Repression of Nitrogen Starvation Responses by Members of the Arabidopsis GARP-Type Transcription Factor NIGT1/HRS1 Subfamily

Two ADP-glucose pyrophosphorylase subunits, OsAGPL1 and OsAGPS1, modulate phosphorus homeostasis in rice

Plant acclimatory responses to phosphate (Pi) starvation stress include the accumulation of carbohydrates, namely sugar and starch. However, whether altered endogenous carbohydrate profile could in turn affect plant Pi starvation responses remains widely unexplored. Here, two genes encoding the large and small subunits of an ADP-glucose pyrophosphorylase (AGP) in rice (Oryza sativa), AGP Large Subunit 1 (AGPL1) and AGP Small Subunit 1 (AGPS1), were functionally characterized with regard to maintenance of phosphorus (P) homeostasis and regulation of Pi starvation signaling. AGPL1 and AGPS1 were both positively responsive to nitrogen (N) or Pi deprivation, and expressed in almost all the tissues except in the meristem and mature zones of root. AGPL1 and AGPS1 physically interacted in chloroplast, and catalyzed the rate-limiting step of starch biosynthesis. Low-N- (LN) and low-Pi (LP)-triggered starch accumulation in leaves was impaired in agpl1, agps1 and apgl1 agps1 mutants compared with the wild-type plants. By contrast, mutation of AGPL1 and/or AGPS1 led to an increase in the content of the major sugar, sucrose, in leaf sheath and root under control and LN conditions. Moreover, the Pi accumulation was enhanced in the mutants under control and LN conditions, but not LP conditions. Notably, the LN-induced suppression of Pi accumulation was compromised attributed to the mutation of AGPL1 and/or AGPS1. Furthermore, the increased Pi accumulation was accompanied by the specific suppression of OsSPX2 and activation of several Pi transporter genes. These results indicate that a balanced level of carbohydrates is vital for maintaining plant P homeostasis.

Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants

Nitrogen (N) is an essential nutrient for plant growth and development; therefore, N deficiency is a major limiting factor in crop production. Plants have evolved mechanisms to cope with N deficiency, and the role of protein-coding genes in these mechanisms has been well studied. In the last decades, regulatory non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long ncRNAs (lncRNAs), have emerged as important regulators of gene expression in diverse biological processes. Recent advances in technologies for transcriptome analysis have enabled identification of N-responsive ncRNAs on a genome-wide scale. Characterization of these ncRNAs is expected to improve our understanding of the gene regulatory mechanisms of N response. In this review, we highlight recent progress in identification and characterization of N-responsive ncRNAs in Arabidopsis thaliana and several other plant species including maize, rice, and Populus.

NIGT1 family proteins exhibit dual mode DNA recognition to regulate nutrient response-associated genes in Arabidopsis

Fine-tuning of nutrient uptake and response is indispensable for maintenance of nutrient homeostasis in plants, but the details of underlying mechanisms remain to be elucidated. NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1) family proteins are plant-specific transcriptional repressors that function as an important hub in the nutrient signaling network associated with the acquisition and use of nitrogen and phosphorus. Here, by yeast two-hybrid assays, bimolecular fluorescence complementation assays, and biochemical analysis with recombinant proteins, we show that Arabidopsis NIGT1 family proteins form a dimer via the interaction mediated by a coiled-coil domain (CCD) in their N-terminal regions. Electrophoretic mobility shift assays defined that the NIGT1 dimer binds to two different motifs, 5'-GAATATTC-3' and 5'-GATTC-N38-GAATC-3', in target gene promoters. Unlike the dimer of wild-type NIGT1 family proteins, a mutant variant that could not dimerize due to amino acid substitutions within the CCD had lower specificity and affinity to DNA, thereby losing the ability to precisely regulate the expression of target genes. Thus, expressing the wild-type and mutant NIGT1 proteins in the nigt1 quadruple mutant differently modified NIGT1-regulated gene expression and responses towards nitrate and phosphate. These results suggest that the CCD-mediated dimerization confers dual mode DNA recognition to NIGT1 family proteins, which is necessary to make proper controls of their target genes and nutrient responses. Intriguingly, two 5'-GATTC-3' sequences are present in face-to-face orientation within the 5'-GATTC-N38-GAATC-3' sequence or its complementary one, while two 5'-ATTC-3' sequences are present in back-to-back orientation within the 5'-GAATATTC-3' or its complementary one. This finding suggests a unique mode of DNA binding by NIGT1 family proteins and may provide a hint as to why target sequences for some transcription factors cannot be clearly determined.

The Transcription Factor NIGT1.2 Modulates Both Phosphate Uptake and Nitrate Influx during Phosphate Starvation in Arabidopsis and Maize

Phosphorus and nitrogen are essential macronutrients for plant growth and crop production. During phosphate (Pi) starvation, plants enhanced Pi but reduced nitrate (NO3 -) uptake capacity, and the mechanism is unclear. Here, we show that a GARP-type transcription factor NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIOANL REPRESSOR1.2 (NIGT1.2) coordinately modulates Pi and NO3 - uptake in response to Pi starvation. Overexpression of NIGT1.2 increased Pi uptake capacity but decreased NO3 - uptake capacity in Arabidopsis (Arabidopsis thaliana). Furthermore, the nigt1.1 nigt1.2 double mutant displayed reduced Pi uptake but enhanced NO3 - uptake under low-Pi stress. During Pi starvation, NIGT1.2 directly up-regulated the transcription of the Pi transporter genes PHOSPHATE TRANSPORTER1;1 (PHT1;1) and PHOSPHATE TRANSPORTER1;4 (PHT1;4) and down-regulated expression of NO3 - transporter gene NITRATE TRANSPORTER1.1 (NRT1.1) by binding to cis-elements in their promoters. Further genetic assays demonstrated that PHT1;1, PHT1;4, and NRT1.1 were genetically epistatic to NIGT1.2 We also identified similar regulatory pathway in maize (Zea mays). These data demonstrate that the transcription factor NIGT1.2 plays a central role in modulating low-Pi-dependent uptake of Pi and NO3 -, tending toward maintenance of the phosphorus to nitrogen balance in plants during Pi starvation.

NRT1.1-centered nitrate signaling in plants

Plants need efficient nitrate (NO3-) sensing systems and sophisticated signaling pathways to develop a wide range of adaptive responses to external fluctuations of NO3- supply. In Arabidopsis thaliana, numerous molecular regulators have been identified to participate in signaling pathways that respond specifically to NO3-. In contrast, only a single NO3- sensing system has been described to date, relying on the NRT1.1 (NPF6.3/CHL1) NO3- transceptor. NRT1.1 governs a wide range of responses to NO3-, from fast reprogramming of genome expression (the primary nitrate response) to longer-term developmental changes (effects on lateral root development). NRT1.1 appears to be at the center of a complex network of signaling pathways, involving numerous molecular players acting downstream and/or upstream of it. Interestingly, some of these regulators are involved in crosstalk with the signaling pathways of other nutrients, such as inorganic phosphate or potassium. Although NRT1.1-mediated NO3- sensing and signaling has mostly been documented in Arabidopsis, recent evidence indicates that similar mechanisms involving NRT1.1 orthologues are operative in rice. This review aims to delineate how the NRT1.1 sensing system and the downstream/upstream transduction cascades are integrated to control both the expression of NO3--responsive genes and the induced plasticity of root development.

Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture

The agricultural green revolution of the 1960s boosted cereal crop yield was in part due to cultivation of semi-dwarf green revolution varieties. The semi-dwarf plants resist lodging and require high nitrogen (N) fertilizer inputs to maximize yield. To produce higher grain yield, inorganic fertilizer has been overused by Chinese farmers in intensive crop production. With the ongoing increase in the food demand of global population and the environmental pollution, improving crop productivity with reduced N supply is a pressing challenge. Despite a great deal of research efforts, to date only a few genes that improve N use efficiency (NUE) have been identified. The molecular mechanisms underlying the coordination of plant growth, carbon (C) and N assimilation is still not fully understood, thus preventing significant improvement. Recent advances have shed light on how explore NUE within an overall plant biology system that considered the co-regulation of plant growth, C and N metabolisms as a whole, rather than focusing specifically on N uptake and assimilation. There are several potential approaches to improve NUE discussed in this review. Increasing knowledge of how plants sense and respond to changes in N availability, as well as identifying new targets for breeding strategies to simultaneously improve NUE and grain yield, could usher in a new green revolution.

Nitrogen and Phosphorus interactions in plants: from agronomic to physiological and molecular insights

Nitrogen (N) and Phosphorus (P) are the two most essential nutrients ensuring food production and security. The ever growing population demands more N and P-based fertilizers. Even though the N provision to the agricultural system is virtually infinite (Haber and Bosch process) it triggers pollution when it is not used by the plant and leaks into the environment. On the other hand, P is predicted to be a limited source worldwide. P use is also responsible for water eutrophication. Thus understanding plant response to combinations of N and P has clear implications for sustainable human development. Recent works have shed new light on how N and P closely interact to control plant responses. Several molecular actors have been revealed controlling the molecular interaction between these two essential elements drafting a working model of N and P interactions. We summarize here these new findings as well as several previous lines of evidence in agronomy and physiology studies preceding this new trend of investigation in the molecular world.

Gene regulatory network and its constituent transcription factors that control nitrogen-deficiency responses in rice

Increase in the nitrogen (N)-use efficiency and optimization of N response in crop species are urgently needed. Although transcription factor-based genetic engineering is a promising approach for achieving these goals, transcription factors that play key roles in the response to N deficiency have not been studied extensively. Here, we performed RNA-seq analysis of root samples of 20 Asian rice (Oryza sativa) accessions with differential nutrient uptake. Data obtained from plants exposed to N-replete and N-deficient conditions were subjected to coexpression analysis and machine learning-based pathway inference to dissect the gene regulatory network required for the response to N deficiency. Four transcription factors, including members of the G2-like and bZIP families, were predicted to function as key regulators of gene transcription within the network in response to N deficiency. Cotransfection assays validated inferred novel regulatory pathways, and further analyses using genome-edited knockout lines suggested that these transcription factors are important for N-deficiency responses in planta. Many of the N deficiency-responsive genes, including those encoding key regulators within the network, were coordinately regulated by transcription factors belonging to different families. Transcription factors identified in this study could be valuable for the modification of N response and metabolism.

Examining the molecular mechanisms contributing to the success of an invasive species across different ecosystems

Invasive species provide an opportune system to investigate how populations respond to new environments. Baby's breath (Gypsophila paniculata) was introduced to North America in the 1800s and has since spread throughout the United States and western Canada. We used an RNA-seq approach to explore how molecular processes contribute to the success of invasive populations with similar genetic backgrounds across distinct habitats. Transcription profiles were constructed from seedlings collected from a sand dune ecosystem in Petoskey, MI (PSMI), and a sagebrush ecosystem in Chelan, WA (CHWA). We assessed differential gene expression and identified SNPs within differentially expressed genes. We identified 1,146 differentially expressed transcripts across all sampled tissues between the two populations. GO processes enriched in PSMI were associated with nutrient starvation, while enriched processes in CHWA were associated with abiotic stress. Only 7.4% of the differentially expressed transcripts contained SNPs differing in allele frequencies of at least 0.5 between populations. Common garden studies found the two populations differed in germination rate and seedling emergence success. Our results suggest the success of G. paniculata in these two environments is likely due to plasticity in specific molecular processes responding to different environmental conditions, although some genetic divergence may be contributing to these differences.

Nitrate in 2020: Thirty Years from Transport to Signaling Networks

Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.

Cytosolic ascorbate peroxidase 1 modulates ascorbic acid metabolism through cooperating with nitrogen regulatory protein P-II in tea plant under nitrogen deficiency stress

Nitrogen (N) element is essential nutrient, and affect metabolism of secondary metabolites in higher plants. Ascorbate peroxidase (APX) plays an important role in ascorbic acid (AsA) metabolism of tea plant. However, the roles of cytosolic ascorbate peroxidase 1 (CsAPX1) in AsA metabolism under N deficiency stress in tea plant remains unclear in detail. In this work, nitrogen regulatory protein P-II (CsGLB1) and CsAPX1 were identified by isobaric tags for relative and absolute quantitation (iTRAQ) from tea plant. The cell growth rates in transgenic Escherichia coli overexpressing CsAPX1 and CsGLB1 were higher than empty vector under N sufficiency condition. Phenotype of shoots and roots, AsA accumulation, and expression levels of AtAPX1 and AtGLB1 genes were changed in transgenic Arabidopsis hosting CsAPX1 under N deficiency stress. These findings suggested that cytosolic CsAPX1 acted a regulator in AsA accumulation through cooperating with GLB1 under N deficiency stress in tea plant.

Glutaredoxin AtGRXS8 represses transcriptional and developmental responses to nitrate in Arabidopsis thaliana roots

Glutaredoxins (GRXs) are small oxidoreductase enzymes that can reduce disulfide bonds in target proteins. The class III GRX gene family is unique to land plants, and Arabidopsis thaliana has 21 class III GRXs, which remain largely uncharacterized. About 80% of A. thaliana class III GRXs are transcriptionally regulated by nitrate, and several recent studies have suggested roles for these GRXs in nitrogen signaling. Our objective was to functionally characterize two nitrate-induced GRX genes, AtGRXS5 and AtGRXS8, defining their roles in signaling and development in the A. thaliana root. We demonstrated that AtGRXS5 and AtGRXS8 are primarily expressed in root and shoot vasculature (phloem), and that the corresponding GRX proteins display nucleo-cytosolic subcellular localization. Ectopic expression of AtGRXS8 in transgenic plants caused major alterations in root system architecture: Normal primary root development, but a near absence of lateral roots. RNA sequencing demonstrated that the roots of AtGRXS8-overexpressing plants show strongly reduced transcript abundance for many primary nitrate response genes, including the major high-affinity nitrate transporters. Correspondingly, high-affinity nitrate uptake and the transport of nitrate from roots to shoots are compromised in AtGRXS8-overexpressing plants. Finally, we demonstrated that the AtGRXS8 protein can physically interact with the TGA1 and TGA4 transcription factors, which are central regulators of early transcriptional responses to nitrate in A. thaliana roots. Overall, these results suggest that AtGRXS8 acts to quench both transcriptional and developmental aspects of primary nitrate response, potentially by interfering with the activity of the TGA1 and TGA4 transcription factors.

Nitrate-inducible NIGT1 proteins modulate phosphate uptake and starvation signalling via transcriptional regulation of SPX genes

Nitrogen and phosphorus are two major soil nutrients required for plant growth. Because requirements of both these elements are interdependent, acquisition of one must be balanced with that of the other. However, the mechanism underlying this balanced acquisition remains unclear. Here, we show by in vivo luciferase imaging that the presence of nitrogen sources is a pre-requisite for strong activation of phosphate starvation responses. In addition, we also show that nitrate rather than ammonium is a potent modulator of phosphate starvation-induced gene expression. Furthermore, protoplast-based transient expression assay and chromatin immunoprecipitation assay demonstrate that NIGT1 GARP-type transcriptional repressors, which are encoded by nitrate-inducible genes, directly bind to and repress the promoters of genes encoding SPX proteins. Consistent with the role of SPX proteins in the suppression of the PHR1 transcriptional activator, the master regulator for phosphate starvation responses, nitrate-dependent enhancement of phosphate starvation responses, such as accumulation of anthocyanin and promotion of root hair growth and phosphate uptake, was less evident in the nigt1.1-nigt1.4 quadruple mutant. Consistently, NIGT1 overexpression alleviated the reduction in phosphate uptake under phosphate-replete conditions. We further reveal the intricate feedback regulations involving PHR1, NIGT1, and SPX family proteins in the phosphate starvation signalling network. Importantly, results of mutant protoplast-based assays and in planta analysis using NIGT1 overexpression in the spx1 spx2 double mutant indicated that the NIGT1-SPX-PHR cascade mediates nitrogen status-responsive regulation of phosphate uptake and starvation signalling. These findings uncover the mechanism underlying the balanced acquisition of nitrogen and phosphorus.

Distinct non-coding RNAs confer root-dependent sense transgene-induced post-transcriptional gene silencing and nitrogen-dependent post-transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots

High-affinity ammonium uptake in roots mediate by AMT1-type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, in addition to the transcriptional and post-translational controls, an organ-dependent and N-dependent post-transcriptional regulation was suggested as an additional regulatory step for fine tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35s:AtAMT1;1-transformed atamt1;1-1 Arabidopsis plants resulted from RDR6-dependent sense transgene-induced post-transcriptional gene silencing (S-PTGS). The siRNAs for S-PTGS may derive from the aberrant RNA, of which the production was co-determined by sequence feature and excessive expression of AtAMT1;1. Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA-targeted hotspots reduced AtAMT1;1-specific siRNAs and overcame S-PTGS in roots. In roots of these lines, however, the steady-state transcript levels of AtAMT1;1 still significantly decreased under conditions of N-sufficiency compared with N-deficiency, confirming a N-dependent post-transcriptional regulatory manner. A crucial role of the 207-bp 3'-end sequence of AtAMT1;1 was further demonstrated by N-dependent accumulation of chimeric-AtAMT1;1 transcript in T-DNA insertion lines and of GFP-tagged chimeric-AtAMT1;1 transcript in transgenic lines. A novel non-coding RNA (ncRNA), which was highly abundant in N-sufficient roots, may target the above-identified 3'-end region for the degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on the AtAMT1;1 transcript at a potential cleavage site (+1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots.

Plant abiotic stress response and nutrient use efficiency

Abiotic stresses and soil nutrient limitations are major environmental conditions that reduce plant growth, productivity and quality. Plants have evolved mechanisms to perceive these environmental challenges, transmit the stress signals within cells as well as between cells and tissues, and make appropriate adjustments in their growth and development in order to survive and reproduce. In recent years, significant progress has been made on many fronts of the stress signaling research, particularly in understanding the downstream signaling events that culminate at the activation of stress- and nutrient limitation-responsive genes, cellular ion homeostasis, and growth adjustment. However, the revelation of the early events of stress signaling, particularly the identification of primary stress sensors, still lags behind. In this review, we summarize recent work on the genetic and molecular mechanisms of plant abiotic stress and nutrient limitation sensing and signaling and discuss new directions for future studies.

Cross-Species Root Transcriptional Network Analysis Highlights Conserved Modules in Response to Nitrate between Maize and Sorghum

Plants have evolved complex mechanisms to respond to the fluctuation of available nitrogen (N) in soil, but the genetic mechanisms underlying the N response in crops are not well-documented. In this study, we generated a time series of NO₃⁻-mediated transcriptional profiles in roots of maize and sorghum, respectively. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes that related to NO₃⁻ treatments. A cross-species comparison revealed 22 conserved modules, of which four were related to hormone signaling, suggesting that hormones participate in the early nitrate response. Three other modules are composed of genes that are mainly upregulated by NO₃⁻ and involved in nitrogen and carbohydrate metabolism, including NRT, NIR, NIA, FNR, and G6PD2. Two G2-like transcription factors (ZmNIGT1 and SbNIGT1), induced by NO₃⁻ stimulation, were identified as hub transcription factors (TFs) in the modules. Transient assays demonstrated that ZmNIGT1 and SbNIGT1 are transcriptional repressors. We identified the target genes of ZmNIGT1 by DNA affinity-purification sequencing (DAP-Seq) and found that they were significantly enriched in catalytic activity, including carbon, nitrogen, and other nutrient metabolism. A set of ZmNIGT1 targets encode transcription factors (ERF, ARF, and AGL) that are involved in hormone signaling and root development. We propose that ZmNIGT1 and SbNIGT1 are negative regulators of nitrate responses that play an important role in optimizing nutrition metabolism and root morphogenesis. Together with conserved N responsive modules, our study indicated that, to encounter N variation in soil, maize and sorghum have evolved an NO₃⁻-regulatory network containing a set of conserved modules and transcription factors.

Nitrogen-phosphorus interplay: old story with molecular tale

Nitrogen (N) and phosphorus (P) are the two most abundant mineral nutrients used by plants, and are also the mostly widely used fertilizer elements driving crop yield improvement in agricultural production. The coordinated utilization of N and P is essential to maintain optimal plant growth and achieve maximal crop yield. The signaling pathways of N and P are generally studied separately, so our understanding of N-P interactions is very limited. A series of recent studies have revealed the critical components regulating N-P interactions in both Arabidopsis thaliana and rice (Oryza sativa), and have shed light on our in-depth understanding of the network integrating N and P signaling pathways. Here, we summarize recent progress on N-P interaction and propose possible working mechanisms integrating these N-P interactive regulation pathways. We further discuss future work that might reveal the N-P interactive regulation network in plants.

Adaptation of Foxtail Millet (Setaria italica L.) to Abiotic Stresses: A Special Perspective of Responses to Nitrogen and Phosphate Limitations

Amongst various environmental constraints, abiotic stresses are increasing the risk of food insecurity worldwide by limiting crop production and disturbing the geographical distribution of food crops. Millets are known to possess unique features of resilience to adverse environments, especially infertile soil conditions, although the underlying mechanisms are yet to be determined. The small diploid genome, short stature, excellent seed production, C₄ photosynthesis, and short life cycle of foxtail millet make it a very promising model crop for studying nutrient stress responses. Known to be a drought-tolerant crop, it responds to low nitrogen and low phosphate by respective reduction and enhancement of its root system. This special response is quite different from that shown by maize and some other cereals. In contrast to having a smaller root system under low nitrogen, foxtail millet enhances biomass accumulation, facilitating root thickening, presumably for nutrient translocation. The low phosphate response of foxtail millet links to the internal nitrogen status, which tends to act as a signal regulating the expression of nitrogen transporters and hence indicates its inherent connection with nitrogen nutrition. Altogether, the low nitrogen and low phosphate responses of foxtail millet can act as a basis to further determine the underlying molecular mechanisms. Here, we will highlight the abiotic stress responses of foxtail millet with a key note on its low nitrogen and low phosphate adaptive responses in comparison to other crops.

Novel Aspects of Nitrate Regulation in Arabidopsis

Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO₃ ^-), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO₃ ^- regulation and starting to unravel the NO₃ ^- regulatory network. Great reviews have been made recently by scientists on the key regulators in NO₃ ^- signaling, NO₃ ^- effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO₃ ^- regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO₃ ^- signaling, and NO₃ ^- regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO₃ ^- regulation and provide a basis for further exploration of NO₃ ^- regulatory network.

Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms

Root systems play a pivotal role in coupling with drought stress, which is accompanied with a substantial transcriptome rebuilding in the root tissues. Here, we present the results of global gene expression profiling of roots of two barley genotypes with contrasting abilities to cope with drought that were subjected to a mild level of the stress. We concentrate our analysis on gene expression regulation processes, which allowed the identification of 88 genes from 39 families involved in transcriptional regulation in roots upon mild drought. They include 13 genes encoding transcription factors (TFs) from AP2 family represented by ERFs, DREB, or B3 domain-containing TFs, eight WRKYs, six NACs, five of the HD-domain, MYB or MYB-related, bHLH and bZIP TFs. Also, the representatives of C3H, CPP, GRAS, LOB-domain, TCP, Tiffy, Tubby, and NF-Ys TFs, among others were found to be regulated by the mild drought in barley roots. We found that drought tolerance is accompanied with a lower number of gene expression changes than the amount observed in a susceptible genotype. The better drought acclimation may be related to the activation of transcription factors involved in the maintenance of primary root growth and in the epigenetic control of chromatin and DNA methylation. In addition, our analysis pointed to fives TFs from ERF, LOB, NAC, WRKY and bHLH families that may be important in the mild but not the severe drought response of barley roots.

The role of nutrient balance in shaping plant root-fungal interactions: facts and speculation

Microbiota colonizing plant roots and their vicinity were shown not to be just random associations, but compose, at least to some extent, host-selected microbial consortia. The plant physiological status, especially the nutrient status, prompts changes in plant morphology and metabolism, which successively imposes a selective pressure on microbial communities. It is well established that a low phosphate status of the host plant activates the molecular machinery underlying the development of mutualistic associations in the host root with arbuscular mycorrhizal fungi (AMF). We hypothesize that the plant´s response to changing nutrient stoichiometry affects processes at the root-mycosphere interface which promote or repress also root interactions with microbial taxa other than AMF. As a consequence, fundamental mechanisms underlying these interactions would be shared in AM host and non-host plants. A detailed understanding of the processes involved in maintenance of plant nutrient homeostasis could contribute to novel strategies in tailoring predominantly parasitic or commensalistic plant-microbe interactions towards beneficial associations.

Transgenerational Response to Nitrogen Deprivation in Arabidopsis thaliana

Nitrogen (N) deficiency is one of the major stresses that crops are exposed to. It is plausible to suppose that a stress condition can induce a memory in plants that might prime the following generations. Here, an experimental setup that considered four successive generations of N-sufficient and N-limited Arabidopsis was used to evaluate the existence of a transgenerational memory. The results demonstrated that the ability to take up high amounts of nitrate is induced more quickly as a result of multigenerational stress exposure. This behavior was paralleled by changes in the expression of nitrate responsive genes. RNAseq analyses revealed the enduring modulation of genes in downstream generations, despite the lack of stress stimulus in these plants. The modulation of signaling and transcription factors, such as NIGTs, NFYA and CIPK23 might indicate that there is a complex network operating to maintain the expression of N-responsive genes, such as NRT2.1, NIA1 and NIR. This behavior indicates a rapid acclimation of plants to changes in N availability. Indeed, when fourth generation plants were exposed to N limitation, they showed a rapid induction of N-deficiency responses. This suggests the possible involvement of a transgenerational memory in Arabidopsis that allows plants to adapt efficiently to the environment and this gives an edge to the next generation that presumably will grow in similar stressful conditions.

Ammonium and nitrate regulate NH4+ uptake activity of Arabidopsis ammonium transporter AtAMT1;3 via phosphorylation at multiple C-terminal sites

In plants, nutrient transporters require tight regulation to ensure optimal uptake in complex environments. The activities of many nutrient transporters are post-translationally regulated by reversible phosphorylation, allowing rapid adaptation to variable environmental conditions. Here, we show that the Arabidopsis root epidermis-expressed ammonium transporter AtAMT1;3 was dynamically (de-)phosphorylated at multiple sites in the cytosolic C-terminal region (CTR) responding to ammonium and nitrate signals. Under ammonium resupply rapid phosphorylation of a Thr residue (T464) in the conserved part of the CTR (CTRC) effectively inhibited AtAMT1;3-dependent NH4+ uptake. Moreover, phosphorylation of Thr (T494), one of three phosphorylation sites in the non-conserved part of the CTR (CRTNC), moderately decreased the NH4+ transport activity of AtAMT1;3, as deduced from functional analysis of phospho-mimic mutants in yeast, oocytes, and transgenic Arabidopsis. Double phospho-mutants indicated a role of T494 in fine-tuning the NH4+ transport activity when T464 was non-phosphorylated. Transient dephosphorylation of T494 with nitrate resupply closely paralleled a transient increase in ammonium uptake. These results suggest that T464 phosphorylation at the CTRC acts as a prime switch to prevent excess ammonium influx, while T494 phosphorylation at the CTRNC fine tunes ammonium uptake in response to nitrate. This provides a sophisticated regulatory mechanism for plant ammonium transporters to achieve optimal ammonium uptake in response to various nitrogen forms.

Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen

Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.

Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants

Nitrate and phosphate ions are major sources of nitrogen and phosphorus for plants. In addition to their vital roles as indispensable macronutrients, these ions function as signalling molecules and induce a variety of responses. Plants adapt to different levels of nutrients by altering their gene expression profile and subsequent physiological and morphological responses. Advances made in recent years have provided novel insights into plant nutrient sensing and modulation of gene expression. Key breakthroughs include elucidation of the mechanisms underlying post-translational regulation of NIN-LIKE PROTEIN (NLP) and PHOSPHATE STARVATION RESPONSE (PHR) family transcription factors, which function as master regulators of responses to nitrate and phosphate starvation, respectively. Determination of the mechanisms whereby these nutrient signals are integrated through NIGT1/HHO family proteins has likewise represented important progress. Further studies have revealed novel roles in nutrient signalling of transcription factors that have previously been shown to be associated with other signals, such as light and phytohormones. Nitrate and phosphate signals are thus transmitted through an intricate gene regulatory network with the help of various positive and negative transcriptional regulators. These complex regulatory patterns enable plants to integrate input signals from various environmental factors and trigger appropriate responses, as exemplified by the regulatory module involving NIGT1/HHO family proteins. These mechanisms collectively support nutrient homeostasis in plants.

Getting to the Root of Plant Mineral Nutrition: Combinatorial Nutrient Stresses Reveal Emergent Properties

In nature, plants have to handle daily fluctuations in light and temperature. In addition, plants face biotic and abiotic stresses that often come in various combinations. For instance, the availability of various nutrients in soil is heterogeneous, resulting in combined nutrient stress. Recent studies reveal that plant responses to multiple nutrient stresses are not the summation of the plant responses to each individual stress. Here, we present and discuss the interactions between phosphate, nitrogen, and zinc to illustrate the effect of macro- and micronutrient interactions on plant growth and ion homeostasis. Solving the mystery of these interactions will pave the way to the development of strategies to improve crop productivity.

Identification of Molecular Integrators Shows that Nitrogen Actively Controls the Phosphate Starvation Response in Plants

Nitrogen (N) and phosphorus (P) are key macronutrients sustaining plant growth and crop yield and ensuring food security worldwide. Understanding how plants perceive and interpret the combinatorial nature of these signals thus has important agricultural implications within the context of (1) increased food demand, (2) limited P supply, and (3) environmental pollution due to N fertilizer usage. Here, we report the discovery of an active control of P starvation response (PSR) by a combination of local and long-distance N signaling pathways in plants. We show that, in Arabidopsis (Arabidopsis thaliana), the nitrate transceptor CHLORINA1/NITRATE TRANSPORTER1.1 (CHL1/NRT1.1) is a component of this signaling crosstalk. We also demonstrate that this crosstalk is dependent on the control of the accumulation and turnover by N of the transcription factor PHOSPHATE STARVATION RESPONSE1 (PHR1), a master regulator of P sensing and signaling. We further show an important role of PHOSPHATE2 (PHO2) as an integrator of the N availability into the PSR since the effect of N on PSR is strongly affected in pho2 mutants. We finally show that PHO2 and NRT1.1 influence each other's transcript levels. These observations are summarized in a model representing a framework with several entry points where N signal influence PSR. Finally, we demonstrate that this phenomenon is conserved in rice (Oryza sativa) and wheat (Triticum aestivum), opening biotechnological perspectives in crop plants.

Nitrate-NRT1.1B-SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants

To ensure high crop yields in a sustainable manner, a comprehensive understanding of the control of nutrient acquisition is required. In particular, the signalling networks controlling the coordinated utilization of the two most highly demanded mineral nutrients, nitrogen and phosphorus, are of utmost importance. Here, we reveal a mechanism by which nitrate activates both phosphate and nitrate utilization in rice (Oryza sativa L.). We show that the nitrate sensor NRT1.1B interacts with a phosphate signalling repressor SPX4. Nitrate perception strengthens the NRT1.1B-SPX4 interaction and promotes the ubiquitination and degradation of SPX4 by recruiting NRT1.1B interacting protein 1 (NBIP1), an E3 ubiquitin ligase. This in turn allows the key transcription factor of phosphate signalling, PHR2, to translocate to the nucleus and initiate the transcription of phosphorus utilization genes. Interestingly, the central transcription factor of nitrate signalling, NLP3, is also under the control of SPX4. Thus, nitrate-triggered degradation of SPX4 activates both phosphate- and nitrate-responsive genes, implementing the coordinated utilization of nitrogen and phosphorus.

The role of protein-protein interactions mediated by the PB1 domain of NLP transcription factors in nitrate-inducible gene expression

BACKGROUND

NIN-LIKE PROTEIN (NLP) transcription factors are master regulators of nitrate-inducible gene expression in higher plants. NLP transcription factors contain a nitrate signal-responsive domain in the amino-terminal region, an RWP-RK-type DNA-binding domain in the middle, and a Phox and Bem1 (PB1) domain at the carboxy terminus. Although the PB1 domain of NLP transcription factors appears to mediate protein-protein interactions associated with nitrate-inducible gene expression in higher plants, its precise role in nitrate-inducible gene expression has not previously been characterized.

RESULTS

Yeast two-hybrid assays with the PB1 domain of the Arabidopsis transcription factor NLP7 revealed NLP-NLP interactions that required the core amino acid residues (K867, D909, D911, and E913) within the PB1 domain. Consistent with previous speculation on redundant and overlapping functions between different Arabidopsis NLP transcription factors, NLP-NLP interactions were observed between a variety of combinations of different NLP transcription factors. Furthermore, a mutated form of NLP7 that harbored amino acid substitutions at K867, D909, D911, and E913 required a far higher level of expression than wild-type NLP7 to restore nitrate-responsive gene expression and growth of nlp6 nlp7-1 double mutants. Surprisingly, however, the ability to transactivate nitrate-responsive promoters in protoplast transient expression assays was similar between wild-type and mutant forms of NLP7, suggesting that the PB1 domain was not required for transcription from naked DNA.

CONCLUSIONS

Protein-protein interactions mediated by the PB1 domain of NLP transcription factors are necessary for full induction of nitrate-dependent expression of target genes in planta. The PB1 domains of NLP transcription factors may act on gene expression from chromosomal DNA via homo- and hetero-oligomerization in the presence of nitrate.

Nitrate signaling and the control of Arabidopsis growth and development

Coordination between plant development and nutrient availability ensures a suitable supply of macromolecules for growth and developmental programs. Nitrate is an important source of nitrogen (N) that acts as a signal molecule to modulate gene expression, physiological, growth and developmental responses throughout the life of the plant. New key players in the nitrate signaling pathway have been described and knowledge of the molecular mechanics of how it impacts growth and developmental processes is increasing fast. Importantly, mechanisms for nitrate-control of growth and developmental processes have been proposed for both local as well as systemic responses. This article provides a synthesis of recent insights into molecular mechanisms by which nitrate impacts growth and development over Arabidopsis life-cycle.

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

Cytokinin is a multifaceted plant hormone that plays major roles not only in diverse plant growth and development processes, but also stress responses. We summarize knowledge of the roles of its metabolism, transport, and signalling in responses to changes in levels of both macronutrients (nitrogen, phosphorus, potassium, sulphur) and micronutrients (boron, iron, silicon, selenium). We comment on cytokinin's effects on plants' xenobiotic resistance, and its interactions with light, temperature, drought, and salinity signals. Further, we have compiled a list of abiotic stress-related genes and demonstrate that their expression patterns overlap with those of cytokinin metabolism and signalling genes.

A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis

Nitrate is a nutrient signal that triggers complex regulation of transcriptional networks to modulate nutrient-dependent growth and development in plants. This includes time- and nitrate concentration-dependent regulation of nitrate-related gene expression. However, the underlying mechanisms remain poorly understood. Here we identify NIGT1 transcriptional repressors as negative regulators of the ArabidopsisNRT2.1 nitrate transporter gene, and show antagonistic regulation by NLP primary transcription factors for nitrate signalling and the NLP-NIGT1 transcriptional cascade-mediated repression. This antagonistic regulation provides a resolution to the complexity of nitrate-induced transcriptional regulations. Genome-wide analysis reveals that this mechanism is applicable to NRT2.1 and other genes involved in nitrate assimilation, hormone biosynthesis and transcription. Furthermore, the PHR1 master regulator of the phosphorus-starvation response also directly promotes expression of NIGT1 family genes, leading to reductions in nitrate uptake. NIGT1 repressors thus act in two transcriptional cascades, forming a direct link between phosphorus and nitrogen nutritional regulation.

Plants respond to nutrients by modulating gene expression. Here, the authors show that nitrate suppresses NRT2.1 nitrate transporter expression via NIGT1 transcriptional repressors and that phosphate starvation enhances this pathway via PHR1, thus linking phosphorus and nitrogen signalling.