How plants tell the time

Cycling of clock genes entrained to the solar rhythm enables plants to tell time: data from Arabidopsis

BACKGROUND AND AIMS

An endogenous rhythm synchronized to dawn cannot time photosynthesis-linked genes to peak consistently at noon since the interval between sunrise and noon changes seasonally. In this study, a solar clock model that circumvents this limitation is proposed using two daily timing references synchronized to noon and midnight. Other rhythmic genes that are not directly linked to photosynthesis, and which peak at other times, also find an adaptive advantage in entrainment to the solar rhythm.

METHODS

Fourteen datasets extracted from three published papers were used in a meta-analysis to examine the cyclic behaviour of the Arabidopsis thaliana photosynthesis-related gene CAB2 and the clock oscillator genes TOC1 and LHY in T cycles and N-H cycles.

KEY RESULTS

Changes in the rhythms of CAB2, TOC1 and LHY in plants subjected to non-24-h light:dark cycles matched the hypothesized changes in their behaviour as predicted by the solar clock model, thus validating it. The analysis further showed that TOC1 expression peaked ∼5·5 h after mid-day, CAB2 peaked close to noon, while LHY peaked ∼7·5 h after midnight, regardless of the cycle period, the photoperiod or the light:dark period ratio. The solar clock model correctly predicted the zeitgeber timing of these genes under 11 different lighting regimes comprising combinations of seven light periods, nine dark periods, four cycle periods and four light:dark period ratios. In short cycles that terminated before LHY could be expressed, the solar clock correctly predicted zeitgeber timing of its expression in the following cycle.

CONCLUSIONS

Regulation of gene phases by the solar clock enables the plant to tell the time, by which means a large number of genes are regulated. This facilitates the initiation of gene expression even before the arrival of sunrise, sunset or noon, thus allowing the plant to 'anticipate' dawn, dusk or mid-day respectively, independently of the photoperiod.

Chronopharmacognosy

This study aims to review the concept of biological rhythms in medicinal plants. Dictionariesgenerally define pharmacognosy as the subject of the study of crude drugs of plant and animal origin. The name is derived from the Greek words pharmakon (drug) and gnosis (knowledge). Today pharmacognosy is also defined as the study of physical, chemical, biochemical and biological properties of drugs, drug substances, or potential drugs or drug substances of natural origin, as well as the search for new drugs from natural sources. Also, another important phenomenon to be taken care of in the production of therapeutic compounds in medicinal plants is the use of circardian clock. The circardian clock is studied by chronobiology, which can be defined as a field of science that examines periodic (cyclic) phenomena in living organisms and their adaptation to solar and lunar related rhythms. Thus, it is the scientific study of the effect of time on living systems and of biological rhythms. Also rhythmic oscillations in plants lead to the enormous production of particular compounds in plants at particular time, which may or may not produce any therapeutic effect in humans. Thus, the study of chronobiology and pharmacognosy can be put together as chronopharmacognosy.

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.

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.

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.

The circadian clock that controls gene expression in Arabidopsis is tissue specific

The expression of CHALCONE SYNTHASE (CHS) expression is an important control step in the biosynthesis of flavonoids, which are major photoprotectants in plants. CHS transcription is regulated by endogenous programs and in response to environmental signals. Luciferase reporter gene fusions showed that the CHS promoter is controlled by the circadian clock both in roots and in aerial organs of transgenic Arabidopsis plants. The period of rhythmic CHS expression differs from the previously described rhythm of chlorophyll a/b-binding protein (CAB) gene expression, indicating that CHS is controlled by a distinct circadian clock. The difference in period is maintained in the wild-type Arabidopsis accessions tested and in the de-etiolated 1 and timing of CAB expression 1 mutants. These clock-affecting mutations alter the rhythms of both CAB and CHS markers, indicating that a similar (if not identical) circadian clock mechanism controls these rhythms. The distinct tissue distribution of CAB and CHS expression suggests that the properties of the circadian clock differ among plant tissues. Several animal organs also exhibit heterogeneous circadian properties in culture but are believed to be synchronized in vivo. The fact that differing periods are manifest in intact plants supports our proposal that spatially separated copies of the plant circadian clock are at most weakly coupled, if not functionally independent. This autonomy has apparently permitted tissue-specific specialization of circadian timing.

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 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.

The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants

We previously identified a novel class of proteins, named pseudo-response regulators (APRRs) in Arabidopsis thaliana, each of which (APRR1, APRR3, APRR5, APRR7, and APRR9) has an intriguing structural design containing an N-terminal pseudo receiver domain and a C-terminal CONSTANS motif. Among them, APRR1 is identical to TOC1, previously proposed to be a candidate component of an Arabidopsis circadian clock. Intriguingly, expressions of the APRR1/TOC1 family of genes are under control of coordinate circadian rhythms at the level of transcription, in the manner that each APRR-transcript starts accumulating sequentially after dawn with 2 to 3 h intervals in the order: APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1. Here we examined this circadian-related event, "circadian waves of the APRR1/TOC1 quintet", by employing CCA1-overexpression (CCA1-ox) transgenic plants, based on the fact that CCA1 is a well-characterized and the most plausible oscillator component. It was found that aberrant overexpression of the CCA1 gene severely perturbed free-running and sequential rhythms of the APRR1/TOC1 family of genes. In the accompanying paper, it was shown that overexpression of APRR1 also results in a marked alteration of the CCA1 circadian rhythm, and vice versa. Taken together, it was suggested that there are intimate and mutual links between these two types of circadian-associated components (APRRs and CCA1).

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.

The heme-oxygenase family required for phytochrome chromophore biosynthesis is necessary for proper photomorphogenesis in higher plants

The committed step in the biosynthesis of the phytochrome chromophore phytochromobilin involves the oxidative cleavage of heme by a heme oxygenase (HO) to form biliverdin IXalpha. Through positional cloning of the photomorphogenic mutant hy1, the Arabidopsis HO (designated AtHO1) responsible for much of phytochromobilin synthesis recently was identified. Using the AtHO1 sequence, we identified families of HO genes in a number of plants that cluster into two subfamilies (HO1- and HO2-like). The tomato (Lycopersicon esculentum) yg-2 and Nicotiana plumbaginifolia pew1 photomorphogenic mutants are defective in specific HO genes. Phenotypic analysis of a T-DNA insertion mutant of Arabidopsis HO2 revealed that the second HO subfamily also contributes to phytochromobilin synthesis. Homozygous ho2-1 plants show decreased chlorophyll accumulation, reduced growth rate, accelerated flowering time, and reduced de-etiolation. A mixture of apo- and holo-phyA was detected in etiolated ho2-1 seedlings, suggesting that phytochromobilin is limiting in this mutant, even in the presence of functional AtHO1. The patterns of Arabidopsis HO1 and HO2 expression suggest that the products of both genes overlap temporally and spatially. Taken together, the family of HOs is important for phytochrome-mediated development in a number of plants and that each family member may uniquely contribute to the phytochromobilin pool needed to assemble holo-phytochromes.

Light response of the circadian waves of the APRR1/TOC1 quintet: when does the quintet start singing rhythmically in Arabidopsis?

We previously identified a novel class of proteins, named A:rabidopsis pseudo-response regulators (APRRs), each of which (APRR1/TOC1, APRR3, APRR5, APRR7, APRR9) has an intriguing structural design containing an N-terminal pseudo-receiver domain and a C-terminal CONSTANS motif. Expression of these APRR1/TOC1 family members is under the control of a coordinate circadian rhythm at the level of transcription such that the APRR-mRNAs start accumulating sequentially after dawn with 2 to 3 h intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1 in a given 24 h photo-period. Based on these data, we previously proposed that these sequential and rhythmic events of transcription, termed 'circadian waves of APRR1/TOC1 quintet', may be a basis of a presumed Arabidopsis biological clock (named 'bar code clock') [Matsushika et al. (2000) Plant and Cell Physiol. 41: 1002]. Here we further characterized the event of circadian waves, by demonstrating that certain light stimuli are crucial determinants to induce the robust circadian waves, and accordingly, the first-boosted and light-induced APRR9 appears to be primarily responsible for this light response of the circadian waves. Also, as such a light stimulus, a red light pulse that is presumably perceived by phytochromes appears to be sufficient to induce (or synchronize) the APRR1/TOC1 circadian waves.

Circadian waves of expression of the APRR1/TOC1 family of pseudo-response regulators in Arabidopsis thaliana: insight into the plant circadian clock

The Arabidopsis pseudo-response regulator, APRR1, has a unique structural design containing a pseudo-receiver domain and a C-terminal CONSTANS motif. This protein was originally characterized as a presumed component of the His-to-Asp phosphorelay systems in Arabidopsis thaliana. Recently, it was reported that APRR1 is identical to the TOC1 gene product, a mutational lesion of which affects the periods of many circadian rhythms in Arabidopsis plants. TOC1 is believed to be a component of the presumed circadian clock (or central oscillator). Based on these facts, in this study four more genes, each encoding a member of the APRR1/TOC1 family of pseudo-response regulators were identified and characterized with special reference to circadian rhythms. It was found that all these members of the APRR1/TOC1 family (APRR1, APRR3, APRR5, APRR7, and APRR9) are subjected to a circadian rhythm at the level of transcription. Furthermore, in a given 24 h period, the APRR-mRNAs started accumulating sequentially after dawn with 2-3 h intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1. These sequential events of transcription, termed 'circadian waves of APRR1/TOCI', were not significantly affected by the photoperiod conditions, if any (e.g. both long and short days), and the expression of APRR9 was first boosted always after dawn. Among these APRRs, in fact, only the expression of APRR9 was rapidly and transiently induced also by white light, whereas such light responses of others were very dull, if any. These results collectively support the view that these members of the APRR1/TOC1 family are together all involved in an as yet unknown mechanism underlying the Arabidopsis circadian clock. Here we propose that the circadian waves of the APRR1/TOC1 family members are most likely a molecular basis of such a biological clock in higher plants.

From biological clock to biological rhythms

The genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output pathways that control diverse rhythmic phenomena.