Functional Profiling Identifies Genes Involved in Organ-Specific Branches of the PIF3 Regulatory Network in Arabidopsis    

Abstract

The phytochrome (phy)-interacting basic helix-loop-helix transcription factors (PIFs) constitutively sustain the etiolated state of dark-germinated seedlings by actively repressing deetiolation in darkness. This action is rapidly reversed upon light exposure by phy-induced proteolytic degradation of the PIFs. Here, we combined a microarray-based approach with a functional profiling strategy and identified four PIF3-regulated genes misexpressed in the dark (MIDAs) that are novel regulators of seedling deetiolation. We provide evidence that each one of these four MIDA genes regulates a specific facet of etiolation (hook maintenance, cotyledon appression, or hypocotyl elongation), indicating that there is branching in the signaling that PIF3 relays. Furthermore, combining inferred MIDA gene function from mutant analyses with their expression profiles in response to light-induced degradation of PIF3 provides evidence consistent with a model where the action of the PIF3/MIDA regulatory network enables an initial fast response to the light and subsequently prevents an overresponse to the initial light trigger, thus optimizing the seedling deetiolation process. Collectively, the data suggest that at least part of the phy/ PIF system acts through these four MIDAs to initiate and optimize seedling deetiolation, and that this mechanism might allow the implementation of spatial (i.e., organ-specific) and temporal responses during the photomorphogenic program.

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

“…A similar study with pif1 defined only two genes as statistically different in expression between the mutant and the wild type, and these differences were less than twofold (Moon et al, 2008). These findings are consistent with the weak or absent visible morphogenic phenotypes in these mutants in the dark (Huq et al, 2004;Leivar et al, 2008aLeivar et al, , 2009Shin et al, 2009;Stephenson et al, 2009;Sentandreu et al, 2011). Profiling of a pif4 pif5 double mutant grown in darkness identified 113 genes that were misregulated in the mutant compared with the wild type .…”

“…Profiling of a pif4 pif5 double mutant grown in darkness identified 113 genes that were misregulated in the mutant compared with the wild type . The degree of overlap of these genes with those misregulated in the pifq mutant suggests that PIF4 and PIF5 together, additively or redundantly, contribute significantly to the combined regulatory activities of the PIF1, 3, 4, 5 quartet (Sentandreu et al, 2011).…”

“…Microarray analysis of darkgrown monogenic pif3 mutant seedlings identified only 14 genes that were differentially expressed, in statistically significant and twofold (SSTF) fashion, between the mutant and the wild type (Monte et al, 2004;Leivar et al, 2009), although the increased number of statistically differentially expressed genes defined by lowering the fold change threshold from 2 to 1.5, in a recent reanalysis of these data, revealed additional targets of PIF3 regulation (Sentandreu et al, 2011). A similar study with pif1 defined only two genes as statistically different in expression between the mutant and the wild type, and these differences were less than twofold (Moon et al, 2008).…”

PIFs: Systems Integrators in Plant Development

“…Microarray studies using dark-grown single mutants for PIF3 (Monte et al, 2004;Leivar et al, 2009;Sentandreu et al, 2011) or PIF1 (Moon et al, 2008), and double mutants for PIF4 and PIF5 , showed relatively modest contributions of individual PIFs in regulating gene expression genome wide, consistent with the absence of robust morphological phenotypes of these mutants in the dark due to genetic redundancy (Leivar et al, 2008b(Leivar et al, , 2012bShin et al, 2009). In sharp contrast, the transcriptomic profile of pifq mutants in the dark largely resemble that of wild-type seedlings grown in the light (Leivar et al, 2009;Shin et al, 2009).…”

“…Also, as detailed below, hormone-related genes are well represented in this table, especially genes related to auxin biosynthesis, transport, and signaling (YUCCA8, YUCCA9, TAA1, CYP79B2, PIN3, WAG2, IAA29, IAA19, and SAUR19) known to be involved in growth responses to shade, diurnal, or high temperature conditions and in hook formation or phototropic responses. Some of these genes participate in the regulation of organ-specific responses (MIDA10/BBX23 and MIDA9), suggesting branching of PIF signaling (Sentandreu et al, 2011. Intriguingly, several PIF-induced targets are negative regulators of PIF-regulated processes (Supplemental Table 1), including some well-known repressors of growth (HFR1, GAI, and PAR1), whereas several PIF-repressed genes are positive regulators of PIFregulated processes (e.g., MIDA9, STO, and JAZ9).…”