Clocking the floral transition from phytochromes to molcular or circadian clocks

Doctoral Seminar 1
BPY-788
Sudershan Mishra
ID-51063
Ph.D First year
Deptt. of Plant Physiology
CBSH, GBPUAT

Why do all of them flowerat the same time,
that too every yearin the same month?
2

Fundamentals questions
• How do plants keep track of the seasons of the year and time
of the day?
• Which environmental signals influence flowering and how are
these signals perceived
• How are environmental signals transduced to bring about the
developmental changes associated with flowering
3

Clocking the floral transition: from
phytochromes to molecular clocks

Overviewoftheseminar
• Basics of the mechanism of flowering
1. What is meant by floral growth
2. Molecular framework for flowering
3. Models related to floral organ formation
• Basics of circadian clocks
1. Basic terminology involved
2. Entrainment and Gating features
3. Simple Arabidopsis oscillator
• Models for clocking flowering time
1. Hourglass Model
2. Bunning’s Hypothesis
3. External Coincidence Model
• CASE STUDIES/UPDATES REGARDING CLOCKING OF FLORAL
TRANSITION
5

What must change to change a vegetative
shoot into a flower
• What is a Flower?
• What is floral evocation?
• Following must change
1. Accumulation of a certain level of biomass so that plant can
change from a state of sexual immaturity into a sexually
mature state
2. the transformation of the apical meristem’s function from a
vegetative meristem into a floral meristem or inflorescence
3. the growth of the flower’s individual organs 6
Wit et al., 2017

Difference between vegetative and floral
growth
• Vegetative Growth
1. Objective organ is a leaf/
shoot
2. Phyllotaxis may be
alternate or opposite or
spiral
3. It may be determined or
not determined
• Floral Growth
1. Objective organ is a
flower or a group of
flowers
2. Phyllotaxis is verticillate
or whorled
3. Always determined
7
Wit et al., 2017

Molecular framework for flower
development
The flower arises from the activity of three classes of genes,
which regulate floral development.
1. Meristem identity genes. Code for the transcription factors
required to
a. Transformation of vegetative meristem to floral meristem
b. Up regulation of organ identity genes
2. Organ identity genes. Directly control organ identity
3. Cadastral genes. Act as spatial regulators for the organ
identity genes
8
Wit et al., 2017

Meristem identity genes
• Include
a. FLORICAULA (FLO) in Antirrhinum
b. SUPRESSOR OF CONSTANS1 (SOC1) also called AGAMOUS
LIKE 20 (AGL20), APETALA 1 (AP1) and LEAFY (LFY) in case of
Arabidopsis
• CAULIFLOWER (CAL) and UNUSUAL FLORAL ORGANS (UFO) are
two another well characterized genes common to many
plants
• TERMINAL FLOWER (TFL) is a special class of genes involved in
maintenance of the floral state of meristem
SOC1/
AGL20
LFY AP1TFL
9
Wit et al., 2017

Organ identity genes
• Floral organ identity genes are homeotic genes which belong to
MADS box family
• 3 classes of genes were delineated initially that led to the ABC
model of flowering
• Genes representing Class A Function- APETALA1 (AP1) &
APETALA2 (AP2)
• Genes representing Class B Function- APETALA3 (AP3) and
PISTILLATA (PI)
• Genes representing Class C Function- AGAMOUS (AG)
10
Wit et al., 2017

MADS Box
• The MADS box is a conserved sequence motif. The genes which
contain this motif are called the MADS-box gene family
• The length of the MADS-box reported by various researchers varies
somewhat, but typical lengths are in the range of 168 to 180 base
pairs (how many amino acids are there in MADS domain then?)
• The MADS box encodes the DNA-binding MADS domain.
• MADS-box gene family got its name later as an acronym referring to
the four founding members
1. MCM1 from the budding yeast, Saccharomyces cerevisiae,
2. AGAMOUS from the thale cress Arabidopsis thaliana,
3. DEFICIENS from the snapdragon Antirrhinum majus
4. SRF from the human Homo sapiens
11
Song et al., 2017

The ABC Model (Coen and Meyerowitz,
1991)
Fig 1- The single or additive expression of the homeotic genes in the right hand column have repercussions
for the development of the organs in the central column and determine the nature of the whorl in the flower
12
Song et al., 2017

Fig 2 - Interpretation
of the phenotypes of
floral homeotic
mutants based on
the ABC model. (A)
Wild type. (B) Loss of
C function results in
expansion of the A
function throughout
the floral meristem.
(C) Loss of A function
results in the spread
of C function
throughout the
meristem. (D) Loss of
B function results in
the expression of
only A and C
functions.
(Source- Principles of
Plant Physiology, Taiz
and Zeiger 5th ed.)
13

The Quadruple Mutant
Fig 3- A quadruple mutant
(api1, ap2, ap3/pi, ag)
results in the production
of leaf like structures in
place of floral organs.
Plant Physiology, Taiz and
Zeiger 5th ed.)
14

ABCDE model of flowering
• Class D gene is represented by SEEDSTICK (STK) which is
involved in ovule development
• Class E genes are required for the functioning of A-, B- and C-
class of genes
• Class E gene are represented by SEPALLATA (SEP) and consist
of four members SEP1, SEP2, SEP3 and SEP4
• According to ABCDE model-
• A+E=sepals
• A+B+E= petals
• B+C+E= stamens
• C+E= carpels
• C+D+E= ovules
15
Song et al., 2017

Competence and determination are two
stages in floral evocation
• A bud is said to be competent if it is able to flower when
given the appropriate developmental signal.
• A bud is said to be determined if it progresses to the next
developmental stage (flowering) even after being removed
from its normal context
Fig 4 - A simplified model for floral evocation at the shoot apex in which the cells of the
vegetative meristem acquire new developmental fates. (Source- Principles of Plant Physiology,
Taiz and Zeiger 5th ed.)
16

Circadian rhythms- the clock within
• An endogenous self sustaining biological rhythm with a
temperature compensated period close to 24 hours which is
normally entrained to day-night cycle
• Endogenous- because the rhythms persist in the absence of
controlling factors
• Endogenousity is possible due to presence of an internal
pacemaker called the oscillator
• Temperature compensation- The oscillator is relatively
unaffected by temperature
• Physiological responses are coupled to specific time point of
endogenous oscillator
Oscillator= Clock Mechanism
Physiological function = Hands of the Clock
17
Lee et al., 2017

Features of Circadian Rhythms- Basic
Fig 5- Basic features of
circadian rhythym
A. A typical circadian
rhythm. The period
is the time between
comparable points in
the repeating cycle;
the phase is any
point in the
repeating cycle
recognizable by its
relationship with the
rest of the cycle; the
amplitude is the
distance between
peak and trough
B. Suspension of a
circadian rhythm in
continuous bright
light and the release
or restarting of the
rhythm following
transfer to darkness.
18
Lee et al., 2017

Features of Circadian Rhythms-
entrainment
Fig 6- A circadian rhythm
entrained to a 24 h light–
dark (L–D) cycle and its
reversion to the free-
running period (26 h in
this example) following
transfer to continuous
darkness.
• Under natural conditions, the endogenous oscillator is entrained
(synchronized) to a true 24-hour period by environmental
signals(zeitgebers) , the most important of which are the light-to-dark
transition at dusk and the dark-to-light transition at dawn
• In absence of zeitgebers rhythm is said to be free-running, and it reverts
to the circadian period that is characteristic of the particular organism
• Only the coupling between the molecular clock and the physiological
function is affected.
• Phytochromes and cryptochromes entrain the clock
19
Lee et al., 2017

Features of Circadian Rhythms- Phase
shifting/gating
Fig 7- Typical phase-
shifting response to a
light pulse given shortly
after transfer to
darkness. The rhythm is
rephased (delayed)
without its period being
changed.
• A single oscillator couples to many processes, still occur on time how?
• Subjective day
• Subjective night
• The phase of the rhythm can be changed if the whole cycle is moved
forward or backward in time without its period being altered
• If a light pulse is given during the first few hours of the subjective night,
the rhythm is delayed; the organism interprets the light pulse as the end
of the previous day
• Gating- regulating when exactly a response will occur
20
Lee et al., 2017

A simple(primitive) model for
Arabidopsis internal oscillator
Fig 8- Circadian oscillator model showing the interactions between the TOC1 and MYB genes LHY and
CCA1. Light acts at dawn to increase LHY and CCA1 expression. LHY and CCA1 act to regulate other
daytime and evening genes. (Source- Principles of Plant Physiology, Taiz and Zeiger 5th ed.)
21

How does the plant decide when to
flower- various models
• Following 3 models are significantly discussed
1. The Hourglass Model
2. Bunning’s Hypothesis
3. The external coincidence model
22
Song et al., 2016

The Discovery of Photoperiodism
• The concept given by W.W.
Garner & H.A. Allard of in
1920.
• M.M. Variety was a single
gene mutant tobacco that
didn't flower in the spring
or summer, like wild type.
• Flowering only occurred if
the day length (amount of
light) was 14 hours or less.
• Maryland Mammoth a
short-day plant because it
required a light period
shorter than a critical
length to flower. 23
Song et al., 2016

Classification into SDP, LDP and DNP
• Short-day plants (SDPs) flower only in short days (qualitative
SDPs), or their flowering is accelerated by short days
(quantitative SDPs)
• Long-day plants (LDPs) flower only in long days (qualitative
LDPs), or their flowering is accelerated by long days
(quantitative LDPs)
• Day-neutral plants do not flower in response to daylight
changes. They flower when they reach a particular stage of
maturity or because of some other cue like temperature or
water, etc.
• LSDPs and SLDPs
25
Song et al., 2016

The Hourglass Model
• The hourglass model assumes the gradual accumulation of a
chemical product in the organism
• A certain quantity of this chemical is necessary to trigger a
physiological response .
• The threshold is reached if the product is not first degraded. It
may be degraded by dark and only accumulates during the light
phase or it may accumulate during dark and be degraded by
light.
• If the light (or the dark) is long enough threshold is reached and
a physiological response, such as maturation of the
reproductive system, is initiated 26
Song et al., 2016

The Hourglass Model contd.
• Phytochrome was proposed as a photoperiodic timer, a concept
that is easily illustrated in plants that flower during short days
• In these plants, when the day is long and the night is short,
fewer Pfr molecules change into Pr during the night, leading to
Pfr-dependent repression of flowering; by contrast
• When the day is short and the night is long, more Pfr molecules
change into Pr during the night, diminishing this repression
• Just the reverse of this happens in case of long day plants
• Plants eventually classified as LDPs or SDPs
27
Song et al., 2016

Phytochrome
• Phytochrome is a homodimer: two identical protein molecules
each conjugated to a light-absorbing molecule.
• Plants make 5 phytochromes: PhyA, PhyB, as well as C, D, and
E.
• There is some redundancy in function of the different
phytochromes, but there also seem to be functions that are
unique to one or another. The phytochromes also differ in
their absorption spectrum; that is, which wavelengths (e.g.,
red vs. far-red) they absorb best.
• Phytochromes exist in two interconvertible forms
• PR because it absorbs red (R; 660 nm) light;
• PFR because it absorbs far-red (FR; 730 nm) light.
• These are the relationships:
• Absorption of red light by PR converts it into PFR.
• Absorption of far-red light by PFR converts it into PR.
• In the dark, PFR spontaneously converts back to PR.
28
Lee et al., 2017

Fig 9 - Structure and interconversion of phytochrome (Figures 39.19 and 39.20, page 769,
Campbell's Biology, 5th Edition)
29

What is the plant actually measuring?
Fig 10 - effect of photoperiodic regulation on LDPs and SDPs Short-day (long-night) plants flower when
night length exceeds a critical dark period. Interruption of the dark period by a brief light treatment (a
night break) prevents flowering. Long-day (short-night) plants flower if the night length is shorter than a
critical period. In some long-day plants, shortening the night with a night break induces flowering.
(Source- Principles of Plant Physiology, Taiz and Zeiger 5th ed.)
30

Experimental evidences- Phytochromes
control flowering
• Red light, of wavelength 660 nm, is the most effective in interrupting
night length.
• Experimental results have confirmed this fact:
1. Short-day (long-night) plants experiencing a long night will not
flower if exposed briefly to 660 nm light sometime during the night.
2. Long-day (short-night) plants exposed briefly to a 660 nm light will
flower even if the total night length exceeds the critical number of
hours.
• Shortening of night length by red light (R) can be negated by a flash
of far-red light (FR) of 730 nm. When this occurs, the plant perceives
no interruption in night length.
• No matter how many times red light is flashed, as long as it is
followed by far-red light the effects of red light are canceled
• True for both LDPs and SDPs 31
Lee et al., 2017

Phytochrome control of flowering
Fig 11 - Phytochrome
control of flowering by
red (R) and far-red (FR)
light. A flash of red light
during the dark period
induces flowering in an
LDP, and the effect is
reversed by a flash of
far-red light. This
response indicates the
involvement of
phytochrome. In SDPs,
a flash of red light
prevents flowering, and
the effect is reversed
by a flash of far-red
light.
Plant Physiology, Taiz
and Zeiger 5th ed.) 32

Bunnings’s Hypothesis, 1960
Fig 11a - Bunning’s hypothesis. In this model, organisms possess 12-h-long photophile and skotophile phases
delimited by an internal oscillator. When daylight lengthens into the skotophile phase, the photoperiodic
response is induced in long-day plants and repressed in short-day plants
33
Song et al., 2016

External Coincidence Model, Pittendrigh
and Minis, 1964
Fig 11b- Fig- The external coincidence model. This model proposes that a photoperiodic response is induced
by the activity of a hypothetical enzyme and the presence of its hypothetical substrate. The enzyme is present
throughout the day, and light triggers the enzyme to change from the inactive form (Ei) to the active form (Ea).
The expression patterns of the substrate are regulated by the circadian clock. Light and temperature change
throughout the day and reset the clock each day by adjusting the phases of the clock components. The time
when resetting occurs changes throughout the year, causing the phase of the substrate to also change slightly.
Therefore, the phases of the maximal amount of the substrate (s-max) are slightly different in long- and short-
day conditions. The photoperiodic response is induced only when the amount of substrate is higher than a
required threshold and Ea is present at the same time.
34
Song et al., 2016

External Coincidence Model contd.
• Instead of the 12-h skotophile phase, the model proposed the
presence of two factors: (a) a substrate whose levels oscillate
throughout the day that induces a photoperiodic response
when it is processed, and (b) an enzyme that is active only
under light. The photoperiodic response is triggered only
when the peak of the substrate coincides with the presence of
the active enzyme.
• Second, because the circadian clock regulates the timing
(phase) of the substrate peak, the phase of this peak changes
depending on day length owing to variations in the timing of
dawn and dusk throughout the year, which entrain (reset) the
circadian clock each day.
• The effects of light entrainment, which can be classified as no
change, phase advance,or phase delay, differ depending on
when the light signals occur 35
Song et al., 2016

Coincidence model is based on alternating
light sensitivity
Fig- 12- Rhythmic flowering in
response to night breaks. SDP
soybean (Glycine max) given cycles of
an 8-hour light period followed by a
64- hour dark period. A 4-hour night
break was given at various times
during the long inductive dark period.
The flowering response, plotted as the
percentage of the maximum, was then
plotted for each night break given . A
night break given at 26 hours induced
maximum flowering, while no
flowering was obtained when the
night break was given at 40 hours.
Note-
1 This shows that sensitivity to the night break shows a circadian rhythm.
2. Flowering in SDPs is induced only when dawn (or a night break) occurs after the
completion of the light-sensitive phase
3. In LDPs the light break must coincide with the light sensitive phase for flowering to occur.
36
Song et al., 2016

Photoperiodic time keeping in Arabidopsis
Fig 13- Molecular basis of coincidence
model in Arabidopsis (A&B).
A- Under short days there is little
overlap between CO mRNA expression
and daylight. CO protein doesn’t
accumulate to sufficient levels in
phloem to promote the expression of
transmissible floral stimulus, FT
protein and the plant remains
vegetative.
B- Under long days, the peak of CO
mRNA abundance (at hours 12
through 16) overlaps with the daylight
(Sensed by phyA and CRY), allowing
CO protein to accumulate. CO
activates mRNA expression in the
phloem which causes flowering when
FT protein is translocated to the apical
meristem
(Source- Principles of Plant Physiology,
37

Photoperiodic time keeping in Rice
Fig 14- Molecular basis of coincidence
model in Rice (C&D).
C- Under short days the lack of
coincidence between Hd1 mRNA
expression and daylight prevents the
accumulation of Hd1 protein, which
acts as a repressor of the gene
encoding the rice transmissible floral
stimulus and FT relative Hd3a. In
absence of Hd1 protein repressor,
Hd3a mRNA is expressed and the
protein it encodes is translocated to
the apical meristem where it causes
flowering
D- Under long days (Sensed by PHY),
the peak of Hd1 mRNA expression
overlaps with the day, allowing
accumulation of Hd1 repressor
protein. As a result Hd2a mRNA is not
expressed and the plant remains
vegetative
(Source- Principles of Plant Physiology,
38

CASE STUDIES/UPDATES REGARDING
CLOCKING OF FLORAL TRANSITION
39

Latest Research Articles
• Burman N, Bhatnagar A, Khurana JP (2018) OsbZIP48, a HY5 transcription
factor ortholog, exerts pleiotropic effects in light-regulated development.
Plant Physiol 176 (1) : 1262–1285
• Charlotte, M. M., & Gommers, S. H. 2018 Spotlight on photobiology Plant
Physiol., 177(2): 437-438
• Krahmer J, Ganpudi A, Abbas A, Romanowski A, Halliday KJ (2018)
Phytochrome, metabolism and growth plasticity. Plant Physiol 176(2): 1039–
1048
• Lee, C. M., Feke, A., Li, M. W., Adamchek, C., Webb, K., Pruneda-Paz, J. &
Gendron, J. M. 2018. Decoys untangle complicated redundancy and reveal
targets of circadian clock F-box proteins. Plant Physiol., 177(1): 331-342
• Muhammad, A.M., Xiaojing, B., & Korff, M.V. 2018. FLOWERING LOCUS T3
controls spikelet initiation but not floral development. Plant physiol., 178(1):
236-255
40

Latest insights into Arabidopsis
molecular clock
Fig 15 - A diagram
showing the putative
relationships among
genes involved in the
photoperiod pathway.
As regulated by the
clock.
Key-
Red- repress flowering
Green- promote
flowering
Simple line- protetin
protein interaction
Arrow- Promotive
effect
Blunt arrow-inhibition
41
Burman et al., 2018

A simple(primitive) model for
Arabidopsis internal oscillator
Fig 8- Circadian oscillator model showing the interactions between the TOC1 and MYB genes LHY
and CCA1. Light acts at dawn to increase LHY and CCA1 expression. LHY and CCA1 act to regulate
other daytime and evening genes. (Source- Principles of Plant Physiology, Taiz and Zeiger 5th ed.)
42

ComponentsofAdvancedmolecularclockof Arabidopsis
• Morning Loop- At dawn, two MYB transcription factors,CCA1 and LHY, repress evening-phased
genes This repression is partly dependent on the function of the CONSTITUTIVE
PHOTOMORPHOGENIC10 (COP10)-DE-ETIOLATED1- DAMAGED DNA BINDING1 complex, a
negative regulator for photomorphogenesis. To repress transcription, CCA1 and LHY bind to
related cis-elements called Evening Element
• Midday Loop- From early in the morning to the first-half part of the night, Pseudo response
regulators PRR9, PRR7, and PRR5 redundantly repress the transcription of CCA1 and LHY via G-
box-like cis elements which activates evening genes like LUX ARRHYTHMO (LUX) , ELF3 and
ELF4
• Evening Loop- LUX, ELF3, and ELF4 form a protein complex referred to as the Evening Complex
that represses PRR9 and LUX expression
• Night Loop- At night, a pseudo-response regulator, TOC1 (also known as PRR1) protein
becomes abundant and contributes to the repression of CCA1 and LHY transcription through
direct binding to G-box related sequences
• TOC1-dependent repression is gradually removed toward the end of the night by TOC1 protein
degradation controlled by ZTL E3 ubiquitin ligase and its homologs, FKF1 and LKP2
43
Burman et al., 2018

Advanced molecular clock of Arabidopsis
Fig 16- The advanced
model of the circadian
clock architecture and
tissue specific expression
profiles of core clock
genes in Arabidopsis
Intricate transcriptional
repression mechanisms
interlocked with core clock
components comprise the
Arabidopsis circadian clock
44
Charlotte et al., 2018

Latest about the mechanism of
flowering in Arabidopsis
• It can be studied under 3 parts
A. Generation of rhythmic expression patterns of CO gene
B. Light dependent control of CO protein stabilization
C. Induction of FT gene expression in long days
45
Muhammad et al., 2018

GenerationofrhythmicexpressionpatternsofCOgene
46
• The CDF family members function as repressors of flowering through direct
repression of CO transcription in the morning, CDF expression is negated by
PRRs and FKF1-GI complex
• The abundance of CCA1 transcript oscillates throughout the day; it is high in
the early morning in both long and short days. CCA1 and its homolog LHY
bind to promoters of PRR5, FKF1, and GI to repress their expression in the
morning. Daily oscillation patterns of PRR5 mRNA expression are antiphasic
to those of CCA1
• During long days, the peak expression of FKF1 and GI proteins, which are
regulated by the circadian clock, occurs in the afternoon. When FKF1
absorbs blue light, it interacts with GI. The photo-induced FKF1-GI complex
accumulates to high levels and degrades CDF proteins on the CO promoter
• Once the repression of CO transcription by CDFs is relieved, FBH proteins
activate CO gene expression by directly binding to the E-box elements in the
CO locus
• FKF1 and GI expression are out of phase under long days

Light dependentControl of CO proteinstabilization
47
• Light signaling modulates the ubiquitin-dependent degradation
mechanisms of CO at different times of day
• PHY B (mediates red light effects) and two RING-finger E3 ubiquitin
ligases, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and HIGH
EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1), are
directly involved in CO degradation in morning
• COP1 and SUPPRESSOR OF PHY A-105 1 (SPA1) degrade the CO
protein during night- particularly important during short days
• Three kinds of photoreceptors—FKF1, PHYA, and cryptochromes
(CRY), especially CRY2—are involved in CO protein stabilization by
sequestration of CO protein away from COP1-SPA complex
• FKF1 directly bind to CO through LOV domain in a blue light
dependent manner and stabilize it

Inductionof FT gene expressionin long days
• CDFs also repress expression of FT which is eventually released by
degaradation of CDFs in blue light dependent manner after which CO
and another transcription factor CRYPTOCHROME-
INTERACTINGBASICHELIX-LOOP-HELIX(CIB) can trigger FT expression
• CO and CIB can act by two ways
• A. Directly binding to the CONSTANS-responsive element (CORE) in
the FT promoter through CCT domain
• B. By physical interaction with certain other proteins like
ASYMMETRIC LEAVES 1 (AS1) protein and the CCAAT-box-binding
nuclear factor Y (NF-Y) proteins
48

Recent insights into flowering mechanism in Arabidopsis
Fig 17 - Photoperiodic regulation of FT induction in Arabidopsis, Muhammad et. al. 2018
49

Photoperiodic sensing in wheat and barley
• Variation in photoperiodic sensitivity within the long-day
cereals is conferred primarily through the PHOTOPERIOD 1
(PPD1) genes
• PPD1 represents a 95-bp region that is conserved across
wheat, barley, rice, and Brachypodium distachyon; this region
likely contains a key cis-regulatory element involved in light
perception and has been proposed to be the binding site of an
unknown transcriptional repressor
• The majority of the photoperiod-insensitive strains of
hexaploid wheat that were instrumental during the green
revolution carry the PPD-D1a allele
50

Photoperiodic ……….barley Contd.
• Wheat and barley PPD1 are homologous to Arabidopsis PRR7,
a gene integral to the circadian clock in Arabidopsis
• Red light acts through PHYC and PPD1 to regulate FT1 and
flowering . Upregulation of PPD1 is accompanied by
upregulation of FT1 (also called VRN3) in long days in
vernalized plants
• It is possible that light signals perceived by PHYC and the
presence of PPD1 represent the point at which external
coincidence occurs
51

Photoperiodicsensingin wheat and barley
Fig 18 - Photoperiodic control in the leaves of the long-day
cereals wheat, barley, and Brachypodium distachyon.
(a) Regulation of FT1 via the vernalization and
photoperiodic pathways.
(b) (b) Diurnal patterns in the gene expression of the key
floral-regulator genes CO1 (or CO in Brachypodium),
PPD1, and FT1 in strains carrying wild type or
hyperfunctional alleles (solid lines) and strains with
reduced or null PHYC activity (dashed red lines)
52

Interaction between vernalization and
photoperiodic response
• During fall, in winter varieties (i.e., those requiring vernalization),
afternoon light causes upregulation of VRN2 gene expression. VRN2
may be downstream of PPD1 and also acts antagonistically to PPD1
to repress FT1 and delay flowering.
• Cold winter temperatures repress VRN2 expression via VRN1. CO1
and PPD1 genes continue to be transcribed.
• In spring, day length acts through PHYC, PPD1, and CO1 to activate
FT1 expression, which feeds back to further upregulate VRN1 and
maintain repression of VRN2.
• In summer, activation by light further facilitates this process. In
wheat, around the time of floral initiation, CO1 begins to decline,
perhaps owing to negative feedback from FT1. CO2 begins to be
upregulated, perhaps maintaining FT1 expression through the
terminal spikelet stage and heading.
53

Interactionbetweenvernalizationand
photoperiodicresponse
Fig 19- The changing influence of day length throughout the year as mediated by PHYC 54

Photoperiodic flowering in Rice-
• Governed by two pathways
• A. Hd1-Hd3a module- for induction in short days
• B. Ghd7-Ehd1-Hd3a/RFT1 module- for induction in long as well as short
days
• Diurnal expression of Hd1 is regulated by a circadian-clock component,
OsGI, an ortholog of Arabidopsis GI
• In long-day afternoons, Hd1 is converted from an activator to a repressor of
Hd3a expression in a functional conversion that is mediated by
phytochromes, specifically PHYB- important for daylength sensing
• Ehd1 promotes flowering independently of Hd1 in short days but also
promotes flowering in long days when Hd1 represses Hd3a expression,
suggesting that Ehd1 and Hd1 determine the degree of florigen expression
through distinct pathways under a given photoperiod
• Ghd7 encodes a CCT-domain protein and negatively regulates
photoperiodic expression of Ehd1 . Lengthening days gradually increase
Ghd7 expression, and this induction requires functional phytochromes
55

Photoperiodicfloweringin Rice
Fig 20- Diurnal expression of floral
regulators. Ghd7 has higher
phytochrome-dependent red-light
inducibility around dawn in long-day
conditions, shifting to midnight in
short-day conditions (orange shaded
area). Ehd1 has higher blue-light-
dependent inducibility around dawn in
both long- and short-day conditions
(blue shaded area). In long days, red
light induces Ghd7 transcription,
leading to suppression of Ehd1 and
Hd3a expression. Accumulation of Hd1
transcript in the presence of light
suppresses Hd3a expression through
PHYB function. In short days, weak
expression of Ghd7 allows induction of
the Ehd1 gene, leading to activation of
Hd3a expression. Under these
conditions and through a parallel
pathway, Hd1 expression occurs mainly
during nighttime and also acts as an
activator of Hd3a
56

TranscriptionalRegulationof RiceFlorigens
via the Ghd7-Ehd1-Hd3a/RFT1Pathway
Fig 21- The regulatory network controlling expression of Hd3a and RFT1. In rice, the critical day
length required for floral induction is determined by two distinct pathways, Hd1-Hd3a and Ghd7-
Ehd1-Hd3a/ RFT1, which are regulated by the circadian clock and light signaling
57

Snapshot-controlof floweringin Arabidopsis
58

Summary
• The floral transition has been well studied at the molecular
level and in addition to discovery of newer components of
molecular clocks, there has been elucidation of specified
modules of transcriptional activators that directly activate or
repress flowering
• Additional roles of photoreceptors in mediating post
transcription stability and abundance of chief floral integrators
have also been well characterized
• Our knowledge about photoperiodic flowering mechanisms in
Arabidopsis has greatly facilitated our understanding of these
mechanisms in major crops (wheat, barley, and rice). This has
been critical in studying mechanisms in plants that are highly
valued in agriculture and horticulture
60

Future Issues
• Circadian rhythms are sensitive to the environment, and plant
rhythms are now being measured in detail under natural
conditions. A current challenge is to understand the link from
circadian timing to physiological traits in the field
• Gating through control by the circadian clock and light-signal
perception has been described in detail in rice, consistent with
the external coincidence model, but much less is known about
parallel mechanisms in wheat and barley
• Although rice is classified as a short-day plant, it possesses the
Ghd7-Ehd1-Hd3a/RFT1 pathway, which enables flowering
responses under various day-length conditions. Investigation
of whether this pathway is conserved in other plants, or
whether it is unique in rice, is of great interest.
61

Clocking the floral transition from phytochromes to molcular or circadian clocks

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