18. Rockwell NC, Su YS, Lagarias JC (2006) Phytochrome structure and signaling mechanisms Annu Rev Plant Biol 57: 837–858. 19. Reed JW, Nagatani A, Elich TD, Fagan M, Chory J (1994) Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol 104: 1139–1149. 20. Kircher S, Kozma-Bognar L, Kim L, A´da´m E, Harter K, et al. (1999) Light quality-dependent nuclear import of the plant photoreceptors phytochrome A and B. Plant Cell 11: 1445–1456. 21. Sweere U, Eichenberg K, Lohrmann J, Mira-Rodado V, Ba¨urle I, et al. (2001) Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling. Science 294: 1108–1111. 22. Khanna R, Shen Y, Marion CM, Tsuchisak A, Theologis A, et al. (2008) The Basic Helix-Loop-Helix Transcription Factor PIF5 Acts on Ethylene Biosyn- thesis and Phytochrome Signaling by Distinct Mechanisms. Plant Cell 19: 3915–3929. 23. Rausenberger J, Hussong A, Kirchenbauer D, Kircher S, Timmer J, et al. (2010) An integrative model for phytochrome B mediated photomorphogenesis: From protein dynamics to physiology. PLoS One 5: e10721. 24. Eichenberg K, Kunkel T, Kretsch T, Speth V, Scha¨fer E (1999) In Vivo Characterization of Chimeric Phytochromes in Yeast. J Biol Chem 274: 354–359. 25. Oka Y, Matsushita T, Mochizuki N, Suzuki T, Tokutomi S, et al. (2004) Functional analysis of a 450-amino acid N-terminal fragment of phytochrome B in Arabidopsis. Plant Cell 16: 2104–2116. 26. Oka Y, Matsushita T, Mochizuki N, Quail PH, Nagatani A (2008) Mutant screen distinquishes between residues necessary for light signal perception and signal transfer by phytochrome B. PLoS Genet 4: e1000158. 27. Mira-Rodado V, Sweere U, Grefen C, Kunkel T, Fejes E, et al. (2007) Functional cross-talk between two-component and phytochrome B signal transduction in Arabidopsis. J Exp Bot 58: 2595–2607. 28. Kircher S, Gil P, Kozma-Bogna´r L, Fejes E, Speth V, et al. (2002) 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: 1541–1555. 29. Chen M, Schwab R, Chory J (2003) Characterization of the requirements for localization of phytochrome B to nuclear bodies. Proc Natl Acad Sci U S A 100: 14493–14498. 30. Chen M (2008) Phytochrome nuclear body: an emerging model to study interphase nuclear dynamics and signaling. Curr Opin Plant Biol 11: 503–506. Regulation of Dark and Photoconversion of phyB-401 31. Bauer D, Viczian A, Kircher S, Nobis T, Nitschke R, et al. (2004) Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signalling in Arabidopsis. Plant Cell 16: 1433–1445. 32. Matsushita T, Mochizuki N, Nagatani A (2003) Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature 424: 571–574. 33. Kretsch T, Poppe C, Scha¨fer E (2000) A new type of mutation in the plant photoreceptor phytochrome B causes loss of photoreversibility and an extremely enhanced light sensitivity. Plant J 22: 177–186. 34. Hennig L, Poppe C, Unger S, Scha¨fer E (1999b) Control of hypocotyl elongation in Arabidopsis thaliana by photoreceptor interaction. Planta 208: 257–263. 35. Su YS, Lagarias JC (2007) Light-independent phytochrome signalling mediated by dominant GAF domain tyrosine mutants of Arabidopsis phytochromes in transgenic plants. Plant Cell 19: 2124–2139. 36. Hu W, Su YS, Lagarias JC (2009) A light-independent allel of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks. Mol Plant 2: 166–182. 37. Essen LO, Mailliet J, Hughes J (2008) The structure of a complete phytochrome sensory module in the Pr ground state. PNAS 105: 14709–14714. 38. Reed JW, Nagpal P, Poole DS, Furuya M, Chory J (1993) Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell 5: 147–157. 39. Gross J, Seyfried M, Fukshansky L, Scha¨fer E (1984) In vivo spectrophotometry. In Technique in Photomorphogenesis Smith HHolmes, ed. London: Academic Press. pp 131–157. 40. Jabben M, Beggs C, Scha¨fer E (1982) Dependence of Pfr/Ptot-ratios on light quality and light quantity. Photochem Photobiol 35: 709–712. 41. Hirschfeld M, Tepperman JM, Clack T, Quail PH, Sharrock RA (1998) Coordination of phytochrome levels in phyB mutants of Arabidopsis as revealed by apoprotein-specific monoclonal antibodies. Genetics 149: 523–535. 42. Livak KJ (1997) User Bulletin No. 2: ABI PRISM 7700 Sequence Detection System. PE Applied Biosystems. Foster City, CA. pp 11–15. 43. Hiltbrunner A, Viczia´n A, Bury E, Tscheuschler A, Kircher S, et al. (2005) Nuclear accumulation of the phytochrome A photoreceptor requires FHY1. Curr Biol 15: 2125–2130. PLoS ONE | www.plosone.org 12 November 2011 | Volume 6 | Issue 11 | e27250