Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) reveals a light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks

ABSTRACT: 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. Experiment 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). Experiment Overall Design: wild type grown in darkness, three independent biological replicates; Experiment Overall Design: phyA-201phyB-5 mutant grown in darkness, three independent biological replicates; Experiment Overall Design: YHB (AtPHYB-YH/phyA-201phyB-5) grown in darkness, two independent transgenic lines, three independent biological replicates; Experiment Overall Design: wild type grown under 15 umol m-2 s-1 Rc, two independent biological replicates; Experiment Overall Design: wild type grown under 50 umol m-2 s-1 Rc, two independent biological replicates; Experiment Overall Design: YHB (AtPHYB-YH/phyA-201phyB-5) grown under 50 umol m-2 s-1 Rc, one transgenic line used, two independent biological replicates

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Wei Hu

PROVIDER: E-GEOD-8951 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks.

Hu Wei W Su Yi-Shin YS Lagarias J Clark JC

Molecular plant 20081216 1

Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su and Lagarias, 2007). In the present study, comparative transcription 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 transcription profiles of dark-grown phyA ...[more]

PMID: 19529817

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Project description:Plant growth and development are strongly affected by light signals perceived by phytochromes (phy) and cryptochromes (cry). The physical interaction between photoreceptors and the cross-talk among downstream signalling steps creates a network of interactions in which the action of one photoreceptor depends on the status of the others. The processes modulated by phy and or cry include seed germination, seedling de-etiolation, plant body formation and flowering. Compared to the wild type the leaves of the phyB mutant are characterised by their extended petioles and pale colour. These features resemble the phenotype of normal plants grown under the low red to far-red ratios typical of dense plant canopies thus providing support to the idea that phyB plays a key role in the perception of high red to far-red ratios. The triple mutant lacking phyA cry1 and cry2 shows little differences in leaf size and shape with the wild typebut the quadruple phyA phyB cry1 cry2 mutant shows severely impaired leaf expansion. In addition to the specific effects on leaf sizeshape and pigmentation the phyB mutation accelerates flowering in the wild type background. This effect can be observed as a reduced number of days between sowing and visible flower buds (time scale) and as a reduced final number of leaves (developmental scale). However in the phyA cry1 cry2 triple mutant background the phyB mutation accelerates flowering on a developmental scale but severely delays flowering on a time scale. The long photoperiods inducing flowering are perceived by the leaves. Flowering signals that could include hormones and sugars migrate from the leaves to the apex in response to the light stimulus. We propose to compare the following mRNA samples of expanding leaves: 1) wild type 2) phyB mutant 3) phyA cry1 cry2 triple mutant 4) phyA phyB cry1 cry2 quadruple mutant. The comparison between the wild type and the phyB mutant will help to uncover the changes in leaf mRNA patterns underlying enhanced petiole growthreduced pigmentation and early flowering in response to the absence of phyB activity. The comparison between the phyA cry1 cry2 triple mutant and the phyA phyB cry1 cry2 quadruple mutant should reveal the mRNA differences between photosynthetic leaves with dramatically different abilities to expand. The added value of the simultaneous analysis of the two comparisons is that effect of phyB is different in both genetic backgrounds and this should provide information on the mechanisms and significance of photoreceptor interactions.

Dataset Information

Transcription profiling of Arabidopsis dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) reveals a light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks

Publications

A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks.

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