Beyond Arabidopsis: The circadian clock in non-model plant species

Seminars in Cell and Developmental Biology

Volumn 24, Issue 5, 2013, Pages 430-436

  McClung, C Robertson ^a  

^a Dartmouth College   (United States)

Author keywords

Circadian clock; Circadian rhythms

Indexed keywords

PROTEIN HISTIDINE KINASE; TRANSCRIPTION FACTOR CCA1; TRANSCRIPTION FACTOR LHY; TRANSCRIPTION FACTOR PRR; TRANSCRIPTION FACTOR TOC1; UNCLASSIFIED DRUG;

ANGIOSPERM; ARABIDOPSIS; BRASSICA RAPA; CANDIDA ALBICANS; CARBOXY TERMINAL SEQUENCE; CASTANEA SATIVA; CIRCADIAN RHYTHM; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GREEN ALGA; MESEMBRIANTHEMUM CRISTALLINUM; MOSS; NONHUMAN; OPUNTIA; OPUNTIA FICUS INDICA; PEA; PHASEOLUS VULGARIS; PLANT; PLANT GROWTH; PLANT METABOLISM; PROMOTER REGION; REVIEW; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; SOYBEAN; TOMATO;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

EID: 84879185726     PISSN: 10849521     EISSN: 10963634     Source Type: Journal    
DOI: 10.1016/j.semcdb.2013.02.007     Document Type: Review

References (146)

1. Whitehead K., Pan M., Masumura K.-i., Bonneau R., Baliga N.S. Diurnally entrained anticipatory behavior in Archaea. PLoS ONE 2009, 4:e5485.
2. Mackey S.R., Golden S.S., Ditty J.L. The itty-bitty time machine: genetics of the cyanobacterial circadian clock. Advances in Genetics 2011, 74:12-53.
3. Edgar R.S., Green E.W., Zhao Y., van Ooijen G., Olmedo M., Qin X., et al. Peroxiredoxins are conserved markers of circadian rhythms. Nature 2012, 485:459-464.
4. Bretzl H. Botanische Forschungen des Alexanderzuges 1903, B.G. Teubner, Leipzig.
5. de Mairan J. Observation botanique. Histoire de l'Academie Royale des Sciences 1729, 35-36.
6. Darwin C., Darwin F. The power of movement in plants 1880, Murray, London.
7. Cumming B.G., Wagner E. Rhythmic processes in plants. Annual Review of Plant Physiology 1968, 19:381-416.
8. Bünning E. The physiological clock 1973, Springer-Verlag, New York. 3rd ed.
9. Kinmonth-Schultz H.A., Golembeski G.S., Imaizumi T. Circadian clock-regulated physiological outputs: dynamic responses in nature. Seminars in Cell and Developmental Biology 2013, 24.
10. Dodd A.N., Salathia N., Hall A., Kevei E., Toth R., Nagy F., et al. Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 2005, 309:630-633.
11. Michael T.P., Breton G., Hazen S.P., Priest H., Mockler T.C., Kay S.A., et al. A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biology 2008, 6:1887-1898.
12. Nozue K., Covington M.F., Duek P.D., Lorrain S., Fankhauser C., Harmer S.L., et al. Rhythmic growth explained by coincidence between internal and external cues. Nature 2007, 448:358-361.
13. Fukushima A., Kusano M., Nakamichi N., Kobayashi M., Hayashi N., Sakakibara H., et al. Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:7251-7256.
14. Graf A., Schlereth A., Stitt M., Smith A.M. Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:9458-9463.
15. Gutiérrez R.A., Stokes T.L., Thum K., Xu X., Obertello M., Katari M.S., et al. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:4939-4944.
16. Kerwin R.E., Jimenez-Gomez J.M., Fulop D., Harmer S.L., Maloof J.N., Kliebenstein D.J. Network quantitative trait loci mapping of circadian clock outputs identifies metabolic pathway-to-clock linkages in Arabidopsis. Plant Cell 2011, 23:471-485.
17. Kunihiro A., Yamashino T., Nakamichi N., Niwa Y., Nakanishi H., Mizuno T. PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) activate the homeobox ATHB2 and auxin-inducible IAA29 genes in the coincidence mechanism underlying photoperiodic control of plant growth of Arabidopsis thaliana. Plant and Cell Physiology 2011, 52:1315-1329.
18. Nozue K., Harmer S.L., Maloof J.N. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis. Plant Physiology 2011, 156:357-372.
19. Harmer S.L. The circadian system in higher plants. Annual Review of Plant Biology 2009, 60:357-377.
20. Doherty C.J., Kay S.A. Circadian control of global gene expression patterns. Annual Review of Genetics 2010, 44:419-444.
21. McClung C.R., Gutiérrez R.A. Network news: prime time for systems biology of the plant circadian clock. Current Opinion in Genetics and Development 2010, 20:588-598.
22. McClung C.R. The genetics of plant clocks. Advances in Genetics 2011, 74:105-138.
23. Haydon M.J., Hearn T.J., Bell L.J., Hannah M.A., Webb A.A.R. Metabolic regulation of circadian clocks. Seminars in Cell and Developmental Biology 2013, 24.
24. Kloppstech K. Diurnal and circadian rhythmicity in the expression of light-induced nuclear messenger RNAs. Planta 1985, 165:502-506.
25. Nagy F., Kay S.A., Chua N.-H. A circadian clock regulates transcription of the wheat Cab-1 gene. Genes and Development 1988, 2:376-382.
26. Giuliano G., Hoffman N.E., Ko K., Scolnik P.A., Cashmore A.R. A light-entrained circadian clock controls transcription of several plant genes. EMBO Journal 1988, 7:3635-3642.
27. Paulsen H., Bogorad L. Diurnal and circadian rhythms in the accumulation and synthesis of mRNA for the light-harvesting chlorophyll a/b-binding protein in tobacco. Plant Physiology 1988, 88:1104-1109.
28. Taylor W.C. Transcriptional regulation by a circadian rhythm. Plant Cell 1989, 1:259-264.
29. Millar A.J., Kay S.A. Circadian control of cab gene transcription and mRNA accumulation in Arabidopsis. Plant Cell 1991, 3:541-550.
30. Rédei G.P. Arabidopsis as a genetic tool. Annual Review of Genetics 1975, 9:111-127.
31. Meyerowitz E.M., Pruitt R.E. Arabidopsis thaliana and plant molecular genetics. Science 1985, 229:1214-1218.
32. Estelle M.A., Somerville C.R. The mutants of Arabidopsis. Trends in Genetics 1986, 2:89-93.
33. Nagel D.H., Kay S.A. Complexity in the wiring and regulation of plant circadian networks. Current Biology 2012, 22:R648-R657.
34. Veflingstad S., Carré I. Emerging design principles in the Arabidopsis circadian clock. Seminars in Cell and Developmental Biology 2013, 24.
35. Chow B.Y., Kay S.A. Global approaches for telling time: omics and the Arabidopsis circadian clock. Seminars in Cell and Developmental Biology 2013, 24.
36. Henriques R., Mas P. Chromatin remodeling and alternative splicing: pre-and post-transcriptional regulation of the Arabidopsis circadian clock. Seminars in Cell and Developmental Biology 2013, 24.
37. Fink G.R. Notes of a bigamous biologist. Genetics 1988, 118:549-550.
38. Song Y.H., Ito S., Imaizumi T. Similarities in the circadian clock and photoperiodism in plants. Current Opinion in Plant Biology 2010, 13:594-603.
39. Kaldis A.D., Kousidis P., Kesanopoulos K., Prombona A. Light and circadian regulation in the expression of LHY and Lhcb genes in Phaseolus vulgaris. Plant Molecular Biology 2003, 52:981-997.
40. Ibanez C., Ramos A., Acebo P., Contreras A., Casado R., Allona I., et al. Overall alteration of circadian clock gene expression in the chestnut cold response. PLoS ONE 2008, 3:e3567.
41. Ramos A., Perez-Solis E., Ibanez C., Casado R., Collada C., Gomez L., et al. Winter disruption of the circadian clock in chestnut. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:7037-7042.
42. Hecht V., Foucher F., Ferrandiz C., Macknight R., Navarro C., Morin J., et al. Conservation of Arabidopsis flowering genes in model legumes. Plant Physiology 2005, 137:1420-1434.
43. Liew L.C., Hecht V., Laurie R.E., Knowles C.L., Vander Schoor J.K., Macknight R.C., et al. DIE NEUTRALIS and LATE BLOOMER 1 contribute to regulation of the pea circadian clock. Plant Cell 2009, 21:3198-3211.
44. Boxall S.F., Foster J.M., Bohnert H.J., Cushman J.C., Nimmo H.G., Hartwell J. Conservation and divergence of circadian clock operation in a stress-inducible crassulacean acid metabolism species reveals clock compensation against stress. Plant Physiology 2005, 137:969-982.
45. Liu H., Wang H., Gao P., Xü J., Xü T., Wang J., et al. Analysis of clock gene homologs using unifoliolates as target organs in soybean (Glycine max). Journal of Plant Physiology 2009, 166:278-289.
46. Hudson K.A. The circadian clock-controlled transcriptome of developing soybean seeds. Plant Genome 2010, 3:3-13.
47. Kim J.A., Kim J.S., Hong J.K., Lee Y.-H., Choi B.-S., Seol Y.-J., et al. Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa. Molecular Genetics and Genomics 2012, 287:373-388.
48. Lou P., Wu J., Cheng F., Cressman L.G., Wang X., McClung C.R. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell 2012, 24:2415-2426.
49. Facella P., Lopez L., Carbone F., Galbraith D.W., Giuliano G., Perrotta G. Diurnal and circadian rhythms in the tomato transcriptome and their modulation by cryptochrome photoreceptors. PLoS ONE 2008, 3:e2798.
50. Mallona I., Egea-Cortines M., Weiss J. Conserved and divergent rhythms of crassulacean acid metabolism-related and core clock gene expression in the cactus Opuntia ficus-indica. Plant Physiology 2011, 156:1978-1989.
51. Miwa K., Serikawa M., Suzuki S., Kondo T., Oyama T. Conserved expression profiles of circadian clock-related genes in two Lemna species showing long-day and short-day photoperiodic flowering responses. Plant and Cell Physiology 2006, 47:601-612.
52. Takata N., Saito S., Saito C.T., Nanjo T., Shinohara K., Uemura M. Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2. New Phytologist 2009, 181:808-819.
53. Takata N., Saito S., Saito C.T., Uemura M. Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of pseudo-response regulators. BMC Evolutionary Biology 2010, 10:126.
54. Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J., et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 2008, 452:991-996.
55. Uemura M., Takata N., Saito S., Saito C.T. Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of pseudo-response regulators. BMC Evolutionary Biology 2010, 10.
56. Murakami M., Ashikari M., Miura K., Yamashino T., Mizuno T. The evolutionarily conserved OsPRR quintet: rice pseudo-response regulators implicated in circadian rhythm. Plant and Cell Physiology 2003, 44:1229-1236.
57. Murakami M., Tago Y., Yamashino T., Mizuno T. Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Plant and Cell Physiology 2007, 48:110-121.
58. Murakami M., Tago Y., Yamashino T., Mizuno T. Characterization of the rice circadian clock-associated pseudo-response regulators in Arabidopsis thaliana. Bioscience, Biotechnology, and Biochemistry 2007, 71:1107-1110.
59. Serikawa M., Miwa K., Kondo T., Oyama T. Functional conservation of clock-related genes in flowering plants: overexpression and RNAi analyses of the circadian rhythm in the monocotyledon Lemna gibba. Plant Physiology 2008, 146:1952-1963.
60. Harmer S.L., Hogenesch J.B., Straume M., Chang H.S., Han B., Zhu T., et al. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 2000, 290:2110-2113.
61. Michael T.P., McClung C.R. Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiology 2003, 132:629-639.
62. Edwards K.D., Anderson P.E., Hall A., Salathia N.S., Locke J.C.W., Lynn J.R., et al. FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 2006, 18:639-650.
63. Covington M.F., Harmer S.L. The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biology 2007, 5:e222.
64. Michael T.P., Mockler T.C., Breton G., McEntee C., Byer A., Trout J.D., et al. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 2008, 4:e14.
65. Covington M.F., Maloof J.N., Straume M., Kay S.A., Harmer S.L. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biology 2008, 9:R130.
66. Bläsing O.E., Gibon Y., Günther M., Höhne M., Morcuende R., Osuna D., et al. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 2005, 17:3257-3281.
67. Smith S.M., Fulton D.C., Chia T., Thorneycroft D., Chapple A., Dunstan H., et al. 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 Physiology 2004, 136:2687-2699.
68. Filichkin S.A., Breton G., Priest H.D., Dharmawardhana P., Jaiswal P., Fox S.E., et al. Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS ONE 2011, 6:e16907.
69. Mockler T.C., Michael T.P., Priest H.D., Shen R., Sullivan C.M., Givan S.A., et al. The Diurnal Project: diurnal and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harbor Symposia on Quantitative Biology 2007, 72:353-363.
70. Nagano Atsushi J., Sato Y., Mihara M., Antonio Baltazar A., Motoyama R., Itoh H., et al. Deciphering and prediction of transcriptome dynamics under fluctuating field conditions. Cell 2012, 151:1358-1369.
71. Khan S., Rowe S.C., Harmon F.G. Coordination of the maize transcriptome by a conserved circadian clock. BMC Plant Biology 2010, 10:126.
72. Hayes K.R., Beatty M., Meng X., Simmons C.R., Habben J.E., Danilevskaya O.N. Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator. PLoS ONE 2010, 5:e12887.
73. Zdepski A., Wang W., Priest H.D., Ali F., Alam M., Mockler T.C., et al. Conserved daily transcriptional programs in Carica papaya. Tropical Plant Biology 2008, 1:236-245.
74. Wang W., Barnaby J.Y., Tada Y., Li H., Tör M., Caldelari D., et al. Timing of plant immune responses by a central circadian regulator. Nature 2011, 470:110-114.
75. Bhardwaj V., Meier S., Petersen L.N., Ingle R.A., Roden L.C. Defence responses of Arabidopsis thaliana to infection by Pseudomonas syringae are regulated by the circadian clock. PLoS ONE 2011, 6:e26968.
76. Goodspeed D., Chehab E.W., Min-Venditti A., Braam J., Covington M.F. Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior. Proceedings of the National Academy of Sciences of the United States of America 2012, 109:4674-4677.
77. Fowler S.G., Cook D., Thomashow M.F. Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiology 2005, 137:961-968.
78. Wilkins O., Bräutigam K., Campbell M.M. Time of day shapes Arabidopsis drought transcriptomes. Plant Journal 2010, 63:715-727.
79. Wilkins O., Waldron L., Nahal H., Provart N.J., Campbell M.M. Genotype and time of day shape the Populus drought response. Plant Journal 2009, 60:703-715.
80. Mikkelsen M.D., Thomashow M.F. A role for circadian evening elements in cold-regulated gene expression in Arabidopsis. Plant Journal 2009, 60:328-339.
81. Dong M.A., Farré E.M., Thomashow M.F. CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:7241-7246.
82. Michael T.P., Salomé P.A., Yu H.J., Spencer T.R., Sharp E.L., Alonso J.M., et al. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 2003, 302:1049-1053.
83. Edwards K.D., Lynn J.R., Gyula P., Nagy F., Millar A.J. Natural allelic variation in the temperature compensation mechanisms of the Arabidopsis thaliana circadian clock. Genetics 2005, 170:387-400.
84. Salathia N., Davis S.J., Lynn J.R., Michaels S.D., Amasino R.M., Millar A.J. FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways. BMC Plant Biology 2006, 6:10.
85. Anwer M.U., Davis S.J. An overview of natural variation studies in the Arabidopsis thaliana circadian clock. Seminars in Cell and Developmental Biology 2013, 24.
86. Salathia N., Lynn J.R., Millar A.J., King G.J. Detection and resolution of genetic loci affecting circadian period in Brassica oleracea. Theoretical and Applied Genetics 2007, 114:683-692.
87. Lou P., Xie Q., Xu X., Edwards C.E., Brock M.T., Weinig C., et al. Genetic architecture of the circadian clock and flowering time in Brassica rapa. Theoretical and Applied Genetics 2011, 123:397-409.
88. Edwards C.E., Ewers B.E., Williams D.G., Xie Q., Lou P., Xu X., et al. The genetic architecture of ecophysiological and circadian traits in Brassica rapa. Genetics 2011, 189:375-390.
89. Edwards C.E., Ewers B.E., McClung C.R., Lou P., Weinig C. Quantitative variation in water-use efficiency across water regimes and its relationship with circadian, vegetative, reproductive, and leaf gas-exchange traits. Molecular Plant 2012, 5:653-668.
90. Hennessey T.L., Field C.B. Oscillations in carbon assimilation and stomatal conductance under constant conditions. Plant Physiology 1991, 96:831-836.
91. Salomé P.A., Michael T.P., Kearns E.V., Fett-Neto A.G., Sharrock R.A., McClung C.R. The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis. Plant Physiology 2002, 129:1674-1685.
92. Martin E.S., Meidner H. Endogenous stomatal movements in Tradescantia virginiana. New Phytologist 1971, 70:923-928.
93. Kerr P.S., Rufty T.W.J., Huber S.C. Endogenous rhythms in photosynthesis, sucrose phosphate synthase activity, and stomatal resistance in leaves of soybean (Glycine max [L.] Merr.). Plant Physiology 1985, 77:275-280.
94. Gorton H.L., Williams W.E., Binns M.E., Gemmell C.N., Leheny E.A., Shepherd A.C. Circadian stomatal rhythms in epidermal peels from Vicia faba. Plant Physiology 1989, 90:1329-1334.
95. Henzler T., Waterhouse R.N., Smyth A.J., Carvajal M., Cooke D.T., Schaffner A.R., et al. Diurnal variations in hydraulic conductivity and root pressure can be correlated with the expression of putative aquaporins in the roots of Lotus japonicus. Planta 1999, 210:50-60.
96. Clarkson D.T., Carvajal M., Henzler T., Waterhouse R.N., Smyth A.J., Cooke D.T., et al. Root hydraulic conductance: diurnal aquaporin expression and the effects of nutrient stress. Journal of Experimental Botany 2000, 51:61-70.
97. Nardini A., Salleo S., Andri S. Circadian regulation of leaf hydraulic conductance in sunflower (Helianthus annuus L. cv Margot). Plant, Cell and Environment 2005, 28:750-759.
98. Aoki S., Kato S., Ichikawa K., Shimizu M. Circadian expression of the PpLhcb2 gene encoding a major light-harvesting chlorophyll a/b-binding protein in the moss Physcomitrella patens. Plant and Cell Physiology 2004, 45:68-76.
99. Okada R., Kondo S., Satbhai S.B., Yamaguchi N., Tsukuda M., Aoki S. Functional characterization of CCA1/LHY homolog genes, PpCCA1a and PpCCA1b, in the moss Physcomitrella patens. Plant Journal 2009, 60:551-563.
100. Holm K., Kallman T., Gyllenstrand N., Hedman H., Lagercrantz U. Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?. BMC Plant Biology 2010, 10:109.
101. Satbhai S.B., Yamashino T., Mizuno T., Aoki S. Heterologous expression and functional characterization of a Physcomitrella pseudo response regulator homolog, PpPRR2, in Arabidopsis. Bioscience, Biotechnology, and Biochemistry 2011, 75:786-789.
102. Más P., Kim W.-Y., Somers D.E., Kay S.A. Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 2003, 426:567-570.
103. Kiba T., Henriques R., Sakakibara H., Chua N.-H. Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by a SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. Plant Cell 2007, 19:2516-2530.
104. Fujiwara S., Wang L., Han L., Suh S.S., Salomé P.A., McClung C.R., et al. Post-translational regulation of the circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins. Journal of Biological Chemistry 2008, 283:23073-23083.
105. Baudry A., Ito S., Song Y.H., Strait A.A., Kiba T., Lu S., et al. F-Box Proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. Plant Cell 2010, 22:606-622.
106. Pohl H. Tagesrhythmus im phototaktischen Verhalten der Eugelna gracilis. Zeitschrift für Naturforschung 1948, 3b:367-374.
107. Mergenhagen D., Mergenhagen E. The biological clock of Chlamydomonas reinhardii in space. European Journal of Cell Biology 1987, 943:203-207.
108. Bruce V.G. Mutants of the biological clock in Chlamydomonas reinhardi. Genetics 1972, 70:537-548.
109. Schulze T., Prager K., Dathe H., Kelm J., Kießling P., Mittag M. How the green alga Chlamydomonas reinhardtii keeps time. Protoplasma 2010, 244:3-14.
110. Matsuo T., Ishiura M. Chlamydomonas reinhardtii as a new model system for studying the molecular basis of the circadian clock. FEBS Letters 2011, 585:1495-1502.
111. Kucho K-i, Okamoto K., Tabata S., Fukuzawa H., Ishiura M. Identification of novel clock-controlled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii. Plant Molecular Biology 2005, 57:889-906.
112. Hwang S., Herrin D.L. Control of lhc gene transcription by the circadian clock in Chlamydomonas reinhardtii. Plant Molecular Biology 1994, 26:557-569.
113. Hwang S., Kawazoe R., Herrin D.L. Transcription of tufA and other chloroplast-encoded genes is controlled by a circadian clock in Chlamydomonas. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:996-1000.
114. Matsuo T., Okamoto K., Onai K., Niwa Y., Shimogawara K., Ishiura M. A systematic forward genetic analysis identified components of the Chlamydomonas circadian system. Genes and Development 2008, 22:918-930.
115. Hazen S.P., Schultz T.F., Pruneda-Paz J.L., Borevitz J.O., Ecker J.R., Kay S.A. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:10387-10392.
116. Onai K., Ishiura M. PHYTOCLOCK1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes to Cells 2005, 10:963-972.
117. Wang Z.-Y., Kenigsbuch D., Sun L., Harel E., Ong M.S., Tobin E.M. A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 1997, 9:491-507.
118. Schaffer R., Ramsay N., Samach A., Corden S., Putterill J., Carré I.A., et al. The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 1998, 93:1219-1229.
119. Kojima S., Shingle D.L., Green C.B. Post-transcriptional control of circadian rhythms. Journal of Cell Science 2011, 124:311-320.
120. Staiger D., Green R. RNA-based regulation in the plant circadian clock. Trends in Plant Science 2011, 16:517-523.
121. Zhang L., Weng W., Guo J. Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms. FEBS Letters 2011, 585:1400-1405.
122. Iliev D., Voytsekh O., Schmidt E.M., Fiedler M., Nykytenko A., Mittag M. A heteromeric RNA-binding protein is involved in maintaining acrophase and period of the circadian clock. Plant Physiology 2006, 142:797-806.
123. Zhao B., Schneid C., Iliev D., Schmidt E.M., Wagner V., Wollnik F., et al. The circadian RNA-binding protein CHLAMY 1 represents a novel type heteromer of RNA recognition motif and lysine homology domain-containing subunits. Eukaryotic Cell 2004, 3:815-825.
124. Courties C., Vaquer A., Troussellier M., Lautier J., Chrétiennot-Dinet M.J., Neveux J., et al. Smallest eukaryotic organism. Nature 1994, 370:255.
125. Corellou F., Schwartz C., Motta J.-P., Djouani-Tahri E.B., Sanchez F., Bouget F.-Y. Clocks in the green lineage: comparative functional analysis of the circadian architecture of the picoeukaryote Ostreococcus. Plant Cell 2009, 21:3436-3449.
126. Troein C., Corellou F., Dixon L.E., van Ooijen G., O'Neill J.S., Bouget F.-Y., et al. Multiple light inputs to a simple clock circuit allow complex biological rhythms. Plant Journal 2011, 66:375-385.
127. Thommen Q., Pfeuty B., Corellou F., Bouget F.Y., Lefranc M. Robust and flexible response of the Ostreococcus tauri circadian clock to light/dark cycles of varying photoperiod. FEBS Journal 2012, 279:3432-3448.
128. Djouani-Tahri E.-B., Christie J.M., Sanchez-Ferandin S., Sanchez F., Bouget F.-Y., Corellou F. A eukaryotic LOV-histidine kinase with circadian clock function in the picoalga Ostreococcus. Plant Journal 2011, 65:578-588.
129. Iwasaki H., Williams S.B., Kitayama Y., Ishiura M., Golden S.S., Kondo T. A KaiC-interacting sensory histidine kinase SasA, necessary to sustain robust circadian oscillation in cyanobacteria. Cell 2000, 101:223-233.
130. Ivleva N.B., Gao T., LiWang A.C., Golden S.S. Quinone sensing by the circadian input kinase of the cyanobacterial circadian clock. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:17468-17473.
131. Heijde M., Zabulon G., Corellou F., Ishikawa T., Brazard J., Usman A., et al. Characterization of two members of the cryptochrome/photolyase family from Ostreococcus tauri provides insights into the origin and evolution of cryptochromes. Plant, Cell and Environment 2010, 33:1614-1626.
132. Pittendrigh C.S. Temporal organization: reflections of a Darwinian clock-watcher. Annual Review of Physiology 1993, 55:17-54.
133. Nakajima M., Imai K., Ito H., Nishiwaki T., Murayama Y., Iwasaki H., et al. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 2005, 308:414-415.
134. Tomita J., Nakajima M., Kondo T., Iwasaki H. No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 2005, 307:251-253.
135. Terauchi K., Kitayama Y., Nishiwaki T., Miwa K., Murayama Y., Oyama T., et al. The ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:16377-16381.
136. Rosbash M. The implications of multiple circadian clock origins. PLoS Biology 2009, 7:e1000062.
137. Tsong A.E., Tuch B.B., Li H., Johnson A.D. Evolution of alternative transcriptional circuits with identical logic. Nature 2006, 443:415-420.
138. Baker C.R., Booth L.N., Sorrells T.R., Johnson A.D. Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification. Cell 2012, 151:80-95.
139. Booth L.N., Tuch B.B., Johnson A.D. Intercalation of a new tier of transcription regulation into an ancient circuit. Nature 2010, 468:959-963.
140. Carroll S.B. Evolution at two levels: on genes and form. PLoS Biology 2005, 3:e245.
141. Wohlbach D.J., Thompson D.A., Gasch A.P., Regev A. From elements to modules: regulatory evolution in Ascomycota fungi. Current Opinion in Genetics and Development 2009, 19:571-578.
142. Nobile C.J., Fox E.P., Nett J.E., Sorrells T.R., Mitrovich Q.M., Hernday A.D., et al. A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell 2012, 148:126-138.
143. Jiao Y., Wickett N.J., Ayyampalayam S., Chanderbali A.S., Landherr L., Ralph P.E., et al. Ancestral polyploidy in seed plants and angiosperms. Nature 2011, 473:97-100.
144. O'Neill J.S., Reddy A.B. Circadian clocks in human red blood cells. Nature 2011, 469:498-503.
145. O'Neill J.S., van Ooijen G., Dixon L.E., Troein C., Corellou F., Bouget F.Y., et al. Circadian rhythms persist without transcription in a eukaryote. Nature 2011, 469:554-558.
146. Brkljacic J., Grotewold E., Scholl R., Mockler T., Garvin D.F., Vain P., et al. Brachypodium as a model for the grasses: today and the future. Plant Physiology 2011, 157:3-13.