Pi Homeostasis In Plants Research Articles

Opportunity for genome engineering to enhance phosphate homeostasis in crops.

Plants maintain cellular homeostasis of phosphate (Pi) through an integrated response pathway regulated by different families of transcription factors including MYB, WRKY, BHLH, and ZFP. The systemic response to Pi limitation showed the critical role played by inositol pyrophosphate (PP-InsPs) as signaling molecule and SPX (SYG1/PHO81/XPR1) domain proteins as sensor of cellular Pi status. Binding of SPX to PP-InsPs regulates the transcriptional activity of the MYB-CC proteins, phosphate starvation response factors (PHR/PHL) as the central regulator of Pi-deficiency response in plants. Vacuolar phosphate transporter, VPT may sense the cellular Pi status by its SPX domain, and vacuolar sequestration is activated under Pi replete condition and the stored Pi is an important resource to be mobilized under Pi deficiency. Proteomic approaches led to new discoveries of proteins associated with Pi-deficient response pathways and post-translational events that may influence plants in achieving Pi homeostasis. This review provides current understanding on the molecular mechanisms at the transcriptional and translational levels for achieving Pi homeostasis in plants. The potential strategies for employing the CRISPR technology to modify the gene sequences of key regulatory and response proteins for attaining plant Pi homeostasis are discussed.

The Arabidopsis PHOSPHATE 1 exporter undergoes constitutive internalization via clathrin-mediated endocytosis.

SUMMARYInorganic phosphate (Pi) homeostasis is essential for plant growth and depends on the transport of Pi across cells. In Arabidopsis thaliana, PHOSPHATE 1 (PHO1) is present in the root pericycle and xylem parenchyma where it exports Pi into the xylem apoplast for its transfer to shoots. PHO1 consists of a cytosolic SPX domain followed by membrane‐spanning α‐helices and ends with the EXS domain, which participates in the steady‐state localization of PHO1 to the Golgi and trans‐Golgi network (TGN). However, PHO1 exports Pi across the plasma membrane (PM), making its localization difficult to reconcile with its function. To investigate whether PHO1 transiently associates with the PM, we inhibited clathrin‐mediated endocytosis (CME) by overexpressing AUXILIN‐LIKE 2 or HUB1. Inhibiting CME resulted in PHO1 re‐localization from the Golgi/TGN to the PM when PHO1 was expressed in Arabidopsis root pericycle or epidermis or Nicotiana benthamiana leaf epidermal cells. A fusion protein between the PHO1 EXS region and GFP was stabilized at the PM by CME inhibition, indicating that the EXS domain plays an important role in sorting PHO1 to/from the PM. PHO1 internalization from the PM occurred independently of AP2 and was not influenced by Pi deficiency, the ubiquitin‐conjugating E2 PHO2, or the potential ubiquitination of cytosolic lysines in the EXS domain. PM‐stabilized PHO1 showed reduced root‐to‐shoot Pi export activity, indicating that CME of PHO1 may be important for its optimal Pi export activity and plant Pi homeostasis.

Phosphate-dependent regulation of vacuolar trafficking of OsSPX-MFSs is critical for maintaining intracellular phosphate homeostasis in rice

Vacuolar storage of inorganic phosphate (Pi) is essential for Pi homeostasis in plants. The SPX-MFS family proteins have been demonstrated to be vacuolar Pi transporters in many plant species. Transcriptional regulation of the predominant transporter among rice SPX-MFSs, OsSPX-MFS3, was only moderately suppressed by Pi starvation. Thus, post-transcriptional mechanisms were hypothesized to regulate the activity of OsSPX-MFS3. In this study, we found that the tonoplast localization of OsSPX-MFSs is inhibited under Pi-depleted conditions, resulting in their retention in the pre-vacuolar compartments (PVCs). A yeast two-hybrid screen identified that two SNARE proteins, OsSYP21 and OsSYP22, interact with the MFS domain of OsSPX-MFS3. Further genetic and cytological analyses indicate that OsSYP21 and OsSYP22 facilitate trafficking of OsSPX-MFS3 from PVCs to the tonoplast. Although a homozygous frameshift mutation in OsSYP22 appeared to be lethal, tonoplast localization of OsSPX-MFS3 was significantly inhibited in transgenic plants expressing a negative-dominant form of OsSYP22 (OsSYP22-ND), resulting in reduced vacuolar Pi concentrations in OsSYP22-ND plants. Under Pi-depleted conditions, the interaction between OsSYP22 and OsSPX-MFS3 was disrupted, and this process depended on the presence of the SPX domain. Deleting the SPX domains of OsSPX-MFSs resulted in their tonoplast localization under both Pi-depleted and Pi-replete conditions. Complementation of the osspx-mfs1/2/3 triple mutants with the MFS domain or the SPX domain of OsSPX-MFS3 confirmed that the MFS and SPX domains are responsive to Pi transport activity and Pi-dependent regulation, respectively. These data indicated that the SPX domains of OsSPX-MFSs sense cellular Pi (InsP) levels and, under Pi-depleted conditions, inhibit the interaction between OsSPX-MFSs and OsSYP21/22 and subsequent trafficking of OsSPX-MFSs from PVCs to the tonoplast.

NIGT1 represses plant growth and mitigates phosphate starvation signaling to balance the growth response tradeoff in rice.

Inorganic phosphate (Pi) availability is an important factor that affects the growth and yield of crops, thus an appropriate and effective response to Pi-fluctuation is critical. However, how crops orchestrate Pi-signaling and growth under Pi-starvation conditions to optimize the growth defense tradeoff remains unclear. Here we show that a Pi-starvation induced transcription factor NIGT1 (NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1) controls plant growth and prevents a hyperresponse to Pi-starvation by directly repressing the expression of growth-related and Pi-signaling genes to achieve a balance between growth and response under a varying Pi environment. NIGT1 directly binds to the promoters of Pi-starvation signaling marker genes, like IPS1, miR827 and SPX2, under Pi-deficient conditions to mitigate the Pi-starvation responsive (PSR). It also directly represses the expression of vacuolar Pi efflux transporter genes VPE1/2 to regulate plant Pi-homeostasis. We further demonstrate that NIGT1 constrains shoot growth by repressing the expression of growth-related regulatory genes, including brassinolide signal transduction master regulator BZR1, cell division regulator CYCB1;1, and DNA replication regulator PSF3. Our findings reveal the function of NIGT1 in orchestrating plant growth and Pi-starvation signaling, and also provide evidence that NIGT1 acts as a safeguard to avoid hyperresponse during Pi-starvation stress in rice. This article is protected by copyright. All rights reserved.

OsIPK2, a rice inositol polyphosphate kinase gene, is involved in phosphate homeostasis and root development.

Phosphorus (P) is one kind of growth-limiting nutrient for plants, which is taken up by root tissue from the environment as inorganic phosphate (Pi). To maintain an appropriate status of cellular Pi, plants have developed sophisticated strategies to sense Pi level and modulate their root system architecture (RSA) under the ever-changing growth condition. However, the molecular basis underlying the mechanism remains elusive. Inositol polyphosphate kinase (IPK2) is a key enzyme in the inositol phosphate metabolism pathway, which catalyzes the phosphorylation of IP3 into IP5 by consuming ATP. In this study, the function of a rice inositol polyphosphate kinase gene (OsIPK2) in plant Pi homeostasis and thus physiological response to Pi signal were characterized. As a biosynthetic gene for phytic acid in rice, overexpression of OsIPK2 led to distinct changes of inositol polyphosphate profiles and an excessive accumulation of Pi level in transgenic rice under Pi-sufficient conditions. The inhibitory effects of OsIPK2 on root growth were alleviated by Pi-deficient treatment compared with wild-type plants, suggesting the involvement of OsIPK2 in the Pi-regulated reconstruction of RSA. In OsIPK2-overexpressing plants, the altered acid phosphatase (APases) activities and misregulation of Pi starvation induced (PSI) genes were observed in roots under different Pi supply conditions. Notably, the expression of OsIPK2 also altered the Pi homeostasis and root system architecture in transgenic Arabidopsis. Taken together, our findings demonstrated that OsIPK2 plays an important role in Pi homeostasis and root system architecture adjustment in response to different environmental Pi levels in plant.

Transcription factor OsNAC016 negatively regulates phosphate-starvation response in rice

Phosphate (Pi), the main form of inorganic phosphorus that can be absorbed by plants, is one of the most limiting macro-nutrients in plants. However, the underlying molecular mechanism determining how plants sense external Pi levels and reprogram transcriptional and adaptive responses is incompletely understood. At present, few rice NAC members have been reported to be involved in the signaling pathways of Pi homeostasis in plants. Here, our research demonstrated that OsNAC016, a Pi-starvation responsive gene in rice, was regulated by PHOSPHATE STARVATION RESPONSE protein 1 (OsPHR1) and OsPHR4. Under Pi-starvation stress, the root growth of OsNAC016-overexpression lines was inhibited more severely, and overexpression plants had lower Pi content than wild type, while osnac016 mutant was hyposensitive to Pi starvation, indicating that OsNAC016 negatively modulates rice Pi-starvation response. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) analysis and transient transactivation assays indicated that OsNAC016 could activate the SPX-domain-containing protein 2 (OsSPX2) gene through binding to its promoter. Further, we found that Pi starvation enhanced OsNAC016 binding to the OsSPX2 promoter, thus strongly promoting OsSPX2 expression. At the same time, Pi starvation induced OsNAC016 protein accumulation in plants. Moreover, similar to OsSPX2, OsNAC016 negatively regulates leaf inclination by repressing the cell elongation in lamina joint in rice under Pi-starvation stress. Together, our findings demonstrate that OsNAC016 negatively regulates rice phosphate-starvation response and leaf inclination by activating OsSPX2 expression under Pi-starvation conditions. These data provide a strategy to create smart crops with ideal shoot architecture and high phosphorus utilization efficiency.

Genome-Wide Analysis of DoSPX Genes and the Function of DoSPX4 in Low Phosphorus Response in Dendrobium officinale.

Dendrobium officinale Kimura et Migo is a famous Chinese herb. D. officinale grows on rocks where the available phosphorus is low. The SPX family plays a critical role in maintaining Pi homeostasis in plants. In this paper, 9 SPX family genes were identified in the genome of D. officinale. Bioinformatics and qRT-PCR analysis showed that DoSPXs were involved in response to −Pi stress and had different expression patterns. DoSPX4, which had a unique expression pattern, was clustered with AtSPX4 and OsSPX4. Under −Pi treatment, the expression level of DoSPX4 reached a peak on 5 d in roots, while showing a downward trend in the aboveground parts. DoSPX4 was located on the cell membrane. Overexpression DoSPX4 promoted Pi content in the stem and the expression level of NtPHT1/2 in Nicotiana tabacum. The results of Yeast two-hybrid showed that DoSPX4 could interact with Phosphate High-Affinity Response factor (DoPHR2). These results highlight the role of DoSPX4 in response to low phosphorus, which provides a theoretical basis for further study on the response mechanism of −Pi in D. officinale.

Mechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 \u2013 PHR2 complex

Phosphate (Pi) starvation response (PHR) transcription factors play key roles in plant Pi homeostasis maintenance. They are negatively regulated by stand-alone SPX proteins, cellular receptors for inositol pyrophosphate (PP-InsP) nutrient messengers. How PP-InsP-bound SPX interacts with PHRs is poorly understood. Here, we report crystal structures of the rice SPX2/InsP6/PHR2 complex and of the PHR2 DNA binding (MYB) domain in complex with target DNA at resolutions of 3.1 Å and 2.7 Å, respectively. In the SPX2/InsP6/PHR2 complex, the signalling-active SPX2 assembles into a domain-swapped dimer conformation and binds two copies of PHR2, targeting both its coiled-coil (CC) oligomerisation domain and MYB domain. Our results reveal that the SPX2 senses PP-InsPs to inactivate PHR2 by establishing severe steric clashes with the PHR2 MYB domain, preventing DNA binding, and by disrupting oligomerisation of the PHR2 CC domain, attenuating promoter binding. Our findings rationalize how PP-InsPs activate SPX receptor proteins to target PHR family transcription factors.

Phosphate starvation responsive GmSPX5 mediates nodule growth through interaction with GmNF-YC4 in soybean (Glycine max).

Phosphorus (P) deficiency adversely affects nodule development as reflected by reduced nodule fresh weight in legume plants. Though mechanisms underlying nodule adaptation to P deficiency have been studied extensively, it remains largely unknown which regulator mediates nodule adaptation to P deficiency. In this study, GUS staining and quantitative reverse transcription-PCR analysis reveal that the SPX member GmSPX5 is preferentially expressed in soybean (Glycine max) nodules. Overexpression of GmSPX5 enhanced soybean nodule development particularly under phosphate (Pi) sufficient conditions. However, the Pi concentration was not affected in soybean tissues (i.e., leaves, roots, and nodules) of GmSPX5 overexpression or suppression lines, which distinguished it from other well-known SPX members functioning in control of Pi homeostasis in plants. Furthermore, GmSPX5 was observed to interact with the transcription factor GmNF-YC4 in vivo and in vitro. Overexpression of either GmSPX5 or GmNF-YC4 significantly upregulated the expression levels of five asparagine synthetase-related genes (i.e., GmASL2-6) in soybean nodules. Meanwhile, yeast one-hybrid and luciferase activity assays strongly suggested that interactions of GmSPX5 and GmNF-YC4 activate GmASL6 expression through enhancing GmNF-YC4 binding of the GmASL6 promoter. These results not only demonstrate the GmSPX5-GmNF-YC4-GmASL6 regulatory pathway mediating soybean nodule development, but also considerably improve our understanding of SPX functions in legume crops.

Effect of AtPAP17 and AtPAP26 genes overexpression on yield and yield components under salt stress in Arabidopsis thaliana plant

Effect of AtPAP17 and AtPAP26 genes overexpression on yield and yield components under salt stress in Arabidopsis thaliana plant

Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis

Phosphorus is an essential nutrient taken up by organisms in the form of inorganic phosphate (Pi). Eukaryotes have evolved sophisticated Pi sensing and signaling cascades, enabling them to stably maintain cellular Pi concentrations. Pi homeostasis is regulated by inositol pyrophosphate signaling molecules (PP-InsPs), which are sensed by SPX domain-containing proteins. In plants, PP-InsP-bound SPX receptors inactivate Myb coiled-coil (MYB-CC) Pi starvation response transcription factors (PHRs) by an unknown mechanism. Here we report that a InsP8–SPX complex targets the plant-unique CC domain of PHRs. Crystal structures of the CC domain reveal an unusual four-stranded anti-parallel arrangement. Interface mutations in the CC domain yield monomeric PHR1, which is no longer able to bind DNA with high affinity. Mutation of conserved basic residues located at the surface of the CC domain disrupt interaction with the SPX receptor in vitro and in planta, resulting in constitutive Pi starvation responses. Together, our findings suggest that InsP8 regulates plant Pi homeostasis by controlling the oligomeric state and hence the promoter binding capability of PHRs via their SPX receptors.

CASEIN KINASE2-Dependent Phosphorylation of PHOSPHATE2 Fine-tunes Phosphate Homeostasis in Rice.

Plants have evolved complex physiological and biochemical mechanisms to adapt to a heterogeneous soil phosphorus environment. PHOSPHATE2 (PHO2) is a phosphate (Pi) starvation-signaling regulator involved in maintaining Pi homeostasis in plants. Arabidopsis (Arabidopsis thaliana) PHO2 targets PHOSPHATE TRANSPORTER1 (PHT1) and PHO1 for degradation, whereas rice (Oryza sativa) PHO2 is thought to mediate PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 degradation. However, it is unclear whether and how PHO2 is post-translationally regulated. Here, we show that in rice, the CASEIN KINASE2 (OsCK2) catalytic subunit OsCK2α3 interacts with OsPHO2 in vitro and in vivo in vascular tissues cells, and phosphorylates OsPHO2 at Ser-841. Phosphorylated OsPHO2 is degraded more rapidly than native OsPHO2 in cell-free degradation assays. OsPHO2 interacts with OsPHO1 and targets it for degradation through a multivesicular body-mediated pathway. PHO1 mutation partially rescued the pho2 mutant phenotype. Further genetic analysis showed that a nonphosphorylatable version of OsPHO2 rescued the Ospho2 phenotype of high Pi accumulation in leaves better than native OsPHO2. In addition to the previously established role of OsCK2 in negatively regulating endoplasmic reticulum exit of PHT1 phosphate transporters, this work uncovers a role for OsCK2α3 in modulating Pi homeostasis through regulating the phosphorylation status and abundance of OsPHO2 in rice.

Inositol Pyrophosphate InsP8 Acts as an Intracellular Phosphate Signal in Arabidopsis

The maintenance of cellular phosphate (Pi) homeostasis is of great importance in living organisms. The SPX domain-containing protein 1 (SPX1) proteins from both Arabidopsis and rice have been proposed to act as sensors of Pi status. The molecular signal indicating the cellular Pi status and regulating Pi homeostasis in plants, however, remains to be identified, as Pi itself does not bind to the SPX domain. Here, we report the identification of the inositol pyrophosphate InsP8 as a signaling molecule that regulates Pi homeostasis in Arabidopsis. Polyacrylamide gel electrophoresis profiling of InsPs revealed that InsP8 level positively correlates with cellular Pi concentration. We demonstrated that the homologs of diphosphoinositol pentakisphosphate kinase (PPIP5K), VIH1 and VIH2, function redundantly to synthesize InsP8, and that the vih1 vih2 double mutant overaccumulates Pi. SPX1 directly interacts with PHR1, the central regulator of Pi starvation responses, to inhibit its function under Pi-replete conditions. However, this interaction is compromised in the vih1 vih2 double mutant, resulting in the constitutive induction of Pi starvation-induced genes, indicating that plant cells cannot sense cellular Pi status without InsP8. Furthermore, we showed that InsP8 could directly bind to the SPX domain of SPX1 and is essential for the interaction between SPX1 and PHR1. Collectively, our study suggests that InsP8 is the intracellular Pi signaling molecule serving as the ligand of SPX1 for controlling Pi homeostasis in plants.

Vacuolar Phosphate Transporters Contribute to Systemic Phosphate Homeostasis Vital for Reproductive Development in Arabidopsis.

Vacuolar storage of phosphate (Pi) is essential for Pi homeostasis in plants. Recent studies have identified a family of vacuolar Pi transporters, VPTs (PHT5s), responsible for vacuolar sequestration of Pi. We report here that both VPT1 and VPT3 contribute to cytosol-to-vacuole Pi partitioning. Although VPT1 plays a predominant role, VPT3 is particularly important when VPT1 is absent. Our data suggested that the vpt1 vpt3 double mutant was more defective in Pi homeostasis than the vpt1 single mutant, as indicated by Pi accumulation capacity, vacuolar Pi influx, subcellular Pi allocation, and plant adaptability to changing Pi status. The remaining member of the VPT family, VPT2 (PHT5;2), did not appear to contribute to Pi homeostasis in such assays. Particularly interesting is the finding that the vpt1 vpt3 double mutant was impaired in reproductive development with shortened siliques and impaired seed set under sufficient Pi, and this phenotype was not found in the vpt1 vpt2 and vpt2 vpt3 double mutants. Measurements of Pi contents revealed Pi over-accumulation in the floral organs of vpt1 vpt3 as compared with the wild type. Further analysis identified excess Pi in the pistil as inhibitory to pollen tube growth, and thus seed yield, in the mutant plants. Reducing the Pi levels in culture medium or mutation of PHO1, a Pi transport protein responsible for root-shoot transport, restored the seed set of vpt1 vpt3 Thus, VPTs, through their function in vacuolar Pi sequestration, control the fine-tuning of systemic Pi allocation, which is particularly important for reproductive development.

Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency.

In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

Heat Stress Affects Pi-related Genes Expression and Inorganic Phosphate Deposition/Accumulation in Barley

Phosphorus (P) in plants is taken from soil as an inorganic phosphate (Pi) and is one of the most important macroelements in growth and development. Plants actively react to Pi starvation by the induced expression of Pi transporters, MIR399, MIR827, and miR399 molecular sponge – IPS1 genes and by the decreased expression of the ubiquitin-conjugating enzyme E2 (PHOSPHATE2 – PHO2) and Pi sensing and transport SPX-MFS genes. The PHO2 protein is involved in the degradation of Pi transporters PHT1;1 (from soil to roots) and PHO1 (from roots to shoots). The decreased expression of PHO2 leads to Pi accumulation in shoots. In contrast, the pho1 mutant shows a decreased level of Pi concentration in shoots. Finally, Pi starvation leads to decreased Pi concentration in all plant tissues. Little is known about plant Pi homeostasis in other abiotic stress conditions. We found that, during the first hour of heat stress, Pi accumulated in barley shoots but not in the roots, and transcriptomic data analysis as well as RT-qPCR led us to propose an explanation for this phenomenon. Pi transport inhibition from soil to roots is balanced by lower Pi efflux from roots to shoots directed by the PHO1 transporter. In shoots, the PHO2 mRNA level is decreased, leading to an increased Pi level. We concluded that Pi homeostasis in barley during heat stress is maintained by dynamic changes in Pi-related genes expression.

Genetic manipulation of a high-affinity PHR1 target cis-element to improve phosphorous uptake in Oryza sativa L.

Phosphorus (P) is an essential macronutrient for crop development and production. Phosphate starvation response 1 (PHR1) acts as the central regulator for Pi-signaling and Pi-homeostasis in plants by binding to the cis-element PHR1 binding sequence (P1BS; GNATATNC). However, how phosphate starvation-induced gene expression is regulated remains obscure. In this work, we investigated the DNA binding affinity of the PHR1 ortholog OsPHR2 to its downstream target genes in Oryza sativa (rice). We confirmed that a combination of P1BS and P1BS-like motifs are essential for stable binding by OsPHR2. Furthermore, we report that variations in P1BS motif bases affected the binding affinity of OsPHR2 and that the highest affinity motif was GaATATtC (designated the A-T-type P1BS). We also found that a combination of two A-T-type P1BS elements in tandem, namely HA-P1BS, was very efficient for binding of OsPHR2. Using the cis-regulator HA-P1BS, we modified the promoters of Transporter Traffic Facilitator 1 (PHF1), a key factor controlling endoplasmic reticulum-exit of phosphate transporters to the plasma membrane, for efficient uptake of phosphorous in an energetically neutral way. Transgenic plants with the modified promoters showed significantly enhanced tolerance to low phosphate stress in both solution and soil conditions, which provides a new strategy for crop improvement to enhance tolerance of nutrient deficiency.

SPX4 Negatively Regulates Phosphate Signaling and Homeostasis through Its Interaction with PHR2 in Rice

PHR2, a central regulator of phosphate signaling in rice, enhanced the expression of phosphate starvation-induced (PSI) genes and resulted in the enhancement of Pi acquisition under Pi deficiency stress. This occurred via PHR2 binding to a cis-element named the PHR1 binding sequences. However, the transcription level of PHR2 was not responsive to Pi starvation. So how is activity of transcription factor PHR2 adjusted to adapt diverse Pi status? Here, we identify an SPX family protein, Os-SPX4 (SPX4 hereafter), involving in Pi starvation signaling and acting as a negative regulator of PHR2. SPX4 is shown to be a fast turnover protein. When Pi is sufficient, through its interaction with PHR2, SPX4 inhibits the binding of PHR2 to its cis-element and reduces the targeting of PHR2 to the nucleus. However, when plants grow under Pi deficiency, the degradation of SPX4 is accelerated through the 26S proteasome pathway, thereby releasing PHR2 into the nucleus and activating the expression of PSI genes. Because the level of SPX4 is responsive to Pi concentration and SPX4 interacts with PHR2 and regulates its activity, this suggests that SPX4 senses the internal Pi concentration under diverse Pi conditions and regulates appropriate responses to maintain Pi homeostasis in plants.

Toward deciphering the genome-wide transcriptional responses of rice to phosphate starvation and recovery

Phosphate (Pi) limitation is one of the major factors negatively impacting crop yield worldwide. Next generation sequencing (NGS) was used to profile the transcriptomes of rice (Oryza sativa) roots and shoots after phosphate starvation and recovery, shedding further light on the complex and dynamic mechanisms involved in Pi homeostasis. The use of NGS also enabled the identification of previously not annotated loci and novel isoforms of genes that are specifically induced by Pi starvation. Furthermore, phosphate re-feeding was observed to have a unique response with a variety of transcription factors and kinases induced in a transient manner. Expression profiles of miRNAs were also assessed upon long-term Pi starvation in roots and shoots revealing several novel miRNAs associated with Pi starvation. Altogether, this study provides key findings regarding Pi homeostasis in plants that will provide a valuable resource for research aimed at generating crops with increased Pi acquisition/use efficiency.

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled. A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several genes also showed induction of unannotated splice isoforms under Pi starvation. Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation-induced isoform, which was associated with increased translation activity. In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250. In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plants.