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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Molecular Mechanisms of Phytochrome Signaling and Gene Regulation

Location: Plant Gene Expression Center

2012 Annual Report


1a. Objectives (from AD-416):
The long-term goal of this research is to define the molecular mechanisms by which the phytochrome (phy) family of photoreceptors perceive informational light signals from the environment and transduce them to photoresponsive nuclear genes, thereby controlling plant growth and development. Using genome-scale microarray-based expression profiling, we have begun to define the global transcriptional network regulated by these photoreceptors and have identified a set of rapidly light-induced or -repressed genes (primarily encoding various transcription factors) that are potential direct targets of the phytochrome signaling pathway. The specific objectives of this project plan are: 1. To identify which phy family members are responsible for signaling to each of these genes, by examining light-induced expression profiles in null mutants of each phytochrome. [NP 301, C 4, PS 4a] 2. To define the cis elements in the promoters of these genes responsible for coordinate light-regulated expression, using computational analysis coupled with targeted mutagenesis and transgenic expression of promoter::reporter fusion constructs. [NP 301, C 4, PS 4a] 3. To identify downstream targets of these genes in the light-regulated transcriptional network, using microarray-based expression profiling in knockout mutants null for each transcription factor, coupled with chromatin immuno- precipitation (ChIP) for target promoter identification and characterization. [NP 301, C 4, PS 4a]


1b. Approach (from AD-416):
The specific objectives of this proposal are: (a) to identify which phys are responsible for signaling to these genes; (b) to define the cis elements in the promoters of these genes responsible for coordinating light-regulated expression; (c) to identify downstream targets of these genes in the light-regulated transcriptional network. The experimental approaches will include: (a) microarray-based expression profiling of mutants null for each phy, both to define the phy-regulated transcriptional networks and to identify rapidly light-responsive genes for targeted reverse-genetic mutagenesis; (b) computational analysis of the promoters of these genes, coupled with targeted mutagenesis and transgenic expression of promoter::reporter fusion constructs; (c) expression profiling in knockout mutants null for each transcription factor, coupled with chromatin immunoprecipitation for identification of promoters that are direct targets of these factors.


3. Progress Report:
Plants respond to light signals informing them of imposed or impending vegetative shade, via the phytochrome (phy) photoreceptor system, by adaptive changes in growth and development, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this perceived information to the transcriptional network, we compared the genome-wide transcription profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry that controls downstream response elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion responses known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. These data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment in response to perturbations in the mutually antagonistic regulatory activities of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses.


4. Accomplishments

Last Modified: 10/19/2017
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