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Research Article

Crosstalk between the Circadian Clock and Innate Immunity in Arabidopsis

  • Chong Zhang,

    Affiliation: Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America

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  • Qiguang Xie,

    Affiliation: Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America

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  • Ryan G. Anderson,

    Affiliation: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America

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  • Gina Ng,

    Affiliation: Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America

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  • Nicholas C. Seitz,

    Affiliation: Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America

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  • Thomas Peterson,

    Affiliation: Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America

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  • C. Robertson McClung,

    Affiliation: Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America

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  • John M. McDowell,

    Affiliation: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America

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  • Dongdong Kong,

    Affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America

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  • June M. Kwak,

    Affiliations: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America, Department of Cell Biology and Molecular Genetics, Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States of America, Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea

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  • Hua Lu mail

    hualu@umbc.edu

    Affiliation: Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America

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  • Published: June 06, 2013
  • DOI: 10.1371/journal.ppat.1003370

Abstract

The circadian clock integrates temporal information with environmental cues in regulating plant development and physiology. Recently, the circadian clock has been shown to affect plant responses to biotic cues. To further examine this role of the circadian clock, we tested disease resistance in mutants disrupted in CCA1 and LHY, which act synergistically to regulate clock activity. We found that cca1 and lhy mutants also synergistically affect basal and resistance gene-mediated defense against Pseudomonas syringae and Hyaloperonospora arabidopsidis. Disrupting the circadian clock caused by overexpression of CCA1 or LHY also resulted in severe susceptibility to P. syringae. We identified a downstream target of CCA1 and LHY, GRP7, a key constituent of a slave oscillator regulated by the circadian clock and previously shown to influence plant defense and stomatal activity. We show that the defense role of CCA1 and LHY against P. syringae is at least partially through circadian control of stomatal aperture but is independent of defense mediated by salicylic acid. Furthermore, we found defense activation by P. syringae infection and treatment with the elicitor flg22 can feedback-regulate clock activity. Together this data strongly supports a direct role of the circadian clock in defense control and reveal for the first time crosstalk between the circadian clock and plant innate immunity.

Author Summary

Plants are frequently challenged by various pathogens. The circadian clock, which is the internal time measuring machinery, has been implicated in regulating plant responses to biotic cues. To better understand the role of the circadian clock in defense control, we tested disease resistance with Arabidopsis mutants disrupted in CCA1 and LHY, two key components of the circadian clock. We found that consistent with their contributions to the circadian clock, cca1 and lhy mutants synergistically affect resistance to both bacterial and oomycete pathogens. Disrupting the circadian clock caused by overexpression of CCA1 or LHY also results in severe disease susceptibility. Thus, our data further demonstrate a direct role of the circadian clock mediated by CCA1 and LHY in defense regulation. We also found that CCA1 and LHY act independently of salicylic acid mediated defense but at least through the downstream target gene GRP7 to regulate both stomata-dependent and -independent pathways. We further show that defense activation by bacterial infection and the treatment with the elicitor flg22 can also feed back to regulate clock activity. Together our study reveals for the first time reciprocal regulation of the circadian clock and plant innate immunity, significantly expanding our view of complex gene networks regulating plant defense responses and development.

Introduction

Plants are challenged by various pathogens on a daily basis. Accumulating evidence implicates a role of the circadian clock in regulating plant innate immunity. The circadian clock is the internal time measuring machinery important for plant growth and development. However, our understanding of the molecular basis of how the circadian clock controls plant innate immunity is still in its infancy.

Plants have evolved various mechanisms, some pre-formed and others induced, to ward off pathogen invasion. An example of pre-formed surface structures is the stomate, the natural opening important for photosynthetic gas exchange. This opening can provide a portal for pathogens to enter leaves; however, plants can also control the aperture of stomata to physically limit pathogens [1], [2]. One type of induced defense is activated when plants recognize pathogen-associated molecular patterns (PAMPs), which are conserved molecules or structures present in groups of related microbes. This defense, also termed PAMP-triggered immunity (PTI), can be highly effective against non-adapted pathogens and provides a basal level of defense even against adapted pathogens [3], [4]. Another type of induced defense is activated by plant resistance (R) proteins, which specifically recognize secreted pathogen effectors and subsequently activate effector-triggered immunity (ETI). ETI, also termed R gene-mediated resistance, is a stronger and faster elaboration of PTI, and frequently results in hypersensitive cell death at the infection site [5], [6], [7]. The small molecule salicylic acid (SA) has been linked to signal transduction in PTI and ETI [8], [9], [10].

The circadian clock has profound influence on the fitness of organisms [11], [12], [13], [14], [15], [16]. The core of the circadian clock is the central oscillator, which in Arabidopsis, is composed of multiple interconnected negative feedback loops that orchestrate biological adjustments independently of external stimuli [17], [18]. Of these clock components, CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and its close homolog LATE ELONGATED HYPOCOTYL (LHY) are transcription factors that are involved in multiple feedback loops and function synergistically to regulate clock activity [19], [20], [21].

The role of the circadian clock in controlling plant innate immunity has long been proposed based on circadian-regulation of defense gene expression [22], [23], [24], [25], [26]. Direct evidence from several research groups has recently emerged to support such a role of the circadian clock. Under free running conditions, wild type Arabidopsis exhibits temporal oscillations in susceptibility to Pseudomonas syringae infection, which are disrupted by overexpression of CCA1 [27]. Misexpression of several clock genes, including CCA1, compromises resistance to the bacterial pathogen Pseudomonas syringae and/or to the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) [27], [28], [29]. Interestingly, although lhy mutants exhibit similarly shortened circadian period as cca1 mutants, LHY was not shown to play a defense role against Hpa [28]. This raises the question of whether CCA1 is a dual function protein, affecting both the circadian clock and other non-clock related processes, as shown in the case of another central oscillator component GIGANTEA [30]. cca1-conferred disease susceptibility might be attributed to a role of CCA1 in regulating non-clock related processes rather than to its direct involvement in the circadian clock [31].

To better understand the role of CCA1 and LHY-mediated circadian clock in defense control, we tested plants misexpressing CCA1 and/or LHY for disease resistance to P. syringae and Hpa. We show that CCA1 and LHY loss-of-function mutants synergistically affect basal resistance and R gene-mediated defense against both pathogens. Disrupting the circadian clock caused by overexpression of CCA1 or LHY also results in severe disease susceptibility to P. syringae. The defense role of CCA1 and LHY against P. syringae is at least partially through circadian control of stomatal aperture but is SA-independent. Furthermore, we found that clock activity is modulated by P. syringae infection or treatment with the elicitor flg22. These data further establish the role of the circadian clock in defense control and for the first time reveal crosstalk between the circadian clock and plant innate immunity.

Results

The effect of CCA1 and LHY on clock activity can manifest in LL and LD

To evaluate defense roles of CCA1 and LHY, we constructed the cca1-1lhy-20 mutant via a genetic cross in a Col-0 background that also contains the LUCIFERASE reporter gene driven by the CCA1 promoter (ProCCA1:LUC). The single loss of function mutants, cca1-1 and lhy-20, have shortened circadian periods of ProCCA1:LUC expression in constant light (LL) [11]. In LL, we confirmed that cca1-1lhy-20 had a much-shortened period (19.9±0.11 hr), compared with wild type (wt) Col-0 (24.4±0.09 hr) (Figure S1A and [19]). Although experiments in LL are important for establishing the involvement of the circadian clock in specific phenotypes, such experimental conditions can also be limiting. In entraining conditions (e.g., a 12 hr L/12 hr D cycle; LD), the altered period of clock mutants like cca1-1 and lhy-20 is not seen due to the entraining cycle, which imposes a 24 hr period (Figure 1). The clock remains important in such LD conditions, though, because the clock determines the phase of specific events with respect to as dawn and dusk. Mutants with altered period in LL typically exhibit altered phase in LD, with short period mutants exhibiting a leading (early) phase and long period mutants exhibiting a lagging (late) phase [32]. Moreover, interactions between the endogenous circadian clock and external LD cycles can results in phase differences, sometimes dramatic, when measured in LD versus LL. For example, the phase of maximal hypocotyl elongation during early seedling growth was shifted 8–12 hours between LD and LL conditions [33], [34]. In their natural environment, plants do not usually encounter LL. Therefore in evaluating the role of the circadian clock on plant defense against pathogens, it is critically important to study plant-pathogen interactions in LD and to consider the potential influence of the circadian clock on the phases of rhythmic events that might influence the plant response to pathogen challenge.

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Figure 1. Clock activity of plants misexpressing CCA1 and/or LHY is disrupted in LD.

Eight-day-old seedlings of Col-0, cca1-1, lhy-20, cca1-1lhy-20, and CCA1ox expressing ProCCA1:LUC reporter were grown from germination in 12 hr light/12 hr dark cycles at 22°C. Luciferase activity was recorded with a Packard TopCount luminometer in LD at 22°C. (A) Mean circadian traces for ProCCA1:LUC activity. (B) Summary of phase value for ProCCA1:LUC in each genotype. Standard error of the mean (SEM) (n = 12–24) was used for (A) and (B). Letters indicate significant difference among the samples (P<0.05; Student's t-test).

doi:10.1371/journal.ppat.1003370.g001

We show here that in LD the phases of cca1-1 and lhy-20 single mutants were leading with respect to that of wild type Col-0, and that the cca1-1 lhy-20 double mutant exhibited a much earlier phase than either single mutant, consistent with the synergistic contribution of CCA1 and LHY in regulating clock activity (Figure 1 and Figure S1B). Early phase was also reported with other cca1lhy mutants [20], [21]. In addition, we found that plants overexpressing CCA1 (CCA1ox), which display arrhythmic clock activity in LL [35], also showed arrhythmic expression of ProCCA1:LUC in LD with an acute peak in response to lights on (Figure 1 and S1B). Low ProCCA1:LUC activity in CCA1ox is consistent with CCA1 being a negative regulator of its own expression [35]. These results emphasize that altered function of the circadian clock can manifest in both LL and LD conditions.

CCA1 and LHY contribute synergistically to resistance to P. syringae

To test disease resistance of cca1-1 and lhy-20 plants, we performed infection experiments at Zeitgeber Time 1 (Zeitgeber Time is the time relative to dawn; ZT1 is 1 hr after lights on) or ZT13 (1 hr after lights off), two times of day associated with drastic changes of light regime. Plant leaves were pressure-infiltrated with virulent P. syringae pv. maculicola ES4326 strain DG3 (PmaDG3) [36]. The infected plants were placed in either LD or LL. Bacterial growth assays at 3 days post infection (3 dpi) revealed no significant difference among Col-0, cca1-1, lhy-20, and cca1-1lhy-20 in either LD or LL (Figure 2 and Figure S2).

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Figure 2. Bacterial growth in plants infiltrated with Pseudomonas syringae pv. maculicola strain DG3 (PmaDG3).

(A) Time scheme used in this report. The white box indicates the light period and black boxes indicate dark periods. (B) ZT1 infection. (C) ZT13 infection. In 12 hr L/12 hr D (LD), 25-day-old plants were grown and infected by infiltration with PmaDG3 at 1×105 colony forming unit (CFU)/ml. Bacterial growth was assessed at 3 dpi. Data represent the average of bacterial numbers in six samples ± standard error. Log transformed bacterial growth was used in statistical analysis (Student's t-test). Letters indicate significant difference among the samples (P<0.05). These experiments were repeated three times with similar results.

doi:10.1371/journal.ppat.1003370.g002

Under natural conditions, P. syringae enters the apoplast of leaves through openings such as stomata and wounds. It is known that stomatal aperture is regulated by the circadian clock [37], [38]. Therefore, infiltration of bacteria directly into plant tissue might bypass the influence of the circadian clock on stomatal defense. To test this possibility, we spray-infected with PmaDG3 Col-0, cca1-1, lhy-20, and cca1-1lhy-20 at ZT1 and ZT13 in LD. We found that Col-0 supported over 10-fold more bacterial growth with ZT1 infection than with ZT13 infection (Figure 3A and 3B), suggesting that Col-0 is more resistant at night than at dawn when spray-infected. Although we did not observe significant difference in bacterial growth between Col-0 and cca1-1 and lhy-20 single mutants, the double mutant cca1-1lhy-20 showed enhanced susceptibility to PmaDG3 when sprayed at ZT13 (Figure 3A to 3C). Consistent with this result, we found that PmaDG6 (an avirulent strain recognized by the resistance protein RPS2 in Col-0) [36]) grew significantly more in cca1-1lhy-20 than in Col-0 and the single mutants with ZT13 infection (Figure 3D and 3E). Together these data suggest that CCA1 and LHY share redundant functions to regulate both basal and RPS2-mediated defense against P. syringae.

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Figure 3. Bacterial growth in plants spray-infected with P. syringae.

(A) ZT1 infection with PmaDG3. (B) ZT13 infection with PmaDG3. (C) Pictures of infected leaves from (A) and (B) at 4 dpi. (D) ZT1 infection with PmaDG6. (E) ZT13 infection with PmaDG6. Twenty five-day-old plants were infected by spraying with the virulent strain PmaDG3 or the avirulent strain PmaDG6 (1×108 CFU/ml) at ZT1 or ZT13. Bacterial growth was assessed at 3 dpi. Data represent the mean bacterial numbers ± SEM (n = 6). Letters indicate significant difference among the samples (P<0.05; Student's t-test). These experiments were repeated three times with similar results.

doi:10.1371/journal.ppat.1003370.g003

Overexpression of CCA1 or LHY confers enhanced susceptibility to P. syringae

To further substantiate the role of CCA1 and LHY in defense regulation, we tested disease resistance of plants overexpressing CCA1 (CCA1ox) or LHY (LHYox), which were shown to have arrhythmic clock activity in LL [35], [39]. CCA1ox plants also exhibited clock arrhythmicity in LD (Figure 1 and S1B). Disease resistance assays indicate that CCA1ox plants were more susceptible to PmaDG3 than Col-0 with infiltration infection in LD or LL (Figure 2 and S2). CCA1ox plants were also more susceptible than Col-0 to PmaDG3 and to PmaDG6 when spray-infected at ZT1 or ZT13 in LD (Figure 3).

LHYox plants are in the Landsberg erecta (Ler) background, with which we used P. syringae pv. tomato DC3000 (DC3000) to test disease resistance because this strain induces stronger disease symptoms in our hands than does PmaDG3. Similar to CCA1ox plants, LHYox plants had more bacterial growth than Ler when infiltrated with DC3000 at ZT1 or ZT13 in LD (Figure 4A). In addition, spray-infection at ZT1 or ZT13 in LD also gave similar results (Figure 4B). Together, disruption of the circadian clock by misexpressing CCA1 and/or LHY compromises disease resistance to P. syringae, supporting a direct role of the circadian clock in defense regulation.

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Figure 4. Overexpression of the LHY gene confers enhanced disease susceptibility to P. syringae.

(A) Infiltration with DC3000. (B) Spray with DC3000. 30-day-old plants were infected with P. syringae pv. tomato strain DC3000 (DC3000) by infiltration (1×105 CFU/ml) or spray (1×108 CFU/ml) at ZT1 or ZT13 in LD. Bacterial growth was assessed at 3 dpi. (C) Cell death staining. The fourth to fifth leaves of Ler and LHYox were stained with trypan blue to visualize cell death [54]. (D) SA quantification. Total SA was extracted from 20- and 30-day old plants. Data represent the average of SA levels (n = 3) ± standard deviation. Statistical analysis was performed with Student's t-test (StatView 5.0.1). Asterisks indicate significant difference between Ler and LHYox at the same time point (P<0.05). These experiments were repeated three times with similar results.

doi:10.1371/journal.ppat.1003370.g004

CCA1 and LHY gate stomatal response to dark and to P. syringae infection

Our data show that cca1-1lhy-20 was more susceptible with spray-infection and CCA1ox and LHYox plants displayed enhanced susceptibility with both spray and infiltration infections. These suggest that both stomata-dependent and -independent defense can be affected by misexpression of either of these two core oscillator genes. Consistent with this notion, a previous study showed that CCA1ox plants had increased CO2 assimilation and stomatal conductance [13]. To further test whether the defense role of CCA1 and LHY is linked to the control of stomatal pore size, we measured plant stomatal aperture at ZT1 and ZT13 in LD. Consistent with Col-0 being more resistant with spray-infection at ZT13 than at ZT1, we found that stomatal aperture of Col-0 was much smaller at ZT13 than at ZT1 (Figure 5A). Compared with Col-0, the cca1-1 and lhy-20 mutants and CCA1ox plants showed similar stomatal aperture at ZT1 but had greater stomatal aperture at ZT13 (Figure 5A). These data suggest that disrupting clock activity mediated by CCA1 and LHY could make plants less responsive to dark-induced stomatal closure at night, thereby enhancing access of P. syringae to the leaf interior.

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Figure 5. Disruption of CCA1 and LHY leads to altered stomatal activity.

(A) Stomatal aperture at ZT1 (left) or ZT13 (right) for Col-0, cca1-1, lhy-20, cca1-1lhy-20, and CCA1ox. (B) Stomatal aperture at ZT1 or ZT13 for Ler and LHYox. (C) Stomatal aperture at 1 hr (top) or 3 hr (bottom) after exposure to PmaDG3 or mock for Col-0, cca1-1, lhy-20, cca1-1lhy-20, and CCA1ox. (D) Stomatal aperture at 1 hr or 3 hr after exposure to DC3000 or mock for Ler and LHYox. For (A) and (B), three leaves from uninfected 25-day-old plants grown in 12 hr light/12 hr dark at 22°C were taken at the indicated times for the measurement of stomatal aperture. For (C) and (D), P. syringae treatment was conducted at ZT4 to ensure that most stomata were open upon treatment. Leaves were immersed in bacterial suspension (108 cfu/ml) or water as mock treatment. At least three leaves of a genotype were collected at the indicated times for stomatal aperture measurement. Data represents the average of three experiments ± SEM. Each of these experiments contains at least 70 randomly chosen stomata. Different letters in (A) indicate significant difference among the samples. Asterisks in (C) and (D) indicate significant difference between mock-treated and infected plants of the same genotype (P<0.001; Student's t-test). These experiments were repeated three times with similar results.

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To further determine how these mutants respond to P. syringae infection, we measured stomatal aperture in the presence of PmaDG3. PmaDG3 treatment was performed at ZT4 after plants had been exposed to light for four hours to ensure the opening of the stomata (Figure S3). At 1 hr post infection (1 hpi), we observed a 48.1% suppression of stomatal aperture in Col-0, compared with mock treatment (Figure 5C top and Table S1). However, this suppression was much reduced in cca1-1 and lhy-20 and largely blocked in cca1-1lhy-20 and CCA1ox. P. syringae-induced stomatal closure was transient since both mock and PmaDG3-treated leaves showed similar stomatal aperture at 3 hpi (Figure 5C bottom). Although exhibiting similar stomatal aperture at ZT1 and ZT13 (Figure 5B), the LHYox plants also showed reduced suppression of DC3000-induced stomatal closure at 1 hpi (16.9%), compared with Ler control (51.6%) (Figure 5D and Table S1). Hence, these results indicate that disrupting the circadian clock by CCA1 and LHY misexpression impairs plants' capacity of inducing stomatal closure in response to P. syringae.

CCA1 and LHY contribute synergistically to Hpa resistance

CCA1 but not LHY was previously shown to regulate resistance to the oomycete pathogen Hpa [28]. To test whether a contribution of LHY to Hpa resistance could be discerned in the double mutant cca1-1lhy-20, we sprayed seven-day-old seedlings at ZT7 in LD with the virulent strain Hpa Emco5 or the avirulent strain Hpa Emoy2 (recognized by the R protein RPP4 in Col-0). We observed significantly more susceptibility to both Hpa strains in the cca1-1lhy-20 double mutant, compared to Col-0 and the single mutants (Figure 6A and 6B) while the CCA1ox plants were substantially more resistant to Hpa Emco5 (Figure 6A). Our data are broadly in agreement with those previously reported [28]. The reason that we did not observe a significant difference between Col-0 and cca1-1 could be due to the difference in the infection time and/or Hpa strains used - Wang et al inoculated plants with the avirulent strain Hpa Emwa1 at dawn [28] while we used Hpa Emco5 (virulent) and Emoy2 (avirulent) in the afternoon in our experiments. Nevertheless, these data, together with the P. syringae data described earlier, demonstrate that CCA1 and LHY contribute synergistically to basal resistance and R-gene mediated defense against both bacterial and oomycete pathogens. What surprises us is the difference in response to P. syringae (decreased resistance) and Hpa (enhanced resistance) strains observed in CCA1ox plants. We speculate that there are distinct mechanisms that these plants use to defend against the two pathogens.

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Figure 6. CCA1 and LHY contribute synergistically to resistance to Hyaloperonospora arabidopsidis (Hpa).

(A) Infection with Hpa Emco5. (B) Infection with Hpa Emoy2. Seven-day-old seedlings were spray-infected at ZT7 in LD with the virulent strain Hpa Emco5 or the avirulent strain Hpa Emoy2 (5×104 spores/ml in water). Sporangiophore production in cotyledons of each genotype was counted at 7 dpi. Data represent the average number of sporangiophores from 20 seedlings for CCA1ox and 50 seedlings for other genotypes ± SEM. Letters indicate significant difference among the samples (P<0.01; Mann-Whitney test). These experiments were repeated three times with similar results.

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Defense-related genes might be preferentially regulated by CCA1 and LHY

Identification of defense-related genes controlled by CCA1 and LHY is critical to gain better understanding of the mechanism of action of CCA1 and LHY in defense regulation. To this end, we analyzed promoters of 571 genes for CCA1-binding site (CBS) and evening element (EE), two cis elements known for CCA1 and LHY binding [40], [41], [42]. These 571 genes had been previously selected to construct mini-microarrays, consisting of three groups, selected (337 defense-related genes based on microarray experiments), empirical (127 empirical marker genes for various pathogen responses), and normalization (107 non-defense related genes whose expression levels were relatively stable among experiments with pathogen infection) [43]. The online tool POBO [44] was used to analyze up to 3000 bp from the promoter regions of these genes, which do not include the coding sequences of neighboring genes, for an enrichment of CBS or EE motifs. The background for this analysis was generated using pseudo-clusters of 100 promoters of up to 3000 bp in length of randomly sampled Arabidopsis genes (1000 bootstrap replications were used in the sampling). Compared with the background, the CBS motif was found as often as expected by chance in the selected and empirical gene promoters (Figure 7A and 7B) but the motifs were found less frequently in the normalization gene promoters (Figure 7C and Table S2). When compared to the normalization genes, there was a greater than 40% increase of the cluster mean for the CBS motif in both selected and empirical genes. These observations suggest that although defense-related genes (selected and empirical genes) are not particularly enriched with the CBS motif, the non-defense related genes (the normalization genes) are slightly depleted of the motif. The enrichment of the EE motif was more pronounced in both selected and empirical genes, with about 200% increase of the cluster means when compared to the normalization genes (Figure 7D–7F and Table S2). Thus, these results suggest that defense-related genes are preferentially regulated by CCA1 and LHY. However, since the sample size in each group is small, caution should be taken when extrapolating this interpretation to the whole genome level.

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Figure 7. Motif enrichment analysis of 571 gene promoters.

A total of 571 promoters from genes in three categories, selected (337 defense-related gene based on microarray experiments), empirical (127 empirical marker genes for various pathogen responses), and normalization (107 non-defense related genes) [43], was analyzed for the enrichment of CBS or EE motifs, using the online tool POBO (http://ekhidna.biocenter.helsinki.fi/pox​o/pobo/) [44]. (A) and (D) are for selected genes, (B) and (E) are for empirical genes, and (C) and (F) are for normalization genes. Panels (A), (B), and (C) are for the CBS motif and panels (D), (E), and (F) are for the EE motif. The red lines represent the background while the blue lines represent one of three sets of genes used in each analysis.

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The defense gene GRP7 acts downstream of CCA1 and LHY

The frequency of CBS or EE motif per promoter region was quantified from the above three sets of genes (Figure S4). Among the genes analyzed, we found that GRP7 (At2g21660; also known as COLD AND CIRCADIAN REGULATED 2 [CCR2]) [45], [46] had the most overrepresentation of the EE motif, with four EE within a 300 bp promoter region. One CBS motif was also found at 1294 bp of the GRP7 promoter. GRP7 is a key constituent of a slave oscillator regulated by the circadian clock [45], [47] and also has been demonstrated to have roles in regulating floral transition and plant defense [48], [49]. Expression of GRP7 was previously shown to be circadian regulated with a shortened circadian period in a cca1lhy double mutant and a disrupted pattern in CCA1ox plants [12], [20], [50]. However, GRP7 had never been explicitly established as a target gene of CCA1 and LHY. Our northern analysis confirmed circadian expression of GRP7 and showed that such expression was slightly affected by the cca1-1 mutation and became arrhythmic in CCA1ox in LL (Figure S5). We also observed disrupted expression of GRP7 in CCA1ox plants in LD (Figure 8A). Thus, these data further confirm that GRP7 is regulated by CCA1.

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Figure 8. CCA1-regulated GRP7 affects disease resistance to P. syringae and stomatal activity.

(A) Expression of GRP7 is disrupted in CCA1ox in LD. Twenty five-day-old Col-0 and CCA1ox plants grown in a chamber with a 12 hr light/12 hr dark cycle and 22°C were harvested at ZT1 at 6 hr interval for 24 hrs followed by RNA extraction and northern blotting. 18S rRNA was used as a loading control. These experiments were repeated twice with similar results. (B) Stomatal aperture at ZT1 or ZT13. (C) Stomatal aperture at 1 hr (left) or 3 hr (right) after exposure to PmaDG3 or mock solution. (D) Bacterial growth assay with ZT1 or ZT13 infection in LD. Asterisks indicate significant difference among the samples at the indicated times in panels (B) and (D) or within the same genotypes in panel (C) (P<0.05; Student's t-test). These experiments were repeated twice with similar results.

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GRP7 was previously demonstrated to regulate stomatal activity [51]. We found that similar to cca1-1lhy-20 and CCA1ox plants, stomatal aperture of grp7-1 was greater than that of Col-0 at ZT13 (Figure 8B). In response to PmaDG3 infection, grp7-1 displayed 14.2% suppression of stomatal aperture whereas Col-0 showed 48.1% suppression at 1 hpi (Figure 8C, S3, and Table S1), suggesting that grp7-1 has reduced responsiveness to PmaDG3 in stomatal closure. We further found that grp7-1 was significantly more susceptible to PmaDG3 than Col-0 when spray-infected at ZT13 in LD (Figure 8D). Together our bioinformatic analysis and experimental evidence indicate that GRP7 is a target of CCA1 and/or LHY that regulates stomatal activity and modulates plant defense.

CCA1 and LHY regulate disease resistance independently of SA

SA is a key signaling molecule involved in both basal resistance and R gene-mediated defense. The accelerated cell death 6-1 (acd6-1) mutant shows constitutive defense, high levels of SA, and extremely small size that is sensitized to the change of SA defense [52], [53]. Thus, acd6-1 has been used as a convenient readout to gauge the effect of some known defense genes in regulating SA-mediated defense [54], [55], [56]. To determine whether CCA1 and LHY act through SA, we crossed cca1-1lhy-20 to acd6-1 and obtained homozygous double (acd6-1cca1-1 and acd6-1lhy-20) and triple (acd6-1cca1-1lhy-20) mutants. We found that both double and triple mutants resembled acd6-1, displaying dwarfism and accumulating similar SA levels (Figure 9A and B). However, when spray-infected with PmaDG3 at ZT13, the double mutants were slightly more susceptible while the triple mutant was much more susceptible than acd6-1 (Figure 9C). These results corroborate a synergistic interaction between CCA1 and LHY in clock and defense regulation. They also suggest that the defense role of CCA1 and LHY is largely SA-independent. Consistent with this notion, we found that in the absence of acd6-1, the SA levels are comparable among Col-0, cca1-1, lhy-20, cca1-1lhy-20, and CCA1ox in LD (Figure S6A). In addition, although more susceptible to P. syringae infection, LHYox plants were dwarf, showed spontaneous cell death, and accumulated high levels of SA (Figure 4C, 4D, and S6B). Together, these results indicate that CCA1 and LHY act independently of SA to regulate resistance to P. syringae.

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Figure 9. CCA1 and LHY conferred disease resistance is SA-independent.

(A) Picture of 25-day-old plants. (B) SA quantitation. Twenty-five-day old plants grown in 12 hr light/12 hr dark cycle (LD) at 22°C were harvested at ZT1, 7, 13, 19 and 25. Total SA were extracted and measured as described [90]. (C) Infection with PmaDG3. Twenty five-day-old plants were infected by spraying with the virulent strain PmaDG3 (1×108 CFU/ml) at ZT13. Bacterial growth was assessed at 3 dpi. Data represent the mean bacterial numbers ± SEM (n = 6). Letters indicate significant difference among the samples (P<0.05; Student's t-test). These experiments were repeated three times with similar results.

doi:10.1371/journal.ppat.1003370.g009

Defense activation reciprocally regulates clock activity

Our data and those from other groups clearly indicate that plant innate immunity is an output event regulated by the circadian clock. However, it is not known whether this regulatory relationship is reciprocal with defense activation feeding back to affect clock activity. To test this, we infected Col-0 expressing the ProCCA1:LUC reporter with both virulent and avirulent P. syringae strains. Bioluminescence analysis indicated that the period of ProCCA1:LUC was significantly shortened in the presence of the virulent strain PmaDG3 or the avirulent strain PmaDG6 at a high dose (OD = 0.1) (Figure 10 and Table S3). Similarly, infection of Col-0 seedlings expressing ProGRP7:LUC also resulted in period shortening of ProGRP7-controlled luciferase activity (Figure S7 and Table S3). These results suggest that clock activity is modulated by both basal and RPS2-mediated defenses.

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Figure 10. Defense activation by P. syringae infection shortens the period of the ProCCA1:LUC reporter activity.

(A) Mean circadian traces for ProCCA1:LUC activity. (B) Mean circadian period of the ProCCA1:LUC reporter. Col-0 seedlings expressing the ProCCA1:LUC reporter were grown from germination in 12 hr light/12 hr dark cycles at 22°C. At ZT7, eight-day-old seedlings were incubated with PmaDG3 or PmaDG6 (1×108 or 1×107 CFU/ml, labeled as 0.1 or 0.01, respectively) for 3 mins, blot dried, and transferred to 96-well plates containing 200 µl of MS media and 30 µl of a 2.5 mM D-luciferin solution. Luciferase activity was recorded with a Packard TopCount luminometer in LL at 22°C. RAE: relative amplitude error. RAE values close to zero indicate strong rhythms while those close to 1 indicate the limit of statistically significant rhythmicity. SEM (n = 12–24) was used for (A) and (B). These experiments were repeated twice with similar results.

doi:10.1371/journal.ppat.1003370.g010

To further investigate which defense signaling pathway(s) are involved in the feedback-regulation of clock activity, we treated Col-0/ProCCA1:LUC seedlings with flg22 or benzo (1,2,3) thiadiazole-7-carbothioic acid (BTH). Flg22 is a 22-aa synthetic peptide from the conserved region of flagellin proteins of P. syringae and elicits plant basal defense in a wide variety of plant species [4], [57]. BTH is an agonist of SA that efficiently activates SA signaling [58]. We found that flg22 at both doses (1 µM and 10 µM) significantly shortened the period of CCA1 expression. However, BTH treatment (10 µM and 300 µM) did not change CCA1 promoter activity (Figure 11A and Table S3). To further test if SA could affect clock activity, we used a cotyledon movement assay [59] to gauge clock activity in the acd6-1 mutant, which constitutively accumulates high levels of SA [52], [53]. We found that acd6-1 showed similar period, phase, and amplitude of the rhythm for cotyledon movement to Col-0 (Figure 11B and S8). Taken together, these data indicate that activation of flg22-triggered basal defense but not SA signaling can feedback to regulate clock activity.

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Figure 11. The clock period is shortened by treatment with flg22 but not with BTH.

(A) Mean circadian period of the ProCCA1:LUC reporter. Eight-day-old Col-0 seedlings expressing the ProCCA1:LUC reporter were grown from germination in 12 hr light/12 hr dark cycles at 22°C. At ZT7, eight-day-old seedlings were treated with flg22 (1 µM or 10 µM) or BTH (10 µM or 300 µM) and transferred to 96-well plates containing 200 µl of MS media and 30 µl of a 2.5 mM D-luciferin solution. Luciferase activity was recorded with a Packard TopCount luminometer in LL at 22°C. (B) Cotyledon movement assay with acd6-1. Eight-day-old acd6-1 seedlings grown in a 12 hr light/121 hr dark cycle at 22°C were transferred to 24-well cloning plates and recorded in LL at 22°C for cotyledon movement. SEM (n = 12–24) was used for (A) and (B). These experiments were repeated twice with similar results.

doi:10.1371/journal.ppat.1003370.g011

Discussion

Increasing evidence has implicated a role of the circadian clock in regulating plant innate immunity. Of the components in the central oscillator of the circadian clock, CCA1 is the first shown to affect plant defense against P. syringae and Hpa [27], [28]. However, its close homolog, LHY, has not been shown such a role, despite the fact that loss-of-function mutants in both genes displayed similarly shortened period. Thus, it was unclear whether plant innate immunity is regulated by the circadian clock mediated by CCA1 or by non-clock related function of CCA1. Here we show that disrupting clock function by misexpression of CCA1 and/or LHY leads to compromised immunity, thus further establishing a direct role of the circadian clock in defense regulation. Our data suggest that one of the mechanisms by which CCA1 and LHY regulate plant innate immunity is through affecting stomatal defense with the downstream target gene GRP7. We further demonstrate that defense activation by P. syringae infection and flg22 treatment shortens circadian period. Thus this study reveals for the first time crosstalk between the circadian clock and plant innate immunity.

The circadian clock mediated by CCA1 and LHY regulates plant defense under LL and LD conditions

Typical studies of the circadian clock have been performed under constant light (LL) conditions to emphasize the endogenous nature of the clock. In LL, perturbations of the circadian clock typically result in altered period length; for instance, loss of CCA1 or LHY function shortens circadian period. However, plants typically grow in LD cycles in which the environmental cycle entrains even a mutant clock to a 24-hour period. Under such LD conditions, perturbations in the circadian clock can manifest as alterations in phase for reporter gene expression (Figure 1 and S1B and [20], [21]) as well as changes in a variety of other traits, including flowering time, metabolism, stomatal activity, gene expression patterns, and defense responses [12], [13], [20], [29], [50], [60], [61]. Thus, the effects of disrupted circadian clock could become apparent under LL and LD conditions.

Several studies indicate that the circadian clock mediated by CCA1 and LHY regulates plant defense in both LL and LD ([27], [28] and this study). For instance, Bhardwaj et. al. showed that CCA1ox plants were more susceptible to P. syringe infection than wt in LL [27]. Here we extend this observation by showing that CCA1ox plants had enhanced susceptibility to P. syringae in both LL and LD (Figure 2, 3, and S2). In LD, enhanced susceptibility was also observed in cca1-1lhy-20 and LHYox plants to P. syringae strains (Figure 3 and 4) and in cca1-1lhy-20 to Hpa strains (Figure 6). Consistent with our data, a single cca1 mutant showed compromised resistance to a different Hpa strain and affected expression of some defense-related genes in LD [28]. Together these studies firmly establish that plant innate immunity is an output regulated by the circadian clock under LL and LD conditions.

While we mainly focus our analyses in this report on defense phenotypes regulated by CCA1 and LHY in LD, we also agree that we should use caution when interpreting our results since the effect of the circadian clock can manifest differently under different light conditions, including both differing daylengths and light intensities. For instance, it is possible that the degree of susceptibility to pathogen infection and the severity of stomatal change in response to dark and P. syringae infection could be different in LD from those in LL in cca1-1lhy-20 (compared with wt). Alternatively, the amplitude, period, and/or phase of defense gene expression could be different in cca1-1lhy-20 (compared with wt) in LD from those in LL. Even different LD conditions could have different effects on clock activity. For example, Michael et al. [62] showed that the set of cycling transcripts increased with the number of different cycling conditions examined. We found that in 12 hr L/12 hr D, expression of GRP7 retained rhythmicity in CCA1ox, compared with that in wt, although the waveform was altered with baseline expression increased (Figure 8A). However, Green et al observed more pronounced alterations in phase of GRP7 expression in CCA1ox (compared with that in wt) in seedlings growing in long or short daylengths (16 hr L/8 hr D or 8 hr L/16 hr D), with maximal transcript accumulation in the dark [12]. Such differences in the patterns of GRP7 transcript abundance could also be due to other reasons besides light conditions. Nonetheless, these observations together with those of Michael et al. [62] emphasize that to better understand the role of the circadian clock in defense control, analyses of defense phenotypes with plants misexpressing CCA1, LHY, and/or other clock genes should be carried out in LL, DD, and different LD conditions for a comprehensive comparison.

Plants employ different mechanisms to defend against pathogens at different times of day

Although encountering pathogens at different times in a day, Arabidopsis plants were suggested to be more resistant in the morning than at night. To support this conclusion, wt plants demonstrated higher resistance and/or defense responses when infiltrated during the day than at night [27], [63]. We also observed similar results in plants infiltrated with P. syringae in LL or LD (Figure 2, 4A, and S2), thus supporting this conclusion. However, with spray-infection in LD, we observed the opposite phenotype; wt plants were more resistant at night than in the morning (Figure 3, 4B and 8D). During spray-infection, P. syringae initially lands on the leaf surface. Further invasion depends on the success of the bacteria in gaining entry into the host tissue via natural openings, such as stomata [1], [2]. Consistent with enhanced disease resistance to sprayed P. syringae, plants in the evening have much smaller stomatal pore sizes than in the morning (Figure 5A, 5B, and 8B).

These two seemly contradicting results actually coalesce to suggest different mechanisms that plants use to defend against pathogens at different times of day, depending on the mode of pathogen invasion. As summarized in Figure 12A, at night plants might rely more on closed stomata to physically restrict pathogen invasion but stomata-independent defense is relatively low. If a pathogen can breach stomatal restriction (i.e. being pressured into host tissue via infiltration in the laboratory) at night, it can be more virulent to the host. However, with stomata widely open during the day, plants apparently compensate for enhanced pathogen access to the leaf interior with enhanced stomata-independent defense that is stronger during the day than at night. This cycling in host resistance means that plants can be more resistant to epiphytic pathogens at night than during the day. But in the presence of apoplastic pathogens, plants can activate stronger defense during the day than at night. Taken together, we conclude that plants rely on distinct mechanisms, involving stomata-dependent and stomata-independent defenses, to respond to pathogen attacks at different times of day.

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Figure 12. A simplified model for crosstalk between the circadian clock and plant innate immunity.

(A) Timing of stomata-dependent and -independent defense in a day. At night, plants might rely more on closed stomata to provide physical constrains to limit pathogen invasion but have relatively lower levels of stomata-independent defense. Once pathogens bypass such constrains (i.e. via infiltration infection in the laboratory), they encounter a plant host that is more susceptible than during the day. During the day, most stomata are wide open. In the presence of pathogens, plants can only transiently reduce stomatal aperture for a few hours (this study and [1]). Thus, during the day plants might depend more on stomata-independent defense to restrict pathogen invasion. Stomata-dependent defense could be stronger at night while stomata-independent defense could be stronger during the day. (B) The circadian clock regulates both stomata-dependent and -independent defense pathways to restrict pathogen growth in Arabidopsis. In a stomata-dependent pathway, CCA1 and LHY act, at least in part, through GRP7 as a direct downstream target to regulate stomatal aperture and thereby defense. Other downstream targets of CCA1 and LHY and other components of the central oscillator of the circadian clock might also be involved in regulating stomata-dependent and –independent defense. On the other hand, pathogen infection can activate PTI, ETI and other defense signaling in the host. PTI induced by flg22 feeds back to regulate clock activity. In addition, flg22-triggered signaling is under circadian clock control [27]. Thus, we conclude that the clock-defense crosstalk involves flg22-mediated signaling. Flg22 can affect stomatal aperture [91]. However, whether this function of flg22 is through its regulation of the circadian clock or through a direct regulation of stomata is unclear. Other questions, such as whether additional PAMPs, effectors, and other defense signaling molecules are involved in clock-defense crosstalk, remain to be answered.

doi:10.1371/journal.ppat.1003370.g012

The circadian clock acts through stomata-dependent and -independent pathways to regulate defense

Our data suggest that both stomata-dependent and -independent defense can be affected by CCA1, LHY, and its downstream target GRP7. Consistent with such a role of CCA1 and GRP7, these proteins are expressed in guard cells [51]. It is conceivable that CCA1 and/or LHY proteins directly affect the abundance of GRP7 via binding to its promoter at different times of day, which in turn regulates stomatal aperture and thereby stomatal defense (Figure 11B). Since both CCA1 and GRP7 proteins are also found in other cell types besides the guard cells [51], [64], it is possible that CCA1/LHY/GRP7 also contribute to stomata-independent defense.

GRP7 is unlikely to be the only target of CCA1 and LHY to regulate pathogen defense. First, our bioinformatic analysis suggests that a number of defense genes besides GRP7 might be preferentially regulated by CCA1 and LHY (Figure 7). And second, plants overexpressing GRP7 are not more susceptible to P. syringae (J. Alfano and H. Kang, personal communications) while CCA1ox and LHYox plants are more susceptible to P. syringae (this study). Thus, CCA1 and LHY presumably act through multiple downstream target genes to regulate plant defense. Identification of these additional defense genes controlled by CCA1 and LHY should advance our understanding of the mechanisms by which the circadian clock regulates plant defense.

Rhythmic variation in stomatal aperture is known to be regulated by the circadian clock [13], [37], [65]. Besides CCA1 and LHY, other genes encoding components of the central oscillator may also affect stomatal defense. For instance, a mutation in EARLY FLOWERING 3 (ELF3) was recently shown to suppress stomatal closure and disease resistance [27], [66]. ELF3 might act through the FLOWERING LOCUS T gene, which is highly expressed in stomata of the elf3 mutant and has been shown to affect stomatal activity [66]. In addition, the timing of cab expression1-1 (toc1-1) mutant also shows defects in stomatal aperture [59], [67]. It is tempting to speculate that ELF3-mediated defense is related to its role in stomatal control and TOC1 could also contribute to plant defense. However, further experiments are necessary to validate these speculations. Nevertheless, these observations suggest that the circadian clock can influence stomatal activity and possibly also stomatal defense via different pathways (Figure 12B).

Stomata have been proposed as a critical battleground during plant-bacterium interactions [1], [2]. However, it is not known whether stomatal defense can also restrict the invasion of pathogens with different life styles from those of bacteria. The oomycete pathogen Hpa does not enter host organs through stomata; rather, germinating spores produce hyphae that penetrate between host epidermal cells and extend through the intracellular space in the mesophyll layer. However, near the end of the infection cycle, hyphal tips emerge through the stomata to the exterior of the leaf and then differentiate into spore-bearing structures [68], [69]. Thus, it is possible that host control of stomatal aperture could influence this stage of the life cycle. Although the role of stomata in defense against Hpa has not been well established, the fact that cca1-1lhy-20 showed enhanced susceptibility to Hpa infection relative to the single mutants and wt suggests such a role of the circadian clock. Interestingly, while conferring enhanced disease susceptibility to P. syringae, CCA1ox heightened resistance to Hpa (Figure 6A and [28]), suggesting that CCA1ox plants employ different mechanisms to defend against these two pathogens. However, it is not clear whether the enhanced Hpa resistance conferred by CCA1ox is related to the circadian clock or to another function resulting from CCA1 overexpression.

Defense activation reciprocally regulates the circadian clock

While regulating multifaceted physiological activities of plants, the circadian clock can also be influenced by external signals, such as changes of light, temperature, hormones, and nutrients [32], [70], [71], [72], [73], [74]. Here we show that infection with both virulent and avirulent P. syringae strains shortens circadian period in Arabidopsis (Figure 10 and S7). We further found that such feedback regulation can be recapitulated with flg22 treatment (Figure 11A). Thus, defense activation can also serve as an input signal to regulate clock activity besides being an output of the circadian clock.

Since flg22-triggered callose deposition and expression of genes involved in flg22 sensing and signal transduction were previously shown to be under circadian clock control [27], we conclude that the clock-defense crosstalk involves flg22 signaling (Figure 12B). Production of SA is circadian regulated [75], however, activation of SA defense does not affect clock activity (Figure 11 and S8 and [74]). Therefore, SA is an output of the circadian clock but does not serve as an input factor. Since our data showed that CCA1 and LHY act largely independently of SA, we speculate that other circadian clock components may act through SA as an output in defense control.

What would be the advantages for plants to have clock-defense crosstalk? A properly tuned circadian clock enhances growth vigor and confers better survival rate and competitive advantage [11], [12], [13], [14], [15], [16]. Regulation of defense by the circadian clock suggests that timing of effective defense against pathogens is crucial for host fitness in the presence of pathogens. However, defense is an energy-costly process intricately connected with plant growth and development. A feedback regulation of the circadian clock by defense activation could be important for the host to balance growth, development, and defense responses, for instance, to redirect the energy from costly disease resistance to primary metabolism. Consistent with this idea, several phytohormones are potential components of the clock-defense circuitry. For instance, auxin regulates clock activity as an input [74] while auxin production and signaling are affected by the circadian clock and thus are clock output events [73], [76], [77]. Other hormones, such as abscisic acid, brassinosteroids, cytokinins, and gibberellic acid, have been shown to serve as clock inputs [74], [78]. Interestingly, cytokinin affects the phase but not the period of the clock [74], [79], [80]. However whether these hormones are also on the output pathways of the circadian clock remains to be investigated. On the other hand, ethylene and jasmonic acid production and/or signaling are on the output pathways of the circadian clock [29], [75], [81], [82], [83] although ethylene does not serve as a clock input in Arabidopsis [82]. The role of jasmonic acid as a clock input is currently unknown. All these phytohormones have been implicated in defense control besides their critical roles in regulating plant growth and development [84], [85], [86]. Therefore further investigating the roles of these phytohormones in clock-defense crosstalk should shed light on the molecular mechanisms by which plants employ to regulate growth, development, and responses to pathogen invasion. Such information could potentially lead to a better control of plant growth and resistance to devastating pathogens, ultimately enhancing productivity of plants.

Materials and Methods

Plant materials

Unless otherwise indicated, all plants used on this paper are in the Columbia-0 (Col-0) background and were grown in growth chambers with a 12 hr light/12 hr dark cycle, light intensity at 200 µmol m−2 s−1, 60% humidity and 22°C. Single mutants (acd6-1, lhy-20, and grp7-1) and plants overexpressing CCA1 (CCA1ox) or LHY (LHYox) were described previously [11], [35], [39], [48], [52]. cca1-1 was originally a Wassilewskija allele but was introgressed into Col-0 via five sequential backcrosses. The mutants cca1-1lhy-20, acd6-1cca1-1, acd6-1lhy-20, and acd6-1cca1-1lhy-20 were made by genetic crosses and confirmed with PCR markers corresponding to individual mutations (Table S4 and [54]). CCA1ox (line #34) and grp7-1 seeds were from Elaine Tobin and James Alfano, respectively.

Disease resistance assays

P. syringae strains were grown at 28°C with King's B medium (10 g proteose peptone, 1.5 g K2HPO4, 3.2 ml 1 M MgSO4, and 5 g glycerol per liter) containing the appropriate antibiotics for selection. Freshly cultured bacteria were collected, washed once, and resuspended to desired final concentrations in 10 mM MgSO4 for infiltration and spray infections or in sterile water for stomatal aperture measurement and bioluminescence analysis. For infiltration infection, the bacterial solution was pressured into the abaxial side of the fifth to seventh leaves of a plant with a 1 ml needleless syringe. For spray infection, the bacterial solution was mixed with Silwet L-77 (Lehle Seeds) at a final concentration of 0.04% and sprayed onto plants until the leaf surface was evenly wet. Bacterial growth and disease symptoms were analyzed as described previously [53]. Log transformed bacterial growth was used in statistical analysis.

Hyaloperonospora arabidopsidis (Hpa) strains were propagated and prepared as previously described [56], [87]. Seven day-old soil-grown seedlings were sprayed with a spore suspension (5×104 spores/ml in water) containing the virulent strain Hpa Emco5 or the avirulent strain Hpa Emoy2. Seven days post inoculation, sporangiophores on both sides of cotyledons were counted to determine the level of resistance. Hpa infections were conducted as blind experiments where plant genotypes were unknown to the experimenters until the completion of the experiments. All bacterial and Hpa infection experiments were repeated at least three times unless otherwise indicated.

Northern blotting

RNA extraction and northern blotting were performed as described [54]. Radioactive probes were made by polymerase chain reaction (PCR) with a specific antisense primer for a gene fragment in the presence of [32P] dCTP. Primers used for making probes were listed in Table S4.

Stomatal aperture measurement

Stomatal aperture was measured with 25-day-old plants as previously described [1]. Briefly, the fifth to seventh leaves were taken at the indicated times and mounted onto a glass slide at the abaxial side using Telesis 5 silicone adhesive (Premiere Products, Inc., CA). The top layer of the leaf was scratched off with a razor blade. Images of at least three random regions of the bottom layer of the leaf were taken immediately with a camera (Canon Digital Rebel xsi, Japan) connected to an inverted microscope (Olympus Model IMT-2). P. syringae treatment was performed at ZT4 when plants had been exposed to light for 4 hr to ensure that most stomata opened. The fifth to seventh leaves of plants were collected and immersed in PmaDG3 or DC3000 resuspensed in sterile water (108 cfu/ml) or in water as mock treatment. At 1 hpi or 3 hpi, treated leaves were harvested and processed for stomata imaging. At least three leaves per genotype and per time point were taken for stomatal images. The stomatal aperture was determined by the ratio between the width and the length of a stoma, which was measured with the assistance of ImageJ (version 1.45).

Bioluminescence analysis

Seedlings expressing the reporter gene LUCIFERASE (LUC) under the control of promoters from CCA1 or GRP7 (At2g21660; also called CCR2) [45], [46] were grown on MS media with 2% sucrose in a 12 hr light/12 hr dark cycle at 22°C for 7–10 days. Seedlings were soaked in P. syringae resuspended in sterile water in the presence of 0.04% Silwet L-77, flg22 (1 µM or 10 µM), or benzo(1,2,3)thiadiazole-7-carbothioic acid (BTH; a SA agonist) (10 µM or 300 µM), and transferred to 96-well plates containing 200 µl of MS media and 30 µl of a 2.5 mM D-luciferin solution. Mock treatments were conducted with sterile water with or without 0.04% Silwet L-77. The seedlings were subsequently transferred to LL at 22°C. LUC activity was detected at 1 hr intervals for 7 days with a TopCount luminometer (Perkin Elmer Life Sciences) and analyzed with MetaMorph image software [88]. Flg22 was purchased from GenScript USA Inc. and BTH was a kind gift from Robert Dietrich (Syngenta).

Cotyledon movement assay

For cotyledon movement, surface sterilized Arabidopsis seeds were grown on MS media with 2% sucrose for 6 days in a 12 hr light/12 hr dark cycle at 22°C and were transferred to 24-well cloning plates, one seedling per well. The seedlings were entrained for two more days in the 12 hr light/12 hr cycle at 22°C and were subsequently released into LL at 22°C. Cotyledon movement was recorded with multiple surveillance cameras every 20 min for 7 days and post-run image analysis was performed as described [88].

Bioinformatic analysis

Up to 3000 bp promoter sequences of 571 genes [43] were downloaded from Athena (http://www.bioinformatics2.wsu.edu/cgi-b​in/Athena/cgi/analysis_select.pl) [89]. These genes were grouped into three sets, selected (337 defense-related gene based on microarray experiments), empirical (127 empirical marker genes for various pathogen responses), and normalization (107 non-defense related genes whose expression levels were relatively stable among experiments with pathogen infection) [43]. Promoters of these genes were analyzed for the enrichment of CBS (AA[AC]AATCT) or EE (AAAATATCT) motifs, using the online tool POBO (http://ekhidna.biocenter.helsinki.fi/pox​o/pobo/) [44]. Pseudo-clusters of 100 promoters of up to 3000 bp in length of Arabidopsis genes, which do not contain the coding sequences of the neighboring genes and were sampled randomly from the entire Arabidopsis genome with 1000 bootstrap replications, were analyzed to generate the background as a control for each motif. The number of the CBS or EE motifs in gene clusters was quantified, using a Perl program.

Supporting Information

Figure S1.

Misexpression of CCA1 and LHY disrupts clock activity in LL and LD. (A) Shortening of circadian period in cca1-1lhy-20 in LL. (B) Phase change of ProCCA1:LUC in cca1-1 and lhy-20 mutants and CCA1ox plants in LD. Eight-day-old Col-0, cca1-1, lhy-20, cca1-1lhy-20, and CCA1ox seedlings expressing ProCCA1:LUC were grown from germination in 12 hr light/12 hr dark cycles at 22°C. Bioluminescence was recorded using a Packard TopCount luminometer in LL (A) or in LD (B) at 22°C. White boxes indicate the light period, black boxes indicate dark periods, and gray boxes indicate subjective dark periods in LL. Panel (B) shows normalized bioluminescence traces shown in Figure 1A.

doi:10.1371/journal.ppat.1003370.s001

(TIF)

Figure S2.

Bacterial growth in plants infiltrated with PmaDG3 in LL. (A) ZT1 infection. (B) ZT13 infection. Plants were grown under the same condition as those used in Figure 2. After infiltration with PmaDG3 at 1×105 CFU/ml, plants were moved to LL. Letters indicate significant difference among the samples (P<0.05; Student's t-test). These experiments were repeated twice with similar results.

doi:10.1371/journal.ppat.1003370.s002

(TIF)

Figure S3.

Stomatal aperture at ZT4. Leaves of uninfected 25-day-old plants grown in a 12 hr light/12 hr dark cycle at 22°C were taken at ZT4 for the measurement of stomatal aperture. Letters indicate significant difference among the samples (P<0.001; Student's t-test). These experiments were repeated three times with similar results.

doi:10.1371/journal.ppat.1003370.s003

(TIF)

Figure S4.

Frequency of motif occurrence on gene promoters. The number of CBS (A) or EE motif (B) occurrence per promoter region for selected, empirical, and normalization genes was quantified, using a Perl program.

doi:10.1371/journal.ppat.1003370.s004

(TIF)

Figure S5.

Expression of GRP7 is CCA1-dependent. Circadian expression of GRP7. Twenty five-day-old Col-0, cca1-1, and CCA1ox plants grown in a chamber with a 12 hr light/12 hr dark cycle and 22°C were transferred to LL at 22°C. Starting from ZT1, plants were harvested at every 4 hr interval for 48 hr for RNA extraction followed by northern blotting. White boxes indicate subjective light periods and gray boxes indicate subjective dark periods in LL. GRP7 transcripts were shown on the top three panels. 18S rRNA from each genotype at different time points, shown on the bottom three panels, was used as a loading control.

doi:10.1371/journal.ppat.1003370.s005

(TIF)

Figure S6.

CCA1 and LHY functions are largely SA-independent. (A) SA quantification. Total SA was extracted from plants and analyzed by HPLC. Data represent the average of SA levels (n = 3) ± standard deviation. (B) Picture of 20- and 30-day-old Ler and LHYox plants. The same batch of plants were used in Figure 4C and 4D for SA and cell death analyses.

doi:10.1371/journal.ppat.1003370.s006

(TIF)

Figure S7.

Defense activation by P. syringae infection shortens the period of the GRP7:LUC reporter. Eight-day-old Col-0 seedlings expressing the ProGRP7:LUC reporter were grown from germination in 12 hr light/12 hr dark cycle at 22°C. Then the seedlings were infected with PmaDG3 or PmaDG6 at OD = 0.1 (1×108 CFU/ml) or OD = 0.01 (1×107 CFU/ml) and transferred to 96-well plates containing 200 µl of MS media and 30 µl of a 2.5 mM D-luciferin solution. Luciferase activity was recorded with a Packard TopCount luminometer in LL at 22°C. (A) Mean circadian traces for ProGRP7:LUC activity. White bars indicate subjective day and gray bars indicate subjective night. (B) Mean circadian period of the ProGRP7:LUC reporter. SEM (n = 12–24) was used for (A) and (B). These experiments were repeated twice with similar results.

doi:10.1371/journal.ppat.1003370.s007

(TIF)

Figure S8.

Cotyledon movement assay with acd6-1. (A) Mean circadian period of cotyledon movement of acd6-1. (B) Summary of period, phase, RAE, and amplitude.

doi:10.1371/journal.ppat.1003370.s008

(TIF)

Table S1.

Suppression of stomatal aperture in the presence of P. syringae.

doi:10.1371/journal.ppat.1003370.s009

(DOCX)

Table S2.

Fold change of cluster means of motif enrichment.

doi:10.1371/journal.ppat.1003370.s010

(DOCX)

Table S3.

Defense activation by P. syringae infection or flg22 treatment shortens the clock period.

doi:10.1371/journal.ppat.1003370.s011

(DOCX)

Table S4.

Primers used in this paper.

doi:10.1371/journal.ppat.1003370.s012

(DOCX)

Acknowledgments

We thank members in the Lu laboratory for assistance in this work. We thank Dr. Maricel Kann for assistance in the bioinformatic analysis, Dr. Xinnian Dong for helpful discussions, and Drs. Jean Greenberg and Gregory Martin for critical comments on the manuscript. We thank Dr. William LaCourse for sharing his HPLC instrument and Mr. Tim Ford for taking pictures for this publication.

Author Contributions

Conceived and designed the experiments: HL. Performed the experiments: CZ QX RGA GN NCS TP DK HL. Analyzed the data: CZ QX RGA GN NCS TP CRM JMM DK JMK HL. Contributed reagents/materials/analysis tools: CRM JMM JMK HL. Wrote the paper: CZ CRM HL. Pseudomonas infection assays: CZ HL. Hpa infection assays: RGA JMM. Clock activity assays: QX CRM. Stomatal assays: CZ DK. Bioinformatic analysis: NCS TP HL. Northern blotting: GN HL. Salicylic acid analysis: CZ HL.

References

  1. 1. Melotto M, Underwood W, Koczan J, Nomura K, He SY (2006) Plant stomata function in innate immunity against bacterial invasion. Cell 126: 969–980. doi: 10.1016/j.cell.2006.06.054
  2. 2. Underwood W, Melotto M, He SY (2007) Role of plant stomata in bacterial invasion. Cell Microbiol 9: 1621–1629. doi: 10.1111/j.1462-5822.2007.00938.x
  3. 3. Zipfel C (2008) Pattern-recognition receptors in plant innate immunity. Curr Opin Immunol 20: 10–16. doi: 10.1016/j.coi.2007.11.003
  4. 4. Boller T, Felix G (2009) A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol 60: 379–406. doi: 10.1146/annurev.arplant.57.032905.105346
  5. 5. Jones JD, Dangl JL (2006) The plant immune system. Nature 444: 323–329. doi: 10.1038/nature05286
  6. 6. Hammond-Kosack KE, Jones JD (1996) Resistance gene-dependent plant defense responses. Plant Cell 8: 1773–1791. doi: 10.1105/tpc.8.10.1773
  7. 7. Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124: 803–814. doi: 10.1016/j.cell.2006.02.008
  8. 8. Ryals JA, Neuenschwander UH, Willits MG, Molina A, Steiner HY, et al. (1996) Systemic acquired resistance. Plant Cell 8: 1809–1819. doi: 10.2307/3870231
  9. 9. Tsuda K, Sato M, Glazebrook J, Cohen JD, Katagiri F (2008) Interplay between MAMP-triggered and SA-mediated defense responses. Plant J 53: 763–775. doi: 10.1111/j.1365-313x.2007.03369.x
  10. 10. Lu H (2009) Dissection of salicylic acid-mediated defense signaling networks. Plant Signal Behav 4: 713–717. doi: 10.4161/psb.4.8.9173
  11. 11. Michael TP, Salome PA, Yu HJ, Spencer TR, Sharp EL, et al. (2003) Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 302: 1049–1053. doi: 10.1126/science.1082971
  12. 12. Green RM, Tingay S, Wang ZY, Tobin EM (2002) Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol 129: 576–584. doi: 10.1104/pp.004374
  13. 13. Dodd AN, Salathia N, Hall A, Kevei E, Toth R, et al. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630–633. doi: 10.1126/science.1115581
  14. 14. Graf A, Schlereth A, Stitt M, Smith AM (2010) Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proc Natl Acad Sci U S A 107: 9458–9463. doi: 10.1073/pnas.0914299107
  15. 15. Dong MA, Farre EM, Thomashow MF (2011) CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci U S A 108: 7241–7246. doi: 10.1073/pnas.1103741108
  16. 16. Ni Z, Kim ED, Ha M, Lackey E, Liu J, et al. (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327–331. doi: 10.1038/nature07523
  17. 17. McClung CR (2008) Comes a time. Curr Opin Plant Biol 11: 514–520. doi: 10.1016/j.pbi.2008.06.010
  18. 18. Harmer S (2009) The circadian system in higher plants. Annual Review of Plant Biology 60: 357–377. doi: 10.1146/annurev.arplant.043008.092054
  19. 19. Lu SX, Knowles SM, Andronis C, Ong MS, Tobin EM (2009) CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiol 150: 834–843. doi: 10.1104/pp.108.133272
  20. 20. Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, et al. (2002) LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev Cell 2: 629–641. doi: 10.1016/s1534-5807(02)00170-3
  21. 21. Alabadi D, Yanovsky MJ, Mas P, Harmer SL, Kay SA (2002) Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Curr Biol 12: 757–761. doi: 10.1016/s0960-9822(02)00815-1
  22. 22. Sauerbrunn N, Schlaich NL (2004) PCC1: a merging point for pathogen defence and circadian signalling in Arabidopsis. Planta 218: 552–561. doi: 10.1007/s00425-003-1143-z
  23. 23. Weyman PD, Pan Z, Feng Q, Gilchrist DG, Bostock RM (2006) A circadian rhythm-regulated tomato gene is induced by Arachidonic acid and Phythophthora infestans infection. Plant Physiol 140: 235–248. doi: 10.1104/pp.105.068874
  24. 24. Wang ZX, Yamanouchi U, Katayose Y, Sasaki T, Yano M (2001) Expression of the Pib rice-blast-resistance gene family is up-regulated by environmental conditions favouring infection and by chemical signals that trigger secondary plant defences. Plant Mol Biol 47: 653–661.
  25. 25. Wang GY, Shi JL, Ng G, Battle SL, Zhang C, et al. (2011) Circadian clock-regulated phosphate transporter PHT4;1 plays an important role in Arabidopsis Defense. Mol Plant 4: 516–526. doi: 10.1093/mp/ssr016
  26. 26. Roden LC, Ingle RA (2009) Lights, rhythms, infection: the role of light and the circadian clock in determining the outcome of plant-pathogen interactions. Plant Cell 21: 2546–2552. doi: 10.1105/tpc.109.069922
  27. 27. Bhardwaj V, Meier S, Petersen LN, Ingle RA, Roden LC (2011) Defence responses of Arabidopsis thaliana to infection by Pseudomonas syringae are regulated by the circadian clock. PLoS One 6: e26968. doi: 10.1371/journal.pone.0026968
  28. 28. Wang W, Barnaby JY, Tada Y, Li H, Tor M, et al. (2011) Timing of plant immune responses by a central circadian regulator. Nature 470: 110–114. doi: 10.1038/nature09766
  29. 29. Shin J, Heidrich K, Sanchez-Villarreal A, Parker JE, Davis SJ (2012) TIME FOR COFFEE represses accumulation of the MYC2 transcription factor to provide time-of-day regulation of jasmonate signaling in Arabidopsis. Plant Cell 24: 2470–2482. doi: 10.1105/tpc.111.095430
  30. 30. Oliverio KA, Crepy M, Martin-Tryon EL, Milich R, Harmer SL, et al. (2007) GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock. Plant Physiol 144: 495–502. doi: 10.1104/pp.107.097048
  31. 31. McClung CR (2011) Plant biology: Defence at dawn. Nature 470: 44–45. doi: 10.1038/470044a
  32. 32. Salomé PA, McClung CR (2005) What makes Arabidopsis tick: Light and temperature entrainment of the circadian clock. Plant, Cell & Environment 28: 21–38. doi: 10.1111/j.1365-3040.2004.01261.x
  33. 33. Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, et al. (2007) Rhythmic growth explained by coincidence between internal and external cues. Nature 448: 358–361. doi: 10.1038/nature05946
  34. 34. Dowson-Day MJ, Millar AJ (1999) Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. Plant J 17: 63–71. doi: 10.1046/j.1365-313x.1999.00353.x
  35. 35. Wang ZY, Tobin EM (1998) Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93: 1207–1217. doi: 10.1016/s0092-8674(00)81464-6
  36. 36. Guttman DS, Greenberg JT (2001) Functional analysis of type III effectors AvrRpt2 and AvrRpm1 of Pseudomonas syringae with the use of a single copy genomic integration system. Mol Plant Microbe Interact 14: 145–155. doi: 10.1094/mpmi.2001.14.2.145
  37. 37. Webb AA (2003) The physiology of circadian rhythms in plants. New Phytol 160: 281–303. doi: 10.1046/j.1469-8137.2003.00895.x
  38. 38. Gorton HL, Williams WE, Binns ME, Gemmell CN, Leheny EA, et al. (1989) Circadian stomatal rhythms in epidermal peels from Vicia faba. Plant Physiol 90: 1329–1334. doi: 10.1104/pp.90.4.1329
  39. 39. Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, et al. (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93: 1219–1229. doi: 10.1016/s0092-8674(00)81465-8
  40. 40. Wang ZY, Kenigsbuch D, Sun L, Harel E, Ong MS, et al. (1997) A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 9: 491–507. doi: 10.2307/3870502
  41. 41. Michael TP, McClung CR (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiol 132: 629–639. doi: 10.1104/pp.021006
  42. 42. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, et al. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110–2113. doi: 10.1126/science.290.5499.2110
  43. 43. Sato M, Mitra RM, Coller J, Wang D, Spivey NW, et al. (2007) A high-performance, small-scale microarray for expression profiling of many samples in Arabidopsis-pathogen studies. Plant J 49: 565–577. doi: 10.1111/j.1365-313x.2006.02972.x
  44. 44. Kankainen M, Holm L (2004) POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res 32: W222–229. doi: 10.1093/nar/gkh463
  45. 45. Heintzen C, Nater M, Apel K, Staiger D (1997) AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc Natl Acad Sci U S A 94: 8515–8520. doi: 10.1073/pnas.94.16.8515
  46. 46. Carpenter CD, Kreps JA, Simon AE (1994) Genes encoding glycine-rich Arabidopsis thaliana proteins with RNA-binding motifs are influenced by cold treatment and an endogenous circadian rhythm. Plant Physiol 104: 1015–1025. doi: 10.1104/pp.104.3.1015
  47. 47. Staiger D, Zecca L, Wieczorek Kirk DA, Apel K, Eckstein L (2003) The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant J 33: 361–371. doi: 10.1046/j.1365-313x.2003.01629.x
  48. 48. Fu ZQ, Guo M, Jeong BR, Tian F, Elthon TE, et al. (2007) A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity. Nature 447: 284–288. doi: 10.1038/nature05737
  49. 49. Streitner C, Danisman S, Wehrle F, Schoning JC, Alfano JR, et al. (2008) The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana. Plant J 56: 239–250. doi: 10.1111/j.1365-313x.2008.03591.x
  50. 50. Niwa Y, Ito S, Nakamichi N, Mizoguchi T, Niinuma K, et al. (2007) Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabidopsis thaliana. Plant Cell Physiol 48: 925–937. doi: 10.1093/pcp/pcm067
  51. 51. Kim JS, Jung HJ, Lee HJ, Kim KA, Goh CH, et al. (2008) Glycine-rich RNA-binding protein 7 affects abiotic stress responses by regulating stomata opening and closing in Arabidopsis thaliana. Plant J 55: 455–466. doi: 10.1111/j.1365-313x.2008.03518.x
  52. 52. Rate DN, Cuenca JV, Bowman GR, Guttman DS, Greenberg JT (1999) The gain-of-function Arabidopsis acd6 mutant reveals novel regulation and function of the salicylic acid signaling pathway in controlling cell death, defenses, and cell growth. Plant Cell 11: 1695–1708. doi: 10.2307/3871047
  53. 53. Lu H, Rate DN, Song JT, Greenberg JT (2003) ACD6, a novel ankyrin protein, is a regulator and an effector of salicylic acid signaling in the Arabidopsis defense response. Plant Cell 15: 2408–2420. doi: 10.1105/tpc.015412
  54. 54. Ng G, Seabolt S, Zhang C, Salimian S, Watkins TA, et al. (2011) Genetic dissection of salicylic acid-mediated defense signaling networks in Arabidopsis. Genetics 189: 851–859. doi: 10.1534/genetics.111.132332
  55. 55. Lu H, Salimian S, Gamelin E, Wang G, Fedorowski J, et al. (2009) Genetic analysis of acd6-1 reveals complex defense networks and leads to identification of novel defense genes in Arabidopsis. Plant J 58: 401–412. doi: 10.1111/j.1365-313x.2009.03791.x
  56. 56. Song JT, Lu H, McDowell JM, Greenberg JT (2004) A key role for ALD1 in activation of local and systemic defenses in Arabidopsis. Plant J 40: 200–212. doi: 10.1111/j.1365-313x.2004.02200.x
  57. 57. Felix G, Duran JD, Volko S, Boller T (1999) Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18: 265–276. doi: 10.1046/j.1365-313x.1999.00265.x
  58. 58. Lawton KA, Friedrich L, Hunt M, Weymann K, Delaney T, et al. (1996) Benzothiadiazole induces disease resistance in Arabidopsis by activation of the systemic acquired resistance signal transduction pathway. Plant J 10: 71–82. doi: 10.1046/j.1365-313x.1996.10010071.x
  59. 59. Millar AJ, Carre IA, Strayer CA, Chua NH, Kay SA (1995) Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267: 1161–1163. doi: 10.1126/science.7855595
  60. 60. Fukushima A, Kusano M, Nakamichi N, Kobayashi M, Hayashi N, et al. (2009) Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proc Natl Acad Sci U S A 106: 7251–7256. doi: 10.1073/pnas.0900952106
  61. 61. Kim JY, Song HR, Taylor BL, Carre IA (2003) Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY. EMBO J 22: 935–944. doi: 10.1093/emboj/cdg075
  62. 62. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, et al. (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14. doi: 10.1371/journal.pgen.0040014
  63. 63. Griebel T, Zeier J (2008) Light regulation and daytime dependency of inducible plant defenses in Arabidopsis: phytochrome signaling controls systemic acquired resistance rather than local defense. Plant Physiol 147: 790–801. doi: 10.1104/pp.108.119503
  64. 64. Yakir E, Hilman D, Kron I, Hassidim M, Melamed-Book N, et al. (2009) Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis. Plant Physiol 150: 844–857. doi: 10.1104/pp.109.137414
  65. 65. Salome PA, Michael TP, Kearns EV, Fett-Neto AG, Sharrock RA, et al. (2002) The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis. Plant Physiol 129: 1674–1685. doi: 10.1104/pp.003418
  66. 66. Kinoshita T, Ono N, Hayashi Y, Morimoto S, Nakamura S, et al. (2011) FLOWERING LOCUS T regulates stomatal opening. Curr Biol 21: 1232–1238. doi: 10.1016/j.cub.2011.06.025
  67. 67. Somers DE, Webb AA, Pearson M, Kay SA (1998) The short-period mutant, toc1-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana. Development 125: 485–494.
  68. 68. Slusarenko AJ, Schlaich NL (2003) Downy mildew of Arabidopsis thaliana caused by Hyaloperonospora parasitica (formerly Peronospora parasitica). Mol Plant Pathol 4: 159–170. doi: 10.1046/j.1364-3703.2003.00166.x
  69. 69. Coates ME, Beynon JL (2010) Hyaloperonospora arabidopsidis as a pathogen model. Annu Rev Phytopathol 48: 329–345. doi: 10.1146/annurev-phyto-080508-094422
  70. 70. Millar AJ (2004) Input signals to the plant circadian clock. J Exp Bot 55: 277–283. doi: 10.1093/jxb/erh034
  71. 71. Gutierrez RA, Stokes TL, Thum K, Xu X, Obertello M, et al. (2008) Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A 105: 4939–4944. doi: 10.1073/pnas.0800211105
  72. 72. Jones MA (2009) Entrainment of the Arabidopsis circadian clock. J Plant Biol 52: 202–209. doi: 10.1007/s12374-009-9030-1
  73. 73. Rawat R, Schwartz J, Jones MA, Sairanen I, Cheng Y, et al. (2009) REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. Proc Natl Acad Sci U S A 106: 16883–16888. doi: 10.1073/pnas.0813035106
  74. 74. Hanano S, Domagalska MA, Nagy F, Davis SJ (2006) Multiple phytohormones influence distinct parameters of the plant circadian clock. Genes Cells 11: 1381–1392. doi: 10.1111/j.1365-2443.2006.01026.x
  75. 75. Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF (2012) Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior. Proc Natl Acad Sci U S A 109: 4674–4677. doi: 10.1073/pnas.1116368109
  76. 76. Covington MF, Harmer SL (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5: e222. doi: 10.1371/journal.pbio.0050222
  77. 77. Jouve L, Gaspar T, Kevers C, Greppin H, Degli Agosti R (1999) Involvement of indole-3-acetic acid in the circadian growth of the first internode of Arabidopsis. Planta 209: 136–142. doi: 10.1007/s004250050615
  78. 78. Robertson FC, Skeffington AW, Gardner MJ, Webb AA (2009) Interactions between circadian and hormonal signalling in plants. Plant Mol Biol 69: 419–427. doi: 10.1007/s11103-008-9407-4
  79. 79. Salome PA, To JP, Kieber JJ, McClung CR (2006) Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period. Plant Cell 18: 55–69. doi: 10.1105/tpc.105.037994
  80. 80. Zheng B, Deng Y, Mu J, Ji Z, Xiang T, et al. (2006) Cytokinin affects circadian-clock oscillation in a phytochrome B- and Arabidopsis response regulator 4-dependent manner. Physiol Plantarum 127: 277–292. doi: 10.1111/j.1399-3054.2006.00660.x
  81. 81. Finlayson SA, Lee IJ, Mullet JE, Morgan PW (1999) The mechanism of rhythmic ethylene production in sorghum. The role of phytochrome B and simulated shading. Plant Physiol 119: 1083–1089. doi: 10.1104/pp.119.3.1083
  82. 82. Thain SC, Vandenbussche F, Laarhoven LJ, Dowson-Day MJ, Wang ZY, et al. (2004) Circadian rhythms of ethylene emission in Arabidopsis. Plant Physiol 136: 3751–3761. doi: 10.1104/pp.104.042523
  83. 83. Jasoni R, Cothren J, Morgan P, Sohan D (2002) Circadian ethylene production in cotton. Plant Growth Regulation 36: 127–133. doi: 10.1023/a:1015073400206
  84. 84. Bari R, Jones JD (2009) Role of plant hormones in plant defence responses. Plant Mol Biol 69: 473–488. doi: 10.1007/s11103-008-9435-0
  85. 85. Spoel SH, Dong X (2008) Making sense of hormone crosstalk during plant immune responses. Cell Host Microbe 3: 348–351. doi: 10.1016/j.chom.2008.05.009
  86. 86. Kazan K, Manners JM (2009) Linking development to defense: auxin in plant-pathogen interactions. Trends Plant Sci 14: 373–382. doi: 10.1016/j.tplants.2009.04.005
  87. 87. McDowell JM, Hoff T, Anderson RG, Deegan D (2010) Propagation, storage, and assays with Hyaloperonospora arabidopsidis: A model oomycete pathogen of Arabidopsis. Methods Mol Biol 712: 137–151. doi: 10.1007/978-1-61737-998-7_12
  88. 88. Kim WY, Salome PA, Fujiwara S, Somers DE, McClung CR (2010) Characterization of pseudo-response regulators in plants. Methods Enzymol 471: 357–378. doi: 10.1016/s0076-6879(10)71019-3
  89. 89. O'Connor TR, Dyreson C, Wyrick JJ (2005) Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21: 4411–4413. doi: 10.1093/bioinformatics/bti714
  90. 90. Wang GF, Seabolt S, Hamdoun S, Ng G, Park J, et al. (2011) Multiple roles of WIN3 in regulating disease resistance, cell death, and flowering time in Arabidopsis. Plant Physiol 156: 1508–1519. doi: 10.1104/pp.111.176776
  91. 91. Zhang W, He SY, Assmann SM (2008) The plant innate immunity response in stomatal guard cells invokes G-protein-dependent ion channel regulation. Plant J 56: 984–996. doi: 10.1111/j.1365-313x.2008.03657.x