Phytochrome-Interacting Factors Have Both Shared and Distinct Biological Roles

Abstract

Phytochromes are plant photoreceptors that perceive red and far-red light. Upon the perception of light in Arabidopsis, light-activated phytochromes enter the nucleus and act on a set of interacting proteins, modulating their activities and thereby altering the expression levels of ∼10% of the organism's entire gene complement. Phytochromeinteracting factors (PIFs) belonging to Arabidopsis basic helix-loop-helix (bHLH) subgroup 15 are key interacting proteins that play negative roles in light responses. Their activities are post-translationally countered by light-activated phytochromes, which promote the degradation of PIFs and directly or indirectly inhibit their binding to DNA. The PIFs share a high degree of similarity, but examinations of pif single and multiple mutants have indicated that they have shared and distinct functions in various developmental and physiological processes. These are believed to stem from differences in both intrinsic protein properties and their gene expression patterns. In an effort to clarify the basis of these shared and distinct functions, we compared recently published genome-wide ChIP data, developmental gene expression maps, and responses to various stimuli for the various PIFs. Based on our observations, we propose that the biological roles of PIFs stem from their shared and distinct DNA binding targets and specific gene expression patterns.

PIFs: Systems Integrators in Plant Development

“…Broad functional categorization of the PIF-induced gene subset during deetiolation, shade, and diurnal growth conditions shows a similar pattern of enrichment in transcription-, cell wall-, and hormone-related genes, consistent with the PIFs functioning in promoting pleiotropic aspects of seedling growth under different light environments (Leivar et al, 2009(Leivar et al, , 2012bShin et al, 2009;Nozue et al, 2011;Hornitschek et al, 2012;Li et al, 2012;Oh et al, 2012;Jeong and Choi, 2013;Zhang et al, 2013). In contrast with this pattern, the PIFq-repressed subset during deetiolation is strongly enriched in photosynthesis/chloroplast-related genes (Leivar et al, 2009;Shin et al, 2009;Oh et al, 2012), consistent with the PIFs functioning in repressing chloroplast development and photosynthetic competency in etiolated seedlings (Leivar et al, 2009;Stephenson et al, 2009).…”

“…Current evidence shows that the direct physical binding of PIFs with the photoactive, nuclear-localized phy Pfr conformer leads to a reduction in PIF abundance and/or activity in the cell (reviewed in Leivar and Quail, 2011;Jeong and Choi, 2013) (Figure 1B). In dark-grown seedlings (i.e., etiolated), PIF proteins accumulate, whereas upon exposure to light (deetiolation response), photoactivated phy Pfr translocates into the nucleus and induces a rapid decline in the abundance of PIFs (particularly the PIF quartet [PIFq] members PIF1, PIF3, PIF4, and PIF5), with half-lives of 5 to 20 min (Bauer et al, 2004;Monte et al, 2004;Shen et al, 2005Shen et al, , 2007Al-Sady et al, 2006;Nozue et al, 2007;Lorrain et al, 2008).…”

“…Interestingly, database analyses have shown that PIFs are differentially expressed in response to environmental and endogenous stimuli (reviewed in Castillon et al, 2007;Jeong and Choi, 2013), suggesting that they might be differentially targeted by transcriptional regulators specific to particular signals. Recent publication of genome-wide binding sites for several Arabidopsis transcriptional regulators allows initial mapping of proteins that have been reported to associate with PIFs potentially to regulate their expression.…”

“…Several excellent reviews have covered the role of PIFs in regulating phy-signaling and transcriptional networks Jeong and Choi, 2013) or have focused on their participation in specific processes, such as seed germination, shade avoidance, thermal-induced responses, or crosstalk with specific hormonal pathways or the circadian clock (Franklin, 2008;Lau and Deng, Leivar et al [2012b], Figure 1B.) 2010; Wang et al, 2012;Casal, 2013;de Wit et al, 2013;KinmonthSchultz et al, 2013;Proveniers and van Zanten, 2013;Shin et al, 2013;Wigge, 2013;Yamashino, 2013).…”

Phytochromes and Phytochrome Interacting Factors

“…some responses are controlled by a single PIF, while others by two or more PIFs; Jeong and Choi, 2013). For example, PIF1 plays a major role in inhibiting light-dependent seed germination (Oh et al, 2004).…”