In silico analysis of the endogenous time-keeping mechanism in citrus

Genetics and Molecular Biology

Volumn 30, Issue 3 SUPPL., 2007, Pages 794-809

  Quecini, Vera ^a  

^a INSTITUTO AGRONÔMICO   (Brazil)

Author keywords

Central oscillator; Circadian clock; Data mining; Photoperiodic responses; Regulatory feedback loop

Indexed keywords

PROTEIN PRR5; PROTEIN SRR1; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; BIOLOGICAL RHYTHM; CITRUS FRUIT; COMPUTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; DATA MINING; EXPRESSED SEQUENCE TAG; FEEDBACK SYSTEM; GENE IDENTIFICATION; GENETIC DISTANCE; GENOMICS; LIGHT DARK CYCLE; NONHUMAN; PHOTOPERIODICITY; PLANT METABOLISM; PLANT PHYSIOLOGY; SEQUENCE DATABASE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CITRUS;

EID: 38049132967     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/s1415-47572007000500008     Document Type: Article

References (103)

1. Abe M, Kobayashi Y, Yamamoto S, Daimon Y, Yamaguchi A, Ikeda Y, Ichinoki H, Notaguchi M, Goto K and Araki T (2005) FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 309:1052-1056.
2. Abied MA and Holland D (1994) Two newly isolated genes from citrus exhibit a different pattern of diurnal expression and light response. Plant Mol Biol 26:165-173.
3. Alabadí D, Oyama T, Yanovsky MJ, Harmon FG, Más P and Kay SA (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293:880-883.
4. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
5. An H, Roussot C, Suarez-Lopez P, Corbesier L, Vincent C, Pineiro M, Hepworth S, Mouradov A, Justin S, Turnbull CGN, et al. (2004) CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development 131:3615-3626.
6. Ayre BG and Turgeon R (2004) Graft transmission of a floral stimulant derived from CONSTANS. Plant Physiol 135:2271-2278.
7. Bell-Pedersen D, Cassone VM, Earnest DJ, Golden SS, Hardin PE, Thomas TL and Zoran MJ (2005) Circadian rhythms from multiple oscillators: Lessons from diverse organisms. Nature Rev Genetics 6:4-13.
8. Blázquez MA (2005) Plant science. The right time and place for making flowers. Science 309:1024-1025.
9. Böhlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Janssen S, Strauss SH and Nilsson O (2006) CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312:1040-1043.
10. Borchert R, Renner SS, Calle Z, Navarrete D, Tye A, Gautier L, Spichiger R and von Hildebrand P (2005) Photoperiodic induction of synchronous flowering near the Equator. Nature 433:627-629.
11. Boylan M, Douglas N and Quail PH (1994) Dominant negative suppression of Arabidopsis photoresponses by mutant phytochrome A sequences identifies spatially discrete regulatory domains in the photoreceptor. Plant Cell 6:449-460.
12. Carré IA (2002) ELF3: A circadian safeguard to buffer effects of light. Trends Plant Sci 7:4-6.
13. Cashmore AR, Jarillo JA, Wu YJ and Liu D (1999) Cryptochromes: Blue light receptors for plants and animals. Science 284:760-765.
14. Cerdán PD and Chory J (2003) Regulation of flowering time by light quality. Nature 423:881-885.
15. Chory J and Peto CA (1990) Mutations in the DET1 gene affect cell-type-specific expression of light-regulated genes and chloroplast development in Arabidopsis. Proc Natl Acad Sci USA 87:8776-8780.
16. Covington MF, Panda S, Liu XL, Strayer CA, Wagner DR and Kay SA (2001) ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell 13:1305-1315.
17. Daniel X, Sugano S and Tobin EM (2004) CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis. Proc Natl Acad Sci USA 101:3292-3297.
18. Devlin PF and Kay SA (2000) Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. Plant Cell 12:2499-2510.
19. Doyle MR, Davis SJ, Bastow RM, McWatters HG, Kozma-Bognar L, Nagy F, Millar AJ and Amasino RM (2002) The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419:74-77.
20. Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, Lynn JR, Straume M, Smith JQ and Millar AJ (2006) FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 18:639-650.
21. Edwards KD, Lynn JR, Gyula P, Nagy F and Millar AJ (2005) Natural allelic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock. Genetics 170:387-400.
22. Eisen MB, Spellman PT, Brown PO and Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863-14868.
23. Endo T, Shimada T, Fujii H, Kobayashi Y, Araki T and Omura M (2005) Ectopic expression of an FT homolog from citrus confers an early flowering phenotype on trifoliate orange (Poncirus trifoliata L. Raf). Transgenic Res 14:703-712.
24. Farré EM, Harmer SL, Harmon FG, Yanovsky MJ and Kay SA (2005) Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol 15:47-54.
25. Fowler S, Lee K, Onouchi H, Samach A, Richardson K, Morris B, Coupland G and Putterill J (1999) GIGANTEA: A circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. EMBO J 18:4679-4688.
26. Frizzo CD, Lorenzo D and Dellacassa E (2004) Composition and seasonal variation of the essential oils from two Mandarin cultivars of southern Brazil. J Agric Food Chem 52:3036-3041.
27. Green RM and Tobin EM (1999) Loss of the circadian clock-associated protein 1 in Arabidopsis results in altered clock-regulated gene expression. Proc Natl Acad Sci USA 96:4176-4179.
28. Griffiths S, Dunford RP, Coupland G and Laurie DA (2003) The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131:1855-1867.
29. Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ and Amasino RM (2003) The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. Plant Cell 15:2719-2729.
30. ZTL complex is required for proper regulation of circadian timing. Plant J 40:291-301.
31. Harmer SL and Kay SA (2005) Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis. Plant Cell 17:1926-1940.
32. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR and Kay SA (2005) LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci USA 102:10387-10392.
33. He Y, Doyle MR and Amasino RM (2004) PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev 18:2774-2784.
34. Hecht V, Foucher F, Ferrandiz C, Macknight R, Navarro C, Morin J, Vardy ME, Ellis N, Beltran JP, Rameau C, et al. (2005) Conservation of Arabidopsis flowering genes in model legumes. Plant Physiol 137:1420-1434.
35. Hicks KA, Albertson TM and Wagner DR (2001) EARLY FLOWERING 3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis. Plant Cell 13:1281-1292.
36. Hicks KA, Millar AJ, Carré IA, Somers DE, Straume MD, Meeks-Wagner R and Kay SA (1996) Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274:790-792.
37. Huang T, Bohlenius H, Eriksson S, Parcy F and Nilsson O (2005) The mRNA of the Arabidopsis gene FT moves from leaf to shoot apex and induces flowering. Science 309:1694-1696.
38. Imaizumi T, Schultz TF, Harmon FG, Ho LA and Kay SA (2005) FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309:293-297.
39. Imaizumi T, Tran HG, Swartz TE, Briggs WR and Kay SA (2003) FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426:302-306.
40. Ito S, Matsushika A, Yamada H, Sato S, Kato T, Tabata S, Yamashino T and Mizuno T (2003) Characterization of the APRR9 pseudo-response regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol 44:1237-1245.
41. Ito S, Nakamichi N, Matsushika A, Fujimori T, Yamashino T and 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.
42. Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M and Shimamoto K (2002) Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev 16:2006-2020.
43. Kikis EA, Khanna R and Quail PH (2005) ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY. Plant J 44:300-313.
44. Kim W-Y, Geng R and Somers DE (2003) Circadian phase-specific degradation of the F-box protein ZTL is mediated by the proteasome. Proc Natl Acad Sci USA 100:4933-4938.
45. Kobayashi Y, Kaya H, Goto K, Iwabuchi M and Araki T (1999) A pair of related genes with antagonistic roles in mediating flowering signals. Science 286:1960-1962.
46. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T and Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43:1096-1105.
47. Komeda Y (2004) Genetic regulation of time to flower in Arabidopsis thaliana. Annu Rev Plant Biol 55:521-535.
48. Lee HS and Castle WS (2001) Seasonal changes of carotenoid pigments and color in Hamlin, Earlygold, and Budd Blood orange juices. J Agric Food Chem 49:877-882.
49. Lin J, Rouseff RL, Barros S and Naim M (2002) Aroma composition changes in early season grapefruit juice produced from thermal concentration. J Agric Food Chem 50:813-819.
50. Liu XL, Covington MF, Fankhauser C, Chory J and Wagner DR (2001) ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell 13:1293-1304.
51. Locke JCW, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, Turner MS and Millar AJ (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 1, doi/10.1038/ msb4100018, http://www.nature.com/msb/journal/v1/n1/full/msb4100018.html.
52. Makino S, Kiba T, Imamura A, Hanaki N, Nakamura A, Suzuki T, Taniguchi M, Ueguchi C, Sugiyama T and Mizuno T (2000) Genes encoding pseudo-response regulators: Insight into His-to-Asp phosphorelay and circadian rhythm in Arabidopsis thaliana. Plant Cell Physiol 41:791-803.
53. Makino S, Matsushika A, Kojima M, Oda Y and 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.
54. Más P, Alabadí D, Yanovsky MJ, Oyama T and Kay SA (2003a) Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis. Plant Cell 15:223-236.
55. Más P, Devlin PF, Panda S and Kay SA (2000) Functional interaction of PHYTOCHROME B and CRYPTOCHROME 2. Nature 408:207-211.
56. Más P, Kim W-Y, Somers DE and Kay SA (2003b) Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426:567-570.
57. Matsushika A, Makino S, Kojima M and Mizuno T (2000) 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 41:1002-1012.
58. Matsushika A, Makino S, Kojima M, Yamashmo T and Mizuno T (2002) The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants. Plant Cell Physiol 43:118-122.
59. McClung CR (2006) Plant circadian rhythms. Plant Cell 18:792-803.
60. McWatters HG, Bastow RM, Hall A and Millar AJ (2000) The ELF3 Zeitnehmer regulates light signaling to the circadian clock. Nature 408:716-20.
61. Michael TP and McClung CR (2002) Phase-specific circadian clock regulatory elements in Arabidopsis thaliana. Plant Physiol 130:627-638.
62. Millar AJ (2004) Input signals to the plant circadian clock. J Exp Bet 55:277-283.
63. Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, Song HR, Carré IA and Coupland G (2002) LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev Cell 2:629-641.
64. Mizuno T and Nakamichi N (2005) Pseudo-response regulators (PRRs) or true oscillator components (TOCs). Plant Cell Physiol 46:677-685.
65. Murakami M, Matsushika A, Ashikari M, Yamashino T and Mizuno T (2005) Circadian-associated rice pseudo response regulators (OsPRRs): Insight into the control of flowering time. Biosci Biotechnol Biochem 69:410-414.
66. Murakami M, Yamashino T and Mizuno T (2004) Characterization of circadian-associated APRR3 Pseudo-Response Regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol 45:645-650.
67. Nakamichi N, Kita M, Ito S, Sato E, Yamashino T and Mizuno T (2005a) 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.
68. Nakamichi N, Kita M, Ito S, Sato E, Yamashino T and Mizuno T (2005b) The Arabidopsis pseudo-response regulators, PRR5 and PRR7, coordinately play essential roles for circadian clock function. Plant Cell Physiol 46:609-619.
69. Nelson DC, Lasswell J, Rogg LE, Cohen MA and Bartel B (2000) FKF1, a clock-controlled gene that regulates the transition to flowering in Arabidopsis. Cell 101:331-340.
70. Ni M, Tepperman JM and Quail PH (1999) Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Nature 400:781-784.
71. Onai K and Ishiura M (2005) PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes Cells 10:963-972.
72. Onouchi H, Igeno MI, Perilleux C, Graves K and Coupland G (2000) Mutagenesis of plants overexpressing CONSTANS demonstrates novel interactions among Arabidopsis flowering-time genes. Plant Cell 12:885-900.
73. Park DH, Somers DE, Kim YS, Choy YH, Li HK, Soh MS, Kim HJ, Kay SA and Nam HG (1999) Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285:1579-1582.
74. Pena L, Martin-Trillo M, Juarez J, Pina JA, Navarro L and Martinez-Zapater JM (2001) Constitutive expression of Arabidopsis LEAFY or APETALA1 genes in citrus reduces their generation time. Nat Biotechnol 19:263-267.
75. Pillitteri LJ, Lovatt CJ and Walling LL (2004) Isolation and characterization of a TERMINAL FLOWER homolog and its correlation with juvenility in citrus. Plant Physiol 135:1540-1551.
76. Putterill J, Robson F, Lee K, Simon R and Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847-857.
77. Robson F, Costa MM, Hepworth SR, Vizir I, Pineiro M, Reeves PH, Putterill J and Coupland G (2001) Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. Plant J 28:619-631.
78. Salomé PA and 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.
79. Salomé PA, Michael TP, Kearns EV, Fett-Neto AG, Sharrock RA and McClung CR (2002) The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis. Plant Physiol 129:1674-1685.
80. Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF and Coupland G (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613-1616.
81. Santelli RV and Siviero F (2001) A search for homologues of plant photoreceptor genes and their signaling partners in the sugarcane expressed sequence tag (Sucest) database. Genet Mol Biol 24:49-53.
82. Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, Carré IA and Coupland G (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and. the photoperiodic control of flowering. Cell 93:1219-1229.
83. Schultz TF, Kiyosue T, Yanovsky M, Wada M and Kay SA (2001) A role for LKP2 in the circadian clock of Arabidopsis. Plant Cell 13:2659-2670.
84. Sharrock RA and Clack T (2002) Patterns of expression and normalized levels of the five Arabidopsis phytochromes. Plant Physiol 130:442-456.
85. Sharrock RA and Quail PH (1989) Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev 3:1745-1757.
86. Smith NG and Wareing PF (1972) The rooting of actively growing and dormant leafy cuttings in relation to endogenous hormone levels and photoperiod. New Phytol 71:483-500.
87. Somers DE, Devlin PF and Kay SA (1998) Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 282:1488-1490.
88. Somers DE, Schultz TF, Milnamow M and Kay SA (2000) ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis. Cell 101:319-329.
89. Song H-R and Carré IA (2005) DET1 regulates the proteasomal degradation of LHY, a component of the Arabidopsis circadian clock. Plant Mol Biol 57:761-771.
90. Staiger D, Allenbach L, Salathia N, Fiechter V, Davis SJ, Millar AJ, Chory J and Fankhauser C (2003). The Arabidopsis SRR1 gene mediates phyB signaling and is required for normal circadian clock function. Genes Dev 17:256-268.
91. Strayer CA, Oyama T, Schultz TF, Raman R, Somers DE, Más P, Panda S, Kreps JA and Kay SA (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289:768-771.
92. Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F and Coupland G (2001) CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410:1116-1120.
93. Sugano S, Andronis C, Green RM, Wang Z-Y and Tobin EM (1998) Protein kinase CK2 interacts with and phosphorylates the Arabidopsis circadian clock-associated 1 protein. Proc Natl Acad Sci USA 95:11020-11025.
94. Sugano S, Andronis C, Ong MS, Green RM and Tobin EM (1999) The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis. Proc Natl Acad Sci USA 96:12362-12366.
95. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG (1997) The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882.
96. Tóth R, Kevei E, Hall A, Millar AJ, Nagy F and Kozma-Bognar L (2001) Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis. Plant Physiol 127:1607-1616.
97. Tseng T-S, Salomé PA, McClung CR and Olszewski NE (2004) SPINDLY and GIGANTEA interact and act in Arabidopsis thaliana pathways involved in light responses, flowering and rhythms in leaf movements. Plant Cell 16:1550-1563.
98. Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A and Coupland G (2004) Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 303:1003-1006.
99. Wang ZY and Tobin EM (1998) Constitutive expression of the circadian clock associated 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93:1207-1217.
100. Wigge PA, Kim MC, Jaeger KE, Busch W, Schmid M, Lohmann JU and Weigel D (2005) Integration of spatial and temporal information during floral induction in Arabidopsis. Science 309:1056-1059.
101. Yano M, Kojima S, Takahashi Y, Lin H and Sasaki T (2001) Genetic control of flowering time in rice, a short-day plant. Plant Physiol 127:1425-1429.
102. Yanovsky MJ and Kay SA (2002) Molecular basis of seasonal time measurement in Arabidopsis. Nature 419:308-312.
103. Yanovsky MJ, Mazzella MA and Casal JJ (2000) A quadruple photoreceptor mutant still keeps track of time. Curr Biol 10:1013-1015.