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First published online January 20, 2006; 10.1104/pp.105.074864 Plant Physiology 140:933-945 (2006) © 2006 American Society of Plant Biologists Forward Genetic Analysis of the Circadian Clock Separates the Multiple Functions of ZEITLUPE1,[W]Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H–6726 Szeged, Hungary (É.K., P.G., B.F., F.N.); School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom (A.H.); Institute of Molecular Plant Science, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom (L.K.-B., A.J.M.); Department of Plant Cellular and Molecular Biology, Ohio State University, Columbus, Ohio 43210 (W.-Y.K., D.E.S.); Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE–901 87 Umea, Sweden (M.E.E.); Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, D–50829 Cologne, Germany (R.T., S.H., S.J.D.); Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom (M.M.S., R.M.B., V.H.); and Biologie II/Institut für Botanik, University of Freiburg, D–79104 Freiburg, Germany (A.V.)
The circadian system of Arabidopsis (Arabidopsis thaliana) includes feedback loops of gene regulation that generate 24-h oscillations. Components of these loops remain to be identified; none of the known components is completely understood, including ZEITLUPE (ZTL), a gene implicated in regulated protein degradation. ztl mutations affect both circadian and developmental responses to red light, possibly through ZTL interaction with PHYTOCHROME B (PHYB). We conducted a large-scale genetic screen that identified additional clock-affecting loci. Other mutants recovered include 11 new ztl alleles encompassing mutations in each of the ZTL protein domains. Each mutation lengthened the circadian period, even in dark-grown seedlings entrained to temperature cycles. A mutation of the LIGHT, OXYGEN, VOLTAGE (LOV)/Period-ARNT-Sim (PAS) domain was unique in retaining wild-type responses to red light both for the circadian period and for control of hypocotyl elongation. This uncoupling of ztl phenotypes indicates that interactions of ZTL protein with multiple factors must be disrupted to generate the full ztl mutant phenotype. Protein interaction assays showed that the ztl mutant phenotypes were not fully explained by impaired interactions with previously described partner proteins Arabidopsis S-phase kinase-related protein 1, TIMING OF CAB EXPRESSION 1, and PHYB. Interaction with PHYB was unaffected by mutation of any ZTL domain. Mutation of the kelch repeat domain affected protein binding at both the LOV/PAS and the F-box domains, indicating that interaction among ZTL domains leads to the strong phenotypes of kelch mutations. Forward genetics continues to provide insight regarding both known and newly discovered components of the circadian system, although current approaches have saturated mutations at some loci.
The circadian systems that drive 24-h biological rhythms in many organisms evolved as an adaptation to the Earth's rotation and its attendant changes in light and temperature conditions. The core of a circadian system can be described as an oscillator; oscillator components (clock genes/proteins) rhythmically regulate their own expression/activity (and that of each other) through one or more negative feedback mechanisms at the transcriptional/translational level, generating a self-sustained oscillation (Young and Kay, 2001  ). Additional clock-associated factors, which do not carry temporal information and which may not be rhythmic, are required to set the period length of this oscillation close to 24 h and to adjust other rhythmic properties. The oscillator regulates the expression of overt rhythms through output pathways. The phase of the oscillator (subjective time) is set to the objective time of the environment by periodic environmental signals (light and temperature) transduced by input pathways. Light signaling to the plant clock is mediated by several photoreceptors of the phytochrome and cryptochrome families, which may themselves be clock regulated (for review, see Fankhauser and Staiger, 2002; Millar, 2003). Increasing light fluence rates shortens the free-running period length in Arabidopsis (Arabidopsis thaliana; Millar et al., 1995b), as in many diurnal animals (Aschoff, 1979).
According to current models (for review, see Hayama and Coupland, 2003
The majority of known components of the Arabidopsis circadian system have been identified by forward genetics (for review, see Southern and Millar, 2005
ZTL was the first component of the plant circadian system to be implicated in regulated proteolysis. ZTL, LOV KELCH PROTEIN 2 (LKP2), and FLAVIN BINDING, KELCH REPEAT, F-BOX 1 (FKF1) form a protein family with a unique signature of three protein domains: an N-terminal Period-ARNT-Sim (PAS)-like LIGHT, OXYGEN, VOLTAGE (LOV) domain, a central F-box motif, and a C-terminal domain of six kelch repeats that are predicted to form a
The unusual LOV/PAS domain of ZTL suggested that ZTL function could be light regulated because the equivalent domain in other proteins (notably FKF1; Imaizumi et al., 2003 We report a large-scale screen to identify circadian clock mutants using a LUC reporter gene under constant darkness. The 104 mutants recovered identify several new clock-affecting genes. In addition, 11 ztl alleles include amino acid substitutions in all three domains of the ZTL protein. Most of the mutants share similar phenotypes. Only mutation of the LOV/PAS domain uncoupled the function of ZTL in red-light responses from its function in the circadian system. Protein interaction assays show that altered interactions with known partner proteins do not explain the phenotype of the ztl mutations, although the strong effects of seemingly disparate mutations are likely due to contributions of multiple domains to each protein interaction.
Isolation of Novel Circadian Mutants
Seeds carrying the CHLOROPHYLL a/b-BINDING PROTEIN (CAB2; also known as LHCB1.1):LUC reporter in the C24 accession (Millar et al., 1995a
Mutants were placed on the genetic map. Greater than five mutant lines were identified that did not map close to clock-associated genes, including lines with a long or short period in constant red light and one line with altered phase but no significant period change; three of these lines are shown in Figure 1. To identify mutants that were allelic with known clock-associated genes, the TOC1, ELF3, GI, or ZTL gene was amplified and sequenced from mutant lines that showed both tight genetic linkage to the relevant locus and the phenotype expected for toc1, elf3, gi, or ztl mutants. This identified two new toc1 alleles with predicted mutations in the pseudoresponse regulator domain (Supplemental Fig. 1; Supplemental Table I) and the short-period phenotype characteristic of previously described toc1 alleles (Fig. 1). One elf3 and two gi alleles will be described elsewhere (L. Kozma-Bognár and A. Hall, unpublished data). Here we characterize 11 new alleles of ZTL (Fig. 2 ), including one with a novel phenotype in red light.
New Mutations within the ZTL Gene
The positions of the 11 newly identified and the two previously published ztl mutations within the ZTL protein sequence are shown in Figure 2 and listed in Supplemental Table I. All are caused by G-to-A transitions in the nucleotide sequence, as expected of EMS mutations. In ztl-21, a G-to-D amino acid substitution is predicted in the second half of the LOV/PAS domain in a residue that is conserved within the ZTL/FKF/LKP2 protein family in Arabidopsis. ztl-22 causes an E-to-K change that lies at a conserved position in the F-box domain of ZTL and other F-box proteins from plants, mammals, and fungi (Patton et al., 1998
Kelch repeat domains form a
Quantitative Differences in the Circadian Phenotypes of ztl Mutants All of the ztl mutants showed a late-phase phenotype of CAB2:LUC(+) expression under the screening conditions (Fig. 4A ; data not shown) and all had a long period of CAB2:LUC(+) expression under constant red or blue or red and blue light (Supplemental Table II). We therefore focused on a subset of alleles that affect each ZTL domain and each genetic background. The rhythmic expression of well-characterized promoter:LUC+ fusions (CAB2, CCR2, or CCA1) was examined in the ztl mutants under constant white, red, or blue light and during dark adaptation. All of the ztl alleles displayed long-period phenotypes in all conditions; in general, ztl-21 plants showed a weaker phenotype compared to the other alleles, whereas ztl-31 plants had the longest periods and also lower rhythmic amplitude (Fig. 4B; Supplemental Fig. 2; Supplemental Table II; data not shown). This quantitative difference in phenotype was replicated when we tested a circadian output that is distinct from gene expression, the leaf movement rhythm (Fig. 4C).
To assess the impact of the ztl mutations under light/dark cycles, the diurnal expression pattern of CCA1:LUC+ and CCR2:LUC+ was tested under short-day conditions (Supplemental Fig. 2, A and C). CCA1:LUC+ activity in wild-type seedlings started to increase in anticipation of lights on, when acute light induction of CCA1 expression sharply increased activity to a peak 1 to 2 h after lights on. The ztl mutants showed evidence of a late circadian phase, with little or no increase in CCA1 expression before dawn. Together with a reduced acute response to light, this led to peak expression at ZT4-6 compared to ZT1-2 in the wild type (Supplemental Fig. 2A). The reduced light response is consistent with CCA1 RNA data for other ztl alleles (Somers et al., 2004 ). CCR2:LUC+ activity also peaked 2 to 4 h later in the night in ztl mutants compared to wild type (Supplemental Fig. 2C).
ZTL protein levels were measured in the mutant plants by western analysis. Data obtained from representative mutant lines carrying single point mutations within each functionally important domain are shown in Figure 5 . The results show that all mutants tested expressed at least the wild-type level of the protein, except ztl-31 (Fig. 5, A and B). ZTL mRNA levels also showed little or no effect of the mutations (Supplemental Fig. 4). ztl-31 was expected to express a protein truncated by 2.6% (16 amino acids; Fig. 2) and, consistent with this, the ZTL antibody recognized a protein with slightly reduced molecular mass in extracts from ztl-31 (Fig. 5B; data not shown). ZTL levels overall were apparently reduced in this line, although ZTL mRNA levels were unaffected or slightly increased (Supplemental Fig. 3), suggesting that the truncated protein was unstable, although an effect on the polyclonal epitope cannot be ruled out.
ZTL protein levels normally oscillate diurnally, with a maximum at ZT13 and a minimum at ZT1 under LD 12:12 cycles. This diurnal oscillation of the protein level is controlled posttranslationally through circadian phase-specific degradation (Kim et al., 2003 ). Although most of the ztl mutant lines showed wild-type oscillations (data not shown), three lines were aberrant. ztl-22, which carries a mutation in the F-box domain, showed strongly elevated levels of ZTL at ZT1 and moderately elevated levels at ZT13 relative to wild type (Fig. 5B). A G-to-D substitution in the fourth kelch repeat (ztl-27) also enhanced ZTL protein accumulation at ZT1 (Fig. 5B). ztl-31 resulted in much lower levels of mutant protein at both times (Fig. 5B). In these three mutants, particularly in the stronger allele ztl-31, phenotypic differences might relate to variation in ZTL protein levels; in the other lines, any differences in the mutant phenotypes are likely to reflect altered function of the mutant proteins rather than differences in their accumulation.
A major aspect of ZTL function is in mediating light responsiveness. The free-running period of circadian rhythms in wild-type Arabidopsis decreases with increasing fluence rates of light. Consequently, fluence rate response curves (FRCs; constructed by plotting period values as a function of the log of fluence rate) for Arabidopsis rhythms show a negative slope. The slope is more negative for ztl-1, ztl-2, and the null ztl-3 mutants than for the wild type because their long-period phenotype is exaggerated at low fluence rates of either red or blue light (Somers et al., 2000 To characterize the effect of the mutant ZTL proteins on light signaling, FRCs were measured for CAB2:LUC(+) rhythms and hypocotyl elongation under red and blue light (Fig. 6 ; Supplemental Fig. 4). Hypocotyl length in dark-grown plants was the same in all genotypes, indicating that the differences observed were light dependent (data not shown). The new alleles were similar to ztl-1 for both circadian and hypocotyl phenotypes under blue light (Supplemental Fig. 4). ztl-31 again showed the greatest lengthening of the circadian period, with slightly weaker effects in ztl-21. Under red light, however, ztl-21 showed qualitatively different behavior from the other alleles (Fig. 6).
At high fluence rates of red light, ztl-21 and the other ztl mutants had a circadian period about 3.5 h longer than wild-type plants. Only ztl-21 maintained this 3.5-h period lengthening across the whole range of red light intensity (Fig. 6B; see also Fig. 4B), giving a FRC with the same gradient as the wild type. The period of the other alleles increased to 8 to 12 h longer than wild type at the lowest fluence rates, as previously reported. ztl-21 seedlings also showed little or no defect in hypocotyl elongation at any fluence rate of red light (Fig. 6D). Under long photoperiods of white light, ztl-21 plants flowered with the wild type in contrast to the modest delay in flowering time observed for kelch mutations (Fig. 4D; Somers et al., 2000 ; Kim et al., 2005). Thus, the LOV/PAS mutant ztl-21 affected the circadian period, but did not affect responses to red light either by shortening the circadian period or by inhibiting hypocotyl elongation or photoperiod sensing. We and others have demonstrated that ZTL affects the circadian period of light-grown plants transferred to constant darkness (dark-adapting plants; Supplemental Fig. 2B). These plants initially have a light-adapted complement of photoreceptors, some of which are thought to remain active for hours to days in darkness. To test the dependence of ZTL function on photoreceptor signaling more stringently, circadian rhythms of CCR2:LUC+ activity were tested in dark-grown seedlings compared to dark-adapting seedlings (Table II ; Supplemental Fig. 5). ztl mutant and wild-type seedlings were grown for 3 d in darkness under entrainment from 12 h 26°C/12 h 22°C temperature cycles, then transferred to constant 22°C for period assays also in darkness. ztl mutants showed an identical, long mean period under these conditions as in dark adaptation, indicating that ZTL regulates the circadian system without ongoing photoreceptor signaling (Table II).
Protein Interactions in ztl Mutants The domain structure of the ZTL protein family, together with published data, suggests that ZTL function might be understood at the molecular level in terms of its physical interactions with degradation targets (including TOC1), the SCF complex (through ASK1), and the phytochrome and cryptochrome photoreceptors. To test this notion, representative mutations located in the three different domains of ZTL (LOV/PAS, ztl-21; F-box, ztl-22; kelch repeats, ztl-27) were introduced into the full-length ZTL cDNA. The corresponding mutant proteins were expressed in yeast (Saccharomyces cerevisiae) and tested for interaction with ASK1, TOC1, and the N-terminal domain (PHYBN; amino acids 1–621), the C-terminal domain (PHYBC; amino acids 645–1,272), or full-length phytochrome B. Protein gel-blot analysis confirmed that the mutated protein fusions were expressed in yeast at similar levels to wild-type protein fusions (data not shown). The ZTL-ASK1 interaction was most severely affected by the mutation in the PAS domain and also reduced by the F-box and kelch mutations (Fig. 7A ). The TOC1-ZTL interaction was abolished by the PAS and kelch mutations, as shown by the absence of yeast growth under selective conditions, whereas the F-box mutation had no significant effect (Fig. 7B).
The interaction between PHYBC and full-length ZTL protein was not affected by the mutations (Fig. 7C). However, reporter activity was significantly increased when PHYBC, fused to the DNA-binding domain of GAL4 (bait), was coexpressed with ZTL fused to the activation domain of GAL4 (prey). Similar results were reported by Jarillo et al. (2001) , who also verified the ZTL-PHYBC interaction with in vitro binding studies. We observed no interaction between PHYBC and ZTL when these proteins were expressed in the inverted configuration (PHYBC as prey, ZTL as bait; data not shown). ZTL failed to interact with PHYBN in the presence or absence of the phycocyanobilin chromophore, regardless of whether reconstituted PHYBN was in the Pr or Pfr conformation (Fig. 7D; Supplemental Fig. 6). In contrast, PHYBN interacted strongly with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) in a Pfr-dependent manner, as reported previously (Shimizu-Sato et al., 2002). Full-length PHYB showed some transactivation of the  -galactosidase reporter gene when expressed alone as bait (Fig. 7D), but expression of ZTL as prey did not enhance this expression, regardless of the chromophore state (Fig. 7D; Supplemental Fig. 6). In the absence of interaction with full-length PHYB and of any effect of ztl mutations, the significance of the ZTL-PHYBC interaction is unclear.
To identify components of the Arabidopsis circadian system, we screened approximately 46,000 M2 seedlings from two EMS-mutagenized populations, recovering 104 mutants with altered temporal patterns of CAB:LUC reporter gene expression (Table I). The short duration of the screen (36 h) allowed a relatively high throughput of up to 4,000 seedlings per week per luminescence counter. Forward genetic screens of this type might seem to be approaching saturation, given that we identified alleles of TOC1, ELF3, GI, and ZTL, and a similar approach using prescreening for mutants with long hypocotyls identified alleles of ELF3, ELF4, and TOC1 (Hazen et al., 2005a ). The success of this direct screen for altered patterns of dynamic gene expression in Arabidopsis is a testament to the power of LUC reporter methods. The screens are not strictly saturated because both screens also identified mutations in genes not previously described as clock affecting. Characterization of these genes is likely to give new insights into the mechanisms of the Arabidopsis circadian system. The screens have not identified new cca1 or lhy loss-of-function alleles (T. Schultz, personal communication), for example, which had clear phenotypes in our conditions (data not shown). However, the proportion of mutants in previously identified genes is high, suggesting that future screens might retain the LUC reporter approach, but monitor different components of the circadian system (as initiated in Onai et al., 2004), perhaps under different environmental conditions.
The LOV/PAS, F-box, and kelch repeat domains of ZTL and their associated biochemical functions were first predicted on the basis of protein sequence homology. These predictions have recently been tested by analysis of the physical interactions between ZTL and various protein partners (Más et al., 2003
The F-box mutant (ztl-22) alone had constitutively higher ZTL levels relative to wild type, although the period was similar to the strongest allele (ztl-31), which had very low levels of ZTL (Fig. 5). This suggests that ZTLztl-22 protein is functionally inactive and that inactivity stabilized the protein. The ztl-22 mutation had no effect on the TOC1-ZTL interaction (Fig. 7B), indicating that reduced interaction with this degradation target did not contribute to the phenotype. A double amino acid substitution in the F-box domain has previously been shown to eliminate interaction with ASK1 in yeast and abrogate SCFZTL complex formation in vivo; the mutant ZTL protein was also stabilized in vivo (Han et al., 2004
The predicted clustering of the new ztl mutations on one face of the
Our data suggest that the kelch domain is important to support intermolecular interactions at the LOV/PAS domain (as previously proposed by Más et al., 2003
ZTL controls the circadian period under all lighting conditions, including in seedlings grown in complete darkness (Table II), resulting in a long-period phenotype in ztl mutants. However, the period phenotype of most ztl alleles is light dependent, being more pronounced at low fluence rates of constant red or blue light (Figs. 4 and 6; Supplemental Fig. 4; Somers et al., 2000
Our results demonstrate directly that ZTL function in the control of hypocotyl elongation by red light is distinct from its role in the circadian system because the LOV/PAS mutant (ztl-21) uncouples these phenotypes. ztl-21 plants had a long circadian period, but showed no defect in hypocotyl elongation under red light (Fig. 6D). The circadian clock in ztl-21 showed no defect in sensitivity to red light: The change in period length across the range of red-light fluence rates was the same as in the wild type (Fig. 6B). Flowering time in long days was also unaffected in ztl-21, although the kelch mutation ztl-25 delayed flowering (Fig. 4D), as previously reported for the null allele ztl-3 (Kim et al., 2005
The LOV/PAS domain alone is sufficient to mediate ZTL interaction with its degradation target TOC1 (data not shown; Más et al., 2003
Plant Material and Growth Conditions
ztl alleles were isolated from EMS-mutagenized populations of the C24 accession carrying the CAB2:LUC reporter gene (Millar et al., 1995a
Unless otherwise indicated, seedlings were grown under LD 12:12 at 22°C prior to analysis and all measurements were carried out at constant 22°C. Illumination was provided by cool-white fluorescent tubes or, where indicated, by monochromatic LED light sources (red,
Seeds were sown on soil and incubated for 2 d in darkness at 4°C. They were subsequently transferred to long-day (16-h white light/8-h dark) conditions. Light sources were fluorescent (cool-white) tubes producing a fluence rate of approximately 60 µmol m–2 s–1. Flowering time was recorded as the number of rosette leaves at the time when inflorescences reached 1-cm height. The experiment was repeated twice using 30 to 40 plants per genotype.
LUC activity was measured either by low-light video imaging (groups of 5–10 seedlings) or with an automated luminometer (single seedlings), essentially as described (Hall et al., 2003
Total RNA extraction, northern blotting, and quantification of ZTL and 18S rRNA specific signals were performed as described (Viczian et al., 2005
Extracts were prepared from 10-d-old Arabidopsis (Arabidopsis thaliana) seedlings grown in LD 12:12. Ground tissue was resuspended in extraction buffer (50 mM Tris-Cl, pH 7.5, 1 mM EDTA, 1 mM dithiothreitol, 1 mM phenylmethylsulfonyl fluoride, 5 µg/mL leupeptin, 1 µg/mL aprotinin, 1 µg/mL pepstatin, 5 µg/mL antipain, and 5 µg/mL chymostatin) by vortexing and clarified by centrifugation at 14,000g for 10 min at 4°C. Supernatant protein concentration was determined (Bio-Rad), concentrated by TCA precipitation, and resuspended in urea/SDS loading buffer (40 mM Tris-Cl, pH 6.8, 8 M urea, 5% SDS, 1 mM EDTA, and 2% 2-mercaptoethanol) to a final concentration of 5 µg/µL. Forty micrograms of protein were separated by SDS-PAGE (8%) and subjected to immunoblot analysis as described previously (Kim et al., 2003
All experimental procedures related to Figure 7, A to C, were performed as described by Chien et al. (1991)
All manipulations involving reconstituted phytochromes (Fig. 7D; Supplemental Fig. 6) were performed as described (Shimizu-Sato et al., 2002
We gratefully acknowledge the assistance of Vilmos Fülöp for protein structure mapping; Tom Schultz, Sam Hazen, and Steve Kay for helpful discussions; Tim Kunkel for providing the purified phycocyanobilin chromophore; and Paul Goode, Nazir Shariff, and Katalin Jószai for expert technical assistance. The empty BD vector, the PHYB-N and PHYB clones in the BD vector, and the PIF3 clone in the AD vector used for yeast two-hybrid assays were kindly provided by Peter H. Quail. Received November 29, 2005; returned for revision November 29, 2005; accepted December 21, 2005.
1 This work was supported in part by a long-term fellowship of the European Molecular Biology Organization (to L.K.B.), by a Marie Curie fellowship of the European Union (to M.E.E.), in part by a Japanese Society for the Promotion of Science postdoctoral fellowship (to S.H.), by a Biotechnology and Biological Science Research Council (BBSRC) postgraduate studentship (to M.M.S.), by a studentship from the Gatsby Charitable Foundation (to R.M.B.), by a Department of Energy Biosciences fellowship of the Life Science Research Foundation (to S.J.D.), by the National Science Foundation (grant no. IBN 0344377) and U.S. Department of Agriculture/Cooperative State Research, Education and Extension Service (grant no.CRIS 2002 35304 12594 to D.E.S.), and by the Alexander von Humboldt Foundation (grant no. IV–UNG/1118446 STP to A.V.); work in Szeged was supported by the Hungarian Scientific Research Fund (grant no. OTKA T046710) and the Howard Hughes Medical Institute (grant no. INTNL 55000325 to F.N.); work in Warwick was supported by the BBSRC (grant nos. G08667, G13967, and G15231) and the imaging facility was supported by grants from the Gatsby Charitable Foundation, the BBSRC, and the Royal Society (to A.J.M.).  The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Andrew J. Millar (andrew.millar{at}ed.ac.uk).
[W] The online version of this article contains Web-only data. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.074864. * Corresponding author; e-mail andrew.millar{at}ed.ac.uk; fax 44–0131–650–5392.
Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293: 880–883 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[CrossRef][ISI][Medline] Aschoff J (1979) Circadian rhythms: influences of internal and external factors on the period measured in constant conditions. Z Tierpsychol 49: 225–247[ISI][Medline] Bauer D, Viczián A, Kircher S, Nobis T, Nitschke R, Kunkel T, Panigrahi KC, Ádám É, Fejes E, Schäfer E, et al (2004) Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signaling in Arabidopsis. Plant Cell 16: 1433–1445 Chien CT, Bartel PL, Sternglanz R, Fields S (1991) The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc Natl Acad Sci USA 88: 9578–9582 Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735–743[CrossRef][ISI][Medline] Dowson-Day MJ, Millar AJ (1999) Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. Plant J 17: 63–71[CrossRef][ISI][Medline] Doyle MR, Davis SJ, Bastow RM, McWatters HG, Kozma-Bognar L, Nagy F, Millar AJ, Amasino RM (2002) The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419: 74–77[CrossRef][Medline] Esnouf RM (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph 15: 133–138 Fankhauser C, Staiger D (2002) Photoreceptors in Arabidopsis thaliana: light perception signal transduction and entrainment of the endogenous clock. Planta 216: 1–16[CrossRef][ISI][Medline] Fowler S, Lee K, Onouchi H, Samach A, Richardson K, Morris B, Coupland G, Putterill J (1999) GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. EMBO J 18: 4679–4688[CrossRef][ISI][Medline] Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ, Amasino RM, et al (2003) The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. Plant Cell 15: 2719–2729 Hall A, Kozma-Bognar L, Toth R, Nagy F, Millar AJ (2001) Conditional circadian regulation of PHYTOCHROME A gene expression. Plant Physiol 127: 1808–1818 Han L, Mason M, Risseeuw EP, Crosby WL, Somers DE (2004) Formation of an SCF complex is required for proper regulation of circadian timing. Plant J 40: 291–301[CrossRef][ISI][Medline] Hayama R, Coupland G (2003) Shedding light on the circadian clock and the photoperiodic control of flowering. Curr Opin Plant Biol 6: 13–19[CrossRef][ISI][Medline] Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA (2005a) Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiol 138: 990–997 Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA (2005b) LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci USA 102: 10387–10392 Hicks KA, Millar AJ, Carré IA, Somers DE, Straume M, Meeks-Wagner R, Kay SA (1996) Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274: 790–792 Imaizumi T, Tran HG, Swartz TE, Briggs WR, Kay SA (2003) FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426: 302–306[CrossRef][Medline] Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker JR, Cashmore AR (2001) An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature 410: 487–490[CrossRef][Medline] Kim WY, Geng R, Somers DE (2003) Circadian phase-specific degradation of the F-box protein ZTL is mediated by the proteasome. Proc Natl Acad Sci USA 100: 4933–4938 Kim WY, Hicks KA, Somers DE (2005) Independent roles for EARLY FLOWERING 3 and ZEITLUPE in the control of circadian timing, hypocotyl length, and flowering time. Plant Physiol 139: 1557–1569 Kiyosue T, Wada M (2000) LKP1 (LOV kelch protein 1): a factor involved in the regulation of flowering time in Arabidopsis. Plant J 23: 807–815[CrossRef][ISI][Medline] Kraulis PJ (1991) MolScript: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946–950[CrossRef][ISI] Li X, Zhang D, Hannink M, Beamer LJ (2004) Crystal structure of the kelch domain of human Keap1. J Biol Chem 279: 54750–54758 Locke JCW, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, Turner MS, Millar AJ (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Sys Biol doi/10.1038/msb4100018 Más P, Kim WY, Somers DE, Kay SA (2003) Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426: 567–570[CrossRef][Medline] Merritt EA, Murphy MEP (1994) Raster3D version 20: a program for photorealistic molecular graphics. Acta Crystallogr D 50: 869–873[CrossRef][Medline] Millar AJ (2003) A suite of photoreceptors entrains the plant circadian clock. J Biol Rhythms 18: 217–226[Abstract] Millar AJ, Carré IA, Strayer CA, Chua N-H, Kay SA (1995a) Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267: 1161–1163 Millar AJ, Straume M, Chory J, Chua N-H, Kay SA (1995b) The regulation of circadian period by phototransduction pathways in Arabidopsis. Science 267: 1163–1166 Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, Song HR, Carre IA, Coupland G (2002) LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev Cell 2: 629–641[CrossRef][ISI][Medline] Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H, Mouradov A, Fowler S, Kamada H, Putterill J, et al (2005) Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis. Plant Cell 17: 2255–2270 Nelson DC, Lasswell J, Rogg LE, Cohen MA, Bartel B (2000) FKF1, a clock-controlled gene that regulates the transition to flowering in Arabidopsis. Cell 101: 331–340[CrossRef][ISI][Medline] Onai K, Ishiura M (2005) PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes Cells 10: 963–972 Onai K, Okamoto K, Nishimoto H, Morioka C, Hirano M, Kami-Ike N, Ishiura M (2004) Large-scale screening of Arabidopsis circadian clock mutants by a high-throughput real-time bioluminescence monitoring system. Plant J 40: 1–11[CrossRef][ISI][Medline] Patton EE, Willems AR, Tyers M (1998) Combinatorial control in ubiquitin-dependent proteolysis: don't Skp the F-box hypothesis. Trends Genet 14: 236–243[CrossRef][ISI][Medline] Plautz JD, Straume M, Stanewsky R, Jamison CF, Brandes C, Dowse HB, Hall JC, Kay SA (1997) Quantitative analysis of Drosophila period gene transcription in living animals. J Biol Rhythms 12: 204–217 Salome PA, McClung CR (2004) The Arabidopsis thaliana clock. J Biol Rhythms 19: 425–4 |
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max = 667 nm; blue,