6 Circadian Regulation of Global Gene Expression and Metabolism
Stacey L. Harmer
Section of Plant Biology Life Sciences Addition, University of California, Room 1002, One Shields Avenue, Davis, CA, 95616-5270 USA
Search for more papers by this authorMichael F. Covington
Section of Plant Biology Life Sciences Addition, University of California, Room 1002, One Shields Avenue, Davis, CA, 95616-5270 USA
Search for more papers by this authorOliver Bläsing
Max-Planck Institut, Molekulare Pflanzenphysiologie, Golm, D-14476 Germany
Search for more papers by this authorMark Stitt
Max-Planck Institut, Molekulare Pflanzenphysiologie, Golm, D-14476 Germany
Search for more papers by this authorStacey L. Harmer
Section of Plant Biology Life Sciences Addition, University of California, Room 1002, One Shields Avenue, Davis, CA, 95616-5270 USA
Search for more papers by this authorMichael F. Covington
Section of Plant Biology Life Sciences Addition, University of California, Room 1002, One Shields Avenue, Davis, CA, 95616-5270 USA
Search for more papers by this authorOliver Bläsing
Max-Planck Institut, Molekulare Pflanzenphysiologie, Golm, D-14476 Germany
Search for more papers by this authorMark Stitt
Max-Planck Institut, Molekulare Pflanzenphysiologie, Golm, D-14476 Germany
Search for more papers by this authorAbstract
The sections in this article are
- Circadian Rhythms in Transcription
- Post-Transcriptional Circadian Regulation
- Circadian Regulation of Transcription – What Kinds of Genes, and Why?
- Regulation of Plant Metabolism
- Circadian Regulation of Plant Growth and Development
- How is Clock-Regulation of Gene Expression Achieved?
- Cross-Species Comparisons
- Comparing Gene Expression in Constant and Diurnal Conditions
- Why Have a Clock Rather Than Relying on Driven Rhythms?
- Future Prospects
- Acknowledgements
References
- Adamska, I., Scheel, B. & Kloppstech, K. (1991) Circadian oscillations of nuclear-encoded chloroplast proteins in pea (Pisum sativum). Plant Mol. Biol., 17, 1055–65.
- Akhtar, R.A., Reddy, A.B., Maywood, E.S., Clayton, J.D., King, V.M., Smith, A.G., Gant, T.W., Hastings, M.H. & Kyriacou, C.P. (2002) Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr. Biol., 12, 540–50.
- Alabadi, D., Oyama, T., Yanovsky, M.J., Harmon, F.G., Mas, P. & Kay, S.A. (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science, 293, 880–3.
- Aoki, S., Kato, S., Ichikawa, K. & Shimizu, M. (2004) Circadian expression of the PpLhcb2 gene encoding a major light-harvesting chlorophyll a/b-binding protein in the moss Physcomitrella patens . Plant Cell Physiol., 45, 68–76.
- Arimura, G., Huber, D.P. & Bohlmann, J. (2004) Forest tent caterpillars (Malacosoma disstria) induce local and systemic diurnal emissions of terpenoid volatiles in hybrid poplar (Populus trichocarpa × deltoides): cDNA cloning, functional characterization, and patterns of gene expression of (-)-germacrene D synthase, PtdTPS1. Plant J., 37, 603–16.
- Athwal, G.S. & Huber, S.C. (2002) Divalent cations and polyamines bind to loop 8 of 14-3-3 proteins, modulating their interaction with phosphorylated nitrate reductase. Plant J., 29, 119–29.
- Bachmann, M., Huber, J.L., Liao, P.C., Gage, D.A. & Huber, S.C. (1996) The inhibitor protein of phosphorylated nitrate reductase from spinach (Spinacia oleracea) leaves is a 14-3-3 protein. FEBS Lett., 387, 127–31.
- Beator, J., Potter, E. & Kloppstech, K. (1992) The effect of heat shock on morphogenesis in barley: coordinated circadian regulation of mRNA levels for light-regulated genes and of the capacity for accumulation of chlorophyll protein complexes. Plant Physiol., 100, 1780–1786.
- Bhattacharya, D., Yoon, H.S. & Hackett, J.D. (2004) Photosynthetic eukaryotes unite: endosymbiosis connects the dots. Bioessays, 26, 50–60.
- Bognar, L.K., Hall, A., Adam, E., Thain, S.C., Nagy, F. & Millar, A.J. (1999) The circadian clock controls the expression pattern of the circadian input photoreceptor, phytochrome B. Proc. Natl. Acad. Sci. USA, 96, 14652–7.
- Borevitz, J.O., Xia, Y., Blount, J., Dixon, R.A. & Lamb, C. (2000) Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell, 12, 2383–2394.
- Boxall, S.F., Foster, J.M., Bohnert, H.J., Cushman, J.C., Nimmo, H.G. & Hartwell, J. (2004) In 13th International Congress of Photosynthesis , Vol. Abstract #165 Montreal, Canada.
- Boxall, S.F., Foster, J.M., Bohnert, H.J., Cushman, J.C., Nimmo, H.G. & Hartwell, J. (2005) Conservation and divergence of the central circadian clock in the stress-inducible CAM plant Mesembryanthemum crystallinum: clock operation in a CAM halophyte reveals clock compensation against abiotic stress. Plant Physiol., 137: 969–82.
- Carpenter, C.D., Kreps, J.A. & Simon, A.E. (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, 1015–25.
- Caspar, T., Huber, S.C. & Somerville, C.R. (1985) Alterations in growth, photosynthesis and respiration in a starch deficient mutant of Arabidopsis thaliana (L.) Heynh deficient in chloroplast phospho-glucomutase. Plant Physiol., 79, 11–17.
- Ceriani, M.F., Hogenesch, J.B., Yanovsky, M., Panda, S., Straume, M. & Kay, S.A. (2002) Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J. Neurosci., 22, 9305–19.
- Chatterton, N.J. & Silvius, J.E. (1979) Photosynthate partitioning into starch in soybean leaves: effects of photoperiod versus photosynthetic period duration. Plant Physiol., 64, 749–53.
- Chatterton, N.J. & Silvius, J.E. (1980) Photosynthate partitioning as affected by daily photosynthetic period duration in six species. Physiol. Plant., 49, 141–144.
- Chatterton, N.J. & Silvius, J.E. (1981) Photosynthate partitioning into starch in soybean leaves: irradiance level and daily photsynthetic period duration effects. Plant Physiol., 67, 257–60.
- Chelius, D., Zhang, T., Wang, G. & Shen, R.F. (2003) Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry. Anal. Chem., 75, 6658–65.
- Claridge-Chang, A., Wijnen, H., Naef, F., Boothroyd, C., Rajewsky, N. & Young, M.W. (2001) Circadian regulation of gene expression systems in the Drosophila head. Neuron, 32, 657–71.
- Correa, A., Lewis, Z.A., Greene, A.V., March, I.J., Gomer, R.H. & Bell-Pedersen, D. (2003) Multiple oscillators regulate circadian gene expression in Neurospora. Proc. Natl. Acad. Sci. USA, 100, 13597–602.
- Covington, M.F., Kay, S., Maloof, J.N., Straume, M. & Harmer, S.L. (2005), In preparation.
- Czechowski, T., Bari, R.P., Stitt, M., Scheible, W.R. & Udvardi, M.K. (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J., 38, 366–79.
- Daniel, X., Sugano, S. & Tobin, E.M. (2004) CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis . Proc. Natl. Acad. Sci. USA, 101, 3292–3297.
- Deng, M.D., Moureaux, T., Leydecker, M.T. & Caboche, M. (1990) Nitrate-reductase expression is under the control of a circadian rhythm and is light inducible in Nicotiana tabacum leaves. Planta, 180, 257–61.
- Dietrich, P., Sanders, D. & Hedrich, R. (2001) The role of ion channels in light-dependent stomatal opening. J. Exp. Bot., 52, 1959–67.
- Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M. & Yoshimura, A. (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev., 18, 926–36.
- Dowson-Day, M.J. & Millar, A.J. (1999) Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis . Plant J., 17, 63–71.
- Dudareva, N., Andersson, S., Orlova, I., Gatto, N., Reichelt, M., Rhodes, D., Boland, W. & Gershenzon, J. (2005) The nonmevalonate pathway supports both monoterpene and sesquiterpene formation in snapdragon flowers. Proc. Natl. Acad. Sci. USA, 102, 933–938.
- Dudareva, N., Murfitt, L.M., Mann, C.J., Gorenstein, N., Kolosova, N., Kish, C.M., Bonham, C. & Wood, K. (2000) Developmental regulation of methyl benzoate biosynthesis and emission in snapdragon flowers. Plant Cell, 12, 949–61.
- Duffield, G.E. (2003) DNA microarray analyses of circadian timing: the genomic basis of biological time. J. Neuroendocrinol., 15, 991–1002.
- Eriksson, M.E., Hanano, S., Southern, M.M., Hall, A. & Millar, A.J. (2003) Response regulator homologs have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta, 218, 159–62.
- Etchegaray, J.P., Lee, C., Wade, P.A. & Reppert, S.M. (2003) Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature, 421, 177–82.
- Fernie, A.R., Geigenberger, P. & Stitt, M. (2005) Flux an important, but neglected, component of functional genomics. Curr. Opin. in Plant Bio., 8: 174–82.
- Fiehn, O. (2002) Metabolomics–the link between genotypes and phenotypes. Plant Mol. Biol., 48, 155–71.
- Finlayson, S.A., Lee, I.J., Mullet, J.E. & Morgan, P.W. (1999) The mechanism of rhythmic ethylene production in sorghum. The role of phytochrome B and simulated shading. Plant Physiol., 119, 1083–9.
- Fondy, B.R. & Geiger, D.R. (1985) Diurnal changes of allocation of newly fixed carbon in exporting sugar beet leaves. Plant Physiol., 78, 753–57.
- Geigenberger, P., Reimholz, R., Deiting, U., Sonnewald, U. & Stitt, M. (1999) Decreased expression of sucrose phosphate synthase strongly inhibits the water stress-induced synthesis of sucrose in growing potato tubers. Plant J., 19, 119–129.
- Geiger, D.R. & Servaites, J.C. (1994) Diurnal regulation of photosynthetic carbon metabolism in C3 plants. Annu. Rev. Plant Biol., 45, 235–56.
- Gibon, Y., Blaesing, O.E., Hannemann, J., Carillo, P., Hohne, M., Hendriks, J.H., Palacios, N., Cross, J., Selbig, J. & Stitt, M. (2004a) A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell, 16, 3304–25.
- Gibon, Y., Blasing, O.E., Palacios-Rojas, N., Pankovic, D., Hendriks, J.H., Fisahn, J., Hohne, M., Gunther, M. & Stitt, M. (2004b) Adjustment of diurnal starch turnover to short days: depletion of sugar during the night leads to a temporary inhibition of carbohydrate utilization, accumulation of sugars and post-translational activation of ADP-glucose pyrophosphorylase in the following light period. Plant J., 39, 847–62.
- Giuliano, G., Hoffman, N.E., Ko, K., Scolnik, P.A. & Cashmore, A.R. (1988) A light-entrained circadian clock controls transcription of several plant genes. Embo J., 7, 3635–42.
- Gordon, W.R. & Koukkari, W.L. (1978) Circadian rhythmicity in the activities of phenylalanine ammonia lyase from Lemna perpusilla and Spirodela polyrhiza . Plant Physiol., 62, 612–615.
- Green, R.M., Tingay, S., Wang, Z.Y. & Tobin, E.M. (2002) Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol., 129, 576–84.
- Gutierrez, R.A., Ewing, R.M., Cherry, J.M. & Green, P.J. (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc. Natl. Acad. Sci. USA, 99, 11513–8.
- Halberg, F., Halberg, E., Barnum, C. & Bittner, J. (1959) In Photoperiodism and related phenomena in plants and animals, Vol. 55 (ed R.B. Withrow), pp. 803–78. American Association for the Advancement of Science, Washington.
- Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A. & Kay, S.A. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science, 290, 2110–3.
- Harmer, S.L. & Kay, S. (2005) Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis . Plant Cell, 17, 1926–40.
- Havaux, M. & Niyogi, K.K. (1999) The violaxanthin cycle protects plants from photooxidative damage by more than one mechanism. Proc. Natl. Acad. Sci. USA, 96, 8762–7.
- Hayama, R., Izawa, T. & Shimamoto, K. (2002) Isolation of rice genes possibly involved in the photoperiodic control of flowering by a fluorescent differential display method. Plant Cell Physiol., 43, 494–504.
- Heintzen, C., Fischer, R., Melzer, S., Kappeler, K., Apel, K. & Staiger, D. (1994a) Circadian oscillations of a transcript encoding a germin-like protein that is associated with cell walls in young leaves of the long-day plant Sinapis alba L. Plant Physiol., 106, 905–15.
- Heintzen, C., Melzer, S., Fischer, R., Kappeler, S., Apel, K. & Staiger, D. (1994b) A light- and temperature-entrained circadian clock controls expression of transcripts encoding nuclear proteins with homology to RNA-binding proteins in meristematic tissue. Plant J., 5, 799–813.
- 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. USA, 94, 8515–20.
- Hennessey, T.L. & Field, C.B. (1991) Circadian rhythms in photosynthesis: Oscillations in carbon assimilation and stomatal conductance under constant conditions. Plant Physiol., 96, 831–36.
- Huber, S.C. & Hanson, K.R. (1992) Carbon partitioning and growth of a starchless mutant of Nicotiana sylvestris . Plant Physiol., 99, 1449–1454.
- Hudson, M.E. & 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, 1605–16.
- Ichikawa, K., Sugita, M., Imaizumi, T., Wada, M. & Aoki, S. (2004) Differential expression on a daily basis of plastid sigma factor genes from the moss physcomitrella patens. Regulatory interactions among PpSig5, the circadian clock, and blue light signaling mediated by cryptochromes. Plant Physiol., 136, 4285–98.
- Izawa, T., Oikawa, T., Sugiyama, N., Tanisaka, T., Yano, M. & Shimamoto, K. (2002) Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev., 16, 2006–20.
- Jackson, M.B. (1982) In Plant Growth Substances (ed P.F. Wareing), pp. 291–301. Academic Press, London.
- Jackson, M.B. (1985) Ethylene and responses of plants to soil waterlogging and submergence. Ann. Rev. Plant Physiol., 36, 145–74.
- Jones, T.L., Tucker, D.E. & Ort, D.R. (1998) Chilling delays circadian pattern of sucrose phosphate synthase and nitrate reductase activity in tomato. Plant Physiol., 118, 149–58.
- 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, 136–42.
- Kerr, P.S., Rufty, T.W. & Huber, S.C. (1985) Endogenous rhythms in photosynthesis, sucrose phosphate synthase activity, and stomatal resistance in leaves of soybean (Glycine max [L.] Merr.). Plant Physiol., 77, 275–80.
- Kim, J.Y., Song, H.R., Taylor, B.L. & Carre, I.A. (2003a) Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY. Embo J., 22, 935–44.
- Kim, W.Y., Geng, R. & Somers, D.E. (2003b) Circadian phase-specific degradation of the F-box protein ZTL is mediated by the proteasome. Proc. Natl. Acad. Sci. USA, 100, 4933–38.
- Kloppstech, K. (1985) Diurnal and circadian rhythmicity in the expression of light-induced plant nuclear messenger RNAs. Planta, 165, 502–506.
- Knypl, J.S., Janas, K.M. & Wolska, M. (1986) Rhythmicity of L-phenylalanine ammonia-lyase activity in Spirodela oligorhiza. Effects of darkening, abscisic acid, and 1-amino-2-phenyl-ethylphosphoric acid. Physiol Plant., 66, 543–549.
- Kolosova, N., Gorenstein, N., Kish, C.M. & Dudareva, N. (2001) Regulation of circadian methyl benzoate emission in diurnally and nocturnally emitting plants. Plant Cell, 13, 2333–47.
- Kopka, J., Fernie, A., Weckwerth, W., Gibon, Y. & Stitt, M. (2004) Metabolite profiling in plant biology: platforms and destinations. Genome Biol., 5, 109.
- Kreps, J.A., Muramatsu, T., Furuya, M. & Kay, S.A. (2000) Fluorescent differential display identifies circadian clock-regulated genes in Arabidopsis thaliana . J. Biol. Rhythms, 15, 208–17.
- Kreps, J.A., Wu, Y., Chang, H.S., Zhu, T., Wang, X. & Harper, J.F. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol., 130, 2129–41.
- Kuno, N., Moller, S.G., Shinomura, T., Xu, X., Chua, N.H. & Furuya, M. (2003) The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis . Plant Cell, 15, 2476–88.
- Lam, H.M., Coschigano, K.T., Oliveira, I.C., Melo-Oliveira, R. & Coruzzi, G.M. (1996) The molecular-genetics of nitrogen assimilation into amino acids in higher plants. Annu. Rev. Plant. Physiol. Plant Mol. Biol., 47, 569–93.
- Lillo, C. & Ruoff, P. (1989) An unusually rapid light-induced nitrate reductase mRNA pulse and circadian oscillations. Naturwissenschaften, 76, 526–8.
- Lin, T.P., Caspar, T., Somerville, C.R. & Preiss, J. (1988) A starch deficient mutant of Arabidopsis thaliana with low ADP-glucose pyrophosphorylase activity lacks one of the two subunits of the enzyme. Plant Physiol., 88, 1175–81.
- Liu, J., Yu, J., McIntosh, L., Kende, H. & Zeevaart, J.A. (2001a) Isolation of a CONSTANS ortholog from Pharbitis nil and its role in flowering. Plant Physiol., 125, 1821–30.
- Liu, X.L., Covington, M.F., Fankhauser, C., Chory, J. & Wagner, D.R. (2001b) ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell, 13, 1293–304.
- Liu, Y., Tsinoremas, N.F., Johnson, C.H., Lebedeva, N.V., Golden, S.S., Ishiura, M. & Kondo, T. (1995) Circadian orchestration of gene expression in cyanobacteria. Genes Dev., 9, 1469–78.
- Mas, P., Kim, W.Y., Somers, D.E. & Kay, S.A. (2003) Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana . Nature, 426, 567–70.
- Matt, P., Schurr, U., Klein, D., Krapp, A. & Stitt, M. (1998) Growth of tobacco in short-day conditions leads to high starch, low sugars, altered diurnal changes in the Nia transcript and low nitrate reductase activity, and inhibition of amino acid synthesis. Planta, 207, 27–41.
- McClure, J.W. (1974) Phytochrome control of oscillating levels of phenylalanine ammonia-lyase in Hordeum vulgare shoots. Phytochemistry, 13, 1065–69.
- McDonald, A.J.S. & Davies, W.J. (1996) Keeping in touch: responses of whole plant to deficits in water and nutrient supply. Adv. Botan. Res., 22, 229–300.
- McDonald, M.J. & Rosbash, M. (2001) Microarray analysis and organization of circadian gene expression in Drosophila . Cell, 107, 567–78.
- Michael, T.P. & McClung, C.R. (2002) Phase-specific circadian clock regulatory elements in Arabidopsis . Plant Physiol., 130, 627–38.
- Michael, T.P. & McClung, C.R. (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis . Plant Physiol., 132, 629–39.
- Michael, T.P., Salome, P.A. & McClung, C.R. (2003) Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proc. Natl. Acad. Sci. USA, 100, 6878–83.
- Millar, A.J., Carre, I.A., Strayer, C.A., Chua, N.H. & Kay, S.A. (1995) Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science, 267, 1161–63.
- Millar, A.J., Short, S.R., Chua, N.H. & Kay, S.A. (1992) A novel circadian phenotype based on firefly luciferase expression in transgenic plants. Plant Cell, 4, 1075–87.
- Mittag, M., Lee, D.H. & Hastings, J.W. (1994) Circadian expression of the luciferin-binding protein correlates with the binding of a protein to the 3' untranslated region of its mRNA. Proc. Natl. Acad. Sci. USA, 91, 5257–61.
- Morse, D., Milos, P.M., Roux, E. & Hastings, J.W. (1989) Circadian regulation of bioluminescence in Gonyaulax involves translational control. Proc. Natl. Acad. Sci. USA, 86, 172–76.
- Moshelion, M., Becker, D., Biela, A., Uehlein, N., Hedrich, R., Otto, B., Levi, H., Moran, N. & Kaldenhoff, R. (2002a) Plasma membrane aquaporins in the motor cells of Samanea saman: diurnal and circadian regulation. Plant Cell, 14, 727–39.
- Moshelion, M., Becker, D., Czempinski, K., Mueller-Roeber, B., Attali, B., Hedrich, R. & Moran, N. (2002b) Diurnal and circadian regulation of putative potassium channels in a leaf moving organ. Plant Physiol., 128, 634–42.
- Murakami, M., Ashikari, M., Miura, K., Yamashino, T. & Mizuno, T. (2003) The evolutionarily conserved OsPRR quintet: rice pseudo-response regulators implicated in circadian rhythm. Plant Cell Physiol., 44, 1229–36.
- Muratani, M. & Tansey, W.P. (2003) How the ubiquitin-proteasome system controls transcription. Nat. Rev. Mol. Cell Biol., 4, 192–201.
- Okamoto, K. & Hastings, J.W. (2003) Novel dinoflagellate clock-related genes identified through microarray analysis. J. Phycol., 39, 519–526.
- 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.
- Ouyang, Y., Andersson, C.R., Kondo, T., Golden, S.S. & Johnson, C.H. (1998) Resonating circadian clocks enhance fitness in cyanobacteria. Proc. Natl. Acad. Sci. USA, 95, 8660–64.
- Overland, L. (1960) Endogenous rhythm in opening and odor of flowers of Cestrum nocturnum . Amer. J. Bot., 47, 378–382.
- Oyama, T. (2005). In preparation.
- Panda, S., Antoch, M.P., Miller, B.H., Su, A.I., Schook, A.B., Straume, M., Schultz, P.G., Kay, S.A., Takahashi, J.S. & Hogenesch, J.B. (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell, 109, 307–20.
- Panda, S., Sato, T.K., Hampton, G.M. & Hogenesch, J.B. (2003) An array of insights: application of DNA chip technology in the study of cell biology. Trends Cell Biol., 13, 151–6.
- Peter, H.-J., Kruger-Alef, C., Knogge, W., Brinkmann, K. & Weissenbock, G. (1991) Diurnal periodicity of chalcone-synthase activity during the development of oat primary leaves. Planta, 183, 409–415.
- Plautz, J.D., Straume, M., Stanewsky, R., Jamison, C.F., Brandes, C., Dowse, H.B., Hall, J.C. & Kay, S.A. (1997) Quantitative analysis of Drosophila period gene transcription in living animals. J. Biol. Rhythms, 12, 204–17.
- Podstolsky, A.J. & Brown, G.N. (1974) L-phenylalanine ammonia-lyase activity in Robinia pseudoacacia seedlings: Cyclic phenomenon activity during continuous light. Plant Physiology, 54, 41–43.
- Pott, M.B., Effmert, U. & Piechulla, B. (2003) Transcriptional and post-translational regulation of S-adenosyl-L-methionine: salicylic acid carboxyl methyltransferase (SAMT) during Stephanotis floribunda flower development. J. Plant Physiol., 160, 635–43.
- Riesselmann, S. & Piechulla, B. (1992) Diurnal and circadian light-harvesting complex and quinone B-binding protein synthesis in leaves of tomato (Lycopersicon esculentum). Plant Physiol., 100, 1840–45.
- Rieu, I., Cristescu, S.M., Harren, F.J., Huibers, W., Voesenek, L.A., Mariani, C. & Vriezen, W.H. (2005) RP-ACS1, a flooding-induced 1-aminocyclopropane-1-carboxylate synthase gene of Rumex palustris, is involved in rhythmic ethylene production. J. Exp. Bot., 56, 841–49.
- Rikin, A., Chalutz, E. & Anderson, J.D. (1984) Rhythmicity in ethylene production in cotton seedlings. Plant Physiol., 75, 493–95.
- Sage-Ono, K., Ono, M., Harada, H. & Kamada, H. (1998) Accumulation of a clock-regulated transcript during flower-inductive darkness in pharbitis nil. Plant Physiol., 116, 1479–85.
- Salghetti, S.E., Muratani, M., Wijnen, H., Futcher, B. & Tansey, W.P. (2000) Functional overlap of sequences that activate transcription and signal ubiquitin-mediated proteolysis. Proc. Natl. Acad. Sci. USA, 97, 3118–23.
- Sato, T.K., Panda, S., Kay, S.A. & Hogenesch, J.B. (2003) DNA arrays: applications and implications for circadian biology. J. Biol. Rhythms, 18, 96–105.
- Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M. & Wisman, E. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis . Plant Cell, 13, 113–23.
- Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carre, I.A. & Coupland, G. (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell, 93, 1219–29.
- Scheible, W.R., Gonzalez-Fontes, A., Lauerer, M., Muller-Rober, B., Caboche, M. & Stitt, M. (1997) Nitrate acts as a signal to induce organic acid metabolism and repress starch metabolism in tobacco. Plant Cell, 9, 783–798.
- Scheible, W.R., Morcuende, R., Czechowski, T., Fritz, C., Osuna, D., Palacios-Rojas, N., Schindelasch, D., Thimm, O., Udvardi, M.K. & Stitt, M. (2004) Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol., 136, 2483–99.
- Shimizu, M., Ichikawa, K. & Aoki, S. (2004) Photoperiod-regulated expression of the PpCOL1 gene encoding a homolog of CO/COL proteins in the moss Physcomitrella patens . Biochem. Biophys. Res. Commun., 324, 1296–301.
- Simkin, A.J., Underwood, B.A., Auldridge, M., Loucas, H.M., Shibuya, K., Schmelz, E., Clark, D.G. & Klee, H.J. (2004) Circadian regulation of the PhCCD1 carotenoid cleavage dioxygenase controls emission of beta-ionone, a fragrance volatile of petunia flowers. Plant Physiol., 136, 3504–14.
- Sivasankar, S. & Oaks, A. (1995) Regulation of nitrate reductase during early seedling growth (A role for asparagine and glutamine). Plant Physiol., 107, 1225–1231.
- Smalle, J., Haegman, M., Kurepa, J., Van Montagu, M. & Van der Straeten, D. (1997) Ethylene can stimulate Arabidopsis hypocotyl elongation in the light. Proc. Natl. Acad. Sci. USA, 94, 2756–2761.
- Smith, S.M., Fulton, D.C., Chia, T., Thorneycroft, D., Chapple, A., Dunstan, H., Hylton, C., Zeeman, S.C. & Smith, A.M. (2004) Diurnal changes in the transcriptome encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves. Plant Physiol., 136, 2687–99.
- Somers, D.E., Devlin, P.F. & Kay, S.A. (1998) Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science, 282, 1488–90.
- Staiger, D., Zecca, L., Wieczorek Kirk, D.A., 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, 361–71.
- Stitt, M. (1996) In Environmental Stress and Photosynthesis, Vol. 3 (ed N. Baker), Academic Press, New York.
- Stitt, M., Bulpin, P.V. & Rees, T. (1978) Pathway of starch breakdown in photosynthetic tissues of Pisum sativum . Biochim. Biophys. Acta, 544, 200–14.
- Stitt, M., Huber, S. & Kerr, P. (1987) In The Biochemistry of Plants, Vol. 10 (eds M.D. Hatch & N.K. Boardman), pp. 327–409, Academic Press, New York.
- Stitt, M. & Krapp, A. (1999) The interaction between elevated carbon dioxide and nitrogen nutrition: the physiological and molecular background. Plant Cell Environ., 22, 583–621.
- Stitt, M., Muller, C., Matt, P., Gibon, Y., Carillo, P., Morcuende, R., Scheible, W.R. & Krapp, A. (2002) Steps towards an integrated view of nitrogen metabolism. J. Exp. Bot., 53, 959–70.
- Storch, K.F., Lipan, O., Leykin, I., Viswanathan, N., Davis, F.C., Wong, W.H. & Weitz, C.J. (2002) Extensive and divergent circadian gene expression in liver and heart. Nature, 417, 78–83.
- Stowe-Evans, E.L., Harper, R.M., Motchoulski, A.V. & Liscum, E. (1998) NPH4, a conditional modulator of auxin-dependent differential growth responses in Arabidopsis . Plant Physiol., 118, 1265–75.
- Stowe-Evans, E.L., Luesse, D.R. & Liscum, E. (2001) The enhancement of phototropin-induced phototropic curvature in Arabidopsis occurs via a photoreversible phytochrome A-dependent modulation of auxin responsiveness. Plant Physiol., 126, 826–34.
- Strayer, C., Oyama, T., Schultz, T.F., Raman, R., Somers, D.E., Mas, P., Panda, S., Kreps, J.A. & Kay, S.A. (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science, 289, 768–71.
- Suarez-Lopez, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F. & Coupland, G. (2001) CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis . Nature, 410, 1116–20.
- Tan, P.K., Downey, T.J., Spitznagel, E.L., Jr., Xu, P., Fu, D., Dimitrov, D.S., Lempicki, R.A., Raaka, B.M. & Cam, M.C. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res., 31, 5676–84.
- Taybi, T., Patil, S., Chollet, R. & Cushman, J.C. (2000) A minimal serine/threonine protein kinase circadianly regulates phosphoenolpyruvate carboxylase activity in crassulacean acid metabolism-induced leaves of the common ice plant. Plant Physiol., 123, 1471–82.
- Thain, S.C., Murtas, G., Lynn, J.R., McGrath, R.B. & Millar, A.J. (2002) The circadian clock that controls gene expression in Arabidopsis is tissue specific. Plant Physiol., 130, 102–10.
- Thain, S.C., Vandenbussche, F., Laarhoven, L.J., Dowson-Day, M.J., Wang, Z.Y., Tobin, E.M., Harren, F.J., Millar, A.J. & Van Der Straeten, D. (2004) Circadian rhythms of ethylene emission in Arabidopsis . Plant Physiol., 136, 3751–61.
- Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L.A., Rhee, S.Y. & Stitt, M. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37, 914–39.
- Tomita, J., Nakajima, M., Kondo, T. & Iwasaki, H. (2004) No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science, 307, 251–54.
- Toth, R., Kevei, E., Hall, A., Millar, A.J., Nagy, F. & Kozma-Bognar, L. (2001) Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis . Plant Physiol., 127, 1607–16.
- Ueda, H.R., Hayashi, S., Chen, W., Sano, M., Machida, M., Shigeyoshi, Y., Iino, M. & Hashimoto, S. (2005) System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat. Genet., 37, 187–92.
- Valverde, F., Mouradov, A., Soppe, W., Ravenscroft, D., Samach, A. & Coupland, G. (2004) Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science, 303, 1003–6.
- Veit, M., Bilger, W., Muhlbauer, T., Brummet, W. & Winter, K. (1996) Diurnal changes in flavonoids. J. Plant Physiol., 148, 478–82.
- Verdonk, J.C., Ric de Vos, C.H., Verhoeven, H.A., Haring, M.A., van Tunen, A.J. & Schuurink, R.C. (2003) Regulation of floral scent production in petunia revealed by targeted metabolomics. Phytochemistry, 62, 997–1008.
- Wang, Z.Y. & Tobin, E.M. (1998) Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell, 93, 1207–17.
- Weckwerth, W., Wenzel, K. & Fiehn, O. (2004) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics, 4, 78–83.
- Weiner, H. & Kaiser, W.M. (1999) 14-3-3 proteins control proteolysis of nitrate reductase in spinach leaves. FEBS Lett., 455, 75–78.
- Woelfle, M.A., Ouyang, Y., Phanvijhitsiri, K. & Johnson, C.H. (2004) The adaptive value of circadian clocks: an experimental assessment in cyanobacteria. Curr. Biol., 14, 1481–6.
- Yanovsky, M.J. & Kay, S.A. (2002) Molecular basis of seasonal time measurement in Arabidopsis . Nature, 419, 308–12.
- Yanovsky, M.J. & Kay, S.A. (2003) Living by the calendar: how plants know when to flower. Nat. Rev. Mol. Cell Biol., 4, 265–75.
- Yoon, H.S., Hackett, J.D., Ciniglia, C., Pinto, G. & Bhattacharya, D. (2004) A molecular timeline for the origin of photosynthetic eukaryotes. Mol. Biol. Evol., 21, 809–18.
- Young, M.W. & Kay, S.A. (2001) Time zones: a comparative genetics of circadian clocks. Nat. Rev. Genet., 2, 702–15.
- Zarembinski, T.I. & Theologis, A. (1994) Ethylene biosynthesis and action: a case of conservation. Plant Mol. Biol., 26, 1579–97.
- Zhang, F., Bartels, M.J. & Stott, W.T. (2004) Quantitation of human glutathione S-transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature peptides. Rapid Commun. Mass. Spectrom, 18, 491–8.
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