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.

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.SPX-domain protein | PHR2 | Pi signaling | Pi-dependent inhibition P hosphorus (P) is an essential macroelement for plant growth and development. Because of high chemical fixation, slow diffusion, and substantial fractions of organic compounds by microorganisms, phosphate (Pi) limitation is usually a constraint for crop production in cultivated soils (1). However, intensive application of P fertilizer to increase agricultural production results in higher cost and environmental pollution and aggravates the shortage of nonrenewable resources worldwide for P fertilizer production (2). Therefore, improving effective Pi use by crops to reduce agricultural dependence on heavy Pi fertilizer application is an important challenge for sustainable agricultural production.The role of Arabidopsis PHOSPHATE STARVATION RESPONSE REGULATOR 1 (AtPHR1) and its orthologs as important regulators in Pi signaling and homeostasis through binding to the PHR1-binding sequence (P1BS) is well established in plants. AtPHR1 binds as a dimer to an imperfect palindromic sequence (GNATATNC), and this DNA-binding ability is dependent on the MYB and coiled-coil (CC) domains present in AtPHR1 and related proteins (3, 4). Orthologs of AtPHR1 have also been described in rice [Oryza sativa ( The SPX domain (Pfam PF03105) is named after the suppressor of yeast gpa1 (SYG1), the yeast cyclin-dependent kinase inhibitor (PHO81), and the human xenotropic and polytropic retrovirus receptor 1 (XPR1). In yeast (Saccharomyces cerevisiae), the SPX domain forms part of the competitive dual-transporter system that prolongs preparation for starvation and faci...

SUMMARYCrop yields are significantly reduced by aluminum (Al) toxicity on acidic soils, which comprise up to 50% of the world's arable land. Al-activated release of ligands (such as organic acids) from the roots is a major Al tolerance mechanism in plants. In maize, Al-activated root citrate exudation plays an important role in tolerance. However, maize Al tolerance is a complex trait involving multiple genes and physiological mechanisms. Recently, transporters from the MATE family have been shown to mediate Al-activated citrate exudation in a number of plant species. Here we describe the cloning and characterization of two MATE family members in maize, ZmMATE1 and ZmMATE2, which co-localize to major Al tolerance QTL. Both genes encode plasma membrane proteins that mediate significant anion efflux when expressed in Xenopus oocytes. ZmMATE1 expression is mostly concentrated in root tissues, is up-regulated by Al and is significantly higher in Al-tolerant maize genotypes. In contrast, ZmMATE2 expression is not specifically localized to any particular tissue and does not respond to Al. [14 C]-citrate efflux experiments in oocytes demonstrate that ZmMATE1 is a citrate transporter. In addition, ZmMATE1 expression confers a significant increase in Al tolerance in transgenic Arabidopsis. Our data suggests that ZmMATE1 is a functional homolog of the Al tolerance genes recently characterized in sorghum, barley and Arabidopsis, and is likely to underlie the largest maize Al tolerance QTL found on chromosome 6. However, ZmMATE2 most likely does not encode a citrate transporter, and could be involved in a novel Al tolerance mechanism.

Summary• Aluminum (Al) toxicity is a major factor limiting crop yields on acid soils. There is considerable genotypic variation for Al tolerance in most common plant species. In maize (Zea mays), Al tolerance is a complex phenomenon involving multiple genes and physiological mechanisms yet uncharacterized.• To begin elucidating the molecular basis of maize Al toxicity and tolerance, a detailed temporal analysis of root gene expression under Al stress was performed using microarrays with Al-tolerant and Al-sensitive genotypes.• Al altered the expression of significantly more genes in the Al-sensitive genotype, presumably as a result of more severe Al toxicity. Nevertheless, several Al-regulated genes exhibited higher expression in the Al-tolerant genotype. Cell wall-related genes, as well as low phosphate-responsive genes, were found to be regulated by Al. In addition, the expression patterns of genes related to Al-activated citrate release indicated that in maize this mechanism is probably regulated by the expression level and/or function of the citrate transporter.• This study is the first comprehensive survey of global transcriptional regulation under Al stress. The results described here will help to further our understanding of how mechanisms of Al toxicity and tolerance in maize are regulated at the transcriptional level.

Phosphorus (P), an essential macronutrient for all living cells, is indispensable for agricultural production. Although Arabidopsis (Arabidopsis thaliana) PHOSPHATE RESPONSE1 (PHR1) and its orthologs in other species have been shown to function in transcriptional regulation of phosphate (Pi) signaling and Pi homeostasis, an integrative comparison of PHR1-related proteins in rice (Oryza sativa) has not previously been reported. Here, we identified functional redundancy among three PHR1 orthologs in rice (OsPHR1, OsPHR2, and OsPHR3) using phylogenetic and mutation analysis. OsPHR3 in conjunction with OsPHR1 and OsPHR2 function in transcriptional activation of most Pi starvation-induced genes. Loss-of-function mutations in any one of these transcription factors (TFs) impaired root hair growth (primarily root hair elongation). However, these three TFs showed differences in DNA binding affinities and messenger RNA expression patterns in different tissues and growth stages, and transcriptomic analysis revealed differential effects on Pi starvation-induced gene expression of single mutants of the three TFs, indicating some degree of functional diversification. Overexpression of genes encoding any of these TFs resulted in partial constitutive activation of Pi starvation response and led to Pi accumulation in the shoot. Furthermore, unlike OsPHR2-overexpressing lines, which exhibited growth retardation under normal or Pi-deficient conditions, OsPHR3-overexpressing plants exhibited significant tolerance to low-Pi stress but normal growth rates under normal Pi conditions, suggesting that OsPHR3 would be useful for molecular breeding to improve Pi uptake/use efficiency under Pi-deficient conditions. We propose that OsPHR1, OsPHR2, and OsPHR3 form a network and play diverse roles in regulating Pi signaling and homeostasis in rice.

Roots are fundamentally important for growth and development, anchoring the plant to its growth substrate, facilitating water and nutrient uptake from the soil, and sensing and responding to environmental signals such as biotic and abiotic stresses. Understanding the molecular mechanisms controlling root architecture is essential for improving nutrient uptake efficiency and crop yields. In this review, we describe the progress being made in the identification of genes and regulatory pathways involved in the development of root systems in rice (Oryza sativa L.), including crown roots, lateral roots, root hairs, and root length. Genes involved in the adaptation of roots to the environmental nutrient status are reviewed, and strategies for further study and agricultural applications are discussed. The growth and development of rice roots are controlled by both genetic factors and environmental cues. Plant hormones, especially auxin and cytokinin, play important roles in root growth and development. Understanding the molecular mechanisms regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0262-x) contains supplementary material, which is available to authorized users.

The plant gaseous hormone ethylene regulates many aspects of plant growth, development and responses to the environment. ETHYLENE INSENSITIVE3 (EIN3) is a transcription factor involved in the ethylene signal transduction pathway in Arabidopsis. To gain a better understanding of the ethylene signal transduction pathway in rice, six EIN3-like genes (designated OsEIL1-6) were identified. OsEIL1, which showed highest similarity with EIN3, was isolated and functionally characterized. Ectopic expression of OsEIL1 in Arabidopsis can partially complement the ein3-1 mutant. The transgenic rice plants with overexpression of OsEIL1 exhibit short root, coiled primary root and slightly short shoot phenotype and elevated response to exogenous ethylene. OsEBP89, an ethylene responsive element binding protein (EREBP) and OsACO1, an ACC (1-aminocyclopropane-1-carboxylic acid) oxidase gene were enhanced in the OsEIL1 overexpressing transgenic plants. These results indicate that OsEIL1 is involved in ethylene signal transduction pathway and acts as a positive regulator of ethylene response in rice.

Phosphorus (P) is an essential macronutrient for plant growth and development, but the molecular mechanism determining how plants sense external inorganic phosphate (Pi) levels and reprogram transcriptional and adaptive responses is incompletely understood. In this study, we investigated the function of OsSPX6 (hereafter SPX6), an uncharacterized member of SPX domain (SYG1, Pho81 and XPR1)-containing proteins in rice, using reverse genetics and biochemical approaches. Transgenic plants overexpressing SPX6 exhibited decreased Pi concentrations and suppression of phosphate starvation-induced (PSI) genes. By contrast, transgenic lines with decreased SPX6 transcript levels or spx6 mutant showed significant Pi accumulation in the leaf and upregulation of PSI genes. Overexpression of SPX6 genetically suppressed the overexpression of PHOSPHATE STARVATION RESPONSE REGULATOR 2 (PHR2) in terms of the accumulation of high Pi content. Moreover, direct interaction of SPX6 with PHR2 impeded PHR2 translocation into the nucleus, and inhibited PHR2 binding to the P1BS (PHR1 binding sequence) element. SPX6 protein was degraded in leaves under Pi-deficient conditions, whereas it accumulated in roots. We conclude that rice SPX6 is another important negative regulator in Pi starvation signaling through the interaction with PHR2. SPX6 shows different responses to Pi starvation in shoot and root, which differ from those of other SPX proteins.