Long-distance nitrate signaling displays cytokinin dependent and independent branches

TaLBD41 interacts with TaNAC2 to regulate nitrogen uptake and metabolism in response to nitrate availability

Nitrate is the main source of nitrogen (N) available to plants and also is a signal that triggers complex regulation of transcriptional networks to modulate a wide variety of physiological and developmental responses in plants. How plants adapt to soil nitrate fluctuations is a complex process involving a fine-tuned response to nitrate provision and N starvation, the molecular mechanisms of which remain largely uncharted. Here, we report that the wheat transcription factor TaLBD41 interacts with the nitrate-inducible transcription factor TaNAC2 and is repressed by nitrate provision. Electrophoretic mobility shift assay and dual-luciferase system show that the TaLBD41-NAC2 interaction confers homeostatic coordination of nitrate uptake, reduction, and assimilation by competitively binding to TaNRT2.1, TaNR1.2, and TaNADH-GOGAT. Knockdown of TaLBD41 expression enhances N uptake and assimilation, increases spike number, grain yield, and nitrogen harvest index under different N supply conditions. We also identified an elite haplotype of TaLBD41-2B associated with increased spike number and grain yield. Our study uncovers a novel mechanism underlying the interaction between two transcription factors in mediating wheat adaptation to nitrate availability by antagonistically regulating nitrate uptake and assimilation, providing a potential target for designing varieties with efficient N use in wheat (Triticum aestivum).

Function of hormone signaling in regulating nitrogen-use efficiency in plants

Nitrogen (N) is one of the most important nutrients for crop plant performance, however, the excessive application of nitrogenous fertilizers in agriculture significantly increases production costs and causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N-use efficiency (NUE) with the aim of developing new crop varieties that combine high yields with improved NUE is an urgent goal for achieving more sustainable agriculture. Plant NUE is a complex trait that is affected by multiple factors, of which hormones are known to play pivotal roles. In this review, we focus on the interaction between the biosynthesis and signaling pathways of plant hormones with N metabolism, and summarize recent studies on the interplay between hormones and N, including how N regulates multiple hormone biosynthesis, transport and signaling and how hormones modulate root system architecture (RSA) in response to external N sources. Finally, we explore potential strategies for promoting crop NUE by modulating hormone synthesis, transport and signaling. This provides insights for future breeding of N-efficient crop varieties and the advancement of sustainable agriculture.

Nitrate, Auxin and Cytokinin-A Trio to Tango

Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.

Auxin efflux carrier ZmPIN1a modulates auxin reallocation involved in nitrate-mediated root formation

BACKGROUND

Auxin plays a crucial role in nitrate (NO₃^-)-mediated root architecture, and it is still unclear that if NO₃^- supply modulates auxin reallocation for regulating root formation in maize (Zea mays L.). This study was conducted to investigate the role of auxin efflux carrier ZmPIN1a in the root formation in response to NO₃^- supply.

RESULTS

Low NO₃^- (LN) promoted primary root (PR) elongation, while repressed the development of lateral root primordia (LRP) and total root length. LN modulated auxin levels and polar transport and regulated the expression of auxin-responsive and -signaling genes in roots. Moreover, LN up-regulated the expression level of ZmPIN1a, and overexpression of ZmPIN1a enhanced IAA efflux and accumulation in PR tip, while repressed IAA accumulation in LRP initiation zone, which consequently induced LN-mediated PR elongation and LR inhibition. The inhibition rate of PR length, LRP density and number of ZmPIN1a-OE plants was higher than that of wild-type plants after auxin transport inhibitor NPA treatment under NN and LN conditions, and the degree of inhibition of root growth in ZmPIN1a-OE plants was more obvious under LN condition.

CONCLUSION

These findings suggest that ZmPIN1a was involved in modulating auxin levels and transport to alter NO₃^--mediated root formation in maize.

Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops

Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.

Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses

Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.

Systemic Regulation of Iron Acquisition by Arabidopsis in Environments with Heterogeneous Iron Distributions

Nutrient distribution within the soil is generally heterogeneous. Plants, therefore, have evolved sophisticated systemic processes enabling them to optimize their nutrient acquisition efficiency. By organ-to-organ communication in Arabidopsis thaliana, for instance, iron (Fe) starvation in one part of a root drives the upregulation of a high-affinity Fe-uptake system in other root regions surrounded by sufficient levels of Fe. This compensatory response through Fe-starvation-triggered organ-to-organ communication includes the upregulation of Iron-regulated transporter 1 (IRT1) gene expression on the Fe-sufficient side of the root; however, the molecular basis underlying this long-distance signaling remains unclear. Here, we analyzed gene expression by RNA-seq analysis of Fe-starved split-root cultures. Genome-wide expression analysis showed that localized Fe depletion in roots upregulated several genes involved in Fe uptake and signaling, such as IRT1, in a distant part of the root exposed to Fe-sufficient conditions. This result indicates that long-distance signaling for Fe demand alters the expression of a subset of genes responsible for Fe uptake and coumarin biosynthesis to maintain a level of Fe acquisition sufficient for the entire plant. Loss of IRON MAN/FE-UPTAKE-INDUCING PEPTIDE (IMA/FEP) leads to the disruption of compensatory upregulation of IRT1 in the root surrounded by sufficient Fe. In addition, our split-root culture-based analysis provides evidence that the IMA3/FEP1-MYB10/72 pathway mediates long-distance signaling in Fe homeostasis through the regulation of coumarin biosynthesis. These data suggest that the signaling of IMA/FEP, a ubiquitous family of metal-binding peptides, is critical for organ-to-organ communication in response to Fe starvation under heterogeneous Fe conditions in the surrounding environment.

Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture

Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.

GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways

Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.

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.

The fast and the furious: rapid long-range signaling in plants

Plants possess a systemic signaling system whereby local stimuli can lead to rapid, plant-wide responses. In addition to the redistribution of chemical messengers that range from RNAs and peptides to hormones and metabolites, a communication system acting through the transmission of electrical, Ca2+, reactive oxygen species and potentially even hydraulic signals has also been discovered. This latter system can propagate signals across many cells each second and researchers are now beginning to uncover the molecular machineries behind this rapid communications network. Thus, elements such as the reactive oxygen species producing NAPDH oxidases and ion channels of the two pore channel, glutamate receptor-like and cyclic nucleotide gated families are all required for the rapid propagation of these signals. Upon arrival at their distant targets, these changes trigger responses ranging from the production of hormones, to changes in the levels of primary metabolites and shifts in patterns of gene expression. These systemic responses occur within seconds to minutes of perception of the initial, local signal, allowing for the rapid deployment of plant-wide responses. For example, an insect starting to chew on just a single leaf triggers preemptive antiherbivore defenses throughout the plant well before it has a chance to move on to the next leaf on its menu.

Nitrogen Systemic Signaling: From Symbiotic Nodulation to Root Acquisition

Plant nutrient acquisition is tightly regulated by resource availability and metabolic needs, implying the existence of communication between roots and shoots to ensure their integration at the whole-plant level. Here, we focus on systemic signaling pathways controlling nitrogen (N) nutrition, achieved both by the root import of mineral N and, in legume plants, through atmospheric N fixation by symbiotic bacteria inside dedicated root nodules. We explore features conserved between systemic pathways repressing or enhancing symbiotic N fixation and the regulation of mineral N acquisition by roots, as well as their integration with other environmental factors, such as phosphate, light, and CO₂ availability.

Role of transporters in plant disease resistance

Plants being sessile have evolved numerous mechanisms to meet the changing environmental and growth conditions. Plant pathogens are responsible for devastating disease epidemics in many species. Transporter proteins are an integral part of plant growth and development, and several studies have documented their role in pathogen disease resistance. In this review, we analyze the studies on genome-wide identifications of plant transporters like sugars will eventually be exported transporters (SWEET), multidrug and toxic compound extrusion (MATE) transporters, ATP-binding cassette (ABC) transporters, natural resistance-associated macrophage proteins (NRAMP), and sugar transport proteins (STPs), all having a significant role in plant disease resistance. The mechanism of action of these transporters, their solute specificity, and the potential application of recent molecular biology approaches deploying these transporters for the development of disease-resistant plants are also discussed. The applications of genome editing tools, such as CRIPSR/Cas9, are also presented. Altogether the information included in this article gives a better understanding of the role of transporter proteins during plant-pathogen interaction.

Nitrogen Deficiency and Synergism between Continuous Light and Root Ammonium Supply Modulate Distinct but Overlapping Patterns of Phytohormone Composition in Xylem Sap of Tomato Plants

Continuous light (CL) or a predominant nitrogen supply as ammonium (NH4+) can induce leaf chlorosis and inhibit plant growth. The similarity in injuries caused by CL and NH4+ suggests involvement of overlapping mechanisms in plant responses to these conditions; however, these mechanisms are poorly understood. We addressed this topic by conducting full factorial experiments with tomato plants to investigate the effects of NO3- or NH4+ supply under diurnal light (DL) or CL. We used plants at ages of 26 and 15 days after sowing to initiate the treatments, and we modulated the intensity of the stress induced by CL and an exclusive NH4+ supply from mild to strong. Under DL, we also studied the effect of nitrogen (N) deficiency and mixed application of NO3- and NH4+. Under strong stress, CL and exclusive NH4+ supply synergistically inhibited plant growth and reduced chlorophyll content. Under mild stress, when no synergetic effect between CL and NH4+ was apparent on plant growth and chlorophyll content, we found a synergetic effect of CL and NH4+ on the accumulation of several plant stress hormones, with an especially strong effect for jasmonic acid (JA) and 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, in xylem sap. This modulation of the hormonal composition suggests a potential role for these plant hormones in plant growth responses to the combined application of CL and NH4+. No synergetic effect was observed between CL and NH4+ for the accumulation of soluble carbohydrates or of mineral ions, indicating that these plant traits are less sensitive than the modulation of hormonal composition in xylem sap to the combined CL and NH4+ application. Under diurnal light, NH4+ did not affect the hormonal composition of xylem sap; however, N deficiency strongly increased the concentrations of phaseic acid (PA), JA, and salicylic acid (SA), indicating that decreased N concentration rather than the presence of NO3- or NH4+ in the nutrient solution drives the hormone composition of the xylem sap. In conclusion, N deficiency or a combined application of CL and NH4+ induced the accumulation of JA in xylem sap. This accumulation, in combination with other plant hormones, defines the specific plant response to stress conditions.

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.

Cytokinin Signaling Downstream of the His-Asp Phosphorelay Network: Cytokinin-Regulated Genes and Their Functions

The plant hormone cytokinin, existing in several molecular forms, is perceived by membrane-localized histidine kinases. The signal is transduced to transcription factors of the type-B response regulator family localized in the nucleus by a multi-step histidine-aspartate phosphorelay network employing histidine phosphotransmitters as shuttle proteins across the nuclear envelope. The type-B response regulators activate a number of primary response genes, some of which trigger in turn further signaling events and the expression of secondary response genes. Most genes activated in both rounds of transcription were identified with high confidence using different transcriptomic toolkits and meta analyses of multiple individual published datasets. In this review, we attempt to summarize the existing knowledge about the primary and secondary cytokinin response genes in order to try connecting gene expression with the multitude of effects that cytokinin exerts within the plant body and throughout the lifespan of a plant.

Nitrate and hormonal signaling crosstalk for plant growth and development

Nitrate is an essential macronutrient for plants, a primary nitrogen source in natural and human-made ecosystems. Nitrate can also act as a signaling molecule that directs genome-wide gene expression changes with an impact on plant metabolism, physiology, growth and development. Nitrate and phytohormone signaling pathways crosstalk to modulate growth and developmental programs in a multifactorial manner. Nitrate-signaling controls plant growth and development using molecular mechanisms that involve phytohormone-signaling pathways. In contrast, many phytohormones modulate or impact nitrate signaling in interconnected pathways. In this review, we explore recent progress in our understanding of well-documented connections between nitrate and phytohormones such as auxin, cytokinin and abscisic acid. We also discuss recent studies connecting nitrate to other phytohormones such as ethylene, salicylic acid, gibberellins and brassinosteroids. While many molecular details remain to be elucidated, a number of core signaling components at the intersection between nitrate and the major hormonal pathways have been described. We focus on established interactions of nitrate and different hormonal pathways to bring about cellular, growth and developmental processes in Arabidopsis thaliana.

Inside out: root cortex-localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti

During Lotus japonicus-Mesorhizobium loti symbiosis, the LOTUS HISTIDINE KINASE1 (LHK1) cytokinin receptor regulates both the initiation of nodule formation and the scope of root infection. However, the exact spatiotemporal mechanism by which this receptor exerts its symbiotic functions has remained elusive. In this study, we performed cell type-specific complementation experiments in the hyperinfected lhk1-1 mutant background, targeting LHK1 to either the root epidermis or the root cortex. We also utilized various genetic backgrounds to characterize expression of several genes regulating symbiotic infection. We show here that expression of LHK1 in the root cortex is required and sufficient to regulate both nodule formation and epidermal infections. The LHK1-dependent signalling that restricts subsequent infection events is triggered before initial cell divisions for nodule primordium formation. We also demonstrate that AHK4, the Arabidopsis orthologue of LHK1, is able to regulate M. loti infection in L. japonicus, suggesting that an endogenous cytokinin receptor could be sufficient for engineering nitrogen-fixing root nodule symbiosis in nonlegumes. Our data provide experimental evidence for the existence of an LHK1-dependent root cortex-to-epidermis feedback mechanism regulating rhizobial infection. This root-localized regulatory module functionally links with the systemic autoregulation of nodulation (AON) to maintain the homeostasis of symbiotic infection.

A Genome-Wide Association Study Identifies New Loci Involved in Wound-Induced Lateral Root Formation in Arabidopsis thaliana

Root systems can display variable architectures that contribute to nutrient foraging or to increase the tolerance of abiotic stress conditions. Root tip excision promotes the developmental progression of previously specified lateral root (LR) founder cells, which allows to easily measuring the branching capacity of a given root as regards its genotype and/or growth conditions. Here, we describe the natural variation among 120 Arabidopsis thaliana accessions in root system architecture (RSA) after root tip excision. Wound-induced changes in RSA were associated with 19 genomic loci using genome-wide association mapping. Three candidate loci associated with wound-induced LR formation were investigated. Sequence variation in the hypothetical protein encoded by the At4g01090 gene affected wound-induced LR development and its loss-of-function mutants displayed a reduced number of LRs after root tip excision. Changes in a histidine phosphotransfer protein putatively involved in cytokinin signaling were significantly associated with LR number variation after root tip excision. Our results provide a better understanding of some of the genetic components involved in LR capacity variation among accessions.

Trichoderma asperellum T42 induces local defense against Xanthomonas oryzae pv. oryzae under nitrate and ammonium nutrients in tobacco

Trichoderma has been explored and found to play a vital role in the defense mechanism of plants. However, its effects on host disease management in the presence of N nutrients remains elusive. The present study aimed to assess the latent effects of Trichoderma asperellum T42 on oxidative burst-mediated defense mechanisms against Xanthomonas oryzae pv. oryzae (Xoo) in tobacco plants fed 10 mM NO₃⁻ and 3 mM NH₄⁺ nutrients. The nitrate-fed tobacco plants displayed an increased HR when Xoo infected, which was enhanced in the Trichoderma-treated plants. This mechanism was enhanced by the involvement of Trichoderma, which elicited NO production and enhanced the expression pattern of NO-modulating genes (NR, NOA and ARC). The real-time NO fluorescence intensity was alleviated in the NH₄⁺-fed tobacco plants compared to that fed NO₃⁻ nutrient, suggesting the significant role of Trichoderma-elicited NO. The nitrite content and NR activity demonstration further confirmed that nitrate metabolism led to NO generation. The production of ROS (H₂O₂) in the plant leaves well-corroborated that the disease resistance was mediated through the oxidative burst mechanism. Nitrate application resulted in greater ROS production compared to NH₄⁺ nutrient after Xoo infection at 12 h post-infection (hpi). Additionally, the mechanism of enhanced plant defense under NO₃⁻ and NH₄⁺ nutrients mediated by Trichoderma involved NO, ROS production and induction of PR1a MEK3 and antioxidant enzyme transcription level. Moreover, the use of sodium nitroprusside (100 μM) with Xoo suspension in the leaves matched the disease resistance mediated via NO burst. Altogether, this study provides novel insights into the fundamental mechanism behind the role of Trichoderma in the activation of plant defense against non-host pathogens under N nutrients.

A hypothetical proposed defense pathway activated during interactions between bacterial pathogen (Xoo) with tobacco plant leaves among treatments.

Nutrient-Related Long-Distance Signals: Common Players and Possible Cross-Talk

Nutrient fluctuations are more a rule rather than an exception in the life of sessile organisms such as plants. Despite this constraint that adds up to abiotic and biotic stresses, plants are able to accomplish their life cycle thanks to an efficient signaling network that reciprocally controls nutrient acquisition and use with growth and development. The majority of nutrients are acquired by the root system where multiple local signaling pathways that rely on nutrient-sensing systems are implemented to direct root growth toward soil resources. Moreover, long-distance signaling plays an essential role in integrating nutrient availability at the whole-plant level and adjusting nutrient acquisition to plant growth requirements. By studying the signaling network for single mineral nutrients, several long-distance signals traveling between roots and shoots and taking a diversity of forms have been identified and are summarized here. However, the nutritional environment is multifactorial, adding a tremendous complexity for our understanding of the nutrient signaling network as a unique system. For instance, long-distance signals are expected to support this nutrient cross-talk in part, but the mechanisms are still largely unknown. Therefore, the involvement of possible long-distance signals as conveyers of nutrient cross-talk is discussed here together with approaches and strategies that are now considered to build a picture from the nutrient signaling puzzle.

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.

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

Our study exploits time—the relatively unexplored fourth dimension of gene regulatory networks (GRNs)—to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. We introduce several conceptual innovations to the analysis of time-series data in the area of predictive GRNs. Our resulting network now provides the “transcriptional logic” for transcription factor perturbations aimed at improving N-use efficiency, an important issue for global food production in marginal soils and for sustainable agriculture. More broadly, the combination of the time-based approaches we develop and deploy can be applied to uncover the temporal “transcriptional logic” for any response system in biology, agriculture, or medicine.

This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our “just-in-time” analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to “prune” the network to 155 TFs and 608 targets. This network precision was reconfirmed using genome-wide TF-target regulation data for four additional TFs (TGA1, HHO5/6, and PHL1) not used in network pruning. These higher-confidence edges in the GRN were further filtered by independent TF-target binding data, used to calculate a TF “N-specificity” index. This refined GRN identifies the temporal relationship of known/validated regulators of N signaling (NLP7/8, TGA1/4, NAC4, HRS1, and LBD37/38/39) and 146 additional regulators. Six TFs—CRF4, SNZ, CDF1, HHO5/6, and PHL1—validated herein regulate a significant number of genes in the dynamic N response, targeting 54% of N-uptake/assimilation pathway genes. Phenotypically, inducible overexpression of CRF4 in planta regulates genes resulting in altered biomass, root development, and ¹⁵NO₃⁻ uptake, specifically under low-N conditions. This dynamic N-signaling GRN now provides the temporal “transcriptional logic” for 155 candidate TFs to improve nitrogen use efficiency with potential agricultural applications. Broadly, these time-based approaches can uncover the temporal transcriptional logic for any biological response system in biology, agriculture, or medicine.

Trichoderma asperellum T42 Reprograms Tobacco for Enhanced Nitrogen Utilization Efficiency and Plant Growth When Fed with N Nutrients

Trichoderma spp., are saprophytic fungi that can improve plant growth through increased nutrient acquisition and change in the root architecture. In the present study, we demonstrate that Trichoderma asperellum T42 mediate enhancement in host biomass, total nitrogen content, nitric oxide (NO) production and cytosolic Ca2+ accumulation in tobacco. T42 inoculation enhanced lateral root, root hair length, root hair density and root/shoot dry mass in tobacco under deprived nutrients condition. Interestingly, these growth attributes were further elevated in presence of T42 and supplementation of NO3- and NH4+ nutrients to tobacco at 40 and 70 days, particularly in NO3- supplementation, whereas no significant increment was observed in nia30 mutant. In addition, NO production was more in tobacco roots in T42 inoculated plants fed with NO3- nutrient confirming NO generation was dependent on NR pathway. NO3- dependent NO production contributed to increase in lateral root initiation, Ca2+ accumulation and activities of nitrate transporters (NRTs) in tobacco. Higher activities of several NRT genes in response to T42 and N nutrients and suppression of ammonium transporter (AMT1) suggested that induction of high affinity NRTs help NO3- acquisition through roots of tobacco. Among the NRTs NRT2.1 and NRT2.2 were more up-regulated compared to the other NRTs. Addition of sodium nitroprusside (SNP), relative to those supplied with NO3-/NH4+ nutrition and T42 treated plants singly, and with application of NO inhibitor, cPTIO, confirmed the altered NO fluorescence intensity in tobacco roots. Our findings suggest that T42 promoted plant growth significantly ant N content in the tobacco plants grown under N nutrients, notably higher in NO3-, providing insight of the strategy for not only tobacco but probably for other crops as well to adapt to fluctuating nitrate availability in soil.

Nitrate supply to grapevine rootstocks - new genome-wide findings

This article comments on: Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert P-F, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V. 2017. Root transcriptomic responses of grafted grapevine to heterogeneous N availability depend on rootstock genotype. Journal of Experimental Botany 68, 4339–4355.

Signals and players in the transcriptional regulation of root responses by local and systemic N signaling in Arabidopsis thaliana

In natural environments, nitrogen (N) concentration in the soil fluctuates greatly and is often limiting for plant growth and development. The ability of plants to respond to changes in N availability is therefore essential for adaptation. The response of plants to N variations consists in particular of adjusting root N uptake systems and root architecture. To do so, plants integrate local sensing and signaling of external N availability with systemic sensing and signaling of their internal N status, in order to tune the functional and structural properties of the root system in accordance with the N demand for growth of the whole plant. Transcriptional regulation of gene expression is one of the most important processes plants use to adapt the properties of the root system in response to local and long-distance N pathways. This review focuses on the mechanisms that give rise to transcriptional responses in Arabidopsis roots under N fluctuations, with an emphasis on those associated with the regulation of nitrate uptake and transport systems. We discuss the putative long-distance signals triggering the gene expression responses, as well as the molecular players that locally induce transcriptional changes. We also highlight several observations revealing the importance of adopting an integrative approach in the regulation of N signaling.

Nitrogen use efficiency in crops: lessons from Arabidopsis and rice

Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.

Phloem-Mobile RNAs as Systemic Signaling Agents

The plant vascular system plays a central role in coordinating physiological and developmental events through delivery of both essential nutrients and long-distance signaling agents. The enucleate phloem sieve tube system of the angiosperms contains a broad spectrum of RNA species. Grafting and transcriptomics studies have indicated that several thousand mRNAs move long distances from source organs to meristematic sink tissues. Ribonucleoprotein complexes play a pivotal role as stable RNA-delivery systems for systemic translocation of cargo RNA. In this review, we assess recent progress in the characterization of phloem and plasmodesmal transport as an integrated local and systemic communication network. We discuss the roles of phloem-mobile small RNAs in epigenetic events, including meristem development and genome stability, and the delivery of mRNAs to specific tissues in response to environmental inputs. A large body of evidence now supports a model in which phloem-mobile RNAs act as critical components of gene regulatory networks involved in plant growth, defense, and crop yield at the whole-plant level.

Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis

In nature and agriculture, nitrate availability is a main environmental cue for plant growth, development and stress responses. Nitrate signaling and regulation are hence at the center of communications between plant intrinsic programs and the environment. It is also well known that endogenous phytohormones play numerous critical roles in integrating extrinsic cues and intrinsic responses, regulating and refining almost all aspects of plant growth, development and stress responses. Therefore, interaction between nitrate and phytohormones, such as auxins, cytokinins, abscisic acid, gibberellins, and ethylene, is prevalent. The growing evidence indicates that biosynthesis, de-conjugation, transport, and signaling of hormones are partly controlled by nitrate signaling. Recent advances with nitrate signaling and transcriptional regulation in Arabidopsis give rise to new paradigms. Given the comprehensive nitrate transport, sensing, signaling and regulations at the level of the cell and organism, nitrate itself is a local and long-distance signal molecule, conveying N status at the whole-plant level. A direct molecular link between nitrate signaling and cell cycle progression was revealed with TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1-20 (TCP20) - NIN-LIKE PROTEIN 6/7 (NLP6/7) regulatory nexus. NLPs are key regulators of nitrogen responses in plants. TCPs function as the main regulators of plant morphology and architecture, with the emerging role as integrators of plant developmental responses to the environment. By analogy with auxin being proposed as a plant morphogen, nitrate may be an environmental morphogen. The morphogen-gradient-dependent and cell-autonomous mechanisms of nitrate signaling and regulation are an integral part of cell growth and cell identification. This is especially true in root meristem growth that is regulated by intertwined nitrate, phytohormones, and glucose-TOR signaling pathways. Furthermore, the nitrate transcriptional hierarchy is emerging. Nitrate regulators in primary nitrate signaling can individually and combinatorially control downstream transcriptional networks and hormonal pathways for signal propagation and amplification. Under the new paradigms, nitrate-induced hormone metabolism and signaling deserve fresh examination. The close interplay and convergent regulation of nitrate and hormonal signaling at morphological, physiological, and molecular levels have significant effects on important agronomic traits, especially nutrient-dependent adaptive root system growth and architecture.

Long-distance transport of phytohormones through the plant vascular system

Phytohormones are a group of low abundance molecules that activate various metabolic and developmental processes in response to environmental and endogenous signals. Like animal hormones, plant hormones often have distinct source and target tissues, hence ensuring long-range communication at the whole-plant level. Plants rely on various hormone distribution mechanisms depending on the distance and the direction of the transport. Here, we highlight the recent findings on the long-distance movement of plant hormones within the vasculature, from the physiological role to the molecular mechanism of the transport.

Hormones and nitrate: a two-way connection

During their sessile mode of life, plants need to endure variations in their environment such as a drastic variability in the nutrient concentration in soil solution. It is almost trivial to say that such fluctuations in the soil modify plant growth, development and phase transitions. However, the signaling pathways underlying the connections between nitrogen related signaling and hormonal signaling controlling growth are still poorly documented. This review is meant to present how nitrate/nitrogen controls hormonal pathways. Furthermore, it is very interesting to highlight the increasing evidence that the hormonal signaling pathways themselves seem to feed back control of the nitrate/nitrogen transport and assimilation to adapt nutrition to growth. This thus defines a feed-forward cycle that finely coordinates plant growth and nutrition.

Nitrate Transport, Sensing, and Responses in Plants

Nitrogen (N) is an essential macronutrient that affects plant growth and development. N is an important component of chlorophyll, amino acids, nucleic acids, and secondary metabolites. Nitrate is one of the most abundant N sources in the soil. Because nitrate and other N nutrients are often limiting, plants have developed sophisticated mechanisms to ensure adequate supply of nutrients in a variable environment. Nitrate is absorbed in the root and mobilized to other organs by nitrate transporters. Nitrate sensing activates signaling pathways that impinge upon molecular, metabolic, physiological, and developmental responses locally and at the whole plant level. With the advent of genomics technologies and genetic tools, important advances in our understanding of nitrate and other N nutrient responses have been achieved in the past decade. Furthermore, techniques that take advantage of natural polymorphisms present in divergent individuals from a single species have been essential in uncovering new components. However, there are still gaps in our understanding of how nitrate signaling affects biological processes in plants. Moreover, we still lack an integrated view of how all the regulatory factors identified interact or crosstalk to orchestrate the myriad N responses plants typically exhibit. In this review, we provide an updated overview of mechanisms by which nitrate is sensed and transported throughout the plant. We discuss signaling components and how nitrate sensing crosstalks with hormonal pathways for developmental responses locally and globally in the plant. Understanding how nitrate impacts on plant metabolism, physiology, and growth and development in plants is key to improving crops for sustainable agriculture.

Transporters Involved in Root Nitrate Uptake and Sensing by Arabidopsis

Most plants use nitrate (NO₃^-) as their major nitrogen (N) source. The NO₃^- uptake capacity of a plant is determined by three interdependent factors that are sensitive to NO₃^- availability: (i) the functional properties of the transporters in roots that contribute to the acquisition of NO₃^- from the external medium, (ii) the density of functional transporters at the plasma membrane of root cells, and (iii) the surface and architecture of the root system. The identification of factors that regulate the NO₃^--sensing systems is important for both fundamental and applied science, because these factors control the capacity of plants to use the available NO₃^-, a process known as the "nitrate use efficiency." The molecular component of the transporters involved in uptake and sensing mechanism in Arabidopsis roots are presented and their relative contribution discussed.