Analysis of far-red light-regulated genome expression profiles of phyochrome a pathway mutants in Arabidopsis

Plant Journal

Volumn 32, Issue 5, 2002, Pages 723-733

  Wang, Haiyang ^a,e   Ma, Ligeng ^a,b   Habashi, Jessica ^a   Li, Jinming ^c,d   Zhao, Hongyu ^c   Deng, Xing Wang ^a,b  

^a YALE UNIVERSITY   (United States)

^b PEKING UNIVERSITY   (China)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^e School of Integrative Plant Science   (United States)

Author keywords

Arabidopsis; Clustering analysis; Genome expression profile; Microarray; Phytochrome A

Indexed keywords

DNA; MUTAGENESIS; PROTEINS;

PHOTORECEPTORS;

PLANTS (BOTANY);

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; INFRARED RAYS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYTOCHROME; PHYTOCHROME A; SIGNAL TRANSDUCTION;

ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA;

EID: 0036909450     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-313X.2002.01462.x     Document Type: Article

References (50)

1. Ang, L.H. and Deng, X.W. (1994) Regulatory hierarchy of photomorphogenic loci: Allele-specific and light-dependent interaction between the HY5 and COP1 loci. Plant Cell, 6, 613-628.
2. Arabidopsis genome initiative (AGI). (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
3. Ballesteros, M., Bolle, C., Lois, L.M., Moore, J.M., Vielle-Calzada, J.-P., Grossniklaus, U. and Chua, N.-H. (2001) LAF1, a MYB transcription activator for phytochrome A signaling. Genes Dev. 15, 2613-2625.
4. Barnes, S.A., Nishizawa, N.K., Quaggio, R.B., Whitelam, G.C. and Chua, N.-H. (1996b) Far-red light blocks greening of Arabidopsis seedlings via a phytochrome A-mediated change in plastid development. Plant Cell, 8, 601-615.
5. Barnes, S.A., Quaggio, R.B., Whitelam, G.C. and Chua, N.-H. (1996a) fhy1 defines a branch point in phytochrome A signal transduction pathways for gene expression. Plant J. 10, 1155-1161.
6. Bolle, C., Koncz, C. and Chua, N.-H. (2000) PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction. Genes Dev. 14, 1269-1278.
7. Borevitz, J.O., Maloof, J.N. et al. (2002) Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics, 160, 683-696.
8. Chattopadhyay, S., Ang, L.H., Puente, P., Deng, X.W. and Wei, N. (1998) Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell, 10, 673-683.
9. Deng, X.W. and Quail, P.H. (1999) Signalling in light-controlled development. Semi. Cell Dev. Biol. 10, 121-129.
10. Desnos, T., Puente, P., Whitelam, G.C. and Harberd, N.P. (2001) FHY1: A phytochrome A-specific signal transducer. Genes Dev. 15, 2980-2990.
11. Dieterle, M., Zhou, Y.-C., Schäfer, E., Funk, M. and Kretsch, T. (2001) EID1, an F-box protein involved in phytochrome A-specific light signaling. Genes Dev. 15, 939-944.
12. Eichenberg, K., Hennig, L., Martin, A. and Schafer, E. (2000) Variation in dynamics of phytochrome A in Arabidopsis ecotypes and mutants. Plant Cell Environ. 23, 311-319.
13. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95, 14883-14868.
14. Enard, W. et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science, 296, 340-343.
15. Fairchild, C.D., Schumaker, M.A. and Quail, P.H. (2000) HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction. Genes Dev. 14, 2377-2391.
16. Fankhauser, C. and Chory, J. (1997) Light control of plant development. Annu. Rev. Cell Dev. Biol. 13, 203-229.
17. Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.-S., Han, B., Wang, X., Kreps, J.A. and Kay, S.A. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science, 290, 2110-2113.
18. Hoecker, U., Tepperman, J.M. and Quail, P.H. (1999) SPA1, a WD-repeat protein specific to phytochrome A signal transduction. Science, 284, 496-499.
19. 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.
20. Hsieh, H.-L., Okamoto, H., Wang, M., Ang, L.-H., Matsui, M., Goodman, H. and Deng, X.W. (2000) FIN219, an auxin-regulated gene, defines a link between phytochrome A and the down-stream regutator COP1 in light control of Arabidopsis development. Genes Dev. 14, 1958-1970.
21. Hudson, M.E. (2000) The genetics of phytochrome signalling in Arabidopsis. Semi. Cell Dev. Biol. 11, 475-483.
22. Hudson, M., Ringli, C., Boylan, M.T. and Quail, P.H. (1999) The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling. Genes Dev. 13, 2017-2027.
23. Kuno, N. and Furuya, M. (2000) Phytochrome regulation of nuclear gene expression in plants. Semi. Cell Dev. Biol. 11, 485-493.
24. Kuno, N., Muramatsu, T., Hamazato, F. and Furuya, M. (2000) Identification by large-scale screening of phytochrome-regulated genes in etiolated seedlings of Arabidopsis using a fluorescent differential display technique. Plant Physiol. 122, 15-24.
25. 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.
26. 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.
27. Maloof, J.N., Borevitz, J.O., Dabi, T., Lutes, J., Nehring, R.B. et al. (2001) Natural variation in light sensitivity of Arabidopsis. Nat. Genet. 29, 441-446.
28. Maloof, J.N., Borevitz, J.O., Weigel, D., Chory, J.et al. (2000) Natural variation in phytochrome signaling. Semi. Cell Dev. Biol. 11, 525-530.
29. Martínez-Garcia, J.F., Huq, E. and Quali, P.H. (2000) Direct targeting of light signals to a promoter element-bound transcription factor. Science, 288, 859-863.
30. MØller, S.G., Kunkel, T. and Chua, N.-H. (2001) A plastidic ABC protein involved in intercompartmental communication of light signaling. Genes Dev. 15, 90-103.
31. Nagatani, A., Reed, J.W. and Chory, J. (1993) Isolation and initial characterization of Arabidopsis mutants that are deficient in phytochrome A. Plant Physiol. 102, 269-277.
32. Nagy, F., Kircher, S. and Schäfer, E. (2000) Nucleo-cytoplasmic partitioning of the plant photoreceptors phytochromes. Semi. Cell Dev. Biol. 11, 505-510.
33. Nagy, F. and Schäfer, E. (2002) Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants. Annu. Rev. Plant Biol. 53, 329-355.
34. Neff, M.M., Fanhauser, C. and Chory, J. (2000) Light: An indicator of time and place. Genes Dev. 14, 257-271.
35. Perez-Amador, M.A., Lidder, P., Johnson, M.A., Landgraf, J., Wisman, E. and Green, P.J. (2001) New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis. Plant Cell, 13, 2703-2717.
36. Puente, P., Wei, N. and Deng, X.W. (1996) Combinatorial interplay of promoter elements constitutes minimal determinants for light and developmental control of gene expression in Arabidopsis. EMBO J. 15, 3732-3743.
37. Quail, P.H. (2002a) Phytochrome photgosensory signalling networks. Nat. Rev. Mol. Cell Biol. 3, 85-93.
38. Quail, P.H. (2002b) Photosensory perception and signalling in plant cells: New paradigms? Curr. Opin. Cell Biol. 14, 180-188.
39. 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.
40. 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.
41. Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M. and Wisman, E. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell, 13, 113-123.
42. Soh, M.S., Kim, Y.M., Han, S.J. and Song, P.S. (2000) REP1, a basic helix-loop-helix protein, is required for a branch pathway of phytochrome A signaling in Arabidopsis. Plant Cell, 12, 2061-2074.
43. 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.
44. Terzaghi, W.B. and Cashmore, A.R. (1995) Light-regulated transcription. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46, 445-474.
45. Wang, H. and Deng, X.W. (2002a) Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1. EMBO J. 21, 1339-1349.
46. Wang, H. and Deng, X.W. (2002b) Phytochrome signaling mechanism. In The Arabidopsis Book (Meyerowitz, E. and Somerville, C., eds). American Society of Plant Biologists). Available at http://www.aspb.org/publications/arabidopsis/.
47. Whitelam, G.C., Johnson, E., Peng, J., Carol, P., Anderson, M.L., Cowl, J.S. and Harberd, N.P. (1993) Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. Plant Cell, 5, 757-768.
48. Yanovsky, M.J., Casal, J.J. and Luppi, J.P. (1997) The VLF loci, polymorphic between ecotypes landsberg erecta and Columbia, dissect two branches of phytochrome A signal transduction that correspond to very-low-fluence and high-irradiance responses. Plant J. 12, 659-667.
49. Yanovsky, M.J., Whitelam, G.C. and Casal, J.J. (2000) fhy3-1 retains inductive responses of phytochrome A. Plant Physiol. 123, 235-242.
50. Yue, H., Eastman, P.S., Wang, B.B., Minor, J., Doctolero, M.H., Nuttall, R.L., Stack, R., Becker, J.W., Montgomery, J.R., vainer, M. and Johnston, R. (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucl. Acids Res. 29, E41.