The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches

Nutrient-hormone relations: Driving root plasticity in plants

Optimal plant development requires root uptake of 14 essential mineral elements from the soil. Since the bioavailability of these nutrients underlies large variation in space and time, plants must dynamically adjust their root architecture to optimize nutrient access and acquisition. The information on external nutrient availability and whole-plant demand is translated into cellular signals that often involve phytohormones as intermediates to trigger a systemic or locally restricted developmental response. Timing and extent of such local root responses depend on the overall nutritional status of the plant that is transmitted from shoots to roots in the form of phytohormones or other systemic long-distance signals. The integration of these systemic and local signals then determines cell division or elongation rates in primary and lateral roots, the initiation, emergence, or elongation of lateral roots, as well as the formation of root hairs. Here, we review the cascades of nutrient-related sensing and signaling events that involve hormones and highlight nutrient-hormone relations that coordinate root developmental plasticity in plants.

Role of Auxin and Nitrate Signaling in the Development of Root System Architecture

The plant root is an important storage organ that stores indole-3-acetic acid (IAA) from the apical meristem, as well as nitrogen, which is obtained from the external environment. IAA and nitrogen act as signaling molecules that promote root growth to obtain further resources. Fluctuations in the distribution of nitrogen in the soil environment induce plants to develop a set of strategies that effectively improve nitrogen use efficiency. Auxin integrates the information regarding the nitrate status inside and outside the plant body to reasonably distribute resources and sustainably construct the plant root system. In this review, we focus on the main factors involved in the process of nitrate- and auxin-mediated regulation of root structure to better understand how the root system integrates the internal and external information and how this information is utilized to modify the root system architecture.

MtNPF6.5 mediates chloride uptake and nitrate preference in Medicago roots

The preference for nitrate over chloride through regulation of transporters is a fundamental feature of plant ion homeostasis. We show that Medicago truncatula MtNPF6.5, an ortholog of Arabidopsis thaliana AtNPF6.3/NRT1.1, can mediate nitrate and chloride uptake in Xenopus oocytes but is chloride selective and that its close homologue, MtNPF6.7, can transport nitrate and chloride but is nitrate selective. The MtNPF6.5 mutant showed greatly reduced chloride content relative to wild type, and MtNPF6.5 expression was repressed by high chloride, indicating a primary role for MtNPF6.5 in root chloride uptake. MtNPF6.5 and MtNPF6.7 were repressed and induced by nitrate, respectively, and these responses required the transcription factor MtNLP1. Moreover, loss of MtNLP1 prevented the rapid switch from chloride to nitrate as the main anion in nitrate-starved plants after nitrate provision, providing insight into the underlying mechanism for nitrate preference. Sequence analysis revealed three sub-types of AtNPF6.3 orthologs based on their predicted substrate-binding residues: A (chloride selective), B (nitrate selective), and C (legume specific). The absence of B-type AtNPF6.3 homologues in early diverged plant lineages suggests that they evolved from a chloride-selective MtNPF6.5-like protein.

Regulation of Nitrate (NO3) Transporters and Glutamate Synthase-Encoding Genes under Drought Stress in Arabidopsis: The Regulatory Role of AtbZIP62 Transcription Factor

Nitrogen (N) is an essential macronutrient, which contributes substantially to the growth and development of plants. In the soil, nitrate (NO₃) is the predominant form of N available to the plant and its acquisition by the plant involves several NO₃ transporters; however, the mechanism underlying their involvement in the adaptive response under abiotic stress is poorly understood. Initially, we performed an in silico analysis to identify potential binding sites for the basic leucine zipper 62 transcription factor (AtbZIP62 TF) in the promoter of the target genes, and constructed their protein–protein interaction networks. Rather than AtbZIP62, results revealed the presence of cis-regulatory elements specific to two other bZIP TFs, AtbZIP18 and 69. A recent report showed that AtbZIP62 TF negatively regulated AtbZIP18 and AtbZIP69. Therefore, we investigated the transcriptional regulation of AtNPF6.2/NRT1.4 (low-affinity NO₃ transporter), AtNPF6.3/NRT1.1 (dual-affinity NO₃ transporter), AtNRT2.1 and AtNRT2.2 (high-affinity NO₃ transporters), and AtGLU1 and AtGLU2 (both encoding glutamate synthase) in response to drought stress in Col-0. From the perspective of exploring the transcriptional interplay of the target genes with AtbZIP62 TF, we measured their expression by qPCR in the atbzip62 (lacking the AtbZIP62 gene) under the same conditions. Our recent study revealed that AtbZIP62 TF positively regulates the expression of AtPYD1 (Pyrimidine 1, a key gene of the de novo pyrimidine biosynthesis pathway know to share a common substrate with the N metabolic pathway). For this reason, we included the atpyd1-2 mutant in the study. Our findings revealed that the expression of AtNPF6.2/NRT1.4, AtNPF6.3/NRT1.1 and AtNRT2.2 was similarly regulated in atzbip62 and atpyd1-2 but differentially regulated between the mutant lines and Col-0. Meanwhile, the expression pattern of AtNRT2.1 in atbzip62 was similar to that observed in Col-0 but was suppressed in atpyd1-2. The breakthrough is that AtNRT2.2 had the highest expression level in Col-0, while being suppressed in atbzip62 and atpyd1-2. Furthermore, the transcript accumulation of AtGLU1 and AtGLU2 showed differential regulation patterns between Col-0 and atbzip62, and atpyd1-2. Therefore, results suggest that of all tested NO₃ transporters, AtNRT2.2 is thought to play a preponderant role in contributing to NO₃ transport events under the regulatory influence of AtbZIP62 TF in response to drought stress.

Posttranslational Modifications: Regulation of Nitrogen Utilization and Signaling

Nitrogen is the most important macroelement required for the composition of key molecules, such as nucleic acids, proteins and other organic compounds. As sessile organisms, plants have evolved sophisticated mechanisms to acquire nitrogen for their normal growth and development. Besides the transcriptional and translational regulation of nitrogen uptake, assimilation, remobilization and signal transduction, posttranslational modifications (PTMs) are shown to participate in these processes in plants. In addition to alterations in protein abundance, PTMs may dramatically increase the complexity of the proteome without the concomitant changes in gene transcription and have emerged as an important type of protein regulation in terms of protein function, subcellular localization and protein activity and stability. Herein, we briefly summarize recent advances on the posttranslational regulation of nitrogen uptake, assimilation, remobilization and nitrogen signaling and discuss the underlying mechanisms of PTMs as well as the signal output of such PTMs. Understanding these regulation mechanisms will provide novel insights for improving the nitrogen use efficiency of plants.

Regulation of Root Nutrient Transporters by CIPK23: 'One Kinase to Rule Them All'

Protein kinases constitute essential regulatory components in the majority of cellular processes in eukaryotic cells. The CBL-INTERACTING PROTEIN KINASE (CIPK) family of plant protein kinases functions in calcium (Ca2+)-related signaling pathways and is therefore involved in the response to a wide variety of signals in plants. By covalently linking phosphate groups to their target proteins, CIPKs regulate the activity of downstream targets, their localization, their stability and their ability to interact with other proteins. In Arabidopsis, the CIPK23 kinase has emerged as a major hub driving root responses to diverse environmental stresses, including drought, salinity and nutrient imbalances, such as potassium, nitrate and iron deficiencies, as well as ammonium, magnesium and non-iron metal toxicities. This review will chiefly report on the prominent roles of CIPK23 in the regulation of plant nutrient transporters and on the underlying molecular mechanisms. We will also discuss the different scenarios explaining how a single promiscuous kinase, such as CIPK23, may convey specific responses to a myriad of signals.

Local auxin biosynthesis acts downstream of brassinosteroids to trigger root foraging for nitrogen

Lateral roots (LRs) dominate the overall root surface of adult plants and are crucial for soil exploration and nutrient acquisition. When grown under mild nitrogen (N) deficiency, flowering plants develop longer LRs to enhance nutrient acquisition. This response is partly mediated by brassinosteroids (BR) and yet unknown mechanisms. Here, we show that local auxin biosynthesis modulates LR elongation while allelic coding variants of YUCCA8 determine the extent of elongation under N deficiency. By up-regulating the expression of YUCCA8/3/5/7 and of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) under mild N deficiency auxin accumulation increases in LR tips. We further demonstrate that N-dependent auxin biosynthesis in LRs acts epistatic to and downstream of a canonical BR signaling cascade. The uncovered BR-auxin hormonal module and its allelic variants emphasize the importance of fine-tuning hormonal crosstalk to boost adaptive root responses to N availability and offer a path to improve soil exploration by expanded root systems in plants.

Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing

In plants, nitrate acts not only as a signaling molecule that affects plant development but also as a nutrient. The development of plant roots, which directly absorb nutrients, is greatly affected by nitrate supply. Alternative gene splicing plays a crucial role in the plant stress response by increasing transcriptome diversity. The effects of nitrate supply on alternative splicing (AS), however, have not been investigated in soybean roots. We used high-quality high-throughput RNA-sequencing data to investigate genome-wide AS events in soybean roots in response to various levels of nitrate supply. In total, we identified 355 nitrate-responsive AS events between optimal and high nitrate levels (NH), 335 nitrate-responsive AS events between optimal and low nitrate levels (NL), and 588 nitrate-responsive AS events between low and high nitrate levels (NLH). RI and A3SS were the most common AS types; in particular, they accounted for 67% of all AS events under all conditions. This increased complex and diversity of AS events regulation might be associated with the soybean response to nitrate. Functional ontology enrichment analysis suggested that the differentially splicing genes were associated with several pathways, including spliceosome, base excision repair, mRNA surveillance pathway and so on. Finally, we validated several AS events using reverse transcription-polymerase chain reaction to confirm our RNA-seq results. In summary, we characterized the features and patterns of genome-wide AS in the soybean root exposed to different nitrate levels, and our results revealed that AS is an important mechanism of nitrate-response regulation in the soybean root.

Genetic variation of BnaA3.NIP5;1 expressing in the lateral root cap contributes to boron deficiency tolerance in Brassica napus

Boron (B) is essential for vascular plants. Rapeseed (Brassica napus) is the second leading crop source for vegetable oil worldwide, but its production is critically dependent on B supplies. BnaA3.NIP5;1 was identified as a B-efficient candidate gene in B. napus in our previous QTL fine mapping. However, the molecular mechanism through which this gene improves low-B tolerance remains elusive. Here, we report genetic variation in BnaA3.NIP5;1 gene, which encodes a boric acid channel, is a key determinant of low-B tolerance in B. napus. Transgenic lines with increased BnaA3.NIP5;1 expression exhibited improved low-B tolerance in both the seedling and maturity stages. BnaA3.NIP5;1 is preferentially polar-localized in the distal plasma membrane of lateral root cap (LRC) cells and transports B into the root tips to promote root growth under B-deficiency conditions. Further analysis revealed that a CTTTC tandem repeat in the 5'UTR of BnaA3.NIP5;1 altered the expression level of the gene, which is tightly associated with plant growth and seed yield. Field tests with natural populations and near-isogenic lines (NILs) confirmed that the varieties carried BnaA3.NIP5;1Q allele significantly improved seed yield. Taken together, our results provide novel insights into the low-B tolerance of B. napus, and the elite allele of BnaA3.NIP5;1 could serve as a direct target for breeding low-B-tolerant cultivars.

Nitrate Modulates Lateral Root Formation by Regulating the Auxin Response and Transport in Rice

Nitrate (NO3-) plays a pivotal role in stimulating lateral root (LR) formation and growth in plants. However, the role of NO3- in modulating rice LR formation and the signalling pathways involved in this process remain unclear. Phenotypic and genetic analyses of rice were used to explore the role of strigolactones (SLs) and auxin in NO3--modulated LR formation in rice. Compared with ammonium (NH4+), NO3- stimulated LR initiation due to higher short-term root IAA levels. However, this stimulation vanished after 7 d, and the LR density was reduced, in parallel with the auxin levels. Application of the exogenous auxin α-naphthylacetic acid to NH4+-treated rice plants promoted LR initiation to levels similar to those under NO3- at 7 d; conversely, the application of the SL analogue GR24 to NH4+-treated rice inhibited LR initiation to levels similar to those under NO3- supply by reducing the root auxin levels at 10 d. D10 and D14 mutations caused loss of sensitivity of the LR formation response to NO3-. The application of NO3- and GR24 downregulated the transcription of PIN-FORMED 2(PIN2), an auxin efflux carrier in roots. LR number and density in pin2 mutant lines were insensitive to NO3- treatment. These results indicate that NO3- modulates LR formation by affecting the auxin response and transport in rice, with the involvement of SLs.

A transceptor-channel complex couples nitrate sensing to calcium signaling in Arabidopsis

Nitrate-induced Ca²⁺ signaling is crucial for the primary nitrate response in plants. However, the molecular mechanism underlying the generation of the nitrate-specific calcium signature remains unknown. We report here that a cyclic nucleotide-gated channel (CNGC) protein, CNGC15, and the nitrate transceptor (NRT1.1) constitute a molecular switch that controls calcium influx depending on nitrate levels. The expression of CNGC15 is induced by nitrate, and its protein is localized at the plasma membrane after establishment of young seedlings. We found that disruption of CNGC15 results in the loss of the nitrate-induced Ca²⁺ signature (primary nitrate response) and retards root growth, reminiscent of the phenotype observed in the nrt1.1 mutant. We further showed that CNGC15 is an active Ca²⁺-permeable channel that physically interacts with the NRT1.1 protein in the plasma membrane. Importantly, we discovered that CNGC15-NRT1.1 interaction silences the channel activity of the heterocomplex, which dissociates upon a rise in nitrate levels, leading to reactivation of the CNGC15 channel. The dynamic interactions between CNGC15 and NRT1.1 therefore control the channel activity and Ca²⁺ influx in a nitrate-dependent manner. Our study reveals a new nutrient-sensing mechanism that utilizes a nutrient transceptor-channel complex assembly to couple nutrient status to a specific Ca²⁺ signature.

Optimal NH4 + /NO3 - ratios enhance the shade tolerance of soybean seedlings under low light conditions

In the maize-soybean intercropping system, shade is the major chronic restraint that affects normal growth of soybean. Different spatial patterns of this system affect the microclimate of soybean through shading from maize plants. However, the negative impacts of shading stress can be mitigated by providing optimal ratios of different fertilizers. Therefore, to test this hypothesis, soybean plants were grown under different light conditions (normal light or shade) to evaluate the response to varying NH4 + /NO3 - ratios. Seeds of soybean (Glycine max L. cv. Nan-99-6) were grown in nutrient solution with a total concentration of 5 mM N using different NH4 + /NO3 - ratios (T0  = 0:0, T1  = 0:100, T2  = 25:75, T3  = 50:50 and T4  = 75:25) for 40 days in a greenhouse at PPFD 320.95 μmol m-2  s-1 (low light) or 967.53 μmol m-2  s-1 (normal light). Under low light, growth and photosynthesis of soybean seedlings significantly decreased as compared to normal light conditions. However, the optimal ratios of NH4 + / NO3 - improved growth and photosynthesis of soybean seedlings under both light conditions. Our results indicated that soybean seedlings supplied with optimal NH4 + /NO3 - ratios (25:75 and 50:50) have maximum biomass yield, chlorophyll pigments, leaf gas exchange, photochemical activity and root growth as compared to low and high NH4 + /NO3 - ratios (T1 and T4 ). High ratios of NH4 + /NO3 - (T4 ) resulted in reduced plant growth due to nutrient accumulation in plant tissues; therefore, we suggest that optimal ratios of NH4 + /NO3 - (T2 and T3 ) can enhance the shade tolerance of soybean seedlings.

HBI1-TCP20 interaction positively regulates the CEPs-mediated systemic nitrate acquisition

Nitrate is the main source of nitrogen for plants but often distributed heterogeneously in soil. Plants have evolved sophisticated strategies to achieve adequate nitrate by modulating the root system architecture. The nitrate acquisition system is triggered by the short mobile peptides C-TERMINALLY ENCODED PEPTIDES (CEPs) that are synthesized on the nitrate-starved roots, but induce the expression of nitrate transporters on the other nitrate-rich roots through an unclear signal transduction pathway. Here, we demonstrate that the transcription factors HBI1 and TCP20 play important roles in plant growth and development in response to fluctuating nitrate supply. HBI1 physically interacts with TCP20, and this interaction was enhanced by the nitrate starvation. HBI1 and TCP20 directly bind to the promoters of CEPs and cooperatively induce their expression. Mutation in HBIs and/or TCP20 resulted in impaired systemic nitrate acquisition response. Our solid genetic and molecular evidence strongly indicate that the HBI1-TCP20 module positively regulates the CEPs-mediated systemic nitrate acquisition.

SPL14/17 act downstream of strigolactone signalling to modulate rice root elongation in response to nitrate supply

Nitrogen (N) is an essential major nutrient for food crops. Although ammonium (NH₄⁺ ) is the primary N source of rice (Oryza sativa), nitrate (NO₃^- ) can also be absorbed and utilized. Rice responds to NO₃^- application by altering its root morphology, such as root elongation. Strigolactones (SLs) are important modulators of root length. However, the roles of SLs and their downstream genes in NO₃^- -induced root elongation remain unclear. Here, the levels of total N and SL (4-deoxyorobanchol) and the responses of seminal root (SR) lengths to NH₄⁺ and NO₃^- were investigated in rice plants. NO₃^- promoted SR elongation, possibly due to short-term signal perception and long-term nutrient function. Compared with NH₄⁺ conditions, higher SL signalling/levels and less D53 protein were recorded in roots of NO₃^- -treated rice plants. In contrast to wild-type plants, SR lengths of d mutants were less responsive to NO₃^- conditions, and application of rac-GR24 (SL analogue) restored SR length in d10 (SL biosynthesis mutant) but not in d3, d14, and d53 (SL-responsive mutants), suggesting that higher SL signalling/levels participate in NO₃^- -induced root elongation. D53 interacted with SPL17 and inhibited SPL17-mediated transactivation from the PIN1b promoter. Mutation of SPL14/17 and PIN1b caused insensitivity of the root elongation response to NO₃^- and rac-GR24 applications. Therefore, we conclude that perception of SLs by D14 leads to degradation of D53 via the proteasome system, which releases the suppression of SPL14/17-modulated transcription of PIN1b, resulting in root elongation under NO₃^- supply.

Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective

Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H⁺-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.

NIN-like protein 7 promotes nitrate-mediated lateral root development by activating transcription of TRYPTOPHAN AMINOTRANSFERASE RELATED 2

Nitrate is essential for plant growth and development. When nitrate availability is low, plants produce more lateral roots (LRs) to seek nitrate from the soil. In this study, by DNA electrophoretic mobility shift and luciferase assays, it was showed that NIN-like protein 7 (NLP7) transcription factor activated expression of TAR2 by directly binding to its promoter. Finally, through genetic analysis, it was speculated that NLP7 regulated LR development through TAR2. In conclusion, NLP7 binds to the TAR2 promoter and activates TAR2 expression, thereby promoting nitrate-dependent LR development.

Modulation of plant root traits by nitrogen and phosphate: transporters, long-distance signaling proteins and peptides, and potential artificial traps

As sessile organisms, plants rely on their roots for anchorage and uptake of water and nutrients. Plant root is an organ showing extensive morphological and metabolic plasticity in response to diverse environmental stimuli including nitrogen (N) and phosphorus (P) nutrition/stresses. N and P are two essential macronutrients serving as not only cell structural components but also local and systemic signals triggering root acclimatory responses. Here, we mainly focused on the current advances on root responses to N and P nutrition/stresses regarding transporters as well as long-distance mobile proteins and peptides, which largely represent local and systemic regulators, respectively. Moreover, we exemplified some of the potential pitfalls in experimental design, which has been routinely adopted for decades. These commonly accepted methods may help researchers gain fundamental mechanistic insights into plant intrinsic responses, yet the output might lack strong relevance to the real situation in the context of natural and agricultural ecosystems. On this basis, we further discuss the established-and yet to be validated-improvements in experimental design, aiming at interpreting the data obtained under laboratory conditions in a more practical view.

Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport

Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate-dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.

Improved Plant Nitrate Status Involves in Flowering Induction by Extended Photoperiod

The floral transition stage is pivotal for sustaining plant populations and is affected by several environmental factors, including photoperiod. However, the mechanisms underlying photoperiodic flowering responses are not fully understood. Herein, we have shown that exposure to an extended photoperiod effectively induced early flowering in Arabidopsis plants, at a range of different nitrate concentrations. However, these photoperiodic flowering responses were attenuated when the nitrate levels were suboptimal for flowering. An extended photoperiod also improved the root nitrate uptake of by NITRATE TRANSPORTER 1.1 (NRT1.1) and NITRATE TRANSPORTER 2.1 (NRT2.1), whereas the loss of function of NRT1.1/NRT2.1 in the nrt1.1-1/2.1-2 mutants suppressed the expression of the key flowering genes CONSTANS (CO) and FLOWERING LOCUS T (FT), and reduced the sensitivity of the photoperiodic flowering responses to elevated levels of nitrate. These results suggest that the upregulation of root nitrate uptake during extended photoperiods, contributed to the observed early flowering. The results also showed that the sensitivity of photoperiodic flowering responses to elevated levels of nitrate, were also reduced by either the replacement of nitrate with its assimilation intermediate product, ammonium, or by the dysfunction of the nitrate assimilation pathway. This indicates that nitrate serves as both a nutrient source for plant growth and as a signaling molecule for floral induction during extended photoperiods.

Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review

Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.

Transcriptional regulators of nitrate metabolism: Key players in improving nitrogen use in crops

Green revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO₃^-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.

Ectopic expression of a grape nitrate transporter VvNPF6.5 improves nitrate content and nitrogen use efficiency in Arabidopsis

BACKGROUND

Nitrate plays an important role in grapevines vegetative and reproductive development. However, how grapevines uptake, translocate and utilize nitrate and the molecular mechanism still remains to be investigated.

RESULTS

In this study, we report the functional characterization of VvNPF6.5, a member of nitrate transporter 1/peptide transporter family (NRT1/PTR/NPF) in Vitis vinifera. Subcellular localization in Arabidopsis protoplasts indicated that VvNPF6.5 is plasma membrane localized. Quantitative RT-PCR analysis indicated that VvNPF6.5 is expressed predominantly in roots and stems and its expression is rapidly induced by nitrate. Functional characterization using cRNA-injected Xenopus laevis oocytes showed that VvNPF6.5 uptake nitrate in a pH dependent way and function as a dual-affinity nitrate transporter involved in both high- and low-affinity nitrate uptake. Further ectopic expression of VvNPF6.5 in Arabidopsis resulted in more ¹⁵NO₃^- accumulation in shoots and roots and significantly improved nitrogen use efficiency (NUE). Moreover, VvNPF6.5 might participate in the nitrate signaling by positively regulating the expression of primary nitrate response genes.

CONCLUSION

Our results suggested that VvNPF6.5 encodes a pH-dependent, dual-affinity nitrate transporter. VvNPF6.5 regulates nitrate uptake and allocation in grapevines and is involved in primary nitrate response.

The K+ and NO3 - Interaction Mediated by NITRATE TRANSPORTER1.1 Ensures Better Plant Growth under K+-Limiting Conditions

K⁺ and NO₃ ^- are the major forms of potassium and nitrogen that are absorbed by the roots of most terrestrial plants. In this study, we observed that a close relationship between NO₃ ^- and K⁺ in Arabidopsis (Arabidopsis thaliana) is mediated by NITRATE TRANSPORTER1.1 (NRT1.1). The nrt1.1 knockout mutants showed disturbed K⁺ uptake and root-to-shoot allocation, and were characterized by growth arrest under K⁺-limiting conditions. The K⁺ uptake and root-to-shoot allocation of these mutants were partially recovered by expressing NRT1.1 in the root epidermis-cortex and central vasculature using SULFATE TRANSPORTER1;2 and PHOSPHATE1 promoters, respectively. Two-way analysis of variance based on the K⁺ contents in nrt1.1-1/K ⁺ transporter1, nrt1.1-1/high-affinity K ⁺ transporter5-3, nrt1.1-1/K ⁺ uptake permease7, and nrt1.1-1/stelar K ⁺ outward rectifier-2 double mutants and the corresponding single mutants and wild-type plants revealed physiological interactions between NRT1.1 and K⁺ channels/transporters located in the root epidermis-cortex and central vasculature. Further study revealed that these K⁺ uptake-related interactions are dependent on an H⁺-consuming mechanism associated with the H⁺/NO₃ ^- symport mediated by NRT1.1. Collectively, these data indicate that patterns of NRT1.1 expression in the root epidermis-cortex and central vasculature are coordinated with K⁺ channels/transporters to improve K⁺ uptake and root-to-shoot allocation, respectively, which in turn ensures better growth under K⁺-limiting conditions.

NITROGEN RESPONSE DEFICIENCY 1-mediated CHL1 induction contributes to optimized growth performance during altered nitrate availability in Arabidopsis

Plants cannot fix nitrogen directly; they must absorb it from the soil through their roots, or in rare cases, form associations with nitrogen-fixing bacteria. The efficiency of nitrogen use in most domesticated crops is low, and more than half of the available nitrogen in the soil can leach into the environment. Understanding the nitrogen signaling pathways is essential for maximizing the efficiency of nitrogen use in crops. In the present study, we characterized the Myeloblastosis (Myb)-like gene NITROGEN RESPONSE DEFICIENCY 1 (NID1). We observed that the growth performance of nid1 knockout (KO) mutant Arabidopsis plants was better than that of wild-type Col-0 plants under very low-nitrate conditions, leading to improved growth performance in the nid1 KO plants. The results of chromatin immunoprecipitation and electrophoretic mobility shift assays indicated that NID1 binds to the promoter of the NITRATE TRANSPORTER (NRT)1.1 gene. Furthermore, nid1 KO plants exhibited similar growth performance to the nid1 KO/chl1-5 (nrt1.1 KO) double mutant and chl1-5 (nrt1.1 KO) plants in response to low-nitrate conditions. We suggest that NID1 plays a crucial role as a transcription factor in optimizing plant growth by modulating the transcript abundance of the nitrate transceptor CHL1, leading to enhanced ABA accumulation in low-nitrate conditions.

The Arabidopsis NRT1/PTR FAMILY protein NPF7.3/NRT1.5 is an indole-3-butyric acid transporter involved in root gravitropism

Active membrane transport of plant hormones and their related compounds is an essential process that determines the distribution of the compounds within plant tissues and, hence, regulates various physiological events. Here, we report that the Arabidopsis NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY 7.3 (NPF7.3) protein functions as a transporter of indole-3-butyric acid (IBA), a precursor of the major endogenous auxin indole-3-acetic acid (IAA). When expressed in yeast, NPF7.3 mediated cellular IBA uptake. Loss-of-function npf7.3 mutants showed defective root gravitropism with reduced IBA levels and auxin responses. Nevertheless, the phenotype was restored by exogenous application of IAA but not by IBA treatment. NPF7.3 was expressed in pericycle cells and the root tip region including root cap cells of primary roots where the IBA-to-IAA conversion occurs. Our findings indicate that NPF7.3-mediated IBA uptake into specific cells is required for the generation of appropriate auxin gradients within root tissues.

Transcriptomic analysis of seed germination improvement of Andrographis paniculata responding to air plasma treatment

The plasma seed treatment is effective for promoting seed germination in many crops. However, the biological mechanism remains unclear. Therefore, mRNA sequencing was used to screen differentially expressed genes in the germination process of Andrographis paniculata seeds treated with air plasma (power density = 8.99 J/cm³). Following plasma treatment, the germination percentages were significantly higher than those of the control, they were 3.5±0.6% vs. 0 at 28 hours after sowing (HAS) and 50.3±2.6% vs. 37.3±1.7% at 48 HAS. After unigenes were assembled and annotated, 125 differentially expressed genes (DEGs) were detected at 28 HAS, compared with nine DEGs at 48 HAS, but no DEGs were detected at 0 HAS, indicating that air plasma treatment mainly changed the gene expression of A. paniculata seeds at 28 HAS. The NCED5 expression level of the treated group was less than one-fifth of the control, and the expressions of three ethylene response factors were significantly higher than the control at 28 HAS, indicating that lower abscisic acid levels play an important role and ethylene signal transduction also participates in radicle protrusion. ACO, NRT1 and PRP3 expressions were significantly higher than in the control at 48 HAS, suggesting that higher ethylene levels cause the endosperm cap to weaken and start to grow root hairs and lateral roots earlier. These findings reveal that plasma promotes seed germination mainly by regulating the expression of hormone-related genes. And the possible signal transduction of related hormones was discussed.

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.

Physiological characteristics and RNA sequencing in two root zones with contrasting nitrate assimilation of Populus × canescens

Different root zones have distinct capacities for nitrate (NO3-) uptake in Populus species, but the underlying physiological and microRNA (miRNA) regulatory mechanisms remain largely unknown. To address this question, two root zones of Populus × canescens (Ait.) Smith. with contrasting capacities for NO3- uptake were investigated. The region of 0-40 mm (root zone I) to the root apex displayed net influxes, whereas the region of 40-80 mm (root zone II) exhibited net effluxes. Concentrations of NO3- and ammonium (NH4+) as well as nitrate reductase activity were lower in zone II than in zone I. Forty one upregulated and twenty three downregulated miRNAs, and 576 targets of these miRNAs were identified in zone II in comparison with zone I. Particularly, growth-regulating factor 4 (GRF4), a target of upregulated ptc-miR396g-5p and ptc-miR396f_L + 1R-1, was downregulated in zone II in comparison with zone I, probably contributing to lower NO3- uptake rates and assimilation in zone II. Furthermore, several miRNAs and their targets, members of C2H2 zinc finger family and APETALA2/ethylene-responsive element binding protein family, were found in root zones, which probably play important roles in regulating NO3- uptake. These results indicate that differentially expressed miRNA-target pairs play key roles in regulation of distinct NO3- uptake rates and assimilation in different root zones of poplars.

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.

Dynamics of localised nitrogen supply and relevance for root growth of Vicia faba ('Fuego') and Hordeum vulgare ('Marthe') in soil

Root growth responds to local differences in N-form and concentration. This is known for artificial systems and assumed to be valid in soil. The purpose of this study is to challenge this assumption for soil mesocosms locally supplied with urea with and without nitrification inhibitor. Soil column experiments with Vicia faba ('Fuego') and Hordeum vulgare ('Marthe') were performed to investigate soil solution chemistry and root growth response of these two species with contrasting root architectures to the different N-supply simultaneously. Root growth was analysed over time and separately for the fertiliser layer and the areas above and below with X-ray CT (via region growing) and WinRHIZO. Additionally, NO3- and NH4+ in soil and soil solution were analysed. In Vicia faba, no pronounced differences were observed, although CT analysis indicated different root soil exploration for high NH4+. In Hordeum vulgare, high NO3- inhibited lateral root growth while high NH4+ stimulated the formation of first order laterals. The growth response to locally distributed N-forms in soil is species specific and less pronounced than in artificial systems. The combination of soil solution studies and non-invasive imaging of root growth can substantially improve the mechanistic understanding of root responses to different N-forms in soil.

ZmCCD10a Encodes a Distinct Type of Carotenoid Cleavage Dioxygenase and Enhances Plant Tolerance to Low Phosphate

Carotenoid cleavage dioxygenases (CCDs) drive carotenoid catabolism to produce various apocarotenoids and immediate derivatives with particular developmental, ecological, and agricultural importance. How CCD genes evolved with species diversification and the resulting functional novelties in cereal crops have remained largely elusive. We constructed a unified four-clade phylogenetic tree of CCDs, revealing a previously unanchored basal clade CCD10 CCD10 underwent highly dynamic duplication or loss events, even in the grass family. Different from cleavage sites of CCD8 and ZAXINONE SYNTHASE (ZAS), maize (Zea mays) ZmCCD10a cleaved differentially structured carotenoids at 5, 6 (5', 6') and 9, 10 (9', 10') positions, generating C8 (6-methyl-5-hepten-2-one) and C13 (geranylacetone, α-ionone, and β-ionone) apocarotenoids in Escherichia coli Localized in plastids, ZmCCD10a cleaved neoxanthin, violaxanthin, antheraxathin, lutein, zeaxanthin, and β-carotene in planta, corroborating functional divergence of ZmCCD10a and ZAS. ZmCCD10a expression was dramatically stimulated in maize and teosinte (Z. mays ssp. parviglumis, Z. mays ssp. huehuetenangensis, Zea luxurians, and Zea diploperennis) roots by phosphate (Pi) limitation. ZmCCD10a silencing favored phosphorus retention in the root and reduced phosphorus and biomass accumulation in the shoot under low Pi. Overexpression of ZmCCD10a in Arabidopsis (Arabidopsis thaliana) enhanced plant tolerance to Pi limitation by preferential phosphorus allocation to the shoot. Thus, ZmCCD10a encodes a unique CCD facilitating plant tolerance to Pi limitation. Additionally, ZmCCD10a silencing and overexpression led to coherent alterations in expression of PHOSPHATE STARVATION RESPONSE REGULATOR 1 (PHR1) and Pi transporters, and cis-regulation of ZmCCD10a expression by ZmPHR1;1 and ZmPHR1;2 implies a probable ZmCCD10a-involved regulatory pathway that adjusts Pi allocation.

Auxin-mediated root branching is determined by the form of available nitrogen

To improve water and nutrient acquisition from the soil, plants can modulate their root system architecture. Despite the importance of changes in root architecture to exploit local nutrient patches occurring in heterogenous soils or after placed fertilization, mechanisms integrating external nutrient signals into the root developmental programme remain poorly understood. Here, we show that local ammonium supply stimulates the accumulation of shoot-derived auxin in the root vasculature and promotes lateral root emergence to build a highly branched root system. Activities of pH and auxin reporters indicate that ammonium uptake mediated by ammonium transporters acidifies the root apoplast, which increases pH-dependent import of protonated auxin into cortical and epidermal cells overlaying lateral root primordia, and subsequently promotes their emergence from the parental root. Thereby, ammonium-induced and H⁺-ATPase-mediated acidification of the apoplast allows auxin to bypass the auxin importers AUX1 and LAX3. In nitrogen-deficient plants, auxin also accumulates in the root vasculature but a more alkaline apoplast leads to retention of auxin in these tissues and prevents lateral root formation. Our study highlights the impact of externally available nitrogen forms on pH-dependent radial auxin mobility and its regulatory function in organ development.

Combined Allosteric Responses Explain the Bifurcation in Non-Linear Dynamics of 15N Root Fluxes Under Nutritional Steady-State Conditions for Nitrate

With regard to thermodynamics out of equilibrium, seedlings are open systems that dissipate energy towards their environment. Accordingly, under nutritional steady-state conditions, changes in external concentrations of one single ion provokes instability and reorganization in the metabolic and structure/architecture of the seedling that is more favorable to the fluxes of energy and matter. This reorganization is called a bifurcation and is described in mathematics as a non-linear dynamic system. In this study, we investigate the non-linear dynamics of ¹⁵N fluxes among cellular compartments of B. napus seedlings in response to a wide range of external NO 3 - 15 concentrations (from 0.05 to 20 mM): this allows to determine whether any stationary states and bifurcations could be found. The biphasic behavior of the root NO 3 - 15 uptake rate (v_in ) was explained by the combined cooperative properties between the v_app (N uptake, storage and assimilation rate) and v_out (N translocation rate) ¹⁵N fluxes that revealed a unique and stable stationary state around 0.28 mM nitrate. The disappearance of this stationary state around 0.5 mM external nitrate concentrations provokes a dramatic bifurcation in ¹⁵N flux pattern. This bifurcation in the v_in and v_out ¹⁵N fluxes fits better with the increase of BnNPF6.3/NRT1.1 expression than BnNRT2.1 nitrate transporter genes, confirming the allosteric property of the BnNPF6/NRT1.1 transporter, as reported in the literature between low and high nitrate concentrations. Moreover, several statistically significant power-law equations were found between variations in the shoots tryptophan concentrations (i.e., IAA precursor) with changes in the v_app and v_out ¹⁵N fluxes as well as a synthetic parameter of plant N status estimated from the root/shoot ratio of total free amino acids concentrations. These relationships designate IAA as one of the major biological parameters related to metabolic and structural-morphological reorganization coupled with the N and water fluxes induced by nitrate. The results seriously challenge the scientific grounds of the concept of high- and low-affinity of nitrate transporters and are therefore discussed in terms of the ecological significance and physiological implications on the basis of recent agronomic, physiological and molecular data of the literature.

NRT1.1s in plants: functions beyond nitrate transport

Arabidopsis AtNRT1.1 (CHL1/AtNPF6.3) is the first nitrate transporter identified in plants and was initially found to play a role in nitrate uptake and transport. AtNRT1.1 also displays auxin transport activity and mediates nitrate-modulated root development, suggesting that it has transport capacity for multiple substrates. Subsequent work revealed that AtNRT1.1 can respond to environmental nitrate fluctuations by altering its nitrate transport activity, modulated by phosphorylation, leading to the critical finding that AtNRT1.1 acts as a transceptor for nitrate sensing. Recent studies have revealed how OsNRT1.1B, the functional homologue of AtNRT1.1 in rice, mediates nitrate signal transduction from the plasma membrane to the nucleus, and how OsNRT1.1B integrates the nitrate and phosphate signaling networks. OsNRT1.1B has also been shown to be involved in regulating the root microbiota to facilitate organic nitrogen mineralization in soil, thus mediating plant-microbe interactions. Furthermore, the divergent functions of OsNRT1.1A and OsNRT1.1B in regulating nitrogen use in rice suggest that the function of NRT1.1 is still far from fully understood. In this review, we focus on the most recent progress on the molecular mechanisms of NRT1.1s in plants, with the aim of providing an up-to-date view of the versatile functions of NRT1.1 in nitrogen utilization in plants.

Signaling pathways underlying nitrogen-dependent changes in root system architecture: from model to crop species

Among all essential mineral elements, nitrogen (N) is required in the largest amounts and thus is often a limiting factor for plant growth. N is taken up by plant roots in the form of water-soluble nitrate, ammonium, and, depending on abundance, low-molecular weight organic N. In soils, the availability and composition of these N forms can vary over space and time, which exposes roots to various local N signals that regulate root system architecture in combination with systemic signals reflecting the N nutritional status of the shoot. Uncovering the molecular mechanisms underlying N-dependent signaling provides great potential to optimize root system architecture for the sake of higher N uptake efficiency in crop breeding. In this review, we summarize prominent signaling mechanisms and their underlying molecular players that derive from external N forms or the internal N nutritional status and modulate root development including root hair formation and gravitropism. We also compare the current state of knowledge of these pathways between Arabidopsis and graminaceous plant species.

Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging

Plants can develop root systems with distinct anatomical features and morphological plasticity to forage nutrients distributed heterogeneously in soils. Lateral root proliferation is a typical nutrient-foraging response to a local supply of nitrate, which has been investigated across many plant species. However, the underlying mechanism in maize roots remains largely unknown. Here, we report on identification of a maize truncated MIKC-type MADS-box transcription factor (ZmTMM1) lacking K- and C-domains, expressed preferentially in the lateral root branching zone and induced by the localized supply of nitrate. ZmTMM1 belongs to the AGL17-like MADS-box transcription factor family that contains orthologs of ANR1, a key regulator for root nitrate foraging in Arabidopsis. Ectopic overexpression of ZmTMM1 recovers the defective growth of lateral roots in the Arabidopsis anr1 agl21 double mutant. The local activation of glucocorticoid receptor fusion proteins for ZmTMM1 and an artificially truncated form of AtANR1 without the K- and C-domains stimulates the lateral root growth of the Arabidopsis anr1 agl21 mutant, providing evidence that ZmTMM1 encodes a functional MADS-box that modulates lateral root development. However, no phenotype was observed in ZmTMM1-RNAi transgenic maize lines, suggesting a possible genetic redundancy of ZmTMM1 with other AGL17-like genes in maize. A comparative genome analysis further suggests that a nitrate-inducible transcriptional regulation is probably conserved in both truncated and non-truncated forms of ZmTMM1-like MADS-box transcription factors found in grass species.

Integrating N signals and root growth: the role of nitrate transceptor NRT1.1 in auxin-mediated lateral root development

This article comments on: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A and Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany 71, 4480–4494.

Nitrate regulation of lateral root and root hair development in plants

Nitrogen (N) is one of the most important macronutrients for plant growth and development. However, the concentration and distribution of N varies in soil due to a variety of environmental factors. In response, higher plants have evolved a developmentally flexible root system to efficiently take up N under N-limited conditions. Over the past decade, significant progress has been made in understanding this form of plant 'root-foraging' behavior, which is controlled by both a local and a long-distance systemic nitrate signaling pathway. In this review, we focus on the key components of nitrate perception, signaling, and transduction and its role in lateral root development. We also highlight recent findings on the molecular mechanisms of the nitrate systemic signaling pathway, including small signaling peptides involved in long-distance shoot-root communication. Furthermore, we summarize the transcription factor networks responsible for nitrate-dependent lateral root and root hair development.

The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate

In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule in plant growth, development, and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). Here we show that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing the cell wall remodeling required for overlying tissue separation during LRP emergence. NRT1.1-mediated repression of both TAR2 and LAX3 is suppressed at high nitrate availability, resulting in nitrate induction of the TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously expected in regulating the nitrate response of root system architecture.

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.

The Root Foraging Response under Low Nitrogen Depends on DWARF1-Mediated Brassinosteroid Biosynthesis

Root developmental plasticity enables plants to adapt to limiting or fluctuating nutrient conditions in the soil. When grown under nitrogen (N) deficiency, plants develop a more exploratory root system by increasing primary and lateral root length. However, mechanisms underlying this so-called foraging response remain poorly understood. We performed a genome-wide association study in Arabidopsis (Arabidopsis thaliana) and we show here that noncoding variations of the brassinosteroid (BR) biosynthesis gene DWARF1 (DWF1) lead to variation of the DWF1 transcript level that contributes to natural variation of root elongation under low N. In addition to DWF1, other central BR biosynthesis genes upregulated under low N include CONSTITUTIVE PHOTOMORPHOGENIC DWARF, DWF4, and BRASSINOSTEROID-6-OXIDASE 2 Phenotypic characterization of knockout and knockdown mutants of these genes showed significant reduction of their root elongation response to low N, suggesting a systemic stimulation of BR biosynthesis to promote root elongation. Moreover, we show that low N-induced root elongation is associated with aboveground N content and that overexpression of DWF1 significantly improves plant growth and overall N accumulation. Our study reveals that mild N deficiency induces key genes in BR biosynthesis and that natural variation in BR synthesis contributes to the root foraging response, complementing the impact of enhanced BR signaling observed recently. Furthermore, these results suggest a considerable potential of BR biosynthesis to genetically engineer plants with improved N uptake.

Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana

Root system architecture (RSA) is required for the acquisition of water and mineral nutrients from the soil. One of the essential nutrients, nitrate (NO₃⁻), is sensed and transported by nitrate transporters NRT1.1 and NRT2.1 in the plants. Nitrate transporter 1.1 (NRT1.1) is a dual-affinity nitrate transporter phosphorylated at the T101 residue by calcineurin B-like interacting protein kinase (CIPKs); it also regulates the expression of other key nitrate assimilatory genes. The differential phosphorylation (phosphorylation and dephosphorylation) strategies and underlying Ca²⁺ signaling mechanism of NRT1.1 stimulate lateral root growth by activating the auxin transport activity and Ca²⁺-ANR1 signaling at the plasma membrane and the endosomes, respectively. NO₃⁻ additionally functions as a signal molecule that forms a signaling system, which consists of a vast array of transcription factors that control root system architecture that either stimulate or inhibit lateral and primary root development in response to localized and high nitrate (NO₃⁻), respectively. This review elucidates the so-far identified nitrate transporters, nitrate sensing, signal transduction, and the key roles of nitrate transporters and its downstream transcriptional regulatory network in the primary and lateral root development in Arabidopsis thaliana under stress conditions.

Towards understanding the hierarchical nitrogen signalling network in plants

Nitrogen (N) is the most abundant mineral elements in plants, and the application of inorganic N fertilizer makes huge contribution to the crop production and global food security. However, low N use efficiency (NUE) and overapplication of N fertilizers causes ever-growing environmental problems. Understanding the molecular mechanisms of N sensing and signalling in plants will provide molecular basis for NUE improvement of crops. Forward genetics screening and functional analysis have characterized the NRT1.1-NLP centered N signalling pathway at the cellular level. With the incorporation of systems biology approaches, a preliminary N regulatory network has been delineated. Meanwhile, long-distance N signalling has also been unveiled at the whole plant level. This review highlights most recent understanding of the N signalling network in plants, and also discusses how to further integrate hierarchical regulation of N signalling in plants.

Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

Nitrate (NO3-) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO3-) supply tends to promote auxin translocation from shoots to roots and vice-versa. This nitrate mediated auxin biosynthesis regulating lateral roots growth is induced by the nitrate transporters and its downstream transcription factors. Most nitrate responsive genes (short-term and long-term) are involved in signalling overlap between nitrate and auxin, thereby inducing lateral roots initiation, emergence, and development. Moreover, in the auxin signalling pathway, the varying nitrate supply regulates lateral roots development by modulating the auxin accumulation in the roots. Here, we focus on the roles of nitrate responsive genes in mediating auxin biosynthesis in Arabidopsis root, and the mechanism involved in the transport of auxin at different nitrate levels. In addition, this review also provides an insight into the significance of nitrate responsive regulatory module and their downstream transcription factors in root system architecture in the model plant Arabidopsis thaliana.

Growth and nitrogen metabolism are associated with nitrogen-use efficiency in cotton genotypes

Crops, including cotton, are sensitive to nitrogen (N) and excessive use can lead to an increase in production costs and environmental problems. We hypothesized that the use of cotton genotypes with substantial root systems and high genetic potentials for nitrogen-use efficiency (NUE) would best address these problems. Therefore, the interspecific variations and traits contributing to NUE in six cotton genotypes having contrasting NUEs were studied in response to various nitrate concentrations. Large genotypic variations were observed in morphophysiological and biochemical traits, especially shoot dry weight, root traits, and N-assimilating enzyme levels. The roots of all the cotton genotypes were more sensitive to low-than high-nitrate concentrations, and the genotype CCRI-69 had the largest root system irrespective of the nitrate concentration. The root morphological traits were positively correlated with N-utilization efficiency and were more affected by genotype than nitrate concentration. Conversely, growth and N-assimilating enzyme levels were more affected by nitrate concentration and were positively correlated with N-uptake efficiency. Based on shoot dry weight, CCRI-69 and XLZ-30 were identified as N-efficient and N-inefficient genotypes, respectively, and these results were confirmed by their contrasting root systems, N metabolism, and NUEs. In the future, multi-omics techniques will be performed to identify key genes/pathways involved in N metabolism, which may have the potential to improve root architecture and increase NUE.

Zn stress facilitates nitrate transporter 1.1-mediated nitrate uptake aggravating Zn accumulation in Arabidopsis plants

Describing the mechanisms of zinc (Zn) accumulation in plants is essential to counteract the effects of excessive Zn uptake in crops grown in contaminated soils. Increasing evidence suggests that there is a positive correlation between nitrate supply and Zn accumulation in plants. However, the role of the primary nitrate transporter NRT1.1 in Zn accumulation in plants remains unknown. In this study, a Zn stress-induced increase in nitrate uptake and an increase in NRT1.1 protein levels in wild-type (Col-0) Arabidopsis plants were measured using microelectrode ion flux and green fluorescent protein (GFP)/β-glucuronidase (GUS) staining, respectively. Both agar and hydroponic cultures showed that mutants lacking the NRT1.1 function in nrt1.1 and chl1-5 (chlorate resistant 1) exhibited lower Zn levels in the roots and shoots of Zn-stressed plants than the wild-type. A lack of NRT1.1 activity also alleviated Zn-induced photosynthetic damage and growth inhibition in plants. Further, we used a rotation system with synchronous or asynchronous uptakes of nitrate and Zn to demonstrate differences in Zn levels between the Col-0 and nrt1.1/chl1-5 mutants. Significantly lower difference in Zn levels were noted in the nitrate/Zn asynchronous treatment than in the nitrate/Zn synchronous treatment. From these results, it can be concluded that NRT1.1 modulates Zn accumulation in plants via a nitrate-dependent pathway.

Untangling the molecular mechanisms and functions of nitrate to improve nitrogen use efficiency

A huge amount of nitrogenous fertilizer is used to increase crop production. This leads to an increase in the cost of production, and to human and environmental problems. It is therefore necessary to improve nitrogen use efficiency (NUE) and to design agronomic, biotechnological and breeding strategies for better fertilizer use. Nitrogen use efficiency relies primarily on how plants extract, uptake, transport, assimilate, and remobilize nitrogen. Many plants use nitrate as a preferred nitrogen source. It acts as a signaling molecule in the various important physiological processes required for growth and development. As nitrate is the main source of nitrogen in the soil, root nitrate transporters are important subjects for study. The latest reports have also discussed how nitrate transporter and assimilation genes can be used as molecular tools to improve NUE in crops. The purpose of this review is to describe the mechanisms and functions of nitrate as a specific factor that can be addressed to increase NUE. Improving factors such as nitrate uptake, transport, assimilation, and remobilization through activation by signaling, sensing, and regulatory processes will improve plant growth and NUE. © 2019 Society of Chemical Industry.

Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots

Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.