A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9

Molecular Systems Biology

Volumn 2, Issue , 2006, Pages

  Zeilinger, Melanie N ^a,c   Farré, Eva M ^b   Taylor, Stephanie R ^a   Kay, Steve A ^b   Doyle III, Francis J ^a  

^a University of California   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF STUTTGART   (Germany)

Author keywords

Arabidopsis; Circadian rhythms; Mathematical modeling; Parameter optimization; Sensitivity analysis

Indexed keywords

PROTEIN; PROTEIN PRR7; PROTEIN PRR9; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CCA1; TRANSCRIPTION FACTOR LHY; TRANSCRIPTION FACTOR TOC1; UNCLASSIFIED DRUG; APRR7 PROTEIN, ARABIDOPSIS; APRR9 PROTEIN, ARABIDOPSIS; ARABIDOPSIS PROTEIN; DNA BINDING PROTEIN; LHY PROTEIN, ARABIDOPSIS;

ARABIDOPSIS; ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; EXPERIMENT; FEEDBACK SYSTEM; GENE EXPRESSION; GENE EXPRESSION REGULATION; HYPOTHESIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR GENETICS; NONHUMAN; PHENOTYPE; PLANT; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; TECHNIQUE; VALIDATION PROCESS; BIOLOGICAL MODEL; BIOLOGICAL RHYTHM; BIOLOGY; COMPUTER SIMULATION; EVALUATION; LIGHT; PHYSIOLOGY; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION;

ANIMALIA; ARABIDOPSIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOLOGICAL CLOCKS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA-BINDING PROTEINS; LIGHT; MODELS, BIOLOGICAL; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 33846085492     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100101     Document Type: Article

References (59)

1. Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293: 880-883
2. Alabadi D, Yanovsky MJ, Mas P, Harmer SL, Kay SA (2002) Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Curr Biol 12: 757-761
3. Covington MF, Panda S, Liu XL, Strayer CA, Wagner DR, Kay SA (2001) ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell 13: 1305-1315
4. Csete ME, Doyle JC (2002) Reverse engineering of biological complexity. Science 295: 1664-1669
5. Devlin PF, Kay SA (2000) Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. Plant Cell 12: 2499-2510
6. Ditty JL, Williams SB, Golden SS (2003) A cyanobacterial circadian timing mechanism. Annu Rev Genet 37: 513-543
7. Doyle JC, Francis BA, Tannenbaum AR (1992) Feedback Control Theory. New York, USA: Macmillan Publishing Company
8. Doyle MR, Davis SJ, Bastow RM, McWatters HG, Kozma-Bognar L, Nagy F, Millar AJ, Amasino RM (2002) The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419: 74-77
9. Dunlap JD, Loros JJ, DeCoursey PJ (eds.) (2004) Chronobiology: Biological Timekeeping. Sunderland, MA: Sinauer Associates, Inc.
10. Farre EM, Harmer SL, Harmon FG, Yanovsky MJ, Kay SA (2005) Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol 15: 47-54
11. Forger DB, Peskin CS (2003) A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci USA 100: 14806-14811
12. Glass L, Kauffman SA (1973) The logical analysis of continuous, nonlinear biochemical control networks. J Theor Biol 39: 103-129
13. Gould PD, Locke JC, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R, Putterill J, Millar AJ, Hall A (2006) The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell 18: 1177-1187
14. Gutierrez RA, Ewing RM, Cherry JM, Green PJ (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: 11513-11518
15. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110-2113
16. Harmer SL, Panda S, Kay SA (2001) Molecular bases of circadian rhythms. Annu Rev Cell Dev Biol 17: 215-253
17. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA (2005) LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci USA 102: 10387-10392
18. Hicks KA, Albertson TM, Wagner DR (2001) EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis. Plant Cell 13: 1281-1292
19. Hicks KA, Millar AJ, Carre IA, Somers DE, Straume M, Meeks-Wagner DR, Kay SA (1996) Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274: 790-792
20. Ingalls BP (2004) Autonomously oscillating biochemical systems: parametric sensitivity of extrema and period. IEE Systems Biol 1: 62-70
21. Ito S, Nakamichi N, Matsushika A, Fujimori T, Yamashino T, 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
22. Kitano H (2002) Systems biology: a brief overview. Science 295: 1662-1664
23. Kramer M, Rabitz H, JM C (1984) Sensitivity analysis of oscillatory systems. Appl Math Mod 8: 328-340
24. Leloup JC, Goldbeter A (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci USA 100: 7051-7056
25. Leloup JC, Gonze D, Goldbeter A (1999) Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora. J Biol Rhythms 14: 433-448
26. Levine W (1996) The Control Handbook. Boca Raton, FL: CRC Press
27. Lidder P, Gutierrez RA, Salome PA, McClung CR, Green PJ (2005) Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. Plant Physiol 138: 2374-2385
28. Locke JCW, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ (2005a) Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 1: 13
29. Locke JCW, Millar AJ, Turner MS (2005b) Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. J Theor Biol 234: 383-393
30. Locke JCW, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ (2006) Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol 2: 59
31. Makino S, Matsushika A, Kojima M, Oda Y, Mizuno T (2001) Light response of the circadian waves of the APRR1/TOC1 quintet: when does the quintet start singing rhythmically in Arabidopsis? Plant Cell Physiol 42: 334-339
32. Mas P, Alabadi D, Yanovsky MJ, Oyama T, Kay SA (2003a) Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis. Plant Cell 15: 223-236
33. Mas P, Kim WY, Somers DE, Kay SA (2003b) Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426: 567-570
34. McWatters HG, Bastow RM, Hall A, Millar AJ (2000) The ELF3 zeitnehmer regulates light signalling to the circadian clock. Nature 408: 716-720
35. Millar AJ (2003) A suite of photoreceptors entrains the plant circadian clock. J Biol Rhythms 18: 217-226
36. Millar AJ, Straume M, Chory J, Chua NH, Kay SA (1995) The regulation of circadian period by phototransduction pathways in Arabidopsis. Science 267: 1163-1166
37. Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, Song HR, Carre IA, Coupland G (2002) LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev Cell 2: 629-641
38. Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H (2002) Robustness as a measure of plausibility in models of biochemical networks. J Theor Biol 216: 19-30
39. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15: 473-497
40. Nakamichi N, Ito S, Oyama T, Yamashino T, Kondo T, Mizuno T (2004) Characterization of plant circadian rhythms by employing Arabidopsis cultured cells with bioluminescence reporters. Plant Cell Physiol 45: 57-67
41. Novak B, Tyson JJ (1997) Modeling the control of DNA replication in fission yeast. Proc Natl Acad Sci USA 94: 9147-9152
42. Onai K, Ishiura M (2005) PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes Cells 10: 963-972
43. Plautz JD, Straume M, Stanewsky R, Jamison CF, Brandes C, Dowse HB, Hall JC, Kay SA (1997) Quantitative analysis of Drosophila period gene transcription in living animals. J Biol Rhythms 12: 204-217
44. Rand DA, Shulgin BV, Salazar D, Millar AJ (2004) Design principles underlying circadian clocks. J Roy Soc Interface 1: 19-30
45. Ruoff P, Vinsjevik M, Monnerjahn C, Rensing L (2001) The Goodwin model: simulating the effect of light pulses on the circadian sporulation rhythm of Neurospora crassa. J Theor Biol 209: 29-42
46. Salome PA, McClung CR (2004) The Arabidopsis thaliana clock. J Biol Rhythms 19: 425-435
47. Salome PA, McClung CR (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
48. Savageau MA (1971) Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 229: 542-544
49. Smolen P, Baxter DA, Byrne JH (2000) Mathematical modeling of gene networks. Neuron 26: 567-580
50. Smolen P, Hardin PE, Lo BS, Baxter DA, Byrne JH (2004) Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK. Biophys J 86: 2786-2802
51. Somers DE, Schultz TF, Milnamow M, Kay SA (2000) ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis. Cell 101: 319-329
52. Somers DE, Kim WY, Geng R (2004) The F-box protein ZEITLUPE confers dosage-dependent control on the circadian clock, photomorphogenesis, and flowering time. Plant Cell 16: 769-782
53. Stanewsky R (2003) Genetic analysis of the circadian system in Drosophila melanogaster and mammals. J Neurobiol 54: 111-147
54. Stelling J, Gilles ED, Doyle III FJ (2004) Robustness properties of circadian clock architectures. Proc Natl Acad Sci USA 101: 13210-13215
55. Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Mas P, Panda S, Kreps JA, Kay SA (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289: 768-771
56. Tomlin CJ, Axelrod JD (2005) Understanding biology by reverse engineering the control. Proc Natl Acad Sci USA 102: 4219-4220
57. Tyson JJ, Hong CI, Thron CD, Novak B (1999) A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys J 77: 2411-2417
58. Varma A, Morbidelli M, Wu H (1999) Parametric Sensitivity in Chemical Systems. Cambridge, UK: Cambridge University Press
59. Weicker K (2002) Evolutionäre Algorithmen. Germany: Teubner, Stuttgart