Woelfle, M. A., Ouyang, Y., Phanvijhitsiri, K. & Johnson, C. H. The adaptive value of circadian clocks?: an experimental assessment in Cyanobacteria. Curr. Biol. 14, 1481–1486 (2004)
Dodd, A. N. et al. Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309, 630–633 (2005)
Harmer, S. L. The circadian system in higher plants. Annu. Rev. Plant Biol. 60, 357–377 (2009)
Bass, J. Circadian topology of metabolism. Nature 491, 348–356 (2012)
Harmer, S. L. et al. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110–2113 (2000)
Lu, Y., Gehan, J. P. & Sharkey, T. D. Daylength and circadian effects on starch degradation and maltose metabolism. Plant Physiol. 138, 2280–2291 (2005)
Graf, A., Schlereth, A., Stitt, M. & Smith, A. M. Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proc. Natl Acad. Sci. USA 107, 9458–9463 (2010)
Noordally, Z. B. et al. Circadian control of chloroplast transcription by a nuclear-encoded timing signal. Science 339, 1316–1319 (2013)
Knight, H., Thomson, A. J. W. & McWatters, H. G. SENSITIVE TO FREEZING6 integrates cellular and environmental inputs to the plant circadian clock. Plant Physiol. 148, 293–303 (2008)
Dalchau, N. et al. The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. Proc. Natl Acad. Sci. USA 108, 5104–5109 (2011)
Bläsing, O. E. et al. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis . Plant Cell 17, 3257–3281 (2005)
Koussevitzky, S. et al. Signals from chloroplasts converge to regulate nuclear gene expression. Science 316, 715–719 (2007)
Lai, A. G. et al. CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc. Natl Acad. Sci. USA 109, 17129–17134 (2012)
Johnson, C. H. in Circadian Clocks from Cell to Human (eds Hiroshige, T. & Honma, K. ) 209–249 (Hokkaido Univ. Press, 1992)
Michael, T. P., Salomé, P. A. & McClung, C. R. Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proc. Natl Acad. Sci. USA 100, 6878–6883 (2003)
Nakamichi, N. et al. PSEUDO-RESPONSE REGULATORS 9, 7 and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell 22, 594–605 (2010)
Gould, P. D. et al. Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants. Plant J. 58, 893–901 (2009)
Moore, B. et al. Role of the Arabidopsis glucose sensor HXK1 in nutrient, light, and hormonal signaling. Science 300, 332–336 (2003)
Kato, T. et al. Mutants of circadian-associated PRR genes display a novel and visible phenotype as to light responses during de-etiolation of Arabidopsis thaliana seedlings. Biosci. Biotechnol. Biochem. 71, 834–839 (2007)
Fukushima, A. et al. Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proc. Natl Acad. Sci. USA 106, 7251–7256 (2009)
Nakamichi, N. et al. Transcriptional repressor PRR5 directly regulates clock-output pathways. Proc. Natl Acad. Sci. USA 109, 17123–17128 (2012)
Damiola, F. et al. Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. Genes Dev. 14, 2950–2961 (2000)
Stokkan, K.-A., Yamazaki, S., Tei, H., Sakaki, Y. & Menaker, M. Entrainment of the circadian clock in the liver by feeding. Science 291, 490–493 (2001)
James, A. B. et al. The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots. Science 322, 1832–1835 (2008)
Johnson, C. H., Kondo, T. & Hastings, J. W. Action spectrum for resetting the circadian phototaxis rhythm in the CW15 strain of Chlamydomonas . Plant Physiol. 97, 1122–1129 (1991)
Nakamichi, N., Kita, M., Ito, S., Yamashino, T. & Mizuno, T. PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana . Plant Cell Physiol. 46, 686–698 (2005)
Para, A. et al. PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell 19, 3462–3473 (2007)
Park, D. H. Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285, 1579–1582 (1999)
Jarillo, J. A. et al. An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature 410, 487–490 (2001)
Cho, Y.-H. & Yoo, S.-D. Signaling role of fructose mediated by FINS1/FBP in Arabidopsis thaliana . PLoS Genet. 7, e1001263 (2011)
González-Guzmán, M. et al. The short-chain alcohol dehydrogenase ABA2 catalyzes the conversion of xanthoxin to abscisic aldehyde. Plant Cell 14, 1833–1846 (2002)
Xiong, L., Ishitani, M., Lee, H. & Zhu, J. K. The Arabidopsis LOS5/ABA3 locus encodes a molybdenum cofactor sulfurase and modulates cold stress- and osmotic stress-responsive gene expression. Plant Cell 13, 2063–2083 (2001)
Leung, J. et al. Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase. Science 264, 1448–1452 (1994)
Gibson, S. I., Laby, R. J. & Kim, D. The sugar-insensitive1 (sis1) mutant of Arabidopsis is allelic to ctr1 . Biochem. Biophys. Res. Commun. 280, 196–203 (2001)
Lehman, A., Black, R. & Ecker, J. R. HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. Cell 85, 183–194 (1996)
Reed, J. W., Nagatani, A., Elich, T. D., Fagan, M. & Chory, J. Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol. 104, 1139–1149 (1994)
Ahmad, M. & Cashmore, A. R. HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 366, 162–166 (1993)
Oyama, T., Shsimura, Y. & Okada, K. The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev. 11, 2983–2995 (1997)
Deng, X. W. et al. COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a Gβ homologous domain. Cell 71, 791–801 (1992)
Hudson, M. E., Lisch, D. R. & Quail, P. H. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J. 34, 453–471 (2003)
Ni, M., Tepperman, J. M. & Quail, P. H. PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95, 657–667 (1998)
Jacobsen, S. E., Binkowski, K. A. & Olszewski, N. E. SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis . Proc. Natl Acad. Sci. USA 93, 9292–9296 (1996)
Talke, I. N., Hanikenne, M. & Krämer, U. Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis halleri . Plant Physiol. 142, 148–167 (2006)
Porra, R. J., Thompson, W. A. & Kreidemann, P. E. Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochim. Biophys. Acta 975, 384–394 (1989)
Kwak, J. M. et al. NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis . EMBO J. 22, 2623–2633 (2003)