylglycerols from lipase action on oils enter glyoxysomes
(specialized peroxisomes)
 Serial β-oxidations produce Acetyl-CoA for the glyoxylate
cycle to yield succinates for conversion to malate in the
mitochondria
Malate is converted through oxaloacetate to PEP, and to
sucrose

Figure 12.19 Conversion of fats into sugars during germination in

oil-storing seeds (Part 1)
Figure 12.19 Conversion of fats into sugars during germination in
oil-storing seeds (Part 2)

LECTURE 13
Assimilation of Mineral Nutrients
Nitrogen
Sulfur
Phosphate and cations
Nitrogen
Complex biogeochemical cycle
Extremely energy expensive process to assimilate
Atmospheric N≡N into ammonium (NH4+) costs 16 ATP per N
via bacterial nitrogen fixation
Nitrate (NO3- ) to Nitrite (NO2-) to NH4+ to glutamine requires
12 ATP/N
12.1 Nitrogen cycles through the atmosphere

Nitrogen assimilation
Nitrate uptake via low affinity and high affinity receptors in the root
Nitrate reductase uses reduced NAD(P)H to drive reduction of
NO3- to NO2-
Molybdenum complex, heme, and Flavin adenine
dinucleotide (FAD) domains
Nitrate reductase dimers use e- from NAD(P)H and protons to
reduce nitrate (NO3-) to nitrite (NO2-) + H2O
Nitrate reductase step
integrates various
factors
Light, nitrate concentration, and carbohydrate availability increase
NR transcription
Circadian regulation
Post-translational phosphorylation by a kinase recruits a 14-3-3
inhibitor protein that inactivates NR in darkness
Light, sugars, and nitrates dephosphorylate NR to restore
activity

12.4 Stimulation of nitrate reductase activity

Nitrite reductase
Nitrite is highly reactive
Reduction of NO2- to NH4+ occurs in plastids via nitrite reductase
using the reducing power of 6 reduced ferredoxins
Upregulated gene expression by light and nitrate
Downregulated transcriptionally by Gln and Asn
Nitrate assimilation
occurs in roots and
shoots
Varies enormously by species and environmental conditions
Nitrate is tolerated to high concentrations in plants, so can be
readily transported
12.6 Relative amounts of nitrate and other nitrogen compounds
in xylem sap

Ammonium metabolism
The Gln synthetase (GS) and Glu synthase (GOGAT) pathways
are present in cytosol and plastids, and regulated differently by
light and carbohydrates
Root GS forms glutamine for transport, root plastid GS as a
source of metabolic N amide substrates, chloroplast GS for
removing photorespiratory NH4+
Different GOGAT enzymes use NADH or Fdred
12.7 Structure and pathways of compounds involved in
ammonium metabolism (Part 1)

Figure 8.8 Operation of the C2 oxidative photosynthetic cycle

Ammonium scavenging as shown in the photorespiratory
pathway
-Preserves nitrogenous compounds
 -Protects the cell from NH4+-induced proton gradient
abolition
Ammonium metabolism
The Glu dehydrogenase (GDH) pathway uses NAD(P)H in
mitochondria and chloroplasts to assimilate NH4+
Primarily for reallocation of N among different pools
13.7 Structure and pathways of compounds involved in
ammonium metabolism (Part 2)

Ammonium metabolism
Transamination reactions interconvert amine carriers for amino
acid and metabolic intermediate syntheses
12.7 Structure and pathways of compounds involved in
ammonium metabolism (Part 3)

Ammonium metabolism
Amino acids, especially Gln and Asn, are used for transport of
organic N compounds
Relative activities of Asn synthetase (AS) and GS/GOGAT
pathways balance N and C assimilation pathways
Abundant carbohydrates or light favor Gln (2N/5C; via
GS/GOGAT upregulation and AS inhibition) and thus rapid
incorporation into new growth
Limiting carbon or energy favor Asn (via AS) as storage and
transporter (2N/4C)
12.7 Structure and pathways of compounds involved in
ammonium metabolism (Part 4)

Amino acid metabolism

Unlike mammals, plants can synthesize all 20 essential amino
acids for protein synthesis
Carbons from glycolysis (3PG, PEP, pyruvate) or the citric acid
cycle (oxaloacetate,
α-ketoglutarate (2-oxoglutarate)) are transaminated from Gln or
Glu
13.8 Biosynthetic pathways for carbon skeletons of the 20
standard amino acids
Nitrogen Fixation
Major source of conversion from atmospheric N2 to NH4+
Fixation occurs in free-living bacteria (largely cyanobacteria) and
symbiotic bacteria
Symbioses may involve simple associations
Azolla and Anabaena
Apoplastic associations of N fixers with grasses
Complex associations
actinorhizal association of Alder with Frankia
legumes with rhizobia such as Rhizobium
Nitrogen fixation
Highly energy-rich intermediates are susceptible to damage from
O2
Nitrogenase enzyme must remain anaerobic
Heterocysts in cyanobacteria
Root nodules

13.10 A heterocyst in a filament of the nitrogen-fixing

cyanobacterium Anabaena
Root nodules
Protect nitrogenase from oxygen
Physical barriers
Leghemoglobin carries respiratory O2 for bacteroid
respiration, accepting e- in a high-affinity oxidase at the end
of the e- transport chain
Allow ready access of carbohydrates to N fixers
Produced by complex “dance” of microbe and host plant
13.9 Root nodules on soybean

Root nodule formation

Host legume recognizes the bacterial
Nod factor via sugar-binding Lys-
motif receptors/kinases on the root
hairs
Ca2+ oscillations
Ca2+/Calmodulin-dependent protein
kinases (CaMK) promote transcription of
Nod factor-inducible genes
initiates infection and nodule
primordium formation
Cytokinin-dependent inhibition of auxin
transport induces nodule cell division
and morphogenesis

Root nodule formation

Plant host nodulin (Nod) gene products and bacterial symbiont
nodulation (nod) gene products interact in signaling and
establishing nodules
Rhizobia migrate toward flavonoid chemical signals from
host roots
These signals induce rhizobial nodD activation, which
upregulates other nod genes
 These nod genes code for enzymes that make lipochitin
oligosaccharide nod factors
Plant specificity comes from fatty acyl chain length and
saturation and modification of the chitin

13.11 Nod factors are lipochitin oligosaccharides

Root nodule formation

Rhizobial Nod factors induce nod-factor-inducible genes,
curling of root hair tip, enclosing bacteria
Localized degradation of cell wall allows bacteria-plant PM
contact
Plant PM invagination forms growing infection thread, while
root cortex cells divide and re-differentiate into a nodule
primordium
Infection thread full of rhizobia grows toward nodule
primordium
13.12 The infection process during nodule organogenesis (Part
1)

13.12 The infection process during nodule organogenesis (Part

2)

Root nodule formation

Infection thread full of rhizobia grows toward nodule primordium
Branching
Fusion with PM
Bacteria differentiate into bacteroids in the nodule, but
remain within plant PM-bounded vesicles (peribacteroid
membrane)
Nodule differentiates to minimize O2, and to extend
vascularization for fixed N export and C uptake
13.12 The infection process during nodule organogenesis (Part
3)
Nitrogenase complex
fixes N2
Fe and MoFe components catalyze:
N2 + 8e-+ 8H++ 16 ATP →
2NH3+ H2+ 16 ADP+ 16 Pi
Electrons come from reduced ferredoxin
O2 can damage both components of the complex
Nitrogenase makes up an enormous fraction of the total bacteroid
protein

13.13 The reaction catalyzed by nitrogenase

Fixed nitrogen is
exported in xylem
Form is species-dependent
Amides (e.g. Asn, Gln) in temperate-originating species
Ureides (allantoic acid, allantoin, citrulline) in tropical-origin
spp
Sulfur assimilation
-2
Primarily absorbed as sulfate (SO ) 4
+ -2
by root H - SO symporter, and
4
assimilated in the leaves.
SO4-2 is reduced to cysteine via
activation to adenosine-5’-
phosphosulfate (APS), then reduction
to sulfite (SO3-2) and then to sulfide
(S-2) for reaction with O-acetylserine
to produce Cys
Some Cys used to synthesize Met
and other derivatives
Export from the leaves as reduced
glutathione (GSH) or oxidized dimer
(GSSG)
13.15 Structure and pathways of compounds involved in sulfur
assimilation

Glutathione (GSH)
Three-amino acid peptide
Oxidized form is a dimer through a disulfide bridge between
cysteine residues (GSSG)
Phosphate assimilation
Primarily absorbed as phosphate (HPO4-2) by root H+- HPO4-2
symporter.
Assimilated into ATP and subsequently transferred to many
substrates
Cation assimilation
Coordination bonds are non-covalent associations of organic
carbon compounds with polyvalent cations
Cation loses positive charge through donation of unshared O
or N electrons from coordinating compounds
Electrostatic bonds are non-covalent attractions between positive
cation and negatively charged groups
Charges are maintained

Figure 13.16 Examples of coordination complexes

12.17 Examples of electrostatic (ionic) complexes

Iron assimilation
Iron is relatively insoluble in soil
Plants use:
soil acidification (root H+ export) to
increase Fe3+ and Pi solubility
reduction of ferric Fe3+ to more soluble
ferrous Fe2+ form, along with Fe2+
transporters
iron chelation with malate, citrate,
phenolics, and other compounds
Grass siderophores chelate Fe3+ and have siderophore-
Fe3+ transporters
3+
Transported as Fe -citrate complex
for insertion into heme precursors or
non-heme FeS proteins
Figure 13.18 Two processes through which plants roots absorb
iron
13.19 The ferrochelatase reaction

13.20 Examples of the two types of oxygenase reactions in cells

of higher plants (Part 1)
Oxygen assimilation:
-Mostly through respiration
-Dioxygenase reactions use both oxygens of O2 to
add to organic compounds
13.20 Examples of the two types of oxygenase reactions in cells
of higher plants (Part 3)
Monooxygenase reactions use one O from
molecular O2 for organic synthesis and the other for
water
Photoassimilation
Assimilation of nutrients is energetically expensive
N fixation can consume up to ¼ of the energy used in the
plant
In C3 plants, photoassimilation uses excess reducing power
and ATP from light reactions to assimilate N in chloroplasts
Abundant CO2 inhibits photoassimilation so reductant is
used in the carbon fixation cycle
Figure 13.20 Summary of the processes involved in the
assimilation of mineral nitrogen in the leaf

LECTURE 14
• Plant cell walls
• Complex structures involved in
– Structure and strength
– Water relations
– Development and morphogenesis
– Defense
• Figure 15.1 Cross-section of a
stem of a buttercup (Ranuculus
repens)
• Figure 15.3 Diversity of cell wall
structure

• Cell walls
• Primary cell wall
– Laid down by growing cells
– Relatively Simple
– Extensible
• Secondary cell wall
 – Laid down largely after growth
ceases
– Internal to 1° cell wall
– May be highly complex,
multilayered
• 15.2 Two views of primary cell
walls
• 15.3 Outer epidermal cell wall
from the growing region of a bean
hypocotyl
• Primary cell walls can also be heavily thickened, and
may differ in morphology across a single cell
• Cell walls
• Primarily consist of sugar
polymers
– Cellulose
– Matrix polysaccharides
• Pectins (extractable with boiling water
or Ca2+ chelators)
 • Hemicelluloses (extractable with hot
NaOH)
• Proteins
• Phenolic lignins and other
components
• Table 14.1 Structural
components of plant cell walls
• 15.5 Conformational structures
of sugars commonly found in
plant cell walls (Part 1)

• 15.5 Conformational structures

of sugars commonly found in
plant cell walls (Part 2)
• (1→4)β-D-glucans
• 15.6 A structural model of a
cellulose microfibril (Part 1)
• Cellulose microfibrils
•
• -Semi-crystalline with abundant H-bonding

-Extremely strong
-inaccessible to
enzymatic attack
-high tensile
strength
• -Crosslinked by matrix polysaccharides and proteins
• 15.6 A structural model of a
cellulose microfibril (Part 2)

• 15.7 Cellulose synthesis by the

cell (Part 1)
• Cellulose microfibrils are constructed on
“rosettes” at the plasma membrane
• -Cellulose synthase (CesA) family
complexes arranged into trimeric to
hexameric subunits, which combine to make
a rosette
• -Construct β-(1-4)-glucans by addition of
UDP-glucoses
• -Associated with microtubules inside cell
membrane
• Figure 14.7 Cellulose
microfibrils are synthesized at the
cell surface by membrane-bound
complexes containing cellulose
synthase (CESA) proteins
• 15.8 Model of cellulose synthesis
by a multisubunit complex
containing cellulose synthase
• Sugar-nucleotide donor
(UDP-Glucose) provides sequential addition of glucoses to
cellulose synthase

• Sterol glucoside may act as “primer” for the glucan chains of

cellulose
• Major structural components of
the primary cell wall and their
likely arrangement
• Matrix polysaccharides
• Produced by glycosyltransferases
in Golgi
• Delivered by exocytosis to the
cell wall

• Hemicelluloses and Pectins

• 15.11 Partial structures of the
most common pectins (Part 1)
• Pectins
• -From fairly simple to very complex and
variable
• -Form soluble hydrophilic gel in cell wall
• -Porosity limits movement of some
macromolecules in the apoplast
• -May bind borate covalently or form ionic
bonds with Ca2+ ions
• 15.11 Partial structures of the
most common pectins (Part 2)
• 15.11 Partial structures of the
most common pectins (Part 3)

• Figure 15.13 Linear arrangement

of various pectin domains to each
other
• Pectins of different types may be linked into long
chains…
• Hemicelluloses
• Linear matrix polysaccharides
with short branches
– Often very long backbones
– Associate tightly with cellulose
• may bind microfibrils together or
• may prevent binding to add
flexibility
• 15.10 Partial structures of
common hemicelluloses (Part 1)
• Xyloglucans are the most abundant hemicelluloses in most
plant groups’ primary cell walls
• -Glucan backbone with attached xylose sidechains
• -Link celluloses together and to other matrix components
• Figure 14.11 Partial structures of
the major hemicelluloses (Part 3)
• Figure 14.11 Partial structures of
the major hemicelluloses (Part 4)
• 15.14 A repeated
hydroxyproline-rich motif from a
molecule of HRGP from tomato
• Cell wall matrix proteins include structural
repeat motifs
• -Hydroxyproline-rich glycoproteins (HRGP)
• -proline-rich proteins (PRP)
• -glycine-rich proteins (GRP)
• 15.15 A highly branched
arabinogalactan molecule
• Arabinogalactan proteins (AGP) may be involved in
developmental signaling and embryogenesis
• New cell walls form
at the cell plate
• Directed by the phragmoplast
(microtubules and membrane
vesicle aggregates)
• Cell walls may form by self-
assembly or by enzyme-mediated
assembly
– self aggregation does occur
– form incomplete cell walls without
additional enzymes such as
Xyloglucan endotransglycosylases
(XETs)
– XETs cut and rejoin xyloglucan
backbones
• Xyloglucan
endotransglucosylases (XET) cut
and join xyloglucan polymers into
new configurations
• Cell wall growth
• As cells grow, cell walls thin and
new material must be added to
retain structural integrity
• Enzymes (such as XET, pectin
methylesterases, glycosylases)
allow integration of new material
into the existing wall;
• expansins allow cellulose
microfibrils to “slide” with
respect to one another

• Cell growth
• Cells can grow by tip growth (e.g.
root hairs, pollen tubes) or by
diffuse growth (most plant cells)
• Expansion of cells depends on
microfibril orientation and cell
wall characteristics
– Isotropic (random) vs. anisotropic
orientation
– Cortical microtubules control where
cellulose microfibrils are deposited

• 15.19 The cell surface expands

differently during tip growth and
diffuse growth

• 15.20 The orientation of newly

deposited cellulose microfibrils
• Cell growth
• Direction and location of cortical
microtubules guiding cellulose
deposition
– Rho-like GTPases (ROPs) activated
by RICs initiate microtubule
formation in specific locations to
orient growth
– Allows complex cellular growth
patterns

• 15.21 Interdigitating cell growth

of leaf pavement cells (Part 1)

• 15.21 Interdigitating cell growth

of leaf pavement cells (Part 2)
• When activated by RIC1, ROP forms “neck”
oriented microtubules; when activated by
RIC4, it orients “lobe” actin filaments
• 15.22 The orientation of
microtubules in the cortical
cytoplasm
• Cellular cortical microtubules (green) coincide with
microfibril orientation (blue)
• 15.23 The disruption of cortical
microtubules

• Figure 15.23 Cortical

microtubules; (C) CesA proteins
and microtubules

• Cell elongation and expansion

• Cell walls must yield for growth
to occur
– Yielding properties (e.g. threshold,
rate)
 – Expansion produces stress
relaxation
• Internal pressure (turgor) drives
expansion
– Stress (force per unit area)
• In growing cells, as water enters
the cell the turgor increases and
causes the wall to yield,
increasing the cell volume and
relieving the ΨP .

• Cell elongation and expansion

• Rate of water uptake = cell area
(A) x membrane permeability (LP)
x (ΔΨW)
• In growing cells, as water enters
the cell
 – turgor increases
– above threshold, causes the wall to
yield,
– increases the cell volume and
relieves the ΨP .
– As water enters, it dilutes the
solutes and makes ΨS less negative
– Thus, the cell must take up or
generate more solutes to drive water
uptake for expansion (turgor stress)
to continue.

• Cell wall loosening

• Changes in Yield threshold (Y) or
cell wall extensibility (m) are
used to change growth rate for a
given ψp
– Loosening enzymes
 – Cell wall acidification (e.g. via
auxin)
• Acid growth hypothesis

• 15.25 Reduction of cell turgor

pressure (water potential) by
stress relaxation
• Auxin induces cell wall acidification, allowing for
rapid stress relaxation and thus loss of turgor
corresponding to increased cell size
--if continued H2O uptake is allowed (control), no loss
of turgor occurs
• 15.26 Acid-induced extension of
isolated cell walls, measured in an
extensometer
• Artificial cell wall acidification increases
extensibility of the cell walls (but only those
cut from growing tissues)
• Acid growth hypothesis
• Acidification of the cell wall (via
auxin or fusicoccin activation of
H+ ATPase) stimulates expansins
and other cell wall enzymes
– Expansins act in catalytic quantities
but do not break covalent bonds
– α-expansins act on cellulose-
cellulose junctions in eudicots,
while β-expansins loosen
glucuranoglycan (GAX) in
gymnosperm primary walls
• Hydrolysis of matrix
polysaccharides
• Cell wall “creep” is irreversible
– extensibility decreases over time:
rigidification
• 15.27 Scheme for the
reconstitution of extensibility of
isolated cell walls (Part 1)

• 15.27 Scheme for the

reconstitution of extensibility of
isolated cell walls (Part 2)
• Freeze-thaw kills cells without destroying
cell-wall enzymes.
• Heat inactivation of tissue denatures cell
wall-loosening enzymes

• Purified expansins added

back to boiled tissue
cell walls allows
elongation again,
but only at
acidic pH
• Cell wall growth cessation
• Older cells lose the ability for
continued expansion
– Incorporation or modification of
matrix components that are less
subject to loosening
– Covalent crosslinking (e.g. lignins,
proteins)
– Newer (2°) cell walls control
growth more than older walls

• Figure 14.20 Alternative

concepts of the structural role of
xyloglucan
• Figure 14.21 Secondary cell
walls
• Figure 15.18 Secondary cell
walls; (D) Structure of poplar
lignin
• Lignins are complex polyphenolics that crosslink
cellulose microfibrils and other cell wall
components, particularly in secondary cell walls
• Figure 14.23 Schematic
representation of Casparian strip
deposition
• Casparian strip is produced by lignification and
suberin deposition in specific regions of endodermal
cell walls
• Cell walls in the Casparian strip membrane
domain are loaded with monolignols via plasma
membrane transporters
• Organized by CASP1 protein
• NADPH oxidase, peroxidase produce reactive
peroxides and radical monolignol intermediates for
polymerization
• ESB1 (Enhanced Suberin 1) may help direct
polymerization

• Another change in the calendar!

• This Friday (3/27) – Wednesday,
April 1 “Recalibration”
• Tuesday, April 7 follows
Wednesday schedule
• “Spring Break” April 8-10

LECTURE 15
Signal Transduction
Process by which information that
is detected by receptors is amplified
and transferred to the site(s) of
action to affect a response
Protein modification
Second messengers
Used in all living organisms
Generic scheme for signal
transduction
Signal transduction may be cell autonomous or
non-cell autonomous
Signal Transduction
Identification
Signal transduction pathways have been
elucidated through genetics
Forward genetic screens looking for mutants
that are affected in a particular set of
responses
Reverse genetics using suspected target
genes (based on homologs, functional
domains, etc.) and targeting those genes for
disruption and/or misexpression/activation
Biochemical methods (e.g. immuno co-
precipitation, yeast two-hybrid, column
purification of activities,
pharmacological agents)
May be based around Physiological
methods
Figure 15.3 Primary locations of
plant hormone receptors and
mechanosensitive receptors (MscS)
in the cell
Kinases in Signal Transduction
Kinases can alter targets through
phosphorylation using ATP (or
GTP)
Ser/Thr, Tyr, His/Asp
Alter charge and shape, which affects
substrate binding, enzymatic activity,
localization, protein interactions,
stability, etc.
Reversible by phosphatases
(dephosphorylation)
May also involve phosphotransferases
for phosphate shuttling
Intracellular Signal
Transduction Cascades
Kinase Cascades
Pass signal through a series of
intermediates
transfer information (e.g. from
membrane to nucleus)
amplify (1 kinase can phosphorylate
many targets or copies of the same
target)
e.g. MAPK (mitogen-activated
protein kinase) cascade

Figure 15.4 Mitogen-activated

protein kinase (MAPK) pathways
amplify signals to achieve a rapid
and massive amplified response to
an environmental or developmental
stimulus
Table 15.1 MAPK signaling
modules identified in plants
Protein Phosphatases
Dephosphorylation can be as
important in signaling as
phosphorylation
e.g. by BSU1 dephosphorylating
BIN2 (a kinase), BIN2 and cannot
enter the nucleus and is degraded
BIN2 thus cannot phosphorylate and
inactivate transcription factors
BES1/BZR1
Result: Transcription factors stay in
nucleus and direct transcription of
brassinosteroid response genes
Inhibiting the inhibitors
e.g. Abscisic acid binding to
phosphatase PP2C complex prevents
 dephosphorylation of SnRK, allowing
this kinase to phosphorylate and
activate transcription factors
Figure 15.5 Calcium ions, pH, and
ROS function as second messengers
that amplify signals and regulate the
activity of target signaling proteins
to trigger physiological responses
Ca++ spike in Physcomitrella
precedes cytokinesis
Figure 15.6 Lipid-modifying
enzymes remodel cellular
membranes and produce lipid
signaling molecules
Figure 15.7 Common scheme for
hormonal regulation
Figure 15.8 Chemical structures of
phytohormones
Figure 15.9 Early experiments on
the chemical nature of auxin
Figure 15.10 Gibberellin
Figure 15.11 Cytokinin enhances
cell division and greening
Figure 15.12 Ethylene responses
Figure 15.13 Stomatal closure in
response to ABA
Figure 15.14 Phenotypes of
Arabidopsis brassinosteroid mutants
Figure 15.15 Rice plants colonized
by root parasitic plants
Hormone homeostasis
Auxin (IAA) biosynthesis
Auxin is synthesized primarily from
Tryptophan via Trp amino transferase
(TAA) and YUCCA, a flavin
monooxygenase
YUCCA6 overexpression (yuc6-ID)
produces excess IAA
IAA functions on numerous processes, in
many tissues, and at all life stages
Auxin is toxic at high concentrations and
must be tightly regulated
reversibly conjugated
sequestered in ER
irreversibly conjugated
degraded
Receptor Auxin binding protein 1 (ABP1)
accumulates in ER

Gibberellic acid (GA)

synthesis
Terpenoid pathway products
Involves plastid, ER, and cytosolic
steps
ER GA13 oxidation pathway is
predominant
Several active GAs (GA4, GA1) that
can be inactivated by further
oxidation
May also be conjugated or methylated
to inactivate

Cytokinin biosynthesis from

nucleotides
Isopentenyl transferase regulation
Derived from adenine with isoprenoid adduct
trans-Zeatin is the most common natural
cytokinin
Sugar-conjugates are inactive
Ethylene biosynthesis
Derived from methionine
ACC synthase is rate limiting step for
ethylene synthesis
Activated by numerous internal and
external stimuli
Inhibited by AOA (aminooxyacetic acid)
and AVG
Yang cycle recycles 5’-
methylthioadenosine from
S-adenosylmethionine to Methionine
ACC oxidase also regulated

Abscisic acid (ABA)

biosynthesis
Derived from terpenoid pathway
carotenoid products
Sesquiterpenoid (C15)
Oxidation and reversible conjugation
may remove ABA
Brassinosteroid biosynthesis
Sterol precursor
Cytochrome P450 monooxygenases
catalyze various steps in Brassinolide
synthesis
Can be hydroxylated to inactivate
Strigolactone synthesis
Also derived from carotenoids
Various active forms

Hormones may act at great distances

(endocrine), near the site of synthesis
(paracrine), or on the cells that produce
them (autocrine)

Hormone transport
 via polar transporters (e.g. auxin)
Xylem stream (e.g. cytokinin, ACC)
Phloem (e.g. auxin, cytokinin)
Membrane transport by ABCG
cassette transporters
air (ethylene, MeJA)
Signaling can also occur by
electrical action potentials
Mimosa
Venus fly trap
Stress responses (e.g. herbivory)
Bacterial two-component
systems
Plant versions modified over
evolutionary time from bacterial
origins
Sensor protein with
 Input domain for sensing
environmental signal
Transmitter domain with histidine
kinase/phosphotransferase activity
Response regulator protein
Receiver domain that accepts
phosphate from transmitter domain
His on an Aspartate
Output domain

Figure 14.4 Plants and bacteria

employ similar signaling
components and mechanisms (B)
Phosphorelays (e.g. cytokinin signaling) are
modified versions of bacterial 2-component
regulatory systems
Hybrid sensor contains transmitter and receiver
domains

Intermediate His-phosphotransfer protein

 Second receiver domain on response regulator
Cytokinin signaling
CRE1 receptor in ER or PM
Cytokinin activates His kinase
Phosphotransferase to AHP, inducing translocation
Phosphotransferase to ARR-As and ARR-Bs
P-ARR-B induces transcription of ARR-A
P-ARRA inhibits cytokinin signaling
P-ARR-B ubiquitinated at SCFKMD
Amount of ARR-B determines expression of other
response genes

Ethylene acts on numerous

receptors
Brassinosteroid (BR) signaling
ABA signaling
IAA and GA signaling involve
polyubiquitination

DELLA class of repressor proteins

in GA signaling
Variations on a theme…
GA can regulate its own production
Signal pathway interactions

Papers
You MUST have your topic
approved before writing your
papers. Topics are very specific.
I’m looking for depth, using recent
primary research papers
I will not accept any paper without
a
pre-approved topic!
Focus on the plant, not on a plant
products’ effect on non-plants
(except where it’s part of a plant
process like the nodule formation
dance)!
LECTURE 16
Plant Photoreceptors and responses to light
Photomorphogenesis
Light regulated growth and development
Phototropism
Growth toward light
Photonasty/nyctinasty
Light-regulated leaf folding

Control of Plant Growth and

Development--Light
Multiple classes of photoreceptors
Phytochromes
Cryptochromes and Phototropins
Dozens of other specific photoreceptors
e.g. UVR8, Zeitlupe
Chromophores
Non-protein pigment compounds that absorb the light
Responsible for the major spectral properties of the
photoreceptor
Associated with the photoreceptor protein
May be covalent or non-covalent attachment
Control of Plant Growth
and Development--Light
Etiolated (dark) growth
(skotomorphogenesis)
Elongated shoots
Pale (no chlorophyll)
Closed cotyledons and apical
hook (e.g. bean) or coleoptile
(e.g. corn)
Photomorphogenesis
Light signals the transition
from dark to light growth
Figure 16.2 Comparison of seedlings grown in the light versus
the dark
17.1 Corn (A and B) and kidney bean (C and D) seedlings grown
either in light or dark

Figure 16.3 Time-lapse photograph of a maize (corn; Zea mays)

coleoptile growing toward unilateral blue light given from the right
Figure 16.4 Plants can use visible light, UV-A, and UV-B
radiation as developmental signals (all wavelengths in nm)
Figure 16.7 The action spectrum of phototropism matches the
absorption spectrum of the light-sensing LOV domain of
phototropin
Phytochromes
Absorb primarily red and far-red light
Control an enormous number and variety of plant processes
Photointerconvertible (photoreversible) between two forms
Slow dark reversion
Pfr is generally the
active form of
phytochrome
17.2 Lettuce seed germination is a typical photoreversible
response controlled by phytochrome

Figure 16.6 The action spectrum of phytochrome function

matches its absorption spectrum
Figure 16.8 Structure of the Pr and Pfr forms of the chromophore
(phytochromobilin) and the peptide region bound to the
chromophore through a thioether linkage
Phytochrome

Overlapping absorption
spectra of Pr and Pfr result in
dynamic photoequilibrium
Photostationary state
in red 85% Pfr and 15% Pr
in far-red 3% Pfr and 97% Pr
 Phytochromes absorb
throughout the visible
spectrum, with additional low
peaks in the blue

Phytochrome proteins
Apoprotein covalently attached to linear tetrapyrrole chromophore
to make the holoprotein
Phytochromobilin chromophore related to heme and
chlorophyll
Autocatalytic thioether linkage to conserved cysteine
Family of related genes (phyA-phyE in Arabidopsis)
Forms homo- and sometimes hetero-dimers
Figure 16.9 Phytochrome domains and their functions
Figure 16.10 After synthesis of phytochromobilin in the plastid
and assembly with the apoprotein, phytochrome is activated by
red light and moves into the nucleus to modulate gene expression
17.11 Nuclear localization of phy–GFP fusion proteins in
epidermal cells of Arabidopsis hypocotyls
Nuclear translocation of phyA-GFP or phyB-GFP
occurs following conversion to Pfr
Uses different mechanisms for entering nucleus
PhyA requires FHY1 or FHL to aid its nuclear
translocation
PhyB can transport with a nuclear localization-like
signal sequence
Phytochrome responses
Phytochromes are made as Pr
Active form is Pfr in most cases

Lag time—time between irradiation and an observed response

Vary widely for light responses
Indicative of the number, complexity, or types of intervening
steps
Escape time from photoreversibility—“point of no return”

Phytochrome responses

Light responses can be

categorized by the amount of
light required to initiate them
Fluence (μmol photons·m-2)
Total photons
Fluence rate (μmol
photons·m-2·s-1) or irradiance

Very-low fluence responses

(VLFR)
 Low fluence responses (LFR)
High irradiance (fluence rate)
responses (HIR)
17.4 Three types of phytochrome responses, based on their
sensitivities to fluence

VLFR
Very low fluence responses
As little as10-4 μmol photons·m-2
Saturate at ~5x10-2 μmol photons·m-2
Converts <0.02% of Pr to Pfr
Not photoreversible by far-red light
Reciprocity applies
“Photon counting”
LFR
3
Range from ~1.0 to 10 μmol
photons·m-2
Photoreversible by far-red
light (e.g. lettuce seed
germination)
Reciprocity applies
17.5 LFR action spectra for the photoreversible stimulation and
inhibition of seed germination

HIR
Magnitude of the response is dependent on fluence rate of
continuous light
Not photoreversible by far-red light
Reciprocity does not apply
May be Red-HIR , FR-HIR, or intermediate action-spectrum
indicating photoequilibrium
Some responses have LFR and HIR components
17.6 HIR action spectrum for the inhibition of hypocotyl
elongation of dark-grown lettuce seedlings

Phytochrome function

Phytochromes are
evolutionarily ancient
Chromophore isomerization
causes protein
conformational change
Redistribution to nucleus and
interaction with transcription
factors
 Autophosphorylating Ser/Thr
kinases
Cytosolic and nuclear targets
Degradation of “type I”
phytochromes
Phytochromes

Genetic mutants used to

dissect functions of
photoreceptors and signaling
components
phyA responsible for FR-HIR
and VLFR
phyB controls most LFR and
red-HIR responses
Other phy proteins are
involved in “fine tuning”
responses to the environment
Figure 17.12 Differences in phytochrome gene family structure
and function

Phytochromes

Genetic studies have some

limitations
Phytochromes regulate each
others’ abundance (e.g. phyB
required for full phyC and
phyD expression)
Heterodimers
Phytochrome function

Phytochromes induce rapid

membrane potential changes
and ion fluxes
 May be involved in rapid
growth responses to Red and
Far-red light
Phytochromes regulate gene
expression
Enormous numbers of genes
are regulated by light
Microarray analysis
Primary response genes
Secondary (“late” or “indirect”)
response genes
Phytochrome function
Primary response genes include nuclear phytochrome interacting
factor (PIF) and PIF-like (PIL) gene products
Some interact specifically with Pfr form of one or more phy
(e.g. PIF3)
Phosphorylation by Pfr may initiate PIF degradation
Some bind DNA to regulate other genes
Phy kinase substrate 1 & 2 (PKS1/PKS2) are phosphorylated in
the cytosol by phyA and interact with phyA and phyB
Phytochrome function
Constitutively
photomorphogenic or
Deetiolated (cop/det/fus)
mutants appear as light-
grown, even in the dark
Phytochrome function
involves protein degradation
Nuclear E3 ligase COP1
ubiquitinates certain
transcription factors and
phyA, inducing degradation
via COP9 complex in
darkness
In light, COP1 shuttled out of
nucleus allowing transcription
factors to function
Figure 16.13 Phytochrome interacting factors (PIFs) act as
regulators of photomorphogenesis
Figure 16.14 COP proteins regulate the turnover of proteins
required for photomorphogenic development
Blue light responses
Cryptochromes (CRY1, CRY2, CRY3, and more…)
Photomorphogenesis (e.g. Hypocotyl growth)
Phototropins (PHOT1 & PHOT2)
Movements (chloroplasts, phototropism)
Zeitlupe family (ZTL)
Circadian rhythms
Figure 16.15 Blue light–induced changes in elongation rates of
etiolated cucumber hypcotyls and membrane depolarization of
hypocotyl cells
Figure 16.16 Cryptochrome domain and chromophore structure

cry1 and cry2 have distinct activities

Cry1
Light stable
Controls hypocotyl elongation
Circadian clock resetting
Interacts with COP1/SPA1 to inactivate their E3 function,
allowing photomorphogenic transcription factors to
accumulate
Cry2
Light labile
Cotyledon expansion
Flowering induction

Figure 16.17 Blue light stimulates the accumulation of

anthocyanin (A) and the inhibition of stem elongation (B) in
transgenic and mutant seedlings of Arabidopsis
Figure 16.18 Model of cry1 interactions with COP1/SPA1 in the
regulation of photomorphogenesis
Photoreceptor systems interact
Phototropins, phytochromes and cryptochromes interact in
slowing stem elongation
Phy/Cry act on anion channels to depolarize Plasma
membrane
Function on different time frames
Phy and Cry interact in flowering regulation

Figure 16.19 Sensory transduction process of blue light–

stimulated inhibition of stem elongation in Arabidopsis
Figure 16.20 Phototropin domain composition, photocycle, and
LOV domain structure
Figure 16.21 Phototropism in Arabidopsis seedlings can be used
as the bioassay for phototropin activity
Figure 16.22 Model for blue light–induced autophosphorylation of
phototropin
Figure 16.23 Schematic diagram of chloroplast distribution
patterns in Arabidopsis palisade cells in response to different light
intensities
Figure 16.24 Model for phototropin-mediated chloroplast
movement in Arabidopsis thaliana
Figure 16.25 Role of the proton-pumping ATPase in the
regulation of stomatal movement
Figure 16.26 Phototropin signal transduction leading to stomatal
opening
Table 16.3 Photomorphogenic responses to UV-B
Figure 16.27 UVR8 structure and dimerization
Figure 16.28 The UVR8 signaling pathway involves COP1 and
SPA1