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Genetics. Jul 2007; 176(3): 1501–1510.
PMCID: PMC1931532

A Complex Genetic Interaction Between Arabidopsis thaliana TOC1 and CCA1/LHY in Driving the Circadian Clock and in Output Regulation

Abstract

It has been proposed that CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) together with TIMING OF CAB EXPRESSION 1 (TOC1) make up the central oscillator of the Arabidopsis thaliana circadian clock. These genes thus drive rhythmic outputs, including seasonal control of flowering and photomorphogenesis. To test various clock models and to disclose the genetic relationship between TOC1 and CCA1/LHY in floral induction and photomorphogenesis, we constructed the cca1 lhy toc1 triple mutant and cca1 toc1 and lhy toc1 double mutants and tested various rhythmic responses and circadian output regulation. Here we report that rhythmic activity was dramatically attenuated in cca1 lhy toc1. Interestingly, we also found that TOC1 regulates the floral transition in a CCA1/LHY-dependent manner while CCA1/LHY functions upstream of TOC1 in regulating a photomorphogenic process. This suggests to us that TOC1 and CCA1/LHY participate in these two processes through different strategies. Collectively, we have used genetics to provide direct experimental support of previous modeling efforts where CCA1/LHY, along with TOC1, drives the circadian oscillator and have shown that this clock is essential for correct output regulation.

CIRCADIAN rhythms are self-sustaining biological oscillations that free run under constant conditions with a periodicity close to 24 hr. The rhythmic clock is prevalent and is found in organisms ranging from prokaryotes to eukaryotes and from animals to plants (Dunlap 1999; Barak et al. 2000; Harmer et al. 2001). This clock can be reset according to environmental cues, such as light and temperature (Liu et al. 1998; Collett et al. 2001; Young and Kay 2001; Samach and Wigge 2005; Carr et al. 2006). Recently, rapid strides have been made in deciphering the molecular bases of the circadian system. A recognizable pattern that is emerging is the recurring trend of autoregulatory positive/negative feedback loops (Alabadi et al. 2001). Further, clock models have been mathematically derived and the resulting equation principals can be applied (Locke et al. 2005a,b; Lakin-Thomas 2006). These models explicitly generate hypothesis-driven questions.

In Arabidopsis thaliana, the proposed negative repressors of the oscillator are the morning-acting myb-related factors CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) (Schaffer et al. 1998; Wang and Tobin 1998; Green and Tobin 1999; Alabadi et al. 2002; Mizoguchi et al. 2002), which are partially redundant genes encoding similar DNA-binding proteins. They act on the proposed positive-activator termed TIMING OF CAB EXPRESSION 1 (TOC1); it works in the evening and encodes a protein of unknown biochemical activity (Somers et al. 1998a; Strayer et al. 2000; Alabadi et al. 2001). TOC1 belongs to the PRR (PSEUDO-RESPONSE REGULATOR) family of proteins, consisting of five members (PRR9, PRR7, PRR5, PRR3, and PRR1/TOC1) (Matsushika et al. 2000; Makino et al. 2002; Eriksson et al. 2003). TOC1 and CCA1/LHY together make up the proposed central circadian loop in Arabidopsis. It is this positive–negative feedback loop between these evening and morning factors that leads to the first genetic model of the plant clock (Alabadi et al. 2001). This regulatory network has consistently and continuously been placed at the core of the molecular oscillator in all published models, but it does not fully describe several experimentally defined features (Schaffer et al. 1998; Wang and Tobin 1998; Harmer et al. 2000; Alabadi et al. 2001; Kim et al. 2003). Mathematical approaches drove experimental approaches to refining a simplistic loop where only CCA1/LHY and TOC1 were the sole elements of the clock. An interlocked two-loop clock model was then proposed to describe oscillatory properties, such as entrainment and response to photoperiods (Locke et al. 2005b). In this model, TOC1 and CCA1/LHY form a central loop, while the flowering-time gene GIGANTEA (GI) works alongside TOC1 to compose a secondary loop. CCA1 and LHY mediate light signal into the clock and GI potentially provides a secondary pathway for light input into the clock (Locke et al. 2005b). More recently, two groups have extended this to a three/four-loop model that includes PRR9 and PRR7 as morning-acting elements in a tertiary CCA1/LHY loop. We note that none of these studies has tested whether a loop with CCA1/LHY and TOC1 is indeed core to the oscillator (Locke et al. 2006; Zeilinger et al. 2006).

The circadian clock has been reported to regulate many processes, such as daily biochemical reactions and other general metabolic aspects of the cell. This in turn coordinates most, if not all, physiological processes. These are collectively called the circadian-output pathways (Harmer et al. 2000). For example, both toc1 and cca1 lhy have defects in flowering time and photomorphogenesis, which correlates with respective mutant circadian phenotypes (Somers et al. 1998b; Strayer et al. 2000; Mizoguchi et al. 2002). In toc1, mutant plants have an early flowering phenotype when grown under a short-day photoperiod. It was found that this phenotype is the result of clock-based misinterpretation of photoperiodic information rather than of the direct effects of toc1 on floral-induction pathways (Somers et al. 1998b; Strayer et al. 2000). Both cca1 and lhy also exhibit an early flowering phenotype under short-day conditions, and this was especially marked in the cca1 lhy double mutant; this double mutant is nearly insensitive to photoperiodic sensing (Mizoguchi et al. 2002). Although both toc1 and cca1 lhy have an early flowering phenotype, they have an inverted phenotype regarding early seeding photomorphogenesis, with toc1 displaying a long hypocotyl whereas cca1 lhy displays a short hypocotyl (Mas et al. 2003; Mizoguchi et al. 2005).

We sought to provide direct experimental evidence for TOC1 and CCA1/LHY as core-loop elements in the clock and to disclose the genetic relationship between TOC1 and CCA1/LHY in output regulation. For this purpose, we established all the possible double mutants and the triple mutant, tested clock responsiveness under a battery of molecular assays, and performed physiological and molecular analysis of clock outputs. We found that the triple mutant cca1 lhy toc1 often exhibited an arrhythmic phenotype under constant light (LL) conditions, which was consistent with the predictions from current mathematical clock models. Interestingly, the triple mutant displayed some limited rhythmic behavior under certain assays. The implication from this experimental data set is that the latest three/four-loop mathematical model (Locke et al. 2006; Zeilinger et al. 2006) will need to be further refined. Also, we found that TOC1 and CCA1/LHY participate in photomorphogenesis and flowering-time promotion through distinct epistatic relationships.

MATERIALS AND METHODS

Plant material and growth condition:

The cca1-11 and lhy-21 mutant alleles have been described (Doyle et al. 2002; Hall et al. 2003; Gould et al. 2005). toc1-21 in Ws-2 was derived from the same mutagenesis as above, and a graphical depiction of the mutation site is shown in supplemental Figure 1 at http://www.genetics.org/supplemental/. We introduced CAB2::LUC (6A), described in Hall et al. (2001), via manual fertilization of this line to the mutants. From the resultant segregants, we selected all the double and triple mutants. Crossing in the marker ensured a single homozygous CAB2::LUC locus. Seedling growth for rhythmicity experiments was, unless otherwise stated, with a fluence rate of white light at ~65 μmol m−2 s−1 at a constant temperature of 22°. Imaging was performed as described via established protocols, where the light was provided from red- and blue-light-emitting diodes at ~2 μmol m−2 s−1 (Dowson-Day and Millar 1999; Thain et al. 2000). Period length and relative amplitude of error were estimated using the fast Fourier transform–nonlinear least squares (FFT–NLLS) program (Plautz et al. 1997). Release assays (Figure 4) were conducted as described (McWatters et al. 2000).

Figure 4.
The clock in cca1 lhy toc1 stops in the middle of the day Wild-type and cca1-11 lhy-21 toc1-21 seedlings were entrained for 7 days to 12L/12D cycles at a constant 22°. (A) At 0 hr (subjective dawn), all seedlings were transferred to LL and 22° ...

Expression analysis by real-time PCR:

Total RNA was extracted with the QIAGEN (Valencia, CA) RNeasy plant mini kit. From 2 μg of RNA, cDNA was synthesized using the Superscript first-strand synthesis system (Invitrogen, San Diego) with oligo(dT) primers. Real-time PCRs were performed in a 20-μl volume comprising primers, cDNA template, and SYBER Green PCR master mix in a Bio-Rad (Hercules, CA) real-time detection system. The efficiency of amplification was assessed relative to a tublin standard. Each RNA sample was assayed in triplicate. RNAs were assayed from two to three independent biological replicates. Expression levels were calculated relative to tublin using a comparative threshold (CT) cycle method method or standard curve method. Levels of samples calculated according to the CT method were normalized to the maximum level of each RNA sample, which was set to 1. The primer sequences were as described (Ding et al. 2007).

Measurement of flowering time:

Flowering-time analysis was carried out on plants grown in a controlled-environment cabinet under SD growth (8 hr light/16 hr dark) at ~20°. Flowering time was measured by counting the number of rosette and cauline leaves. Data are presented as mean ± SE (n = 20–24). These flowering-time experiments were replicated with similar results.

Analysis of hypocotyl length:

For hypocotyl-length analysis, seeds were stratified in the dark at 4° for 3 days on 3% sucrose–Murashige and Skoog plates (as used in luminescence assays) and then transferred to short-day growth conditions (8 hr light/16 hr dark). Hypocotyl length was measured after 1 week of growth, as described (Davis et al. 2001), and the mean value ± SE was calculated (n = 20–30 for each genotype).

RESULTS

Defective clock responses of multiple mutants between toc1 and cca1/lhy:

In Arabidopsis, an interlocked feedback-loop clock model has been developed to describe much of the genetic data collected from clock mutants (e.g., Zeilinger et al. 2006). In all such models, the three genes TOC1, CCA1, and LHY are placed centrally within a core loop and, if this multiple-loop model is correct, then whenever all are mutated, rhythmic responses should be dramatically attenuated. [Again, we note that cca1, lhy, and toc1 mutations alone do not block clock function (Somers et al. 1998b; Alabadi et al. 2002; Mizoguchi et al. 2002).] To test this hypothesis, we constructed the cca1 lhy toc1 triple mutant and assayed the free-running response using CAB2::LUC as a reporter. The cca1 toc1 and the lhy toc1 double mutants were also selected to further expand our understanding of their genetic interactions within the proposed core. A driven rhythm after release from entraining conditions was detected in cca1 lhy toc1 in the first day under constant light conditions. This is compared to the cca1 lhy double that, as expected, maintained rhythmic expression of CAB2, albeit with an earlier phase of the first peak (Figure 1A). Through FFT–NLLS analysis, most cca1 lhy toc1 seedlings lacked detectable rhythmicity, as these lines had a very high error compared to wild-type plants (Figure 1B). Therefore, the circadian clock in cca1 lhy toc1 was severely disrupted. Both cca1 toc1 and lhy toc1 maintained a relatively strong rhythm, similar to that seen with cca1 lhy (Figure 1, B–D). All double-mutant lines displayed short periodicity. However, the period length in cca1 toc1 and lhy toc1 was ~2–3 hr longer than that in cca1 lhy under the same conditions (Figure 1, C and D), which suggested to us that TOC1 is not redundant to CCA1 and LHY with regard to period-length control in the same manner as CCA1 and LHY are to each other.

Figure 1.
toc1 enhanced the circadian phenotype of cca1 and lhy. Seedlings of the Ws wild type, cca1-11 lhy-21, cca1-11 toc1-21, lhy-21 toc1-21, and cca1-11 lhy-21 toc1-21 were grown under standard 12L/12D conditions and then transferred to LL, and CAB2:LUC luminescence ...

To further examine the clock defects present within cca1 lhy toc1, we performed real-time PCR on RNA extracted from replicate time points from mutant seedlings that were released into constant light after 1-week entraining under 12 hr light/12 hr darkness (12L/12D). With this assay, we found that the expression patterns of other clock-regulated genes were disrupted. For example, GI exhibited an earlier peak of expression that shifted ~4 hr earlier compared to the wild type. Further, the cca1 lhy toc1 triple mutant dramatically dampened rhythmic expression of GI after one very short period cycle (Figure 2A). LUX ARRHYTHMO (LUX), which is another presumably critical activator of CCA1 and LHY (Hazen et al. 2005), was also found to have an earlier peak of expression in cca1 lhy toc1, compared to the wild type, and the early phase was shifted by ~8 hr. Rhythmic expression of LUX was also abolished after one very short period peak (Figure 2, A and B). With regard to a morning gene mathematically important for a tertiary circadian loop (Zeilinger et al. 2006), we note published work that the peak of PRR9 expression was greatly reduced in cca1 lhy (Farre et al. 2005). We thus examined PRR9 expression in cca1 lhy toc1. We found that PRR9 lost rhythmic expression once the plants were transferred into constant-light conditions and there was markedly low abundance of PRR9 transcript over a circadian cycle (Figure 2C).

Figure 2.
Disrupted rhythms in the cca1 lhy toc1 triple mutant. Ws and cca1-11 lhy-21 toc1-21 mutant seedlings were grown for 7 days in standard 12L/12D conditions, and then entrained seedlings were transferred into constant light conditions and harvested every ...

The collective requirement of cca1 lhy toc1 for rhythmicity after temperature entrainment:

Temperature serves as an important environmental time cue and entrainment to temperature cycles has been reported (Somers et al. 1998a,b; Michael et al. 2003). We sought to test the roles of TOC1 and CCA1/LHY with regard to perception of temperature entrainment. We tested the driven responsiveness and circadian behavior under LL of genotypes grown under LL at 22° after entrainment for 1 week to 12 hr warm 22°/12 hr cool 18° (WC) cycles. We first noted that, for WC-cycle entrained seedlings, both cca1 lhy and wild-type plants maintained strong rhythmic expression. In contrast, cca1 lhy toc1 lost its driven rhythm after one cycle at 22° under LL (Figure 3A). Although rhythms could be fit to ~50% of triple-mutant seedlings with FFT–NLLS analysis, most had a very high error compared to the wild type (Figure 3B). The residual one cycle of CAB2 expression suggested to us that, under constant light conditions, the cca1 lhy toc1 phenotype could be partially rescued when plants were exposed to WC cycles. However, the free-running rhythm under LL after a WC entrainment was arrested within a day after transfer to constant conditions (Figure 3A). Collectively, we interpret these data as the cca1 lhy toc1 triple mutant being capable of both light/dark and warm/cool perception.

Figure 3.
In plants entrained to temperature cycles, rhythms are severely disrupted in cca1 lhy toc1. (A) Wild-type, the cca1-11 lhy-21 double mutant, and the cca1-11 lhy-21 toc1-21 triple-mutant seedlings were grown for 1 week in a temperature-entraining regimen ...

A diurnally entrained clock stops in the middle of a circadian day in cca1 lhy toc1:

Since the clock in cca1 lhy toc1 was apparently disrupted, we sought to define the arrest time point of this triple mutant. To this end, we performed a release assay (McWatters et al. 2000). For this, we grew seedlings under 12L/12D before transfer to LL at subjective dawn (0 hr). Replicate samples were then transferred to darkness every 2 hr for imaging of the first peak of CAB2 expression. The average time of the first peak of CAB2 expression in constant darkness (DD) was plotted against the duration of the preceding light interval. We found, as previously reported (Hall et al. 2003), that the circadian clock in wild-type plants continued to oscillate and that the peak phase was only marginally affected by the single light–dark transition. Note that the peak of CAB2 expression occurred close to the phase predicted from the discontinued light–dark (LD) cycle at 24–30 hr or 46–56 hr after the last dark–light transition at 0 hr (Figure 4A). In this assay, the cca1 lhy toc1 triple displayed no evidence of gating and thus no evidence of circadian regulation after seedlings where exposed to light for any duration >10 hr. After this point, the peak time of CAB2 expression was clearly set by the final light–dark transition, whatever the duration, and not by the entraining LD cycle (Figure 4B). Since CAB2 expression in cca1 lhy toc1 was arrhythmic under LL (Figures 1 and and2),2), we did not expect to detect a clock-regulated peak of CAB2 after anything more than a day of continuous light. However, even seedlings that had been exposed to LL for >30 hr were still found to maintain a circadian-inducible CAB2 peak, which was not a result from an acute response to light (Figure 4B). We suggest that the cca1 lhy toc1 triple mutant could restart the clock making use of the dusk signal. This implies that an as-of-yet-undescribed component(s) of a residual clock is present in the cca1 lhy toc1 triple mutant and that cca1 lhy toc1 is sensitive to the “light-off” signal.

toc1 enhanced the inhibitory effect of cca1 and lhy on PRR9 and less so on PRR7:

It was reported that both PRR9 and PRR7 expression levels were reduced in the cca1 lhy double mutant (Farre et al. 2005). To test if TOC1 also participates in regulating PRR9 and PRR7 expression, as indirectly implied by a three/four-loop model, we performed real-time PCR on RNA extracted from replicate time points from wild type and cca1, lhy, toc1, and all double- and triple-mutant seedlings grown under 8L/16D cycles and examined evident PRR9 and PRR7 transcript abundance. With this assay, we did not detect any differences in PRR9 expression between wild-type plants and toc1 (Figure 5, A and B). In the cca1 single mutant, the peak of PRR9 expression was reduced, consistent with published data (Farre et al. 2005). Although the transcript level of PRR9 in lhy was also reduced, its expression was higher than that in cca1 (Figure 5, A and B). Accordingly, the expression of PRR9 was higher in lhy toc1 than that in cca1 toc1, which had a similarly low-level PRR9 transcript as that of cca1 lhy and cca1 lhy toc1 (Figure 5, A and B). In both the cca1 toc1 double mutant and the cca1 lhy toc1 triple mutant, the peak of PRR9 accumulation was reduced to a level similar to that seen in the cca1 lhy double mutant. We suggest that TOC1 activates PRR9 expression through a pathway controlled by CCA1 and LHY (Figure 5, A and B). Mutations in CCA1 and LHY did not influence PRR7 expression as strongly as the effect on PRR9. The peak of PRR7 transcript accumulation was only slightly reduced in the double mutants cca1 lhy and cca1 toc1 and in the cca1 lhy toc1 triple mutant (Figure 5, C and D). It was also noted that no major difference in PPR7 was detected between wild-type plants and any single mutant assayed (Figure 5, C and D).

Figure 5.
TOC1 regulates PRR9 expression through CCA1 and LHY and has a smaller effect on PRR7. Seedlings of the Ws wild type, cca1-11, lhy-21, toc1-21, cca1-11 lhy-21, cca1-11 toc1-21, lhy-21 toc1-21, and cca1-11 lhy-21 toc1-21 were grown under standard 8L/16D ...

Genetic interactions between TOC1 and CCA1/LHY in the control of flowering time:

It was previously reported that, under short days, both the lhy and the cca1 single mutants flowered earlier than wild-type plants and that the cca1 lhy double mutant flowered significantly earlier than either of the two single mutants (Mizoguchi et al. 2002). The toc1-1 allele was also found to have an earlier-flowering phenotype under short-day conditions, which resulted from the circadian defect (Somers et al. 1998b; Strayer et al. 2000). To disclose a relationship between TOC1 and CCA1/LHY in flowering-time control, we measured flowering time of the double mutants cca1 lhy, cca1 toc1, and lhy toc1, as well as the triple mutant cca1 lhy toc1 and all respective single mutants under short-day conditions. All single mutants were marginally early flowering, and the cca1 lhy double mutant was significantly early flowering (Figure 6A), in agreement with published findings (Alabadi et al. 2001; Mizoguchi et al. 2002, 2005). Any double-mutant combination with toc1 flowered earlier than any single mutant and, strikingly, the cca1 lhy toc1 triple mutant flowered similarly as the cca1 lhy double mutant (Figure 6A).

Figure 6.
Interactions between TOC1 and CCA1/LHY in the control of flowering time. (A) Flowering time of Ws wild type, cca1-11, lhy-21, toc1-21, cca1-11 lhy-21, cca1-11 toc1-21, lhy-21 toc1-21, and cca1-11 lhy-21 toc1-21 was measured under standard 8L/16D conditions. ...

A previous report indicted that the earlier-flowering phenotype of cca1 lhy was the result of an early phase of GI expression. This in turn resulted in a higher expression of FT (Mizoguchi et al. 2005). To detect if the early flowering phenotype of the cca1 toc1 and the lhy toc1 double mutants and the cca1 lhy toc1 triple mutant was also a result from earlier phased expression of GI and the resultant increased FT, we examined GI and FT expression by real-time PCR from RNA extracted from plants grown under 8L/16D. In wild-type plants, GI had a peak of expression ~8 hr after lights were turned on. In contrast, the peak expression of GI shifted earlier by 4 hr in cca1 toc1, lhy toc1, and cca1 lhy toc1, and, as expected, cca1 lhy (Figure 6B). Accordingly, FT expression was increased compared to the wild type in cca1 toc1, lhy toc1, and cca1 lhy toc1, as it was in cca1 lhy (Mizoguchi et al. 2005).

TOC1 is required for the short-hypocotyl phenotype of the cca1 lhy double mutant:

TOC1 is a proposed positive factor in the light-mediated repression of hypocotyl elongation during seedling deetiolation (Mas et al. 2003). The cca1 lhy double mutant under short-day growth conditions displays a short hypocotyl compared to the wild type. This has led to the suggestion that CCA1 and LHY are negative regulators in seedling deetiolation (Mizoguchi et al. 2005). To test the epistatic relationship between toc1 and cca1/lhy in the photomorphogenic response, we measured hypocotyl lengths of the cca1 toc1 and lhy toc1 double mutants and the cca1 lhy toc1 triple mutant under short-day conditions. We found that the cca1 toc1 and the lhy toc1 double mutants and the cca1 lhy toc1 triple mutant exhibited a hypocotyl length similar to that seen with the toc1 mutant. All displayed a much longer hypocotyl than that of cca1, lhy, cca1 lhy, and wild-type plants (Figure 7). Therefore, the short-hypocotyl phenotype of the lhy cca1 double mutant under short-day conditions was dependent on TOC1 activity.

Figure 7.
TOC1 is required for short hypocotyl length phenotype in the cca1 lhy double mutant. Hypocotyl elongation after 6 days of growth under standard 8L/16D conditions. Hypocotyl lengths are mean ±SE (n = 20–30). This experiment was ...

toc1 coupled with cca1 or lhy is capable of light detection:

It was shown before that the transcript of PRR9 rapidly and transiently accumulated when etiolated seedlings were exposed to white light and that the light-dependent acute response of PRR9 is a phytochrome-mediated event (Makino et al. 2001; Ito et al. 2003). Since the cca1 lhy toc1 mutant was hyposensitive to light under the photomorphogenic assay (Figure 7), it was plausible that light-induced PRR9 expression might be accordingly affected. To this end, we examined PRR9 expression through real-time PCR from RNA extracted from wild-type and mutant seedlings grown in darkness that were harvested after being exposed to a 1-hr white-light treatment or, as the control, without such a light pulse. Interestingly, we found that light-induced PRR9 expression was not reduced in cca1 lhy toc1. On the contrary, it was marginally increased (Figure 8). Moreover, PRR9 levels were slightly increased in cca1, lhy, toc1, cca1 toc1, lhy toc1, and cca1 lhy mutants (Figure 8). The increased PRR9 expression in toc1 was consistent with the low expression level of PRR9 in TOC1 overexpression lines (Ito et al. 2003). What is clear is that any combination of mutations involving cca1, lhy, and toc1 is per se capable of light perception.

Figure 8.
Light-induced PRR9 accumulation was regulated by TOC1 and CCA1/LHY. Five-day-old etiolated seedlings of Ws wild type, cca1-11, lhy-21, toc1-21, cca1-11 lhy-21, cca1-11 toc1-21, lhy-21 toc1-21, and cca1-11 lhy-21 toc1-21 were exposed to white light, and ...

DISCUSSION

Previous research revealed a reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. The myb-related transcription factors LHY/CCA1 act as negative elements that repress TOC1 expression, and, conversely, TOC1 appears to be a positive element for LHY and CCA1 expression (Alabadi et al. 2001). The data presented here provide further evidence that TOC1 and CCA1/LHY interact in a complicated network in driving clock regulation and in output control. The disrupted clock function of cca1 lhy toc1 under constant light conditions provides direct experimental support for elements of the clock model proposed by Locke et al. (2005b), and its extensions (Locke et al. 2006; Zeilinger et al. 2006). Interestingly, the requirement of TOC1 in the floral transition was found to be a CCA1/LHY-dependent mechanism, whereas the CCA1/LHY requirement for photomorphogenesis was found to require TOC1. This collectively demonstrates that TOC1 and CCA1/LHY participate in a complex epistatic manner perhaps consistent with their action as a loop.

We found drastic rhythm disruptions for CAB2::LUC reporter activity in cca1 lhy toc1 after one 24-hr cycle under constant light (Figure 1A). Our real-time PCR data also revealed the rapid loss of rhythmicity in cca1 lhy toc1. Both GI and LUX, evening-expressed regulators of CCA1/LHY (Fowler et al. 1999; Hazen et al. 2005), lost rhythmic amplitude in the triple mutant after one constant-light cycle (Figure 2, A and B). Similarly, PRR9, a morning-clock gene (Matsushika et al. 2000; Makino et al. 2002; Eriksson et al. 2003), exhibited markedly dampened expression in cca1 lhy toc1. Under constant-light conditions, PRR9 expression in cca1 lhy toc1 was arrhythmic and virtually undetectable (Figure 2C), and evident defects were also detected during a diurnal light–dark cycle (Figure 5A). Collectively, we found circadian disruptions in both morning and evening clock-controlled genes in cca1 lhy toc1.

Our studies lead us to suggest that the cca1 lhy toc1 triple mutant exhibited a clock phenotype similar to that of the cca1 lhy gi triple mutant. The latter was key in providing experimental evidence to support a relationship between a core loop and a secondary loop, as extended from the latest mathematical model (Locke et al. 2006). According to this three-loop clock model, and even when one considers a four-loop model (Zeilinger et al. 2006), after CCA1, LHY, and GI were mutated, all loops would be “opened.” This could explain the collapsed clock in the cca1 lhy gi triple mutant. Correspondingly, since all the loops would be “opened” in cca lhy toc1, it is not difficult to understand why cca1 lhy toc1 also had the same strong clock defect phenotype as that in cca1 lhy gi. What is further obvious is that the cca1 lhy toc1 mutant displays one driven oscillation in response to the last light-to-dark transition (Figures 1 and and2).2). As such, the secondary and tertiary loops derived from the three/four-loop mathematical models either must have interconnections between them or there is another “complete” loop(s) yet to be discovered that does not require CCA1/LHY and/or TOC1 as components. The nature of such a hypothetical partial loop is as of yet unknown.

Both CCA1 and LHY were reported to have a positive effect on PRR9 transcript accumulation. In the cca1 lhy double mutant, PRR9 expression was dramatically reduced (Farre et al. 2005). As negative repressors in the clock, CCA1 and LHY can also be activated by TOC1, as both overexpression of either myb gene resulted in reduced expression of TOC1 (Alabadi et al. 2001). Therefore, TOC1 perhaps indirectly regulates PRR9 expression. Interestingly, we did not detect any difference in PRR9 accumulation when comparing toc1 and the wild type (Figure 5, A and B). However, we found that toc1 could enhance the inhibitory effect of cca1 and lhy on PRR9 accumulation (Figure 5, A and B). Although PRR9 expression was greatly reduced in cca1 (Farre et al. 2005), lhy had a higher peak of PRR9 expression compared to cca1. Accordingly, lhy toc1 also had a higher peak of PRR9 expression compared to cca1 toc1 (Figure 5, A and B).

It was reported that the peak of PRR7 expression was modestly reduced in cca1 lhy (Farre et al. 2005). We found that both cca1 toc1 and cca1 lhy toc1 displayed similar peak levels of PRR7. Further, no detectable differences were found in PRR7 expression between toc1 and wild-type plants (Figure 5C). However, we found no clear difference in the peak of PRR7 expression among cca1, lhy, and wild-type plants, which was contradictory to a previous report (Farre et al. 2005). This might be result of the different growth conditions, as we grew our plants under short-day conditions. Under our conditions, we found the peak of PRR7 expression was ~4 hr after the transition to light, whereas it was previously reported the peak of PRR7 expression was 8 hr after the transition to light during growth under 12L/12D condition (Figure 5, C and D) (Farre et al. 2005). Alternatively, or in addition to, this mild discrepancy could be due to an accession difference (as the wild type, we report Ws-2 whereas Farre et al. reported Col-0). In addition, LHY was found to have a reduced effect on PRR7 expression, as major differences were not found regarding the peak of PRR7 expression between lhy toc1 and wild-type plants (Figure 5, C and D). Collectively, our studies lead us to propose that TOC1 was also involved in the activation of PRR9 and perhaps of PRR7. Here, this regulation was dependent on CCA1/LHY action. Our data thus provide direct experimental support for the latest three/four-loop clock models (Locke et al. 2006; Zeilinger et al. 2006). Accordingly to these models, after TOC1 is mutated, CCA1 and LHY expression would be reduced, and this results in the indirect decrease of PRR9 and PRR7 expression.

The cca1 lhy double mutant was revealed to have an early flowering phenotype under short-day conditions (Mizoguchi et al. 2005). In our studies, we found that the cca1 lhy toc1 triple mutant flowered identically to the cca1 lhy double mutant (Figure 5A). The double cca1 toc1 and lhy toc1 flowered slightly later than cca1 lhy and cca1 lhy toc1 under short-day conditions, whereas both double mutants flowered much earlier than the cca1, the lhy, and the toc1 single mutant (Figure 5A). These single mutants also exhibited an earlier flowering phenotype under short-day conditions (Alabadi et al. 2001; Mizoguchi et al. 2005). In addition, we observed that in cca1 lhy toc1, cca1 toc1, and lhy toc1, the phase of GI expression was shifted earlier, resulting in a correlative increase in FT expression level (Figure 5, B–E). Taken together, our results support a model where the early flowering phenotype of toc1 is a result of the low expression of CCA1 and LHY, which, in turn, leads to a phase shift of GI and an increase in FT (Mizoguchi et al. 2005).

Our epistatic studies revealed that under short-day conditions the cca1 lhy toc1 triple mutant had a hypocotyl length similar to that of toc1. Moreover, both cca1 toc1 and lhy toc1 were found to have a long hypocotyl, similar to that of toc1 and cca1 lhy toc1 (Figure 7). As the cca1 lhy double mutant exhibited a short-hypocotyl length, compared to wild-type plants under short-day conditions (Mizoguchi et al. 2005), our observation led us to suggest that TOC1 functions downstream of CCA1/LHY in this photomorphogenic process. In addition, we also observed that light-induced PRR9 expression in cca1, lhy, toc1, and all combinations of double and triple mutants was slightly increased compared to wild-type plants (Figure 7). Clearly, etiolated combinations of these clock mutations had full light sensitivity for acute induction of PRR9 transcript. The increased PRR9 expression level with the light induction in toc1 was consistent with the low expression level of PRR9 in TOC1 overexpression lines (Ito et al. 2005). Accordingly, the slightly increased light-induced PRR9 expression in cca1 toc1, lhy toc1, and cca1 lhy toc1 could be explained by downstream regulation of TOC1 on CCA1 and LHY. However, this observation is contradictory to the long hypocotyl of toc1, cca1 toc1, lhy toc1, and cca1 lhy toc1. This lends even further support to the idea that the hypocotyl defects in these lines were due to an underlying clock phenotype, and not to a light-perception defect per se. This collectively implies that TOC1 has a negative role in this photomorphogenic response and that the interaction between TOC1 and CCA1/LHY in this response is clock driven.

Acknowledgments

Z.D. was supported by a postdoctoral fellowship provided jointly by the Max Plank Society and the Chinese Academy of Sciences. This work was additionally funded in the S.J.D. lab by the Max Planck Society and the Life Sciences Research Foundation. Work in R.M.A.'s laboratory was supported by the College of Agricultural and Life Sciences and the Graduate School of the University of Wisconsin and by the National Science Foundation (grant no. 0209786).

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