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.
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.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Leivar
authors.forename: James M
authors.initials: JM
authors.lastname: Tepperman
authors.forename: Megan M
authors.initials: MM
authors.lastname: Cohn
authors.forename: Elena
authors.initials: E
authors.lastname: Monte
authors.forename: Bassem
authors.initials: B
authors.lastname: Al-Sady
authors.forename: Erika
authors.initials: E
authors.lastname: Erickson
authors.forename: Peter H
authors.initials: PH
authors.lastname: Quail
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000528:radiation effects*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D051792:Basic Helix-Loop-Helix Proteins / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000528:radiation effects; D053263:Gene Regulatory Networks / Q000187:drug effects / Q000235:genetics* / Q000528:radiation effects; D017343:Genes, Plant / Q000235:genetics; D007210:Indoleacetic Acids / Q000494:pharmacology; D008027:Light; D055537:Light Signal Transduction / Q000187:drug effects / Q000528:radiation effects; D009024:Morphogenesis / Q000187:drug effects / Q000528:radiation effects; D009154:Mutation / Q000235:genetics; D059372:Nucleotide Motifs / Q000235:genetics; D010641:Phenotype; D010834:Phytochrome / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D036226:Seedlings / Q000187:drug effects / Q000254:growth & development / Q000378:metabolism / Q000528:radiation effects; D014158:Transcription, Genetic / Q000187:drug effects / Q000528:radiation effects
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D007210:Indoleacetic Acids; D010834:Phytochrome