References
- 1Dodd, AN, Belbin, FE, Frank, A and Webb, AAR. Interactions between circadian clocks and photosynthesis for the temporal and spatial coordination of metabolism. Frontiers in Plant Science. 2015; 6: 245. DOI: 10.3389/fpls.2015.00245
- 2Grundy, J, Stoker, C and Carré, IA. Circadian regulation of abiotic stress tolerance in plants. Frontiers in Plant Science. 2015; 6: 1–15. DOI: 10.3389/fpls.2015.00648
- 3Yazdanbakhsh, N, Sulpice, R, Graf, A, Stitt, M and Fisahn, J. Circadian control of root elongation and C partitioning in Arabidopsis thaliana. Plant, Cell and Environment. 2011; 34: 877–894. DOI: 10.1111/j.1365-3040.2011.02286.x
- 4Dodd, AN. Plant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage. Science. 2005; 309: 630–633. DOI: 10.1126/science.1115581
- 5Green, RM, Tingay, S, Wang, ZY and Tobin, EM. Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant physiology. 2002; 129: 576–584. DOI: 10.1104/pp.004374
- 6Davis, SJ and Millar, AJ. Watching the hands of the Arabidopsis biological clock. Genome biology. 2001; 2: 1008.1–1008.4. DOI: 10.1186/gb-2001-2-3-reviews1008
- 7Turek, FW, Joshu, C, Kohsaka, A, Lin, E, Ivanova, G, Mcdearmon, E, et al. Obesity and Metabolic Syndrome in Circadian Clock Mutant Mice. Science. 2005; 308: 1043–1045. DOI: 10.1126/science.1108750
- 8Bell-Pedersen, D, Shinohara, ML, Loros, JJ and Dunlap, JC. Circadian clock controlled genes isolated from Neurospora crassa are late night to early morning-specific. Proceedings of the National Academy of Sciences. 1996; 93: 13096–13101. DOI: 10.1073/pnas.93.23.13096
- 9Guo, F, Yu, J, Jung, HJ, Abruzzi, KC, Luo, W, Griffith, LC, et al. Circadian neuron feedback controls the Drosophila sleep-activity profile. Nature. 2016; 536: 292–297. DOI: 10.1038/nature19097
- 10Welkie, DG, Rubin, BE, Chang, YG, Diamond, S, Rifkin, SA, LiWang, A, et al. Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA. Proceedings of the National Academy of Sciences. 2018; 115: E7174–E7183. DOI: 10.1073/pnas.1802940115
- 11De Caluwé, J, Xiao, Q, Hermans, C, Verbruggen, N, Leloup, JC and Gonze, D. A Compact Model for the Complex Plant Circadian Clock. Frontiers in Plant Science. 2016; 7: 1–15. DOI: 10.3389/fpls.2016.00074
- 12Fogelmark, K and Troein, C. Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock. PLoS Computational Biology. 2014; 10:
e1003705 . DOI: 10.1371/journal.pcbi.1003705 - 13Pokhilko, A, Mas, P and Millar, AJ. Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. BMC Systems Biology. 2013; 7: 23. DOI: 10.1186/1752-0509-7-23
- 14Rust, MJ, Markson, JS, Lane, WS, Fisher, DS and O’Shea, EK.
Ordered phospho rylation governs oscillation of a three-protein circadian clock . Science (New York, NY). 2007; 318: 809–12. DOI: 10.1126/science.1148596 - 15Kurosawa, G, Aihara, K and Iwasa, Y. A Model for the Circadian Rhythm of Cyanobacteria that Maintains Oscillation without Gene Expression. Biophysical Journal. 2006; 91: 2015–2023. DOI: 10.1529/biophysj.105.076554
- 16Lerner, I, Bartok, O, Wolfson, V, Menet, JS, Weissbein, U, Afik, S, et al. Clk post-transcriptional control denoises circadian transcription both temporally and spatially. Nature Communications. 2015; 6: 7056. DOI: 10.1038/ncomms8056
- 17Fathallah-Shaykh, HM, Bona, JL and Kadener, S. Mathematical model of the Drosophila circadian clock: loop regulation and transcriptional integration. Biophysical journal. 2009; 97: 2399–408. DOI: 10.1016/j.bpj.2009.08.018
- 18Bellman, J, Kim, JK, Lim, S and Hong, CI. Modeling Reveals a Key Mechanism for Light-Dependent Phase Shifts of Neurospora Circadian Rhythms. Biophysical Journal. 2018; 115: 1093–1102. DOI: 10.1016/j.bpj.2018.07.029
- 19Crosthwaite, SK, Loros, JJ and Dunlap, JC. Light-Induced Resetting of a Circadian Clock Is Mediated by a Rapid Increase in frequency Transcript. Cell. 1995; 81: 1003–1012. DOI: 10.1016/S0092-8674(05)80005-4
- 20Reló Gio, A, Westermark, PO, Wallach, T, Schellenberg, K and Kramer, A. Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops. PLoS Comput Biol. 2011; 7:
e1002309 . DOI: 10.1371/journal.pcbi.1002309 - 21Geier, F, Becker-Weimann, S, Kramer, A and Herzel, H. Entrainment in a Model of the Mammalian Circadian Oscillator. J Biol Rhythms. 2005; 20: 83–93. DOI: 10.1177/0748730404269309
- 22Podkolodnaya, OA, Tverdokhleb, NN and Podkolodnyy, NL. Computational modeling of the cell-autonomous mammalian circadian oscillator. BMC Systems Biology. 2017; 11: 27–42. DOI: 10.1186/s12918-016-0379-8
- 23Hevia, MA, Canessa, P and Larrondo, LF. Circadian clocks and the regulation of virulence in fungi: Getting up to speed. Seminars in Cell & Developmental Biology. 2016; 57: 147–155. DOI: 10.1016/j.semcdb.2016.03.021
- 24Bujdoso, N and Davis, SJ. Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana. Frontiers in Plant Science. 2013; 4: 1–8. DOI: 10.3389/fpls.2013.00003
- 25Hogenesch, JB and Ueda, HR. Understanding systems-level properties: Timely stories from the study of clocks. Nature Reviews Genetics. 2011; 12: 407–416. DOI: 10.1038/nrg2972
- 26Bell-Pedersen, D, Cassone, VM, Earnest, DJ, Golden, SS, Hardin, PE, Thomas, TL, et al. Circadian rhythms from multiple oscillators: Lessons from diverse organisms. Nature Reviews Genetics. 2005; 6: 544–556. DOI: 10.1038/nrg1633
- 27Pokhilko, A, Fernández, AP, Edwards, KD, Southern, MM, Halliday, KJ and Millar, AJ. The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Molecular Systems Biology. 2012; 8: 574. DOI: 10.1038/msb.2012.6
- 28Pokhilko, A, Hodge, SK, Stratford, K, Knox, K, Edwards, KD, Thomson, AW, et al. Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Molecular Systems Biology. 2010; 6: 416. DOI: 10.1038/msb.2010.69
- 29Herrero, E, Kolmos, E, Bujdoso, N, Yuan, Y, Wang, M, Berns, MC, et al. EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. The Plant cell. 2012; 24: 428–43. DOI: 10.1105/tpc.111.093807
- 30Kolmos, E, Nowak, M, Werner, M, Fischer, K, Schwarz, G, Mathews, S, et al. Integrating ELF4 into the circadian system through combined structural and functional studies. HFSP journal. 2009; 3: 350–66. DOI: 10.2976/1.3218766
- 31Zeilinger, MN, Farré, EM, Taylor, SR, Kay, SA and Doyle, FJ. A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9. Molecular Systems Biology. 2006; 2: 58. DOI: 10.1038/msb4100101
- 32Locke, JCW, Kozma-Bognár, L, Gould, PD, Fehér, B, Kevei, É, Nagy, F, et al. Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Molecular Systems Biology. 2006; 2: 59. DOI: 10.1038/msb4100102
- 33Locke, JCW, Southern, MM, Kozma-Bognár, L, Hibberd, V, Brown, PE, Turner, MS, et al. Extension of a genetic network model by iterative experimentation and mathematical analysis. Molecular Systems Biology. 2005; 1: 0013. DOI: 10.1038/msb4100018
- 34Locke, JCW, Millar, AJ and Turner, MS. Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. Journal of Theoretical Biology. 2005; 234: 383–393. DOI: 10.1016/j.jtbi.2004.11.038
- 35Shin, J and Davis, SJ. Recent advances in computational modeling as a conduit to understand the plant circadian clock. F1000 biology reports. 2010; 2: 5–8. DOI: 10.3410/B2-49
- 36Harmer, SL. The Circadian System in Higher Plants. Annual Review of Plant Biology. 2009; 60: 357–377. DOI: 10.1146/annurev.arplant.043008.092054
- 37Johnson, CH, Elliott, JA and Foster, R. Entrainment of circadian programs. Chronobiology International. 2003; 20: 741–774. DOI: 10.1081/CBI-120024211
- 38Millar, AJ. The Intracellular Dynamics of Circadian Clocks Reach for the Light of Ecology and Evolution. Annual Review of Plant Biology. 2016; 67: 595–618. DOI: 10.1146/annurev-arplant-043014-115619
- 39Hsu, PY and Harmer, SL. Wheels within wheels: The plant circadian system. Trends in Plant Science. 2014; 19: 240–249. DOI: 10.1016/j.tplants.2013.11.007
- 40Gould, PD, Locke, JCW, Larue, C, Southern, MM, Davis, SJ, Hanano, S, et al. The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell. 2006; 18: 1177–1187. DOI: 10.1105/tpc.105.039990
- 41Edwards, K, Anderson, P, Hall, A, Salathia, N, Locke, J, Lynn, J, et al. FLOWERING LOCUS C Mediates Natural Variation in the High-Temperature Response of the Arabidopsis Circadian Clock. The Plant cell. 2006; 18: 639–650. DOI: 10.1105/tpc.105.038315
- 42Jones, MA, Morohashi, K, Grotewold, E and Harmer, SL. Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation. Frontiers in Plant Science. 2019; 10: 57. DOI: 10.3389/fpls.2019.00057
- 43Gould, PD, Ugarte, N, Domijan, M, Costa, M, Foreman, J, MacGregor, D, et al. Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Molecular Systems Biology. 2013; 9: 650. DOI: 10.1038/msb.2013.7
- 44Wigge, PA. Ambient temperature signalling in plants. 2013; 16: 661–666. DOI: 10.1016/j.pbi.2013.08.004
- 45Akman, OE, Locke, JCW, Tang, S, Carré, I, Millar, AJ and Rand, DA. Isoform switching facilitates period control in the Neurospora crassa circadian clock. Molecular Systems Biology. 2008; 4: 164. DOI: 10.1038/msb.2008.28
- 46Ruoff, P, Zakhartsev, M and Westerhoff, HV. Temperature compensation through systems biology. FEBS Journal. 2007; 274: 940–950. DOI: 10.1111/j.1742-4658.2007.05641.x
- 47Ruoff, P and Rensing, L. The temperature-compensated goodwin model simulates many circadian clock properties. Journal of Theoretical Biology. 1996; 179: 275–285. DOI: 10.1006/jtbi.1996.0067
- 48Ruoff, P. Introducing temperature-compensation in any reaction kinetic oscillator model. Journal of Interdisiplinary Cycle Research. 1992; 23: 92–99. DOI: 10.1080/09291019209360133
- 49Leloup, JC and Goldbeter, A. Temperature Compensation of Circadian Rhythms: Control of the Period in a Model for Circadian Oscillations of the Per Protein in Drosophila. Chronobiology International. 1997; 14: 511–520. DOI: 10.3109/07420529709001472
- 50Nagao, R, Epstein, IR, Gonzalez, ER and Varela, H. Temperature (over)compensation in an oscillatory surface reaction. Journal of Physical Chemistry A. 2008; 112: 4617–4624. DOI: 10.1021/jp801361j
- 51Kolmos, E, Herrero, E, Bujdoso, N, Millar, AJ, Tóth, R, Gyula, P, et al. A Reduced-Function Allele Reveals That EARLY FLOWERING3 Repressive Action on the Circadian Clock Is Modulated by Phytochrome Signals in Arabidopsis. The Plant Cell. 2011; 23: 3230–3246. DOI: 10.1105/tpc.111.088195
- 52Ruoff, P, Vinsjevik, M and Rensing, L. Temperature compensation in biological oscillators: a challenge for joint experimental and theoretical analysis. Comments Theor Biol. 2000; 5: 361–382.
- 53Salomé, PA, Weigel, D and McClung, CR. The role of the Arabidopsis morning loop components CCA1, LHY, PRR7, and PRR9 in temperature compensation. The Plant cell. 2010; 22: 3650–61. DOI: 10.1105/tpc.110.079087
- 54Sidaway-Lee, K, Costa, MJ, Rand, DA, Finkenstadt, B and Penfield, S. Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response. Genome Biology. 2014; 15: R45. DOI: 10.1186/gb-2014-15-3-r45
- 55Blair, EJ, Bonnot, T, Hummel, M, Hay, E, Marzolino, JM and Quijada, IA, et al. Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis. Scientific Reports. 2019; 9: 4814. DOI: 10.1038/s41598-019-41234-w
- 56Ripel, L, Wendell, M, Rognli, OA, Torre, S, Lee, Y and Olsen, JE. Thermoperiodic Control of Floral Induction Involves Modulation of the Diurnal FLOWERING LOCUS T Expression Pattern. Plant and Cell Physiology. 2017; 58: 466–477. DOI: 10.1093/pcp/pcw221
- 57Bours, R, van Zanten, M, Pierik, R, Bouwmeester, H and van der Krol, A. Antiphase Light and Temperature Cycles Affect PHYTOCHROME B-Controlled Ethylene Sensitivity and Biosynthesis, Limiting Leaf Movement and Growth of Arabidopsis. 2013; 163: 882–895. DOI: 10.1104/pp.113.221648
- 58De Caluwé, J, de Melo, JRF, Tosenberger, A, Hermans, C, Verbruggen, N, Leloup, JC, et al. Modeling the photoperiodic entrainment of the plant circadian clock. Journal of Theoretical Biology. 2017; 420: 220–231. DOI: 10.1016/j.jtbi.2017.03.005
- 59Davis, AM, Ronald, J, Ma, Z, Wilkinson, AJ, Philippou, K, Shindo, T, et al. HSP90 Contributes to Entrainment of the Arabidopsis Circadian Clock via the Morning Loop. Genetics. 2018; 210: 1383–1390. DOI: 10.1534/genetics.118.301586
- 60Somers, DE, Webb, AA, Pearson, M and Kay, SA. The short-period mutant, toc1-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana. 1998; 125: 485–494.
- 61Boikoglou, E, Ma, Z, von Korff, M, Davis, AM, Nagy, F and Davis, SJ. Environmental Memory from a Circadian Oscillator: The Arabidopsis thaliana Clock Differentially Integrates Perception of Photic vs. Thermal Entrainment. 2011; 189: 655–664. DOI: 10.1534/genetics.111.131417
- 62Salomé, PA and McClung, CR. PSEUDO-RESPONSE REGULATOR 7 and 9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock. Plant Cell. 2005; 17: 791–803. DOI: 10.1105/tpc.104.029504
