Light signal transduction: An infinite spectrum of possibilities

Plant Journal

Volumn 61, Issue 6, 2010, Pages 982-991

  Chory, Joanne ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Arabidopsis; Light signaling; Photoreceptors

Indexed keywords

ARABIDOPSIS; COMPLEX NETWORKS; GENETIC STUDIES; HIGHER PLANTS; IN-PLANTS; LIGHT-SIGNAL TRANSDUCTION; SIGNALING COMPONENTS; SIGNALING NETWORKS;

MAMMALS; SIGNAL TRANSDUCTION; VISION;

SIGNALING;

PHYTOCHROME;

ARABIDOPSIS; ARTICLE; DNA MICROARRAY; GENETICS; GROWTH, DEVELOPMENT AND AGING; HISTORY; METABOLISM; PHOTOTRANSDUCTION;

ARABIDOPSIS; HISTORY, 20TH CENTURY; LIGHT SIGNAL TRANSDUCTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYTOCHROME;

ARABIDOPSIS; EMBRYOPHYTA; MAMMALIA;

EID: 77950377798     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2009.04105.x     Document Type: Article

References (122)

1. Ahmad, M. Cashmore, A.R. (1993) HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature, 366, 162 166.
2. Alonso, J.M. Ecker, J.R. (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat. Rev. Genet. 7, 524 536.
3. Al-Sady, B., Ni, W., Kircher, S., Schafer, E. Quail, P.H. (2006) Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Mol. Cell, 23, 439 446.
4. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796 815.
5. Bae, G. Choi, G. (2008) Decoding of light signals by plant phytochromes and their interacting proteins. Annu. Rev. Plant Biol. 59, 281 311.
6. Balasubramanian, S., Sureshkumar, S., Agrawal, M., Michael, T.P., Wessinger, C., Maloof, J.N., Clark, R., Warthmann, N., Chory, J. Weigel, D. (2006) The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat. Genet. 38, 711 715.
7. Barton, K.A., Binns, A.N., Matzke, A.J. Chilton, M.D. (1983) Regeneration of intact tobacco plants containing full length copies of genetically engineered T-DNA, and transmission of T-DNA to R1 progeny. Cell, 32, 1033 1043.
8. Benvenuto, G., Formiggini, F., Laflamme, P., Malakhov, M. Bowler, C. (2002) The photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a nucleosome context. Curr. Biol. 12, 1529 1534.
9. Borevitz, J.O., Maloof, J.N., Lutes, J. et al. (2002) Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics, 160, 683 696.
10. Briggs, W.R. (2007) The LOV domain: a chromophore module servicing multiple photoreceptors. J. Biomed. Sci. 14, 499 504.
11. Briggs, W.R. Olney, M.A. (2001) Photoreceptors in plant photomorphogenesis to date. Five phytochromes, two cryptochromes, one phototropin, and one superchrome. Plant Physiol. 125, 85 88.
12. Brock, M.T., Tiffin, P. Weinig, C. (2007) Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana. Mol. Ecol. 16, 3050 3062.
13. Bruce, W.B., Christensen, A.H., Klein, T., Fromm, M. Quail, P.H. (1989) Photoregulation of a phytochrome gene promoter from oat transferred into rice by particle bombardment. Proc. Natl Acad. Sci. USA, 86, 9692 9696.
14. Burr, B. Burr, F.A. (1982) Ds controlling elements of maize at the shrunken locus are large and dissimilar insertions. Cell, 29, 977 986.
15. Butler, W.L., Norris, K.H., Siegelman, H.W. Hendricks, S.B. (1959) Detection, assay, and preliminary purification of the pigment controlling photoresponsive development of plants. Proc. Natl Acad. Sci. USA, 45, 1703 1708.
16. Caplan, A., Herrera-Estrella, L., Inze, D., Van Haute, E., Van Montagu, M., Schell, J. Zambryski, P. (1983) Introduction of genetic material into plant cells. Science, 222, 815 821.
17. Cashmore, A.R., Jarillo, J.A., Wu, Y.J. Liu, D. (1999) Cryptochromes: blue light receptors for plants and animals. Science, 284, 760 765.
18. Castillon, A., Shen, H. Huq, E. (2007) Phytochrome interacting factors: central players in phytochrome-mediated light signaling networks. Trends Plant Sci. 12, 514 521.
19. Ceriani, M.F., Darlington, T.K., Staknis, D., Mas, P., Petti, A.A., Weitz, C.J. Kay, S.A. (1999) Light-dependent sequestration of TIMELESS by CRYPTOCHROME. Science, 285, 553 556.
20. Chamovitz, D.A., Wei, N., Osterlund, M.T., von Arnim, A.G., Staub, J.M., Matsui, M. Deng, X.-W. (1996) The COP9 complex, a novel multisubunit nuclear regulator involved in light control of a plant developmental switch. Cell, 86, 115 121.
21. Chattopadhyay, S., Puente, P., Deng, X.W. Wei, N. (1998) Combinatorial interaction of light-responsive elements plays a critical role in determining the response characteristics of light-regulated promoters in Arabidopsis. Plant J. 15, 69 77.
22. Chen, M. (2008) Phytochrome nuclear body: an emerging model to study interphase nuclear dynamics and signaling. Curr. Opin. Plant Biol. 11, 503 508.
23. Chen, E., Swartz, T.E., Bogomolni, R.A. Kliger, D.S. (2007) A LOV story: the signaling state of the phot1 LOV2 photocycle involves chromophore-triggered protein structure relaxation, as probed by far-UV time-resolved optical rotatory dispersion spectroscopy. Biochemistry, 46, 4619 4624.
24. Choi, G., Yi, H., Lee, J., Kwon, Y.K., Soh, M.S., Shin, B., Luka, Z., Hahn, T.R. Song, P.S. (1999) Phytochrome signalling is mediated through nucleoside diphosphate kinase 2. Nature, 401, 610 613.
25. Chory, J. (1992) A genetic model for light-regulated seedling development in Arabidopsis. Development, 115, 337 354.
26. Chory, J. Peto, C.A. (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.
27. Chory, J., Peto, C., Feinbaum, R., Pratt, L. Ausubel, F. (1989) Arabidopsis thaliana mutant that develops as a light-grown plant in the absence of light. Cell, 58, 991 999.
28. Christie, J.M., Reymond, P., Powell, G.K., Bernasconi, P., Raibekas, A.A., Liscum, E. Briggs, W.R. (1998) Arabidopsis NPH1: a flavoprotein with the properties of a photoreceptor for phototropism. Science, 282, 1698 1701.
29. Christie, J.M., Swartz, T.E., Bogomolni, R.A. Briggs, W.R. (2002) Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function. Plant J. 32, 205 219.
30. Clark, R.M., Schweikert, G., Toomajian, C. et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 317, 338 342.
31. Cornilescu, G., Ulijasz, A.T., Cornilescu, C.C., Markley, J.L. Vierstra, R.D. (2008) Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J. Mol. Biol. 383, 403 413.
32. Donald, R.G.K. Cashmore, A.R. (1990) Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J. 9, 1717 1726.
33. El-Assal, S.E.D., Alonso-Blanco, C., Hanhart, C.J. Koornneef, M. (2004) Pleiotropic effects of the Arabidopsis cryptochrome 2 allelic variation underlie fruit trait-related QTL. Plant Biol. (Stuttg.) 6, 370 374.
34. El-Din El-Assal, S., Alonso-Blanco, C., Peeters, A.J., Raz, V. Koornneef, M. (2001) A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat. Genet. 29, 435 440. Erratum: Nat. Genet. (2002) 30, 123.
35. Endo, M. Nagatani, A. (2008) Flowering regulation by tissue specific functions of photoreceptors. Plant Signal. Behav. 3, 47 48.
36. Endo, M., Nakamura, S., Araki, T., Mochizuki, N. Nagatani, A. (2005) Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles. Plant Cell, 17, 1941 1952.
37. Endo, M., Mochizuki, N., Suzuki, T. Nagatani, A. (2007) CRYPTOCHROME2 in vascular bundles regulates flowering in Arabidopsis. Plant Cell, 19, 84 93.
38. Essen, L.O., Mailliet, J. Hughes, J. (2008) The structure of a complete phytochrome sensory module in the Pr ground state. Proc. Natl Acad. Sci. USA, 105, 14709 14714.
39. Fankhauser, C. (2000) Phytochromes as light-modulated protein kinases. Semin. Cell Dev. Biol. 11, 467 473.
40. Fankhauser, C., Yeh, K.C., Lagarias, J.C., Zhang, H., Elich, T.D. Chory, J. (1999) PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis. Science, 284, 1539 1541.
41. Fedoroff, N., Wessler, S. Shure, M. (1983) Isolation of the transposable maize controlling elements Ac and Ds. Cell, 35, 235 242.
42. Filiault, D.L., Wessinger, C.A., Dinneny, J.R., Lutes, J., Borevitz, J.O., Weigel, D., Chory, J. Maloof, J.N. (2008) Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc. Natl Acad. Sci. USA, 105, 3157 3162.
43. Finlayson, S.A., Lee, I.J., Mullet, J.E. Morgan, P.W. (1999) The mechanism of rhythmic ethylene production in sorghum. The role of phytochrome B and simulated shading. Plant Physiol. 119, 1083 1089.
44. Finlayson, S.A., Hays, D.B. Morgan, P.W. (2007) phyB-1 sorghum maintains responsiveness to simulated shade, irradiance and red light: far-red light. Plant Cell Environ. 30, 952 962.
45. Folta, K.M., Lieg, E.J., Durham, T. Spalding, E.P. (2003) Primary inhibition of hypocotyl growth and phototropism depend differently on phototropin-mediated increases in cytoplasmic calcium induced by blue light. Plant Physiol. 133, 1464 1470.
46. Fraley, R.T., Rogers, S.G., Horsch, R.B. et al. (1983) Expression of bacterial genes in plant cells. Proc. Natl Acad. Sci. USA, 80, 4803 4807.
47. Gallagher, S., Short, T.W., Ray, P.M., Pratt, L.H. Briggs, W.R. (1988) Light-mediated changes in two proteins found associated with plasma membrane fractions from pea stem sections. Proc. Natl Acad. Sci. USA, 85, 8003 8007.
48. Geiser, M., Weck, E., Dorng, H.P., Werr, W., Courage-Tebbe, U., Tillmann, E. Starlinger, P. (1982) Genomic clones of a wild-type allele and a transposable element-induced mutant allele of the sucrose synthase gene of Zea mays L. EMBO J. 1, 1455 1460.
49. Gilmartin, P.M., Sarokin, L., Memelink, J. Chua, N.-H. (1990) Molecular light switches for plant genes. Plant Cell, 2, 369 378.
50. Harper, R.M., Stowe-Evans, E.L., Luesse, D.R., Muto, H., Tatematsu, K., Watahiki, M.K., Yamamoto, K. Liscum, E. (2000) The NPH4 locus encodes the auxin response factor ARF7, a conditional regulator of differential growth in aerial Arabidopsis tissue. Plant Cell, 12, 757 770.
51. Harper, S.M., Neil, L.C., Day, I.J., Hore, P.J. Gardner, K.H. (2004) Conformational changes in a photosensory LOV domain monitored by time-resolved NMR spectroscopy. J. Am. Chem. Soc. 126, 3390 3391.
52. Herrera-Estrella, L., Block, M.D., Messens, E., Hernalsteens, J.P., Montagu, M.V. Schell, J. (1983) Chimeric genes as dominant selectable markers in plant cells. EMBO J. 2, 987 995.
53. Hershey, H.P., Colbert, J.T., Lissemore, J.L., Barker, R.F. Quail, P.H. (1984) Molecular cloning of cDNA for Avena phytochrome. Proc. Natl Acad. Sci. USA, 81, 2332 2336.
54. Hitomi, K., DiTacchio, L., Arvai, A.S., Yamamoto, J., Kim, S.T., Todo, T., Tainer, J.A., Iwai, S., Panda, S. Getzoff, E.D. (2009) Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc. Natl Acad. Sci. USA, 106, 6962 6967.
55. Huq, E., Al-Sady, B., Hudson, M., Kim, C., Apel, K. Quail, P.H. (2004) Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis. Science, 305, 1937 1941.
56. Jiao, Y., Lau, O.S. Deng, X.W. (2007) Light-regulated transcriptional networks in higher plants. Nat. Rev. Genet. 8, 217 230.
57. Jones, A.M., Chory, J., Dangl, J.L., Estelle, M., Jacobsen, S.E., Meyerowitz, E.M., Nordborg, M. Weigel, D. (2008) The impact of Arabidopsis on human health: diversifying our portfolio. Cell, 133, 939 943.
58. Kagawa, T., Sakai, T., Suetsugu, N., Oikawa, K., Ishiguro, S., Kato, T., Tabata, S., Okada, K. Wada, M. (2001) Arabidopsis NPL1: a phototropin homolog controlling the chloroplast high-light avoidance response. Science, 291, 2138 2141.
59. Kebrom, T.H. Brutnell, T.P. (2007) The molecular analysis of the shade avoidance syndrome in the grasses has begun. J. Exp. Bot. 58, 3079 3089.
60. Khanna, R., Huq, E., Kikis, E.A., Al-Sady, B., Lanzatella, C. Quail, P.H. (2004) A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. Plant Cell, 16, 3033 3044.
61. Khanna, R., Shen, Y., Marion, C.M., Tsuchisaka, A., Theologis, A., Schafer, E. Quail, P.H. (2007) The basic helix-loop-helix transcription factor PIF5 acts on ethylene biosynthesis and phytochrome signaling by distinct mechanisms. Plant Cell, 19, 3915 3929.
62. Kinoshita, T., Doi, M., Suetsugu, N., Kagawa, T., Wada, M. Shimazaki, K. (2001) Phot1 and phot2 mediate blue light regulation of stomatal opening. Nature, 414, 656 660.
63. Koornneef, M., Rolff, E. Spruit, C.J.P. (1980) Genetic control of light-inhibited hypocotyl elongation in Arabidopsis thaliana (L.) Heynh. Z. Pflanzenphysiol. 100S, 147 160.
64. Koornneef, M., van Eden, J., Hanhart, C.J., Stam, P., Braaksma, F.J. Feenstra, W.J. (1983) Linkage map of Arabidopsis thaliana. J. Hered. 74, 265 272.
65. Kwok, S.F., Piekos, B., Miséra, S. Deng, X.-W. (1996) A complement of ten essential and pleiotropic arabidopsis COP/DET/FUS genes is necessary for repression of photomorphogenesis in darkness. Plant Physiol. 110, 731 742.
66. Lam, E. Chua, N.-H. (1990) GT-1 binding site confers light responsive expression in transgenic tobacco. Science, 248, 471 474.
67. Lazarova, G.I., Kerckhoffs, L.H., Brandstadter, J., Matsui, M., Kendrick, R.E., Cordonnier-Pratt, M.M. Pratt, L.H. (1998) Molecular analysis of PHYA in wild-type and phytochrome A-deficient mutants of tomato. Plant J. 14, 653 662.
68. Leung, D.W., Otomo, C., Chory, J. Rosen, M.K. (2008) Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway. Proc. Natl Acad. Sci. USA, 105, 12797 12802.
69. Levskaya, A., Weiner, O.D., Lim, W.A. Voigt, C.A. (2009) Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature, 461, 997 1001.
70. Lin, C., Yang, H., Guo, H., Mockler, T., Chen, J. Cashmore, A.R. (1998) Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2. Proc. Natl Acad. Sci. USA, 95, 2686 2690.
71. Liscum, E. Briggs, W.R. (1995) Mutations in the NPH1 locus of Arabidopsis disrupt the perception of phototropic stimuli. Plant Cell, 7, 473 485.
72. Lister, R., Gregory, B.D. Ecker, J.R. (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr. Opin. Plant Biol. 12, 107 118.
73. Litts, J.C., Kelly, J.M. Lagarias, J.C. (1983) Structure-function studies on phytochrome. J. Biol. Chem. 258, 11025 11031.
74. Liu, Y., Roof, S., Ye, Z., Barry, C., van Tuinen, A., Vrebalov, J., Bowler, C. Giovannoni, J. (2004) Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc. Natl Acad. Sci. USA, 101, 9897 9902.
75. Liu, H., Yu, X., Li, K., Klejnot, J., Yang, H., Lisiero, D. Lin, C. (2008) Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science, 322, 1535 1539.
76. Lloyd, A.M., Barnason, A.R., Rogers, S.G., Byrne, M.C., Fraley, R.T. Horsch, R.B. (1986) Transformation of Arabidopsis thaliana with Agrobacterium tumefaciens. Science, 234, 464 466.
77. Loudet, O., Michael, T.P., Burger, B.T., Le Mette, C., Mockler, T.C., Weigel, D. Chory, J. (2008) A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 105, 17193 17198.
78. Ma, L., Zhao, H. Deng, X.W. (2003) Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development, 130, 969 981.
79. Maloof, J.N., Borevitz, J.O., Weigel, D. Chory, J. (2000) Natural variation in phytochrome signaling. Semin. Cell Dev. Biol. 11, 523 530.
80. Maloof, J.N., Borevitz, J.O., Dabi, T. et al. (2001) Natural variation in light sensitivity of Arabidopsis. Nat. Genet. 29, 441 446.
81. Mas, P., Devlin, P.F., Panda, S. Kay, S.A. (2000) Functional interaction of phytochrome B and cryptochrome 2. Nature, 408, 207 211.
82. Menon, S., Chi, H., Zhang, H., Deng, X.W., Flavell, R.A. Wei, N. (2007) COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptor-induced entry into the cell cycle from quiescence. Nat. Immunol. 8, 1236 1245.
83. Monte, E., Al-Sady, B., Leivar, P. Quail, P.H. (2007) Out of the dark: how the PIFs are unmasking a dual temporal mechanism of phytochrome signalling. J. Exp. Bot. 58, 3125 3133.
84. Motchoulski, A. Liscum, E. (1999) Arabidopsis NPH3: a NPH1 photoreceptor-interacting protein essential for phototropism. Science, 286, 961 964.
85. Murai, N., Kemp, J.D., Sutton, D.W. et al. (1983) Phaseolin gene from bean is expressed after transfer to sunflower via tumor-inducing plasmid vectors. Science, 222, 476 482.
86. Mustilli, A.C., Fenzi, F., Ciliento, R., Alfano, F. Bowler, C. (1999) Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. Plant Cell, 11, 145 157.
87. Nagatani, A. (2004) Light-regulated nuclear localization of phytochromes. Curr. Opin. Plant Biol. 7, 708 711.
88. Neff, M.M., Fankhauser, C. Chory, J. (2000) Light: an indicator of time and place. Genes Dev. 14, 257 271.
89. Ni, M., Tepperman, J.M. Quail, P.H. (1999) Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Nature, 400, 781 784.
90. Ogura, Y., Komatsu, A., Zikihara, K., Nanjo, T., Tokutomi, S., Wada, M. Kiyosue, T. (2008) Blue light diminishes interaction of PAS/LOV proteins, putative blue light receptors in Arabidopsis thaliana, with their interacting partners. J. Plant. Res. 121, 97 105.
91. Rockwell, N.C., Su, Y.S. Lagarias, J.C. (2006) Phytochrome structure and signaling mechanisms. Annu. Rev. Plant Biol. 57, 837 858.
92. Sakamoto, K. Nagatani, A. (1996) Nuclear localization activity of phytochrome B. Plant J. 10, 859 868.
93. Schroeder, D.F., Gahrtz, M., Maxwell, B.B., Cook, R.K., Kan, J.M., Alonso, J.M., Ecker, J.R. Chory, J. (2002) De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis. Curr. Biol. 12, 1462 1472.
94. Sharrock, R.A. Quail, P.H. (1989) Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 3, 1745 1757.
95. Shen, Y., Khanna, R., Carle, C.M. Quail, P.H. (2007) Phytochrome induces rapid PIF5 phosphorylation and degradation in response to red-light activation. Plant Physiol. 145, 1043 1051.
96. Short, T.W. Briggs, W.R. (1994) The transduction of blue light signals in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 45, 143 171.
97. Shu, X., Royant, A., Lin, M.Z., Aguilera, T.A., Lev-Ram, V., Steinbach, P.A. Tsien, R.Y. (2009) Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science, 324, 804 807.
98. Siegelman, H.W., Turner, B.C. Hendricks, S.B. (1966) The chromophore of phytochrome. Plant Physiol. 41, 1289 1292.
99. Silverthorne, J. Tobin, E.M. (1984) Demonstration of transcriptional regulation of specific genes by phytochrome action. Proc. Natl Acad. Sci. USA, 81, 1112 1116.
100. Simpson, J., Timko, M.P., Cashmore, A.R., Schell, J., Van Montagu, M. Herrera-Estrella, L. (1985) Light-inducible and tissue-specific expression of a chimaeric gene under control of the 5′-flanking sequence of a pea chlorophyll a/b-binding protein gene. EMBO J. 4, 2723 2729.
101. Strickland, D., Moffat, K. Sosnick, T.R. (2008) Light-activated DNA binding in a designed allosteric protein. Proc. Natl Acad. Sci. USA, 105, 10709 10714.
102. Tanaka, S., Nakamura, S., Mochizuki, N. Nagatani, A. (2002) Phytochrome in cotyledons regulates the expression of genes in the hypocotyl through auxin-dependent and -independent pathways. Plant Cell Physiol. 43, 1171 1181.
103. Tepperman, J.M., Hudson, M.E., Khanna, R., Zhu, T., Chang, S.H., Wang, X. Quail, P.H. (2004) Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J. 38, 725 739.
104. Tepperman, J.M., Hwang, Y.S. Quail, P.H. (2006) phyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of Arabidopsis seedling de-etiolation. Plant J. 48, 728 742.
105. Timko, M.P., Kausch, A.P., Castresana, C., Fassler, J., Herrera-Estrella, L., Van den Broeck, G., Van Montagu, M., Schell, J. Cashmore, A.R. (1985) Light regulation of plant gene expression by an upstream enhancer-like element. Nature, 318, 579 582.
106. Tokutomi, S., Matsuoka, D. Zikihara, K. (2008) Molecular structure and regulation of phototropin kinase by blue light. Biochim. Biophys. Acta, 1784, 133 142.
107. Vierstra, R.D. Quail, P.H. (1983) Photochemistry of 124 kilodalton Avena phytochrome in vitro. Plant Physiol. 82, 264 267.
108. Wagner, J.R., Zhang, J., Brunzelle, J.S., Vierstra, R.D. Forest, K.T. (2007) High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. J. Biol. Chem. 282, 12298 12309.
109. Wei, N. Deng, X.W. (2003) The COP9 signalosome. Annu. Rev. Cell Dev. Biol. 19, 261 286.
110. Wei, N., Tsuge, T., Serino, G., Dohmae, N., Takio, K., Matsui, M. Deng, X.W. (1998) The COP9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex. Curr. Biol. 8, 919 922.
111. Weigel, D. Mott, R. (2009) The 1001 genomes project for Arabidopsis thaliana. Genome Biol. 10, 107.
112. Wertz, I.E., O'Rourke, K.M., Zhang, Z., Dornan, D., Arnott, D., Deshaies, R.J. Dixit, V.M. (2004) Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. Science, 303, 1371 1374.
113. Wu, Y.I., Frey, D., Lungu, O.I., Jaehrig, A., Schlichting, I., Kuhlman, B. Hahn, K.M. (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature, 461, 104 108.
114. Yamaguchi, R., Nakamura, M., Mochizuki, N., Kay, S.A. Nagatani, A. (1999) Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus in transgenic Arabidopsis. J. Cell Biol. 145, 437 445.
115. Yanagawa, Y., Sullivan, J.A., Komatsu, S. et al. (2004) Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes. Genes Dev. 18, 2172 2181.
116. Yang, X., Kuk, J. Moffat, K. (2008) Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction. Proc. Natl Acad. Sci. USA, 105, 14715 14720.
117. Yazaki, J., Gregory, B.D. Ecker, J.R. (2007) Mapping the genome landscape using tiling array technology. Curr. Opin. Plant Biol. 10, 534 542.
118. Yeh, K.C. Lagarias, J.C. (1998) Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc. Natl Acad. Sci. USA, 95, 13976 13981.
119. Yeh, K.C., Wu, S.H., Murphy, J.T. Lagarias, J.C. (1997) A cyanobacterial phytochrome two-component light sensory system. Science, 277, 1505 1508.
120. Yi, C. Deng, X.W. (2005) COP1 - from plant photomorphogenesis to mammalian tumorigenesis. Trends Cell Biol. 15, 618 625.
121. Zhang, Y., Feng, S., Chen, F., Chen, H., Wang, J., McCall, C., Xiong, Y. Deng, X.W. (2008) Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. Plant Cell, 20, 1437 1455.
122. Zhulin, I.B., Taylor, B.L. Dixon, R. (1997) PAS domain S-boxes in Archaea, bacteria, and sensors for oxygen and redox. Trends Biochem. Sci. 9, 331 333.