Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis

Plant Cell

Volumn 17, Issue 7, 2005, Pages 1926-1940

  Harmer, Stacey L ^a   Kay, Steve A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FEEDBACK; GENES; MUTAGENESIS;

EVENING ELEMENT (EE); SCANNING MUTAGENESIS; TRANSCRIPTIONAL REGULATION;

PLANTS (BOTANY);

FEEDBACK; GENES; PLANTS;

ARABIDOPSIS;

ARABIDOPSIS PROTEIN; CCA1 PROTEIN, ARABIDOPSIS; DNA BINDING PROTEIN; LHY PROTEIN, ARABIDOPSIS; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; BIOLOGICAL RHYTHM; CIRCADIAN RHYTHM; DNA FLANKING REGION; GENE EXPRESSION REGULATION; GENETICS; PROMOTER REGION; REGULATORY SEQUENCE;

3' FLANKING REGION; 5' FLANKING REGION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOLOGICAL CLOCKS; CIRCADIAN RHYTHM; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, PLANT; PROMOTER REGIONS (GENETICS); REGULATORY ELEMENTS, TRANSCRIPTIONAL; REPRESSOR PROTEINS; TRANSCRIPTION FACTORS;

EID: 33644813858     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.105.033035     Document Type: Article

References (48)

1. Alabadi, D., Oyama, T., Yanovsky, M.J., Harmon, F.G., Mas, P., and Kay, S.A. (2001). Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293, 880-883.
2. Alabadi, D., Yanovsky, M.J., Mas, P., Harmer, S.L., and Kay, S.A. (2002). Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Curr. Biol. 12, 757-761.
3. Clough, S.J., and Bent, A.F. (1998). Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
4. Cyran, S.A., Buchsbaum, A.M., Reddy, K.L., Lin, M.C., Glossop, N.R., Hardin, P.E., Young, M.W., Stortl, R.V., and Blau, J. (2003). vrille, Pdp1, and dClock form a second feedback loop in the Drosophila circadian clock. Cell 112, 329-341.
5. Darlington, T.K., Lyons, L.C., Hardin, P.E., and Kay, S.A. (2000). The period E-box is sufficient to drive circadian oscillation of transcription in vivo. J. Biol. Rhythms 15, 462-471.
6. Doyle, M.R., Davis, S.J., Bastow, R.M., McWatters, H.G., Kozma-Bognar, L., Nagy, F., Millar, A.J., and Amasino, R.M. (2002). The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419, 74-77.
7. Duffield, G.E. (2003). DNA microarray analyses of circadian timing: The genomic basis of biological time. J. Neuroendocrinol. 15, 991-1002.
8. Emery, P., and Reppert, S.M. (2004). A rhythmic Ror. Neuron 43, 443-446.
9. Eriksson, M.E., Hanano, S., Southern, M.M., Hall, A., and Millar, A.J. (2003). Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta 218, 159-162.
10. Farre, E.M., Harmer, S.L., Harmon, F.G., Yanovsky, M.J., and Kay, S.A. (2005). Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr. Biol. 15, 47-54.
11. Foley, R.C., and Singh, K.B. (2004). TGA5 acts as a positive and TGA4 acts as a negative regulator of ocs element activity in Arabidopsis roots in response to defence signals. FEBS Lett. 563, 141-145.
12. Glossop, N.R., Houl, J.H., Zheng, H., Ng, F.S., Dudek, S.M., and Hardin, P.E. (2003). VRILLE feeds back to control circadian transcription of Clock in the Drosophila circadian oscillator. Neuron 37, 249-261.
13. Green, R.M., Tingay, S., Wang, Z.Y., and Tobin, E.M. (2002). Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol. 129, 576-584.
14. Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A., and Kay, S.A. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110-2113.
15. Harmer, S.L., Panda, S., and Kay, S.A. (2001). Molecular bases of circadian rhythms. Annu. Rev. Cell Dev. Biol. 17, 215-253.
16. Hudson, M.E., and Quail, P.H. (2003). Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data. Plant Physiol. 133, 1605-1616.
17. Ito, S., Nakamichi, N., Matsushika, A., Fujimori, T., Yamashino, T., and Mizuno, T. (2005). Molecular dissection of the promoter of the light-induced and circadian-controlled APRR9 gene encoding a clock-associated component of Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 69, 382-390.
18. Kim, J.Y., Song, H.R., Taylor, B.L., and Carre, I.A. (2003). Light- regulated translation mediates gated induction of the Arabidopsis clock protein LHY. EMBO J. 22, 935-944.
19. Lyons, L.C., Darlington, T.K., Hao, H., Houl, J., Kay, S.A., and Hardin, P.E. (2000). Specific sequences outside the E-box are required for proper per expression and behavioral rescue. J. Biol. Rhythms 15, 472-482.
20. Matsushika, A., Makino, S., Kojima, M., and Mizuno, T. (2000). Circadian waves of expression of the APRR1/TOC1 family of pseudo-response regulators in Arabidopsis thaliana: Insight into the plant circadian clock. Plant Cell Physiol. 41, 1002-1012.
21. Matsushika, A., Makino, S., Kojima, M., Yamashino, T., and Mizuno, T. (2002). The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants. Plant Cell Physiol. 43, 118-122.
22. Michael, T.P., and McClung, C.R. (2002). Phase-specific circadian clock regulatory elements in Arabidopsis. Plant Physiol. 130, 627-638.
23. Michael, T.P., and McClung, C.R. (2003). Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiol. 132, 629-639.
24. Michael, T.P., Salome, P.A., Yu, H.J., Spencer, T.R., Sharp, E.L., McPeek, M.A., Alonso, J.M., Ecker, J.R., and McClung, C.R. (2003). Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 302, 1049-1053.
25. Millar, A.J., Carre, I.A., Strayer, C.A., Chua, N.H., and Kay, S.A. (1995). Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267, 1161-1163.
26. Mitsui, S., Yamaguchi, S., Matsuo, T., Ishida, Y., and Okamura, H. (2001). Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes Dev. 15, 995-1006.
27. Mizoguchi, T., Wheatley, K., Hanzawa, Y., Wright, L., Mizoguchi, M., Song, H.R., Carre, I.A., and Coupland, G. (2002). LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev. Cell 2, 629-641.
28. Nakamichi, N., Kita, M., Ito, S., Sato, E., Yamashino, T., and Mizuno, T. (2005b). The Arabidopsis pseudo-response regulators, PRR5 and PRR7, coordinately play essential roles for circadian clock function. Plant Cell Physiol. 46, 609-619.
29. Nakamichi, N., Kita, M., Ito, S., Yamashino, T., and Mizuno, T. (2005a). Pseudo-response regulators, PRR9, PRR7, and PRR5, play together essential roles close to the circadian clock of Arabidopsis thaliana. Plant Cell Physiol., in press.
30. Ouyang, Y., Andersson, C.R., Kondo, T., Golden, S.S., and Johnson, C.H. (1998). Resonating circadian clocks enhance fitness in cyanobacteria. Proc. Natl. Acad. Sci. USA 95, 8660-8664.
31. Park, D.H., Somers, D.E., Kim, Y.S., Choy, Y.H., Lim, H.K., Soh, M.S., Kim, H.J., Kay, S.A., and Nam, H.G. (1999). Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285, 1579-1582.
32. Piechulla, B., Merforth, N., and Rudolph, B. (1998). Identification of tomato Lhc promoter regions necessary for circadian expression. Plant Mol. Biol. 38, 655-662.
33. Plautz, J.D., Straume, M., Stanewsky, R., Jamison, C.F., Brandes, C., Dowse, H.B., Hall, J.C., and Kay, S.A. (1997). Quantitative analysis of Drosophila period gene transcription in living animals. J. Biol. Rhythms 12, 204-217.
34. Preitner, N., Damiola, F., Lopez-Molina, L., Zakany, J., Duboule, D., Albrecht, U., and Schibler, U. (2002). The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110, 251-260.
35. Puente, P., Wei, N., and Deng, X.W. (1996). Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis. EMBO J. 15, 3732-3743.
36. Roenneberg, T., and Merrow, M. (2003). The network of time: Understanding the molecular circadian system. Curr. Biol. 13, R198-R207.
37. Salome, P.A., and McClung, C.R. (2004). The Arabidopsis thaliana clock. J. Biol. Rhythms 19, 425-435.
38. Salome, P.A., and McClung, C.R. (2005). PSEUDO-RESPONSE REGULATOR 7 and 9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock. Plant Cell 17, 791-803.
39. Sato, T.K., Panda, S., Kay, S.A., and Hogenesch, J.B. (2003). DNA arrays: Applications and implications for circadian biology. J. Biol. Rhythms 18, 96-105.
40. Sato, T.K., Panda, S., Miraglia, L.J., Reyes, T.M., Rudic, R.D., McNamara, P., Naik, K.A., FitzGerald, G.A., Kay, S.A., and Hogenesch, J.B. (2004). A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 43, 527-537.
41. Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M., and Wisman, E. (2001). Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13, 113-123.
42. Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carre, I.A., and Coupland, G. (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93, 1219-1229.
43. Strayer, C., Oyama, T., Schultz, T.F., Raman, R., Somers, D.E., Mas, P., Panda, S., Kreps, J.A., and Kay, S.A. (2000). Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289, 768-771.
44. Suarez-Lopez, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., and Coupland, G. (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410, 1116-1120.
45. Tomita, J., Nakajima, M., Kondo, T., and Iwasaki, H. (2005). No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 307, 251-254.
46. Ueda, H.R., Hayashi, S., Chen, W., Sano, M., Machida, M., Shigeyoshi, Y., Iino, M., and Hashimoto, S. (2005). System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat. Genet. 37, 187-192.
47. Wang, Z.Y., Kenigsbuch, D., Sun, L., Harel, E., Ong, M.S., and Tobin, E.M. (1997). A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 9, 491-507.
48. Wang, Z.Y., and Tobin, E.M. (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93, 1207-1217.