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Integrating circadian dynamics with
physiological processes in plants
Kathleen Greenham and C. Robertson McClung
Abstract | The plant circadian clock coordinates the responses to multiple and often
simultaneous environmental challenges that the sessile plant cannot avoid. These responses
must be integrated efficiently into dynamic metabolic and physiological networks essential
for growth and reproduction. Many of the output pathways regulated by the circadian
clock feed back to modulate clock function, leading to the appreciation of the clock as a
central hub in a sophisticated regulatory network. In this Review, we discuss the circadian
regulation of growth, flowering time, abiotic and biotic stress responses, and metabolism,
as well as why temporal ‘gating’ of these processes is important to plant fitness.
Self-sustaining periodicity
Continued rhythmicity in the
absence of environmental
stimuli.
Entrainment
Setting of period and phase
by external cues, termed
zeitgeber (‘time giver’ in
German), the strongest of
which is light. Temperature
cycles can also be effective
zeitgebers.
Temperature compensation
The close maintenance of
circadian periods within a
physiological range at varying
temperatures by buffering to
compensate for changes in the
rates of biochemical reactions.
Department of Biological
Sciences, Dartmouth College,
Hanover, New Hampshire
03755, USA.
Correspondence to C.R.M. e-mail: c.robertson.mcclung@
dartmouth.edu
doi:10.1038/nrg3976
Published online
15 September 2015;
corrected online 13 October
2015
In 1729, the French astronomer de Mairan demonstrated that rhythmic leaf movement of a heliotrope
plant, most likely Mimosa pudica, persisted in constant
darkness and therefore was of endogenous origin. The
periodicity of this rhythm was approximately 24 hours,
revealing an internal mechanism resonating with the
light–dark cycle present on Earth1. Endogenous circadian oscillators occur in all domains of life (Bacteria,
Archaea and Eukaryota)2 and share common properties
of self-sustaining periodicity, entrainment and temperature
compensation1. Central to all oscillators are autoregulatory feedback loops that drive the rhythmic behaviour
of genes, proteins and metabolites.
Most studies of the plant circadian clock have considered Arabidopsis thaliana. In A. thaliana, and plants in
general, the circadian clock comprises interlocked feedback loops regulated both transcriptionally and posttranscriptionally, including through post-translational
modification and protein turnover 3. Components of
the circadian oscillator can be described based on the
timing of their expression patterns with morning‑,
daytime‑ and evening‑phased genes. Extensive transcriptional and post-transcriptional feedback loops
maintain proper timing of expression of each gene and
their downstream targets throughout the day 3–7 (FIG. 1).
Thus, the circadian clock modifies responsiveness to
environmental stimuli throughout the day, a property
known as ‘gating’. In silico modelling of an evolving
clock system required varying photoperiods coupled
with environmental changes to generate a circadian
clock with interlocked feedback loops 8, suggesting
that the complexity of the plant circadian clock is an
adaptive response to the changing environment.
Accumulating evidence supports the importance of
circadian rhythms; fitness costs are associated with disrupting the circadian clocks of cyanobacteria and plants9.
To dissociate circadian from diurnal control, experiments
are performed under free-running conditions in which the
oscillator drives rhythmicity in the absence of environmental time cues and clock function is assessed via the
free-running period and phase. External time cues, or
resetting stimuli, vary in effect depending on the time of
day. For example, a pulse of light in the morning advances
the phase of the clock whereas a pulse late in the day
delays the phase. Differences in free-running period
translate to differences in phase under 24‑hour conditions. In general, a long period confers a lagging phase
whereas a short period confers a leading phase1. However,
circadian phase can also vary independently of period10,11.
Regulation of plant physiology by the circadian clock
is widespread. This Review considers a few of the bestcharacterized outputs, including growth, flowering time,
abiotic and biotic stress responses, and metabolism
(FIG. 2). This focus, although limited, should nonetheless
illustrate the breadth of regulatory mechanisms by which
the circadian clock coordinates plant physiology and
behaviour with the daily and seasonal cycles imposed
by the Earth’s rotation and axial tilt. We emphasize the
synchrony of responses driven by the oscillator and the
importance of integrating circadian information into
predictive network models for improved crop breeding.
Circadian gene regulation
Transcriptional regulation. A common theme in circadian output pathway regulation is the overarching transcriptional control imposed by the circadian oscillator
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CCA1
and LHY
PRR9
TOC1
PRR7
ELF4
ELF3
LUX
RVE8
PRR5
GI
ZTL
Morning-phased
genes
Protein
Positive transcriptional regulation
Negative transcriptional regulation
Evening-expressed
genes
EC
Post-translational regulation
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| Genetics
Figure 1 | Model of the Arabidopsis thaliana circadian clock. Nature
The circadian
clock
network comprises a series of interlocked feedback loops with transcriptional,
post-transcriptional and post-translational regulation. The morning-phased genes
LATE‑ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK‑ASSOCIATED 1 (CCA1),
whose expression peaks at dawn, activate the daytime‑expressed genes
PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, which together with PRR5 repress
CCA1 and LHY. The PRRs also repress REVEILLE 8 (RVE8), which induces the expression
of evening-phased genes, including TIMING OF CAB EXPRESSION 1 (TOC1), LUX
ARRHYTHMO (LUX) and EARLY FLOWERING 4 (ELF4). ELF3, ELF4 and LUX form the
evening complex (EC), a multi-protein complex that represses the expression of
day-phased genes, PRR7 and PRR9. TOC1 also inhibits the expression of morning-phased
CCA1, LHY, PRR9 and PRR7. As well as from transcriptional regulation, there is substantial
post‑translational regulation of the network. TOC1 and PRR5 protein levels are regulated
through SKP‑, CULLIN‑ and F box‑containing complex-dependent degradation mediated
by the F box protein ZEITLUPE (ZTL), which is stabilized by GIGANTEA (GI). Transcriptional
regulation is emphasized in this model and depicted by solid red and black lines. Genes
with peak expression during the day are indicated with yellow boxes and evening genes
are indicated with blue boxes. Dashed lines indicate post-translational regulation with
ZTL, the only protein in the model and depicted as an oval. The EC is represented by the
light blue circle surrounding ELF3, ELF4, and LUX. Lines that meet the edge of the light
blue circle indicate regulation of the entire EC, whereas lines leading to specific boxes
indicate regulation of that single gene, as seen for TOC1 negative regulation of ELF4 and
LUX but not of ELF3. For additional details of the circadian clock model, we refer the
reader to REFS 3–7. Adapted with permission from REF. 132, Wiley.
Circadian clock
An endogenous time-keeping
mechanism that requires
approximately 24 hours to
complete a single cycle.
Photoperiods
The duration of light in
one day.
in response to environmental cues. The feedback model
inherent in the oscillator provides a network of input
and output pathways that are temporally and spatially
regulated. Transcriptional studies have assigned large
portions of the transcriptome to circadian-regulated
gene sets that include growth, stress response, hormone
signalling and metabolism12–14. Most studies have been
performed in A. thaliana, but other plants, including
Oryza sativa and Populus trichocarpa, similarly exhibit
circadian regulation of a large portion of the transcriptome15. These transcriptome studies have enabled the
identification of circadian‑regulated genes in diurnal
expression studies.
A model generated from field-grown rice sampled
for temporal transcriptome data that incorporated meteorological data successfully predicted transcriptome
dynamics of the following growing season. Critical to the
predictive performance of the model was the incorporation of a gating function to account for the circadian control of the response to the environment. Genes known to
be circadian regulated required a gate model to properly
predict their expression dynamics16. Using the expression
patterns for a subset of circadian clock genes in relation to
the physical time of day, the progression of internal time
over the course of one growing season was calculated.
Although individual clock genes were strongly affected by
solar radiation or temperature, the overall progression of
the internal time was relatively constant17. Further experimental data are needed to test this concept of averaging
clock gene expression to achieve an internal time; however,
it argues for caution when interpreting the implications
of expression changes of individual clock genes.
The breadth of circadian regulation of transcription is
further substantiated by chromatin immunoprecipitation
followed by sequencing (ChIP–seq) studies using circadian clock transcription factors. One such experiment
estimated that 40% of known circadian‑regulated genes,
including clock components, are TIMING OF CAB
EXPRESSION 1 (TOC1; also known as APRR1) targets,
with TOC1 acting as a repressor of morning-phased
genes18. Similarly, PSEUDO-RESPONSE REGULATOR 5
(PRR5) binds to the promoters of genes enriched for
morning-phased expression involved in functions such as
hypocotyl elongation, flowering time and cold response.
This is also consistent with the evening expression
of PRR5 and its role in repressing morning‑phased
genes19. PRR7 ChIP-seq revealed binding to end‑of‑night
and early morning‑phased genes with enrichment for
transcriptional regulators involved in the circadian clock,
growth, stress response and light signalling 20. Combining
ChIP-seq and transcriptome studies provides a powerful tool for dissecting the distinct roles of circadian clock
genes in regulating specific output pathways.
In addition to temporal regulation, spatial regulation
contributes to circadian dynamics in the plant. Spatial
organization of clock function was first indicated by the
ability to entrain the two cotyledons and shoot apex to
out‑of‑phase light–dark cycles21. More recently, diurnal
microarray analysis of tissue‑specific expression has
revealed different expression profiles of several circadian clock genes in different tissues and according to day
length22. Comparison of whole‑leaf, mesophyll, vascular
and epidermal tissues revealed the mesophyll to be the
predominant tissue contributing to transcript abundance
cycles in whole‑leaf samples22. Application of cell‑sorting
technology and more‑accurate cell-type‑specific markers will improve associations between transcriptional
changes and metabolic processes and refine existing
whole‑leaf and whole‑seedling expression studies.
Post‑transcriptional regulation. In addition to transcriptional regulation, there is substantial posttranscriptional and post-translational regulation of
the network. Examples include regulated mRNA and
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and PRR9 (REFS 31–33); however, whether this process
is stress‑dependent remains to be seen. Further study is
needed to determine how these various splice forms contribute to mature mRNA accumulation in response to
environmental cues.
Light signalling
Photoperiodic
flowering
Biotic stress
Hormone
signalling
Metabolism
O
OH
COOH
Abiotic
stress
Growth responses
Figure 2 | The circadian system of plants. The circadian clockNature
occupies
a central
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| Genetics
position in the regulatory network of plants. The traditional view has been of a linear
pathway in which environmental stimuli, such as light and temperature, entrain the clock,
which then regulates output pathways. However, extensive data have accumulated in
support of a more complex networked view in which the clock regulates its own
sensitivity to entraining stimuli, for example through regulated expression of
photoreceptors. Metabolic pathways, as well as abiotic‑ and biotic‑stress responses,
often show circadian regulation, but metabolic intermediates, hormones and
stress‑signalling pathways feed back to modulate clock function (indicated by
bidirectional arrows). In addition, there is considerable crosstalk among clock-modulated
signalling pathways (indicated by coloured arrows for each output pathway). Thus, the
circadian clock has a central role in an integrated system to temporally coordinate
physiological and metabolic responses with the environment.
Free-running conditions
Experimental environment
under constant light and
temperature, permitting
assessment of the
endogenous periodicity
and phase of a rhythm.
Period
The time to complete
a single cycle under
constant conditions of
light and temperature.
Phase
The time in the circadian
rhythm at which a
particular rhythmic output
occurs. Typically, acrophase
(peak of the rhythm) is
measured but trough, mid-rise
and mid-fall are also used.
protein stability, nucleocytoplasmic partitioning and
post-translational modification23–25. Recent studies have
implicated regulated alternative splicing in circadian
clock function; for example, thermosensitive alternative
splicing, in which isoform accumulation varies with
temperature, occurs for several clock genes26–28. The
production of premature in‑frame termination codons
(PTCs), referred to as unproductive alternative splicing
(UAS), often leads to mRNA decay but can yield stable truncated proteins. Cold regulation of CIRCADIAN
CLOCK‑ASSOCIATED 1 (CCA1) alternative splicing
contributes to freezing tolerance — CCA1 alternative
splicing generates two PTC isoforms with differences in
the length of retention of the fourth intron29. These isoforms accumulate to varying levels in response to abiotic
and biotic stresses and involve the serine/arginine-rich
SR45 splicing factor 26,30. A PTC‑containing isoform of
CCA1 retaining the full fourth intron increased with a
phase delay of several hours in response to a 4–25 °C
cold‑acclimation thermocycle and a 4–37 °C transition while the mature mRNA maintained its phasing
across conditions. Differences in phasing between the
two PTC isoforms suggest they contribute differentially
to CCA1 mature mRNA levels30. The splicing factor
PROTEIN ARGININE METHYLTRANSFERASE 5
(PRMT5) contributes to the alternative splicing of PRR7
Growth
Complex circadian gene regulation is needed to coordinate the many pathways involved in specific aspects of
plant growth. The well-characterized growth of the germinating seedling stem (hypocotyl elongation) provides
an excellent example of circadian regulation of growth.
Rhythmic elongation in constant light establishes the
circadian regulation of this growth process34, although
growth under constant darkness is arrhythmic35, demonstrating that light is required for circadian‑regulated
hypocotyl elongation. Light-dependent rhythmic
growth relies on two basic helix–loop–helix (bHLH)
transcription factors, PHYTOCHROME‑INTERACTING
FACTOR 4 (PIF4) and PIF5, whose mRNA and protein
levels correlate with growth35. PIF4 and PIF5 integrate
several growth‑promoting pathways, including the circadian clock, light, sucrose, temperature and hormone
signalling 36–39. PIF4 and PIF5 are positive regulators of
hypocotyl growth, and their expression patterns coincide
with the end‑of‑night phase of elongation. PIF4 and PIF5
are targeted for degradation through a light‑regulated,
PHYTOCHROME B (PHYB)-dependent process40. The
proper circadian regulation of PIF4 and PIF5 expression depends on early evening repression by the evening complex (EC)41. The carboxy‑terminal domain of
the EC component EARLY FLOWERING 3 (ELF3)
interacts with PIF4 to inhibit its activity as a transcriptional regulator 42 in the early night 35. Arrhythmic,
CCA1‑overexpressing (CCA1‑OX) plants have elevated
PIF4 and PIF5 levels, so they lack early night growth
repression and elongate throughout the night. Light
maintains the inactivation of PIF4 and PIF5 during the
day, resulting in similar growth repression in CCA1‑OX
and wild‑type plants during the day 42. The internal
regulation by the circadian clock coupled with external
photoperiod cues reveals an elegant external coincidence
mechanism for hypocotyl elongation43.
Other environmental cues affecting hypocotyl elongation include temperature and shading, both of which
involve the EC component ELF3. Quantitative trait
locus (QTL) mapping with A. thaliana natural accessions revealed variation in thermoresponsive hypocotyl
growth and implicated ELF3, a second EC component,
LUX ARRHYTHMO (LUX; also known as PCL1), and
PHYB. The elf3‑1 loss‑of‑function mutant exhibits
enhanced growth under control temperatures and does
not increase growth at high temperature, coinciding with
elevated PIF4 levels under both conditions. This mutant
also loses high‑temperature induction of LUX expression, suggesting that ELF3 is required for this rapid
thermoresponsiveness44. Natural allelic variation in ELF3
also alters the hypocotyl elongation response to shading;
QTL mapping in an A. thaliana Bayreuth and Shahdara
(Bay‑0 × Sha) recombinant inbred line (RIL) population
revealed that the Bay‑0 ELF3 allele confers longer period
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Phytochrome
Red (~650 nm) and far-red
(~740 nm) light-absorbing
photoreceptors. In
Arabidopsis thaliana,
phytochromes are encoded by
a five-member gene family,
PHYTOCHROME A (PHYA)–
PHYE. The phytochrome
apoproteins are covalently
bound to a linear tetrapyrrole
chromophore.
External coincidence
The coincidence of an
internal rhythm driven by the
circadian clock with external
photoperiodic information.
For example, on short days,
CONSTANS (CO) mRNA and
protein are synthesized
after dusk; in the dark,
CO is unstable and fails to
accumulate. By contrast,
on long days, CO mRNA
accumulates before dusk,
so newly translated CO is
stabilized in the light and
accumulates.
Florigens
Molecules (or molecular
complexes) responsible for
floral induction. Florigens are
produced in the leaves and
transmitted through the
phloem to the shoot apical
meristem of buds and
growing tips.
Internal coincidence
The coincidence of two internal
rhythms driven by the
circadian clock. For example,
GIGANTEA (GI) accumulates
at about dusk on short days,
whereas FLAVIN-BINDING
KELCH REPEAT F-BOX 1 (FKF1)
peaks after dark. However,
under long-day conditions, the
peaks of both proteins coincide
in the late afternoon, enabling
the accumulation of an
FKF1–GI complex.
Long-day plant
A plant that exhibits a
photoperiodic behaviour (for
example, accelerated flowering)
when the day length is greater
than a threshold value.
Cryptochrome
(CRY). Blue‑light‑absorbing
photoreceptors. In
Arabidopsis thaliana,
CRYs are encoded by two
genes, CRY1 and CRY2.
The CRY apoproteins are
non‑covalently bound to pterin
and flavin chromophores,
which absorb light at 380 nm
and 450 nm, respectively.
and greater response to shade than the Sha allele45,46. Loss
of ELF3 also disrupts rhythmic root growth rates under
diurnal and free‑running conditions47.
ELF3 is essential for maintaining rhythmic leaf
growth and movement. Maximal leaf growth occurs several hours after dawn, a pattern inconsistent with PIF4
and PIF5 expression levels, which contribute to but are
not essential for rhythmic leaf growth in A. thaliana48.
Rhythmic leaf growth can be maintained under freerunning conditions in other dicotyledonous plants,
including Ricinus communis, but not in the monocotyledonous Zea mays or O. sativa 49. In Brachypodium
distachyon, growth rate seems to be controlled by temperature and not by the circadian clock50. These studies
highlight the versatility of the circadian clock network,
which temporally regulates growth processes through
multiple output pathways.
Photoperiodic flowering
Many plants use day length to coordinate flowering
with the season, thereby improving reproductive success (fitness) (FIG. 3). Day length is measured in the
leaves via complex networks that regulate the expression of florigens that are transmitted to the shoot apical
meristem to induce floral meristem identity (FMI) genes
(FIG. 3a). The measurement of day length requires the circadian clock — mutations that disrupt clock function
are often associated with altered flowering timing 51–53.
Studies, most advanced in A. thaliana, have elucidated
a molecular network for the photoperiodic regulation
of flowering time that includes features consistent with
both internal coincidence and external coincidence models51–53. Therefore, the coincidence mechanism coordinating flowering in A. thaliana shares properties with the
model of hypocotyl elongation: both integrate external
cues with internal control by the circadian clock54.
Photoperiodic flowering in A. thaliana. Clock function
specifically in the phloem companion cells of the leaf
(where FLOWERING LOCUS T (FT), CONSTANS (CO)
and other critical regulators of photoperiodic flowering
are expressed51–53) and not, for example, in the mesophyll,
is critical for photoperiodic flowering 22. In A. thaliana,
a long-day plant, expression of the florigen genes FT and
TWIN SISTER OF FT (TSF) increases in the afternoon
of long days51–53, mainly in response to the accumulation of
CO, a critical transcriptional activator (FIG. 3a). The accumulation of CO under long-day conditions entails both
transcriptional and post-transcriptional regulation. Clock
information is transmitted to CO via clock-regulated
activators and suppressors of CO transcription, and via
the cycling clock protein GIGANTEA (GI)51–53.
CYCLING DOF FACTORs (CDFs) repress CO transcription in the morning. In the afternoon, CDF transcription is repressed51–53, and on long days CDFs are degraded
by a complex of FLAVIN-BINDING KELCH REPEAT
F-BOX 1 (FKF1; also known as ADO3) and GI 55.
Transcription of both FKF1 and GI is clock‑regulated.
On short days, GI protein accumulates to a peak at dusk,
whereas FKF1 protein peaks after dark, so FKF1 and GI
do not interact (FIG. 3b). However, under long days, the
peaks of both proteins coincide in late afternoon, permitting accumulation of the FKF1–GI complex (FIG. 3e).
Light enhances the interaction of FKF1, a blue-light photoreceptor, with GI, an example of external coincidence
of the environmental light–dark cycle with the internally
cycling FKF1–GI complex. Thus, in the afternoon of
long days, FKF1 and GI form a ubiquitin ligase complex
that targets CDFs for proteasomal degradation (FIG. 3f),
thereby derepressing CO56.
The outcome of the regulatory network governing CO
transcription is that CO mRNA accumulates after dusk
under short days (FIG. 3c). CO fails to accumulate in the
dark (FIG. 3d) because the protein is degraded by a complex of CONSTITUTIVE PHOTOMORPHOGENESIS 1
(COP1) and SUPPRESSOR OF PHYA‑105 1 (SPA1)57,58.
However, under long days, CO mRNA and protein
accumulate in the afternoon light, which stabilizes
CO in another example of external coincidence51–53,59.
Photoactivated CRYPTOCHROME 2 (CRY2) complexes with
COP1 and SPA1 to suppress CO degradation60. Blue-light
activation of FKF1 also enhances its interaction with, and
stabilization of, CO through an unknown mechanism56.
FT transcription is also induced independently of
CO. Several CRY2‑INTERACTING bHLH (CIB) transcription factors accumulate under long days and bind
as heterodimers to the FT promoter to activate FT transcription61,62. The CIBs are activated in the afternoon by
blue-light‑dependent interaction with CRY2 (REFS 62,63).
In addition, CIB protein stability is enhanced in blue light
via interaction with the FKF1 relatives ZEITLUPE (ZTL;
also known as ADO1) and LOV KELCH PROTEIN 2
(LKP2; also known as ADO2), although not with FKF1
(REF. 63). Thus, this CO‑independent induction of FT is
mediated in the afternoon and/or evening of long days
via two classes of blue‑light photoreceptors, CRY2 for
CIB activation and ZTL and LKP2 for CIB stabilization. FT and TSF are transmitted via the phloem to the
shoot apical meristem, where they complex with FD to
activate several SQUAMOSA PROMOTER‑BINDING
PROTEIN‑LIKE (SPL) transcription factors, which in
turn activate FMI genes51 (FIG. 3a).
In summary, photoperiodic flowering in A. thaliana
relies on oscillating components driven by the circadian
clock and features elements of both internal and external coincidence. Particularly prominent are examples
of external coincidence, in which light signalling in
the afternoon of long days leads to the degradation of
flowering repressors, such as the CDFs, and stabilizes or
activates flowering inducers, such as CO and the CIBs.
Photoperiodic flowering in long‑day cereals. The role of
the clock in photoperiodic flowering of long-day cereals,
such as wheat and barley, is incompletely understood,
although the function of CO and FT homologues seems
conserved with A. thaliana 51–53. Photoperiod insensitivity is conferred by disrupting the wheat and barley
homologues of PRR7, PHOTOPERIOD 1 (PPD1) or
PPD‑H1 (REFS 64,65). Although both PPD1 and PPD‑H1
are clock-regulated66,67, their disruption fails to alter circadian period68,69, suggesting that they are clock outputs
but not essential for clock function. Another distinction
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a
CO
GI
FT
FMIs
FKF1
FT
FT
Short day
b
Light
FD
Long day
e
Dark
Light
Dark
Internal
and external
coincidence
GI protein
FKF1 protein
GI–FKF1 complex
c
f
CDF protein
CO mRNA
d
PHYA
g
CO protein
CRY2
FKF1
External
coincidence
FT mRNA
CO protein
FT mRNA
Photoperiodic transition
Vegetative
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◀ Figure 3 | Photoperiodic regulation of flowering initiation in Arabidopsis thaliana. a | Photoperiodic sensing occurs in the phloem companion cells of the leaf.
Clock-regulated GIGANTEA (GI) and FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1)
activate FLOWERING LOCUS T (FT) transcription through a coherent feed-forward loop,
and FT protein (a florigen) is transmitted to the shoot apical meristem (SAM) via the
phloem. In the SAM, FT complexes with FD to activate the transcription of several
floral meristem identity (FMI) genes, including LEAFY (LFY), SUPPRESSOR OF
OVEREXPRESSION OF CONSTANS 1 (SOC1), APETALA1 (AP1) and FRUITFULL (FUL; also
known as AGL8). The induction of the FMIs by FT–FD is indirect. FT–FD induces several
SQUAMOSA PROMOTER‑BINDING PROTEIN‑LIKE (SPL) transcription factors, which in
turn directly activate the FMIs but which have been omitted for simplicity and clarity.
b | GI transcript abundance oscillates owing to transcriptional regulation by the clock,
such that on short days GI protein accumulates to a maximum at or near dusk. Although
FKF1 transcript and protein abundance also oscillate, the maximum accumulation
of FKF1 protein occurs after dusk. Thus, the GI–FKF1 complex accumulates to low levels
in the dark and does not include light-activated FKF1. c | Clock‑regulated transcription
of the CYCLING DOF FACTOR (CDF) genes results in accumulation of CDF mRNA (not
shown) and protein in the morning. CDF protein binds to the CONSTANS (CO) promoter
to repress transcription. d | Repression of CO transcription is relieved after dusk, but
unstable CO protein fails to accumulate. As a consequence, FT transcription and mRNA
and protein levels remain low. e | On long days, the peak accumulation of GI protein is
phase‑delayed and coincides with the peak accumulation of FKF1 protein; both
proteins attain maximal levels when it is light, an example of the internal coincidence
of two endogenous circadian oscillations. As a result, greater levels of the GI–FKF1
complex accumulate and contain light-activated FKF1. This is an example of external
coincidence of light with the endogenous oscillation in FKF1 protein abundance.
f | GI–FKF1 complex including light-activated FKF1 degrades CDF proteins, permitting
CO transcription, mRNA accumulation and translation of CO protein in the light.
g | Light signalling through PHYTOCHROME A (PHYA), CRYPTOCHROME 2 (CRY2) and
FKF1 stabilizes CO protein, providing a second example of external coincidence of
light, in this case with the endogenous oscillation in CO translation. Stabilized CO
protein accumulates and binds to the FT promoter to induce transcription, with
subsequent mRNA accumulation. In addition, light-activated FKF1 protein is recruited
to the FT promoter to directly stimulate FT transcription and mRNA accumulation. Thus,
on long days, FT mRNA abundance increases, permitting translation of FT protein to
levels sufficient to induce the transition from vegetative to reproductive growth. Parts
b–g are adapted with permission from REF. 53, Annual Reviews.
from A. thaliana is that PHYC has a central role in photoperiodic flowering in wheat and barley. In the light,
PHYC homodimerizes and heterodimerizes with PHYB
and induces transcription of PPD1 and FT1 (also known
as VRN3 or VRN-H3 in these plants)70. Thus, PHYC
contributes to a mechanism of external coincidence in
long‑day cereals53.
Short-day plants
Plants that exhibit a
photoperiodic behaviour
(for example, accelerated
flowering) when the day length
is less than a threshold value.
Vernalization
A prolonged period of chilling
that results in the acquisition
or acceleration of the ability
to flower.
Photoperiodic flowering in short‑day plants. The clock
is also involved in photoperiodic flowering in short‑day
plants, such as rice. As in A. thaliana, florigens encoded
by rice FT homologues, in this case HEADING DATE 3A
(HD3A) and RICE FLOWERING LOCUS T 1 (RFT1), are
expressed in the leaf vasculature under inductive conditions (short days) and move to the shoot apical meristem
to induce flowering 71. These florigens are regulated by
two distinct pathways: the HD1–HD3A module resembles A. thaliana CO–FT, but the GRAIN NUMBER,
PLANT HEIGHT AND HEADING DATE 7 (GHD7)–
EARLY HEADING DATE 1 (EHD1)–HD3A–RFT1
pathway lacks an A. thaliana counterpart.
HD1, the rice CO orthologue, is induced by GI and
encodes a bifunctional protein that promotes HD3A
transcription under short days but inhibits HD3A under
long days. This conversion from activator to repressor
is an example of external coincidence entailing light
signalling via PHYB53,72,73. A second bifunctional transcriptional regulator of HD3A, LATE HEADING 8
(LH8)–HD5–DAYS TO HEADING 8 (DTH8)–GHD8,
activates under short days and represses under long
days53. Thus, although the A. thaliana CO–FT axis has
been preserved in rice as HD1–HD3A, there are clear
differences in mechanistic detail.
In the second pathway, EHD1, a B‑type response regulator, upregulates HD3A expression to promote flowering mainly on short days, when blue‑light signalling
coincides with the morning phase set by the circadian
clock74,75. Photoperiodic input is also achieved through
phytochrome signalling during a photosensitive phase
on long days to increase expression of GHD7, which
inhibits EHD1 expression76. The regulation of GHD7
expression is multifaceted and includes circadian clock
input via inhibition by ELF3‑1–HD17–ELF7 (REFS 77,78).
Rice ELF3‑1 also activates HD3A expression indirectly
by inhibiting PRR37, a suppressor of HDA3 (but not
RFT1) expression under long days78.
Thus, flowering time determination in rice, as in
A. thaliana, features external coincidence in which light
signalling must coincide with sensitive phases established by endogenously cycling circadian components53,73.
Although the rice orthologues of key A. thaliana genes
contribute to flowering time, the regulatory networks
differ considerably in mechanistic detail as well as in the
recruitment of new components and, indeed, of whole
new pathways in rice. These substantial differences in
flowering time regulation may reflect phylogenetic differences between monocots and dicots or, instead, regulatory changes associated with the switch from long‑ to
short‑day sensitivity. There is a need for additional
comparative analyses to determine whether the regulatory networks currently defined in A. thaliana and rice
will prove adequate to explain flowering throughout the
angiosperms.
Abiotic stress
A consequence of circadian integration of environmental cues is the gating of the response to a given stimulus;
the magnitude or the very occurrence of the response
depends on the time of day (FIG. 4). Time of day often
contributes more to transcriptome variation than the
given stress79–81. For example, cold treatment can cause
substantial amplitude damping for circadian clock and
output genes, which can be misattributed as a direct
cold response rather than a consequence of a general
damping of circadian‑regulated genes81. This strongly
argues for sampling at multiple time points when studying any stress response, to ensure the full transcriptional
response is captured and rhythmically expressed genes
are properly compared.
Cold responses. In many plant species, cold temperatures
provide developmental cues, such as overwintering to
break seed dormancy and vernalization to induce flowering. Freezing temperatures encroaching on the growing
season challenge crop production and focus attention
on plant response and acclimation to low temperatures.
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a Wild type
b Wild type
c Wild type
d Disrupted clock
Reviews
| Genetics
Figure 4 | Circadian clock gating of abiotic stress response. Nature
An example
of an
abio­ticstress‑responding gene (expression level shown by the wavy lines) that is regulated by
the clock and shows a ‘gated’ response to a stress stimulus (indicated by a lightning
bolt). White and purple bars represent day and night, respectively. a | Under normal
growth conditions, the stress‑responding gene is rhythmically expressed, as observed
for the C‑REPEAT BINDING FACTOR (CBF) genes, for example. b | When a stress stimulus
is given at different times of day, the magnitude of the transcriptional response varies
depending on the circadian gating of the response. In the case of the CBFs, a greater
response is seen 4 hours after dawn (indicated by a black arrow and line) compared with
16 hours after dawn (indicated by a red arrow and line)84. c | When exposed to prolonged
stress conditions, stress-responding genes may exhibit a time‑of‑day-dependent
response that coincides with the timing of their expression patterns under normal
conditions (indicated by a black line). This is observed for the drought response79.
d | When the clock is disrupted, such as in the CIRCADIAN CLOCK‑ASSOCIATED 1‑over
expressing (CCA1‑OX) line, the gated induction of the CBFs is lost and the transcriptional
response to cold is similar at different times of day (indicated by black and red arrows
and lines)84. These examples demonstrate the difficulties with studies of transcriptome
changes in response to stress that do not account for circadian gating of the response
by incorporating temporal data.
C‑REPEAT BINDING FACTOR (CBF; also known as
DEHYDRATION‑RESPONSIVE ELEMENT‑BINDING
(DREB)) transcription factors are induced within
15 minutes in response to cold (4 °C). In A. thaliana,
CBFs regulate more than 100 cold-responsive genes,
collectively known as the CBF regulon82. Components
of this pathway have been elucidated in crops such
as wheat, rice and tomato83, making them targets for
cold‑tolerance improvement because the induction of
these genes is sufficient to induce freezing tolerance82.
Induction of the CBFs in response to cold is gated by
the circadian clock, such that higher transcript levels are induced by a cold treatment 4 hours compared
to 16 hours after dawn84. The magnitude of the cold
induction of CBFs parallels the endogenous rhythm
in CBF‑transcript accumulation in plants grown without cold (FIG. 4), similar to the gated light induction of
LIGHT‑HARVESTING CHLOROPHYLL A/B‑BINDING
PROTEIN 1.1 (LHCB1.1; also known as CAB2)85. The
CBFs are among a list of cold‑ and drought‑responsive
rhythmically expressed genes in A. thaliana12. The circadian regulation of CBF1–3 genes is disrupted in plants
with clock gene mutations in both CCA1 (cca1‑11 allele)
and LATE‑ELONGATED HYPOCOTYL (LHY; lhy‑21
allele), probably owing to loss of both CCA1 and LHY
binding to the promoters of these genes 86. In addition to the CCA1 regulation of the CBF cold‑response
pathway, PRR7 binds to the CBF promoters as well as
to promoters of genes involved in abscisic acid (ABA)
and drought signalling 20. The involvement of CCA1 and
PRR7 is consistent with the drought‑ and cold‑resistant
phenotypes of the prr5‑11 prr7‑11 prr9‑10 triple mutant,
which shows increased CBF expression as well as an
overall disruption of circadian associated gene expression87. Similarly, the toc1‑101 mutant exhibits increased
expression of CBF3 and freezing tolerance88. A circadian
clock model simulation predicted negative regulation
of CBF3 by TOC1, which binds to the CBF3 promoter
and contributes to its gated cold response88. Although
constitutive expression of CBFs in wheat, barley and
rice confers tolerance to drought and cold stress, there
are often adverse effects on growth83. This suggests that
the circadian regulation of the cold‑response pathway is
coordinated with the unstressed temporal structure of
metabolic processes to maximize the efficiency of the
response while maintaining growth.
Many clock-regulated targets are identified through
known regulatory elements. Cold‑responsive genes
show enrichment for the CCA1‑binding site (CBS)
and the evening element (EE) motif 89, the binding targets of CCA1, LHY and the related REVEILLE (RVE)
transcription factors, which contribute to the induction of evening‑expressed genes3,90. EE and EE‑like
(EEL) motifs or the CBS are enriched in association
with the ABA-responsive element-like (ABREL) motif
in cold‑responsive genes. A synthetic promoter containing four EEs and three ABREL motifs confers cold
induction in A. thaliana89. ABREL motifs have also been
found in Ca2+‑responsive genes91, providing a possible
link to circadian gating of low‑temperature‑induced Ca2+
oscillations92,93. Consistent with the network structure
of the circadian clock, cold also acts as a clock input,
as evidenced by the damping of circadian clock gene
expression at 4 °C81 and the low‑temperature regulation
of CCA1 splicing 29. One possible mechanism for the cold
response to feed back to affect clock function is through
CBF1 binding to the LUX promoter 94. How these various mechanisms of cold input to the clock coordinate to
regulate freezing tolerance has yet to be seen.
Drought responses. The cold-responsive genes that
make up the CBF regulon also respond to drought,
demonstrating extensive overlap between these two
stress‑response pathways82,95. The rhythmic expression of drought‑responsive genes confers rhythmic
modulation of the response to drought throughout the
day, as seen in A. thaliana and poplar 79,80. ABA has an
important role during the drought response, mediating
drought-induced stomatal closure. The clock gates ABA
responses, and ABA acts as a clock input, lengthening
the circadian period4,96. The ABA induction of TOC1
expression is gated by the circadian clock, altering
TOC1 induction depending on the time of ABA treatment, again with the maximum level of induction corresponding to the peak of TOC1 expression (FIG. 4),
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REVIEWS
similar to the gated cold induction of the CBFs 97. ABA
treatment does not affect LHY or CCA1 expression,
resulting in differential sensitivity to ABA that coincides with the increased sensitivity of the stomata to
ABA in the afternoon and an overall reduction in stomatal aperture in toc1 mutants4,97. ABA biosynthesis and
signalling‑pathway genes are enriched in the circadian
transcriptome12,98, consistent with the diurnal oscillations of ABA observed in several species99,100. The pervasiveness of circadian control extends to members of all
plant hormone signalling pathways12,98, providing insight
into the mechanism for producing the gating response.
By altering the timing of expression of biosynthesis and
signalling genes within the various hormone pathways,
the plant is continuously shifting from a sensitized to
desensitized state, thereby modulating response.
Nutrient availability. An often-overlooked abiotic stress
condition is nutrient availability and homeostasis, which
is critical for growth. The transcriptional pathways
responding to various nutrients have been interrogated
in A. thaliana, and several studies have uncovered the
involvement of the circadian clock. Analysis of the nitrogen transcriptional response network revealed CCA1 as
a regulator of nitrogen assimilation genes and demonstrated the ability of nitrogen metabolites to alter the
phase of CCA1 expression, suggesting a mechanism for
nitrogen input into the circadian oscillator 101. Similarly,
several iron‑homeostasis genes are circadian regulated, resulting in time‑of‑day‑dependent expression
patterns102. Iron deficiency modulates clock function,
lengthening period in wild–type plants, and analysis of
circadian clock mutants showed that CCA1, LHY, ZTL
and GI are necessary for this response102–104. A linear relationship between increased iron deficiency and period
lengthening 104 suggests a finely tuned response mechanism. This mechanism was not observed for copper, zinc
or manganese103,104, implying that not all nutrients act as
clock inputs.
Biotroph
A plant pathogen that does not
kill the plant as part of the
infection process, instead
establishing a long-term
feeding relationship with the
living cells of the host.
Necrotrophic fungus
A fungal plant pathogen that
kills plant cells as part of the
infection process, feeding on
the dead cells of the host.
ROS and circadian control. Reactive oxygen species
(ROS) are natural by‑products of photosynthesis and
respiration that act as secondary messengers during plant
stress responses105. Under standard growth conditions,
ROS levels follow a diurnal cycle, with peak production
corresponding to peak levels of the ROS scavenger catalase106. These time‑of‑day‑specific peaks are maintained
under constant light conditions, so they are dependent
on the circadian clock. ROS-signalling genes with timeof-day-specific phases show disrupted patterns in cca1‑1
lhy‑11, toc1‑1, elf3‑1 and lux‑1 clock mutants106. CCA1
binds to several ROS-responsive gene promoters, identifying a direct link between circadian control of ROS
response and a circadian gated response to ROS production106. The presence of reduction–oxidation (redox)
cycles of ROS-scavenging peroxiredoxins in all domains
of life has led to the speculation that circadian oscillators co‑evolved from this redox homeostasis system
following oxygenation on Earth2. As abiotic and biotic
stress conditions continue to afflict annual crop production, the proper regulation of ROS homeostasis must be
considered when breeding for increased yield through
metabolic optimization. Given the conservation of these
redox cycles, a phylogenetic approach might shed light on
the evolution of these interactions within the circadian
oscillator.
Biotic stress
As with responses to abiotic stresses, constitutive expression of defence pathways that confer resistance to pathogens and herbivores is deleterious. The optimal defence
hypothesis (ODH) posits that a plant should allocate
defensive resources to tissues that are most valuable and
most vulnerable to pathogens or herbivores. Indeed,
young sink tissues and reproductive structures typically
contain higher basal levels of defence compounds and
show stronger induced‑defence responses than other
parts107. This minimizes the fitness trade-offs associated
with the activation of defence pathways. In recent years,
the ODH has expanded to include a temporal component, and compelling evidence has established that
plants use the circadian clock to temporally restrict both
the basal expression and the induction of defence pathways to the time of day when the threat posed by pathogens and herbivores is maximal, thereby minimizing
fitness costs.
In lima beans, herbivory damage at night is more
effective than daytime damage at eliciting accumulation
of defence compounds, such as jasmonic acid (JA), and
emission of defence‑associated volatiles108. Similarly, secondary metabolites associated with herbivory defence
show both tissue-specific and diurnal patterns of
accumulation in Nicotiana attenuata109.
The first indication of a potential role of the clock
in pathogen responses came when it was observed that
PATHOGEN AND CIRCADIAN CONTROLLED 1
(PCC1), a gene that is rapidly induced after Pseudomonas
syringae infection, oscillates with an evening peak110.
Subsequently, the EE motif was found to be overrepresented in the promoters of novel components of
RECOGNITION OF PERONOSPORA PARASITICA 4
(RPP4)-mediated resistance to the oomycete biotroph
Hyaloperonospora arabidopsidis 111. These new defence
genes are transcribed under circadian control, mediated
by CCA1, even in the absence of pathogen challenge,
allowing plants to anticipate infection at dawn, when
the oomycete spores are typically released. Similarly,
clock‑regulated transcripts are over-represented in the
set of transcripts responding to infection of A. thaliana
with the necrotrophic fungus Botrytis cinerea112. The clock
modulates the ability of A. thaliana to respond to infection by both H. arabidopsidis and P. syringae113–115 (FIG. 5a).
Disruption of the clock (arrhythmia) resulting from overexpression of CCA1 or LHY113,114 or from mutational loss
of LUX function115 dramatically increased susceptibility
to pathogen challenge (FIG. 5b). Interestingly, plants are
more susceptible to pathogen entry in the early morning,
when the stomata are maximally open. Owing to this
vulnerability, the plants activate defence pathways in the
morning, providing more resistance to bacteria infiltrating the leaves in the morning than in the evening 114,115.
CCA1 and LHY act, at least in part, through GLYCINE
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a
b
Pathogen
Open
stoma
Closed stoma
Stomatal aperture and immune response
c
Stomatal aperture and immune response
d
JA
JA
JA synthesis and signalling, and looper feeding activity
JA synthesis and signalling, and looper feeding activity
Figure 5 | Circadian regulation of resistance to pathogens and herbivores. a | Circadian ‘gating’ of maximal
Nature Reviews | Genetics
stomatal aperture to early morning allows pathogens access to the leaf interior. Coincident with the period of
vulnerability to pathogen access, plant immune defences are maximal, affording resistance to challenge. b | Circadian
dysfunction results in failure to close stomata and reduced resistance to pathogen challenge. c | The circadian clock of
cabbage loopers gates feeding activity to the daytime, and the plant circadian clock maximizes jasmonic acid (JA)
synthesis and signalling during the day, maximizing resistance to looper herbivory. d | Circadian dysfunction in the
plant results in a failure to induce JA accumulation and signalling during the day, permitting increased looper feeding
and growth and allowing increased herbivory damage.
RICH PROTEIN 7 (GRP7; also known as RBG7 and
CCR2)-mediated control of stomatal aperture114. GRP7
is an RNA-binding protein that functions in a slave oscillator loop important for full resistance to P. syringae116.
TIME FOR COFFEE (TIC) has also been implicated in circadian modulation of pathogen sensitivity
via the circadian regulation of stomatal aperture115.
As seen with abiotic stress responses, many clockregulated output pathways feed back to modulate clock
function. Pathogen challenge is no exception, and infection of A. thaliana with B. cinerea dampens the oscillation of multiple clock genes112. Defence activation by
P. syringae infection or by the bacterial elicitor flg22
perturbs clock function to shorten period114.
Analysis of the circadian transcriptome of
A. thaliana suggests circadian regulation of JA and
salicylic acid (SA) biosynthesis and signalling pathways 12 and, indeed, the accumulation of both JA
and SA cycles117. Expression of both the JA receptor,
CORONATINE-INSENSITIVE 1 (COI1), and the
key bHLH transcription factor MYC2, which activates
the transcription of JA‑responsive genes, is gated by the
clock118. TIC contributes to this circadian gating by
inhibiting both MYC2 and COI1 expression; thus, tic
mutants are defective in rhythmic JA responses to pathogen infection118. Consistent with the ODH, the phase at
which rhythmic JA accumulation peaks coincides with
the daytime maximal feeding activity of cabbage loopers (Trichoplusia ni) (FIG. 5c). When the circadian clocks
of A. thaliana and the cabbage loopers were entrained
out of phase with one another, looper activity at the
novel phase (night for the plants), when the plants
were not anticipating attack, devastated the plants.
Similarly, plant mutants with disrupted clocks failed to
enhance herbivory resistance during the day (FIG. 5d).
Collectively, these experiments demonstrate the importance of plant defensive preparations in anticipation
of herbivore activity 117.
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Carbon partitioning
The distribution of carbon
assimilates from
photosynthetic tissues to
non‑photosynthetic organs.
Conclusions and perspective
The breadth of physiological processes regulated by the
plant circadian clock impels further integration of circadian dynamics in future studies. Integrating spatial and
temporal information is essential for truly understanding the network response rather than that of individual
pathways. Ultimately, an effective model will incorporate the changing sensitivity of the network to environmental stimuli, as determined by the circadian gating
of the response, and whether the stimuli feed back to
modulate clock function. The changing sensitivity of the
network to stimuli has significant implications on stress‑
treatment experiments, as the timing of both treatment
and response must be considered.
Throughout crop domestication, cultivars with
optimized flowering time were selected; many of
these contain mutations in circadian clock genes128.
Including circadian traits into current breeding practices may enhance crop performance by selecting for
improved responses to various stresses while maintaining synchrony with metabolic processes needed for
a
Relative starch levels
Wild type
Short period
∗
Dusk
Time of day
Dawn
b
Relative starch levels
Metabolism
Circadian and diurnal regulation of metabolism provides coordinated growth and efficient use of resources.
A study of metabolite levels estimated that 30% of primary metabolite accumulation is under circadian control at 20 °C119. Specific clock components contribute
differentially to metabolite regulation, as seen by the
more extreme changes in primary metabolite levels
observed in the prr5‑11 prr7‑11 prr9‑10 triple mutant
compared with the CCA1‑OX line120. These results suggest output regulation by the PRRs that is distinct from
regulation by CCA1.
The importance of circadian regulation of metabolism is illustrated by the control of starch degradation.
The rate of starch degradation is tightly regulated such
that energy stores are not depleted before photosynthesis
can resume (FIG. 6). Plants shifted into the dark earlier in
the day have slower rates of starch degradation at night
compared with control plants, resulting in similar levels
of starch depletion at dawn121. This adjustment in the
rate of degradation is dictated by the anticipation of
dawn, as determined by the circadian clock. Circadian
short‑period mutants show increased rates of degradation, resulting in depletion of starch before the end of
the night and sucrose starvation121. This controlled rate
of degradation is not unique to A. thaliana; for example,
it also occurs in the grass B. distachyon, even though the
two plants diverged 140‑million years ago122.
Carbon partitioning towards starch also depends on
clock function. The short‑period mutant cca1‑11 lhy‑21
has an earlier peak of carbon partitioning towards starch
compared with wild type. Interestingly, the prr7‑3 prr9‑1
long‑period mutant shows general disruption in carbon partitioning patterns compared with wild type123,
suggesting that PRR7 and PRR9 may have a more general role in metabolic homeostasis, consistent with the
altered metabolic profile in the prr5‑11 prr7‑11 prr9‑10
triple mutant 120. Root growth exhibits a similar pattern,
with a drop in growth rate observed late in the night in
cca1‑1 lhy‑11 mutants compared with wild type due to a
depleted carbon source at the end of the night that can be
rescued by the addition of exogenous sucrose47. Several
carbon flux models have incorporated these experimental data to predict the dynamics of carbon partitioning
and assess the contributions of day length, circadian
clock and source and sink relationships124,125. Consistent
with the stress‑response pathways, photosynthetically
derived sucrose also acts as an input to entrain circadian
rhythms of clock gene expression126,127. As metabolomics
studies become more widespread among temporal abiotic and biotic stress response studies, more‑elaborate
models will undoubtedly incorporate these changes and
predict the necessary modifications to key regulators
required for maximum growth.
Dawn
Dusk
Dawn
Time of day
Figure 6 | Circadian regulation of
starch
degradation. Nature
Reviews
| Genetics
a | Wild‑type plants grown in a light–dark cycle accumulate
starch during the day and degrade starch at a linear rate
that is coordinated with the length of the night, as
anticipated by the circadian clock. A plant with short
circadian period incorrectly anticipates an early dawn and
adjusts the rate of starch degradation to be more rapid,
with the consequence that starch is exhausted before
dawn, leading to carbon starvation stress (indicated by an
asterisk), which is detrimental to plant performance. b | The
amount of photosynthate accumulated on any given day
cannot be readily anticipated, owing to environmental
conditions being unpredictable; for example, more
photosynthate is available to be partitioned into starch on
sunny compared to cloud-covered days. Based on the
levels of starch at the end of the day and the duration of
the night predicted by the circadian clock, the rate
of starch degradation is adjusted to efficiently use
accumulated starch without inducing carbon starvation.
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growth. A current restriction to crop improvement is
the limited amount of circadian data available in crop
species. With the impending threat of climate change,
it is imperative that we translate our knowledge from
A. thaliana to important crop plants to appreciate both
conservation and innovation among these diverse species. Whole‑genome duplications and hybridization
are common among angiosperms, and many valuable
crops are polyploid, with expanded circadian gene families. For example, a study of the Brassica rapa genome
revealed preferential retention of circadian clock genes,
resulting in most clock genes being retained in two or
three copies129. The PRR gene family seems to have
expanded across species, with the ancestor to flowering plants having three clades, the PRR1 and TOC1
clade, the PRR5 and PRR9 clade and the PRR7 and
PRR3 clade. Following monocot and dicot divergence,
it seems that individual genes within the PRR5 and
PRR9 clade versus the PRR7 and PRR3 clade duplicated
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Acknowledgements
The authors thank three anonymous reviewers for their comments and apologize to those whose work has not been cited
owing to length constraints. This work was supported by
grants from the US National Science Foundation
(IOS‑1202779 to K.G. and IOS‑0923752, IOS‑1025965 and
IOS‑1257722 to C.R.M.) and from the Rural Development
Administration, Republic of Korea (Next-Generation BioGreen
21 Programme, Systems and Synthetic Agrobiotech Center
(PJ01106904 to C.R.M.)).
Competing interests statement
The authors declare no competing interests.
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CORRIGENDUM
Integrating circadian dynamics with physiological processes in plants
Kathleen Greenham and C. Robertson McClung
Nature Reviews Genetics 16, 598–610 (2015)
In this article, the authors have updated Figure 1 by removing the repressive post-translational regulation arrow originally
linking ZEITLUPE (ZTL) to the evening complex (EC), which is a multi-protein complex consisting of EARLY FLOWERING 4
(ELF4), ELF3 and LUX ARRHYTHMO (LUX). This alteration is because this regulatory relationship is not supported by the
current literature. The authors apologize for this error.
© 2015 Macmillan Publishers Limited. All rights reserved