PIFs: pivotal components in a cellular signaling hub

Abstract

A small subset of basic helix-loop-helix transcription factors called PIFs (phytochrome-interacting factors) act to repress seed germination, promote seedling skotomorphogenesis and promote shade-avoidance through regulated expression of over a thousand genes. Light-activated phytochrome molecules directly reverse these activities by inducing rapid degradation of the PIF proteins. Here, we review recent advances in dissecting this signaling pathway and examine emerging evidence that indicates that other pathways also converge to regulate PIF activity, including the gibberellin pathway, the circadian clock and high temperature. Thus PIFs have broader roles than previously appreciated, functioning as a cellular signaling hub that integrates multiple signals to orchestrate regulation of the transcriptional network that drives multiple facets of downstream morphogenesis. The relative contributions of the individual PIFs to this spectrum of regulatory functions ranges from quantitatively redundant to qualitatively distinct.

Figure 1

The PIF-subfamily of phy-interacting basic helix–loop–helix (bHLH) transcription factors. (a) PIF3 domain structure. Schematic of the PIF3 polypeptide showing the location of the consensus bHLH domain, which defines this class of transcription factors, as well as the binding sites for photoactivated phyB (APB) and phyA (APA). The bHLH domain is responsible for dimerization and DNA-binding of the protein. The Arabidopsis PIFs bind to the conserved G-box DNA-sequence motif shown. (b) Subfamily 15 of the Arabidopsis bHLH family showing the phylogeny, nomenclature, domain structures, phy-interaction activity and in vivo functional activity of the PIF proteins. Pfr-specific interaction with phyA and/or phyB is indicated as A and/or B, and lack of interaction as (−). The asterisk indicates evidence of PIF8 binding to phyB (Y. Oka and P.H. Quail, unpublished). Evidence of functional involvement in phy signaling in vivo is indicated as (+), and lack of such evidence as (−). ND = not determined. Modified from [5, 10].

Figure 2

Simplified schematic summary of PIF-mediated signaling pathways. phy photoactivation (Pfr formation) triggers rapid nuclear-localized proteolysis of the PIF proteins. Under long-term light exposure, a direct, mutually negative feedback loop from the PIFs to phyB emerges, whereby the PIFs modulate phyB abundance concomitantly with the converse, by inducing COP1-catalyzed ubiquitylation and degradation of phyB. In addition to this direct regulation of PIF protein abundance, photoactivated phys regulate PIF activity indirectly (i) at the transcriptional level via control of the circadian clock, which in turn induces circadian oscillations in PIF4 and PIF5 gene expression in the light, (ii) at the post-translational level via modulation of the GA signaling pathway, which controls the abundance of DELLA proteins, which, in turn, act negatively on PIF transcriptional activity through binding to the bHLH domain, and, potentially, (iii) by an unknown mechanism via the COP1–SPA regulatory pathway (broken line). PIF4 and PIF5 are also subject to negative feedback regulation via inhibitory heterodimer formation with HFR1, whose gene expression level is promoted by PIF4 and PIF5 in response to vegetational shade. These alterations in abundance or activity result in activation or repression of PIF target-genes, leading in turn to propagation of the cascade of transcriptional changes that drive the overt morphogenic responses. High temperature acts specifically through PIF4 by an unknown mechanism to induce enhanced elongation growth.

Figure 3

Light reverses PIF-promoted skotomorphogenesis by phy-induced degradation of the PIF proteins. (a) PIFs promote skotomorphogenesis in dark-grown wild-type (WT) seedlings. This developmental state is reversed either in the dark by constitutive genetic removal of PIF1, PIF3, PIF4 and PIF5 in the quadruple pifq mutant, or by exposing the WT to light (2 days continuous R light). (b) The phenotype of dark-grown pifq-mutant seedlings resembles that of dark-grown cop1-mutant seedlings, such as the weak cop1-6 mutant allele shown in the picture [92]. (c) PIFs regulate expression of rapidly light-responsive genes such as PIL1. PIFs promote high-level expression of the PIL1 gene in dark-grown (D) WT seedlings (time zero). This expression is strongly repressed in the absence of the PIF quartet in the dark-grown pifq mutant (time zero). Light induces rapid repression of PIL1 gene expression in the WT, in parallel with similarly rapid photoactivated-phy-induced degradation of PIF5 (and other PIFs). Abbreviation: PP2A, SERINE/THREONINE PROTEIN PHOSPHATASE 2A. Modified from [38], [51].and [54].

Figure 4

The PIFs function redundantly and differentially in a cellular signaling hub at the convergence of multiple pathways. Schematic summary of the network of known overlapping and differential activities of the PIF and related non-PIF Subfamily-15 members in integrating responses to both environmental and endogenous signaling pathways.