Time for circadian rhythms: plants get synchronized

Current Opinion in Plant Biology

Volumn 12, Issue 5, 2009, Pages 574-579

  Más, Paloma ^a   Yanovsky, Marcelo J ^b  

^a CSIC   (Spain)

^b UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA; SPACER DNA; UNTRANSLATED RNA;

ARABIDOPSIS; BIOLOGICAL RHYTHM; CIRCADIAN RHYTHM; FLOWER; GENE EXPRESSION REGULATION; GENETICS; INTRON; LIGHT; METABOLISM; PHYSIOLOGY; PLANT GENE; REVIEW; SIGNAL TRANSDUCTION; TEMPERATURE;

ARABIDOPSIS; BIOLOGICAL CLOCKS; CIRCADIAN RHYTHM; DNA, INTERGENIC; DNA, PLANT; FLOWERS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; INTRONS; LIGHT; RNA, UNTRANSLATED; SIGNAL TRANSDUCTION; TEMPERATURE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 70349546322     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2009.07.010     Document Type: Review

References (63)

1. Wijnen H., and Young M.W. Interplay of circadian clocks and metabolic rhythms. Annu Rev Genet 40 (2006) 409-448
2. Hall A.J.W., and McWatters H.G.E. Endogenous Plant Rhythms (2005), Blackwell Publishing Ltd
3. Harmer S.L. The circadian system in higher plants. Annu Rev Plant Biol 60 (2009) 357-377
4. McClung C.R. Plant circadian rhythms. Plant Cell 18 (2006) 792-803
5. Covington M., Maloof J., Straume M., Kay S.A., and Harmer S. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9 (2008) R130. By integrating the data from multiple Arabidopsis circadian microarrays, the authors identify clock-related elements connected with phase-specific transcript accumulation. Circadian genes were found to be over-represented among plant hormone and stress response pathways, suggesting that all of these pathways are modulated by the circadian clock.
6. Hazen S.P., Naef F., Quisel T., Gendron J., Chen H., Ecker J., Borevitz J., and Kay S. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10 (2009) R17. By using tiling arrays, the authors demonstrate that the circadian clock regulates not only the expression of protein coding genes but also the rhythmic oscillation of introns, intergenic regions and non-coding RNAs.
7. Michael T.P., Breton G., Hazen S.P., Priest H., Mockler T.C., Kay S.A., and Chory J. A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol 6 (2008) e225. In this manuscript, the authors examine the Arabidopsis transcriptome under multiple growth conditions and mutant backgrounds using DNA microarrays. They found that genes related to plant hormones were co-expressed at the time of day when hypocotyl growth is maximal. The authors show that the coincidence of phytohormone signaling with darkness is required to coordinate plant growth.
8. Michael T.P., Mockler T.C., Breton G., McEntee C., Byer A., Trout J.D., Hazen S.P., Shen R., Priest H.D., Sullivan C.M., et al. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4 (2008) e14. In this manuscript, the authors examine global transcriptomic profiles to obtain conclusions about the interplay between thermocycles and photocycles, and their influence on the daily transcription program. The study provides a comprehensive analysis of conserved promoter motifs that might be involved in controlling phase-specific expression.
9. Wang Z.Y., and Tobin E.M. Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93 (1998) 1207-1217
10. Schaffer R., Ramsay N., Samach A., Corden S., Putterill J., Carré I.A., and Coupland G. The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93 (1998) 1219-1229
11. Strayer C. Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289 (2000) 768-771
12. Matsushika A., Makino S., Kojima M., and Mizuno T. 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 (2000) 1002-1012
13. Alabadí D., Oyama T., Yanovsky M.J., Harmon F.G., Más P., and Kay S.A. Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293 (2001) 880-883
14. Stratmann T., and Más P. Chromatin, photoperiod and the Arabidopsis circadian clock: a question of time. Semin Cell Dev Biol 19 (2008) 554-559
15. Perales M., and Más P. A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. Plant Cell 19 (2007) 2111-2123
16. Lu S.X., Knowles S.M., Andronis C., Ong M.S., and Tobin E.M. CIRCADIAN CLOCK ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiol (2009) 10.1104/pp.108.133272
17. Farré E.M., Harmer S.L., Harmon F.G., Yanovsky M.J., and Kay S.A. Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol 15 (2005) 47-54
18. Nakamichi N., Kita M., Ito S., Yamashino T., and 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 (2005) 686-698
19. Salomé P.A., and McClung C.R. PSEUDO-RESPONSE REGULATOR 7 and 9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock. Plant Cell 17 (2005) 791-803
20. Locke J.C., Kozma-Bognar L., Gould P.D., Feher B., Kevei E., Nagy F., Turner M.S., Hall A., and Millar A.J. Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol 2 (2006) 59
21. Ito S., Kawamura H., Niwa Y., Nakamichi N., Yamashino T., and Mizuno T. A genetic study of the Arabidopsis circadian clock with reference to the TIMING OF CAB EXPRESSION 1 (TOC1) gene. Plant Cell Physiol 50 (2009) 290-303
22. Martin-Tryon E.L., Kreps J.A., and Harmer S.L. GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation. Plant Physiol 143 (2007) 473-486
23. McClung C. Comes a time. Curr Opin Plant Biol 11 (2008) 514-520
24. Pruneda-Paz J.L., Breton G., Para A., and Kay S.A. A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323 (2009) 1481-1485. The authors describe a new feedback loop in the Arabidopsis circadian system between the components of the morning loop CCA1 and LHY and a new transcription factor denominated CHE. The study also reports the direct interaction between CHE and TOC1, a component of the evening oscillator in shoots.
25. Henriques R., Jang I.-C., and Chua N.-H. Regulated proteolysis in light-related signaling pathways. Curr Opin Plant Biol 12 (2009) 49-56
26. Más P. Circadian clock function in Arabidopsis thaliana: time beyond transcription. Trends Cell Biol 18 (2008) 273-281
27. Hotta C.T., Gardner M.J., Hubbard K.E., Baek S.J., Dalchau N., Suhita D., Dodd A.N., and Webb A.A.R. Modulation of environmental responses of plants by circadian clocks. Plant Cell Environ 30 (2007) 333-349
28. Yanovsky M.J., and Kay S.A. Signaling networks in the plant circadian system. Curr Opin Plant Biol 4 (2001) 429-435
29. Casal J.J., and Yanovsky M.J. Regulation of gene expression by light. Int J Dev Biol 49 (2005) 501-511
30. Yu J.-W., Rubio V., Lee N.-Y., Bai S., Lee S.-Y., Kim S.-S., Liu L., Zhang Y., Irigoyen M.L., Sullivan J.A., et al. COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol Cell 32 (2008) 617-630. This report sheds some light on the mechanism by which COP1 regulates flowering time and circadian rhythms. The authors describe that light antagonizes COP1 activity in the nucleus, where modulates GI protein stability through an interaction facilitated by the clock and flowering-related component ELF3.
31. Michael T.P., Salome P.A., and McClung C.R. Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proc Natl Acad Sci U S A 100 (2003) 6878-6883
32. Mazzella M.A., Bertero D., and Casal J.J. Temperature-dependent internode elongation in vegetative plants of Arabidopsis thaliana lacking phytochrome B and cryptochrome 1. Planta 210 (2000) 497-501
33. Halliday K.J., and Whitelam G.C. Changes in photoperiod or temperature alter the functional relationships between phytochromes and reveal roles for PHYD and PHYE. Plant Physiol 131 (2003) 1913-1920
34. Yamashino T., Ito S., Niwa Y., Kunihiro A., Nakamichi N., and Mizuno T. Involvement of Arabidopsis clock-associated pseudo-response regulators in diurnal oscillations of gene expression in the presence of environmental time cues. Plant Cell Physiol 49 (2008) 1839-1850
35. Salomé P.A., Xie Q., and McClung C.R. Circadian timekeeping during early Arabidopsis development. Plant Physiol 147 (2008) 1110-1125
36. Davidson A.J., Castanon-Cervantes O., Leise T.L., Molyneux P.C., and Harrington M.E. Visualizing jet lag in the mouse suprachiasmatic nucleus and peripheral circadian timing system. S Eur J Neurosci 29 (2009) 171-180
37. James A.B., Monreal J.A., Nimmo G.A., Kelly C.L., Herzyk P., Jenkins G.I., and Nimmo H.G. The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots. Science 322 (2008) 1832-1835. This manuscript reports for the first time the existence of different oscillators in shoots and roots of Arabidopsis plants. The root clock lacks the canonical evening loop found in shoots. The authors also propose that a photosynthesis-related signal from shoots is involved in the synchronization of the morning loop in roots.
38. Hall A., Kozma-Bognar L., Bastow R.M., Nagy F., and Millar A.J. Distinct regulation of CAB and PHYB gene expression by similar circadian clocks. Plant J 32 (2002) 529-537
39. Thain S.C., Murtas G., Lynn J.R., McGrath R.B., and Millar A.J. The circadian clock that controls gene expression in Arabidopsis is tissue specific. Plant Physiol 130 (2002) 102-110
40. Pitts S., Perone E., and Silver R. Food-entrained circadian rhythms are sustained in arrhythmic Clk/Clk mutant mice. Am J Physiol Regul Integr Comp Physiol 285 (2003) R57-R67
41. Mohawk J.A., Baer M.L., and Menaker M. The methamphetamine-sensitive circadian oscillator does not employ canonical clock genes. Proc Natl Acad Sci U S A 106 (2009) 3519-3524
42. Dodd A.N., Salathia N., Hall A., Kevei E., Toth R., Nagy F., Hibberd J.M., Millar A.J., and Webb A.A. Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309 (2005) 630-633
43. Green R.M., Tingay S., Wang Z.Y., and Tobin E.M. Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol 129 (2002) 576-584
44. 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. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 302 (2003) 1049-1053
45. Ni Z., Kim E.-D., Ha M., Lackey E., Liu J., Zhang Y., Sun Q., and Chen Z.J. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457 (2009) 327-331. The authors show that the increased growth vigour seen in Arabidopsis hybrids and allotetraploids is caused by enhanced chlorophyll and starch accumulation resulting from alterations in the expression of clock genes. Thus, the circadian regulation of physiological and metabolic pathways has a prominent role in the control of biomass production.
46. Kant P., Gordon M., Kant S., Zolla G., Davydov O., Heimer Y.M., Chalifa-Caspi V., Shaked R., and Barak S. Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses. Plant Cell Environ 31 (2008) 697-714
47. Covington M.F., and Harmer S.L. The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5 (2007) e222. By using transcriptome analysis, the authors show that the circadian clock regulates auxin signaling pathways by modulating the plant sensitivity to this plant hormone. The circadian clock also modulates the growth responses controlled by exogenous auxin.
48. Mizuno T., and Yamashino T. Comparative transcriptome of diurnally oscillating genes and hormone-responsive genes in Arabidopsis thaliana: insight into circadian clock-controlled daily responses to common ambient stresses in plants. Plant Cell Physiol 49 (2008) 481-487. A comprehensive analysis of global transcriptome data unravels the connection between the circadian clock and plant responses to environmental stresses mostly mediated by abscisic acid and methyl jasmonate.
49. Bancos S., Szatmari A.-M., Castle J., Kozma-Bognar L., Shibata K., Yokota T., Bishop G.J., Nagy F., and Szekeres M. Diurnal regulation of the brassinosteroid-biosynthetic CPD gene in Arabidopsis. Plant Physiol 141 (2006) 299-309
50. Blázquez M.A., Trenor M., and Weigel D. Independent control of gibberellin biosynthesis and flowering time by the circadian clock in Arabidopsis. Plant Physiol 130 (2002) 1770-1775
51. Jouve L., Gaspar T., Kevers C., Greppin H., and Degli Agosti R. Involvement of indole-3-acetic acid in the circadian growth of the first internode of Arabidopsis. Planta 209 (1999) 136-142
52. Thain S.C., Vandenbussche F., Laarhoven L.J., Dowson-Day M.J., Wang Z.Y., Tobin E.M., Harren F.J., Millar A.J., and Straeten D. Circadian rhythms of ethylene emission in Arabidopsis. Plant Physiol 136 (2004) 3751-3761
53. Hanano S., Domagalska M.A., Nagy F., and Davis S.J. Multiple phytohormones influence distinct parameters of the plant circadian clock. Genes to Cells 11 (2006) 1381-1392
54. Salome P.A., To J.P.C., Kieber J.J., and McClung C.R. Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period. Plant Cell 18 (2006) 55-69
55. Nakamichi N., Kusano M., Fukushima A., Kita M., Ito S., Yamashino T., Saito K., Sakakibara H., and Mizuno T. Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol 50 (2009) 447-462
56. Bieniawska Z., Espinoza C., Schlereth A., Sulpice R., Hincha D.K., and Hannah M.A. Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol 147 (2008) 263-279
57. Fowler S.G., Cook D., and Thomashow M.F. Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 137 (2005) 961-968
58. Franklin K.A., and Whitelam G.C. Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat Genet 39 (2007) 1410-1413
59. Blasing O.E., Gibon Y., Gunther M., Hohne M., Morcuende R., Osuna D., Thimm O., Usadel B., Scheible W.-R., and Stitt M. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17 (2005) 3257-3281
60. Gutiérrez R.A., Stokes T.L., Thum K., Xu X., Obertello M., Katari M.S., Tanurdzic M., Dean A., Nero D.C., McClung C.R., et al. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A 105 (2008) 4939-4944. This article reports the implication of CCA1 in nitrogen assimilation. The regulation of CCA1 by glutamate (or a glutamate-derived metabolite) also modulates the expression of key nitrogen assimilatory genes.
61. Usadel B., Blasing O.E., Gibon Y., Retzlaff K., Hohne M., Gunther M., and Stitt M. Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol 146 (2008) 1834-1861
62. Gibon Y., Usadel B., Blaesing O., Kamlage B., Hoehne M., Trethewey R., and Stitt M. Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol 7 (2006) R76
63. 2+ oscillations. The study also connects cADPR with clock function and with the regulation of essential clock genes.