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United States Department of Agriculture

Agricultural Research Service

Research Project: Molecular Mechanisms of Phytochrome Signaling and Gene Regulation Title: Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis

Authors
item Leivar, Pablo -
item Tepperman, James -
item Cohn, Megan -
item Monte, Elana -
item Bassem, Al-Sady -
item Erickson, Erika -
item Quail, Peter -

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 5, 2012
Publication Date: April 24, 2012
Citation: Leivar, P., Tepperman, J.M., Cohn, M.M., Monte, E., Bassem, A., Erickson, E., Quail, P.H. 2012. Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis. The Plant Cell. 24:1398-1419.

Interpretive Summary: Genome-wide expression profiling in this study identifies core elements of a transcriptional network that is regulated rapidly and reciprocally by light and vegetational shade signals, via a phytochrome-transcription factor transduction interface. The data establish that this signaling hub functions continuously to control early seedling and juvenile plant growth and development in response to the prevailing light environment. The components of this system thus provide potential molecular targets for manipulation in producing crops with superior food or cellulosic-biofeul productivity.

Technical Abstract: Plants respond to shade-modulated light signals via phytochrome (phy)-induced adaptive changes, termed shade avoidance. To examine the roles of Phytochrome-Interacting basic helix-loop-helix Factors, PIF1, 3, 4, and 5, in relaying such signals to the transcriptional network, we compared the shade-responsive transcriptome profiles of wild-type and quadruple pif (pifq) mutants. We identify a subset of genes, enriched in transcription factor–encoding loci, that respond rapidly to shade, in a PIF-dependent manner, and contain promoter G-box motifs, known to bind PIFs. These genes are potential direct targets of phy-PIF signaling that regulate the primary downstream transcriptional circuitry. A second subset of PIF-dependent, early response genes, lacking G-box motifs, are enriched for auxin-responsive loci, and are thus potentially indirect targets of phy-PIF signaling, mediating the rapid cell expansion induced by shade. Comparing deetiolation- and shade-responsive transcriptomes identifies another subset of G-box–containing genes that reciprocally display rapid repression and induction in response to light and shade signals. These data define a core set of transcriptional and hormonal processes that appear to be dynamically poised to react rapidly to light-environment changes via perturbations in the mutually antagonistic actions of the phys and PIFs. Comparing the responsiveness of the pifq and triple pif mutants to light and shade confirms that the PIFs act with overlapping redundancy on seedling morphogenesis and transcriptional regulation but that each PIF contributes differentially to these responses.

Last Modified: 11/23/2014
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