A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis

Abstract

Plants respond to different stresses by inducing or repressing transcription of partially overlapping sets of genes. In Arabidopsis, the PHR1 transcription factor (TF) has an important role in the control of phosphate (Pi) starvation stress responses. Using transcriptomic analysis of Pi starvation in phr1, and phr1 phr1-like (phl1) mutants and in wild type plants, we show that PHR1 in conjunction with PHL1 controls most transcriptional activation and repression responses to phosphate starvation, regardless of the Pi starvation specificity of these responses. Induced genes are enriched in PHR1 binding sequences (P1BS) in their promoters, whereas repressed genes do not show such enrichment, suggesting that PHR1(-like) control of transcriptional repression responses is indirect. In agreement with this, transcriptomic analysis of a transgenic plant expressing PHR1 fused to the hormone ligand domain of the glucocorticoid receptor showed that PHR1 direct targets (i.e., displaying altered expression after GR:PHR1 activation by dexamethasone in the presence of cycloheximide) corresponded largely to Pi starvation-induced genes that are highly enriched in P1BS. A minimal promoter containing a multimerised P1BS recapitulates Pi starvation-specific responsiveness. Likewise, mutation of P1BS in the promoter of two Pi starvation-responsive genes impaired their responsiveness to Pi starvation, but not to other stress types. Phylogenetic footprinting confirmed the importance of P1BS and PHR1 in Pi starvation responsiveness and indicated that P1BS acts in concert with other cis motifs. All together, our data show that PHR1 and PHL1 are partially redundant TF acting as central integrators of Pi starvation responses, both specific and generic. In addition, they indicate that transcriptional repression responses are an integral part of adaptive responses to stress. As sessile organisms, plants are often exposed to stress conditions, and have evolved adaptive responses to protect themselves from different types of stress. Some responses are stress type-specific whereas others are common to different stress types. Understanding how these responses are controlled is crucial for rational improvement of stress tolerance, a limiting factor in crop productivity. Here we examined the physiological and molecular responses to phosphate starvation and found that a single transcription factor family, represented by PHOSPHATE STARVATION RESPONSE REGULATOR 1 (PHR1), has a central role in the control of specific and shared phosphate starvation stress responses. In consonance with the importance of PHR1, we found that the PHR1-binding sequence, present in most PHR1 direct targets, is a crucial cis motif for Pi starvation responsiveness. An artificial promoter controlled by PHR1 recapitulates responsiveness to Pi starvation and to modulators of this response, qualifying PHR1 family members as central integrators in Pi starvation signalling. This central integrator system also controls most transcriptional repression responses to Pi starvation, indicating that they are an integral part of the adaptive response, and not a consequence of plant malfunction due to stress.