Báo cáo khoa học: Regulation of output from the plant circadian clock pot

REVIEW ARTICLE
Regulation of output from the plant circadian clock
Esther Yakir, Dror Hilman, Yael Harir and Rachel M. Green
Department of Plant Sciences and the Environment, Institute for Life Sciences, Hebrew University, Jerusalem, Israel
What is a circadian system?
2
Circadian systems are widespread endogenous mecha-
nisms that allow organisms to time their physiological
changes to predictable day ⁄ night cycles. They have
evolved in a wide range of organisms, from cyano-
bacteria to mammals, indicating their importance in
life processes. Among an enormous variety of 24 h
rhythms that are controlled by the circadian system
are nitrogen-fixation in cyanobacteria, olfactory
responses in Drosophila and sleep patterns in humans
[1]. The basic oscillator mechanism that generates the
rhythms is being elucidated in several model organisms
[1] and consists of transcriptional–translational posit-
ive ⁄ negative feedback loops involving a group of clock
genes. The oscillator can be set (entrained) by signals
from the environment, such as the daily changes in
light and temperature, transduced via input pathways.
Finally, output pathways link the oscillator to the var-
ious biological processes whose rhythms it controls.
The Arabidopsis circadian oscillator
Most of the work on the circadian oscillator in plants
has been carried out using the model plant Arabidopsis
thaliana. The plant oscillator appears to be comprised
Keywords
circadian; Arabidopsis; plant; output;
pathway; transcription; oscillator; hormone;

calcium
Correspondence
R. M. Green, Department of Plant Sciences
and the Environment, Institute for Life
Sciences, Hebrew University, Givat Ram,
Jerusalem 91904, Israel
Fax: +972 2 658 4425
Tel. +972 2 658 5391
E-mail:
(Received 24 October 2006, accepted
23 November 2006)
doi:10.1111/j.1742-4658.2006.05616.x
Plants, like many other organisms, have endogenous biological clocks that
enable them to organize their physiological, metabolic and developmental
processes so that they occur at optimal times. The best studied of these biolo-
gical clocks are the circadian systems that regulate daily ( 24 h) rhythms.
At the core of the circadian system in every organism are oscillators respon-
sible for generating circadian rhythms. These oscillators can be entrained
(set) by cues from the environment, such as daily changes in light and tem-
perature. Completing the circadian clock model are the output pathways that
provide a link between the oscillator and the various biological processes
whose rhythms it controls. Over the past few years there has been a tremen-
dous increase in our understanding of the mechanisms of the oscillator and
entrainment pathways in plants and many useful reviews on the subject. In
this review we focus on the output pathways by which the oscillator regulates
rhythmic plant processes. In the first part of the review we describe the role of
the circadian system in regulation at all stages of a plant’s development, from
germination and growth to reproductive development as well as in multiple
cellular processes. Indeed, the importance of a circadian clock for plants can
be gauged by the fact that so many facets of plant development are under its

control. In the second part of the review we describe what is known about the
mechanisms by which the circadian system regulates these output processes.
Abbreviations
APRR7, ARABIDOPSIS PSEUDORESPONSE REGULATOR 7; APRR9, ARABIDOPSIS PSEUDORESPONSE REGULATOR 9; CAT3,
CATALASE 3; CBS, CCA1-binding site; CCA1, CIRCADIAN CLOCK ASSOCIATED 1
1
; CCL, CCR-LIKE; CCR1, COLD CIRCADIAN RHYTHM
RNA BINDING 1; CCR2, COLD CIRCADIAN RHYTHM RNA BINDING 2; CK, cytokinin; CO, CONSTANS; DST, downstream element;
EE, evening element; FT, FLOWERING LOCUS T; GA, gibberellin; Hd1, heading date 1; Hd3A, heading date 3A; IAA, indole-3-acetic acid;
LHY, LATE ELONGATED HYPOCOTYLS; LUX, LUX ARRYTHMO; RCA, RUBISCO ACTIVASE; SEN1, SENESCENCE-ASSOCIATED GENE 1;
TOC1, TIMING OF CAB1.
FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS 335
of components analogous to those described in other
model organisms. Over the past decade, several puta-
tive Arabidopsis clock components have been identified
through mutational analysis and have been proposed
to form a positive ⁄ negative feedback loop to generate
circadian rhythms. Towards the end of the night, the
positive element, TIMING OF CAB1 (TOC1), is
involved in inducing the expression of CIRCADIAN
CLOCK ASSOCIATED 1 (CCA1) and LATE ELON-
GATED HYPOCOTYL (LHY) [2]. CCA1 and LHY
are known to encode transcription factors that,
in vitro, can be phosphorylated [3,4] and can bind the
TOC1 promoter [2]. Thus, during the day, CCA1 and
LHY might directly repress the expression of TOC1.
Towards evening, following a drop in levels of CCA1
and LHY, TOC1 expression increases, completing the
feedback loop. More recently, additional genes, inclu-
ding EARLY FLOWERING 4 (ELF4), GIGANTEA

(GI) and LUX ARRYTHMO (LUX), and feedback
loops have been identified suggesting that the oscillator
is more complex and may be composed of several
interlocking feedback loops [2,5–9]. Such an arrange-
ment is likely to be important for conferring stability
to the oscillator and is part of the mechanism ensuring
that the circadian system is able to function accurately
under a range of environmental conditions [10–12].
Clearly, to be of use to an organism, an oscillator
needs to be entrained by environmental signals [13].
Light and temperature are the most important of such
signals. Phytochromes, cryptochromes and members of
the ZTL ⁄ FKF1 ⁄ LPK2 family of proteins [14–16] have
all been shown to be light receptors for entrainment
[17,18]. Several genes, including EARLY FLOWER-
ING 3 (ELF3) and TIME FOR COFFEE (TIC) have
also been implicated in the input signaling pathways
from light to the clock [19,20].
There is not always, however, a clear distinction
between oscillator and input elements in the circadian
system. For example, the TOC1 paralogs, ARABI-
DOPSIS PSEUDORESPONSE REGULATORS 7
and 9 (APRR7 and APRR9) both appear to function
as part of the oscillatory mechanism, possibly forming
an additional regulatory feedback loop similar to those
found in other organisms [21,22]. At the same time,
APRR7 and APRR9 also have a role in regulating
light and temperature input to the oscillator [13,21].
Output processes regulated by the
circadian oscillator

Because there are already many excellent recent
reviews on the mechanism of the oscillator and its
entrainment [13,23,24], we focus on output from the
oscillator. We start with an overview of the multiple
roles that the circadian system has in regulation at all
stages of a plant’s life before describing what is known
about the mechanisms by which the circadian system
regulates these output processes.
The role of the circadian system during
development
The circadian clock controls many developmental pro-
cesses throughout the life cycle of the plant. Some of
these processes take place on a daily basis and are
directly regulated by the circadian clock. Others occur
annually and are controlled by changes in day-length
(photoperiod) that are detected by the circadian system.
Germination
At the earliest stage of development the circadian sys-
tem may regulate seed germination (Fig. 1A). In many
species, including downy birch (Betula pubescens), Lap-
land diapensia (Diapensia lapponica) and leatherleaf
(Chamaedaphne calyculata), germination is controlled
by day-length [25–28]. The existence of photoperiodic
control of germination suggests that, at least in some
plant species, the circadian system is functioning in
seeds. Consistent with this idea, imbibition (the absorb-
ance of water) by Arabidopsis seeds synchronizes circa-
dian-controlled gene expression [29]. Furthermore, in
dry (quiescent) onion (Allium cepa) seeds there is a
circadian rhythm in gas exchange that continues in con-

stant darkness [30], indicating that there may be a func-
tioning oscillator in seeds even before germination.
Growth
The circadian system continues to regulate many devel-
opmental processes that occur shortly after germina-
tion. For example, Arabidopsis hypocotyls elongate
with a circadian pattern immediately upon germination
(Fig. 1B). The rate of hypocotyl growth is greatest in
the evening and minimal in the morning, and can be
entrained by light even before the cotyledons emerge
from the seed coat [31]. A similar pattern of elongation
has also been found in adult plants such as tomato
(Lycopersicon esculentum) and red goosefoot (Chenopo-
dium rubrum) [32–34]. Cotyledon and leaf movements
are regulated by the circadian system in Arabidopsis
and other species like legumes (Fig. 1C) [31,35]. How-
ever, the mechanisms, for example, changes in cell
turgor and differential cell growth, controlling the
movements vary between species. The rate of Arabid-
opsis stem circumnutations is also under circadian
Circadian clock output in plants E. Yakir et al.
336 FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS
control (Fig. 1D), and is greatest at dawn [36]. During
the growth period, the circadian clock also regulates
shade-avoidance responses (Fig. 1E) that enable plants
to detect competition from other plants for light
energy and react by enhancing stem and petiole growth
[37].
Reproductive development
The best-characterized developmental phenomenon

regulated by the circadian clock is the transition from
vegetative to reproductive development via the photo-
periodic pathway (Fig. 1F). Some 70 years ago a
model was proposed for photoperiodic sensing [38].
According to this model, called the external coinci-
dence model, the circadian clock controls the expres-
sion of a light-sensitive component. When there is a
coincidence between light and sufficiently high levels of
the light-sensitive component in the leaves, flowering is
promoted. In recent years, research on Arabidopsis (a
plant that flowers earlier under conditions of long
days) has shown that the protein encoded by the CON-
STANS (CO) gene is the light-sensitive component
[39]. Briefly, the circadian clock controls CO mRNA
levels so that under long days CO transcript levels
start to rise well before sunset and stay high till the
next morning. Under short days CO mRNA accumu-
lates to significant levels only after sunset [40] and
although CO translation occurs rapidly the protein is
unstable in the dark. By contrast, during the day far-
red and blue light stabilize CO protein, and CO
accumulates in the nucleus [41]. CO then activates the
transcription of the floral regulator FLOWERING
LOCUS T (FT) [42]. FT mRNA, and possibly protein,
moves from the leaf to the shoot apex and promotes
flowering [43].
Interestingly, the components of the photoperiodic
flowering pathway appear to be conserved even in
plants that have a very different developmental
response to increasing day-length. Thus, in rice (Oryza

sativa), a plant that flowers early under short days, the
CONSTANS homolog Hd1 also acts as the component
integrating between the circadian clock and light sig-
nal, however, instead of activating the FT homolog
(Hd3a) under long days, Hd1 repress Hd3a under these
conditions [44,45].
Pollination
Following the transition to reproductive development,
the circadian clock continues to control physiological
events, such as pollination, that are important for suc-
cessful seed formation. Many plants rely on pollinators
that are active during a specific time of the day. In
some species, in order to maximize the possibility of
pollination and minimize the chances of damage, the
circadian system regulates flower opening so that it
occurs only during part of the day when potential poll-
inators are most active (Fig. 1G). Thus Arabidopsis
[46] petals open in the morning and close at midday,
whereas night-blooming cestrum (Cestrum nocturnum)
[47] petals open in the evening and close around dawn.
A
B
C
F
M
N
G
H
I
J

K
L
D
E
Fig. 1. The circadian system has a regulatory role in nearly all aspects of a plant’s life. (A) Germination, (B) hypocotyl elongation, (C) leaf
movements, (D) circumnutations, (E) shade avoidance, (F) flowering time, (G) flower opening, (H) scent production, (I) tuberization, (J) winter
dormancy, (K) stomatal opening, (L) photosynthesis, (M) photoprotection, and (N) protection from temperature extremes.
E. Yakir et al. Circadian clock output in plants
FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS 337
Another important feature of the plant–pollinator
relationship is the plant’s signature scent, which is a
combination of volatile compounds unique for each
plant species. Some volatiles are regulated by the circa-
dian clock so that they are emitted in the correct phase
with the plant’s pollinator activity (Fig. 1H) [47]. For
example, in snapdragon (Antirrhinum majus) flowers
which are pollinated by bees, the emission of methyl
benzoate, myrcene and (E)-b-ocimene, is high during
the day [48,49]. By contrast, methyl benzoate, is emit-
ted at night by tobacco (Nicotiana suaveolens) and
petunia flowers (Petunia · hybrida) in order to attract
moths [49]. These rhythms are controlled by the clock
and are probably a result of circadian changes in
mRNA levels and enzyme activity in the biosynthesis
pathway and in the levels of available substrate [48–50].
Nectar secretion is a further factor affecting success-
ful pollination that may be timed to correspond with
pollinator activity. In some species of the family Com-
positae, nectar secretion is under diurnal control and
very possibly also under circadian control [51].

Other photoperiod-regulated processes
In addition to the transition from vegetative to repro-
ductive development, several other processes in the
plant’s life circle are controlled, at least in part, by
photoperiod and thus, probably, the circadian system.
One of these processes is the development of storage
organs (Fig. 1I). In many cultivars of potatoes, inclu-
ding Solanum tuberosum ssp. Andigena, tuberization
depends on photoperiod and there is evidence that a
potato ortholog of CONSTANS might be involved
[52]. Another photoperiod-controlled process is the
winter dormancy of temperate-zone woody plants
(Fig. 1J). In chestnut (Castanea sativa) trees LHY and
TOC1 orthologs might play a part in regulating the
dormant state [53], and in aspen (Populus tremula) and
black cottonwood (Populus trichocarpa) trees short-
day-induced dormancy is controlled by CO and FT
[54].
The role of the circadian system in the regulation
of cellular processes
Stomatal opening
Circadian regulation can also be seen at the level of a
single cell. One important example is the circadian
rhythm observed in stomatal (leaf pore) opening
(Fig. 1K). In Arabidopsis, stomatal conductance is
higher during the day than at night [55], whereas in
crassulacean acid metabolism
3
plants, stomatal opening
has an opposite phase [56]. In addition the circadian

clock gates sensitivity of stomata to extracellular sig-
nals, such as light [57].
Photosynthesis and carbon dioxide fixation
Photosynthesis and carbon fixation are two of the
many important cellular processes that take place at a
specific time of day (Fig. 1L). The expression of many
Arabidopsis genes participating in the light-harvesting
reactions of photosynthesis is under clock control
[58,59]. Among them are the LHCA and LHCB gene
families, which encode chlorophyll a ⁄ b binding poly-
peptides for photosystems I and II, as well as genes
that are involved in the biosynthesis of chlorophyll
and RUBISCO SMALL SUBUNIT (RBCS) and
RUBISCO ACTIVASE ( RCA) that participate in car-
bon fixation [58,60]. It is not yet clear whether the
circadian expression of mRNA in these pathways is
always matched by circadian regulation at the level of
protein synthesis. However, in some cases protein lev-
els are under circadian control, for example, the syn-
thesis of LHCB and RCA in tomato is regulated by
the circadian system [61]. The rhythm of expression of
photosynthesis genes appears to be correlated with the
circadian rhythms observed in stomatal opening and
CO
2
assimilation [62]. The circadian system also regu-
lates post-translational modification of photosynthetic
components such as phosphorylation of the D1 protein
in duckweed (Spirodela oligorrhiza) [63].
Beside genes that encode proteins with a role in pho-

tosynthesis reactions, some genes encode proteins that
are involved in photorespiration, and sugar metabo-
lism and transport are also under circadian control
[58,64,65]. Furthermore, it has been suggested that
there is a clock-controlled correlation between the
energy-producing process of photosynthesis and the
expression of genes involved in energy-consuming pro-
cesses such as nitrogen assimilation [58].
Stress responses
The circadian system appears to have a role in regula-
ting responses to both abiotic and biotic stresses. For
example, although plants need sun in order to pro-
duce energy, high light levels can also be very dam-
aging. Thus, before sunrise plants express genes
encoding enzymes in the biosynthesis of photoprotect-
ing pigments [58] and this expression is under
circadian regulation (Fig. 1M). Similarly, the mRNA
levels of some genes involved in cold protection are
highest at dusk (Fig. 1N) [58]. Furthermore, the up-
regulation by cold of some major genes is gated by
the circadian clock to a specific time during the day
Circadian clock output in plants E. Yakir et al.
338 FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS
[66], as is sensitivity of the plants themselves to high
and low temperatures. Thus cotton (Gossypium hirsu-
tum) is most sensitive to cold at the beginning of the
day and to high temperatures in the evening [67]. It
has been suggested that this circadian-controlled gat-
ing of the timing of sensitivity to extreme tempera-
tures might be a way for the plant to distinguish

between changes in temperatures during the course of
the day and seasonal changes in temperature. In addi-
tion, the circadian clock also regulates mRNA levels
of some pathogen-related genes in Arabidopsis [59]. As
an indication of the importance of the circadian sys-
tem in regulating stress responses, microarray experi-
ments have shown that around 70% of the known
clock-controlled genes may also be regulated by cold,
salt or drought stresses [68].
Mechanisms for regulating output
In contrast with mammals, which have a central pace-
maker in the brain to regulate the other oscillators in
the body, plant circadian clocks appear to be auto-
nomous. Thus, different plant organs can maintain
rhythmic expression of genes with different phases [69].
Futhermore, genes can cycle with varying periods in
different cells [70]. These differences in phase and per-
iod may be a result either of tissue-specific changes in
input pathways and ⁄ or of modifications in the oscilla-
tor mechanism itself, although the available evidence
suggests that the basic oscillator mechanism is funda-
mentally conserved [70]. It seems unlikely, however,
that tissue-specific differences in the oscillator mechan-
ism are sufficient to regulate a wide range of output
processes with different phases.
In general, despite extensive evidence, gathered over
the years, that the circadian system has a regulatory
role in nearly all aspects of a plant’s life, remarkably
little is known about the actual mechanisms by which
the oscillator regulates these outputs. Indeed, one of

the most intriguing, but least understood, questions is
how the oscillator can regulate so many different plant
processes, including gene expression, with a wide vari-
ety of phases throughout the day.
Transcriptional control
Transcriptional control is probably one of the
most important levels of regulation for controlling
developmental, physiological and metabolic outputs.
Research in mice, Drosophila and Neurospora has
shown that a large percentage of the genome in a vari-
ety of organisms is under clock control [71–73]. An
extreme case of transcription clock control was found
in the cyanobacterium Synechococcus elongates
PCC 7942 which has most of its genome under clock
control [74]. A two-component signaling system seems
to be one of the mechanisms by which the cyanobacte-
rial clock regulates transcription [75,76].
In Arabidopsis as much as 36% of the genome is
controlled by the circadian system [58,59,77,78] and
because at least two components of the circadian oscil-
lator are transcription factors (CCA1 and LHY), an
appealing idea is that plant oscillator components
directly control the expression of some genes. Several
motifs have been identified in the promoters of circa-
dian-regulated genes and have been suggested as tar-
gets for binding by CCA1 and LHY. One such motif,
AAATATCT, also known as the Evening Element
(EE), is over-represented in the promoters of circadian
clock-controlled genes that show a peak of expression
in the evening [58,77,78]. In vitro assays show that

CCA1 and LHY can bind directly to the EE element
[2,6,79]. Moreover, an artificial promoter containing
four tandem repeats of the EE separated by 16 ran-
dom nucleotides confer evening-phased gene expression
to a luciferase reporter, confirming that the EE may be
sufficient to determine the phase of gene expression
[79]. Furthermore, mutations in the EE alter circadian
rhythms of gene expression, demonstrating that this
motif is necessary for evening phase of these genes
[2,58,80]. By contrast, many of the circadian-regulated
genes with an evening phase do not contain EEs in
their promoters, whereas EEs have been found in the
promoters of morning genes.
The EE differs in only one base pair from another
important circadian motif, the CCA1-binding site
(CBS) sequence, AAAAATCT. Wang et al. [81] first
characterized the CBS as the site for CCA1 binding in
CAB1 promoter. However, the CBS does not appear
to be over-represented in circadian gene promoters
[78]. Furthermore, there is contradictory evidence
regarding the role of the CBS in phase determination.
Harmer and Kay [79] found that changing the EE to a
CBS in a synthetic promoter based on the COLD
CIRCADIAN RHYTHM RNA BINDING 2 (CCR2)
promoter did not alter the peak expression phase of
the gene. By contrast, Michael and McClung [80]
showed that altering the EE motif in CATALASE 3
(CAT3)
4
promoter to a CBS could change the peak

expression phase of the gene from evening to morning.
Together, the results from these two groups suggest
that other elements in CAT3 promoter are required for
phase determination and that the context of the motif
is important.
Clearly, therefore, the EE and CBS are insufficient
to explain circadian expression of all the clock-
E. Yakir et al. Circadian clock output in plants
FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS 339
controlled genes and combinations of known and
unknown motifs are necessary for the correct phasing
of circadian genes. Recently, Harmer and Kay [79]
have identified a morning element (AACCACGA
AAAT) sequence that might have a role in determining
circadian expression and phase by binding of a yet
unknown transcription activator. Other motifs might
include the light-activation sequence G-box (CAC
GTG) and the related Hex element, but these have not
yet been tested experimentally [77,78,82].
Post-transcriptional control
The oscillator also regulates post-transcriptional con-
trol. For example, CCR2 mRNA accumulation is a
result of both transcriptional and post-transcriptional
regulation. CCR2 regulates the splicing of its own
transcript and that of the closely related COLD CIR-
CADIAN RHYTHM RNA BINDING 1 (CCR1), thus
circadian-regulated changes in the levels of CCR2 pro-
tein affect CCR1 and CCR2 mRNA accumulation [83–
86]. Another example is circadian control of the half-
life of some transcripts. CCR-LIKE

5
(CCL) and
SENESCENCE ASSOCIATED GENE 1 (SEN1 ) have
a longer half-life in the morning than in the afternoon
even under conditions of constant light and tempera-
ture [87]. CCL and SEN1 have in their 3¢-UTRs a
downstream element (DST) that can mediate transcript
stability [88]. Furthermore, CCL and SEN1 mRNA
decay is altered in a mutant that affects the DST decay
pathway [87]. Thus, DST may be involved in circadian
regulation of transcript stability.
Included in the cohort of plant genes controlled by
the circadian system are many genes that encode regu-
latory proteins such as kinases and phosphatases.
These proteins may act as secondary regulators of cir-
cadian output pathways. For example, the circadian
system controls expression of the gene encoding phos-
phoenolpyruvate carboxylase kinase that regulates
phosophorylation of phosphoenolpyruvate carboxylase
to catalyse fixation of CO
2
in crassulacean acid meta-
bolism plants [89].
The role of hormones in regulating circadian
output
Hormones affect most of the known circadian-con-
trolled processes in plants and it is likely that, at least
in some cases, the clock operates through changes in
hormone levels or hormone perception. However, to
date, there is only limited evidence for the role of

hormones in delivering information from the clock to
output processes.
In many plant species, including Arabidopsis, barley
(Hordeum distychum), wheat (Triticum aestivum), rye
(Secale cereale), red goosefoot and cotton, ethylene
production is under circadian control [90,91]. In Ara-
bidopsis, ethylene levels peak in the middle of the sub-
jective day. This pattern of ethylene accumulation is
correlated with the circadian regulation of expression
of ACC SYNTHASE which encodes the enzyme
responsible for the synthesis of the ethylene precursor,
1-amino-cyclopropane-1-carboxilic acid. The fact that
ethylene production is regulated by the circadian oscil-
lator might suggest that ethylene has a role in regula-
ting output processes. However, mutant plants that are
affected in ethylene biosynthesis and signaling show no
differences in rhythmic hypocotyl elongation or leaf
movement, two rhythmic growth processes that circa-
dian-controlled oscillations of ethylene might be expec-
ted to regulate [92]. Thus the biological significance of
rhythmic ethylene production is still unclear.
Greater success has been achieved in connecting
auxin to circadian regulation of growth. The levels of
free indole-3-acetic acid (IAA) and its conjugated form,
IAA–aspartate, were shown to cycle in continuous light
both in floral stems and in rosette leaves of Arabidopsis
[93]. There is also a circadian control of the expression
of genes involved in auxin transport and auxin
response [58,59]. More interestingly, the abolition of
rhythmic stem elongation following removal of the

floral stem, the endogenous source of auxin, can be res-
cued by the application of exogenous auxin [93].
The relationship between the circadian clock and
gibberellins (GAs) is more complicated. Both the
clock, via the photoperiod pathway, and GAs affect
flowering time in Arabidopsis, but most evidence
reveals genetic differences between the photoperiod
pathway and the GA pathway [94]. However in other
plants, such as darnel ryegrass (Lolium temulentum),
GAs may have a role in regulating photoperiodic
flowering [95–98]. Thus, it is possible that GAs have a
role in regulating circadian output.
There is some circumstantial evidence that other
hormones may be involved in regulating circadian out-
put. In carrot (Daucus carota), the levels of cytokinins
(CKs) are under circadian control [99]. While in
tobacco, CKs, as well as IAA and abscisic acid, are
rhythmic under diurnal condition [100]. It has been
suggested that CKs may also be a part of an input
pathway to the Arabidopsis clock [101,102].
The role of calcium in regulating circadian output
Calcium (Ca
2+
) is a second messenger in many differ-
ent processes in the plant cell and there is evidence
Circadian clock output in plants E. Yakir et al.
340 FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS
that it may play this role in the regulation of output
pathways from the circadian clock. Consistent with a
potential role in regulating circadian output, circadian

oscillations in free Ca
2+
have been demonstrated in
the cytosol and chloroplast of tobacco (Nicotiana
plumbaginifolia) and in the cytosol of Arabidopsis
[103,104]. However, there are differences in the circa-
dian oscillations of Ca
2+
; cytosolic oscillations of
Ca
2+
continue in constant light, whereas chloroplastic
oscillations of Ca
2+
continue only in constant dark
[103]. Furthermore, circadian oscillations of cytosolic
Ca
2+
in tobacco seedlings have different phases in dif-
ferent tissues and in Arabidopsis the phase of circadian
oscillations of cytosolic Ca
2+
is modulated by the
entraining photoperiod [104,105]. These results may
reflect a possible role for calcium in mediating different
clock controlled processes, including photoperiodism, in
different cells. Finally there is evidence that Ca
2+
has
a role in the circadian regulation of leaf movement in

legumes, and in stomatal opening and photoperiod-
controlled flowering in morning glory (Pharbitis nil)
[35,106]. Together these results strongly suggest that
Ca
2+
is part of the output signaling from the clock.
As yet, however, no molecular decoders of the circa-
dian Ca
2+
oscillations, such as calcium-binding pro-
teins, have been experimentally proven in plants
although a number of potential Ca
2+
decoders have
been identified [106].
Conclusions
The circadian system clearly plays an extremely
important role in the life of plants, and indeed other
organisms. However, despite this significance, and in
spite of the considerable advances in our understand-
ing of how the oscillator and input pathways func-
tion, there is still much we do not understand of how
the circadian system is able to accurately regulate so
many output processes. Deciphering the mechanisms
by which these output processes are controlled may
allow us to modify specific pathways that are regula-
ted by the circadian system. It will also give us a bet-
ter understanding of this important aspect of the lives
of plants.
Acknowledgements

The authors would like to thank Miri Hassidim, Shai
Yerushalmi, Ido Kron and David Greenberg for their
critical reading of the manuscript. Our apologies to the
many researchers whose work was not cited due to
limitation of space. This work was supported by ISF
grants (0397232 and 0397386).
References
1 Young MW & Kay SA (2001) Time zones: a compara-
tive genetics of circadian clocks. Nat Rev Genet 2, 702–
715.
2 Alabadi D, Oyama T, Yanovsky MJ, Harmon FG,
Mas P & Kay SA (2001) Reciprocal regulation
between TOC1 and LHY ⁄ CCA1 within the Arabidopsis
circadian clock. Science 293, 880–883.
3 Sugano S, Andronis C, Green RM, Wang Z-Y &
Tobin EM (1998) Protein kinase CK2 interacts with
and phosphorylates the Arabidopsis circadian clock-
associated 1 protein. Proc Natl Acad Sci USA 95,
11020–11025.
4 Sugano S, Andronis C, Ong MS, Green RM & Tobin
EM (1999) The protein kinase CK2 is involved in regu-
lation of circadian rhythms in Arabidopsis. Proc Natl
Acad Sci USA 96, 12362–12366.
5 Doyle MR, Davis SJ, Bastow RM, McWatters HG,
Kozma-Bognar L, Nagy F, Millar AJ & Amasino RM
(2002) The ELF4 gene controls circadian rhythms and
flowering time in Arabidopsis thaliana. Nature 419,
74–77.
6 Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO,
Ecker JR & Kay SA (2005) LUX ARRHYTHMO

encodes a Myb domain protein essential for circadian
rhythms. Proc Natl Acad Sci USA 102, 10387–
10392.
7 Kikis EA, Khanna R & Quail PH (2005) ELF4 is a
phytochrome-regulated component of a negative-feed-
back loop involving the central oscillator components
CCA1 and LHY. Plant J 44, 300–313.
8 Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K,
Onouchi H, Mouradov A, Fowler S, Kamada H,
Putterill J et al. (2005) Distinct roles of GIGANTEA
in promoting flowering and regulating circadian
rhythms in Arabidopsis. Plant Cell 17, 2255–2270.
9 Paltiel J, Amin R, Gover A, Ori N & Samach A
(2006) Novel roles for GIGANTEA revealed under
environmental conditions that modify its expression in
Arabidopsis and Medicago truncatula. Planta 224,
1255–1268.
6
10 Locke JC, Millar AJ & Turner MS (2005) Modelling
genetic networks with noisy and varied
experimental data: the circadian clock in Arabidopsis
thaliana. J Theoret Biol 234, 383–393.
11 Edwards KD, Lynn JR, Gyula P, Nagy F & Millar AJ
(2005) Natural allelic variation in the temperature-
compensation mechanisms of the Arabidopsis thaliana
circadian clock. Genetics 170, 387–400.
12 Gould PD, Locke JC, Larue C, Southern MM, Davis
SJ, Hanano S, Moyle R, Milich R, Putterill J, Millar
AJ et al. (2006) The molecular basis of temperature
compensation in the Arabidopsis circadian clock.

Plant
Cell 18, 1177–1187.
E. Yakir et al. Circadian clock output in plants
FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS 341
13 Salom AP & McClung CR (2005) What makes the
Arabidopsis clock tick on time? A review on entrain-
ment. Plant, Cell Environ 28, 21–38.
14 Nelson DC, Lasswell J, Rogg LE, Cohen MA & Bartel
B (2000) FKF1, a clock-controlled gene that regulates
the transition to flowering in Arabidopsis. Cell 101,
331–340.
15 Schultz TF, Kiyosue T, Yanovsky M, Wada M & Kay
SA (2001) A role for LKP2 in the circadian clock of
Arabidopsis. Plant Cell 13, 2659–2670.
16 Somers DE, Schultz TF, Milnamow M & Kay SA
(2000) ZEITLUPE encodes a novel clock-associated
PAS protein from Arabidopsis. Cell 101 , 319–329.
17 Devlin PF & Kay SA (2001) Circadian photopercep-
tion. Annu Rev Physiol 63, 677–694.
18 Imaizumi T, Tran HG, Swartz TE, Briggs WR & Kay
SA (2003) FKF1 is essential for photoperiodic-specific
light signalling in Arabidopsis. Nature 426, 302–306.
19 Hall A, Bastow RM, Davis SJ, Hanano S, McWatters
HG, Hibberd V, Doyle MR, Sung S, Halliday KJ,
Amasino RM et al. (2003) The TIME FOR COFFEE
gene maintains the amplitude and timing of Arabidop-
sis circadian clocks. Plant Cell 15, 2719–2729.
20 McWatters HG, Bastow RM, Hall A & Millar AJ
(2000) The ELF3 zeitnehmer regulates light signalling
to the circadian clock. Nature 408, 716–720.

21 Farre EM, Harmer SL, Harmon FG, Yanovsky MJ &
Kay SA (2005) Overlapping and distinct roles of PRR7
and PRR9 in the Arabidopsis circadian clock. Curr Biol
15, 47–54.
22 Yamamoto Y, Sato E, Shimizu T, Nakamich N, Sato
S, Kato T, Tabata S, Nagatani A, Yamashino T &
Mizuno T (2003) Comparative genetic studies on the
APRR5 and APRR7 genes belonging to the APRR1 ⁄
TOC1 quintet implicated in circadian rhythm, control
of flowering time, and early photomorphogenesis.
Plant Cell Physiol 44, 1119–1130.
23 Gardner MJ, Hubbard KE, Hotta CT, Dodd AN &
Webb AAR (2006) How plants tell the time. Biochem
J 397, 15–24.
24 McClung CR (2006) Plant circadian rhythms. Plant
Cell 18, 792–803.
25 Baskin JM & Baskin CC (1976) Effect of photoperiod
on germination of Cyperus inflexus seeds.
Bot Gaz 137,
269–273.
26 Black M & Wareing PF (1954) Photoperiodic control
of germination in seed of birch (Betula pubescens
Ehrh.). Nature 174, 705–706.
27 Black M & Wareing PF (1955) Growth studies in
woody species VII. Photoperiodic control of germina-
tion in Betula pudescens Ehrh. Physiologia Plantarum
8, 300–316.
28 Densmore RV (1997) Effect of day length on germina-
tion of seeds collected in Alaska. Am J Bot 84, 274–
278.

29 Zhong HH, Painter JE, Salome PA, Straume M &
McClung CR (1998) Imbibition, but not release from
stratification, sets the circadian clock in Arabidopsis
seedlings. Plant Cell 10 , 2005–2018.
30 Bryant TR (1972) Gas exchange in dry seeds: circadian
rhythmicity in the absence of DNA replication, tran-
scription, and translation. Science 178, 634–636.
31 Dowson-Day MJ & Millar AJ (1999) Circadian dys-
function causes aberrant hypocotyl elongation patterns
in Arabidopsis. Plant J 17, 63–71.
32 Fernandez SR & Wagner E (1994) New method of
measurement and analysis of the stem extension
growth rate to demonstrate complete synchronisation
of Chenopodium rubrum plants by environmental con-
ditions. J Plant Physiol 144, 362–369.
33 Lecharny A & Wagner E (1984) Stem extension rate in
light-grown plants. Evidence for an endogenous circa-
dian rhythm in Chenopodium rubrum. Physiologia Plan-
tarum 60, 437–443.
34 Tukey HB & Ketellapper HJ Jr (1963) Length of the
light–dark cycle and plant growth. Am J Bot 50, 110–
115.
35 Webb AAR (2003) The physiology of circadian
rhythms in plants. New Phytologist 160, 281–303.
36 Niinuma K, Someya N, Kimura M, Yamaguchi I &
Hamamoto H (2005) Circadian rhythm of circumnuta-
tion in inflorescence stems of Arabidopsis. Plant Cell
Physiol 46, 1423–1427.
37 Salter MG, Franklin KA & Whitelam GC (2003) Gat-
ing of the rapid shade-avoidance response by the circa-

dian clock in plants. Nature 426, 680–683.
38 Bu
¨
nning E (1936) Die endogene tagesrhythmik als
grundlage der photoperiodischen reaktion. Ber Dtsch
Bot Ges 54, 590–607.
39 Searle I & Coupland G (2004) Induction of flowering
by seasonal changes in photoperiod. EMBO J 23,
1217–1222.
40 Suarez-Lopez P, Wheatley K, Robson F, Onouchi H,
Valverde F & Coupland G (2001) CONSTANS med-
iates between the circadian clock and the control of
flowering in Arabidopsis. Nature 410, 1116–1120.
41 Valverde F, Mouradov A, Soppe W, Ravenscroft D,
Samach A & Coupland G (2004) Photoreceptor regula-
tion of CONSTANS protein in photoperiodic flower-
ing. Science 303, 1003–1006.
42 Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-
Sommer Z, Yanofsky MF & Coupland G (2000) Dis-
tinct roles of CONSTANS target genes in reproductive
development of Arabidopsis. Science 288, 1613–1616.
43 Huang T, Bohlenius H, Eriksson S, Parcy F &
Nilsson O (2005) The mRNA of the Arabidopsis gene
FT moves from leaf to shoot apex and induces flower-
ing. Science 309, 1694–1696.
44 Hayama R, Yokoi S, Tamaki S, Yano M & Shima-
moto K (2003) Adaptation of photoperiodic control
Circadian clock output in plants E. Yakir et al.
342 FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS
pathways produces short-day flowering in rice. Nature

422, 719–722.
45 Kojima S, Takahashi Y, Kobayashi Y, Monna L,
Sasaki T, Araki T & Yano M (2002) Hd3a, a rice
ortholog of the Arabidopsis FT gene, promotes transi-
tion to flowering downstream of Hd1 under short-day
conditions. Plant Cell Physiol 43, 1096–1105.
46 van Doorn WG & van Meeteren U (2003) Flower open-
ing and closure: a review. J Exp Bot 54, 1801–1812.
47 Overland L (1960) Endogenous rhythm in opening and
odor of flowers of Cestrum nocturnm. Am J Bot 47,
378–382.
48 Dudareva N, Martin D, Kish CM, Kolosova N,
Gorenstein N, Faldt J, Miller B & Bohlmann J (2003)
(E)-a-Ocimene and myrcene synthase genes of floral
scent biosynthesis in snapdragon: function and expres-
sion of three terpene synthase genes of a new terpene
synthase subfamily. Plant Cell 15, 1227–1241.
49 Kolosova N, Gorenstein N, Kish CM & Dudareva N
(2001) Regulation of circadian methyl benzoate emis-
sion in diurnally and nocturnally emitting plants. Plant
Cell 13, 2333–2347.
50 Verdonk JC, Ric de Vos CH, Verhoeven HA, Haring
MA, van Tunen AJ & Schuurink RC (2003) Regula-
tion of floral scent production in petunia revealed by
targeted metabolomics. Phytochemistry 62, 997–1008.
51 Pesti J (1976) Daily fluctuations in the sugar content of
nectar and periodicity of secretion in the Compositae.
Acta Agron Acad Sci Hung 25, 5–17.
52 Martinez-Garcia JF, Virgos-Soler A & Prat S (2002)
Control of photoperiod-regulated tuberization in

potato by the Arabidopsis flowering-time gene CON-
STANS. Proc Natl Acad Sci USA 99, 15211–15216.
53 Ramos A, Perez-Solis E, Ibanez C, Casado R, Collada
C, Gomez L, Aragoncillo C & Allona I (2005) Winter
disruption of the circadian clock in chestnut. Proc Natl
Acad Sci USA 102, 7037–7042.
54 Bohlenius H, Huang T, Charbonnel-Campaa L, Brun-
ner AM, Jansson S, Strauss SH & Nilsson O (2006)
CO ⁄ FT regulatory module controls timing of flowering
and seasonal growth cessation in trees. Science 312,
1040–1043.
55 Somers DE, Webb AAR, Pearson M & Kay SA (1998)
The short-period mutant, toc1-1, alters circadian clock
regulation of multiple outputs throughout development
in Arabidopsis thaliana. Development 125, 485–494.
56 Thimann KV, Tan Z-Y & Park J (1992) Cycling of
stomatal aperture in leaves of plants with crassulacean
acid metabolism under constant conditions. Am J Bot
79, 23–27.
57 Gorton HL, Williams WE & Assmann SM (1993) Cir-
cadian rhythms in stomatal responsiveness to red and
blue light. Plant Physiol 103, 399–406.
58 Harmer SL, Hogenesch JB, Straume M, Chang H-S,
Han B, Zhu T, Wang X, Kreps JA & Kay SA (2000)
Orchestrated transcription of key pathways in
Arabi-
dopsis by the circadian clock. Science 290, 2110–2113.
59 Schaffer R, Landgraf J, Accerbi M, Simon V, Larson
M & Wisman E (2001) Microarray analysis of diurnal
and circadian-regulated genes in Arabidopsis. Plant Cell

13, 113–123.
60 Pilgrim ML & McClung CR (1993) Differential invol-
vement of the circadian clock in the expression of
genes required for ribulose-1,5-bisphosphate
carboxylase ⁄ oxygenase synthesis, assembly, and activa-
tion in Arabidopsis thaliana. Plant Physiol 103, 553–
564.
61 Martino-Catt S & Ort DR (1992) Low temperature
interrupts circadian regulation of transcriptional activ-
ity in chilling-sensitive plants. Proc Natl Acad Sci USA
89, 3731–3735.
62 Salome PA, Michael TP, Kearns EV, Fett-Neto AG,
Sharrock RA & McClung CR (2002) The out of phase
1 mutant defines a role for PHYB in circadian phase
control in Arabidopsis. Plant Physiol 129, 1674–1685.
63 Booij-James IS, Swegle WM, Edelman M & Mattoo
AK (2002) Phosphorylation of the D1 photosystem II
reaction center protein is controlled by an endogenous
circadian rhythm. Plant Physiol 130, 2069–2075.
64 Lu Y, Gehan JP & Sharkey TD (2005) Daylength and
circadian effects on starch degradation and maltose
metabolism. Plant Physiol 138, 2280–2291.
65 McClung CR, Hsu M, Painter JE, Gagne JM, Karls-
berg SD & Salome PA (2000) Integrated temporal reg-
ulation of the photorespiratory pathway. Circadian
regulation of two Arabidopsis genes encoding serine
hydroxymethyltransferase. Plant Physiol 123, 381–392.
66 Fowler SG, Cook D & Thomashow MF (2005) Low
temperature induction of Arabidopsis CBF1, 2, and 3 is
gated by the circadian clock. Plant Physiol 137, 961–

968.
67 Rikin A, Dillwith JW & Bergman DK (1993) Correla-
tion between the circadian rhythm of resistance to
extreme temperatures and changes in fatty acid compo-
sition in cotton seedlings. Plant Physiol 101, 31–36.
68 Kreps JA, Wu Y, Chang H-S, Zhu T, Wang X & Har-
per JF (2002) Transcriptome changes for Arabidopsis
in response to salt, osmotic, and cold stress. Plant
Physiol 130, 2129–2141.
69 Thain SC, Hall A & Millar AJ (2000) Functional inde-
pendence of circadian clocks that regulate plant gene
expression. Curr Biol 10, 951–956.
70 Thain SC, Murtas G, Lynn JR, McGrath RB & Millar
AJ (2002) The circadian clock that controls gene
expression in Arabidopsis is tissue specific. Plant Phy-
siol 130, 102–110.
71 Ceriani MF, Hogenesch JB, Yanovsky M, Panda S,
Straume M & Kay SA (2002) Genome-wide expression
analysis in Drosophila reveals genes controlling circa-
dian behavior. J Neurosci 22, 9305–9319.
E. Yakir et al. Circadian clock output in plants
FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS 343
72 Nowrousian M, Duffield GE, Loros JJ & Dunlap JC
(2003) The frequency gene is required for temperature-
dependent regulation of many clock-controlled genes
in Neurospora crassa. Genetics 164, 923–933.
73 Panda S, Antoch MP, Miller BH, Su AI, Schook AB,
Straume M, Schultz PG, Kay SA, Takahashi JS &
Hogenesch JB (2002) Coordinated Transcription of key
pathways in the mouse by the circadian clock. Cell

109, 307–320.
74 Liu Y, Tsinoremas NF, Johnson CH, Lebedeva NV,
Golden SS, Ishiura M & Kondo T (1995) Circadian
orchestration of gene expression in cyanobacteria.
Genes Dev 9, 1469–1478.
75 McClung CR (2006) Two-component signaling pro-
vides the major output from the cyanobacterial circa-
dian clock. Proc Natl Acad Sci USA 103, 11819–11820.
76 Takai N, Nakajima M, Oyama T, Kito R, Sugita C,
Sugita M, Kondo T & Iwasaki H (2006) A KaiC-asso-
ciating SasA–RpaA two-component regulatory system
as a major circadian timing mediator in cyanobacteria.
Proc Natl Acad Sci USA 103, 12109–12114.
77 Edwards KD, Anderson PE, Hall A, Salathia NS,
Locke JCW, Lynn JR, Straume M, Smith JQ &
Millar AJ (2006) FLOWERING LOCUS C mediates
natural variation in the high-temperature response of
the Arabidopsis circadian clock. Plant Cell 18, 639–
650.
78 Michael TP & McClung CR (2003) Enhancer trapping
reveals widespread circadian clock transcriptional con-
trol in Arabidopsis. Plant Physiol 132, 629–639.
79 Harmer SL & Kay SA (2005) Positive and negative
factors confer phase-specific circadian regulation of
transcription in Arabidopsis. Plant Cell 17, 1926–1940.
80 Michael TP & McClung CR (2002) Phase-specific cir-
cadian clock regulatory elements in Arabidopsis. Plant
Physiol 130, 627–638.
81 Wang ZY, Kenigsbuch D, Sun L, Harel E, Ong MS &
Tobin EM (1997) A Myb-related transcription factor is

involved in the phytochrome regulation of an Arabi-
dopsis Lhcb gene. Plant Cell 9, 491–507.
82 Hudson ME & Quail PH (2003) Identification of pro-
moter motifs involved in the network of phytochrome
A-regulated gene expression by combined analysis of
genomic sequence and microarray data. Plant Physiol
133, 1605–1616.
83 Heintzen C, Nater M, Apel K & Staiger D (1997)
AtGRP7, a nuclear RNA-binding protein as a compo-
nent of a circadian-regulated negative feedback loop in
Arabidopsis thaliana. Proc Natl Acad Sci USA 94,
8515–8520.
84 Schoning JC & Staiger D (2005) At the pulse of time:
protein interactions determine the pace of circadian
clocks. FEBS Lett 579, 3246–3252.
85 Staiger D, Apel K & Trepp G (1999) The Atger3 pro-
moter confers circadian clock-regulated transcription
with peak expression at the beginning of the night.
Plant Mol Biol 40, 873–882.
86 Staiger D, Zecca L, Kirk DAW, Apel K & Eckstein L
(2003) The circadian clock regulated RNA-binding
protein AtGRP7 autoregulates its expression by influ-
encing alternative splicing of its own pre-mRNA. Plant
J 33, 361–371.
87 Lidder P, Gutierrez RA, Salome PA, McClung CR &
Green PJ (2005) Circadian control of messenger RNA
stability. Association with a sequence-specific messenger
RNA decay pathway. Plant Physiol 138, 2374–2385.
88 Newman TC, Ohme-Takagi M, Taylor CB & Green PJ
(1993) DST sequences, highly conserved among plant

SAUR genes, target reporter transcripts for rapid
decay in tobacco. Plant Cell 5, 701–714.
89 Hartwell J, Gill A, Nimmo GA, Wilkins MB, Jenkins
GI & Nimmo HG (1999) Phosphoenolpyruvate car-
boxylase kinase is a novel protein kinase regulated at
the level of expression. Plant J 20, 333–342.
90 Jasoni RL, Cothren T, Morgan PW & Sohan DE
(2004) Circadian ethylene production in cotton. Plant
Growth Regulation 36, 127–133.
91 McClung CR (2000) Circadian rhythms in plants: a
millennial view. Physiologia Plantarum 109, 359–371.
92 Thain SC, Vandenbussche F, Laarhoven LJJ, Dowson-
Day MJ, Wang Z-Y, Tobin EM, Harren FJM, Millar
AJ & Van Der Straeten D (2004) Circadian rhythms of
ethylene emission in Arabidopsis. Plant Physiol 136,
3751–3761.
93 Jouve L, Gaspar T, Kevers C, Greppin H & Degli
Agosti R (1999) Involvement of indole-3-acetic acid in
the circadian growth of the first internode of Arabidop-
sis. Planta 209, 136–142.
94 Boss PK, Bastow RM, Mylne JS & Dean C (2004)
Multiple pathways in the decision to flower: enabling,
promoting, and resetting. Plant Cell 16, S18–S31.
95 King RW & Evans LT (2003) GIBBERELLINS and
FLOWERING OF GRASSES and CEREALS: prizing
open the lid of the ‘florigen’ black box. Annu Rev Plant
Biol 54, 307–328.
96 King RW, Evans LT, Mander LN, Moritz T, Pharis R
& Twitchin B (2003) Synthesis of gibberellin GA6 and
its role in flowering of Lolium temulentum. Phytochem-

istry 62, 77–82.
97 King RW, Moritz T, Evans LT, Martin J, Andersen
CH, Blundell C, Kardailsky I & Chandler PM (2006)
Regulation of flowering in the long-day grass Lolium
temulentum by gibberellins and the FLOWERING
LOCUS T cene. Plant Physiol 141, 498–507.
98 MacMillan CP, Blundell CA & King RW (2005) Flow-
ering of the grass Lolium perenne. Effects of vernaliza-
tion and long days on gibberellin biosynthesis and
signaling. Plant Physiol 138, 1794–1806.
99 Stiebeling B & Neumann K-H (1986) Identification
and concentation of endogenous cytokinins in carrots
Circadian clock output in plants E. Yakir et al.
344 FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS
(Daucus carota L.) as influenced by development and a
circadian rhythm. J Plant Physiol 127 , 111–121.
100 Novakova M, Motyka V, Dobrev PI, Malbeck J,
Gaudinova A & Vankova R (2005) Diurnal variation
of cytokinin, auxin and abscisic acid levels in tobacco
leaves. J Exp Bot 56, 2877–2883.
101 Salome PA, To JPC, Kieber JJ & McClung CR (2006)
Arabidopsis response regulators ARR3 and ARR4 play
cytokinin-independent roles in the control of circadian
period. Plant Cell 18, 55–69.
102 Zheng B, Deng Y, Mu J, Ji Z, Xiang T, Niu Q-W,
Chua N-H & Zuo J (2006) Cytokinin affects circadian-
clock oscillation in a phytochrome B- and Arabidopsis
response regulator 4-dependent manner. Physiologia
Plantarum 127, 277–292.
103 Johnson CH, Knight MR, Kondo T, Masson P, Sed-

brook J, Haley A & Trewavas A (1995) Circadian
oscillations of cytosolic and chloroplastic free calcium
in plants. Science 269, 1863–1865.
104 Wood NT, Haley A, Viry-Moussaid M, Johnson CH,
van der Luit AH & Trewavas AJ (2001) The calcium
rhythms of different cell types oscillate with different
circadian phases. Plant Physiol 125, 787–796.
105 Love J, Dodd AN & Webb AAR (2004) Circadian and
diurnal calcium oscillations encode photoperiodic
information in Arabidopsis. Plant Cell 16, 956–966.
106 Dodd AN, Love J & Webb AAR (2005) The plant
clock shows its metal: circadian regulation of cytosolic
free Ca
2+
. Trends Plant Sci 10, 15–21.
E. Yakir et al. Circadian clock output in plants
FEBS Journal 274 (2007) 335–345 ª 2006 The Authors Journal compilation ª 2006 FEBS 345