Genetic linkages between circadian clock-associated components and phytochrome-dependent red light signal transduction in Arabidopsis thaliana

Cold-induced degradation of core clock proteins implements temperature compensation in the Arabidopsis circadian clock

The period of circadian clocks is maintained at close to 24 hours over a broad range of physiological temperatures due to temperature compensation of period length. Here, we show that the quantitative control of the core clock proteins TIMING OF CAB EXPRESSION 1 [TOC1; also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)] and PRR5 is crucial for temperature compensation in Arabidopsis thaliana. The prr5 toc1 double mutant has a shortened period at higher temperatures, resulting in weak temperature compensation. Low ambient temperature reduces amounts of PRR5 and TOC1. In low-temperature conditions, PRR5 and TOC1 interact with LOV KELCH PROTEIN 2 (LKP2), a component of the E3 ubiquitin ligase Skp, Cullin, F-box (SCF) complex. The lkp2 mutations attenuate low temperature-induced decrease of PRR5 and TOC1, and the mutants display longer period only at lower temperatures. Our findings reveal that the circadian clock maintains its period length despite ambient temperature fluctuations through temperature- and LKP2-dependent control of PRR5 and TOC1 abundance.

Emerging Molecular Links Between Plant Photomorphogenesis and Virus Resistance

Photomorphogenesis refers to photoreceptor-mediated morphological changes in plant development that are triggered by light. Multiple photoreceptors and transcription factors (TFs) are involved in the molecular regulation of photomorphogenesis. Likewise, light can also modulate the outcome of plant-virus interactions since both photosynthesis and many viral infection events occur in the chloroplast. Despite the apparent association between photosynthesis and virus infection, little is known about whether there are also interplays between photomorphogenesis and plant virus resistance. Recent research suggests that plant-virus interactions are potentially regulated by several photoreceptors and photomorphogenesis regulators, including phytochromes A and B (PHYA and PHYB), cryptochromes 2 (CRY2), phototropin 2 (PHOT2), the photomorphogenesis repressor constitutive photomorphogenesis 1 (COP1), the NAM, ATAF, and CUC (NAC)-family TF ATAF2, the Aux/IAA protein phytochrome-associated protein 1 (PAP1), the homeodomain-leucine zipper (HD-Zip) TF HAT1, and the core circadian clock component circadian clock associated 1 (CCA1). Particularly, the plant growth promoting brassinosteroid (BR) hormones play critical roles in integrating the regulatory pathways of plant photomorphogenesis and viral defense. Here, we summarize the current understanding of molecular mechanisms linking plant photomorphogenesis and defense against viruses, which represents an emerging interdisciplinary research topic in both molecular plant biology and virology.

ZmCCA1a on Chromosome 10 of Maize Delays Flowering of Arabidopsis thaliana

Maize (Zea mays) is a major cereal crop that originated at low latitudes, and thus photoperiod sensitivity is an important barrier to the use of tropical/subtropical germplasm in temperate regions. However, studies of the mechanisms underlying circadian regulation in maize are at an early stage. In this study we cloned ZmCCA1a on chromosome 10 of maize by map-based cloning. The gene is homologous to the Myb transcription factor genes AtCCA1/AtLHY in Arabidopsis thaliana; the deduced Myb domain of ZmCCA1a showed high similarity with that of AtCCA1/AtLHY and ZmCCA1b. Transiently or constitutively expressed ZmCCA1a-YFPs were localized to nuclei of Arabidopsis mesophyll protoplasts, agroinfiltrated tobacco leaves, and leaf and root cells of transgenic seedlings of Arabidopsis thaliana. Unlike AtCCA1/AtLHY, ZmCCA1a did not form homodimers nor interact with ZmCCA1b. Transcripts of ZmCCA1a showed circadian rhythm with peak expression around sunrise in maize inbred lines CML288 (photoperiod sensitive) and Huangzao 4 (HZ4; photoperiod insensitive). Under short days, transcription of ZmCCA1a in CML288 and HZ4 was repressed compared with that under long days, whereas the effect of photoperiod on ZmCCA1a expression was moderate in HZ4. In ZmCCA1a-overexpressing A. thaliana (ZmCCA1a-ox) lines, the circadian rhythm was disrupted under constant light and flowering was delayed under long days, but the hypocotyl length was not affected. In addition, expression of endogenous AtCCA1/AtLHY and the downstream genes AtGI, AtCO, and AtFt was repressed in ZmCCA1a-ox seedlings. The present results suggest that the function of ZmCCA1a is similar, at least in part, to that of AtCCA1/AtLHY and ZmCCA1b, implying that ZmCCA1a is likely to be an important component of the circadian clock pathway in maize.

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PIF proteins

Light-environment signals, sensed by plant phytochrome photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown "trans factors" modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of colocalization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator to regulate the expression of PIF-DTGs through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF-signaling hub.

Daily humidity oscillation regulates the circadian clock to influence plant physiology

Early circadian studies in plants by de Mairan and de Candolle alluded to a regulation of circadian clocks by humidity. However, this regulation has not been described in detail, nor has its influence on physiology been demonstrated. Here we report that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1. Under simulated natural light and humidity cycles, humidity oscillation increases the amplitude of the circadian clock and further improves plant fitness-related traits. In addition, humidity oscillation enhances effector-triggered immunity at night possibly to counter increased pathogen virulence under high humidity. These results indicate that the humidity oscillation regulates specific circadian outputs besides those co-regulated with the light-dark cycle.

SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis

Light is the most important exogenous stimulus regulating plant growth and various developmental processes. Phytochromes, especially PHYTOCHROME B (PHYB) mediates the various light-mediated processes in Arabidopsis. SPATULA (SPT) is an important transcription factor, which has been reported previously to participate in temperature-mediated transition from seed dormancy to germination. Here we investigate the function of SPT in the floral transition under long day conditions and photomorphogenesis in Arabidopsis. In this study, spt-2 shows significantly delayed flowering time. But mutation of SPT in the background of phyb-1 rescues the phenotype of spt-2. The flowering time of double mutant of spt-2/phyb-1 is similar with the wild type. These results indicate that SPT promotes the transition from vegetative stage to floral stage and it regulates this transition in a PHYB-dependent manner. With qRT-PCR analysis, it is found that SPT regulates flowering time via FLC, SVP, FT and SOC1. Furthermore, SPT also controls photomorphogenesis. spt-2 displays shortened hypocotyls and increased chlorophylls contents compared with the wild type. These phenotypes are also rescued in the double mutant of spt-2/phyb-1. These results indicate that SPT is also involved in photomorphogenic development in Arabidopsis and SPT regulates photomorphogenesis in a PHYB-dependent manner. Collectively, SPT is not only a temperature responder but it is also an important light regulator during plant growth and development.

Computing and Visualizing Gene Function Similarity and Coherence with NaviGO

Gene ontology (GO) is a controlled vocabulary of gene functions across all species, which is widely used for functional analyses of individual genes and large-scale proteomic studies. NaviGO is a webserver for visualizing and quantifying the relationship and similarity of GO annotations. Here, we walk through functionality of the NaviGO webserver ( http://kiharalab.org/web/navigo/ ) using an example input and explain what can be learned from analysis results. NaviGO has four main functions, accessed from each page of the webserver: "GO Parents," "GO Set", "GO Enrichment", and "Protein Set." For a given list of GO terms, the "GO Parents" tab visualizes the hierarchical relationship of GO terms, and the "GO Set" tab calculates six functional similarity and association scores and presents results in a network and a multidimensional scaling plot. For a set of proteins and their associated GO terms, the "GO Enrichment" tab calculates protein GO functional enrichment, while the "Protein Set" tab calculates functional association between proteins. The NaviGO source code can be also downloaded and used locally or integrated into other software pipelines.

AtHESPERIN: a novel regulator of circadian rhythms with poly(A)-degrading activity in plants

We report the identification and characterization of a novel gene, AtHesperin (AtHESP) that codes for a deadenylase in Arabidopsis thaliana. The gene is under circadian clock-gene regulation and has similarity to the mammalian Nocturnin. AtHESP can efficiently degrade poly(A) substrates exhibiting allosteric kinetics. Size exclusion chromatography and native electrophoresis coupled with kinetic analysis support that the native enzyme is oligomeric with at least 3 binding sites. Knockdown and overexpression of AtHESP in plant lines affects the expression and rhythmicity of the clock core oscillator genes TOC1 and CCA1. This study demonstrates an evolutionary conserved poly(A)-degrading activity in plants and suggests deadenylation as a mechanism involved in the regulation of the circadian clock. A role of AtHESP in stress response in plants is also depicted.

The Blue Light-Dependent Polyubiquitination and Degradation of Arabidopsis Cryptochrome2 Requires Multiple E3 Ubiquitin Ligases

Cryptochromes are blue light receptors regulated by light-dependent ubiquitination and degradation in both plant and animal lineages. The Arabidopsis genome encodes two cryptochromes, CRY1 and CRY2, of which CRY2 undergoes blue light-dependent ubiquitination and 26S proteasome-dependent degradation. The molecular mechanism regulating blue light-dependent proteolysis of CRY2 is still not fully understood. We found that the F-box proteins ZEITLUPE (ZTL) and Lov Kelch Protein2 (LKP2), which mediate blue light suppression of degradation of the CRY2 signaling partner CIB1, are not required for the blue light-dependent CRY2 degradation. We further showed that the previously reported function of the COP1-SPA1 protein complex in blue light-dependent CRY2 degradation is more likely to be attributable to its cullin 4 (CUL4)-based E3 ubiquitin ligase activity than its activity as the cryptochrome signaling partner. However, the blue light-dependent CRY2 degradation is only partially impaired in the cul4 mutant, the cop1-5 null mutant and the spa1234 quadruple mutant, suggesting a possible involvement of additional E3 ubiquitin ligases in the regulation of CRY2. Consistent with this hypothesis, we demonstrated that the blue light-dependent CRY2 degradation is significantly impaired in the temperature-sensitive cul1 mutant allele (axr6-3), especially under the non-permissive temperature. Based on these and other results presented, we propose that photoexcited CRY2 undergoes Lys48-linked polyubiquitination catalyzed by the CUL4- and CUL1-based E3 ubiquitin ligases.

The EC night-time repressor plays a crucial role in modulating circadian clock transcriptional circuitry by conservatively double-checking both warm-night and night-time-light signals in a synergistic manner in Arabidopsis thaliana

During the last decade, significant research progress has been made in Arabidopsis thaliana in defining the molecular mechanisms behind the plant circadian clock. The circadian clock must have the ability to integrate both external light and ambient temperature signals into its transcriptional circuitry to regulate its function properly. We previously showed that transcription of a set of clock genes including LUX (LUX ARRHYTHMO), GI (GIGANTEA), LNK1 (NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 1), PRR9 (PSEUDO-RESPONSE REGULATOR 9) and PRR7 is commonly regulated through the evening complex (EC) night-time repressor in response to both moderate changes in temperature (Δ6°C) and differences in steady-state growth-compatible temperature (16-28°C). Here, we further show that a night-time-light signal also feeds into the circadian clock transcriptional circuitry through the EC night-time repressor, so that the same set of EC target genes is up-regulated in response to a night-time-light pulse. This light-induced event is dependent on phytochromes, but not cryptochromes. Interestingly, both the warm-night and night-time-light signals negatively modulate the activity of the EC night-time repressor in a synergistic manner. In other words, an exponential burst of transcription of the EC target genes is observed only when these signals are simultaneously fed into the repressor. Taken together, we propose that the EC night-time repressor plays a crucial role in modulating the clock transcriptional circuitry to keep track properly of seasonal changes in photo- and thermal cycles by conservatively double-checking the external light and ambient temperature signals.

Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana

An interlocking multiloop model has been generally accepted to describe the transcriptional circuitry of core clock genes, through which robust circadian rhythms are generated in Arabidopsis thaliana. The circadian clock must have the ability to integrate ambient temperature signals into the clock transcriptional circuitry to regulate clock function properly. Clarification of the underlying mechanism is a longstanding subject in the field. Here, we provide evidence that temperature signals feed into the clock transcriptional circuitry through the evening complex (EC) night-time repressor consisting of EARLY FLOWERING 3 (ELF3, ELF4) and LUX ARRHYTHMO (LUX; also known as PCL1). Chromatin immunoprecipitation assays showed that PSEUDO-RESPONSE REGULATOR7 (PRR7), GIGANTEA (GI) and LUX are direct targets of the night-time repressor. Consequently, transcription of PRR9/PRR7, GI and LUX is commonly regulated through the night-time repressor in response to both moderate changes in temperature (Δ6°C) and differences in the steady-state growth-compatible temperature (16-28°C). A warmer temperature inhibits EC function more, whereas a cooler temperature stimulates it more. Consequently, the expression of these target genes is up-regulated in response to a warm temperature specifically during the dark period, whereas they are reversibly down-regulated in response to a cool temperature. Transcription of another EC target, the PIF4 (PHYTOCHROME-INTERACTING FACTOR 4) gene, is modulated through the same thermoregulatory mechanism. The last finding revealed the sophisticated physiological mechanism underlying the clock-controlled output pathway, which leads to the PIF4-mediated temperature-adaptive regulation of hypocotyl elongation.

GNC and CGA1 modulate chlorophyll biosynthesis and glutamate synthase (GLU1/Fd-GOGAT) expression in Arabidopsis

Chloroplast development is an important determinant of plant productivity and is controlled by environmental factors including amounts of light and nitrogen as well as internal phytohormones including cytokinins and gibberellins (GA). The paralog GATA transcription factors GNC and CGA1/GNL up-regulated by light, nitrogen and cytokinin while also being repressed by GA signaling. Modifying the expression of these genes has previously been shown to influence chlorophyll content in Arabidopsis while also altering aspects of germination, elongation growth and flowering time. In this work, we also use transgenic lines to demonstrate that GNC and CGA1 exhibit a partially redundant control over chlorophyll biosynthesis. We provide novel evidence that GNC and CGA1 influence both chloroplast number and leaf starch in proportion to their transcript level. GNC and CGA1 were found to modify the expression of chloroplast localized GLUTAMATE SYNTHASE (GLU1/Fd-GOGAT), which is the primary factor controlling nitrogen assimilation in green tissue. Altering GNC and CGA1 expression was also found to modulate the expression of important chlorophyll biosynthesis genes (GUN4, HEMA1, PORB, and PORC). As previously demonstrated, the CGA1 transgenic plants demonstrated significantly altered timing to a number of developmental events including germination, leaf production, flowering time and senescence. In contrast, the GNC transgenic lines we analyzed maintain relatively normal growth phenotypes outside of differences in chloroplast development. Despite some evidence for partial divergence, results indicate that regulation of both GNC and CGA1 by light, nitrogen, cytokinin, and GA acts to modulate nitrogen assimilation, chloroplast development and starch production. Understanding the mechanisms controlling these processes is important for agricultural biotechnology.

REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock

Circadian rhythms provide organisms with an adaptive advantage, allowing them to regulate physiological and developmental events so that they occur at the most appropriate time of day. In plants, as in other eukaryotes, multiple transcriptional feedback loops are central to clock function. In one such feedback loop, the Myb-like transcription factors CCA1 and LHY directly repress expression of the pseudoresponse regulator TOC1 by binding to an evening element (EE) in the TOC1 promoter. Another key regulatory circuit involves CCA1 and LHY and the TOC1 homologs PRR5, PRR7, and PRR9. Purification of EE-binding proteins from plant extracts followed by mass spectrometry led to the identification of RVE8, a homolog of CCA1 and LHY. Similar to these well-known clock genes, expression of RVE8 is circadian-regulated with a dawn phase of expression, and RVE8 binds specifically to the EE. However, whereas cca1 and lhy mutants have short period phenotypes and overexpression of either gene causes arrhythmia, rve8 mutants have long-period and RVE8-OX plants have short-period phenotypes. Light input to the clock is normal in rve8, but temperature compensation (a hallmark of circadian rhythms) is perturbed. RVE8 binds to the promoters of both TOC1 and PRR5 in the subjective afternoon, but surprisingly only PRR5 expression is perturbed by overexpression of RVE8. Together, our data indicate that RVE8 promotes expression of a subset of EE-containing clock genes towards the end of the subjective day and forms a negative feedback loop with PRR5. Thus RVE8 and its homologs CCA1 and LHY function close to the circadian oscillator but act via distinct molecular mechanisms.

Copper homeostasis influences the circadian clock in Arabidopsis

Almost every aspect of plant physiology is influenced by diurnal and seasonal environmental cycles which suggests that biochemical oscillations must be a pervasive phenomenon in the underlying molecular organization. The circadian clock is entrained by light and temperature cycles, and controls a wide variety of endogenous processes that enable plants to anticipate the daily periodicity of environmental conditions. Several previous reports suggest a connection between copper (Cu) homeostasis and the circadian clock in different organisms other than plants. However, the nature of the Cu homeostasis influence on chronobiology remains elusive. Cytosolic Cu content could oscillate since Cu regulates its own transporters expression. We recently reported how the deregulation of Cu homeostasis in Arabidopsis transgenic plants affects the expression of two MYB transcription factors which are nuclear components of the circadian clock. In this addendum, we hypothesize the advantages that could be derived from the influence of metal homeostasis on plant circadian rhythms and their significance.

Deregulated copper transport affects Arabidopsis development especially in the absence of environmental cycles

Copper is an essential cofactor for key processes in plants, but it exerts harmful effects when in excess. Previous work has shown that the Arabidopsis (Arabidopsis thaliana) COPT1 high-affinity copper transport protein participates in copper uptake through plant root tips. Here, we show that COPT1 protein localizes to the plasma membrane of Arabidopsis cells and the phenotypic effects of transgenic plants overexpressing either COPT1 or COPT3, the latter being another high-affinity copper transport protein family member. Both transgenic lines exhibit increased endogenous copper levels and are sensitive to the copper in the growth medium. Additional phenotypes include decreased hypocotyl growth in red light and differentially affected flowering times depending on the photoperiod. Furthermore, in the absence of environmental cycles, such as light and temperature, the survival of plants overexpressing COPT1 or COPT3 is compromised. Consistent with altered circadian rhythms, the expression of the nuclear circadian clock genes CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) is substantially reduced in either COPT1- or COPT3-overexpressing plants. Copper affects the amplitude and the phase, but not the period, of the CCA1 and LHY oscillations in wild-type plants. Copper also drives a reduction in the expression of circadian clock output genes. These results reveal that the spatiotemporal control of copper transport is a key aspect of metal homeostasis that is required for Arabidopsis fitness, especially in the absence of environmental cues.

The 5'UTR of CCA1 includes an autoregulatory cis element that segregates between light and circadian regulation of CCA1 and LHY

The transcription factor CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) participates in both light and circadian clock regulation in Arabidopsis. Two sets of transgenic plants in which GFP was fused to the CCA1 promoter with (1.3-kb fragment) or without (1.01-kb fragment) its 5'UTR were engineered. The transgenic plants transformed with the promoter including the 5'UTR had altered circadian regulation resulting in elongated hypocotyls, a bushy appearance and delayed flowering. In contrast, the transgenic plants transformed with the promoter without the 5'UTR showed earlier flowering than the wild type. Changes in CCA1, LHY and TOC1 gene expression were investigated under light-dark (L:D) fluctuations, continuous darkness (D:D) and continuous light (L:L). The circadian expression of CCA1 was altered in both sets of transgenic plants, being repressed in the plants transformed with the 1.01-kb fragment and constitutively overexpressed in those transformed with the 1.3-kb fragment. Under L:D conditions, regulation of LHY and TOC1 expression was separated from CCA1 regulation in both sets of transgenic plants, with intact rhythmic expression of both LHY and TOC1. Under D:D conditions, the rhythmic expression of LHY and TOC1 was lost in the 1.3 plants but retained with some erratic pattern under L:L conditions. In the 1.01 plants, under both D:D and L:L conditions the rhythmic expression was retained. These results indicate separate light-induced signal-transmission pathways for LHY and CCA1.

Arabidopsis thaliana life without phytochromes

Plants use light as a source of energy for photosynthesis and as a source of environmental information perceived by photoreceptors. Testing whether plants can complete their cycle if light provides energy but no information about the environment requires a plant devoid of phytochromes because all photosynthetically active wavelengths activate phytochromes. Producing such a quintuple mutant of Arabidopsis thaliana has been challenging, but we were able to obtain it in the flowering locus T (ft) mutant background. The quintuple phytochrome mutant does not germinate in the FT background, but it germinates to some extent in the ft background. If germination problems are bypassed by the addition of gibberellins, the seedlings of the quintuple phytochrome mutant exposed to red light produce chlorophyll, indicating that phytochromes are not the sole red-light photoreceptors, but they become developmentally arrested shortly after the cotyledon stage. Blue light bypasses this blockage, rejecting the long-standing idea that the blue-light receptors cryptochromes cannot operate without phytochromes. After growth under white light, returning the quintuple phytochrome mutant to red light resulted in rapid senescence of already expanded leaves and severely impaired expansion of new leaves. We conclude that Arabidopsis development is stalled at several points in the presence of light suitable for photosynthesis but providing no photomorphogenic signal.

Integrating ELF4 into the circadian system through combined structural and functional studies

The circadian clock is a timekeeping mechanism that enables anticipation of daily environmental changes. In the plant Arabidopsis thaliana, the circadian system is a multiloop series of interlocked transcription-translation feedbacks. Several genes have been arranged in these oscillation loops, but the position of the core-clock gene ELF4 in this network was previously undetermined. ELF4 lacks sequence similarity to known domains, and functional homologs have not yet been identified. Here we show that ELF4 is functionally conserved within a subclade of related sequences, and forms an alpha-helical homodimer with a likely electrostatic interface that could be structurally modeled. We support this hypothesis by expression analysis of new elf4 hypomorphic alleles. These weak mutants were found to have expression level phenotypes of both morning and evening clock genes, implicating multiple entry points of ELF4 within the multiloop network. This could be mathematically modeled. Furthermore, morning-expression defects were particular to some elf4 alleles, suggesting predominant ELF4 action just preceding dawn. We provide a new hypothesis about ELF4 in the oscillator-it acts as a homodimer to integrate two arms of the circadian clock.

The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana

The plant circadian clock generates rhythms with a period close to 24 h, and it controls a wide range of physiological and developmental oscillations in habitats under natural light/dark cycles. Among clock-controlled developmental events, the best characterized is the photoperiodic control of flowering time in Arabidopsis thaliana. Recently, it was also reported that the clock regulates a daily and rhythmic elongation of hypocotyls. Here, we report that the promotion of hypocotyl elongation is in fact dependent on changes in photoperiods in such a way that an accelerated hypocotyl elongation occurs especially under short-day conditions. In this regard, we provide genetic evidence to show that the circadian clock regulates the photoperiodic (or seasonal) elongation of hypocotyls by modulating the expression profiles of the PIF4 and PIF5 genes encoding phytochrome-interacting bHLH (basic helix-loop-helix) factors, in such a manner that certain short-day conditions are necessary to enhance the expression of these genes during the night-time. In other words, long-day conditions are insufficient to open the clock-gate for triggering the expression of PIF4 and PIF5 during the night-time. Based on these and other results, the photoperiodic control of hypocotyl elongation is best explained by the accumulation of PIF4 and PIF5 during the night-time of short days, due to coincidence between the internal (circadian rhythm) and external (photoperiod) time cues. This mechanism is a mirror image of the photoperiod-dependent promotion of flowering in that plants should experience long-day conditions to initiate flowering promptly. Both of these clock-mediated coincidence mechanisms may coordinately confer ecological fitness to plants growing in natural habitats with varied photoperiods.

Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response

Arabidopsis PSEUDO RESPONSE REGULATOR (PRR) genes are components of the circadian clock mechanism. In order to understand the scope of genome-wide transcriptional regulation by PRR genes, a comparison survey of gene expression in wild-type Arabidopsis and a prr9-11 prr7-10 prr5-10 triple mutant (d975) using mRNA collected during late daytime was conducted using an Affymetrix ATH-1 GeneChip. The expression of 'night genes' increased and the expression of 'day genes' decreased toward the end of the diurnal light phase, but expression of these genes was essentially constant in d975. The expression levels of 'night genes' were lower, whereas the expression of 'day genes' was higher in d975 than in the wild type. Bioinformatics approaches have indicated that the set of up-regulated genes in d975 and the set of cold-responsive genes have significant overlap. We found that d975 is more tolerant to cold, high salinity and drought stresses than the wild type. In addition, dehydration-responsive element B1/C-repeat-binding factor (DREB1/CBF), which is expressed around mid-day, is more highly expressed in d975. Raffinose and L-proline accumulated at higher levels in d975 even when plants were grown under normal conditions. These results suggest that PRR9, PRR7 and PRR5 are involved in a mechanism that anticipates diurnal cold stress and which initiates a stress response by mediating cyclic expression of stress response genes, including DREB1/CBF.

The circadian system in higher plants

The circadian clock regulates diverse aspects of plant growth and development and promotes plant fitness. Molecular identification of clock components, primarily in Arabidopsis, has led to recent rapid progress in our understanding of the clock mechanism in higher plants. Using mathematical modeling and experimental approaches, workers in the field have developed a model of the clock that incorporates both transcriptional and posttranscriptional regulation of clock genes. This cell-autonomous clock, or oscillator, generates rhythmic outputs that can be monitored at the cellular and whole-organism level. The clock not only confers daily rhythms in growth and metabolism, but also interacts with signaling pathways involved in plant responses to the environment. Future work will lead to a better understanding of how the clock and other signaling networks are integrated to provide plants with an adaptive advantage.

Characterization of genetic links between two clock-associated genes, GI and PRR5 in the current clock model of Arabidopsis thaliana

The GI (GIGANTEA) and PRR5 (PSEUDO-RESPONSE REGULATOR 5) genes are crucially implicated in the Arabidopsis circadian clock. We characterized a gi prr5 double loss-of-function mutant for the first time with reference to circadian clock-associated phenotypes. The results of this study revealed the genetic linkages between GI and PRR5 in the control of free running circadian oscillation of gene expression, early photomorphogenesis and flowering time. A mathematical clock model consisting of three interactive transcriptional feedback loops has recently been proposed. The model includes the hypothetical evening Y-TOC1 feedback loop, in which "Y" is suspected to be GI and/or PRR5. This issue was also addressed in this study; perhaps GI and PRR5 are not sufficient to fulfill the Y role.

Comes a time

The circadian clock is a selfsustaining oscillator with an endogenous period of approximately 24 hours. The Arabidopsis clock is composed of a set of interlocking negative feedback loops entailing transcriptional, post-transcriptional, and post-translational, particularly regulated proteolysis, control. Clock control of the transcriptome is widespread; up to 90% of the transcriptome cycles in at least one condition in seedlings exposed to a variety of environmental cycles. Clock control extends to the metabolome, though diurnal oscillations in enzyme activities and metabolites are less dramatic than oscillations in cognate transcripts. Metabolites, including organic nitrogen intermediates, feed back to modulate clock function, consistent with the view of the circadian clock as a key integrator of metabolic signals to coordinate metabolism and physiology with the environment.

The function of the clock-associated transcriptional regulator CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) in Arabidopsis thaliana

In the model higher plant Arabidopsis thaliana, the CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) gene plays important circadian clock-associated roles. The CCA1 protein is a member of a small subfamily of single MYB-related transcription factors. This family consists of several homologous CCA1-like transcription factors, including the closest homolog LHY (LATE ELONGATED HYPOCOTYL). To gain insight into the molecular function of CCA1 and its homologs, here we took a unique genetic approach that was recently developed for Arabidopsis thaliana. Through this strategy, referred to as CRES-T (Chimeric REpressor Silencing Technology), a transgenic plant was constructed to produce a dominant negative transcriptional repressor (designated CCA1-SRDX). By employing the resulting transgenic lines, together with previously established cca1 lhy double mutant and CCA1-ox (over-expressing) plants, their circadian clock-associated phenotypes were examined and compared with each other. The observed clock-associated phenotypes of the CCA1-SRDX plants were very similar to those of CCA1-ox, but not to those of cca1 lhy, suggesting that CCA1 acts predominantly as a transcriptional repressor in nature. However, the developmental morphology (or architecture) of adult CCA1-SRDX plants were quite different from that of CCA1-ox, suggesting that CCA1 might also be implicated, directly or indirectly, in an as yet unknown circadian-associated output pathway at a late developmental stage.

Are there multiple circadian clocks in plants?

We have reported that Arabidopsis might have genetically distinct circadian oscillators in multiple cell-types.1 Rhythms of CHLOROPHYLL A/B BINDING PROTEIN2 (CAB2) promoter activity are 2.5 h longer in phytochromeB mutants in constant red light and in cryptocrome1 cry2 double mutant (hy4-1 fha-1) in constant blue light than the wild-type.2 However, we found that cytosolic free Ca(2+) ([Ca(2+)](cyt)) oscillations were undetectable in these mutants in the same light conditions.1 Furthermore, mutants of CIRCADIAN CLOCK ASSOCIATED1 (CCA1) have short period rhythms of leaf movement but have arrhythmic [Ca(2+)](cyt) oscillations. More important, the timing of cab1-1 (toc1-1) mutant has short period rhythms of CAB2 promoter activity ( approximately 21 h) but, surprisingly, has a wild-type period for circadian [Ca(2+)](cyt) oscillations ( approximately 24 h). In contrast, toc1-2, a TOC1 loss-of-function mutant, has a short period of both CAB2 and [Ca(2+)](cyt) rhythms ( approximately 21 h). Here we discuss the difference between the phenotypes of toc1-1 and toc1-2 and how rhythms of CAB2 promoter activity and circadian [Ca(2+)](cyt) oscillations might be regulated differently.

The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels

We show that a previously uncharacterized Arabidopsis thaliana basic helix-loop-helix (bHLH) phytochrome interacting factor (PIF), designated PIF7, interacts specifically with the far-red light-absorbing Pfr form of phyB through a conserved domain called the active phyB binding motif. Similar to PIF3, upon light exposure, PIF7 rapidly migrates to intranuclear speckles, where it colocalizes with phyB. However, in striking contrast to PIF3, this process is not accompanied by detectable light-induced phosphorylation or degradation of PIF7, suggesting that the consequences of interaction with photoactivated phyB may differ among PIFs. Nevertheless, PIF7 acts similarly to PIF3 in prolonged red light as a weak negative regulator of phyB-mediated seedling deetiolation. Examination of pif3, pif4, and pif7 double mutant combinations shows that their moderate hypersensitivity to extended red light is additive. We provide evidence that the mechanism by which these PIFs operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner, via a process likely involving the proteasome pathway. These data suggest that the role of these phyB-interacting bHLH factors in modulating seedling deetiolation in prolonged red light may not be as phy-activated signaling intermediates, as proposed previously, but as direct modulators of the abundance of the photoreceptor.

Mechanistic duality of transcription factor function in phytochrome signaling

The phytochrome (phy) family of sensory photoreceptors (phyA-E in Arabidopsis) elicit changes in gene expression after light-induced migration to the nucleus, where they interact with basic helix-loop-helix transcription factors, such as phytochrome-interacting factor 3 (PIF3). The mechanism by which PIF3 relays phy signals, both early after initial light exposure and later during long-term irradiation, is not understood. Using transgenically expressed PIF3 variants, carrying site-specific amino acid substitutions that block the protein from binding either to DNA, phyA, and/or phyB, we examined the involvement of PIF3 in early, phy-induced marker gene expression and in modulating long-term, phy-imposed inhibition of hypocotyl cell elongation under prolonged, continuous irradiation. We describe an unanticipated dual mechanism of PIF3 action that involves the temporal uncoupling of its two most central molecular functions. We find that in early signaling, PIF3 acts positively as a transcription factor, exclusively requiring its DNA-binding capacity. Contrary to previous proposals, PIF3 functions as a constitutive coactivator in this process, without the need for phy binding and subsequent phy-induced modifications. This finding implies that another factor(s) is conditionally activated by phy and functions in concert with PIF3, to induce target gene transcription. In contrast, during long-term irradiations, PIF3 acts exclusively through its phyB-interacting capacity to control hypocotyl cell elongation, independently of its ability to bind DNA. Unexpectedly, PIF3 uses this capacity to regulate phyB protein abundance (and thereby global photosensory sensitivity) to modulate this long-term response rather than participating directly in the transduction chain as a signaling intermediate.

Rhythmic and light-inducible appearance of clock-associated pseudo-response regulator protein PRR9 through programmed degradation in the dark in Arabidopsis thaliana

In Arabidopsis thaliana, it is currently believed that the members of a small family of PSEUDO-RESPONSE REGULATOR (PRR) proteins, including TOC1 (TIMING OF CAB EXPRESSION 1), coordinately play roles close to the circadian clock. Among these PRR members, the PRR9 gene is unique in that not only does its transcription oscillate diurnally, but it is also rapidly induced by light in a manner dependent on phytochromes. These events at the level of transcription must be crucial for the clock-associated functions of PRR9. Nonetheless, little is known about the expression of the PRR9 protein product itself in plant cells. Here, we show that PRR9 polypeptides themselves oscillate diurnally, and that they accumulate rapidly in response to light. Our work further suggests that the presence of PRR9 polypeptides is controlled through proteasome-mediated programmed degradation in the dark.

Genetic Linkages of the Circadian Clock-Associated Genes, TOC1, CCA1 and LHY, in the Photoperiodic Control of Flowering Time in Arabidopsis thaliana

In Arabidopsis thaliana, the flowering time is regulated through the circadian clock that measures day-length and modulates the photoperiodic CO-FT output pathway in accordance with the external coincidence model. Nevertheless, the genetic linkages between the major clock-associated TOC1, CCA1 and LHY genes and the canonical CO-FT flowering pathway are less clear. By employing a set of mutants including an extremely early flowering toc1 cca1 lhy triple mutant, here we showed that CCA1 and LHY act redundantly as negative regulators of the photoperiodic flowering pathway. The partly redundant CCA1/LHY functions are largely, but not absolutely, dependent on the upstream TOC1 gene that serves as an activator. The results of examination with reference to the expression profiles of CO and FT in the mutants indicated that this clock circuitry is indeed linked to the CO-FT output pathway, if not exclusively. For this linkage, the phase control of certain flowering-associated genes, GI, CDF1 and FKF1, appears to be crucial. Furthermore, the genetic linkage between TOC1 and CCA1/LHY is compatible with the negative and positive feedback loop, which is currently believed to be a core of the circadian clock. The results of this study suggested that the circadian clock might open an exit for a photoperiodic output pathway during the daytime. In the context of the current clock model, these results will be discussed in connection with the previous finding that the same clock might open an exit for the early photomorphogenic output pathway during the night-time.