Inorganic phosphate (Pi) represents the main source of phosphorus for plants, yet this crucial macroelement is often found in very low concentrations, and is insoluble and unevenly distributed in soil. To counter these constraints, plants have developed various strategies to detect Pi distribution in their environment and to adapt their physiology to variations in Pi concentration.
It was previously shown that a local supply of Pi can simulate soil heterogeneity, demonstrating the capacity of plants to stimulate root development in the Pi-enriched area (Drew, 1975; Linkohr et al., 2002). Furthermore, numerous physiological traits of root growth are associated with a local response to Pi deficiency, including: a reduction in the size of the root cells (Reymond et al., 2006); an increase in the length of the root hair (Bates and Lynch, 1996); a cell cycle arrest of the primary root meristem, promoted by a sensing mechanism located in the root tip (Ticconi et al., 2004; Svistoonoff et al., 2007; Arnaud et al., 2010); and an altered development affecting secondary roots (Linkohr et al., 2002; Lopez-Bucio et al., 2002; Reymond et al., 2006).
In addition, there is also an integration of the global Pi status of the plant involving a systemic response (also known as a long-distance response). For example, it has been demonstrated with a split-root experimental design that communication takes place between the root parts of a single plant submitted to uneven distribution of Pi concentrations (Liu et al., 1998; Burleigh and Harrison, 1999; Franco-Zorrilla et al., 2005). This was revealed by the downregulation of Mt4 and several high-affinity Pi transporters in the phosphate-starved part of the root of Medicago (Burleigh and Harrison, 1999), Solanum lycopersicum (tomato; Liu et al., 1998) and Arabidopsis (Franco-Zorrilla et al., 2005), respectively.
The primary signal involved in long-distance signaling has been directly linked to Pi present in the medium and/or the plant cell, as evidenced by a non-metabolizable form of Pi, such as phosphite (Ticconi et al., 2001; Varadarajan et al., 2002), which suppresses phosphate starvation traits. This effect has also been shown by phosphate-sequestering intracellular metabolites, which induce Pi starvation-responsive ribonuclease genes (Köck et al., 1998). Recent genetic evidence corroborates these previous studies, with the identification of phf1, a mutant of the Pi transporter traffic facilitator 1 gene. In this mutant, the activity in several high-affinity phosphate transporters is abolished, resulting in a constitutive low level of intracellular Pi. Such mutant plants express many Pi starvation genes constitutively, even when grown on a phosphate-rich medium (Gonzalez et al., 2005). The factors involved in the long-distance signaling pathway are controversial, but they seem to require components other than Pi. Genetic approaches have further identified some elements of the pathway. For instance, the pho2 mutant, which was selected on the basis of Pi accumulation in leaves (Delhaize and Randall, 1995), is affected in the production of an E2 ubiquitin conjugase enzyme. This enzyme was found to modulate the expression of genes such as High-affinity transporters (PHT1;8 and PHT1;9) and members of the IPS1/At4 family. A complex regulatory system has been identified involving the degradation of PHO2 mRNA through the action of microRNA399 (mir399). This mir399, regulated by At4 (Franco-Zorrilla et al., 2007), moves through the phloem, and might act as a long-distance signal (Aung et al., 2006; Bari et al., 2006). Although these elements appear to be involved in the systemic regulation of genes that respond to Pi starvation, only a limited number of targets have been investigated, as it is unknown which genes are systemically regulated by phosphate deficiency at the whole-genome level. Nevertheless, transcriptional control is a key level of regulation for the response to Pi starvation, and one of its major actors has been identified as the Myb transcription factor PHR1 (Rubio et al., 2001). Recently, exhaustive genome-wide analyses on Arabidopsis thaliana (Misson et al., 2005; Morcuende et al., 2007) have identified numerous genes regulated by Pi starvation; however, neither of these studies was able to distinguish between local and systemic regulations. In the present work, we have addressed this issue by performing a split-root experiment, in which two parts of the same root were supplied with independent media that differ in their Pi content. RNA extracted from the different root parts was then analyzed with Affymetrix ATH1 DNA chips for a full genome analysis. Such experiments gave a global view of the transcripts that are regulated locally or systemically by Pi supply, and lead to a detailed characterization of the roles of external versus internal Pi, and of elements involved in the Pi transduction pathway.