Inter-Domain Signal Transmission within the Phytochromes

Journal of Biochemistry and Molecular Biology

Volumn 32, Issue 3, 1999, Pages 215-225

  Song, Pill Soon ^a,b  

^a Kumho Life and Environmental Science Laboratory   (South Korea)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

Conformational changes; Inter domain signaling; Light signaling; Phytochromes; Plant photomorphogenesis; Post translational modification; Protein phosphorylation

Indexed keywords

EID: 0033454757     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (72)

1. Bhoo, S. H., Hirano, T., Jeong, H.-Y., Lee, J.-G., Furuya, M. and Song, P.-S. (1997) Phytochrome photochromism probed by site-directed mutations and chromophore esterification. J. Am. Chem. Soc. 119: 11717-11718.
2. Boylan, M. T. and Quail, P. H. (1996) Are the phytochromes protein kinases? Protoplasma 195: 12-17.
3. Braslavsky, S. E., Gartner, W. and Schaffner, K. (1997) Phytochrome photoconversion. Plant Cell Environ. 20: 700-706.
4. Chen, F., Parker, W., Lewis, J. W., Song, P.-S. and Kliger, D. S. (1993) Time-resolved UV circular dichroism of phytochrome A: Folding of the N-terminal region. J. Am. Chem. Soc. 115: 9854-9855.
5. Cherry, J. R., Hondred, D., Walker, J. M., Keller, J. M., Hershey, H. and Vierstra, R. D. (1993) Carboxy-terminal deletion analysis of oat phytochrome A reveals the presence of separate domains required for structure and biological activity. Plant Cell 5: 565-575.
6. Choi, G. T., Soh, M.-S., Yi, H., Luka, Z., Lee, J. H., Hahn, T.-R., Kwon, Y.-K. and Song, P.-S. (1999) Phytochrome-regulated light signaling is mediated through nucleotide diphosphate kinase 2. Nature, submitted.
7. Deforce, L., Tomizawa, K., Ito, N., Farrens, D. L., Song, P.-S. and Furuya, M. (1991) In vitro assembly of apophytochrome and apophytochrome deletion mutants expressed in yeast with phycocyanobilin. Proc. Natl. Acad. Sci. USA 88: 10392-10396.
8. Deforce, L., Furuya, M. and Song, P.-S. (1993) Mutational analysis of the pea phytochrome A chromophore pocket: Chromophore assembly with apophytochrome A and photoreversibility. Biochemistry 32: 14165-14172.
9. Deforce, L., Tokutomi, S. and Song, P.-S. (1994) Phototransformation of pea phytochrome A induces an increase in α-helical folding of the apoprotein: comparison with a monocot phytochrome A and CD analysis by different methods. Biochemistry 33: 4918-4922.
10. Edgerton, M. D. and Jones, A. M. (1992) Localization of protein-protein interactions between subunits of phytochrome. Plant Cell 4: 161-171.
11. Edgerton, M. D. and Jones, A. M. (1993) Subunit interactions in the carboxy-terminal domain of phytochrome. Biochemistry 32: 8239-8243.
12. Eichenberg, K., Kunkel, T., Kretsch, T., Speth, V. and Schafer, E. (1999) In vivo characterization of chimeric phytochromes in yeast. J. Biol. Chem. 274: 354-359.
13. Elich, T. D. and Chory, J. (1997) Phytochrome: If it looks and smells like a histidine kinase, is it a histidine kinase? Cell 91: 713-716.
14. Fankhauser, C. and Chory, J. (1999) Photomorphogenesis: Light receptor kinases in plants! Curr. Opinion in Biol. in press.
15. Farrens, D., Holt, R., Rospendowski, B., Song, P.-S. and Cotton, T. (1989) Surface-enhanced resonance Raman Scattering (SERRS) Spectroscopy applied to phytochrome and its model compounds. II. Phytochrome and phycocyanin chromophores. J. Am. Chem. Soc. 111: 9162-9169.
16. Fodor, S., Lagarias, J. C. and Mathies, R. (1990) Resonance Raman analysis of the Pr and Pfr forms of phytochrome. Biochemistry 29: 11141-11146.
17. Furuya, M. (1993) Phytochromes: Their molecular species, gene families, and functions. Annu. Rev. Plant Physiol. Plant Mol. Biol. 44: 617-645.
18. Furuya, M. and Song, P.-S. (1994) Assembly and properties of holophytochrome. In: Photomorphogenesis in Plants, Kendrick, R. E. and Kronenberg, G. H. M. (eds.), Kluwer Academic Publishers, Dordrecht, pp. 105-140.
19. Grimm, R., Gast, D. and Rudiger, W. (1989) Characterization of a protein-kinase activity associated with phytochrome from etiolated oat (Avena sativa L) seedlings. Planta 178: 199-206.
20. Hahn, T. R. and Song, P.-S. (1981) The hydrophobic properties of phytochrome as probed by 8-anilinonaphthalene sulfonate fluorescence. Biochemistry 20: 2602-2609.
21. Hahn, T. R. and Song, P.-S. (1987) Molecular structure of phytochrome as probed by intrinsic phosphorescence of degraded 59 kilodalton chromopeptide. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 20: 87-90.
22. Han, B. D. and Chae, Q. (1993) Determination of the cytoplasmic free-calcium. Ion concentration changes by phytochrome action in oat cell using Fluo-3/AM. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 26: 346-351.
23. Hershey, H. P., Barker, R. F., Idler, K. B., Lissemore, J. L. and Quail, P. H. (1985) Analysis of cloned cDNA and genomic sequences for phytochrome: complete amino acid sequences for two gene products expressed in etiolated Avena. Nucleic Acids Res. 13: 8543-8559.
24. Hoecker, U., Xu, Y. and Quail, P. H. (1998) SPA1: A new genetic locus involved in phytochrome A-specific signal transduction. Plant Cell 10: 19-33.
25. Hoecker, U., Tepperman, J. and Quail, P. H. (1999) SPA1, a WD-repeat protein specific to phytochrome A signal transduction. Science 284: 496-499.
26. Jones, A. M. and Erickson, H. P. (1989) Domain structure of phytochrome from Avena sativa. Photochem. Photobiol. 49: 479-483.
27. Kim, H. Y. and Chae, Q. (1987) The binding of phytochrome-cyclic AMP and phytochrome-estriol complexes to the liposome. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 20: 199-207.
28. Kim, I. S. and Song, P.-S. (1987) Hydrophobic sites on the protein surfaces of the Pr and Pfr forms of phytochrome. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 20: 149-156.
29. Kim, I. S., Bai, U. and Song, P.-S. (1989) A purified 124-kDa oat phytochrome does not possess a protein kinase activity. Photochem. Photobiol. 49: 319-323.
30. Kim, I. S., Lim, M. H. and Song, P.-S. (1991) Delivery of phytochrome into plant protoplasts by lipsome. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 24: 103-110.
31. Kosower, N. S., Kosower, E. M., Newton, G. I. and Ranney, H. M. (1979) Bimane fluorescent labels: Labeling of normal human red cells under physiological conditions. Proc. Natl. Acad. Sci. USA 76: 3382-3286.
32. Kosower, N. S. and Kosower, E. M. (1987) Thiol labeling with bromobimanes. Methods Enzymol. 143: 76-84.
33. Lagarias, J. C. and Rapoport, H. (1980) Chromopeptides from phytochrome. The structure and linkage of the Pr form of the phytochrome chromophore. J. Am. Chem. Soc. 102: 4821-4828.
34. Lapko, V. N., Wells, T. A. and Song, P.-S. (1996) Protein kinase A-catalyzed phosphorylation and conformational changes in phytochrome A. Biochemistry 35: 6585-6594.
35. Lapko, V. N., Jiang, X.-Y., Smith, D. L. and Song, P.-S. (1997) Post-translational modification of oat phytochrome A: Phosphorylation of a specific serine in a multiple serine cluster. Biochemistry 36: 10595-10599.
36. Lapko, V. N., Jiang, X.-Y., Smith, D. L. and Song, P.-S. (1998) Surface topography of phytochrome A deduced from specific chemical modification with iodoacetamide. Biochemistry 36: 12526-12535.
37. Lapko, V. N., Jiang, X.-Y., Smith, D. L. and Song, P.-S. (1999) Mass spectrometric characterization of oat phytochrome A: Isoforms and posttranslational modifications. Protein Science 8: 1-13.
38. Nakasako, M., Wada, M., Tokutomi, S., Yamamoto, K. T., Sakai, J., Kataoka, M., Tokunaga, F. and Furuya, M. (1990) Quaternary structure of pea phytochrome I dimer studied with small-angle X-ray scattering and rotary-shadowing electron microscopy. Photochem. Photobiol. 52: 3-12.
39. Ni, M., Tepperman, J. M. and Quail, P. H. (1998) PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction is a novel basic helix-loop-helix protein. Cell 95: 657-667.
40. Park, C., Park, M. H. and Chae, Q. (1996) Identification and characterization of phytochrome-regulated phospholipase D in oat cells (Avena sativa L.). J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 29: 535-540.
41. Park, M. H. and Chae, Q. (1992) The phytochrome-mediated protein dephosphorylation of the phosphoproteins in oat cells. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 25: 33.
42. Park, Y.-I., Kim, J.-H., Lee, J.-D., Kim, Y. W. and Kim, I.-S. (1998) Three protein kinases from the etiolated oat seedlings phosphorylate oat phytochrome A in vitro. J. Biochem. Mol. Biol. (formerly Korean Biochem. J.) 31: 221-226.
43. Partis, M. D. and Grimm, R. (1990) Computer analysis of phytochrome sequences from five species: Implications for the mechanism of action. Z. Naturforsch. 45c: 987-998.
44. Quail, P. H. (1997a) An emerging molecular map of the phytochromes. Plant Cell Environ. 20: 657-685.
45. Quail, P. H. (1997b) The phytochromes: a biochemical mechanism of signaling in sight? BioEssays 19: 571-579.
46. Quail, P. H. (1998) The phytochrome family: dissection of functional roles and signalling pathways among family members. Phil. Trans. Royal Soc. London: Biol. Sci. 353: 1399-1403.
47. Quail, P. H., Boylan, M. T., Parks, B. M., Short, T. W., Xu, Y. and Wagner, D. (1995) Phytochromes: Photosensory perception and signal transduction. Science 268: 675-680.
48. Robertson, D. E., Farid, R. S., Moser, C. C., Urbauer, J. L., Mulholland, S. E., Pidikiti, R., Lear, J. D., Ward, A. J., Degrado, W. F. and Dutton, P. L. (1994) Design and synthesis of multi-haem proteins. Nature 368: 425-432.
49. Romanowski, M. and Song, P.-S. (1992) Structural domains of phytochrome deduced from homologies in amino acid sequences. J. Protein Chem. 11: 139-155.
50. Romero, L. C., Biswal, B. and Song, P.-S. (1991) Protein phosphorylation in isolated nuclei from etiolated Avena seedlings: Effects of red/far-red light and cholera toxin. FEBS Lett. 282: 347-350.
51. Rospendowski, B. N., Farrens, D. L., Cotton, T. M. and Song, P.-S. (1989) Surface enhanced resonance Raman scattering as a probe of the structural differences between the Pr and Pfr forms of phytochrome. FEBS. Lett. 258: 1-4.
52. Sarkar, H. K., Song, P.-S., Chang, T. H. and Yu, H. (1984) The tertiary structure of phytochrome probed by quasi-elastic light scattering and rotational relaxation time measurements. Biochemistry 23: 1882-1888.
53. Schneider-Poetsch, H. A. W. (1992) Signal transduction by phytochrome: Phytochromes have a module related to the transmitter modules of bacterial sensor proteins. Photochem. Photobiol. 56: 839-846.
54. Schwarzer, A., Kim, T. S. Y., Hagen, V., Molday, R. S. and Bauer, P. J. (1997) The Na/Ca-K exchange of rod photoreceptor exists as dimer in the plasma membrane. Biochemistry 36: 13667-13676.
55. Sharp, R. E., Diers, J. R., Bocian, D. F. and Dutton, P. L. (1998) Differential binding of iron(III) and zinc(II) protoporphyrin IX to synthetic four-helix bundles. J. Am. Chem. Soc. 120: 7103-7104.
56. Shinomura, T., Nagatani, A., Hanzawa, H., Kubota, M., Watanabe, M. and Furuya, M. (1996) Action spectra for phytochrome A-and B-specific photoinduction of seed germination in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 93: 8129-8133.
57. Singh, B. R. and Song, P.-S. (1989) Interactions between phytochrome and tetrapyrroles: Conformation changes probed by CD spectroscopy. Biochim. Biophys. Acta 996: 62-69.
58. Singh, B. R. and Song, P.-S. (1990) Phytochrome and protein phosphorylation. Photochem. Photobiol. 52: 249-254.
59. 2+-induced chromophore modification. Biochemistry 29: 1943-1948.
60. Sommer, D., Wells, T. A. and Song, P.-S. (1996) A possible tyrosine phosphorylation in phytochrome A. FEBS Lett. 393: 161-166.
61. Song, P.-S. (1993) Phytochrome as a light switch for gene expression in plants. Mol. Cells 3: 353-361.
62. Song, P.-S. (1998) Intra-and inter-molecular signaling by plant molecular light switches, phytochromes. Proc. Internatl. Symp. on Perspectives in Life Science Toward 21st Century, Cho, M. J. (ed.), Korean Society for Molecular Biology and Gyeongsang National University Press, Chinju, pp. 64-79.
63. Song, P.-S., Park, M. H. and Furuya, M. (1997) Chromophore: apoprotein interactions in phytochrome A. Plant Cell Environ. 20: 707-712.
64. Vierstra, R. D., Quail, P. H., Hahn, T. R. and Song, P.-S. (1987) Comparison of the protein conformations between different forms (Pr vs Pfr) of native (124 kDa) and degraded (118/ 114 kDa) phytochromes from Avena. Photochem. Photobiol. 45: 429-432.
65. Wells, T. A., Nakazawa, M., Manabe, K. and Song, P.-S. (1994) A conformational change associated with the phototransformation of Pisum phytochrome A as probed by fluorescence quenching. Biochemistry 33: 708-712.
66. Wells, T. A., Lapko, V. N., Bhoo, S. H., Moon, D.-K. and Song, P.-S. (1996a) Spectroscopic and structural requirements for photoreceptors: Phytochromes, In: Regulation of Plant Growth and Development by Light: Current Topics in Plant Physiology: An American Society of Plant Physiologists Series volume 17, Briggs, W. R., Heath, R. L. and Tobin, E. M. (eds.), American Society of Plant Physiologists, Rockville, MD, pp. 9-29.
67. Wells, T. A., Lapko, V., Moon, D.-K., Bhoo, S. H., Hirano, T. and Song, P.-S. (1996b) Phytochromes: Molecular light switches. In: Proc. 50th Anniversary Conf. Kor. Chem. Soc., Korean Chem. Soc., Seoul, Korea, pp. 313-325.
68. Whitelam, G. C. (1998) Phytochromes and photomorphogenesis in Arabidopsis. Phil. Trans. Royal Soc. London: Biol. Sci. 353: 1445-1453.
69. Wong, Y.-S., McMichael, Jr., R. W. and Lagarias, J. C. (1989) Properties of a polycation-stimulated protein kinase associated with purified Avena phytochrome. Plant Physiol. 91: 709-718.
70. Yeh, K. C. and Lagarias, J. C. (1998) Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc. Natl. Acad. Sci. USA 95: 13976-13981.
71. Yeh, K. C., Wu, S.-H., Murphy, J. T. and Lagarias, J. C. (1997) A cyanobacterial phytochrome two-component light sensory system. Science 277: 1505-1508.
72. Yi, H., Song, P.-S. and Choi, G. (1998) Cloning and characterization of nucleoside diphosphate kinase 2 from Arabidopsis thaliana (Plant Gene Register 98-056). Plant Physiol. 116: 1604.