phyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of Arabidopsis seedling de-etiolation

Plant Journal

Volumn 48, Issue 5, 2006, Pages 728-742

  Tepperman, James M ^a   Hwang, Yong Sic ^a   Quail, Peter H ^a  

^a NONE

Author keywords

Microarray; Photosensory perception; Phytochromes; Signaling; Transcriptional networks

Indexed keywords

GENES; MUTAGENESIS; PROTEINS;

MICROARRAYS; PHOTOSENSORY PERCEPTION; PHYTOCHROMES; TRANSCRIPTIONAL NETWORKS;

PLANTS (BOTANY);

ARABIDOPSIS PROTEIN; BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; PHYA PROTEIN, ARABIDOPSIS; PHYB PROTEIN, ARABIDOPSIS; PHYTOCHROME A; PHYTOCHROME B; PIF3 PROTEIN, ARABIDOPSIS;

ARABIDOPSIS; ARTICLE; COLOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; PHOTOTRANSDUCTION; RADIATION EXPOSURE; SEEDLING;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; COLOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; LIGHT; PHOTOTRANSDUCTION; PHYTOCHROME A; PHYTOCHROME B; SEEDLING;

GENES; MUTATION; PLANTS; PROTEINS; SEEDLINGS;

ARABIDOPSIS;

EID: 33749237560     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2006.02914.x     Document Type: Article

References (44)

1. Al-Sady, B., Ni, W., Kircher, S., Schäfer, E. and Quail, P.H. (2006) Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Mol. Cell, 23, 439-446.
2. Allison, L.A. (2000) The role of sigma factors in plastid transcription. Biochimie, 82, 12.
3. von Arnim, A. and Deng, X.-W. (1996) Light control of seedling development. Ann. Rev. Plant Physiol. Plant Mol. Biol. 47, 215-243.
4. Bauer, D., Viczian, A., Kircher, S. et al. (2004) Constitutive Photomorphogenesis 1 and multiple photoreceptors control degradation of Phytochrome Interacting Factor 3, a transcription factor required for light signaling in Arabidopsis. Plant Cell, 16, 1433-1445.
5. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B57, 289-300.
6. Cantón, F.R. and Quail, P.H. (1999) Both phyA and phyB mediate light-imposed repression of PHYA gene expression in Arabidopsis. Plant Physiol. 121, 1207-1215.
7. Chen, M., Chory, J., Frankhauser, C. (2004) Light signal transduction in higher plants. Annu. Rev. Genet. 38, 87-117.
8. Duek, P.D. and Fankhauser, C. (2005) bHLH class transcription factors take centre stage in phytochrome signalling. Trends Plant Sci. 10, 51-54.
9. Franklin, K.A. and Whitelam, G.C. (2004) Light signals, phytochromes and cross-talk with other environmental cues. J. Exp. Bot. 55, 271-276.
10. Franklin, K.A., Praekelt, U., Stoddart, W.M., Billingham, O.E., Halliday, K. and Whitelam, G.C. (2003) Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis. Plant Physiol. 131, 1-7.
11. Gentleman, R., Carey, V., Bates, D. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80.
12. Hirschfeld, M., Tepperman, J.M., Clack, T., Quail, P.H. and Sharrock, R.A. (1998) Coordination of phytochrome levels in phyB mutants of Arabidopsis as revealed by apoprotein-specific monoclonal antibodies. Genetics, 149, 523-535.
13. Huq, E., Al-Sady, B., Hudson, M., Kim, C., Apel, K. and Quail, P.H. (2004) Phytochrome-interacting factor 1, a basic helix-loop-helix transcription factor, is a critical regulator of the chlorophyll biosynthetic pathway. Science, 305, 1937-1941.
14. Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B. and Speed, T.P. (2003) Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res. 31, E15.
15. Jiao, Y., Ma, L., Strickland, E. and Deng, X.W. (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and arabidopsis. Plant Cell, 17, 3239-3256.
16. Khanna, R., Huq, E., Kikis, E.A., Al-Sady, B., Lanzatella, C. and Quail, P.H. (2004) A novel molecular recognition motif necessary for targeting photoactivated Phytochrome signalling to specific basic helix-loop-helix transcription factors. Plant Cell, 16, 3033-3044.
17. Kim, J., Yi, H., Choi, G., Shin, B., Song, P.-S. and Choi, G. (2003) Functional characterization of phytochrome interacting factor 3 in phytochrome-mediated light signal transduction. Plant Cell, 15, 2399-2407.
18. Lissemore, J.L. and Quail, P.H. (1988) Rapid transcriptional regulation by phytochrome of the genes for phytochrome and chlorophyll a/b-binding protein in Avena sativa. Mol. Cell. Biol. 8, 4840-4850.
19. Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H. and Deng, X.-W. (2001) Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell, 13, 2589-2607.
20. Ma, L., Gao, Y., Qu, L., Chen, Z., Li, J., Zhao, H. and Deng, X.W. (2002) Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis? Plant Cell, 14, 2383-2398.
21. Ma, L., Sun, N., Liu, X., Jiao, Y., Zhao, H. and Deng, X.W. (2005) Organ-Specific Expression of Arabidopsis Genome during Development. Plant Physiol. 138, 80-91.
22. Makino, S., Matsushika, A., Kojima, M., Yamashino, T. and Mizuno, T. (2002) The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. characterization with APRR1-overexpressing plants. Plant Cell Physiol. 43, 58-69.
23. Mazzella, M.A., Arana, M.V., Staneloni, R.J. et al. (2005) Phytochrome control of the Arabidopsis transcriptome anticipates seedling exposure to light. Plant Cell, 17, 2507-2516.
24. McCormac, A.C., Wagner, D., Boylan, M.T., Quail, P.H., Smith, H. and Whitelam, G.C. (1993) Photoresponses of transgenic Arabidopsis seedlings expressing introduced phytochrome B-encoding cDNAs: evidence that phytochrome A and phytochrome B have distinct photoregulatory functions. Plant J. 4, 19-27.
25. Monte, E., Tepperman, J.M., Al-Sady, B., Kaczorowski, K.A., Alonso, J.M., Ecker, J.R., Li, X., Zhang, Y. and Quail, P.H. (2004) The phytochrome- Interacting transcription factor, PIF3, acts early, selectively, and positively and light-induced chloroplast development. Proc. Natl Acad. Sci. USA, 101, 16091-16098.
26. Morelli, G. and Ruberti, I. (2002) Light and shade in the photocontrol of Arabidopsis growth. Trends Plant Sci. 7, 399-404.
27. Nagatani, A. (2004) Light-regulated nuclear localization of phytochromes. Curr. Opin. Plant Biol. 7, 708-711.
28. Parks, B.M. (2003) The red side of photomorphogenesis. Plant Physiol. 133, 1437-1444.
29. Parks, B.M. and Spalding, E.P. (1999) Sequential and coordinated action of phytochromes A and B during Arabidopsis stem growth revealed by kinetic analysis. Proc. Natl Acad. Sci. USA, 96, 14142-14146.
30. Parks, B.M., Folta, K.M. and Spalding, E.P. (2001) Photocontrol of stem growth. Curr. Opin. Plant Biol. 4, 436-440.
31. Quail, P.H. (2002) Phytochrome photosensory signalling networks. Nat. Rev. Mol. Cell Biol. 3, 85-93.
32. Reed, J.W., Nagpal, P., Poole, D.S., Furuya, M. and 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.
33. Reed, J.W., Nagatani, A., Elich, T.D., Fagan, M. and Chory, J. (1994) Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol. 104, 1139-1149.
34. Salter, M.G., Franklin, K.A. and Whitelam, G.C. (2003) Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature, 426, 680-683.
35. Schaefer, E. and Nagy, F. (2006) Photomorphogenesis in plants and bacteria. Dordrecht: Springer.
36. Shen, H., Moon, J. and Huq, E. (2005) PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis. Plant J. 44, 1023-1035.
37. Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 1, Article 3. available at: http://www.bepress.com/sagmb/vol3/ iss1/art3/. (Last accessed 29 September 2006).
38. Somers, D.E., Sharrock, R.A., Tepperman, J.M. and Quail, P.H. (1991) The hy3 long hypocotyl mutant of Arabidopsis is deficient in phytochrome B. Plant Cell, 3, 1263-1274.
39. Storey, J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc. B64, 479-498.
40. Tepperman, J.M., Zhu, T., Chang, H.S., Wang, X. and Quail, P.H. (2001) Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc. Natl Acad. Sci. USA, 98, 9437-9442.
41. Tepperman, J.M., Hudson, M.E., Khanna, R., Zhu, T., Chang, S.H., Wang, X. and 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.
42. Valvekens, D., Van Montagu, M. and Van Lijsebettens, M. (1988) Agrobacterium tumefaciens-mediated transformation of arabidopsis thaliana root explants by using kanamycin selection. Proc. Natl. Acad. Sci. USA. 85, 5536-5540.
43. Wang, H., Ma, L., Habashi, J., Li, J., Zhao, H. and Deng, X.W. (2002) Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J. 32, 723-733.
44. Whitelam, G.C., Patel, S. and Devlin, P.F. (1998) Phytochromes and photomorphogenesis in Arabidopsis. Phil. Trans. R. Soc. Lond. B Biol. Sci. 353, 1445-1453.