Basic Information:
Series_titleA light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks
Series_summaryDominant 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.
Series_overall_design16 samples: 9 are dark-grown samples (3 samples x 3 replicates), 6 are continuous red light (Rc)-grown samples (3 samples x 2 replicates).
Series_overall_designwild type grown in darkness, three independent biological replicates;
Series_overall_designphyA-201phyB-5 mutant grown in darkness, three independent biological replicates;
Series_overall_designYHB (AtPHYB-YH/phyA-201phyB-5) grown in darkness, two independent transgenic lines, three independent biological replicates;
Series_overall_designwild type grown under 15 umol m-2 s-1 Rc, two independent biological replicates;
Series_overall_designwild type grown under 50 umol m-2 s-1 Rc, two independent biological replicates;
Series_overall_designYHB (AtPHYB-YH/phyA-201phyB-5) grown under 50 umol m-2 s-1 Rc, one transgenic line used, two independent biological replicates
Series_typeExpression profiling by array
Series_sample_idGSM226267 GSM226268 GSM226269 GSM226270 GSM226271 GSM226272 GSM226273 GSM226274 GSM226275 GSM226276 GSM226277 GSM226278 GSM226279 GSM226280 GSM226281