Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Subscribe

Logo for

Science 323 (5920): 1481-1485

Copyright © 2009 by the American Association for the Advancement of Science

A Functional Genomics Approach Reveals CHE as a Component of the Arabidopsis Circadian Clock

Jose L. Pruneda-Paz, Ghislain Breton, Alessia Para, Steve A. Kay*

Abstract: Transcriptional feedback loops constitute the molecular circuitry of the plant circadian clock. In Arabidopsis, a core loop is established between CCA1 and TOC1. Although CCA1 directly represses TOC1, the TOC1 protein has no DNA binding domains, which suggests that it cannot directly regulate CCA1. We established a functional genomic strategy that led to the identification of CHE, a TCP transcription factor that binds specifically to the CCA1 promoter. CHE is a clock component partially redundant with LHY in the repression of CCA1. The expression of CHE is regulated by CCA1, thus adding a CCA1/CHE feedback loop to the Arabidopsis circadian network. Because CHE and TOC1 interact, and CHE binds to the CCA1 promoter, a molecular linkage between TOC1 and CCA1 gene regulation is established.

Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.

* To whom correspondence should be addressed. E-mail: skay{at}ucsd.edu

THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
BRANCHED1 Promotes Axillary Bud Dormancy in Response to Shade in Arabidopsis.
E. Gonzalez-Grandio, C. Poza-Carrion, C. O. S. Sorzano, and P. Cubas (2013)
PLANT CELL 25, 834-850
   Abstract »    Full Text »    PDF »
The TIE1 Transcriptional Repressor Links TCP Transcription Factors with TOPLESS/TOPLESS-RELATED Corepressors and Modulates Leaf Development in Arabidopsis.
Q. Tao, D. Guo, B. Wei, F. Zhang, C. Pang, H. Jiang, J. Zhang, T. Wei, H. Gu, L.-J. Qu, et al. (2013)
PLANT CELL 25, 421-437
   Abstract »    Full Text »    PDF »
Circadian Clock Regulates Dynamic Chromatin Modifications Associated with Arabidopsis CCA1/LHY and TOC1 Transcriptional Rhythms.
H. Hemmes, R. Henriques, I.-C. Jang, S. Kim, and N.-H. Chua (2012)
Plant Cell Physiol. 53, 2016-2029
   Abstract »    Full Text »    PDF »
Transcriptional repressor PRR5 directly regulates clock-output pathways.
N. Nakamichi, T. Kiba, M. Kamioka, T. Suzuki, T. Yamashino, T. Higashiyama, H. Sakakibara, and T. Mizuno (2012)
PNAS 109, 17123-17128
   Abstract »    Full Text »    PDF »
Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks.
G. W. Bassel, A. Gaudinier, S. M. Brady, L. Hennig, S. Y. Rhee, and I. De Smet (2012)
PLANT CELL 24, 3859-3875
   Abstract »    Full Text »    PDF »
Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis.
O. Windram, P. Madhou, S. McHattie, C. Hill, R. Hickman, E. Cooke, D. J. Jenkins, C. A. Penfold, L. Baxter, E. Breeze, et al. (2012)
PLANT CELL 24, 3530-3557
   Abstract »    Full Text »    PDF »
Ubiquitin-Mediated Control of Plant Hormone Signaling.
D. R. Kelley and M. Estelle (2012)
Plant Physiology 160, 47-55
   Full Text »    PDF »
TCP transcription factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), is required for normal tassel branch angle formation in maize.
F. Bai, R. Reinheimer, D. Durantini, E. A. Kellogg, and R. J. Schmidt (2012)
PNAS 109, 12225-12230
   Abstract »    Full Text »    PDF »
In silico analyses of pericycle cell populations reinforce their relation with associated vasculature in Arabidopsis.
B. Parizot, I. Roberts, J. Raes, T. Beeckman, and I. De Smet (2012)
Phil Trans R Soc B 367, 1479-1488
   Abstract »    Full Text »    PDF »
A Self-Regulatory Circuit of CIRCADIAN CLOCK-ASSOCIATED1 Underlies the Circadian Clock Regulation of Temperature Responses in Arabidopsis.
P. J. Seo, M.-J. Park, M.-H. Lim, S.-G. Kim, M. Lee, I. T. Baldwin, and C.-M. Park (2012)
PLANT CELL 24, 2427-2442
   Abstract »    Full Text »    PDF »
Preferential Retention of Circadian Clock Genes during Diploidization following Whole Genome Triplication in Brassica rapa.
P. Lou, J. Wu, F. Cheng, L. G. Cressman, X. Wang, and C. R. McClung (2012)
PLANT CELL 24, 2415-2426
   Abstract »    Full Text »    PDF »
Newly Described Components and Regulatory Mechanisms of Circadian Clock Function in Arabidopsis thaliana.
M. A. Troncoso-Ponce and P. Mas (2012)
Mol Plant 5, 545-553
   Abstract »    Full Text »    PDF »
Time for a Nuclear Meeting: Protein Trafficking and Chromatin Dynamics Intersect in the Plant Circadian System.
E. Herrero and S. J. Davis (2012)
Mol Plant 5, 554-565
   Abstract »    Full Text »    PDF »
Linking photoreceptor excitation to changes in plant architecture.
L. Li, K. Ljung, G. Breton, R. J. Schmitz, J. Pruneda-Paz, C. Cowing-Zitron, B. J. Cole, L. J. Ivans, U. V. Pedmale, H.-S. Jung, et al. (2012)
Genes & Dev. 26, 785-790
   Abstract »    Full Text »    PDF »
Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator.
W. Huang, P. Perez-Garcia, A. Pokhilko, A. J. Millar, I. Antoshechkin, J. L. Riechmann, and P. Mas (2012)
Science 336, 75-79
   Abstract »    Full Text »    PDF »
Evolution and Diversification of the CYC/TB1 Gene Family in Asteraceae--A Comparative Study in Gerbera (Mutisieae) and Sunflower (Heliantheae).
S. Tahtiharju, A. S. Rijpkema, A. Vetterli, V. A. Albert, T. H. Teeri, and P. Elomaa (2012)
Mol. Biol. Evol. 29, 1155-1166
   Abstract »    Full Text »    PDF »
Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes.
A. B. James, N. H. Syed, S. Bordage, J. Marshall, G. A. Nimmo, G. I. Jenkins, P. Herzyk, J. W. S. Brown, and H. G. Nimmo (2012)
PLANT CELL 24, 961-981
   Abstract »    Full Text »    PDF »
FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis.
S. Ito, Y. H. Song, A. R. Josephson-Day, R. J. Miller, G. Breton, R. G. Olmstead, and T. Imaizumi (2012)
PNAS 109, 3582-3587
   Abstract »    Full Text »    PDF »
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor.
J. M. Gendron, J. L. Pruneda-Paz, C. J. Doherty, A. M. Gross, S. E. Kang, and S. A. Kay (2012)
PNAS 109, 3167-3172
   Abstract »    Full Text »    PDF »
Determinants of the DNA Binding Specificity of Class I and Class II TCP Transcription Factors.
I. L. Viola, R. Reinheimer, R. Ripoll, N. G. U. Manassero, and D. H. Gonzalez (2012)
J. Biol. Chem. 287, 347-356
   Abstract »    Full Text »    PDF »
The Arabidopsis Transcription Factor AtTCP15 Regulates Endoreduplication by Modulating Expression of Key Cell-cycle Genes.
Z.-Y. Li, B. Li, and A.-W. Dong (2012)
Mol Plant 5, 270-280
   Abstract »    Full Text »    PDF »
The class I protein AtTCP15 modulates plant development through a pathway that overlaps with the one affected by CIN-like TCP proteins.
N. G. Uberti-Manassero, L. E. Lucero, I. L. Viola, A. C. Vegetti, and D. H. Gonzalez (2012)
J. Exp. Bot. 63, 809-823
   Abstract »    Full Text »    PDF »
The Arabidopsis O-Linked N-Acetylglucosamine Transferase SPINDLY Interacts with Class I TCPs to Facilitate Cytokinin Responses in Leaves and Flowers.
E. Steiner, I. Efroni, M. Gopalraj, K. Saathoff, T.-S. Tseng, M. Kieffer, Y. Eshed, N. Olszewski, and D. Weiss (2012)
PLANT CELL 24, 96-108
   Abstract »    Full Text »    PDF »
The Pea TCP Transcription Factor PsBRC1 Acts Downstream of Strigolactones to Control Shoot Branching.
N. Braun, A. de Saint Germain, J.-P. Pillot, S. Boutet-Mercey, M. Dalmais, I. Antoniadi, X. Li, A. Maia-Grondard, C. Le Signor, N. Bouteiller, et al. (2012)
Plant Physiology 158, 225-238
   Abstract »    Full Text »    PDF »
Antagonistic Action of Strigolactone and Cytokinin in Bud Outgrowth Control.
E. A. Dun, A. de Saint Germain, C. Rameau, and C. A. Beveridge (2012)
Plant Physiology 158, 487-498
   Abstract »    Full Text »    PDF »
Transcriptomic Analysis Reveals Calcium Regulation of Specific Promoter Motifs in Arabidopsis.
H. J. Whalley, A. W. Sargeant, J. F. C. Steele, T. Lacoere, R. Lamb, N. J. Saunders, H. Knight, and M. R. Knight (2011)
PLANT CELL 23, 4079-4095
   Abstract »    Full Text »    PDF »
A Role for Protein Kinase Casein Kinase2 {alpha}-Subunits in the Arabidopsis Circadian Clock.
S. X. Lu, H. Liu, S. M. Knowles, J. Li, L. Ma, E. M. Tobin, and C. Lin (2011)
Plant Physiology 157, 1537-1545
   Abstract »    Full Text »    PDF »
Molecular Mechanisms Underlying the Arabidopsis Circadian Clock.
N. Nakamichi (2011)
Plant Cell Physiol. 52, 1709-1718
   Abstract »    Full Text »    PDF »
Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development.
X. Ouyang, J. Li, G. Li, B. Li, B. Chen, H. Shen, X. Huang, X. Mo, X. Wan, R. Lin, et al. (2011)
PLANT CELL 23, 2514-2535
   Abstract »    Full Text »    PDF »
High time for a roll call: gene duplication and phylogenetic relationships of TCP-like genes in monocots.
M. Mondragon-Palomino and C. Trontin (2011)
Ann. Bot. 107, 1533-1544
   Abstract »    Full Text »    PDF »
A High-Throughput Screening System for Arabidopsis Transcription Factors and Its Application to Med25-Dependent Transcriptional Regulation.
B. Ou, K.-Q. Yin, S.-N. Liu, Y. Yang, T. Gu, J. M. Wing Hui, L. Zhang, J. Miao, Y. Kondou, M. Matsui, et al. (2011)
Mol Plant 4, 546-555
   Abstract »    Full Text »    PDF »
CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis.
M. A. Dong, E. M. Farre, and M. F. Thomashow (2011)
PNAS 108, 7241-7246
   Abstract »    Full Text »    PDF »
Circadian Clock Parameter Measurement: Characterization of Clock Transcription Factors Using Surface Plasmon Resonance.
J. S. O'Neill, G. van Ooijen, T. Le Bihan, and A. J. Millar (2011)
J Biol Rhythms 26, 91-98
   Abstract »    PDF »
Interactions between plant circadian clocks and solute transport.
M. J. Haydon, L. J. Bell, and A. A. R. Webb (2011)
J. Exp. Bot. 62, 2333-2348
   Abstract »    Full Text »    PDF »
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.
R. Yang, C. Zhang, and Z. Su (2011)
Bioinformatics 27, 1023-1025
   Abstract »    Full Text »    PDF »
The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose.
N. Dalchau, S. J. Baek, H. M. Briggs, F. C. Robertson, A. N. Dodd, M. J. Gardner, M. A. Stancombe, M. J. Haydon, G.-B. Stan, J. M. Goncalves, et al. (2011)
PNAS 108, 5104-5109
   Abstract »    Full Text »    PDF »
BROTHER OF LUX ARRHYTHMO Is a Component of the Arabidopsis Circadian Clock.
S. Dai, X. Wei, L. Pei, R. L. Thompson, Y. Liu, J. E. Heard, T. G. Ruff, and R. N. Beachy (2011)
PLANT CELL 23, 961-972
   Abstract »    Full Text »    PDF »
LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 Form a Positive Feedback Regulatory Loop in the Arabidopsis Circadian Clock.
Y. Wang, J.-F. Wu, N. Nakamichi, H. Sakakibara, H.-G. Nam, and S.-H. Wu (2011)
PLANT CELL 23, 486-498
   Abstract »    Full Text »    PDF »
The Jumonji C Domain-Containing Protein JMJ30 Regulates Period Length in the Arabidopsis Circadian Clock.
S. X. Lu, S. M. Knowles, C. J. Webb, R. B. Celaya, C. Cha, J. P. Siu, and E. M. Tobin (2011)
Plant Physiology 155, 906-915
   Abstract »    Full Text »    PDF »
Jumonji domain protein JMJD5 functions in both the plant and human circadian systems.
M. A. Jones, M. F. Covington, L. DiTacchio, C. Vollmers, S. Panda, and S. L. Harmer (2010)
PNAS 107, 21623-21628
   Abstract »    Full Text »    PDF »
Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana.
S. Hong, H.-R. Song, K. Lutz, R. A. Kerstetter, T. P. Michael, and C. R. McClung (2010)
PNAS 107, 21211-21216
   Abstract »    Full Text »    PDF »
TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock in Arabidopsis thaliana.
E. Giraud, S. Ng, C. Carrie, O. Duncan, J. Low, C. P. Lee, O. Van Aken, A. H. Millar, M. Murcha, and J. Whelan (2010)
PLANT CELL 22, 3921-3934
   Abstract »    Full Text »    PDF »
Digital Gene Expression Signatures for Maize Development.
A. L. Eveland, N. Satoh-Nagasawa, A. Goldshmidt, S. Meyer, M. Beatty, H. Sakai, D. Ware, and D. Jackson (2010)
Plant Physiology 154, 1024-1039
   Abstract »    Full Text »    PDF »
Plant Biology in the Fourth Dimension.
S. Harmer (2010)
Plant Physiology 154, 467-470
   Full Text »    PDF »
On reverse engineering of gene interaction networks using time course data with repeated measurements.
E. R. Morrissey, M. A. Juarez, K. J. Denby, and N. J. Burroughs (2010)
Bioinformatics 26, 2305-2312
   Abstract »    Full Text »    PDF »
Robust Circadian Rhythms of Gene Expression in Brassica rapa Tissue Culture.
X. Xu, Q. Xie, and C. R. McClung (2010)
Plant Physiology 153, 841-850
   Abstract »    Full Text »    PDF »
Identification of Specific DNA Binding Residues in the TCP Family of Transcription Factors in Arabidopsis.
P. Aggarwal, M. Das Gupta, A. P. Joseph, N. Chatterjee, N. Srinivasan, and U. Nath (2010)
PLANT CELL 22, 1174-1189
   Abstract »    Full Text »    PDF »
F-Box Proteins FKF1 and LKP2 Act in Concert with ZEITLUPE to Control Arabidopsis Clock Progression.
A. Baudry, S. Ito, Y. H. Song, A. A. Strait, T. Kiba, S. Lu, R. Henriques, J. L. Pruneda-Paz, N. H. Chua, E. M. Tobin, et al. (2010)
PLANT CELL 22, 606-622
   Abstract »    Full Text »    PDF »
PSEUDO-RESPONSE REGULATORS 9, 7, and 5 Are Transcriptional Repressors in the Arabidopsis Circadian Clock.
N. Nakamichi, T. Kiba, R. Henriques, T. Mizuno, N. H. Chua, and H. Sakakibara (2010)
PLANT CELL 22, 594-605
   Abstract »    Full Text »    PDF »
Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks.
L. Pu and S. Brady (2010)
Plant Physiology 152, 411-419
   Full Text »    PDF »
Phytochrome functions in Arabidopsis development.
K. A. Franklin and P. H. Quail (2010)
J. Exp. Bot. 61, 11-24
   Abstract »    Full Text »    PDF »
Profile of Steve Kay.
B. Trivedi (2009)
PNAS 106, 18051-18053
   Full Text »    PDF »
Evolutionarily Conserved Regulatory Motifs in the Promoter of the Arabidopsis Clock Gene LATE ELONGATED HYPOCOTYL.
M. Spensley, J.-Y. Kim, E. Picot, J. Reid, S. Ott, C. Helliwell, and I. A. Carre (2009)
PLANT CELL 21, 2606-2623
   Abstract »    Full Text »    PDF »
A timing mechanism for stem cell maintenance and differentiation in the Arabidopsis floral meristem.
B. Sun, Y. Xu, K.-H. Ng, and T. Ito (2009)
Genes & Dev. 23, 1791-1804
   Abstract »    Full Text »    PDF »
Functional Analysis of Transcription Factors in Arabidopsis.
N. Mitsuda and M. Ohme-Takagi (2009)
Plant Cell Physiol. 50, 1232-1248
   Abstract »    Full Text »    PDF »
CIRCADIAN RHYTHMS: Linking the Loops.
C. R. McClung (2009)
Science 323, 1440-1441
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882