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| Status |
Public on Nov 10, 2008 |
| Title |
A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su & Lagarias 2007 Plant Cell 19, 2124-2139). In the present study, comparative transcript profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole genome transcriptional profiles of dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to, but quantitatively greater than those of wild-type seedlings grown under 15 or 50 umol m-2 m-1 continuous red light (Rc). Among the 2977 genes statistically significant two-fold (SSTF) regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-modulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway(s) strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.
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| Overall design |
16 samples: 9 are dark-grown samples (3 samples x 3 replicates), 6 are continuous red light (Rc)-grown samples (3 samples x 2 replicates).
wild type grown in darkness, three independent biological replicates;
phyA-201phyB-5 mutant grown in darkness, three independent biological replicates;
YHB (AtPHYB-YH/phyA-201phyB-5) grown in darkness, two independent transgenic lines, three independent biological replicates;
wild type grown under 15 umol m-2 s-1 Rc, two independent biological replicates;
wild type grown under 50 umol m-2 s-1 Rc, two independent biological replicates;
YHB (AtPHYB-YH/phyA-201phyB-5) grown under 50 umol m-2 s-1 Rc, one transgenic line used, two independent biological replicates
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| Contributor(s) |
Hu W, Lagarias CJ |
| Citation(s) |
19529817 |
| Submission date |
Sep 04, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Wei Hu |
| Organization name |
Univ of California at Davis
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| Department |
Department of Molecular and Cellular Biology
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| Lab |
J Clark Lagarias
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| Street address |
One Shields Ave.
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
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| Samples (15)
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| Relations |
| Affiliated with |
GSE69995 |
| BioProject |
PRJNA102383 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8951_RAW.tar |
30.6 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
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