Phytochrome-regulated gene expression

Journal of Integrative Plant Biology

Volumn 49, Issue 1, 2007, Pages 11-20

  Quail, Peter H ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b WESTERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

Auxin related genes; Expression profiling; Functional profiling; Microarrays; Phytochrome signaling; Reverse genetics; Transcription factors; Transcriptional networks

Indexed keywords

GENE EXPRESSION; GENOME; MORPHOGENESIS; PLANT; SEEDLING;

ARABIDOPSIS;

EID: 33846115053     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2006.00422.x     Document Type: Review

References (36)

1. Al-Sady B, Ni W, Kircher S, Schäfer E, Quail PH (2006). Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Mol Cell 23, 439-446.
2. Allison LA (2000). The role of sigma factors in plastid transcription. Biochimie 82, 12.
3. Ang LH, Chattopadhyay S, Wei N, Oyama T, Okada K, Batschauer A et al. (1998). Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. Mol Cell 1, 213-222.
4. Bauer D, Viczian A, Kircher S, Nobis T, Nitschke R, Kunkel T 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. Chen M, Chory J, Fankhauser C (2004). Light signal transduction in higher plants. Annu Rev Genet 38, 87-117.
6. Eriksson ME, Hanano S, Southern MM, Hall A, Millar AJ (2003). Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta 218, 159-162.
7. Fankhauser C, Yeh KC, Lagarias JC, Zhang H, Elich TD, Chory J (1999). PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis. Science 284, 1539-1541.
8. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S et al. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391.
9. Hoecker U, Tepperman JM, Quail PH (1999). SPA1, a WD-repeat protein specific to phytochrome A signal transduction. Science 284, 496-499.
10. Hoecker U, Xu Y, Quail PH (1998). SPA1: A new genetic locus involved in phytochrome A-specific signal transduction. Plant Cell 10, 19-33.
11. Jiao Y, Ma L, Strickland E, Deng XW (2005). Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17, 3239-3256.
12. Khanna R, Kikis EA, Quail PH (2003). Early Flowering 4 (ELF4) functions in phytochrome B regulated seedling deetiolation. Plant Physiol 133, 1530-1538.
13. Khanna R, Shen Y, Toledo-Ortiz G, Kikis EA, Johannesson H, Hwang Y-S et al. (2006). Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation. Plant Cell tpc.106.042200.
14. Kim JH, Choi D, Kende H (2003). The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J 36, 94-104.
15. Koornneef M, Rolff E, Spruit C (1980). Genetic control of light-inhibited hypocotyl elongation in Arabidopsis thaliana (L.) Heynh. Z Pflanzenphysiol 100, 147-160.
16. Kuno N, Furuya M (2000). Phytochrome regulation of nuclear gene expression in plants. Sem Cell Devel Biol 11, 485-493.
17. Lariguet P, Boccalandro HE, Alonso JM, Ecker JR, Chory J, Casal JJ et al. (2003). A growth regulatory loop that provides homeo-stasis to phytochrome A signaling. Plant Cell 15, 2966-2978.
18. Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR (2004). Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Dev Cell 7, 193-204.
19. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ (1999). High density synthetic oligonucleotide arrays. Nat Genet Suppl 21, 20-24.
20. Ma L, Gao Y, Qu L, Chen Z, Li J, Zhao H et al. (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, Li J, Qu L, Hager J, Chen Z, Zhao H et al. (2001). Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13, 2589-2607.
22. Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng XW (2005). Organ-specific expression of Arabidopsis genome during development. Plant Physiol 138, 80-91.
23. Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker JR et al. (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.
24. Morelli G, Ruberti I (2002). Light and shade in the photocontrol of Arabidopsis growth. Trends Plant Sci 7, 399-404.
25. Nagatani, Akira (2004). Light-regulated nuclear localization of phytochromes. Curr Opin Plant Biol 7, 708-711.
26. Quail PH (2002). Phytochrome photosensory signalling networks. Nat Rev/ Mol Cell Biol 3, 85-93.
27. Quail PH (2006). Phytochrome signal transduction network. In: Schäfer E, Nagy F, eds. Photomorphogenesis in Plants and Bacteria, 3rd Edition. Springer, Dordrecht, The Netherlands. pp. 335-356.
28. Salter MG, Michael G, Franklin KA, Keara A, Whitelam GC, Garry C (2003). Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature 426, 680-683.
29. Schäfer E, Nagy F (2006). Photomorphogenesis in Plants and Bacteria, Springer, Dordrecht, The Netherlands.
30. Tepperman JM, Hudson ME, Khanna R, Zhu T, Chang SH, Wang X et al. (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.
31. Tepperman JM, Hwang YS, Quail PH (2006). phyA dominates in transduction of red-light signals to rapidly-responding genes at the Initiation of Arabidopsis seedling deetiolation. Plant J 48, 728-742.
32. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH (2001). Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci USA 98, 9437-9442.
33. Terzaghi WB, Cashmore AR (1995). Light-regulated transcription. Annu Rev Plant Physiol Plant Mol Biol 46, 445-474.
34. Tobin E, Kehoe DM (1994). Phytochrome regulated gene expression. Seminars Cell Biol 5, 335-346.
35. Tu SL, Lagarias JC (2005). The Phytochromes. In: Briggs WR, Spudich J, eds. Handbook of Photosensory Receptors. Wiley-VCH, Wenheim, Germany. pp. 121-145.
36. Wang H, Ma L, Habashi J, Li J, Zhao H, Deng XW (2002). Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J 32, 723-733.