Regulation of OsSPX1 and OsSPX3 on expression of OsSPX domain genes and Pi-starvation signaling in rice

Altered Expression of OsNLA1 Modulates Pi Accumulation in Rice (Oryza sativa L.) Plants

Current agricultural practices rely on heavy use of fertilizers for increased crop productivity. However, the problems associated with heavy fertilizer use, such as high cost and environmental pollution, require the development of crop species with increased nutrient use efficiency. In this study, by using transgenic approaches, we have revealed the critical role of OsNLA1 in phosphate (Pi) accumulation of rice plants. When grown under sufficient Pi and nitrate levels, OsNLA1 knockdown (Osnla1-1, Osnla1-2, and Osnla1-3) lines accumulated higher Pi content in their shoot tissues compared to wild-type, whereas, over-expression lines (OsNLA1-OE1, OsNLA1-OE2, and OsNLA1-OE3) accumulated the least levels of Pi. However, under high Pi levels, knockdown lines accumulated much higher Pi content compared to wild-type and exhibited Pi toxicity symptoms in the leaves. In contrast, the over-expression lines had 50-60% of the Pi content of wild-type and did not show such symptoms. When grown under limiting nitrate levels, OsNLA1 transgenic lines also displayed a similar pattern in Pi accumulation and Pi toxicity symptoms compared to wild-type suggesting an existence of cross-talk between nitrogen (N) and phosphorous (P), which is regulated by OsNLA1. The greater Pi accumulation in knockdown lines was a result of enhanced Pi uptake/permeability of roots compared to the wild-type. The cross-talk between N and P was found to be nitrate specific since the knockdown lines failed to over-accumulate Pi under low (sub-optimal) ammonium level. Moreover, OsNLA1 was also found to interact with OsPHO2, a known regulator of Pi homeostasis, in a Yeast Two-Hybrid (Y2H) assay. Taken together, these results show that OsNLA1 is involved in Pi homeostasis regulating Pi uptake and accumulation in rice plants and may provide an opportunity to enhance P use efficiency by manipulating nitrate supply in the soil.

Phosphorus remobilization from rice flag leaves during grain filling: an RNA-seq study

The physiology and molecular regulation of phosphorus (P) remobilization from vegetative tissues to grains during grain filling is poorly understood, despite the pivotal role it plays in the global P cycle. To test the hypothesis that a subset of genes involved in the P starvation response are involved in remobilization of P from flag leaves to developing grains, we conducted an RNA-seq analysis of rice flag leaves during the preremobilization phase (6 DAA) and when the leaves were acting as a P source (15 DAA). Several genes that respond to phosphate starvation, including three purple acid phosphatases (OsPAP3, OsPAP9b and OsPAP10a), were significantly up-regulated at 15 DAA, consistent with a role in remobilization of P from flag leaves during grain filling. A number of genes that have not been implicated in the phosphate starvation response, OsPAP26, SPX-MFS1 (a putative P transporter) and SPX-MFS2, also showed expression profiles consistent with involvement in P remobilization from senescing flag leaves. Metabolic pathway analysis using the KEGG system suggested plastid membrane lipid synthesis is a critical process during the P remobilization phase. In particular, the up-regulation of OsPLDz2 and OsSQD2 at 15 DAA suggested phospholipids were being degraded and replaced by other lipids to enable continued cellular function while liberating P for export to developing grains. Three genes associated with RNA degradation that have not previously been implicated in the P starvation response also showed expression profiles consistent with a role in P mobilization from senescing flag leaves.

Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses

The huge variation in root system architecture (RSA) among different rice (Oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. Unlike model plant Arabidopsis, the molecular basis of such variation in RSA is very poorly understood in rice. Cultivars with stable variation are valuable resources for identification of genes involved in RSA and related physiological traits. We have screened for RSA and identified two such indica rice cultivars, IR-64 (OsAS83) and IET-16348 (OsAS84), with stable contrasting RSA. OsAS84 produces robust RSA with more crown roots, lateral roots and root hairs than OsAS83. Using comparative root transcriptome analysis of these cultivars, we identified genes related to root development and different physiological responses like abiotic stress responses, hormone signaling, and nutrient acquisition or transport. The two cultivars differ in their response to salinity/dehydration stresses, phosphate/nitrogen deficiency, and different phytohormones. Differential expression of genes involved in salinity or dehydration response, nitrogen (N) transport, phosphate (Pi) starvation signaling, hormone signaling and root development underlies more resistance of OsAS84 towards abiotic stresses, Pi or N deficiency and its robust RSA. Thus our study uncovers gene-network involved in root development and abiotic stress responses in rice.

Identification and expression analysis of OsLPR family revealed the potential roles of OsLPR3 and 5 in maintaining phosphate homeostasis in rice

BACKGROUND

Phosphorus (P), an essential macronutrient, is often limiting in soils and affects plant growth and development. In Arabidopsis thaliana, Low Phosphate Root1 (LPR1) and its close paralog LPR2 encode multicopper oxidases (MCOs). They regulate meristem responses of root system to phosphate (Pi) deficiency. However, the roles of LPR gene family in rice (Oryza sativa) in maintaining Pi homeostasis have not been elucidated as yet.

RESULTS

Here, the identification and expression analysis for the homologs of LPR1/2 in rice were carried out. Five homologs, hereafter referred to as OsLPR1-5, were identified in rice, which are distributed on chromosome1 over a range of 65 kb. Phylogenetic analysis grouped OsLPR1/3/4/5 and OsLPR2 into two distinct sub-clades with OsLPR3 and 5 showing close proximity. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed higher expression levels of OsLPR3-5 and OsLPR2 in root and shoot, respectively. Deficiencies of different nutrients ie, P, nitrogen (N), potassium (K), magnesium (Mg) and iron (Fe) exerted differential and partially overlapping effects on the relative expression levels of the members of OsLPR family. Pi deficiency (-P) triggered significant increases in the relative expression levels of OsLPR3 and 5. Strong induction in the relative expression levels of OsLPR3 and 5 in osphr2 suggested their negative transcriptional regulation by OsPHR2. Further, the expression levels of OsLPR3 and 5 were either attenuated in ossiz1 and ospho2 or augmented in rice overexpressing OsSPX1.

CONCLUSIONS

The results from this study provided insights into the evolutionary expansion and a likely functional divergence of OsLPR family with potential roles of OsLPR3 and 5 in the maintenance of Pi homeostasis in rice.

Phosphate starvation promoted the accumulation of phenolic acids by inducing the key enzyme genes in Salvia miltiorrhiza hairy roots

Phosphate starvation increased the production of phenolic acids by inducing the key enzyme genes in a positive feedback pathway in Saliva miltiorrhiza hairy roots. SPX may be involved in this process. Salvia miltiorrhiza is a wildly popular traditional Chinese medicine used for the treatment of coronary heart diseases and inflammation. Phosphate is an essential plant macronutrient that is often deficient, thereby limiting crop yield. In this study, we investigated the effects of phosphate concentration on the biomass and accumulation of phenolic acid in S. miltiorrhiza. Results show that 0.124 mM phosphate was favorable for plant growth. Moreover, 0.0124 mM phosphate was beneficial for the accumulation of phenolic acids, wherein the contents of danshensu, caffeic acid, rosmarinic acid, and salvianolic acid B were, respectively, 2.33-, 1.02-, 1.68-, and 2.17-fold higher than that of the control. By contrast, 12.4 mM phosphate inhibited the accumulation of phenolic acids. The key enzyme genes in the phenolic acid biosynthesis pathway were investigated to elucidate the mechanism of phosphate starvation-induced increase of phenolic acids. The results suggest that phosphate starvation induced the gene expression from the downstream pathway to the upstream pathway, i.e., a feedback phenomenon. In addition, phosphate starvation response gene SPX (SYG1, Pho81, and XPR1) was promoted by phosphate deficiency (0.0124 mM). We inferred that SPX responded to phosphate starvation, which then affected the expression of later responsive key enzyme genes in phenolic acid biosynthesis, resulting in the accumulation of phenolic acids. Our findings provide a resource-saving and environmental protection strategy to increase the yield of active substance in herbal preparations. The relationship between SPX and key enzyme genes and the role they play in phenolic acid biosynthesis during phosphate deficiency need further studies.

Characterization of the AtSPX3 Promoter Elucidates its Complex Regulation in Response to Phosphorus Deficiency

AtSPX3, responding to phosphate (Pi) deficiency by its expression, is an important gene involved in Pi homeostasis in Arabidopsis. To understand its transcriptional regulation, we characterized the AtSPX3 promoter by distal truncation, internal deletion and mutation of the predicted cis-elements, and identified multiple cis-elements responsive to Pi status. The P1BS (AtPHR-binding site) and AtMyb4 (putative MYB4-binding site) elements were two main cis-elements in the AtSPX3 promoter. P1BS is essential and has a dosage effect for activating expression of the gene under Pi deficiency, while the element AtMyb4 possesses a dual function: one is to enhance AtSPX3 expression in roots under Pi deficiency, and the other one is to repress AtSPX3 expression in shoots under both Pi deficiency and sufficiency. Moreover, we confirmed that AtPHR1, a key transcription factor in Pi homeostasis of plants, was required for the negative regulation function of the AtMyb4 element in shoots. Additionally, we also found that the AtSPX3 promoter had a length limitation for activating gene expression. Generally, our findings in this work are useful for understanding the molecular regulation mechanism of genes involved in Pi uptake and homeostasis.

Soybean SPX1 is an important component of the response to phosphate deficiency for phosphorus homeostasis

Phosphate (Pi) homeostasis is required for plant growth and development, but the Pi-signaling pathways in plants still remain largely unknown. Proteins only containing the SPX domain are very important in phosphate (Pi) homeostasis and signaling transduction. In the T-DNA insertion Arabidopsis mutant spx3, AtPHT1-4, AtPHT1-5, AtACP5, AtRNS, and AtAT4 expression levels were increased under Pi-sufficient condition and low Pi condition compared with WT. Meanwhile, the expression levels of these phosphate starvation genes was inhibited in OXSPX1 and spx3/OXSPX1 compared with WT, only under Pi-sufficient condition. These imply that GmSPX1 may negatively control the transcription of Pi starvation responsive genes indirectly. However, there were no differences between expression levels of these PSI genes in spx3 and those in WT under -Pi conditions. These facts imply that the negative regulation of GmSPX1 and AtSPX3 on PSI genes is depending on Pi concentration. Consistent with this, GmSPX1 overexpression in the WT and spx3 decreased the total Pi concentration in plants and changed root hair morphology, suppressing the elongation and number of root hairs compared with the WT and spx3. The yeast two-hybrid assays and BiFC assays demonstrated that GmSPX1 could interact with GmMYB48.The qRT-PCR analysis showed that GmMYB48 is a new phosphate starvation induced transcription factor in soybean. Also, GmSPX1 overexpression led to decreased transcripts of AtMYB4, an ortholog of GmMYB48, in OXSPX1. Together, these results suggest that GmSPX1 is a negative regulator in the Pi signaling network of soybean, and the interaction of GmSPX1/GmMYB48 can be considered a potential candidate suppressor.

Deciphering Phosphate Deficiency-Mediated Temporal Effects on Different Root Traits in Rice Grown in a Modified Hydroponic System

Phosphate (Pi), an essential macronutrient for growth and development of plant, is often limiting in soils. Plants have evolved an array of adaptive strategies including modulation of root system architecture (RSA) for optimal acquisition of Pi. In rice, a major staple food, RSA is complex and comprises embryonically developed primary and seminal roots and post-embryonically developed adventitious and lateral roots. Earlier studies have used variant hydroponic systems for documenting the effects of Pi deficiency largely on primary root growth. Here, we report the temporal effects of Pi deficiency in rice genotype MI48 on 15 ontogenetically distinct root traits by using easy-to-assemble and economically viable modified hydroponic system. Effects of Pi deprivation became evident after 4 days- and 7 days-treatments on two and eight different root traits, respectively. The effects of Pi deprivation for 7 days were also evident on different root traits of rice genotype Nagina 22 (N22). There were genotypic differences in the responses of primary root growth along with lateral roots on it and the number and length of seminal and adventitious roots. Notably though, there were attenuating effects of Pi deficiency on the lateral roots on seminal and adventitious roots and total root length in both these genotypes. The study thus revealed both differential and comparable effects of Pi deficiency on different root traits in these genotypes. Pi deficiency also triggered reduction in Pi content and induction of several Pi starvation-responsive (PSR) genes in roots of MI48. Together, the analyses validated the fidelity of this modified hydroponic system for documenting Pi deficiency-mediated effects not only on different traits of RSA but also on physiological and molecular responses.

Genome-Wide Small RNA Analysis of Soybean Reveals Auxin-Responsive microRNAs that are Differentially Expressed in Response to Salt Stress in Root Apex

Root growth and the architecture of the root system in Arabidopsis are largely determined by root meristematic activity. Legume roots show strong developmental plasticity in response to both abiotic and biotic stimuli, including symbiotic rhizobia. However, a global analysis of gene regulation in the root meristem of soybean plants is lacking. In this study, we performed a global analysis of the small RNA transcriptome of root tips from soybean seedlings grown under normal and salt stress conditions. In total, 71 miRNA candidates, including known and novel variants of 59 miRNA families, were identified. We found 66 salt-responsive miRNAs in the soybean root meristem; among them, 22 are novel miRNAs. Interestingly, we found auxin-responsive cis-elements in the promoters of many salt-responsive miRNAs, implying that these miRNAs may be regulated by auxin and auxin signaling plays a key role in regulating the plasticity of the miRNAome and root development in soybean. A functional analysis of miR399, a salt-responsive miRNA in the root meristem, indicates the crucial role of this miRNA in modulating soybean root developmental plasticity. Our data provide novel insight into the miRNAome-mediated regulatory mechanism in soybean root growth under salt stress.

Disruption of OsEXO70A1 Causes Irregular Vascular Bundles and Perturbs Mineral Nutrient Assimilation in Rice

Normal uptake, transportation, and assimilation of primary nutrients are essential to plant growth. Tracheary elements (TEs) are tissues responsible for the transport of water and minerals and characterized by patterned secondary cell wall (SCW) thickening. Exocysts are involved in the regulation of SCW deposition by mediating the targeted transport of materials and enzymes to specific membrane areas. EXO70s are highly duplicated in plants and provide exocysts with functional specificity. In this study, we report the isolation of a rice mutant rapid leaf senescence2 (rls2) that exhibits dwarfism, ferruginous spotted necrotic leaves, decreased hydraulic transport, and disordered primary nutrient assimilation. Histological analysis of rls2-1 mutants has indicated impaired cell expansion, collapsed vascular tissues, and irregular SCW deposition. Map-based cloning has revealed that RLS2 encodes OsEXO70A1, which is one of the 47 members of EXO70s in rice. RLS2 was widely expressed and spatially restricted in vascular bundles. Subcellular localization analysis demonstrated that RLS2 was present on both membrane and nuclear regions. Expression analysis revealed that mutations in rls2 triggers transcriptional fluctuation of orthologous EXO70 genes and affects genes involved in primary nutrient absorption and transport. In brief, our study revealed that RLS2 is required for normal vascular bundle differentiation and primary nutrient assimilation.

OsSIZ1, a SUMO E3 Ligase Gene, is Involved in the Regulation of the Responses to Phosphate and Nitrogen in Rice

SIZ1-mediated SUMOylation regulates hormone signaling as well as abiotic and biotic stress responses in plants. Here, we investigated the expression profile of OsSIZ1 in rice using quantitative reverse transcription-PCR (qRT-PCR) and pOsSIZ1-GUS transgenic plants, and the function of OsSIZ1 in the responses to phosphate and nitrogen using a reverse genetics approach. OsSIZ1 is constitutively expressed throughout the vegetative and reproductive growth of rice, with stronger promoter activities in vascular bundles of culms. ossiz1 mutants had shorter primary roots and adventitious roots than wild-type plants, suggesting that OsSIZ1 is associated with the regulation of root system architecture. Total phosphorus (P) and phosphate (Pi) concentrations in both roots and shoots of ossiz1 mutants were significantly increased irrespective of Pi supply conditions compared with the wild type. Pi concentration in the xylem sap of ossiz1 mutants was significantly higher than that of the wild type under a Pi-sufficient growth regime. Total nitrogen (N) concentrations in the most detected tissues of ossiz1 mutants were significantly increased compared with the wild type. Analysis of mineral contents in ossiz1 mutants indicated that OsSIZ1 functions specifically in Pi and N responses, not those of other nutrients examined, in rice. Further, qRT-PCR analyses revealed that the expression of multiple genes involved in Pi starvation signaling and N transport and assimilation were altered in ossiz1 mutants. Together, these results suggested that OsSIZ1 may act as a regulator of the Pi (N)-dependent responses in rice.

Stress responsive miRNAs and isomiRs in cereals

Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.

Replace, reuse, recycle: improving the sustainable use of phosphorus by plants

The 'phosphorus problem' has recently received strong interest with two distinct strands of importance. The first is that too much phosphorus (P) is entering into waste water, creating a significant economic and ecological problem. Secondly, while agricultural demand for phosphate fertilizer is increasing to maintain crop yields, rock phosphate reserves are rapidly declining. Unravelling the mechanisms by which plants sense, respond to, and acquire phosphate can address both problems, allowing the development of crop plants that are more efficient at acquiring and using limited amounts of phosphate while at the same time improving the potential of plants and other photosynthetic organisms for nutrient recapture and recycling from waste water. In this review, we attempt to synthesize these important but often disparate parts of the debate in a holistic fashion, since solutions to such a complex problem require integrated and multidisciplinary approaches that address both P supply and demand. Rapid progress has been made recently in our understanding of local and systemic signalling mechanisms for phosphate, and of expression and regulation of membrane proteins that take phosphate up from the environment and transport it within the plant. We discuss the current state of understanding of such mechanisms involved in sensing and responding to phosphate stress. We also discuss approaches to improve the P-use efficiency of crop plants and future direction for sustainable use of P, including use of photosynthetic organisms for recapture of P from waste waters.

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.

SPX proteins regulate Pi homeostasis and signaling in different subcellular level

To cope with low phosphate (Pi) availability, plants have to adjust its gene expression profile to facilitate Pi acquisition and remobilization. Sensing the levels of Pi is essential for reprogramming the gene expression profile to adapt to the fluctuating Pi environment. AtPHR1 in Arabidopsis and OsPHR2 in rice are central regulators of Pi signaling, which regulates the expression of phosphate starvation-induced (PSI) genes by binding to the P1BS elements in the promoter of PSI genes. However, how the Pi level affects the central regulator to regulate the PSI genes have puzzled us for a decade. Recent progress in SPX proteins indicated that the SPX proteins play important role in regulating the activity of central regulator AtPHR1/OsPHR2 in a Pi dependent manner at different subcellular levels.

OsCYCP1;1, a PHO80 homologous protein, negatively regulates phosphate starvation signaling in the roots of rice (Oryza sativa L.)

Phosphorus is one of the most essential and limiting nutrients in all living organisms, thus the organisms have evolved complicated and precise regulatory mechanisms for phosphorus acquisition, storage and homeostasis. In the budding yeast, Saccharomyces cerevisiae, the modification of PHO4 by the PHO80 and PHO85 complex is a core regulation system. However, the existence and possible functions in phosphate signaling of the homologs of the PHO80 and PHO85 components in plants has yet to be determined. Here we describe the identification of a family of seven PHO80 homologous genes in rice named OsCYCPs. Among these, the OsCYCP1;1 gene was able to partially rescue the pho80 mutant strain of yeast. The OsCYCP1;1 protein was predominantly localized in the nucleus, and was ubiquitously expressed throughout the whole plant and during the entire growth period of rice. Consistent with the negative role of PHO80 in phosphate signaling in yeast, OsCYCP1;1 expression was reduced by phosphate starvation in the roots. This reduction was dependent on PHR2, the central regulator of phosphate signaling in rice. Overexpression and suppression of the expression of OsCYCP1;1 influenced the phosphate starvation signaling response. The inducible expression of phosphate starvation inducible and phosphate transporter genes was suppressed in the OsCYCP1;1 overexpression lines and was relatively enhanced in the OsCYCP1;1 RNAi plants by phosphate starvation. Together, these results demonstrate the role of PHO80 homologs in the phosphate starvation signaling pathway in rice.

Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner

In plants, sensing the levels of external and internal nutrients is essential for reprogramming the transcriptome and adapting to the fluctuating environment. Phosphate (Pi) is a key plant nutrient, and a large proportion of Pi starvation-responsive genes are under the control of Phosphate Starvation Response Regulator 1 (PHR1) in Arabidopsis (AtPHR1) and its homologs, such as Oryza sativa (Os)PHR2 in rice. AtPHR1 and OsPHR2 expression is not very responsive to Pi starvation, raising the question as to how plants sense changes in cellular Pi levels to activate the central regulator. SPX [named after SYG1 (suppressor of yeast gpa1), Pho81 (CDK inhibitor in yeast PHO pathway), and XPR1 (xenotropic and polytropic retrovirus receptor)] proteins that harbor only the SPX domain are reported to be involved in the negative regulation of Pi starvation responses. Here, we show that the nuclear localized SPX proteins SPX1 and SPX2 are Pi-dependent inhibitors of the activity of OsPHR2 in rice. Indeed, SPX1 and SPX2 proteins interact with PHR2 through their SPX domain, inhibiting its binding to P1BS (the PHR1-binding sequence: GNATATNC). In vivo data, as well as results from in vitro experiments using purified SPX1, SPX2, and OsPHR2 proteins, showed that SPX1 and SPX2 inhibition of OsPHR2 activity is Pi-dependent. These data provide evidence to support the involvement of SPX1 and SPX2 in the Pi-sensing mechanism in plants.

Comparative characterization of GmSPX members reveals that GmSPX3 is involved in phosphate homeostasis in soybean

BACKGROUND AND AIMS

Proteins containing the SPX (SYG1/Pho81/XPR1) domain are vital components in the phosphorus (P) signalling pathway, and regulate phosphate (Pi) homeostasis in plants. However, the characteristics and functions of GmSPX members in soybean (Glycine max) remain largely unknown.

METHODS

BLAST searching revealed nine GmSPX members in the soybean genome. Subsequently, expression patterns of GmSPX members were investigated in various tissues of soybean grown in nutrient solution or sand culture through quantitative real-time PCR (qPCR) analysis. Sub-cellular localization of GmSPX was examined via transient expression of 35S:GmSPX-GFP in epidermal cells of onion (Allium cepa). Finally, soybean transgenic composite plants were generated to study GmSPX3 functions.

KEY RESULTS

Nine GmSPX members were identified, which were classified into three groups based on phylogenetic analysis. Diverse responses of GmSPX members to deficiencies of nutrients (nitrogen, phosphorus, potassium and iron) or inoculation of arbuscular mycorrhizal fungi and rhizobia were observed in soybean. In addition, variations of sub-cellular localization of GmSPX members were found. Among them, GmSPX3, GmSPX7 and GmSPX8 were localized in the nuclei, and the other GmSPX members were confined to the nuclei and cytoplasm. The nuclear-localized and Pi starvation responsive-gene, GmSPX3, was functionally analysed in soybean transgenic composite plants. Overexpression of GmSPX3 led to increased P concentrations in both shoots and roots in the high-P treatment, and increased transcription of seven Pi starvation-responsive genes in soybean hairy roots.

CONCLUSIONS

Taken together, the results suggest that GmSPX3 is a positive regulator in the P signalling network, and controls Pi homeostasis in soybean.

Overexpression of OsMYB4P, an R2R3-type MYB transcriptional activator, increases phosphate acquisition in rice

R2R3 MYB transcription factors play regulatory roles in plant responses to various environmental stresses and nutrient deficiency. In this study, we isolated and designated OsMYB4P, an R2R3 MYB transcription factor, from rice (Oryza sativa L. 'Dongjin') under phosphate-deficient conditions. OsMYB4P was localized in the nucleus and acted as a transcriptional activator. Transcriptional levels of OsMYB4P in cell suspension, shoots, and roots of rice increased under phosphate-deficient conditions. Shoots and roots of OsMYB4P-overexpressing plants grew well in high- and phosphate-deficient conditions. In addition, root system architecture was altered considerably as a result of OsMYB4P overexpression. Under both phosphate-sufficient and -deficient conditions, more Pi accumulated in shoots and roots of OsMYB4P-overexpressing plants than in the wild type. Overexpression of OsMYB4P led to greater expression of Pi transporter-family proteins OsPT1, OsPT2, OsPT4, OsPT7, and OsPT8 in shoots, and to decreased or unchanged expression of these proteins in roots, with the exception of OsPT8. These results demonstrate that OsMYB4P may be associated with efficient utilization of Pi in rice through transcriptional activation of Pi homeostasis-related genes.

SPX1 is an important component in the phosphorus signalling network of common bean regulating root growth and phosphorus homeostasis

Proteins containing the SPX domain are believed to play vital roles in the phosphorus (P) signalling network in plants. However, the functions of SPX proteins in legumes remain largely unknown. In this study, three SPX members, PvSPX1-PvSPX3 were cloned from common bean (Phaseolus vulgaris L.). It was found that the transcripts of all three PvSPX members were significantly enhanced in both bean leaves and roots by phosphate (Pi) starvation. Among them, the expression of nuclear localized PvSPX1 showed more sensitive and rapid responses to Pi starvation. Consistently, only overexpression of PvSPX1 resulted in increased root P concentration and modified morphology of transgenic bean hairy roots, such as inhibited root growth and an enlarged root hair zone. It was further demonstrated that PvSPX1 transcripts were up-regulated by overexpressing PvPHR1, and overexpressing PvSPX1 led to increased transcripts of 10 Pi starvation-responsive genes in transgenic bean hairy roots. Taken together, it is suggested that PvSPX1 is a positive regulator in the P signalling network of common bean, and is downstream of PvPHR1.

RNA sequencing analysis reveals transcriptomic variations in tobacco (Nicotiana tabacum) leaves affected by climate, soil, and tillage factors

The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq) analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs), soil factors (SFs), and tillage factors (TFs). We detected 4980, 2916, and 1605 differentially expressed genes (DEGs) that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs), respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.

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.

The paralogous SPX3 and SPX5 genes redundantly modulate Pi homeostasis in rice

The importance of SPX-domain-containing proteins to phosphate (Pi) homeostasis and signalling transduction has been established in plants. In this study, phylogenetic analysis revealed that OsSPX3 and OsSPX5 (SPX3/5) are paralogous SPX genes ( SYG1/Pho81/XPR1) in cereal crops. SPX3/5 are specifically responsive to Pi starvation at both the transcriptional and post-transcriptional levels. Similar tissue expression patterns of the two genes and proteins were identified by in situ hybridization and the transgenic plants harbouring SPX3pro-SPX3-GUS or SPX5pro-SPX5-GUS fusions, respectively. Both SPX3/5 are localized in the nucleus and cytoplasm in rice protoplasts and plants. SPX3/5 negatively regulate root-to-shoot Pi translocation with redundant function. The data showed that the Pi-starvation-accumulated SPX3/5 proteins are players in restoring phosphate balance following phosphate starvation. In vitro and in vivo protein-protein interaction analyses indicated that these two proteins can form homodimers and heterodimers, also implying their functional redundancy. Genetic interaction analysis indicated that SPX3/5 are functional repressors of OsPHR2 (PHR2), the rice orthologue of the central regulator AtPHR1 for Pi homeostasis and Pi signalling. These results suggest that the evolution of the additional redundant paralogous SPX genes is beneficial to plants recovering Pi homeostasis after Pi starvation by PHR2 pathway.

Fine characterization of OsPHO2 knockout mutants reveals its key role in Pi utilization in rice

Previous research using forward genetics approaches demonstrated that OsPHO2 regulates multiple phosphate-starvation responses in rice. In this work, we finely characterized two independent OsPHO2 knockout rice mutants under inorganic phosphate (Pi)-sufficient conditions. The ospho2 mutants exhibited defects in growth and reproductive development in the whole growing period. The cells in the elongation zone of ospho2 seedling roots were much shorter than those of the wild type. The phosphorus concentration in the blades of ospho2 mutants was 5.8-fold higher than those of wild-type plants, whereas it was only slightly higher in the sheaths, culms, spikelets, and seeds. Furthermore, Pi levels in the ospho2 mutants were highest in the oldest leaf and lowest in the youngest leaf, whereas there was no significant difference in the corresponding leaves of wild-type plants. These results suggest that ospho2 mutant phenotype results from a partial defect in Pi translocation and remobilization in the shoot of rice. This study thus provides evidence that OsPHO2, which functions at the downstream of OsPHF1, modulates Pi utilization by regulating the expression of Pht1 transporters in rice.

Phosphate nutrition: improving low-phosphate tolerance in crops

Phosphorus is an essential nutrient that is required for all major developmental processes and reproduction in plants. It is also a major constituent of the fertilizers required to sustain high-yield agriculture. Levels of phosphate--the only form of phosphorus that can be assimilated by plants--are suboptimal in most natural and agricultural ecosystems, and when phosphate is applied as fertilizer in soils, it is rapidly immobilized owing to fixation and microbial activity. Thus, cultivated plants use only approximately 20-30% of the applied phosphate, and the rest is lost, eventually causing water eutrophication. Recent advances in the understanding of mechanisms by which wild and cultivated species adapt to low-phosphate stress and the implementation of alternative bacterial pathways for phosphorus metabolism have started to allow the design of more effective breeding and genetic engineering strategies to produce highly phosphate-efficient crops, optimize fertilizer use, and reach agricultural sustainability with a lower environmental cost. In this review, we outline the current advances in research on the complex network of plant responses to low-phosphorus stress and discuss some strategies used to manipulate genes involved in phosphate uptake, remobilization, and metabolism to develop low-phosphate-tolerant crops, which could help in designing more efficient crops.

Auxin response factor (OsARF12), a novel regulator for phosphate homeostasis in rice (Oryza sativa)

Phosphorus (P) is crucial nutrient element for crop growth and development. However, the network pathway regulating homeostasis of phosphate (Pi) in crops has many molecular breeding unknowns. Here, we report that an auxin response factor, OsARF12, functions in Pi homeostasis. Measurement of element content, quantitative reverse transcription polymerase chain reaction analysis and acid phosphatases (APases) activity assay showed that the osarf12 mutant and osarf12/25 double mutant with P-intoxicated phenotypes had higher P concentrations, up-regulation of the Pi transporter encoding genes and increased APase activity under Pi-sufficient/-deficient (+Pi/-Pi, 0.32/0 mM NaH2 PO4) conditions. Transcript analysis revealed that Pi-responsive genes--Phosphate starvation (OsIPS)1 and OsIPS2, SYG1/Pho81/XPR1(OsSPX1), Sulfoquinovosyldiacylglycerol 2 (OsSQD2), R2R3 MYB transcription factor (OsMYB2P-1) and Transport Inhibitor Response1 (OsTIR1)--were more abundant in the osarf12 and osarf12/25 mutants under +Pi/-Pi conditions. Knockout of OsARF12 also influenced the transcript abundances of the OsPHR2 gene and its downstream components, such as OsMiR399j, OsPHO2, OsMiR827, OsSPX-MFS1 and OsSPX-MFS2. Results from -Pi/1-naphthylphthalamic acid (NPA) treatments, and auxin reporter DR5::GUS staining suggest that root system alteration and Pi-induced auxin response were at least partially controlled by OsARF12. These findings enrich our understanding of the biological functions of OsARF12, which also acts in regulating Pi homeostasis.

Down-regulation of OsSPX1 causes high sensitivity to cold and oxidative stresses in rice seedlings

Rice SPX domain gene, OsSPX1, plays an important role in the phosphate (Pi) signaling network. Our previous work showed that constitutive overexpression of OsSPX1 in tobacco and Arabidopsis plants improved cold tolerance while also decreasing total leaf Pi. In the present study, we generated rice antisense and sense transgenic lines of OsSPX1 and found that down-regulation of OsSPX1 caused high sensitivity to cold and oxidative stresses in rice seedlings. Compared to wild-type and OsSPX1-sense transgenic lines, more hydrogen peroxide accumulated in seedling leaves of OsSPX1-antisense transgenic lines for controls, cold and methyl viologen (MV) treatments. Glutathione as a ROS scavenger could protect the antisense transgenic lines from cold and MV stress. Rice whole genome GeneChip analysis showed that some oxidative-stress marker genes (e.g. glutathione S-transferase and P450s) and Pi-signaling pathway related genes (e.g. OsPHO2) were significantly down-regulated by the antisense of OsSPX1. The microarray results were validated by real-time RT-PCR. Our study indicated that OsSPX1 may be involved in cross-talks between oxidative stress, cold stress and phosphate homeostasis in rice seedling leaves.

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles

Rice has developed several morphological and physiological strategies to adapt to phosphate starvation in the soil. In order to elucidate the molecular basis of response to phosphate starvation, we performed mRNA sequencing of 4 rice cultivars with variation in growth response to Pi starvation as indicated by the shoot/root dry weight ratio. Approximately 254 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence and an average of about 5,000 transcripts from each cultivar were found to be responsive under phosphate starvation. Comparative analysis of the RNA-Seq profiles of the 4 cultivars revealed similarities as well as distinct differences in expression of these responsive transcripts. We elucidated a set of core responsive transcripts including annotated and unannotated transcripts commonly expressed in the 4 cultivars but with different levels of expression. De novo assembly of unmapped reads to the Nipponbare genome generated a set of sequence contigs representing potential new transcripts that may be involved in tolerance to phosphate starvation. This study can be used for identification of genes and gene networks associated with environmental stress and the development of novel strategies for improving tolerance to phosphate starvation in rice and other cereal crops.

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.

A phosphate starvation response regulator Ta-PHR1 is involved in phosphate signalling and increases grain yield in wheat

BACKGROUND AND AIMS

Phosphorus deficiency is a major limiting factor for crop yield worldwide. Previous studies revealed that PHR1 and it homologues play a key role in regulating the phosphate starvation response in plants. However, the function of PHR homologues in common wheat (Triticum aestivum) is still not fully understood. The aim of the study was to characterize the function of PHR1 genes in regulating phosphate signalling and plant growth in wheat.

METHODS

Wheat transgenic lines over-expressing a wheat PHR1 gene were generated and evaluated under phosphorus-deficient and -sufficient conditions in hydroponic culture, a soil pot trial and two field experiments.

KEY RESULTS

Three PHR1 homologous genes Ta-PHR1-A1, B1 and D1 were isolated from wheat, and the function of Ta-PHR1-A1 was analysed. The results showed that Ta-PHR1-A1 transcriptionally activated the expression of Ta-PHT1.2 in yeast cells. Over-expressing Ta-PHR1-A1 in wheat upregulated a subset of phosphate starvation response genes, stimulated lateral branching and improved phosphorus uptake when the plants were grown in soil and in nutrient solution. The data from two field trials demonstrated that over-expressing Ta-PHR1-A1 increased grain yield by increasing grain number per spike.

CONCLUSIONS

TaPHR1 is involved in phosphate signalling in wheat, and was valuable in molecular breeding of crops, with improved phosphorus use efficiency and yield performance.

Improvement of phosphorus efficiency in rice on the basis of understanding phosphate signaling and homeostasis

Rice is one of the most important cereal crops feeding a large segment of the world's population. Inefficient utilization of phosphate (Pi) fertilizer by the plant in rice production increases cost and pollution. Developing cultivars with improved Pi use efficiency is essential for the sustainability of agriculture. Pi uptake, translocation and remobilization are regulated by complex molecular mechanisms through the functions of Pi transporters (PTs) and other downstream Pi Starvation Induced (PSI) genes. Expressions of these PSI genes are regulated by the Pi Starvation Response Regulator (OsPHR2)-mediated transcriptional control and/or PHO2-mediated ubiquitination. SPX-domain containing proteins and the type I H(+)-PPase AVP1 involved in the maintenance and utilization of the internal phosphate. The potential application of posttranscriptional regulation of PT1 through OsPHF1 for Pi efficiency is proposed.

Understanding plant responses to phosphorus starvation for improvement of plant tolerance to phosphorus deficiency by biotechnological approaches

In both prokaryotes and eukaryotes, including plants, phosphorus (P) is an essential nutrient that is involved in various biochemical processes, such as lipid metabolism and the biosynthesis of nucleic acids and cell membranes. P also contributes to cellular signaling cascades by function as mediators of signal transduction and it also serves as a vital energy source for a wide range of biological functions. Due to its intensive use in agriculture, P resources have become limited. Therefore, it is critically important in the future to develop scientific strategies that aim to increase P use efficiency and P recycling. In addition, the biologically available soluble form of P for uptake (phosphate; Pi) is readily washed out of topsoil layers, resulting in serious environmental pollution. In addition to this environmental concern, the wash out of Pi from topsoil necessitates a continuous Pi supply to maintain adequate levels of fertilization, making the situation worse. As a coping mechanism to P stress, plants are known to undergo drastic cellular changes in metabolism, physiology, hormonal balance and gene expression. Understanding these molecular, physiological and biochemical responses developed by plants will play a vital role in improving agronomic practices, resource conservation and environmental protection as well as serving as a foundation for the development of biotechnological strategies, which aim to improve P use efficiency in crops. In this review, we will discuss a variety of plant responses to low P conditions and various molecular mechanisms that regulate these responses. In addition, we also discuss the implication of this knowledge for the development of plant biotechnological applications.

The emerging importance of the SPX domain-containing proteins in phosphate homeostasis

Plant growth and development are strongly influenced by the availability of nutrients in the soil solution. Among them, phosphorus (P) is one of the most essential and most limiting macro-elements for plants. In the environment, plants are often confronted with P starvation as a result of extremely low concentrations of soluble inorganic phosphate (Pi) in the soil. To cope with these conditions, plants have developed a wide spectrum of mechanisms aimed at increasing P use efficiency. At the molecular level, recent studies have shown that several proteins carrying the SPX domain are essential for maintaining Pi homeostasis in plants. The SPX domain is found in numerous eukaryotic proteins, including several proteins from the yeast PHO regulon, involved in maintaining Pi homeostasis. In plants, proteins harboring the SPX domain are classified into four families based on the presence of additional domains in their structure, namely the SPX, SPX-EXS, SPX-MFS and SPX-RING families. In this review, we highlight the recent findings regarding the key roles of the proteins containing the SPX domain in phosphate signaling, as well as providing further research directions in order to improve our knowledge on P nutrition in plants, thus enabling the generation of plants with better P use efficiency.

Comprehensive sequence and whole-life-cycle expression profile analysis of the phosphate transporter gene family in rice

Plant phosphate transporter (PT) genes comprise a large family with important roles in various physiological and biochemical processes. In this study, a database search yielded 26 potential PT family genes in rice (Oryza sativa). Analysis of these genes led to identification of eight conserved motifs and 5-12 trans-membrane segments, most of them conserved. A total of 237 putative cis elements were found in the 2-kb upstream region of these genes. Of these, a majority were Pi-response and other stress-related cis regulatory elements, such as PHO-like, TATA-box-like, PHR1, or Helix-loop-helix elements, and WRKY1 and ABRE elements, suggesting gene regulation by these signals. Comprehensive expression analysis of these genes was performed using data from microarrays hybridized with RNA from 27 tissues covering the entire lifecycle from three rice genotypes: Minghui 63, Zhenshan 97, and Shanyou 63. Real-time PCR analysis confirmed that three rice PT genes are preferentially expressed in stamen at 1 d before flowering, two in panicle at the heading stage, and two in flag leaf at 14 d after the heading stage. Hormone-treatment experiments revealed differential up-regulation or down-regulation of 11 rice PT genes in seedlings exposed to five hormones, respectively. These results will be useful for elucidating the roles of these genes in the growth, development, and stress response of the rice plant.

Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I

BACKGROUND

Developmental cues to start meiosis occur late in plants. Ameiotic1 (Am1) encodes a plant-specific nuclear protein (AM1) required for meiotic entry and progression through early prophase I. Pollen mother cells (PMCs) remain mitotic in most am1 mutants including am1-489, while am1-praI permits meiotic entry but PMCs arrest at the leptotene/zygotene (L/Z) transition, defining the roles of AM1 protein in two distinct steps of meiosis. To gain more insights into the roles of AM1 in the transcriptional pre-meiotic and meiotic programs, we report here an in depth analysis of gene expression alterations in carefully staged anthers at 1 mm (meiotic entry) and 1.5 mm (L/Z) caused by each of these am1 alleles.

RESULTS

1.0 mm and 1.5 mm anthers of am1-489 and am1-praI were profiled in comparison to fertile siblings on Agilent® 4 × 44 K microarrays. Both am1-489 and am1-praI anthers are cytologically normal at 1.0 mm and show moderate transcriptome alterations. At the 1.5-mm stage both mutants are aberrant cytologically, and show more drastic transcriptome changes. There are substantially more absolute On/Off and twice as many differentially expressed genes (sterile versus fertile) in am1-489 than in am1-praI. At 1.5 mm a total of 4,418 genes are up- or down-regulated in either am1-489 or am1-praI anthers. These are predominantly stage-specific transcripts. Many putative meiosis-related genes were found among them including a small subset of allele-specific, mis-regulated genes specific to the PMCs. Nearly 60% of transcriptome changes in the set of transcripts mis-regulated in both mutants (N = 530) are enriched in PMCs, and only 1% are enriched in the tapetal cell transcriptome. All array data reported herein will be deposited and accessible at MaizeGDB http://www.maizegdb.org/.

CONCLUSIONS

Our analysis of anther transcriptome modulations by two distinct am1 alleles, am1-489 and am1-praI, redefines the role of AM1 as a modulator of expression of a subset of meiotic genes, important for meiotic progression and provided stage-specific insights into the genetic networks associated with meiotic entry and early prophase I progression.

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.

Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation

Here we report on the characterization of rice osa-miR827 and its two target genes, OsSPX-MFS1 and OsSPX-MFS2, which encode SPX-MFS proteins predicted to be implicated in phosphate (Pi) sensing or transport. We first show by Northern blot analysis that osa-miR827 is strongly induced by Pi starvation in both shoots and roots. Hybridization of osa-miR827 in situ confirms its strong induction by Pi starvation, with signals concentrated in mesophyll, epidermis and ground tissues of roots. In parallel, we analyzed the responses of the two OsSPX-MFS1 and OsSPX-MFS2 gene targets to Pi starvation. OsSPX-MFS1 mRNA is mainly expressed in shoots under sufficient Pi supply while its expression is reduced on Pi starvation, revealing a direct relationship between induction of osa-miR827 and down-regulation of OsSPX-MFS1. In contrast, OsSPX-MFS2 responds in a diametrically opposed manner to Pi starvation. The accumulation of OsSPX-MFS2 mRNA is dramatically enhanced under Pi starvation, suggesting the involvement of complex regulation of osa-miR827 and its two target genes. We further produced transgenic rice lines overexpressing osa-miR827 and T-DNA knockout mutant lines in which the expression of osa-miR827 is abolished. Compared with wild-type controls, both target mRNAs exhibit similar changes, their expression being reduced and increased in overexpressing and knockout lines, respectively. This suggests that OsSPX-MFS1 and OsSPX-MFS2 are both negatively regulated by osa-miR827 abundance although they respond differently to external Pi conditions. We propose that this is a complex mechanism comprising fine tuning of spatial or temporal regulation of both targets by osa-miR827.

Does OsPHR2, central pi-signaling regulator, regulate some unknown factors crucial for plant growth?

OsPHR2, the homolog of AtPHR1, is a central Pi-signaling regulator. The Pi-signaling pathway downstream of AtPHR1, similarly of OsPHR2,1,2 involves a noncoding RNA which targets mimicry of miR399. miRNA399 mediates cleavage of PHO2. (3,4) The regulating pathway downstream of OsPHR2 is negatively regulated by the Pi-signaling responsive gene OsSPX1. (5,6) Overexpression of AtPHR1 and OsPHR2 leads to an increased concentration of Pi in the shoot tissues with leaf toxic symptom and growth retardation similar as the phenotype of pho2 mutant, especially under Pi abundant conditions. (7,2,6) It has been known that the low affinity Pi transporter OsPT2 mainly contributes to the shoot Pi accumulation mediated by OsPHR2, and overexpression of OsPT2 results in shoot Pi accumulation and leaf toxic symptom and growth retardation under Pi abundant conditions. (6) Two curious questions are emerging from the reported results: How Os SPX1 functions on the negative regulation of the pathway and what mechanism of the growth retardation mediated by OsPHR2. For the second question, our favored hypothesis is that the growth inhibition mediated by overexpression of OsPHR2 is caused by toxic physiological effects due to excessive Pi accumulation in shoots (Pi toxicity). In fact, the toxic symptoms become diminished with decreased Pi levels in growth medium. However, the plant growth retardation mediated by overexpression of OsPHR2 may be caused by some unknown genetic factor(s) regulated by OsPHR2.

OsSPX1 suppresses the function of OsPHR2 in the regulation of expression of OsPT2 and phosphate homeostasis in shoots of rice

Phosphate (Pi) homeostasis in plants is required for plant growth and development, and is achieved by the coordination of Pi acquisition, translocation from roots to shoots, and remobilization within plants. Previous reports have demonstrated that over-expression of OsPHR2 (the homolog of AtPHR1) and knockdown of OsSPX1 result in accumulation of excessive shoot Pi in rice. Here we report that OsPHR2 positively regulates the low-affinity Pi transporter gene OsPT2 by physical interaction and upstream regulation of OsPHO2 in roots. OsPT2 is responsible for most of the OsPHR2-mediated accumulation of excess shoot Pi. OsSPX1 suppresses the regulation on expression of OsPT2 by OsPHR2 and the accumulation of excess shoot Pi, but it does not suppress induction of OsPT2 or the accumulation of excessive shoot Pi in the Ospho2 mutant. Our data also show that OsSPX1 is a negative regulator of OsPHR2 and is involved in the feedback of Pi-signaling network in roots that is defined by OsPHR2 and OsPHO2. This finding provides new insight into the regulatory mechanism of Pi uptake, translocation, allocation and homeostasis in plants.

Regulation of phosphate starvation responses in higher plants

BACKGROUND

Phosphorus (P) is often a limiting mineral nutrient for plant growth. Many soils worldwide are deficient in soluble inorganic phosphate (P(i)), the form of P most readily absorbed and utilized by plants. A network of elaborate developmental and biochemical adaptations has evolved in plants to enhance P(i) acquisition and avoid starvation.

SCOPE

Controlling the deployment of adaptations used by plants to avoid P(i) starvation requires a sophisticated sensing and regulatory system that can integrate external and internal information regarding P(i) availability. In this review, the current knowledge of the regulatory mechanisms that control P(i) starvation responses and the local and long-distance signals that may trigger P(i) starvation responses are discussed. Uncharacterized mutants that have P(i)-related phenotypes and their potential to give us additional insights into regulatory pathways and P(i) starvation-induced signalling are also highlighted and assessed.

CONCLUSIONS

An impressive list of factors that regulate P(i) starvation responses is now available, as is a good deal of knowledge regarding the local and long-distance signals that allow a plant to sense and respond to P(i) availability. However, we are only beginning to understand how these factors and signals are integrated with one another in a regulatory web able to control the range of responses demonstrated by plants grown in low P(i) environments. Much more knowledge is needed in this agronomically important area before real gains can be made in improving P(i) acquisition in crop plants.

Regulation of phosphate starvation responses in plants: signaling players and cross-talks

Phosphate (Pi) availability is a major factor limiting growth, development, and productivity of plants. In both ecological and agricultural contexts, plants often grow in soils with low soluble phosphate content. Plants respond to this situation by a series of developmental and metabolic adaptations that are aimed at increasing the acquisition of this vital nutrient from the soil, as well as to sustain plant growth and survival. The development of a comprehensive understanding of how plants sense phosphate deficiency and coordinate the responses via signaling pathways has become of major interest, and a number of signaling players and networks have begun to surface for the regulation of the phosphate-deficiency response. In practice, application of such knowledge to improve plant Pi nutrition is hindered by complex cross-talks, which are emerging in the face of new data, such as the coordination of the phosphate-deficiency signaling networks with those involved with hormones, photo-assimilates (sugar), as well as with the homeostasis of other ions, such as iron. In this review, we focus on these cross-talks and on recent progress in discovering new signaling players involved in the Pi-starvation responses, such as proteins having SPX domains.