We are taking genetic approaches in Arabidopsis thaliana to dissect Pi sensing and developed several screens for isolating Pi-deficiency-response (pdr) mutants. We are focusing on pdr mutant isolation and characterization, as well as on gene identification and functional analysis of PDR gene products.
Two classes of conditional pdr mutants are of particular interest: Class I mutations, typified by pdr2 and similar mutants disrupt local Pi sensing and reveal a Pi-sensitive checkpoint in root development that regulates stem cell fate and meristem activity in response to external Pi availability. On the other hand, class II mutations, typified by pdr1 and additional mutants impair metabolic adjustments and systemic responses to Pi limitation. Continued forward genetic screens for new pdr loci, isolation of suppressors or enhancers of identified pdr mutations, and complementary strategies for functional gene identification will be essential for understanding plant Pi sensing.
Environmental Pi availability profoundly impacts root development. When challenged by Pi shortage, plants adjust root system architecture and enhance root exudation to better facilitate interception and uptake of the nutrient, which becomes more limiting with increasing soil depth. Thus, Pi deprivation stimulates formation of a shallow root system and expansion of root surface area by attenuating primary root extension rate, promoting development of lateral roots, and intensifying root hair formation. Physiological and molecular studies indicate that external Pi status is sensed locally at root tips to adjust meristem activity.
We have isolated and characterized a collection of pdr mutants (pdr2-pdr4) that display hypersensitive inhibition of primary root growth in response to Pi deprivation, leading to a truncated root system. A second set of mutants, named low phosphate root (lpr1, lpr2), were isolated in the collaborating Desnos/Nussaume laboratory and show an insensitive, long root phenotype on low Pi. Our phenotypic studies revealed a Pi-sensitive checkpoint in root development that adjusts stem cell identity and meristem activity in response to local Pi availability. Genetic analyses indicate that genes of both mutant collections functionally interact in a common pathway to regulate cell-to-cell communication via extensive cell wall modification of cells in the stem cell niche, which is dependent on dynamic changes in Fe uptake and tissue-specific distribution in root meristems.
Core components of this pathway are PDR3, a putative subunit of a histone deacetylase complex, PDR2, the P5-type ATPase in Arabidopsis, and two multicopper oxidases (MCO), LPR1 and LPR2. These proteins of unknown specificities are expressed in the distal root meristem and targeted to the cell nucleus and endoplasmatic reticulum (ER). Considering the epistatic relationship between lpr1/lpr2, pdr2 and pdr3 mutations as well as their respective phenotypes, PDR3 and PDR2 likely restrict LPR function, either by negatively regulating LPR biogenesis or by removing/inactivating products generated by their associated MCO activity. Our results indicate that partially antagonistic interactions between Pi and Fe availability mediate local Pi sensing. We observed that the pdr2 mutation sensitizes root meristem activity not only to the inhibitory effect of decreasing Pi, but also to increasing external Fe, which is counteracted by loss of LPR genes. Although the substrate specificity of LPR1 remains to be established, it is tempting to speculate that PDR2/LPR1-dependent Fe transport and Fe-mediated redox signaling modulates root meristem activity in response to Pi deficiency via cell-to-cell signaling in the root stem cell niche.
Because the ER-localized PDR2-LPR1 module likely affects the secretory pathway, the role of root exudation for external Pi sensing is currently studied in a project within the Leibniz Association center grant “Chemical Communication in the Rhizosphere”. In collaboration with other IPB departments, we are developing protocols for sterile hydroponic growth of Arabidopsis plants and non-targeted metabolite analysis of root exudates.
Our characterization of pdr mutants revealed complex interactions between P, Fe and N sensing. Pi deprivation causes elevated Fe accumulation in plants and modifies the expression of genes regulating Fe homeostasis. When compared to wild type, loss of PDR2 and PDR3 sensitizes the response of root meristems to the inhibitory effect of external Fe. Given that LPR1 encodes a multicopper oxidase, it is feasible that Pi availability interacts with Fe homeostasis and possibly with the production of reactive oxygen species (ROS) to adjust root meristem activity via proteins of the ER and cell nucleus. On the other hand, class II pdr mutations such as pdr1, which alter both metabolic and developmental responses to Pi limitation (e.g. root system architecture, Pi homeostasis, expression of Pi-responsive genes) not only reduce the sensitivity of Pi deficiency responses, but also enhance the sensitivity to nitrate and other N sources in the medium. Thus, two factors contribute to the conditional phenotype of pdr1: a decreased sensitivity to low Pi and an increased sensitivity to high nitrate and other N compounds. We hypothesize that PDR1 encodes a regulatory component upstream of Pi starvation-inducible gene expression, which may further play a role in sensing external N status. Cloning and molecular characterization of PDR1 and other class I PDR genes will illuminate the emerging connection between Pi and N sensing.