Signaling Mechanisms of Higher Plant Photoreceptors: A Structure-Function Perspective

Current Topics in Developmental Biology

Volumn 68, Issue , 2005, Pages 227-261

  Wang, Haiyang ^a  

^a United States Department of Agriculture   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYPTOCHROME; FLAVOPROTEIN; PHYTOCHROME;

ARABIDOPSIS; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; GENE; GENETICS; METABOLISM; MULTIGENE FAMILY; PHOSPHORYLATION; PHOTOSYNTHESIS; REVIEW; SIGNAL TRANSDUCTION;

ARABIDOPSIS; FLAVOPROTEINS; GENES, PLANT; MODELS, BIOLOGICAL; MOLECULAR STRUCTURE; MULTIGENE FAMILY; PHOSPHORYLATION; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; PHYTOCHROME; SIGNAL TRANSDUCTION;

EID: 25144446374     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0070-2153(05)68008-8     Document Type: Review

References (196)

1. Ahmad M., and Cashmore A.R. HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 366 (1993) 162-166
2. Ahmad M., Lin C., and Cashmore A.R. Mutations throughout an Arabidopsis blue-light photoreceptor impair blue-light-responsive anthocyanin accumulation and inhibition of hypocotyl elongation. Plant J. 8 (1995) 653-658
3. Ahmad M., and Cashmore A.R. The blue-light receptor cryptochrome 1 shows functional dependence on phytochrome A or phytochrome B in Arabidopsis thaliana. Plant J. 11 (1997) 421-427
4. Ahmad M., Jarillo J.A., Smirnova O., and Cashmore A.R. The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro. Mol. Cell 1 (1998) 939-948
5. Ahmad M., Jarillo J.A., Smirnova O., and Cashmore A.R. Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism. Nature 392 (1998) 720-723
6. Ahmad M., Grancher N., Heil M., Black R.C., Giovani B., Galland P., and Lardemer D. Action spectrum for cryptochrome-dependent hypocotyl growth inhibition in Arabidopsis. Plant Physiol. 129 (2002) 774-785
7. Andel III F., Lagarias J.C., and Mathies R.A. Resonance Raman analysis of chromophore structure in the lumi-R photoproduct of phytochrome. Biochemistry 35 (1996) 15997-16008
8. Aukerman M.J., Hirschfeld M., Wester L., Weaver M., Clack T., Amasino R.M., and Sharrock R.A. A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing. Plant Cell 9 (1997) 1317-1326
9. Blazquez M.A., Soowal L.N., Lee I., and Weigel D. LEAFY expression and flower initiation in Arabidopsis. Development 124 (1997) 3835-3844
10. Blazquez M.A., and Weigel D. Independent regulation of flowering by phytochrome B and gibberellins in Arabidopsis. Plant Physiol. 120 (1999) 1025-1032
11. Bognar L.K., Hall A., Adam E., Thain S.C., Nagy F., and Millar A.J. The circadian clock controls the expression pattern of the circadian input photoreceptor, phytochrome B. Proc. Natl. Acad. Sci. USA 96 (1999) 14652-14657
12. Borthwick H.A., Hendricks S.B., Parker M.W., Toole E.H., and Toole V.K. A reversible photoreaction controlling seed germination. Proc. Natl. Acad. Sci. USA 38 (1952) 662-666
13. Botto J.F., Sanchez R.A., Whitelam G.C., and Casal J.J. Phytochrome A mediates the promotion of seed germination by very low fluences of light and canopy shade light in Arabidopsis. Plant Physiol. 110 (1996) 439-444
14. Brautigam C.A., Smith B.S., Ma Z., Palnitkar M., Tomchick D.R., Machius M., and Deisenhofer J. Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 101 (2004) 12142-12147
15. Briggs W.R., and Olney M.A. Photoreceptors in plant photomorphogenesis to date. Five phytochromes, two cryptochromes, one phototropin, and one superchrome. Plant Physiol. 125 (2001) 85-88
16. Briggs W.R., and Christie J.M. Phototropins 1 and 2: Versatile plant blue-light receptors. Trends Plant Sci. 7 (2002) 204-210
17. Brudler R., Hitomi K., Daiyasu H., Toh H., Kucho K., Ishiura M., Kanehisa M., Roberts V.A., Todo T., Tainer J.A., and Getzoff E.D. Identification of a new cryptochrome class. Structure, function, and evolution. Mol. Cell 11 (2003) 59-67
18. Canton F.R., and Quail P.H. Both phyA and phyB mediate light-imposed repression of PHYA gene expression in Arabidopsis. Plant Physiol. 121 (1999) 1207-1216
19. Casal J.J., and Mazzella M.A. Conditional synergism between cryptochrome 1 and phytochrome B is shown by the analysis of phyA, phyB, and hy4 simple, double, and triple mutants in Arabidopsis. Plant Physiol. 118 (1998) 19-25
20. Casal J.J., Sánchez R.A., and Botto J.F. Modes of action of phytochromes. J. Exp. Bot. 49 (1998) 127-138
21. Cashmore A.R., Jarillo J.A., Wu Y.J., and Liu D. Cryptochromes: Blue light receptors for plants and animals. Science 284 (1999) 760-765
22. Cashmore A.R. Cryptochromes: Enabling plants and animals to determine circadian time. Cell 114 (2003) 537-543
23. Chen M., Schwab R., and Chory J. Characterization of the requirements for localization of phytochrome B to nuclear bodies. Proc. Natl. Acad. Sci. USA 100 (2003) 14493-14498
24. Cherry J.R., Hondred D., Walker J.M., and Vierstra R.D. Phytochrome requires the 6-kDa N-terminal domain for full biological activity. Proc. Natl. Acad. Sci. USA 89 (1992) 5039-5043
25. Cherry J.R., Hondred D., Walker J.M., Keller J.M., Hershey H.P., and Vierstra R.D. Carboxy-terminal deletion analysis of oat phytochrome A reveals the presence of separate domains required for structure and biological activity. Plant Cell 5 (1993) 565-575
26. Choi G., Yi H., Lee J., Kwon Y.K., Soh M.S., Shin B., Luka S., Hahn T.R., and Song P.S. Phytochrome signaling is mediated through nucleoside diphosphate kinase 2. Nature 401 (1999) 610-613
27. Christie J.M., and Briggs W.R. Blue light sensing in higher plants. J. Biol. Chem. 276 (2001) 11457-11460
28. Christie J.M., Reymond P., Powell G.K., Bernasconi P., Raibekas A.A., Liscum E., and Briggs W.R. Arabidopsis NPH1: A flavoprotein with the properties of a photoreceptor for phototropism. Science 282 (1998) 1698-1701
29. Christie J.M., Salomon M., Nozue K., Wada M., and Briggs W.R. LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): Binding sites for the chromophore flavin mononucleotide. Proc. Natl. Acad. Sci. USA 96 (1999) 8779-8783
30. Christie J.M., Swartz T.E., Bogomolni R.A., and Briggs W.R. Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function. Plant J. 32 (2002) 205-219
31. Clack T., Mathews S., and Sharrock R.A. The phytochrome apoprotein family in Arabidopsis is encoded by five genes: The sequences and expression of PHYD and PHYE. Plant Mol. Biol. 25 (1994) 413-427
32. Clough R.C., Jordan-Beebe E.T., Lohman K.N., Marita J.M., Walker J.M., Gatz C., and Vierstra R.D. Sequences within both the N- and C-terminal domains of phytochrome A are required for PFR ubiquitination and degradation. Plant J. 17 (1999) 155-167
33. Colón-Carmona A., Chen D.L., Yeh K.-C., and Abel S. Aux/IAA proteins are phosphorylated by phytochrome in vitro. Plant Physiol. 124 (2000) 1728-1738
34. Corchnoy S.B., Swartz T.E., Lewis J.W., Szundi I., Briggs W.R., and Bogomolni R.A. Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1. J. Biol. Chem. 278 (2003) 724-731
35. Crosson S., and Moffat K. Structure of a flavin-binding plant photoreceptor domain: Insights into light-mediated signal transduction. Proc. Natl. Acad. Sci. USA 98 (2001) 2995-3000
36. Crosson S., and Moffat K. Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Plant Cell 14 (2002) 1067-1075
37. Crosson S., Rajagopal S., and Moffat K. The LOV domain family: Photoresponsive signaling modules coupled to diverse output domains. Biochemistry 42 (2003) 2-10
38. Cutler S.R., Ehrhardt D.W., Griffitts J.S., and Somerville C.R. Random GFP::cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency. Proc. Natl. Acad. Sci. USA 97 (2000) 3718-3723
39. Deng X.W., and Quail P.H. Signalling in light-controlled development. Semin. Cell Dev. Biol. 10 (1999) 121-129
40. Devlin P.F., Halliday K.J., Harberd N.P., and Whitelam G.C. The rosette habit of Arabidopsis thaliana is dependent upon phytochrome action: Novel phytochromes control internode elongation and flowering time. Plant J. 10 (1996) 1127-1134
41. Devlin P.F., Patel S.R., and Whitelam G.C. Phytochrome E influences internode elongation and flowering time in Arabidopsis. Plant Cell 10 (1998) 1479-1487
42. Devlin P.F., Robson P.R., Patel S.R., Goosey L., Sharrock R.A., and Whitelam G.C. Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time. Plant Physiol. 119 (1999) 909-915
43. El-Din El-Assal S., Alonso-Blanco C., Peeters A.J., Raz V., and Koornneef M. A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat. Genet. 29 (2001) 435-440
44. Elich T.D., and Chory J. Biochemical characterization of Arabidopsis wild-type and mutant phytochrome B holoproteins. Plant Cell 9 (1997) 2271-2280
45. Fankhauser C., Yeh K.C., Lagarias J.C., Zhang H., Elich T.D., and Chory J. PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis. Science 284 (1999) 1539-1541
46. Fankhauser C. Phytochromes as light-modulated protein kinases. Semin. Cell. Dev. Biol. 11 (2000) 467-473
47. Fankhauser C. The phytochromes, a family of red/far-red absorbing photoreceptors. J. Biol. Chem. 276 (2001) 11453-11456
48. Federov R., Schlichting I., Hartmann E., Domratcheva T., Fuhrmann M., and Hegemann P. Crystal structures and molecular mechanism of a light-induced signaling switch: The phot1-LOV domain from Chlamydomonas reinhartii. Biophys. J. 84 (2003) 2474-2482
49. Folta K.M., and Spalding E.P. Unexpected roles for cryptochrome 2 and phototropin revealed by high-resolution analysis of blue light-mediated hypocotyl growth inhibition. Plant J. 26 (2001) 471-478
50. Folta K.M. Green light stimulates early stem elongation, antagonizing light-mediated growth inhibition. Plant Physiol. 135 (2004) 1407-1416
51. Franklin K.A., Davis S.J., Stoddart W.M., Vierstra R.D., and Whitelam G.C. Mutant analyses define multiple roles for phytochrome C in Arabidopsis photomorphogenesis. Plant Cell 15 (2003) 1981-1989
52. Franklin K.A., Praekelt U., Stoddart W.M., Billingham O.E., Halliday K.J., and Whitelam G.C. Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis. Plant Physiol. 131 (2003) 1340-1346
53. Frechilla S., Zhu J., Talbott L.D., and Zeiger E. Stomata from npq1, a zeaxanthin-less Arabidopsis mutant, lack a specific response to blue light. Plant Cell Physiol. 40 (1999) 949-954
54. Furuya M., and Song P.-S. Assembly and properties of holophytochrome. In: Kendrick R.E., and Kronenberg G.H.M. (Eds). "Photomorphogenesis in Plants" (1994), Kluwer Academic Publishers, Dordrecht, The Netherlands 105-140
55. Gallagher S., Short T.W., Ray P.M., Pratt L.H., and Briggs W.R. Light-mediated changes in two proteins found associated with plasma membrane fractions from pea stem sections. Proc. Natl. Acad. Sci. USA 85 (1988) 8003-8007
56. Garner W.W., and Allard H.A. Effect of the relative length of day and night and other factors of the environment on growth and reproduction in plants. J. Agric. Res. 18 (1920) 553-606
57. Giovani B., Brrdin M., Ahmad M., and Brettel K. Light-induced electron transfer in a cryptochrome blue-light photoreceptor. Nat. Struct. Biol. 10 (2003) 489-490
58. Guo H., Yang H., Mockler T.C., and Lin C. Regulation of flowering time by Arabidopsis photoreceptors. Science 279 (1998) 1360-1363
59. Guo H., Duong H., Ma N., and Lin C. The Arabidopsis blue light receptor cryptochrome 2 is a nuclear protein regulated by a blue light-dependent post-transcriptional mechanism. Plant J. 19 (1999) 279-287
60. Gyula P., Schafer E., and Nagy F. Light perception and signalling in higher plants. Curr. Opin. Plant Biol. 6 (2003) 446-452
61. Hager A., and Brich M. Blue-light-induced phosphorylation of a plasma-membrane protein from phototropically sensitive tips of maize coleoptiles. Planta 189 (1993) 567-576
62. Hamazato F., Shinomura T., Hanzawa H., Chory J., and Furuya M. Fluence and wavelength requirements for Arabidopsis CAB gene induction by different phytochromes. Plant Physiol. 115 (1997) 1533-1540
63. Harper S.M., Neil L.C., and Gardner K.H. Structural basis of a phototropin light switch. Science 301 (2003) 1541-1544
64. Harper S.M., Neil L.C., Day I.J., Hore P.J., and Gardner K.H. Conformational changes in a photosensory LOV domain monitored by time-resolved NMR spectroscopy. J. Am. Chem. Soc. 126 (2004) 3390-3391
65. Haupt W., and Häder D.P. Photomovement. In: Kendrick R.E., and Kronenberg G.H.M. (Eds). "Photomorphogenesis in Plants" (1994), Kluwer Academic Publishers, Dordrecht, The Netherlands 707-732
66. Hennig L., Buche C., Eichenberg K., and Schafer E. Dynamic properties of endogenous phytochrome A in Arabidopsis seedlings. Plant Physiol. 121 (1999) 571-577
67. Hennig L., Stoddart W.M., Dieterle M., Whitelam G.C., and Schafer E. Phytochrome E controls light-induced germination of Arabidopsis. Plant Physiol. 128 (2002) 194-200
68. Hirschfeld M., Tepperman J.M., Clack T., Quail P.H., and Sharrock R.A. Coordination of phytochrome levels in phyB mutants of Arabidopsis as revealed by apoprotein-specific monoclonal antibodies. Genetics 149 (1998) 523-535
69. Huala E., Oeller P.W., Liscum E., Han I.S., Larsen E., and Briggs W.R. Arabidopsis NPH1: A protein kinase with a putative redox-sensing domain. Science 278 (1997) 2120-2123
70. Huang K., and Beck C.F. Phototropin is the blue-light receptor that controls multiple steps in the sexual life cycle of the green alga Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 100 (2003) 6269-6274
71. Hughes J., and Lamparter T. Prokaryotes and phytochrome. The connection to chromophores and signaling. Plant Physiol. 121 (1999) 1059-1068
72. Huq E., and Quail P.H. PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J. 21 (2002) 2441-2450
73. Huq E., Al-Sady B., and Quail P.H. Nuclear translocation of the photoreceptor phytochrome B is necessary for its biological function in seedling photomorphogenesis. Plant J. 35 (2003) 660-664
74. Imaizumi T., Tran H.G., Swartz T.E., Briggs W.R., and Kay S.A. FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426 (2003) 302-306
75. Jackson J.A., and Jenkins G.I. Extension-growth responses and expression of flavonoid biosynthesis genes in the Arabidopsis hy4 mutant. Planta 197 (1995) 233-239
76. Janoudi A.K., Gordon W.R., Wagner D., Quail P., and Poff K.L. Multiple phytochromes are involved in red-light-induced enhancement of first-positive phototropism in Arabidopsis thaliana. Plant Physiol. 113 (1997) 975-979
77. Jansen M., Gaba V., and Greenberg B. Higher plants and UV-B radiation: Balancing damage, repair and acclimation. Trends Plant Sci. 3 (1998) 131-135
78. Jarillo J.A., Capel J., Tang R.H., Yang H.Q., Alonso J.M., Ecker J.R., and Cashmore A.R. An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature 410 (2001) 487-490
79. Jenkins G.I., Christie J.M., Fuglevand G., Long J.C., and Jackson J.A. Plant responses to UV and blue light: Biochemical and genetic approaches. Plant Sci. 112 (1995) 117-138
80. Jordan E.T., Cherry J.R., Walker J.M., and Vierstra R.D. The amino-terminus of phytochrome A contains two distinct functional domains. Plant J. 9 (1996) 243-257
81. Jordan E.T., Marita J.M., Clough R.C., and Vierstra R.D. Characterization of regions within the N-terminal 6-kilodalton domain of phytochrome A that modulate its biological activity. Plant Physiol. 115 (1997) 693-704
82. Kagawa T., Sakai T., Suetsugu N., Oikawa K., Ishiguro S., Kato T., Tabata S., Okada K., and Wada M. Arabidopsis NPL1: A phototropin homolog controlling the chloroplast high-light avoidance response. Science 291 (2001) 2138-2141
83. Kawai H., Kanegae T., Christensen S., Kiyosue T., Sato Y., Imaizumi T., Kadota A., and Wada M. Responses of ferns to red light are mediated by an unconventional photoreceptor. Nature 421 (2003) 287-290
84. Kendrick R.E., and Kronenberg G.H.M. "Photomorphogenesis in Plants." (1994), Academic Publishers, Kluwer Dordrecht, The Netherlands
85. Kennis J.T., Crosson S., Gauden M., van Stokkum I.H., Moffat K., and van Grondelle R. Primary reactions of the LOV2 domain of phototropin, a plant blue-light photoreceptor. Biochemistry 42 (2003) 3385-3392
86. Khanna R., Huq E., Kikis E.A., Al-Sady B., Lanzatella C., and Quail P.H. A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. Plant Cell 16 (2004) 3033-3044
87. Kim B.C., Tennessen D.J., and Last R.L. UV-B-induced photomorphogenesis in Arabidopsis thaliana. Plant J. 15 (1998) 667-674
88. Kim D.-H., Kang J.-G., Yang S.-S., Chung K.-S., Song P.-S., and Park C.-M. A phytochrome associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis. Plant Cell 14 (2002) 3043-3056
89. Kim J., Yi H., Choi G., Shin B., and Song P.S. Functional characterization of phytochrome interacting factor 3 in phytochrome-mediated light signal transduction. Plant Cell 15 (2003) 2399-2407
90. Kim J.-I., Shen Y., Han Y.-J., Park J.-E., Kirchenbauer D., Soh M.-S., Nagy F., Schäfer E., and Song P.-S. Phytochrome phosphorylation modulates light signaling by influencing the protein-protein interaction. Plant Cell 16 (2004) 2629-2640
91. Kinoshita T., Doi M., Suetsugu N., Kagawa T., Wada M., and Shimazaki K. Phot1 and phot2 mediate blue light regulation of stomatal opening. Nature 414 (2001) 656-660
92. Kircher S., Kozma-Bognar L., Kim L., Adam E., Harter K., Schafer E., and Nagy F. Light quality-dependent nuclear import of the plant photoreceptors phytochrome A and B. Plant Cell 11 (1999) 1445-1456
93. Kircher S., Gil P., Kozma-Bognar L., Fejes E., Speth V., Husselstein-Muller T., Bauer D., Adam E., Schafer E., and Nagy F. Nucleocytoplasmic partitioning of the plant photoreceptors phytochrome A, B, C, D, and E is regulated differentially by light and exhibits a diurnal rhythm. Plant Cell 14 (2002) 1541-1555
94. Kleine T., Lockhart P., and Batschauer A. An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles. Plant J. 35 (2003) 93-103
95. Kleiner O., Kircher S., Harter K., and Batschauer A. Nuclear localization of the Arabidopsis blue light receptor cryptochrome 2. Plant J. 19 (1999) 289-296
96. Krall L., and Reed J.W. The histidine kinase-related domain participates in phytochrome B function but is dispensable. Proc. Natl. Acad. Sci. USA 97 (2000) 8169-8174
97. Kretsch T., Poppe C., and Schafer E. A new type of mutation in the plant photoreceptor phytochrome B causes loss of photoreversibility and an extremely enhanced light sensitivity. Plant J. 22 (2000) 177-186
98. Lapko V.N., Jiang X.-Y., Smith D.L., and Song P.-S. Post-translational modification of oat phytochrome A: Phosphorylation of a specific serine in a multiple serine cluster. Biochemistry 36 (1997) 10595-10599
99. Lapko V.N., Jiang X.-Y., Smith D.L., and Song P.-S. Mass spectrometric characterization of oat phytochrome A: Isoforms and posttranslational modifications. Protein Sci. 8 (1999) 1032-1044
100. Lasceve G., Leymarie J., Olney M.A., Liscum E., Christie J.M., Vavasseur A., and Briggs W.R. Arabidopsis contains at least four independent blue-light-activated signal transduction pathways. Plant Physiol. 120 (1999) 605-614
101. Lin C., Robertson D.E., Ahmad M., Raibekas A.A., Jorns M.S., Dutton P.L., and Cashmore A.R. Association of flavin adenine dinucleotide with the Arabidopsis blue light receptor CRY1. Science 269 (1995) 968-970
102. Lin C., Yang H., Guo H., Mockler T., Chen J., and Cashmore A.R. Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2. Proc. Natl. Acad. Sci. USA 95 (1998) 2686-2690
103. Lin C. Photoreceptors and regulation of flowering time. Plant Physiol. 123 (2000) 39-50
104. Lin C. Blue light receptors and signal transduction. Plant Cell 14 Suppl. (2002) S207-S225
105. Lin C. Phototropin blue light receptors and light-induced movement responses in plants. Sci. STKE 2002 (2002) PE5
106. Lin C., and Shalitin D. Cryptochrome structure and signal transduction. Annu. Rev. Plant Biol. 54 (2003) 469-496
107. Liscum E., and Briggs W.R. Mutations in the NPH1 locus of Arabidopsis disrupt the perception of phototropic stimuli. Plant Cell 7 (1995) 473-485
108. Liscum E. Phototropism, mechanisms and outcomes. In: Somerville C., and Meyerowitz E. (Eds). "The Arabidopsis Book" (2002), American Society of Plant Biologists, Rockville, MD. http://www.aspb.org/publications/arabidopsis/doi/10.1199/tab.0074/
109. Liscum E., Hodgson D.W., and Campbell T.J. Blue light signaling through the cryptochromes and phototropins. So that's what the blues is all about. Plant Physiol. 133 (2003) 1429-1436
110. Losi A. The bacterial counterparts of plant phototropins. Photochem. Photobiol. Sci. 3 (2004) 566-574
111. Ma L., Li J., Qu L., Hager J., Chen Z., Zhao H., and Deng X.W. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13 (2001) 2589-2607
112. Malhotra K., Kim S.T., Batschauer A., Dawut L., and Sancar A. Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity. Biochemistry 34 (1995) 6892-6899
113. Maloof J.N., Borevitz J.O., Dabi T., Lutes J., Nehring R.B., Redfern J.L., Trainer G.T., Wilson J.M., Asami T., Berry C.C., Weigel D., and Chory J. Natural variation in light sensitivity of Arabidopsis. Nat. Genet. 29 (2001) 441-446
114. Mancinelli A.L. The physiology of phytochrome action. In: Kendrick R.E., and Kronenberg G.H.M. (Eds). "Photomorphogenesis in Plants" (1994), Kluwer Academic Publishers, Dordrecht, The Netherlands 211-269
115. Martinez-Garcia J.F., Huq E., and Quail P.H. Direct targeting of light signals to a promoter element-bound transcription factor. Science 288 (2000) 859-863
116. Mas P., Devlin P.F., Panda S., and Kay S.A. Functional interaction of phytochrome B and cryptochrome 2. Nature 408 (2000) 207-211
117. Mathews S., and Sharrock R.A. Phytochrome gene diversity. Plant Cell Environ. 20 (1997) 666-671
118. Matsushita T., Mochizuki N., and Nagatani A. Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature 424 (2003) 571-574
119. McClung C.R. Circadian rhythms in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52 (2001) 139-162
120. Mockler T.C., Guo H., Yang H., Duong H., and Lin C. Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction. Development 126 (1999) 2073-2082
121. Mockler T., Yang H., Yu X., Parikh D., Cheng Y.C., Dolan S., and Lin C. Regulation of photoperiodic flowering by Arabidopsis photoreceptors. Proc. Natl. Acad. Sci. USA 100 (2003) 2140-2145
122. Monte E., Alonso J.M., Ecker J.R., Zhang Y., Li X., Young J., Austin-Phillips S., and Quail P.H. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. Plant Cell 15 (2003) 1962-1980
123. Montgomery B.L., and Lagarias J.C. Phytochrome ancestry: Sensors of bilins and light. Trends Plant Sci. 7 (2002) 357-366
124. Motchoulski A., and Liscum E. Arabidopsis NPH3: A NPH1 photoreceptor-interacting protein essential for phototropism. Science 286 (1999) 961-964
125. Mouradov A., Cremer F., and Coupland G. Control of flowering time: Interacting pathways as a basis for diversity. Plant Cell 14 (2002) S111-S130
126. Nagatani A., Reed J.W., and Chory J. Isolation and initial characterization of Arabidopsis mutants that are deficient in phytochrome A. Plant Physiol. 102 (1993) 269-277
127. Nagy F., Kircher S., and Schafer E. Nucleo-cytoplasmic partitioning of the plant photoreceptors phytochromes. Semin. Cell. Dev. Biol. 11 (2000) 505-510
128. Neff M.M., and Van Volkenburgh E. Light-stimulated cotyledon expansion in arabidopsis seedlings (the role of phytochrome B). Plant Physiol. 104 (1994) 1027-1032
129. Neff M.M., and Chory J. Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during Arabidopsis development. Plant Physiol. 118 (1998) 27-35
130. Neff M.M., Fankhauser C., and Chory J. Light: An indicator of time and place. Genes Dev. 14 (2000) 257-271
131. Ni M., Tepperman J.M., and Quail P.H. PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95 (1998) 657-667
132. Nilsson O., Lee I., Blazquez M.A., and Weigel D. Flowering-time genes modulate the response to LEAFY activity. Genetics 150 (1998) 403-410
133. Oka Y., Matsushita T., Mochizuki N., Suzuki T., Tokutomi S., and Nagatani A. Functional analysis of a 450-amino acid N-terminal fragment of phytochrome B in Arabidopsis. Plant Cell 16 (2004) 2104-2116
134. Palmer J.M., Short T.W., Gallagher S., and Briggs W.R. Blue light-induced phosphorylation of a plasma membrane-associated protein in Zea mays L. Plant Physiol. 102 (1993) 1211-1218
135. Park C.M., Bhoo S.H., and Song P.S. Inter-domain crosstalk in the phytochrome molecules. Semin. Cell. Dev. Biol. 11 (2000) 449-456
136. Parks B.M., Quail P.H., and Hangarter R.P. Phytochrome A regulates red-light induction of phototropic enhancement in Arabidopsis. Plant Physiol. 110 (1996) 155-162
137. Putterill J., Robson F., Lee K., Simon R., and Coupland G. The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80 (1995) 847-857
138. Quail P.H. An emerging molecular map of the phytochromes. Plant Cell Environ. 20 (1997) 657-665
139. Quail P.H. Photosensory perception and signalling in plant cells: New paradigms?. Curr. Opin. Cell. Biol. 14 (2002) 180-188
140. Quail P.H. Phytochrome photosensory signalling networks. Nat. Rev. Mol. Cell. Biol. 3 (2002) 85-93
141. Quail P.H., Boylan M.T., Parks B.M., Short T.W., Xu Y., and Wagner D. Phytochromes: Photosensory perception and signal transduction. Science 268 (1995) 675-680
142. Reed J.W., Nagatani A., Elich T.D., Fagan M., and Chory J. Phytochrome A and Phytochrome B Have Overlapping but Distinct Functions in Arabidopsis Development. Plant Physiol. 104 (1994) 1139-1149
143. Reymond P., Short T.W., Briggs W.R., and Poff K.L. Light-induced phosphorylation of a membrane protein plays an early role in signal transduction for phototropism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 89 (1992) 4718-4721
144. Roux S.J. Signal transduction in phytochrome responses. In: Kendrick R.E., and Kronenberg G.H.M. (Eds). "Photomorphogenesis in Plants" (1994), Kluwer Academic Publishers, Dordrecht, The Netherlands 187-209
145. Saijo Y., Sullivan J.A., Wang H., Yang J., Shen Y., Rubio V., Ma L., Hoecker U., and Deng X.W. The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. Genes Dev. 17 (2003) 2642-2647
146. Sakai T., Kagawa T., Kasahara M., Swartz T.E., Christie J.M., Briggs W.R., Wada M., and Okada K. Arabidopsis nph1 and npl1: Blue light receptors that mediate both phototropism and chloroplast relocation. Proc. Natl. Acad. Sci. USA 98 (2001) 6969-6974
147. Sakamoto K., and Briggs W.R. Cellular and subcellular localization of phototropin 1. Plant Cell 14 (2002) 1723-1735
148. Salomon M., Christie J.M., Knieb E., Lempert U., and Briggs W.R. Photochemical and mutational analysis of the FMN-binding domains of the plant blue light receptor, phototropin. Biochemistry 39 (2000) 9401-9410
149. Salomon M., Eisenreich W., Durr H., Schleicher E., Knieb E., Massey V., Rudiger W., Muller F., Bacher A., and Richter G. An optomechanical transducer in the blue light receptor phototropin from Avena sativa. Proc. Natl. Acad. Sci. USA 98 (2001) 12357-12361
150. Salomon M., Knieb E., von Zeppelin T., and Rudiger W. Mapping of low- and high-fluence autophosphorylation sites in phototropin 1. Biochemistry 42 (2003) 4217-4225
151. Salomon M., Lempert U., and Rudiger W. Dimerization of the plant photoreceptor phototropin is probably mediated by the LOV1 domain. FEBS Lett. 572 (2004) 8-10
152. Sancar A. Structure and function of DNA photolyase. Biochemistry 33 (1994) 2-9
153. Sancar A. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem. Rev. 103 (2003) 2203-2237
154. Schepens I., Duek P., and Fankhauser C. Phytochrome-mediated light signalling in Arabidopsis. Curr. Opin. Plant Biol 7 (2004) 564-569
155. Schneider-Poetsch H.A. Signal transduction by Phytochrome: Phytochromes have a module related to the transmitter modules of bacterial sensor proteins. Photochem. Photobiol. 56 (1992) 839-846
156. Senger H. Cryptochrome, some terminological thoughts. "Blue Light Effects in Biological Systems," (1984), Springer-Verlag, Berlin, Germany 72
157. Seo H.S., Yang J.-Y., Ishikawa M., Bolle C., Ballesteros M., and Chua N.-H. LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. Nature 423 (2003) 995-999
158. Seo H.S., Watanabe E., Tokutomi S., Nagatani A., and Chua N.H. Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Genes Dev. 18 (2004) 617-622
159. Shalitin D., Yang H., Mockler T.C., Maymon M., Guo H., Whitelam G.C., and Lin C. Regulation of Arabidopsis cryptochrome 2 by blue-light-dependent phosphorylation. Nature 417 (2002) 763-767
160. Shalitin D., Yu X., Maymon M., Mockler T., and Lin C. Blue light-dependent in vivo and in vitro phosphorylation of Arabidopsis cryptochrome 1. Plant Cell 15 (2003) 2421-2429
161. Sharrock R.A., and Quail P.H. Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 3 (1989) 1745-1757
162. Sharrock R.A., and Clack T. Heterodimerization of type II phytochromes in Arabidopsis. Proc. Natl. Acad. Sci. USA 101 (2004) 11500-11505
163. Shinomura T., Nagatani A., Hanzawa H., Kubota M., Watanabe M., and Furuya M. Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 93 (1996) 8129-8133
164. Short T.W., Reymond P., and Briggs W.R. A pea plasma membrane protein exhibiting blue light-induced phosphorylation retains photosensitivity following triton solubilization. Plant Physiol. 101 (1993) 647-655
165. Smith H., and Whitelam G.C. The shade avoidance syndrome: Multiple responses mediated by multiple phytochromes. Plant Cell Environ. 20 (1997) 840-844
166. Somers D.E., and Quail P.H. Temporal and spatial expression patterns of PHYA and PHYB genes in Arabidopsis. Plant J. 7 (1995) 413-427
167. Somers D.E., Devlin P.F., and Kay S.A. Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 282 (1998) 1488-1490
168. Song P.-S. Inter-domain signal transmission within the phytochromes. J. Biochem. Mol. Biol. 32 (1999) 215-225
169. Spalding E.P. Ion channels and the transduction of light signals. Plant Cell Environ. 23 (2000) 665-674
170. Stockhaus J., Nagatani A., Halfter U., Kay S., Furuya M., and Chua N.H. Serine-to-alanine substitutions at the amino-terminal region of phytochrome A result in an increase in biological activity. Genes Dev. 6 (1992) 2364-2372
171. Suesslin C., and Frohnmeyer H. An Arabidopsis mutant defective in UV-B light-mediated responses. Plant J. 33 (2003) 591-601
172. Swartz T.E., Wenzel P.J., Corchnoy S.B., Briggs W.R., and Bogomolni R.A. Vibration spectroscopy reveals light-induced chromophore and protein structural changes in the LOV2 domain of the plant blue-light receptor phototropin 1. Biochemistry 41 (2002) 7183-7189
173. Talbott L.D., Shmayevich I.J., Chung Y., Hammad J.W., and Zeiger E. Blue light and phytochrome-mediated stomatal opening in the npq1 and phot1 phot2 mutants of Arabidopsis. Plant Physiol. 133 (2003) 1522-1529
174. Tepperman J.M., Zhu T., Chang H.S., Wang X., and Quail P.H. Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc. Natl. Acad. Sci. USA 98 (2001) 9437-9442
175. Todo T. Functional diversity of the DNA photolyase/blue light receptor family. Mutat. Res. 434 (1999) 89-97
176. Toth R., Kevei E., Hall A., Millar A.J., Nagy F., and Kozma-Bognar L. Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis. Plant Physiol. 127 (2001) 1607-1616
177. Vierstra R.D., and Davis S.J. Bacteriophytochromes: New tools for understanding phytochrome signal transduction. Semin. Cell Dev. Biol. 11 (2000) 511-521
178. Vince-Prue D. The duration of light and photoperiodic responses. In: Kendrick R.E., and Kronenberg G.H.M. (Eds). "Photomorphogenesis in Plants" (1994), Kluwer Academic Publishers, Dordrecht, The Netherlands 447-490
179. Wada M., Kagawa T., and Sato Y. Chloroplast movement. Annu. Rev. Plant Biol. 54 (2003) 455-468
180. Wagner D., and Quail P.H. Mutational analysis of phytochrome B identifies a small COOH-terminal-domain region critical for regulatory activity. Proc. Natl. Acad. Sci. USA 92 (1995) 8596-8600
181. Wagner D., Fairchild C.D., Kuhn R.M., and Quail P.H. Chromophore-bearing NH2-terminal domains of phytochromes A and B determine their photosensory specificity and differential light lability. Proc. Natl. Acad. Sci. USA 93 (1996) 4011-4015
182. Wagner D., Koloszvari M., and Quail P.H. Two small spatially distinct regions of phytochrome B are required for efficient signaling rates. Plant Cell 8 (1996) 859-871
183. Wang H., Ma L.-G., Li J.-M., Zhao H.-Y., and Deng X.W. Direct interaction of Arabidopsis cryptochromes with COP1 in light control development. Science 294 (2001) 154-158
184. Wang H., and Deng X.W. Dissecting the phytochrome A-dependent signaling network in higher plants. Trends Plant Sci. 8 (2003) 172-178
185. Wang H., and Deng X.W. Phytochrome signaling mechanism. In: Somerville C.R., and Meyerowitz E. (Eds). "The Arabidopsis Book" (2004), American Society of Plant Biologists, Rockville, MD. http://www.bioone.org/pdfserv/i1543-8120-018-01-0001.pdf
186. Wei N., and Deng X.W. The role of the COP/DET/FUS genes in light control of arabidopsis seedling development. Plant Physiol. 112 (1996) 871-878
187. Whitelam G.C., Johnson E., Peng J., Carol P., Anderson M.L., Cowl J.S., and Harberd N.P. Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. Plant Cell 5 (1993) 757-768
188. Whitelam G.C., and Devlin P.F. Roles of different phytochromes in Arabidopsis photomorphogenesis. Plant Cell Environ. 20 (1997) 752-758
189. Wu S.H., and Lagarias J.C. Defining the bilin lyase domain: Lessons from the extended phytochrome superfamily. Biochemistry 39 (2000) 13487-13495
190. Yamaguchi R., Nakamura M., Mochizuki N., Kay S.A., and Nagatani A. Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus in transgenic Arabidopsis. J. Cell Biol. 145 (1999) 437-445
191. Yang H.Q., Wu Y.J., Tang R.H., Liu D., Liu Y., and Cashmore A.R. The C termini of Arabidopsis cryptochromes mediate a constitutive light response. Cell 103 (2000) 815-827
192. Yang H.Q., Tang R.H., and Cashmore A.R. The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1. Plant Cell 13 (2001) 2573-2587
193. Yanovsky M.J., Luppi J.P., Kirchbauer D., Ogorodnikova O.B., Sineshchekov V.A., Adam E., Kircher S., Staneloni R.J., Schafer E., Nagy F., and Casal J.J. Missense mutation in the PAS2 domain of phytochrome A impairs subnuclear localization and a subset of responses. Plant Cell 14 (2002) 1591-1603
194. Yeh K.C., and Lagarias J.C. Eukaryotic phytochromes: Light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc. Natl. Acad. Sci. USA 95 (1998) 13976-13981
195. Zeiger E. Sensory transduction of blue light in guard cells. Trends Plant Sci. 5 (2000) 183-185
196. Zhu Y., Tepperman J.M., Fairchild C.D., and Quail P.H. Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3. Proc. Natl. Acad. Sci. USA 97 (2000) 13419-13424