PLANT PHYSIOLOGY

Phytochrome
Prof. Dr. S.M. Sitompul
mtom Lab. Plant Physiology, Faculty of Agriculture, Universitas Brawijaya
Email : dl@ub.ac.id

MODUL
Hak cipta dilindungi undang-undang. ©Modul ini tidak boleh digandakan seluruhnya atau sebagian tanpa izin dari penulis

Phytochrome adalah suatu pigment

(molekul) protein biru tanaman yang
terlibat dalam pengendalian
perkembangan tanaman seperti
perkecambahan biji, pertumbuhan
batang, perluasan daun, sintesis
08
pigment, dan pembungaan.
Photoreversibility, pertubahan dapat
balik akibat cahaya, adalah sifat

SELF-PROPAGATING ENTREPRENEURIAL EDUCATION DEVELOPMENT

paling istimewa dari phytochrome.
Perubahan sifat ini berhubungan
Photoreversibility is the most
dengan posisi dari suatu gugusan
distinctive property of
dalam molekul phytochrome dari
phytochrome posisi (isomer) cis ke trans.

Most biological processes have been considered to be irreversible for a long time, but
some recent studies have shown the possibility of their reversion at a cellular level
(Cho et al., 2016)

LECTURE OUTCOMES (SPEED)

After the completion of this lecture and mastering the lecture
materials, students should be able to
1. explain phytochrome including its discovery and initial studies.
2. explain the phytochemistry and biochemistry of phytochrome
3. explain characteristics of phytocrome-induced responses
4. explain structure and function of phytochrome proteins
5. explain signaling pathways of phytochrome
6. explain ecological functions of phytochrome

LECTURE OUTLINE
1. INTRODUCTION 4. STRUCTURE AND FUNCTION OF
2. PHYTROCHEMISTRY AND BIOCHEMISTRY PHYTOCHROME PROTEINS
OF PHYTOCHROME 5. SIGNALING PATHWAY
3. CHARACTERISTICS OF PHYTOCROME- 6. ECOLOGICAL FUNCTIONS
INDUCED RESPONSES

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Plant Physiology/Phytochrome/S.M. Sitompul The University of Brawijaya 2017

1. INTRODUCTION

1. Initial Studies
 The discovery of phytochrome is
closely associated with studies on
flowering.
 Phytochrome is a blue protein
pigment with a molecular mass
of about 125 kDa that plants,
and some bacteria and fungi, use
to detect light.
- The term phytochrome (“plant
color”) was originally coined to
describe the proteinous pigment
that controls photope-riod
detection and floral induction of
certain short-day plants (e.g. Fig. 24.22 A flash of red (R) light during the
cocklebur and soybean) (Garner dark period induces flowering in an LDP but
and Allard, 1920). prevents flowering in an SDP (1), and the
- Essentially all proteins absorb effect is reversed by a flash of far-red (Fr)
light in the near-UV region due to light (2). This response indicates the
the presence of aromatic amino involvement of phytochrome.
acids, and proteins that sense
visible light possess chromophore
cofactors that confer the desired
wavelength sensitivity.
 In 1932, Beltsville research
group of the USDA headed by
Borthwick and Hendricks showed
that red light (630 to 680 nm)
elicits the germination of lettuce
seeds, whereas far-red light (710
to 740 nm) inhibits the process.

Irradiations Germination
(%)
R 88
R, Fr 22 Fig. 17.2 Lettuce seed germination
R, Fr, R 84
R, Fr, R, Fr 18
R, Fr, R, Fr, R 72
R, Fr, R, Fr, R, Fr 22
R = red, Fr = Far red

Notes:

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2. Chemical Structure
 Native phytochrome is a soluble
protein with a molecular mass of
about 250 kDa, and exist as
homodimers (a protein complex
composed of two subunits).
- Each subunit consists of two
components: a light-absorbing
pigment molecule called the
chromophore, and a polypeptide
chain called the apoprotein (Fig.
17.6).
- The chromophore is an open–
chain tetrapyrrole which is
covalently linked to the protein
moiety through a cysteine residue
(a sulfur linkage).
- Apoprotein consists of a 60 kDa Fig. 17.6 Structure of the Pr and Pfr forms of
amino-terminal domain, and a 55 the chromophore (phytochromobilin) and
kDa carboxyl- terminal domain. the peptide region bound to the
chromophore through a thioether linkage.
The chromophore undergoes a cis-trans
isomerization at carbon 15 in response to
red and far-red light. (After Andel et al.
1997.)

 The absorption of red light appears to provide the energy required to

overcome high activation energy for rotation around double bond, a
transition that is not possible at normal temperature.
- The apoprotein monomer has a molecular mass of about 125 kDa and is encoded
in angiosperms by a small family of genes. Together, the apoprotein and its
chromophore make up the holoprotein.

 In higher plants the chromophore of phytochrome is a linear tetrapyrrole

called phytochromobilin.
 Light (R or FR) cannot be absorbed by the phytochrome apoprotein alone,
and can be absorbed only when the polypeptide is covalently linked with
phytochromobilin to form the holoprotein.
 Phytochromobilin, synthesized inside plastids, is derived from heme via a
pathway that branches from the chlorophyll biosynthetic pathway.
- The phytochromobilin is exported to the cytosol where it attaches to the
apoprotein through a thioether linkage to a cysteine residue (Fig. 17.6).
- Assembly of the phytochrome apoprotein with its chromophore is autocatalytic
(it occurs spontaneously).
Notes:

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2. PHYTROCHEMISTRY AND BIOCHEMISTRY OF

PHYTOCHROME
1. Photoreversibility
 Photoreversibility is the conversion/reconversion of phytochrome which is
the most distinctive property of this pigment, and it may be expressed in
abbreviated form as follows:

 It is important to note that the

phytochrome pool is never fully
converted to the Pfr or Pr forms
following-red or far-red
irradiation, because the
absorption spectra of the Pfr and
Pr forms overlap.
 Thus, when Pr molecules are
exposed to red light, most of
them absorb the photons and are
converted to Pfr, but some of the
Pfr made also absorbs the red
light and is converted back to Pr Fig. 17.3 Absorption spectra of purified oat
(Fig. 17.3). phytochrome in the Pr (red line) and Pfr
 The proportion of phytochrome (green line) forms overlap. At the top of the
in the Pfr form after saturating canopy, there is a relatively uniform
irradiation by red light is only distribution of visible spectrum light (blue
about 88%. line), but under a dense canopy much of the
 Similarly, the very small amount red light is absorbed by plant pigments,
resulting in transmittance of mostly far-red
of far-red light absorbed by Pr
light. The black line shows the spectral
makes it impossible to convert properties of light that is filtered through a
Pfr entirely to Pr by broad- leaf. Thus, the relative proportions of Pr and
spectrum far-red light. Pfr are determined by the degree of
 Instead, an equilibrium of 98% vegetative shading in the canopy. (After
Pr and 2% Pfr is achieved. This Kelly and Lagarias 1985, courtesy of Patrice
equilibrium is termed the Dubois.)
photostationary state.
 In addition to absorbing red
light, both forms of phyto- Notes:
chrome absorb light in the
blue region of the spectrum
that can convert Pr to Pfr and
vice versa.
 Blue-light responses can also
result from the action of one
or more specific blue-light
photoreceptors.
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2. The Physiologically Active Form of Phytochrome

 Because phytochrome responses are induced by red light, hypothetically
they could result from either the appearance of Pfr or the disappearance of
Pr.
 In most cases studied, a quantitative relationship holds between the
magnitude of the physiological response and the amount of Pfr generated
by light.
 No such relationship holds between the physiological response and the loss
of Pr.
 Evidence such as this has led to the conclusion that Pfr is the physiologi-
cally active form of phytochrome.
 The use of narrow waveband red and far-red light was central to the
discovery and eventual isolation of phytochrome.
 However, a plant growing outdoors is never exposed to strictly "red" or "far-
red" light, as are plants used in laboratory-based photobiological
experiments.
 In natural settings plants are exposed to a much broader spectrum of light,
and it is under these conditions that phytochrome must work to regulate
developmental responses to changes in the light environment.

Notes:

3. CHARACTERISTICS OF PHYTOCROME-INDUCED
RESPONSES
1. Variety of Phytochrome Responses
 The variety of different phytochrome responses in intact plants is extensive,
in terms of both the kinds of responses (Table 17.1) and the quantity of
light needed to induce the responses.
 These phytochrome-induced responses, for ease of discussion, may be
logically grouped into two types:
- Rapid biochemical events
- Slower morphological changes, including movements and growth
 Such responses can be classified into various types depending on the
amount and duration of light required and on their action spectra.

Notes:

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Table 17.1 Typical photoreversible responses induced by phytochrome in a

variety of higher and lower plants

Group Genus Stage of development/Effect of red light

Angiosperms Lactuca (lettuce) Seed/Promotes germination
Avena (oat) Seedling (etiolated)/Promotes de-etiolation (e.g., leaf unrolling)
Sinapis (mustard) Seedling/Promotes formation of leaf primordia, development of primary leaves,
and production of anthocyanin
Pisum (pea) Adult/Inhibits internode elongation
Xanthium (cocklebur) Adult/Inhibits flowering (photoperiodic response)
Gymnosperms Pinus (pine) Seedling /Enhances rate of chlorophyll accumulation
Pteridophytes Onoclea (sensitive Young gametophyte/Promotes growth
fern)
Bryophytes Polytrichum (moss) Germling/Promotes replication of plastids
Chlorophytes Mougeotia (alga) Mature gametophyte/Promotes orientation of chloroplasts to directional dim
light
Group Genus Stage of development/Effect of red light
Angiosperms Lactuca (lettuce) Seed/Promotes germination
Avena (oat) Seedling (etiolated)/Promotes de-etiolation (e.g., leaf unrolling)
Sinapis (mustard) Seedling/Promotes formation of leaf primordia, development of primary leaves,
and production of anthocyanin
Pisum (pea) Adult/Inhibits internode elongation
Xanthium (cocklebur) Adult/Inhibits flowering (photoperiodic response)
Gymnosperms Pinus (pine) Seedling /Enhances rate of chlorophyll accumulation
Pteridophytes Onoclea (sensitive Young gametophyte/Promotes growth
fern)
Bryophytes Polytrichum (moss) Germling/Promotes replication of plastids
Chlorophytes Mougeotia (alga) Mature gametophyte/Promotes orientation of chloroplasts to directional dim
light

Notes:

2. Lag and Escape Time of Phytochrome Responses

 Morphological responses to the photoactivation of phytochrome may be
observed visually after a lag time-the time between stimulation and
observed response.
 The lag time may be as brief as a few minutes or as long as several weeks.
 The more rapid of these responses are usually reversible movements of
organelles or reversible volume changes (swelling, shrinking) in cells, but
even some growth responses are remarkably fast.
 Variety in phytochrome responses can also be seen in the phenomenon
called escape from photoreversibility.
- Red light-induced events are reversible by far-red light for only a limited
period of time, after which the response is said to have "escaped" from
reversal control by light.
 This escape phenomenon can be explained by a model based on the
assumption that phytochrome-controlled morphological responses are the
end result of a multi-step sequence of linked biochemical reactions in the

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responding cells.
 Early stages in the sequence may be fully reversible by removing Pfr, but at
some point in the sequence a point of no return is reached, beyond which
the reactions proceed irreversibly toward the response.
 Therefore the escape time represents the amount of time it takes before the
overall sequence of reactions becomes irreversible; essentially, the time it
takes for Pfr to complete its primary action.
 The escape time for different responses ranges remarkably, from less than a
minute to hours.

4. Phytochrome Responses and Light Quantity

 Phytochrome responses can be distinguished by the amount of light
required to induce them.
 The amount of light is referred to as the fluence, the number of photons
impinging on a unit surface area.
- The standard units for fluence are micromoles of quanta per square
meter (mol m-2).
- Some phytochrome responses are sensitive not only to the fluence, but
also to the irradiance* or fluence rate of light. The units of irradiance
are micromoles of quanta per square meter per second (mol m-2 s-1).

Notes:

 Phytochrome responses fall into

three major categories based on
the amount of light required:
very low-fluence responses
(VLFRs), low-fluence responses
(LFRs), and high-irradiance
responses (HIRs) (Fig. 17.4).

 VLFRs are nonphotoreversible

- Some phytochrome responses
can be initiated by fluences as
low as 0.0001 mol m-2 (one-
tenth of the amount of light
emitted by a firefly in a single
flash), and saturated (i.e., Fig. 17.4 Three types of phytochrome
reach a maximum) at about responses, based on their sensitivi-ties to
0.05 mol m-2. For example, fluence. The relative magni-tudes of
Arabidopsis seeds can be representative responses are plotted against
induced to germinate with red increasing fluences of red light. Short light
pulses activate VLFRs and LFRs. Because
light (0.001 to 0.1 mol m-2).
HIRs are proportional to irradiance as well as
to fluence, the effects of three different
 LFRs are photoreversible. irradiances !aiven continuously are
- These phytochrome responses illustrated (11 > 12 > 1 3). (After Briggs et
cannot be initiated until the al. 1984.)
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fluence reaches 1.0 mol m-2,

and are saturated at about
1000 mol m-2.
- These include most of the
red/far-red photoreversible
responses, such as the
promotion of lettuce and
Arabidopsis seed germination
(Fig. 17.5).
- LFR spectra include a main
peak for stimulation in the red
region (660 nm), and a major Fig. 17.5 LFR action spectra for the
peak for inhibition in the far- photoreversible stimulation and inhibition of
seed germination in Arabidopsis. (After
red region (720 nm).
Shropshire et al. 1961.)

 Both VLFRs and LFRs can be induced by brief pulses of light, provided that
the total amount of light energy adds up to the required fluence.
 The total fluence is a function of two factors: the fluence rate (mol m-2 s-1)
and the time of irradiation.
 Thus, a brief pulse of red light will induce a response, provided that the
light is sufficiently bright, and conversely, very dim light will work if the
irradiation time is long enough.
 This reciprocal relationship between fluence rate and time is known as the
law of reciprocity, which was first formulated by R. W. Bunsen and H. E.
Roscoe in 1850.
 VLFRs and LFRs both obey the law of reciprocity; the magnitude of the
response (e.g. % germination or degree of inhibition of hypocotyl
elongation) is dependent on the product of the fluence rate and the time of
irradiation.
 HIRs require prolonged or continuous exposure to light of relatively high
irradiance. The response is proportional to the irradiance until the response
saturates and additional light has no further effect.
 These responses are proportional to fluence ratethe number of photons
striking the plant tissue per secondrather than fluencethe total number of
photons striking it in a given period of illumination that leads to the term of
HIRs (high-irradiance responses).
 HIRs saturate at much higher fluences than LFRsat least 100 times higher.
 HIRs obey the law of reciprocity as suggested by inhibition of hypocotyl
elongation in response to short pulses of FR light, suggesting that
photoperception by phytochrome is rate-limiting for this response.
Notes:

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4. STRUCTURE AND FUNCTION OF PHYTOCHROME

PROTEINS
1. Functional Domains of
Phytochrome
 Several of the structural domains
in phytochrome have been
identified including the diversity
of cellular changes mediated in
response to light (Fig. 17.7).
 The N-terminal half of
phytochrome contains a PAS
domain, a GAF domain with
bilin-lyase activity, which is
necessary for autocatalytic
assembly of the chromophore,
and the PHY domain, which
stabilizes phytochrome in the Pfr
form.
 A hinge region separates the N-
terminal and C-terminal halves
of the molecule and plays a
critical role in conversion of the
inactive, Pr form of phytochrome
to the active, Pfr form.
 Downstream of the hinge regions
are two PAS-related domain
(PRD) repeats that mediate
phytochrome dimerization.
 Within the PRD are two nuclear
localization sequences (NLSs)
that when exposed, direct the Fig 17.7 After synthesis and assembly (1),
phytochrome is activated by red light (2)
active, Pfr form of phytochrome
and moves into the nucleus (3) to modulate
to the nucleus.
gene expression. A small pool of
 A major breakthrough in phytochrome remains in the cytosol, where
phytochrome research was it may regulate rapid biochemical changes
achieved with the three- (4). Several conserved domains within the
dimensional structure for the N- phytochrome are shown: PAS, GAF (contains
terminal region of a bacterial bilin-lyase domain), PHY, PRID (PAS-related
phytochrome bound to its domain), and HKRD (HIS kinase-related
chromophore, biliverdin, from domain). POB, phytochromobilin. (After
the radiation-resistant, Montgomery and Lagarias 2002.)
extremophilic bacterium
Deinococcus radiodurans
(Wagner et al. 2005). Notes:
 Unlike plant phytochromes,
bacterial phytochromes utilize a
range of tetrapyrrole
chromophores and likely mediate
very different downstream
responses. Nevertheless, the
structure of the chromophore-
binding pocket is likely to be
highly conserved, and the
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chromophore is tightly associated PAS domain

with a pocket in the GAF domain GAF domain
(Fig. 17. 8).

2. Phytochrome as a Light-
Regulated Protein Kinase
 Phytochrome is a light-regulated
protein kinase that is necessary
for its activation.
 Higher-plant phytochromes,
having some homology with the
Comserved
histidine kinase domains cystein Chromophore
(bacterial phytochromes), are Fig. 17.8 A three-dimensional crystal
serine/threonine kinases (Fig. structure is shown for the N-terminal portion
17.9B) and likely phosphory-late of a bacterial phytochrome from Deinococcus
other proteins. radiodurans. The chromophore, biliverdin
(shown in purple), is covalently attached to
a conserved cysteine residue (shown in pink)
3. Cytosol and Nucleus
and is closely associated with the protein
Phytochrome backbone of the GAF domain. (After Wagner
 In the cytosol, phytochrome et al. 2005.)
holoproteins dimerize in the
inactive Pr state.
- Upon absorption of light, the Pr
chromophore undergoes a cis-
trans isomerization of the double
bond between carbons 15 and 16
and rotation of the C14C15 single
bond (Fig. 17.16).
- During the conversion of Pr to Pfr,
the protein moiety of the
phytochrome holoprotein also
undergoes a conformational
change in the hinge region that
exposes a nuclear localization
signal (NLS) in the C-terminal half
of phytochrome resulting in the
movement of phytochrome
molecules from the cytosol to the
nucleus (Fig. 17.7).
 The movement of phytochromes
Fig. 17.9 (B) Plant phytochrome is an
from the cytosol to the nucleus is autophosphorylating serine/threonine kinase
light quality-dependent, in that that phosphorylates other proteins (shapes
the Pfr form of phytochrome is containing X).
selectively imported into the
nucleus.

Notes:

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4. Multigene Family of Phytochrome

 Early biochemical studies provided hints that there were different forms of
phytochrome.
 Two different classes of phytochrome have been found; the light-labile form
(Type I) and the light-stable form (Type II). Actually, it is the Pfr form of
Type I phytochromes that is unstable.
- In Arabidopsis the family is composed of five structurally related members: PHYA,
PHYB, PHYC, PHYD, and PHYE (Sharrock and Quail 1989). In rice, a monocot,
there are only three phytochrome-encoding genes: PHYA, PHYB, and PHYC
(Mathews and Sharrock 1997).
 The apoprotein by itself (without the chromophore) is designated PHY; the
holoprotein (with the chromophore) is designated phy.

5. SIGNALING PATHWAYS
1. Early Steps in Phytochrome Action
 All phytochrome-regulated changes in plants begin with absorption of light
by the pigment.
 After light absorption, the molecular properties of phytochrome are altered,
probably affecting the interaction of the phytochrome protein with other
cellular components that ultimately bring about changes in the growth,
development, or position of an organ.
 The early steps in phytochrome action and the signal transduction pathways
that lead to physiological or developmental responses fall into two general
categories:
- Ion fluxes, which cause relatively rapid turgor responses
- Altered gene expression, which result in slower, long-term processes.

2. Phytochrome and Membrane Potentials

 Phytochrome can rapidly alter the properties of membranes, within seconds
of a light pulse.
 Such rapid modulation has been measured in individual cells, and has been
inferred from the effects of red and far-red light on the surface potential of
roots and oat (Avena) coleoptiles.
 The lag time between the production of Pfr and the onset of measurable
hyperpolarization (membrane potential changes), found in the above
studies, is 4.5 seconds.
 Changes in the bioelectric potential of cells imply changes in the flux of ions
across the plasma membrane and suggest that some of the cytosolic
responses of phytochrome are initiated at or near the plasma membrane.

3. Phytochrome and Gene Expression

 Phytochrome regulates gene expression, and the stimulation and repression
of transcription by light can be very rapid, with lag times as short as 5
minutes.
 Some of the early gene products that are rapidly upregula-ted following a
shift from darkness to light are transcript-tion factors that activate the
expression of other genes.
 The genes encoding these rapidly up-regulated proteins are called primary
response genes.
 Expression of the primary response genes depends on signal transduction
pathways and is independent of protein synthesis.

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 In contrast, the expression of the late genes, or secondary response

genes, requires the synthesis of new proteins.

4. Phytochrome Interacting Factors (PIFs)

 Several phytochrome-interacting factors (PIFs) have been identified in
Arabidopsis by two methods (yeast two-hybrid library screens and co-
immunoprecipitation).
 One of the most extensively characterized of these factors is PIF3, a basic
helix-loop-helix (bHLH) transcription factor that interacts with both phyA and
phyB.
 Recent studies of PIF-family members have indicated that they act primarily
as negative regulators of phytochrome response.
 Phytochromes appear to initiate the degradation of PIF proteins through
phosphorylation, followed by degradation through the proteasome complex.

5. Protein Kinases and Phosphatases

 In addition to nucleus-localized transcription factors, two-hybrid screens also
identified cytosolic proteins as potential partners for phy proteins.
 Phytochrome kinase substrate 1 (PKS1) is capable of interacting with
phyA and phyB in both the active Pfr and inactive Pr form.
 This protein can accept a phosphate from phyA, further highlighting the
importance of phosphorylation in phytochrome signaling.
 Phytochrome-associated protein phosphatase 5 (PAPP5) is another
factor that interacts with phytochromes and is probably involved in
accentuating phytochrome response through dephosphorylation of the active
phytochrome.
 A possible model for the regulation of phy activity by phosphorylation is
shown in Fig. 17.13.

Fig. 17.13 Phytochrome activity is modulated by phosphorylation status. Following

activation by red light, the phytochrome-associated phosphatase PAPP5 and as-yet
unidentified kinases modulate phytochrome activity in response to the intensity or
quality of light. (After Ryu et al. 2005.)

Notes:

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6. Gene Expression and Protein Degradation

 The cloning of several COP/DET/FUS genes has revealed an essential role for
protein degradation in the regulation of the light response.
 COP1 encodes an E3 ubiquitin ligase that is essential for placing a small
peptide tag known as ubiquitin onto proteins.
 Once tagged by ubiquitin, the proteins are transported to the 26S
proteasome, a cellular garbage disposal that chews up proteins into their
constituent amino acids.
 COP9 and several other COP proteins compose the COP9 signalosome
(CSN), which forms the lid of this garbage disposal, helping to determine
which proteins enter the complex.
 COP1 has been shown to interact with several proteins involved in the light
response, including the transcription factors HFRI, HY5, and LAFI, targeting
them for degradation in the dark (Fig. 17.14, ).
 In the light, COP1 is exported from the nucleus to the cytosol (Fig. 17.14),
excluding it from interaction with many of the nucleus-localized transcription
factors.
 These transcription factors can then bind to promoter elements in genes that
mediate photomorphogenic development.
 COP1 is also responsible for the degradation of the flowering regulators CO
and GI as well as proteins involved in auxin and GA response.

Fig. 17.14 COP proteins regulate the turnover of proteins required for
photomorphogenic development. During the night, COP1 enters the nucleus, and
the COP1/SPA1 complex adds ubiquitin to a subset of transcriptional activators. The
transcription factors are then degraded by the COP9 signalosome-proteasome
complex. During the day, COP1 exits the nucleus, allowing the transcriptional
activators to accumulate. Blue tails represent ubiquitin tags on proteins destined for
the COP9 signalosome complex (CSN) that serves as the gatekeeper of the 26S
proteasome.

Notes:

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6. ECOLOGICAL FUNCTIONS
1. Plant Adaptation to Light
 The ratio of red light (R) to far-red light (FR) varies remarkably in different
environments (Table 17.3).

Table 17.3 Ecologically important light parameters

Fluence rate
Light type and Environment R:FRa
(mol m-2s-1)
Daylight 1900 1.19
Sunset 26.5 0.96
Moonlight 0.005 0.94
Ivy canopy 17.7 0.13
Lakes, at a depth of 1 m
Black Loch 680 17.2
Loch Leven 300 3.1
Loch Borralie 1200 1.2
Soil, at a depth of 5 mm 8.6 0.88
Source: Smith 1982, p. 493.
Note: The light intensity factor (400-800 nm) is given as the photon flux density, and
phytochrome-active light is given as the RTR ratio.
*Absolute values taken from spectroradiometer scans; the values should be taken to
indicate the relationships between the various natural conditions and not as actual
environmental means.

- As shading increases, the R:FR ratio decreases, and a higher proportion of

FR light converts more Pfr to Pr, and the ratio of Pfr/Ptotal decreases.

An important function of

phytochrome is that it enables
plants to sense shading by other
plants.
 Plants that increase stem
extension in response to shading
are said to exhibit a shade
avoidance response.
 When sun plants were grown in
natural light with natural F:FR
ratio, stem extension rates
increased in response to a higher
FR content (i.e., a lower Pfr:Ptotal
ratio) (Fig. 17.16).

2. Role of Hormones in Shade

Avoidance
 Evidence is also emerging for the
Fig.17.16 Phytochromes appear to play a
integration of a number of
predominant role in controlling stem
hormonal pathways in the control elongation rate in sun plants (solid line), but
of shade avoidance responses not in shade plants (dashed line). (After
including those of auxin, Morgan and Smith 1979.)
gibberellins, and ethylene.
 Several recent reports have
suggested that the PIF proteins
play important roles in mediating
responses to shade and at least
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Plant Physiology/Phytochrome/S.M. Sitompul The University of Brawijaya 2017

some of these responses are

mediated through GA signaling
pathways (Fig. 17.17).
 When plants are grown under
high R:FR, as in an open canopy,
phy proteins become nuclear
localized and inactivate PIF
proteins.
 In darkness or under low R:FR, a
pool of phytochrome is excluded
from the nucleus, enabling the
accumulation of PIF proteins that
promote elongation responses.
Fig. 17.17 In the dark, the growth-
3. Crop Yield and Shade promoting hormone gibberellic acid (GA)
Avoidance binds to its receptor and mediates the
 In recent years, yield gains in ubiquitination of DELLA proteins. The DELLA
crops such as maize have come proteins are then targeted to the 26S
largely through the breeding of proteasome for degradation. In the absence
new maize varieties with a higher of the DELLA proteins, PIFs can act as both
tolerance to crowding (which positive and negative regulators of gene
induces shade avoidance expression, likely through interaction with
responses) than through
different partners, perhaps mediated
increases in basic yield per plant.
through different cis-regulatory elements
 As a consequence, today's maize
upstream of target genes. In the light,
crops can be grown at higher
DELLA proteins bind PIF proteins, preventing
densities than older varieties
them from interacting with genes. PHY
without suffering decreases in
plant yield (Fig. 17.18). proteins also target PIF proteins, through
phosphorylation, eventually leading to their
ubiquitination and degradation. In the
absence of PIF proteins, genes required for
cell expansion are not expressed, and plant
growth is retarded.

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Plant Physiology/Phytochrome/S.M. Sitompul The University of Brawijaya 2017

QUIZ
1. What is phytochrome and its function?
2. What was that found in 1932 by Beltsville research group of the USDA?
3. What are the components of phytochrome?
4. What does the Pr chromophore experience when it absorbs light?
5. What does it mean by photoreversibility of phytochrome?
6. What is the proportion of phytochrome in the Pfr form after saturating
irradiation by red light?
7. What is photostationary state?
8. What is the physiologically active form of phytochrome?
9. What is the lag time of morphological responses to the photoactivation of
phytochrome?
10. What does it mean by escape from photoreversibility?
11. What is the escape time for different responses?
12. What does it mean by fluence?
13. What are the major categories of phytochrome responses?.
14. What is an example of phytochrome responses categorized as LFR?.
15. What are the domains contained in the N-terminal half of phytochrome?
16. What is it called that separates the N-terminal and C-terminal halves of the
phytochrome?.
17. Where is the component phytochromobilin of phytochrome synthesized?.
18. Where is the complete phytochrome synthesized?.
19. What is the form of phytochrome imported selectively into the nucleus?.
20. What is the type of phytochromes that is unstable?.
21. How many are phytochromes found in rice that are encoded by genes?.
22. What are the early steps in phytochrome action and the signal transduction
pathways that lead to physiological responses?.
23. How long does it take for phytochrome to alter the properties of membranes?.
24. What are the early gene products that are rapidly upregula-ted following a
shift from darkness to light?.

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