Loss of the circadian clock-associated protein 1 in Arabidopsis results in altered clock-regulated gene expression

Characterization of the APRR9 Pseudo-Response Regulator Belonging to the APRR1/TOC1 Quintet in Arabidopsis thaliana

In Arabidopsis thaliana, a number of circadian-associated factors have been identified, including TOC1 (TIMING OF CAB EXPRESSION1) that is believed to be a component of the central oscillator. TOC1 is a member of a small family of proteins, designated as ARABIDOPSIS PSEUDO-RESPONSE REGULATORS (APRR1/TOC1, APRR3, APRR5, APRR7, and APRR9). As demonstrated previously, these APRR1/TOC1 quintet members are crucial for a better understanding of the molecular links between circadian rhythms and photosensory signal transduction. Here we focused on the light-induced quintet member, APRR9, and three critical issues with regard to this member were simultaneously addressed: (i) clarification of the mechanism underlying the light-dependent acute response of APRR9, (ii) clarification of the phenotype of a null mutant of APRR9, (iii) identification of protein(s) that interacts with APRR9. In this study, we present the results that support the following views. (i) A phytochrome-mediated signaling pathway(s) activates the transcription of APRR9, leading to the acute light response of APRR9. (ii) The severe mutational lesion of APRR9 singly, if not directly, affects the period (and/or phase) of free-running rhythms, in continuous light, of every circadian-controlled gene tested, including the clock genes, APRR1/TOC1, CCA1, and LHY. (iii) The APRR9 protein is capable of interacting with APRR1/TOC1, suggesting a hetrodimer formation between these cognate family members. These results are discussed within the context of a current consistent model of the Arabidopsis circadian oscillator.

Enhanced Fitness Conferred by Naturally Occurring Variation in the Circadian Clock

Natural variation in clock parameters is necessary for the circadian clock to contribute to organismal fitness over a broad geographic range. Considerable variation is evident in the period, phase, and amplitude of 150 Arabidopsis accessions, and the period length is correlated with the day length at the latitude of origin, implying the adaptive significance of correctly regulated circadian timing. Quantitative trait loci analysis of recombinant inbred lines indicates that multiple loci interact to determine period, phase, and amplitude. The loss-of-function analysis of each member of the ARABIDOPSIS PSEUDO-RESPONSE REGULATOR family suggests that they are candidates for clock quantitative trait loci.

The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks

Plants synchronize developmental and metabolic processes with the earth's 24-h rotation through the integration of circadian rhythms and responses to light. We characterize the time for coffee (tic) mutant that disrupts circadian gating, photoperiodism, and multiple circadian rhythms, with differential effects among rhythms. TIC is distinct in physiological functions and genetic map position from other rhythm mutants and their homologous loci. Detailed rhythm analysis shows that the chlorophyll a/b-binding protein gene expression rhythm requires TIC function in the mid to late subjective night, when human activity may require coffee, in contrast to the function of EARLY-FLOWERING3 (ELF3) in the late day to early night. tic mutants misexpress genes that are thought to be critical for circadian timing, consistent with our functional analysis. Thus, we identify TIC as a regulator of the clock gene circuit. In contrast to tic and elf3 single mutants, tic elf3 double mutants are completely arrhythmic. Even the robust circadian clock of plants cannot function with defects at two different phases.

Comparative genetic studies on the APRR5 and APRR7 genes belonging to the APRR1/TOC1 quintet implicated in circadian rhythm, control of flowering time, and early photomorphogenesis

In Arabidopsis thaliana, a number of circadian-associated factors have been identified. Among those, TOC1 (TIMING OF CAB EXPRESSION 1) is believed to be a component of the central oscillator. TOC1 is a member of a small family of proteins, designated as Arabidopsis PSEUDO-RESPONSE REGULATORS (APRR1/TOC1, APRR3, APRR5, APRR7, and APRR9). Nonetheless, it is not very clear whether or not the APRR family members other than APRR1/TOC1 are also implicated in the mechanisms underlying the circadian rhythm. To address this issue further, here we characterized a set of T-DNA insertion mutants, each of which is assumed to have a severe lesion in each one of the quintet genes (i.e. APRR5 and APRR7). For each of these mutants (aprr5-11 and aprr7-11) we demonstrate that a given mutation singly, if not directly, affects the circadian-associated biological events simultaneously: (i) flowering time in the long-day photoperiod conditions, (ii) red light sensitivity of seedlings during the early photomorphogenesis, and (iii) the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light. These results suggest that, although the quintet members other than APRR1/TOC1 may not be directly integrated into the framework of the central oscillator, they are crucial for a better understanding of the molecular mechanisms underlying the Arabidopsis circadian clock.

The evolutionarily conserved OsPRR quintet: rice pseudo-response regulators implicated in circadian rhythm

In Arabidopsis thaliana, a number of circadian-associated factors have been identified, including TOC1 (TIMING OF CAB EXPRESSION 1) that is believed to be a component of the central oscillator. TOC1 is a member of a small family of proteins, designated as ARABIDOPSIS PSEUDO-RESPONSE REGULATORS (APRR1/TOC1, APRR3, APRR5, APRR7, and APRR9). As demonstrated previously, these APRR1/TOC1 quintet members are crucial for a better understanding of the molecular links between circadian rhythms, control of flowering time through photoperiodic pathways, and also photosensory signal transduction in this dicotyledonous plant. In this respect, both the dicotyledonous (e.g. A. thaliana) and monocotyledonous (e.g. Oryza sativa) plants might share the evolutionarily conserved molecular mechanism underlying the circadian rhythm. Based on such an assumption, and as the main objective of this study, we asked the question of whether rice also has a set of pseudo-response regulators, and if so, whether or not they are associated with the circadian rhythm. Here we showed that rice has five members of the OsPRR family (Oryza sativa Pseudo-Response Regulator), and also that the expressions of these OsPRR genes are under the control of circadian rhythm. They are expressed in a diurnal and sequential manner in the order of OsPRR73 (OsPRR37)-->OsPRR95 (OsPRR59)-->OsPRR1, which is reminiscent of the circadian waves of the APRR1/TOC1 quintet in A. thaliana. These and other results of this study suggested that the OsPRR quintet, including the ortholog of APRR1/TOC1, might play important roles within, or close to, the circadian clock of rice.

The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis

Using fluorescent differential display, we identified, from approximately 8000 displayed bands, a DNA fragment showing rapid induction in response to red light irradiation. This EARLY-PHYTOCHROME-RESPONSIVE1 gene (EPR1) encodes a novel nucleus-localized MYB protein harboring a single MYB domain that is highly similar to the circadian oscillator proteins CCA1 and LHY. EPR1 is regulated by both phytochrome A and phytochrome B, and the red-light induction of EPR1 is not inhibited by cycloheximide, demonstrating that EPR1 represents a primary phytochrome-responsive gene. Our results show that EPR1 overexpression results in enhanced far-red light-induced cotyledon opening and delayed flowering. In wild-type Arabidopsis plants grown in continuous light, the EPR1 transcript exhibits circadian rhythmicity similar to that of CCA1 and LHY. Moreover, EPR1 suppresses its own expression, suggesting that this protein is part of a regulatory feedback loop. Constitutive expression of CCA1 and LHY results in the loss of EPR1 rhythmicity, whereas increased levels of EPR1 have no effect on the central oscillator. We propose that EPR1 is a component of a slave oscillator that contributes to the refinement of output pathways, ultimately mediating the correct oscillatory behavior of target genes.

Light and circadian regulation in the expression of LHY and Lhcb genes in Phaseolus vulgaris

In order to understand some aspects of the circadian clock function in Phaseolus vulgaris, we analyzed the temporal transcript profile of Lhcb genes, typical clock reporters in plants, and that of PvLHY, an orthologue of Arabidopsis thaliana LHY which is a putative transcription factor of Lhcb genes. Under different light regimes, Lhcb and PvLHY exhibit a clear circadian pattern of expression. Moreover, the rhythm of Lhcb genes appears to be tightly coupled to that of PvLHY with the latter having a slightly earlier phase. This supports the idea that the oscillating capacity of PvLHY may be one of the causes of the rhythmic expression of Lhcb genes in bean. In addition to their circadian regulation, Lhcb and PvLHY are induced by light with similar and relatively slow induction kinetics. Moreover, this light induction is gated by the circadian oscillator: minimal responses occur at times around peaks of the pre-existing rhythm, while maximal ones occur at troughs of the pre-existing rhythm. This pattern of gating is opposite to that observed in Arabidopsis. The failure to block the light induction pathways at pre-existing troughs appears to have a detrimental effect to the subsequent circadian rhythmicity. Briefly, the overall regulation of PvLHY and Lhcb genes by light and the circadian clock reveals different strategies between Phaseolus and Arabidopsis in the adaptation to photoperiodic conditions.

Toward a detailed computational model for the mammalian circadian clock

We present a computational model for the mammalian circadian clock based on the intertwined positive and negative regulatory loops involving the Per, Cry, Bmal1, Clock, and Rev-Erb alpha genes. In agreement with experimental observations, the model can give rise to sustained circadian oscillations in continuous darkness, characterized by an antiphase relationship between Per/Cry/Rev-Erbalpha and Bmal1 mRNAs. Sustained oscillations correspond to the rhythms autonomously generated by suprachiasmatic nuclei. For other parameter values, damped oscillations can also be obtained in the model. These oscillations, which transform into sustained oscillations when coupled to a periodic signal, correspond to rhythms produced by peripheral tissues. When incorporating the light-induced expression of the Per gene, the model accounts for entrainment of the oscillations by light-dark cycles. Simulations show that the phase of the oscillations can then vary by several hours with relatively minor changes in parameter values. Such a lability of the phase could account for physiological disorders related to circadian rhythms in humans, such as advanced or delayed sleep phase syndrome, whereas the lack of entrainment by light-dark cycles can be related to the non-24h sleep-wake syndrome. The model uncovers the possible existence of multiple sources of oscillatory behavior. Thus, in conditions where the indirect negative autoregulation of Per and Cry expression is inoperative, the model indicates the possibility that sustained oscillations might still arise from the negative autoregulation of Bmal1 expression.

A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana

APRR1 (ARABIDPSIS PSUEDO-RESPONSE REGULATOR 1) (or TOC1, TIMING OF CAB EXPRESSION 1) is believed to be a crucial component of biological clocks of Arabidopsis thaliana. Nevertheless, its molecular function remains to be fully elucidated. Based on the results of yeast two-hybrid and in vitro binding assays, we previously showed that APRR1/TOC1 interacts with certain bHLH factors (i.e. PIF3 and PIL1, which are PHYTOCHROME INTERACTING FACTOR 3 and its homolog (PIF3-LIKE 1), respectively). To critically examine the relevance of PIL1 with reference to the function of APRR1/TOC1, T-DNA insertion mutants were isolated for PIL1. No phenotype was observed for such homozygous pil1 mutants, in terms of circadian-associated events in plants. We then examined more extensively a certain set of bHLH factors, which are considerably similar to PIL1 in their structural designs. The results of extensive analyses of such bHLH factors (namely, HFR1, PIL2, PIF4, PIL5 and PIL6) in wild-type and APRR1-overexressing (APRR1-ox) transgenic lines provided us with several new insights into a link between APRR1/TOC1 and these bHLH factors. In yeast two-hybrid assays, APRR1/TOC1 showed the ability to interact with these proteins (except for HFR1), as well as PIL1 and PIF3. Among them, it was found that the expressions of PIF4 and PIL6 were regulated in a circadian-dependent manner, exhibiting free-running robust rhythms. The expressions of PIF4 and PIL6 were regulated also by light in a manner that their transcripts were rapidly accumulated upon exposure of etiolated seedlings to light. The light-induced expressions of PIF4 and PIL6 were severely impaired in APRR1-ox transgenic lines. Taken together, here we propose the novel view that these bHLH factors (PIF4 and PIL6) might play roles, in concert with APRR1/TOC1, in the integration of light-signals to control both circadian and photomorphogenic processes.

Cell autonomous circadian waves of the APRR1/TOC1 quintet in an established cell line of Arabidopsis thaliana

A small family of genes, named Arabidopsis Pseudo Response Regulator (APRR), are intriguing with special reference to circadian rhythms in plants, based on the fact that one of the members (APRR1) is identical to TOC1 (Timing of CAB Expression 1) that is believed to encode a clock component. In Arabidopsis plants, each transcript of the APRR1/TOC1 quintet genes starts accumulating after dawn rhythmically and one after another at intervals in the order of APRR9 --> APRR7 --> APRR5 --> APRR3 --> APRR1/TOC1. To characterize such intriguing circadian-associated events, we employed an established Arabidopsis cell line (named T87). When T87 cells were grown in an appropriate light and dark cycle, cell autonomous diurnal oscillations of the APRR1/TOC1 quintet genes were observed at the level of transcription, as seen in intact plants. After transfer to the conditions without any environmental time cues, particularly in constant dark, we further showed that free-running circadian rhythms persisted in the cultured cells, not only for the APRR1/TOC1 quintet genes, but also other typical circadian-controlled genes including CCA1 (Circadian Clock Associated 1), LHY (Late Elongated Hypocotyl) and CCR2 (Cold Circadian Rhythm RNA Binding 2). To our knowledge, this is the first indication of cell autonomous circadian rhythms in cultured cells in Arabidopsis thaliana, which will provide us with an alternative and advantageous means to characterize the plant biological clock.

Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY

The transcription factor LHY and the related protein CCA1 perform overlapping functions in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis: Overexpression of LHY abolished function of the circadian clock in constant light, but rhythmic expression of several circadian clock-regulated transcripts was observed under light- dark cycles. These oscillations correlated with high amplitude changes in LHY protein levels, caused by light-induced translation of the LHY transcript. Increases in LHY protein levels were also observed in light-grown wild-type plants, when light signals coincided with the circadian-regulated peak of LHY transcription at dawn. Unexpectedly, translational induction coincided with acute downregulation of LHY transcript levels. We suggest that the simultaneous translational induction and transcriptional repression of LHY expression play a role to narrow the peak of LHY protein synthesis at dawn and increase the robustness and accuracy of circadian oscillations. Strong phase shifting responses to light signals were observed in plants lacking function of LHY, CCA1 or both, suggesting that light-regulated expression of these proteins does not mediate entrainment of the clock to light-dark cycles.

Shedding light on the circadian clock and the photoperiodic control of flowering

Recently, notable progress has been made towards understanding the genetic interactions that underlie the function of the circadian clock in plants, and how these functions are related to the seasonal control of flowering time. The LHY/CCA1 and TOC1 genes have been proposed to participate in a negative feedback loop that is part of the central oscillator of the circadian clock. Furthermore, analysis of a flowering-time pathway has suggested how transcriptional regulation by the circadian clock, combined with post-transcriptional regulation by light, could activate proteins that control flowering time in response to appropriate daylengths.

The Arabidopsis SRR1 gene mediates phyB signaling and is required for normal circadian clock function

Plants possess several photoreceptors to sense the light environment. In Arabidopsis cryptochromes and phytochromes play roles in photomorphogenesis and in the light input pathways that synchronize the circadian clock with the external world. We have identified SRR1 (sensitivity to red light reduced), a gene that plays an important role in phytochrome B (phyB)-mediated light signaling. The recessive srr1 null allele and phyB mutants display a number of similar phenotypes indicating that SRR1 is required for normal phyB signaling. Genetic analysis suggests that SRR1 works both in the phyB pathway but also independently of phyB. srr1 mutants are affected in multiple outputs of the circadian clock in continuous light conditions, including leaf movement and expression of the clock components, CCA1 and TOC1. Clock-regulated gene expression is also impaired during day-night cycles and in constant darkness. The circadian phenotypes of srr1 mutants in all three conditions suggest that SRR1 activity is required for normal oscillator function. The SRR1 gene was identified and shown to code for a protein conserved in numerous eukaryotes including mammals and flies, implicating a conserved role for this protein in both the animal and plant kingdoms.

Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis

To examine the role of the TOC1 (TIMING OF CAB EXPRESSION1) gene in the Arabidopsis circadian system, we generated a series of transgenic plants expressing a gradation in TOC1 levels. Silencing of the TOC1 gene causes arrhythmia in constant darkness and in various intensities of red light, whereas in blue light, the clock runs faster in silenced plants than in wild-type plants. Increments in TOC1 gene dosage delayed the pace of the clock, whereas TOC1 overexpression abolished rhythmicity in all light conditions tested. Our results show that TOC1 RNA interference and toc1-2 mutant plants displayed an important reduction in sensitivity to red and far-red light in the control of hypocotyl elongation, whereas increments in TOC1 gene dosage clearly enhanced light sensitivity. Furthermore, the red light-mediated induction of CCA1/LHY expression was decreased in TOC1 RNA interference and toc1-2 mutant plants, indicating a role for TOC1 in the phytochrome regulation of circadian gene expression. We conclude that TOC1 is an important component of the circadian clock in Arabidopsis with a crucial function in the integration of light signals to control circadian and morphogenic responses.

Aberrant expression of the Arabidopsis circadian-regulated APRR5 gene belonging to the APRR1/TOC1 quintet results in early flowering and hypersensitiveness to light in early photomorphogenesis

In Arabidopsis thaliana, the transcripts of the APRR1/TOC1 family genes each start accumulating after dawn rhythmically and one after another at intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1 under continuous light. Except for the well-characterized APRR1/TOC1, however, no evidence has been provided that other APRR1/TOC1 family genes are indeed implicated in the mechanisms underlying circadian rhythms. We here attempted to provide such evidence by characterizing transgenic plants that constitutively express the APRR5 gene. The resulting APRR5-overexpressing (APRR5-ox) plants showed intriguing properties with regard to not only circadian rhythms, but also control of flowering time and light response. First, the aberrant expression of APRR5 in such transgenic plants resulted in a characteristic phenotype with regard to transcriptional events, in which free-running rhythms were considerably altered for certain circadian-regulated genes, including CCA1, LHY, APRR1/TOC1, other APRR1/TOC1 members, GI and CAB2, although each rhythm was clearly sustained even after plants were transferred to continuous light. With regard to biological events, APRR5-ox plants flowered much earlier than wild-type plants, more or less, in a manner independent of photoperiodicity (or under short-day conditions). Furthermore, APRR5-ox plants showed an SRL (short-hypocotyls under red light) phenotype that is indicative of hypersensitiveness to red light in early photomorphogenesis. Both APRR1-ox and APRR9-ox plants also showed the same phenotype. Therefore, APRR5 (together with APRR1/TOC1 and APRR9) must be taken into consideration for a better understanding of the molecular links between circadian rhythms, control of flowering time through the photoperiodic long-day pathway, and also light signaling-controlled plant development.

Aberrant expression of the light-inducible and circadian-regulated APRR9 gene belonging to the circadian-associated APRR1/TOC1 quintet results in the phenotype of early flowering in Arabidopsis thaliana

Several Arabidopsis genes have been proposed to encode potential clock-associated components, including the Myb-related CCA1 and LHY transcription factors and a member (APRR1/TOC1) of the family of pseudo-response regulators. We previously showed that transcripts of the APRR1/TOC1 family genes each start accumulating after dawn rhythmically and sequentially at intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1, under the conditions of continuous light. Nevertheless, no evidence has been provided that each member of the APRR1/TOC1 quintet, except for APRR1/TOC1, is indeed relevant to the mechanisms underlying circadian rhythms. Here we attempt to provide such evidence by characterizing transgenic plants that aberrantly (or constitutively) express the APRR9 gene in a manner independent of circadian rhythms. The resulting APRR9-ox plants showed intriguing phenotypes with regard to circadian rhythms, in two aspects. First, the aberrant expression of APRR9 resulted in a characteristic phenotype with regard to transcriptional events, in which short-period rhythms were commonly observed for certain circadian-regulated genes, including CCA1, LHY, APRR1/TOC1, other APRR1/TOC1 members, ELF3, and CAB2. With regard to biological consequences, such APRR9-ox plants flowered much earlier than wild-type plants, in a manner independent of photoperiodicity (or under short-day conditions). These results suggest that APRR9 (and perhaps other members of the APRR1/TOC1 quintet) must also be taken into consideration for a better understanding of the molecular mechanisms underlying circadian rhythms, and also underlying control of the flowering time through the photoperiodic long-day pathway.

The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis

Arabidopsis displays circadian rhythms in stomatal aperture, stomatal conductance, and CO(2) assimilation, each of which peaks around the middle of the day. The rhythmic opening and closing of stomata confers a rhythm in sensitivity and resistance, respectively, to the toxic gas sulfur dioxide. Using this physiological assay as a basis for a mutant screen, we isolated mutants with defects in circadian timing. Here, we characterize one mutant, out of phase 1 (oop1), with the circadian phenotype of altered phase. That is, the timing of the peak (acrophase) of multiple circadian rhythms (leaf movement, CO(2) assimilation, and LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING PROTEIN transcription) is early with respect to wild type, although all circadian rhythms retain normal period length. This is the first such mutant to be characterized in Arabidopsis. oop1 also displays a strong photoperception defect in red light characteristic of phytochrome B (phyB) mutants. The oop1 mutation is a nonsense mutation of PHYB that results in a truncated protein of 904 amino acids. The defect in circadian phasing is seen in seedlings entrained by a light-dark cycle but not in seedlings entrained by a temperature cycle. Thus, PHYB contributes light information critical for proper determination of circadian phase.

The APRR3 component of the clock-associated APRR1/TOC1 quintet is phosphorylated by a novel protein kinase belonging to the WNK family, the gene for which is also transcribed rhythmically in Arabidopsis thaliana

In higher plants, clock-controlled circadian rhythms are a longstanding issue in physiology, and a newly emerging paradigm of molecular biology. In the model higher plant Arabidopsis thaliana, several genes have been proposed to encode potential clock-associated components, including a member (APRR1/TOC1) of the pseudo-response regulator family. We previously showed that transcripts of the APRR1/TOC1 family start accumulating after dawn rhythmically and sequentially at approximately 2 h intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/ TOC1. This and other results led us to propose that this APRR1/TOC1 quintet might play coordinate roles in the mechanism underlying circadian rhythms in higher plants. To gain further insight as to such an idea, we here attempt to identify proteins that interact with one of the quintet members, APRR3. The identified component is a novel protein kinase, named WNK1, which is considerably similar to, but clearly distinct from, mitogen-activated protein kinases (MAPKs). It was found that APRR3 is a substrate of this novel protein kinase, the gene for which also shows a rhythmic transcription profile that is well coincident with the APRR3 rhythm. These findings give new insight into the mechanisms underlying the circadian rhythm in A. thaliana, providing a molecular link between the putative clock component, APRR3, and WNK1, a novel protein kinase that might be implicated as a signal transducer.

Circadian rhythms confer a higher level of fitness to Arabidopsis plants

Circadian rhythms have been demonstrated in organisms across the taxonomic spectrum. In view of their widespread occurrence, the adaptive significance of these rhythms is of interest. We have previously shown that constitutive expression of the CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) gene in Arabidopsis plants (CCA1-ox) results in loss of circadian rhythmicity. Here, we demonstrate that these CCA1-ox plants retain the ability to respond to diurnal changes in light. Thus, transcript levels of several circadian-regulated genes, as well as CCA1 itself and the closely related LHY, oscillate robustly if CCA1-ox plants are grown under diurnal conditions. However, in contrast with wild-type plants in which transcript levels change in anticipation of the dark/light transitions, the CCA1-ox plants have lost the ability to anticipate this daily change in their environment. We have used CCA1-ox lines to examine the effects of loss of circadian regulation on the fitness of an organism. CCA1-ox plants flowered later, especially under long-day conditions, and were less viable under very short-day conditions than their wild-type counterparts. In addition, we demonstrate that two other circadian rhythm mutants, LHY-ox and elf3, have low-viability phenotypes. Our findings demonstrate the adaptive advantage of circadian rhythms in Arabidopsis.

The role of CCA1 and LHY in the plant circadian clock

Our understanding of plant circadian rhythms has been advanced by two papers investigating the roles of the transcription factors CCA1 and LHY in the circadian oscillator.

LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis

Several genes are known to regulate circadian rhythms in Arabidopsis, but the identity of the central oscillator has not been established. LHY and CCA1 are related MYB-like transcription factors proposed to be closely involved. Here we demonstrate that, as shown previously for CCA1, inactivation of LHY shortens the period of circadian rhythms in gene expression and leaf movements. By constructing lhy cca1-1 double mutants, we show that LHY and CCA1 are partially redundant and essential for the maintenance of circadian rhythms in constant light. Under light/dark cycles the lhy cca1-1 plants show dramatically earlier phases of expression of GI and TOC1, genes associated with the generation of circadian rhythms and the promotion of LHY and CCA1 expression. We conclude that LHY and CCA1 appear to be negative regulatory elements required for central oscillator function.

Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis

Circadian clocks are autoregulatory, endogenous mechanisms that allow organisms, from bacteria to humans, to advantageously time a wide range of activities within 24-hr environmental cycles. CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) are thought to be important components of the circadian clock in the model plant Arabidopsis. The similar circadian phenotypes of lines overexpressing either CCA1 or LHY have suggested that the functions of these two transcription factors are largely overlapping. cca1-1 plants, which lack CCA1 protein, show a short-period phenotype for the expression of several genes when assayed under constant light conditions. This suggests that LHY function is able to only partially compensate for the lack of CCA1 protein, resulting in a clock with a faster pace in cca1-1 plants. We have obtained plants lacking CCA1 and with LHY function strongly reduced, cca1-1 lhy-R, and show that these plants are unable to maintain sustained oscillations in both constant light and constant darkness. However, these plants exhibit some circadian function in light/dark cycles, showing that the Arabidopsis circadian clock is not entirely dependent on CCA1 and LHY activities.

Photosensory perception and signalling in plant cells: new paradigms?

Plants monitor informational light signals using three sensory photoreceptor families: the phototropins, cryptochromes and phytochromes. Recent advances suggest that the phytochromes act transcriptionally by targeting light signals directly to photoresponsive promoters through binding to a transcriptional regulator. By contrast, the cryptochromes appear to act post-translationally, by disrupting extant proteosome-mediated degradation of a key transcriptional activator through direct binding to a putative E3 ubiquitin ligase, thereby elevating levels of the activator and consequently of target gene expression.

The Arabidopsis circadian system

Rhythms with periods of approximately 24 hr are widespread in nature. Those that persist in constant conditions are termed circadian rhythms and reflect the activity of an endogenous biological clock. Plants, including Arabidopsis, are richly rhythmic. Expression analysis, most recently on a genomic scale, indicates that the Arabidopsis circadian clock regulates a number of key metabolic pathways and stress responses. A number of sensitive and high-throughput assays have been developed to monitor the Arabidopsis clock. These assays have facilitated the identification of components of plant circadian systems through genetic and molecular biological studies. Although much remains to be learned, the framework of the Arabidopsis circadian system is coming into focus.DedicationThis review is dedicated to the memory of DeLill Nasser, a wonderful mentor and an unwavering advocate of both Arabidopsis and circadian rhythms research.

Phytochrome photosensory signalling networks

Light is life for plants. To continuously assess and adapt to fluctuations in the quality and quantity of this essential commodity, plants deploy sensory photoreceptors, including the phytochromes. Having captured an incoming photon, the activated phytochrome molecule must relay this information to nuclear genes that are poised to respond by directing appropriate adjustments in growth and development. Defining the intricate intracellular signalling networks through which this sensory information is transduced is an area of intense research activity.

Molecular bases of circadian rhythms

Circadian rhythms are found in most eukaryotes and some prokaryotes. The mechanism by which organisms maintain these roughly 24-h rhythms in the absence of environmental stimuli has long been a mystery and has recently been the subject of intense research. In the past few years, we have seen explosive progress in the understanding of the molecular basis of circadian rhythms in model systems ranging from cyanobacteria to mammals. This review attempts to outline these primarily genetic and biochemical findings and encompasses work done in cyanobacteria, Neurospora, higher plants, Drosophila, and rodents. Although actual clock components do not seem to be conserved between kingdoms, central clock mechanisms are conserved. Somewhat paradoxically, clock components that are conserved between species can be used in diverse ways. The different uses of common components may reflect the important role that the circadian clock plays in adaptation of species to particular environmental niches.

The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants

Several Arabidopsis genes have been proposed to encode potential clock-associated components, including the Myb-related CCA1 and LHY transcription factors and a member of the novel family of pseudo response regulators (APRR1/TOC1). We previously showed that mRNAs of the APRR1/TOC1 family of genes start accumulating after dawn rhythmically and sequentially at approximately 2 h intervals in the order: APRR9--> APRR7-->APRR5-->APRR3-->APRR1/TOC1. Here we constructed APRR1-overexpressing (APRR1-ox) plants, and examined certain circadian profiles for APRRs, CCA1, LHY, GI, CCR2, and CAB2. The free-running circadian rhythms of the APRR1/TOC1 family of genes, including APRR1, were dampened in APRR1-ox plants. In particular, the light-inducible expression of APRR9 was severely repressed in APRR1-ox plants, suggesting that there is a negative APRR1-->APRR9 regulation. The free-running robust rhythm of CAB2 was also dampened in APRR1-ox. The circadian profiles of potential clock-associated genes, CCA1, LHY, GI, and CCR2 were all markedly altered in APRR1-ox, each in characteristic fashion. To gain further insight into the molecular function of APRR1, we then identified a novel Myc-related bHLH transcription factor, which physically associated with APRR1. This protein (named PIL1) is similar in its amino acid sequence to PIF3, which has been identified as a phytochrome-interacting transcription factor. These results are discussed in relation to the current idea that APRR1 (TOC1) plays a role within, or close to, the Arabidopsis central oscillator.

RNA-binding proteins and circadian rhythms in Arabidopsis thaliana

An Arabidopsis transcript preferentially expressed at the end of the daily light period codes for the RNA-binding protein AtGRP7. A reverse genetic approach in Arabidopsis thaliana has revealed its role in the generation of circadian rhythmicity: AtGRP7 is part of a negative feedback loop through which it influences the oscillations of its own transcript. Biochemical and genetic experiments indicate a mechanism for this autoregulatory circuit: Atgrp7 gene transcription is rhythmically activated by the circadian clock during the day. The AtGPR7 protein accumulates with a certain delay and represses further accumulation of its transcript, presumably at the post-transcriptional level. In this respect, the AtGRP7 feedback loop differs from known circadian oscillators in the fruitfly Drosophila and mammals based on oscillating clock proteins that repress transcription of their own genes with a 24 h rhythm. It is proposed that the AtGRP7 feedback loop may act within an output pathway from the Arabidopsis clock.

Picking out parallels: plant circadian clocks in context

Molecular models have been described for the circadian clocks of representatives of several different taxa. Much of the work on the plant circadian system has been carried out using the thale cress, Arabidopsis thaliana, as a model. We discuss the roles of genes implicated in the plant circadian system, with special emphasis on Arabidopsis. Plants have an endogenous clock that regulates many aspects of circadian and photoperiodic behaviour. Despite the discovery of components that resemble those involved in the clocks of animals or fungi, no coherent model of the plant clock has yet been proposed. In this review, we aim to provide an overview of studies of the Arabidopsis circadian system. We shall compare these with results from different taxa and discuss them in the context of what is known about clocks in other organisms.

The Neurospora circadian clock: simple or complex?

The fungus Neurospora crassa is being used by a number of research groups as a model organism to investigate circadian (daily) rhythmicity. In this review we concentrate on recent work relating to the complexity of the circadian system in this organism. We discuss: the advantages of Neurospora as a model system for clock studies; the frequency (frq), white collar-1 and white collar-2 genes and their roles in rhythmicity; the phenomenon of rhythmicity in null frq mutants and its implications for clock mechanisms; the study of output pathways using clock-controlled genes; other rhythms in fungi; mathematical modelling of the Neurospora circadian system; and the application of new technologies to the study of Neurospora rhythmicity. We conclude that there may be many gene products involved in the clock mechanism, there may be multiple interacting oscillators comprising the clock mechanism, there may be feedback from output pathways onto the oscillator(s) and from the oscillator(s) onto input pathways, and there may be several independent clocks coexisting in one organism. Thus even a relatively simple lower eukaryote can be used to address questions about a complex, networked circadian system.

Clock-associated genes in Arabidopsis: a family affair

The identification of components of the plant circadian clock has been advanced recently with the success of two forward genetics approaches. The ZEITLUPE and TOC1 loci were cloned and each was found to be part of two separate, larger gene families with intriguing domain structures. The ZTL family of proteins contains a subclass of the PAS domain coupled to an F box and kelch motifs, suggesting that they play a role in a novel light-regulated ubiquitination mechanism. TOC1 shares similarity to the receiver domain of the well-known two-component phosphorelay signalling systems, combined with a strong similarity to a region of the CONSTANS transcription factor, which is involved in controlling flowering time. When added to the repertoire of previously identified clock-associated genes, it is clear that both similarities and differences with other circadian systems will emerge in the coming years.

Flowering in time: genes controlling photoperiodic flowering in Arabidopsis

Successful sexual reproduction in plants relies upon the strict coordination of flowering time with favourable seasons of the year. One of the most important seasonal cues for the model plant Arabidopsis thaliana (Arabidopsis) is day length. Genes influencing flowering time in Arabidopsis have been isolated, some of which are involved in the perception and signalling of day length. This review discusses recent progress that has been made in understanding how Arabidopsis integrates environmental and internal signals to ensure a sharp transition to flowering and new insights on the role of the circadian clock in controlling the expression of genes that promote flowering in response to day length.

Time zones: a comparative genetics of circadian clocks

The circadian clock is a widespread cellular mechanism that underlies diverse rhythmic functions in organisms from bacteria and fungi, to plants and animals. Intense genetic analysis during recent years has uncovered many of the components and molecular mechanisms comprising these clocks. Although autoregulatory genetic networks are a consistent feature in the design of all clocks, the weight of evidence favours their independent evolutionary origins in different kingdoms.

Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock

The interactive regulation between clock genes is central for oscillator function. Here, we show interactions between the Arabidopsis clock genes LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), and TIMING OF CAB EXPRESSION 1 (TOC1). The MYB transcription factors LHY and CCA1 negatively regulate TOC1 expression. We show that both proteins bind to a region in the TOC1 promoter that is critical for its clock regulation. Conversely, TOC1 appears to participate in the positive regulation of LHY and CCA1 expression. Our results indicate that these interactions form a loop critical for clock function in Arabidopsis.

The molecular genetics of circadian rhythms in Arabidopsis

While a number of physiological and biochemical processes in plants have been found to be regulated in a circadian manner, the mechanism underlying the circadian oscillator remains to be elucidated. Advances in the identification and characterization of components of the plant circadian system have been made largely through the use of genetics in Arabidopsis thaliana. Results so far indicate that the generation of rhythmicity by the Arabidopsis clock relies on molecular mechanisms that are similar to those described for other organisms, but that a totally different set of molecular components has been recruited to perform these functions.

Multiple transcription-factor genes are early targets of phytochrome A signaling

The phytochrome family of sensory photoreceptors directs adaptational changes in gene expression in response to environmental light signals. Using oligonucleotide microarrays to measure expression profiles in wild-type and phytochrome A (phyA) null-mutant Arabidopsis seedlings, we have shown that 10% of the genes represented on the array are regulated by phyA in response to a continuous far-red light signal. Strikingly, 44% of the genes responding to the signal within 1 h are predicted to encode multiple classes of transcriptional regulators. Together with previous data, this observation suggests that phyA may regulate seedling photomorphogenesis by direct targeting of light signals to the promoters of genes encoding a master set of diverse transcriptional regulators, responsible in turn for orchestrating the expression of multiple downstream target genes in various branches of a phyA-regulated transcriptional network.

Endogenous timekeepers in photosynthetic organisms

Circadian and photoperiodic timing mechanisms were first described in photosynthetic organisms. These organisms depend upon sunlight for their energy, so adaptation to daily and seasonal fluctuations in light must have generated a strong selective pressure. Studies of the endogenous timekeepers of photosynthetic organisms provide evidence for both a fitness advantage and for selective pressures involved in early evolution of circadian clocks. Photoperiodic timing mechanisms in plants appear to use their circadian timers as the ruler by which the day/night length is measured. As in animals, the overall clock system in plants appears to be complex; the system includes multiple oscillators, several input pathways, and a myriad of outputs. Genes have now been isolated from plants that are likely to encode components of the central clockwork or at least that act very close to the central mechanism. Genetic and biochemical analyses of the central clockwork of a photosynthetic organism are most highly advanced in cyanobacteria, where a cluster of clock genes and interacting factors have been characterized.

shygrl1 is a mutant affected in multiple aspects of photomorphogenesis

We have used a counter-selection strategy based on aberrant phytochrome regulation of an Lhcb gene to isolate an Arabidopsis mutant designated shygrl1 (shg1). shg1 seedlings have reduced phytochrome-mediated induction of the Lhcb gene family, but normal phytochrome-mediated induction of several other genes, including the rbcS1a gene. Additional phenotypes observed in shg1 plants include reduced chlorophyll in leaves and additional photomorphogenic abnormalities when the seedlings are grown on medium containing sucrose. Mutations in the TATA-proximal region of the Lhcb1*3 promoter that are known to be important for phytochrome regulation affected reporter gene expression in a manner similar to the shg1 mutation. Our results are consistent with the possibility that the mutation either leads to defective chloroplast development or to aberrant phytochrome regulation. They also add to the evidence of complex interactions between light- and sucrose-regulated pathways.

EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis

Higher plants use photoperiodic cues to regulate many aspects of development, including the transition from vegetative to floral development. The EARLY FLOWERING3 (ELF3) gene is required for photoperiodic flowering and normal circadian regulation in Arabidopsis. We have cloned ELF3 by positional methods and found that it encodes a novel 695-amino acid protein that may function as a transcriptional regulator. ELF3 transcript level is regulated in a circadian manner, as is expected of a zeitnehmer input pathway component. Overexpression of the LATE ELONGATED HYPOCOTYL gene, which has been proposed to function as a clock component, did not abolish circadian regulation of ELF3 transcription, providing further evidence that ELF3 is a circadian clock input pathway component.

CIRCADIAN RHYTHMS IN PLANTS

Circadian rhythms, endogenous rhythms with periods of approximately 24 h, are widespread in nature. Although plants have provided many examples of rhythmic outputs and our understanding of photoreceptors of circadian input pathways is well advanced, studies with plants have lagged in the identification of components of the central circadian oscillator. Nonetheless, genetic and molecular biological studies, primarily in Arabidopsis, have begun to identify the components of plant circadian systems at an accelerating pace. There also is accumulating evidence that plants and other organisms house multiple circadian clocks both in different tissues and, quite probably, within individual cells, providing unanticipated complexity in circadian systems.

CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis

Flowering is often triggered by exposing plants to appropriate day lengths. This response requires an endogenous timer called the circadian clock to measure the duration of the day or night. This timer also controls daily rhythms in gene expression and behavioural patterns such as leaf movements. Several Arabidopsis mutations affect both circadian processes and flowering time; but how the effect of these mutations on the circadian clock is related to their influence on flowering remains unknown. Here we show that expression of CONSTANS (CO), a gene that accelerates flowering in response to long days, is modulated by the circadian clock and day length. Expression of a CO target gene, called FLOWERING LOCUS T (FT), is restricted to a similar time of day as expression of CO. Three mutations that affect circadian rhythms and flowering time alter CO and FT expression in ways that are consistent with their effects on flowering. In addition, the late flowering phenotype of such mutants is corrected by overexpressing CO. Thus, CO acts between the circadian clock and the control of flowering, suggesting mechanisms by which day length regulates flowering time.

Arabidopsis gene knockout: phenotypes wanted

Gene knockout is considered to be a major component of the functional genomics toolbox, and is aimed at revealing the function of genes discovered through large-scale sequencing programs. In the past few years, several Arabidopsis populations mutagenized with insertion elements, such as the T-DNA of Agrobacterium or transposons, have been produced. These large populations are routinely screened for insertions into specific genes, allowing mass-isolation of knockout lines. Although many Arabidopsis knockouts have already been obtained, few of them have been reported to present informative phenotypes that provide a direct clue to gene function. Although functional redundancy explains the lack of phenotypical alterations in some cases, it also appears that many mutations are conditional and/or do not alter plant morphology even in the presence of severe physiological defects. Consequently, gene knockout per se is not sufficient to assess gene function and must be integrated into a more global approach for determining biological functions.

Analysis of the function of two circadian-regulated CONSTANS-LIKE genes

The Arabidopsis genes CONSTANS-LIKE 1 (COL1) and CONSTANS-LIKE 2 (COL2) are predicted to encode zinc finger proteins with approximately 67% amino acid identity to the protein encoded by the flowering-time gene CONSTANS (CO). We show that the circadian clock regulates expression of COL1 and COL2 with a peak in transcript levels around dawn. We analyzed transgenic plants misexpressing COL1, COL2 and CO. Unlike CO, altered expression of COL1 and COL2 in transgenic plants had little effect on flowering time. However, analysis of circadian phenotypes in the transgenic plants showed that over-expression of COL1 can shorten the period of two distinct circadian rhythms. Experiments with the highest COL1 over-expressing line indicate that its circadian defects are fluence rate-dependent, suggesting an effect on a light input pathway(s).

Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis

Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional nonrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY, CCA1, and GI, suggesting that other key circadian clock genes might be found within these clusters.

All in good time: the Arabidopsis circadian clock

Biological time-keeping mechanisms have fascinated researchers since the movement of leaves with a daily rhythm was first described >270 years ago. The circadian clock confers a approximately 24-hour rhythm on a range of processes including leaf movements and the expression of some genes. Molecular mechanisms and components underlying clock function have been described in recent years for several animal and prokaryotic organisms, and those of plants are beginning to be characterized. The emerging model of the Arabidopsis clock has mechanistic parallels with the clocks of other model organisms, which consist of positive and negative feedback loops, but the molecular components appear to be unique to plants.

Phytochrome-interacting factors

The phytochrome family of sensory photoreceptors transduces environmental light signals to responsive nuclear genes by poorly defined pathways. The recent application of yeast two-hybrid library screens to the identification of components that physically interact with members of the phytochrome family has dramatically altered previous views of the likely intracellular signaling pathways. The evidence indicates that one pathway involves light-triggered translocation of the photoreceptor molecule from cytoplasm to nucleus where it binds specifically in its biologically active form to a promoter-bound basic helix-loop-helix protein. The phytochrome molecules are proposed to function as integral, light-switchable components of transcriptional regulator complexes targeting environmental light signals directly and instantly to specific gene promoters.