Hormones and nitrate: a two-way connection

High nitrogen application in maize enhances insecticide tolerance of the polyphagous herbivore Spodoptera litura by induction of detoxification enzymes and intensification of cuticle

Nitrogen (N) is one of the most intensively used fertilizers in cropping system and could exert a variety of bottom-up effects on the ecological fitness of herbivores. However, the effects of increased N inputs on insect pesticide tolerance have not been comprehensively understood. Bioassays showed that high N (HN) applied to maize plants significantly increased larval tolerance of Spodoptera litura to multiple insecticides. Activities of detoxification enzymes were significantly higher in the larvae fed on maize plants supplied with HN. RNA-seq analysis showed that numerous GST and cuticle-related genes were induced in the larvae fed on HN maize. RT-qPCR analysis further confirmed four GST genes and larval-specific cuticle gene LCP167. Furthermore, when injected with dsRNA specific to GSTe1, GSTs5, and LCP167, the mortality of larvae treated with methomyl was about 3-fold higher than that of dsGFP-injected larvae. Electron microscope observation showed that cuticle of the larvae fed on HN maize was thicker than the medium level of N. These findings suggest that increased application of N fertilizer enhances insecticide tolerance of lepidopteran pests via induction of detoxification enzymes and intensification of cuticle. Thus, overuse of N fertilizer may increase pest insecticide tolerance and usage of chemical insecticides.

Genome-Wide Identification and Expression Analysis of Nitrate Transporter (NRT) Gene Family in Eucalyptus grandis

Eucalyptus grandis is an important planted hardwood tree worldwide with fast growth and good wood performance. The nitrate transporter (NRT) gene family is a major core involved in nitrogen (N) absorption and utilization in plants, but the comprehensive characterization of NRT genes in E. grandis remains mostly elusive. In this study, a total of 75 EgNRT genes were identified from the genome of E. grandis that were distributed unevenly across ten chromosomes, except Chr9. A phylogenetic analysis showed that the EgNRT proteins could be divided into three classes, namely NRT1, NRT2 and NRT3, which contained 69, 4 and 2 members, respectively. The cis-regulatory elements in the promoter regions of EgNRT genes were mainly involved in phytohormone and stress response. The transcriptome analysis indicated that the differentially expressed genes of leaf and root in E. grandis under different N supply conditions were mainly involved in the metabolic process and plant hormone signal transduction. In addition, the transcriptome-based and RT-qPCR analysis revealed that the expression of 13 EgNRT genes, especially EgNRT1.3, EgNRT1.38, EgNRT1.39 and EgNRT1.52, was significantly upregulated in the root under low-N-supply treatment, suggesting that those genes might play a critical role in root response to nitrate deficiency. Taken together, these results would provide valuable information for characterizing the roles of EgNRTs and facilitate the clarification of the molecular mechanism underlying EgNRT-mediated N absorption and distribution in E. grandis.

Peculiarity of the early metabolomic response in tomato after urea, ammonium or nitrate supply

Nitrogen (N) is the nutrient most applied in agriculture as fertilizer (as nitrate, Nit; ammonium, A; and/or urea, U, forms) and its availability strongly constrains the crop growth and yield. To investigate the early response (24 h) of N-deficient tomato plants to these three N forms, a physiological and molecular study was performed. In comparison to N-deficient plants, significant changes in the transcriptional, metabolomic and ionomic profiles were observed. As a probable consequence of N mobility in plants, a wide metabolic modulation occurred in old leaves rather than in young leaves. The metabolic profile of U and A-treated plants was more similar than Nit-treated plant profile, which in turn presented the lowest metabolic modulation with respect to N-deficient condition. Urea and A forms induced some changes at the biosynthesis of secondary metabolites, amino acids and phytohormones. Interestingly, a specific up-regulation by U and down-regulation by A of carbon synthesis occurred in roots. Along with the gene expression, data suggest that the specific N form influences the activation of metabolic pathways for its assimilation (cytosolic GS/AS and/or plastidial GS/GOGAT cycle). Urea induced an up-concentration of Cu and Mn in leaves and Zn in whole plant. This study highlights a metabolic reprogramming depending on the N form applied, and it also provide evidence of a direct relationship between urea nutrition and Zn concentration. The understanding of the metabolic pathways activated by the different N forms represents a milestone in improving the efficiency of urea fertilization in crops.

Nitrate Signaling and Its Role in Regulating Flowering Time in Arabidopsis thaliana

Plant growth is coordinated with the availability of nutrients that ensure its development. Nitrate is a major source of nitrogen (N), an essential macronutrient for plant growth. It also acts as a signaling molecule to modulate gene expression, metabolism, and a variety of physiological processes. Recently, it has become evident that the calcium signal appears to be part of the nitrate signaling pathway. New key players have been discovered and described in Arabidopsis thaliana (Arabidopsis). In addition, knowledge of the molecular mechanisms of how N signaling affects growth and development, such as the nitrate control of the flowering process, is increasing rapidly. Here, we review recent advances in the identification of new components involved in nitrate signal transduction, summarize newly identified mechanisms of nitrate signaling-modulated flowering time in Arabidopsis, and suggest emerging concepts and existing open questions that will hopefully be informative for further discoveries.

Auxin synthesis promotes N metabolism and optimizes root structure enhancing N acquirement in maize (Zea mays L.)

MAIN CONCLUSION

Foliar NAA increases photosynthate supplied by enhancing photosynthesis, to strengthen root activity and provide a large sink for root carbohydrate accumulation, which is beneficial to acquire more nitrogen. The improvement of grain yield is an effective component in the food security. Auxin acts as a well-known plant hormone, plays an important role in maize growth and nutrient uptake. In this study, with maize variety Zhengdan 958 (ZD958) as material, the effects of auxin on nitrogen (N) uptake and assimilation of seedling maize were studied by hydroponic experiments. With water as the control, naphthalene acetic acid (NAA, 0.1 mmol/L) and aminoethoxyvinylglycine (AVG, 0.1 mmol/L, an auxin synthesis inhibitor) were used for foliar spraying. The results showed that NAA significantly improved photosynthetic rate and plant biomass by 58.6% and 91.7%, respectively, while the effect of AVG was opposite to that of NAA. At the same time, key enzymes activities related N assimilation in NAA leaves were significantly increased, and the activities of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase (GOGAT) were increased by 32.3%, 22.9%, and 16.2% in new leaves. Furthermore, NAA treatment promoted underground growth. When compared with control, total root length, root surface area, root tip number, branch number and root activity were significantly increased by 37.8%, 22.2%, 35.1%, 28.8% and 21.2%. Root growth is beneficial to N capture in maize. Ultimately, the total N accumulation of NAA treatment was significantly increased by 74.5%, as compared to the control. In conclusion, NAA foliar spraying increased endogenous IAA content, and enhanced the activity of N assimilation-related enzymes and photosynthesis rate, in order to build a large sink for carbohydrate accumulation. In addition, NAA strengthened root activity and regulated root morphology and architecture, which facilitated further N uptake and plant growth.

Physiological and Transcriptomic Analysis Provides Insights into Low Nitrogen Stress in Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop that is well adapted to nutrient-poor soils. However, our understanding of how different LN-tolerant foxtail millet varieties adapt to long-term low nitrogen (LN) stress at the physiological and molecular levels remains limited. In this study, two foxtail millet varieties with contrasting LN tolerance properties were investigated through analyses of physiological parameters and transcriptomics. The physiological results indicate that JG20 (high tolerance to LN) exhibited superior biomass accumulation both in its shoots and roots, and higher nitrogen content, soluble sugar concentration, soluble protein concentration, zeatin concentration in shoot, and lower soluble sugar and soluble protein concentration in its roots compared to JG22 (sensitive to LN) under LN, this indicated that the LN-tolerant foxtail millet variety can allocate more functional substance to its shoots to sustain aboveground growth and maintain high root activity by utilizing low soluble sugar and protein under LN conditions. In the transcriptomics analysis, JG20 exhibited a greater number of differentially expressed genes (DEGs) compared to JG22 in both its shoots and roots in response to LN stress. These LN-responsive genes were enriched in glycolysis metabolism, photosynthesis, hormone metabolism, and nitrogen metabolism. Furthermore, in the shoots, the glutamine synthetase gene SiGS5, chlorophyll apoprotein of photosystem II gene SiPsbQ, ATP synthase subunit gene Sib, zeatin synthesis genes SiAHP1, and aldose 1-epimerase gene SiAEP, and, in the roots, the high-affinity nitrate transporter genes SiNRT2.3, SiNRT2.4, glutamate synthase gene SiGOGAT2, fructose-bisphosphate aldolase gene SiFBA5, were important genes involved in the LN tolerance of the foxtail millet variety. Hence, our study implies that the identified genes and metabolic pathways contribute valuable insights into the mechanisms underlying LN tolerance in foxtail millet.

Nitrogen nutrition and xylem sap composition in Zea mays: effect of urea, ammonium and nitrate on ionomic and metabolic profiles

In plants the communication between organs is mainly carried out via the xylem and phloem. The concentration and the molecular species of some phytohormones, assimilates and inorganic ions that are translocated in the xylem vessel play a key role in the systemic nutritional signaling in plants. In this work the composition of the xylem sap of maize was investigated at the metabolic and ionomic level depending on the N form available in the nutrient solution. Plants were grown up to 7 days in hydroponic system under N-free nutrient solution or nutrient solution containing N in form of nitrate, urea, ammonium or a combination of urea and ammonium. For the first time this work provides evidence that the ureic nutrition reduced the water translocation in maize plants more than mineral N forms. This result correlates with those obtained from the analyses of photosynthetic parameters (stomatal conductance and transpiration rate) suggesting a parsimonious use of water by maize plants under urea nutrition. A peculiar composition in amino acids and phytohormones (i.e. S, Gln, Pro, ABA) of the xylem sap under urea nutrition could explain differences in xylem sap exudation in comparison to plants treated with mineral N forms. The knowledge improvement of urea nutrition will allow to further perform good agronomic strategies to improve the resilience of maize crop to water stress.

Involvement of plant signaling network and cell metabolic homeostasis in nitrogen deficiency-induced early leaf senescence

Nitrogen (N) is a basic building block that plays an essential role in the maintenance of normal plant growth and its metabolic functions through complex regulatory networks. Such the N metabolic network comprises a series of transcription factors (TFs), with the coordinated actions of phytohormone and sugar signaling to sustain cell homeostasis. The fluctuating N concentration in plant tissues alters the sensitivity of several signaling pathways to stressful environments and regulates the senescent-associated changes in cellular structure and metabolic process. Here, we review recent advances in the interaction between N assimilation and carbon metabolism in response to N deficiency and its regulation to the nutrient remobilization from source to sink during leaf senescence. The regulatory networks of N and sugar signaling for N deficiency-induced leaf senescence is further discussed to explain the effects of N deficiency on chloroplast disassembly, reactive oxygen species (ROS) burst, asparagine metabolism, sugar transport, autophagy process, Ca2+ signaling, circadian clock response, brassinazole-resistant 1 (BZRI), and other stress cell signaling. A comprehensive understanding for the metabolic mechanism and regulatory network underlying N deficiency-induced leaf senescence may provide a theoretical guide to optimize the source-sink relationship during grain filling for the achievement of high yield by a selection of crop cultivars with the properly prolonged lifespan of functional leaves and/or by appropriate agronomic managements.

Analysis of Functional Single-Nucleotide Polymorphisms (SNPs) and Leaf Quality in Tea Collection under Nitrogen-Deficient Conditions

This study discusses the genetic mutations that have a significant association with economically important traits that would benefit tea breeders. The purpose of this study was to analyze the leaf quality and SNPs in quality-related genes in the tea plant collection of 20 mutant genotypes growing without nitrogen fertilizers. Leaf N-content, catechins, L-theanine, and caffeine contents were analyzed in dry leaves via HPLC. Additionally, the photochemical yield, electron transport efficiency, and non-photochemical quenching were analyzed using PAM-fluorimetry. The next generation pooled amplicon-sequencing approach was used for SNPs-calling in 30 key genes related to N metabolism and leaf quality. The leaf N content varied significantly among genotypes (p ≤ 0.05) from 2.3 to 3.7% of dry mass. The caffeine content varied from 0.7 to 11.7 mg g-1, and the L-theanine content varied from 0.2 to 5.8 mg g-1 dry leaf mass. Significant positive correlations were detected between the nitrogen content and biochemical parameters such as theanine, caffeine, and most of the catechins. However, significant negative correlations were observed between the photosynthetic parameters (Y, ETR, Fv/Fm) and several biochemical compounds, including rutin, Quercetin-3-O-glucoside, Kaempferol-3-O-rutinoside, Kaempferol-3-O-glucoside, Theaflavin-3'-gallate, gallic acid. From our SNP-analysis, three SNPs in WRKY57 were detected in all genotypes with a low N content. Moreover, 29 SNPs with a high or moderate effect were specific for #316 (high N-content, high quality) or #507 (low N-content, low quality). The use of a linear regression model revealed 16 significant associations; theaflavin, L-theanine, and ECG were associated with several SNPs of the following genes: ANSa, DFRa, GDH2, 4CL, AlaAT1, MYB4, LHT1, F3'5'Hb, UFGTa. Among them, seven SNPs of moderate effect led to changes in the amino acid contents in the final proteins of the following genes: ANSa, GDH2, 4Cl, F3'5'Hb, UFGTa. These results will be useful for further evaluations of the important SNPs and will help to provide a better understanding of the mechanisms of nitrogen uptake efficiency in tree crops.

Molecular bases for the stronger plastic response to high nitrate in the invasive plant Xanthium strumarium compared with its native congener

MAIN CONCLUSION

High expressions of nitrate use and photosynthesis-related transcripts contribute to the stronger plasticity to high nitrate for the invader relative to its native congener, which may be driven by hormones. Strong phenotypic plasticity is often considered as one of the main mechanisms underlying exotic plant invasions. However, few studies have been conducted to investigate the related molecular mechanisms. Here, we determined the differences in the plastic responses to high nitrate between the invasive plant X. strumarium and its native congener, and the molecular bases by transcriptome analysis and quantitative real-time PCR validation. Our results showed that the invader had higher plasticity of growth, nitrogen accumulation and photosynthesis in responses to high nitrate than its native congener. Compared with its congener, more N utilization-related transcripts, including nitrate transporter 1/peptide transporter family 6.2 and nitrate reductase 1, were induced by high nitrate in the root of X. strumarium, improving its N utilization ability. More transcripts coding for photosynthetic antenna proteins were also induced by high nitrate in the shoot of X. strumarium, enhancing its photosynthesis. Hormones may be involved in the regulation of the plastic responses to high nitrate in the two species. Our study contributes to understanding the molecular mechanisms underlying the stronger plasticity of the invader in responses to high nitrate, and the potential function of plant hormones in these processes, providing bases for precise control of invasive plants using modern molecular techniques.

Effect of ipt Gene Induction in Transgenic Tobacco Plants on Hydraulic Conductance, Formation of Apoplastic Barriers and Aquaporin Activity under Heat Shock

Cytokinins are known to keep stomata open, which supports gas exchange and correlates with increased photosynthesis. However, keeping the stomata open can be detrimental if the increased transpiration is not compensated for by water supply to the shoots. In this study, we traced the effect of ipt (isopentenyl transferase) gene induction, which increases the concentration of cytokinins in transgenic tobacco plants, on transpiration and hydraulic conductivity. Since water flow depends on the conductivity of the apoplast, the deposition of lignin and suberin in the apoplast was studied by staining with berberine. The effect of an increased concentration of cytokinins on the flow of water through aquaporins (AQPs) was revealed by inhibition of AQPs with HgCl₂. It was shown that an elevated concentration of cytokinins in ipt-transgenic plants increases hydraulic conductivity by enhancing the activity of aquaporins and reducing the formation of apoplastic barriers. The simultaneous effect of cytokinins on both stomatal and hydraulic conductivity makes it possible to coordinate the evaporation of water from leaves and its flow from roots to leaves, thereby maintaining the water balance and leaf hydration.

LjNRT2.3 plays a hierarchical role in the control of high affinity transport system for root nitrate acquisition in Lotus japonicus

Nitrate is a key mineral nutrient required for plant growth and development. Plants have evolved sophisticated mechanisms to respond to changes of nutritional availability in the surrounding environment and the optimization of root nitrate acquisition under nitrogen starvation is crucial to cope with unfavoured condition of growth. In this study we present a general description of the regulatory transcriptional and spatial profile of expression of the Lotus japonicus nitrate transporter NRT2 family. Furthermore, we report a phenotypic characterization of two independent Ljnrt2.3 knock out mutants indicating the involvement of the LjNRT2.3 gene in the root nitrate acquisition and lateral root elongation pathways occurring in response to N starvation conditions. We also report an epistatic relationship between LjNRT2.3 and LjNRT2.1 suggesting a combined mode of action of these two genes in order to optimize the Lotus response to a prolonged N starvation.

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.

Nitrate-responsive transcriptome analysis reveals additional genes/processes and associated traits viz. height, tillering, heading date, stomatal density and yield in japonica rice

Our transcriptomic analysis expanded the repertoire of nitrate-responsive genes/processes in rice and revealed their phenotypic association with root/shoot, stomata, tiller, panicle/flowering and yield, with agronomic implications for nitrogen use efficiency. Nitrogen use efficiency (NUE) is a multigenic quantitative trait, involving many N-responsive genes/processes that are yet to be fully characterized. Microarray analysis of early nitrate response in excised leaves of japonica rice revealed 6688 differentially expressed genes (DEGs), including 2640 hitherto unreported across multiple functional categories. They include transporters, enzymes involved in primary/secondary metabolism, transcription factors (TFs), EF-hand containing calcium binding proteins, hormone metabolism/signaling and methytransferases. Some DEGs belonged to hitherto unreported processes viz. alcohol, lipid and trehalose metabolism, mitochondrial membrane organization, protein targeting and stomatal opening. 1158 DEGs were associated with growth physiology and grain yield or phenotypic traits for NUE. We identified seven DEGs for shoot apical meristem, 66 for leaf/culm/root, 31 for tiller, 70 for heading date/inflorescence/spikelet/panicle, 144 for seed and 78 for yield. RT-qPCR validated nitrate regulation of 31 DEGs belonging to various important functional categories/traits. Physiological validation of N-dose responsive changes in plant development revealed that relative to 1.5 mM, 15 mM nitrate significantly increased stomatal density, stomatal conductance and transpiration rate. Further, root/shoot growth, number of tillers and grain yield declined and panicle emergence/heading date delayed, despite increased photosynthetic rate. We report the binding sites of diverse classes of TFs such as WRKY, MYB, HMG etc., in the 1 kb up-stream regions of 6676 nitrate-responsive DEGs indicating their role in regulating nitrate response/NUE. Together, these findings expand the repertoire of genes and processes involved in genomewide nitrate response in rice and reveal their physiological, phenotypic and agronomic implications for NUE.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Nitrate signaling promotes plant growth by upregulating gibberellin biosynthesis and destabilization of DELLA proteins

Nitrate, one of the main nitrogen (N) sources for crops, acts as a nutrient and key signaling molecule coordinating gene expression, metabolism, and various growth processes throughout the plant life cycle. It is widely accepted that nitrate-triggered developmental programs cooperate with hormone synthesis and transport to finely adapt plant architecture to N availability. Here, we report that nitrate, acting through its signaling pathway, promotes growth in Arabidopsis and wheat, in part by modulating the accumulation of gibberellin (GA)-regulated DELLA growth repressors. We show that nitrate reduces the abundance of DELLAs by increasing GA contents through activation of GA metabolism gene expression. Consistently, the growth restraint conferred by nitrate deficiency is partially rescued in global-DELLA mutant that lacks all DELLAs. At the cellular level, we show that nitrate enhances both cell proliferation and elongation in a DELLA-dependent and -independent manner, respectively. Our findings establish a connection between nitrate and GA signaling pathways that allow plants to adapt their growth to nitrate availability.

Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge

Background

Treatment of wheat with the phytohormones abscisic acid (ABA) and gibberellic acid (GA) has been shown to affect Fusarium head blight (FHB) disease severity. However, the molecular mechanisms underlying the elicited phenotypes remain unclear. Toward addressing this gap in our knowledge, global transcriptomic profiling was applied to the FHB-susceptible wheat cultivar ‘Fielder’ to map the regulatory responses effected upon treatment with ABA, an ABA receptor antagonist (AS6), or GA in the presence or absence of Fusarium graminearum (Fg) challenge.

Results

Spike treatments resulted in a total of 30,876 differentially expressed genes (DEGs) identified in ‘Fielder’ (26,004) and the Fg (4872) pathogen. Topology overlap and correlation analyses defined 9689 wheat DEGs as Fg-related across the treatments. Further enrichment analyses demonstrated that these included expression changes within ‘Fielder’ defense responses, cell structural metabolism, molecular transport, and membrane/lipid metabolism. Dysregulation of ABA and GA crosstalk arising from repression of ‘Fielder’ FUS3 was noted. As well, expression of a putative Fg ABA-biosynthetic cytochrome P450 was detected. The co-applied condition of Fg + ABA elicited further up-regulation of phytohormone biosynthesis, as well as SA and ET signaling pathways and cell wall/polyphenolic metabolism. In contrast, co-applied Fg + GA mainly suppressed phytohormone biosynthesis and signaling, while modulating primary and secondary metabolism and flowering. Unexpectedly, co-applied Fg + AS6 did not affect ABA biosynthesis or signaling, but rather elicited antagonistic responses tied to stress, phytohormone transport, and FHB disease-related genes.

Conclusions

Observed exacerbation (misregulation) of classical defense mechanisms and cell wall fortifications upon ABA treatment are consistent with its ability to promote FHB severity and its proposed role as a fungal effector. In contrast, GA was found to modulate primary and secondary metabolism, suggesting a general metabolic shift underlying its reduction in FHB severity. While AS6 did not antagonize traditional ABA pathways, its impact on host defense and Fg responses imply potential for future investigation. Overall, by comparing these findings to those previously reported for four additional plant genotypes, an additive model of the wheat-Fg interaction is proposed in the context of phytohormone responses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08069-0.

CALMODULIN-LIKE-38 and PEP1 RECEPTOR 2 integrate nitrate and brassinosteroid signals to regulate root growth

Plants exhibit remarkable developmental plasticity, enabling them to adapt to adverse environmental conditions such as low nitrogen (N) in the soil. Brassinosteroids (BRs) promote root foraging for nutrients under mild N deficiency, but the crosstalk between the BR- and N-signaling pathways in the regulation of root growth remains largely unknown. Here, we show that CALMODULIN-LIKE-38 (CML38), a calmodulin-like protein, specifically interacts with the PEP1 RECEPTOR 2 (PEPR2), and negatively regulates root elongation in Arabidopsis (Arabidopsis thaliana) in response to low nitrate (LN). CML38 and PEPR2 are transcriptionally induced by treatments of exogenous nitrate and BR. Compared with Col-0, the single mutants cml38 and pepr2 and the double mutant cml38 pepr2 displayed enhanced primary root growth and produced more lateral roots under LN. This is consistent with their higher nitrate absorption abilities, and their stronger expression of nitrate assimilation genes. Furthermore, CML38 and PEPR2 regulate common downstream genes related to BR signaling, and they have positive roles in BR signaling. Low N facilitated BR signal transmission in Col-0 and CML38- or PEPR2-overexpressing plants, but not in the cml38 and pepr2 mutants. Taken together, our results illustrate a mechanism by which CML38 interacts with PEPR2 to integrate LN and BR signals for coordinating root development to prevent quick depletion of N resources in Arabidopsis.

Transcriptomic and metabolomic profiles of Zea mays fed with urea and ammonium

The simultaneous presence of different N-forms in the rhizosphere leads to beneficial effects on nitrogen (N) nutrition in plants. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants. Maize fed with a mixture of urea and ammonium displayed a better N-uptake efficiency than ammonium- or urea-fed plants (Buoso et al., Plant Physiol Biochem, 2021a; 162: 613-623). Through multiomic approaches, we provide the molecular characterization of maize response to urea and ammonium nutrition. Several transporters and enzymes involved in N-nutrition were upregulated by all three N-treatments (urea, ammonium, or urea and ammonium). Already after 1 day of treatment, the availability of different N-forms induced specific transcriptomic and metabolomic responses. The combination of urea and ammonium induced a prompt assimilation of N, characterized by high levels of some amino acids in shoots. Moreover, ZmAMT1.1a, ZmGLN1;2, ZmGLN1;5, ZmGOT1, and ZmGOT3, as well transcripts involved in glycolysis-TCA cycle were induced in roots by urea and ammonium mixture. Depending on N-form, even changes in the composition of phytohormones were observed in maize. This study paves the way to formulate guidelines for the optimization of N fertilization to improve N-use efficiency in maize and therefore limit N-losses in the 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.

Interaction of BTB-TAZ protein MdBT2 and DELLA protein MdRGL3a regulates nitrate-mediated plant growth

Nitrate acts as a vital signal molecule in the modulation of plant growth and development. The phytohormones gibberellin (GA) is also involved in this process. However, the exact molecular mechanism of how nitrate and GA signaling pathway work together in regulating plant growth remains poorly understood. In this study, we found that a nitrate-responsive BTB/TAZ protein MdBT2 participates in regulating nitrate-induced plant growth in apple (Malus × domestica). Yeast two-hybridization, protein pull-down, and bimolecular fluorescence complementation (BiFC) assays showed that MdBT2 interacts with a DELLA protein MdRGL3a, which is required for the ubiquitination and degradation of MdRGL3a proteins via a 26S proteasome-dependent pathway. Furthermore, heterologous expression of MdBT2 partially rescued growth inhibition caused by overexpression of MdRGL3a in Arabidopsis. Taken together, our findings indicate that MdBT2 promotes nitrate-induced plant growth partially through reducing the abundance of the DELLA protein MdRGL3a.

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.

Nitrogen Supply Alters Rice Defense Against the Striped Stem Borer Chilo suppressalis

Plant nutrition status is closely associated with plant defense against insect herbivores. However, the way nitrogen supply regulates rice anti-herbivore is not clear. This study investigated the effects of low (LN, 0.3 mM) and high (HN, 3 mM) nitrate levels on rice resistance against the striped stem borer Chilo suppressalis (SSB), one of the major destructive rice pests. Seven-day-old rice seedlings were cultured with different nitrate levels for 30 days and then inoculated with third instars of SSB. LN significantly enhanced rice anti-herbivore defense and lowered the total nitrogen content in the plants, but increased the content of free amino acids after SSB infestation. Additionally, LN significantly increased the accumulation of phenolic acids and flavonoids, especially lignin, resulting in enhanced constitutive defense in SSB-infested plants. SSB feeding led to a rapid accumulation of secondary metabolites. HN application led to the accumulation of metabolites derived from cinnamic acid, p-coumaric acid, p-coumaric CoA, feruloyl CoA, and apigenin, while LN led to the accumulation of metabolites derived from 3-dehydroquinic acid, phenylalanine, acetyl CoA, and aspartic acid. Collectively, our finding suggests that nitrogen deficiency enhances rice anti-herbivore defense via constitutive defense by the accumulation of phenolic acids and flavonoids.

The Photosynthetic Bacterium Rhodopseudomonas palustris Strain PS3 Exerts Plant Growth-Promoting Effects by Stimulating Nitrogen Uptake and Elevating Auxin Levels in Expanding Leaves

Rhodopseudomonas palustris strain PS3, a phototrophic bacterium, was originally isolated from a paddy field located in Taipei city, Taiwan, and showed positive effects on the growth of leafy vegetables. The aim of this study was to clarify the mechanism of the beneficial effects exerted by PS3 on plants. An ineffective R. palustris strain, YSC3, isolated from a paddy field located in Yilan County, was used as the negative control for comparative analyses. We cultivated non-heading Chinese cabbage (Brassica rapa var. chinensis) in 1/2 strength Hoagland hydroponic solution, in which nitrate is the main nitrogen source. We evaluated various plant physiological responses to inoculation with different bacterial inoculants. The N use efficiency (NUE) of PS3-inoculated plants was dramatically higher than that of YSC3-inoculated plants. The nitrate uptake efficiency (NUpE) was significantly elevated in plants treated with PS3; however, no excess nitrate accumulation was observed in leaves. We also noticed that the endogenous indole-3-acetic acid (IAA) levels as well as the cell division rate in the leaves of PS3-inoculated plants were significantly higher than those in the leaves of YSC3-inoculated plants. We examined the bacterial transcription of some genes during root colonization, and found that the expression level of IAA synthesis related gene MAO was almost the same between these two strains. It suggests that the elevated endogenous IAA in the PS3-inoculated plants was not directly derived from the exogenous IAA produced by this bacterium. Taken together, we deduced that PS3 inoculation could promote plant growth by enhancing nitrate uptake and stimulating the accumulation of endogenous auxin in young expanding leaves to increase the proliferation of leaf cells during leaf development.

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.

Low auxin sensitivity of diageotropica tomato mutant alters nitrogen deficiency response

Plant responses to nitrogen supply are dependent on auxin signaling, but much still remains to be elucidated regarding N deficiency in tomato. Thus, the objective of this work was to evaluate how low auxin sensitivity regulates the responses of tomato plants to N deficiency. For this purpose, we used the tomato diageotropica mutant, with low auxin sensitivity, and a near isogenic line cv. Micro-Tom grown in nutrient solutions under absence and presence of nitrogen. Plant height, stem diameter, root and shoot dry mass, area and root density, number of lateral roots, leaf area, chlorophylls and carotenoids content, nitrogen accumulation and nitrogen use efficiency were evaluated. We observed a clear interaction between the tomato genotype and nitrogen. When the plants were grown with nitrogen, 'Micro-Tom' showed higher growth than the diageotropica mutant. Under nitrogen deficiency condition, the mutant showed improved growth, nitrogen use efficiency and higher contents of pigments. In general, the low sensitivity to auxin in diageotropica caused reduced growth in both shoot and root. However, the diageotropica tomato showed a positive regulation of the nitrogen use efficiency under nitrogen deficiency. In general, our data revealed that the reduced sensitivity to auxin increased the adaptive capacity to the nitrogen deficiency.

Low nitrogen induces root elongation via auxin-induced acid growth and auxin-regulated target of rapamycin (TOR) pathway in maize

Under low nitrogen (N) supply, an important adaption of the maize root system is to promote the root elongation so as to increase N uptake from a larger soil space. The underlying physiological mechanism is largely unknown. In the present study, two maize inbred lines (Ye478 and Wu312) were used to study the possible involvement of the auxin and target of rapamycin (TOR) pathway in low-N-induced root elongation. Compared to Wu312, primary root elongation of Ye478 was more sensitive to low nitrate supply. Correspondingly, more auxin was accumulated in the root tip, and more protons were secreted, increasing the acidity of the apoplast space. On the other hand, low-N-induced root elongation was greatly reduced when shoot-to-root auxin transport was inhibited by applying N-1-naphthylphthalamic acid (NPA) at the plant base or by pruning the top leaf where auxin is mostly synthesized. Furthermore, exogenous application of TOR inhibitor also eliminated the response of root elongation under low N. The content of TOR kinase and the expression of TOR pathway-related genes were significantly changed when shoot-to-root auxin transport was reduced by NPA treatment. Taken together, it is concluded that low-N stress increases shoot-to-root auxin transport which enhances root elongation via auxin-dependent acid growth and the auxin-regulated TOR pathway in maize.

The auxin-resistant dgt tomato mutant grows less than the wild type but is less sensitive to ammonium toxicity and nitrogen deficiency

The low-auxin-sensitivity tomato mutant, dgt, despite displaying reduced plant growth, has been linked to greater resistance to N deficiency. This led us to test the role of auxin resistance of dgt in NH₄⁺ toxicity and N deficiency, compared to wild type tomato (cv. Micro-Tom, MT), grown in hydroponic media. A completely randomized design with three replications in a 2 × 4 factorial scheme was adopted, corresponding to the two tomato genotypes (MT and dgt), involving four nutritional treatments: NO₃^- (5 mM); NH₄⁺ (5 mM); NO₃^- (5 mM) plus exogenous auxin (10 μM IAA); and N omission. The results show that NH₄⁺ was toxic to MT but not to dgt. Under N deficiency, MT displayed a lower shoot NO₃^- content, a lower photosynthetic rate, and a decrease in both shoot and root dry weight. However, in dgt, no difference was observed in shoot NO₃^- content and photosynthetic rate between plants grown on NO₃^- or under N deficiency. In addition, dgt showed an increase in shoot dry weight under N deficiency. We highlight the role of auxin resistance in the adaptation of plants to NH₄⁺ toxicity and N deficiency.

Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture

The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant’s response to low nitrogen (N) availability. The global expression profiles of root tissues collected from low and high N treatments at different time points in two rice genotypes, Pokkali and Bengal, with contrasting responses to N stress and contrasting root architectures were examined. Overall, the number of differentially expressed genes (DEGs) in Pokkali (indica) was higher than in Bengal (japonica) during low N and early N recovery treatments. Most low N DEGs in both genotypes were downregulated whereas early N recovery DEGs were upregulated. Of these, 148 Pokkali-specific DEGs might contribute to Pokkali’s advantage under N stress. These DEGs included transcription factors and transporters and were involved in stress responses, growth and development, regulation, and metabolism. Many DEGs are co-localized with quantitative trait loci (QTL) related to root growth and development, chlorate-resistance, and NUE. Our findings suggest that the superior growth performance of Pokkali under low N conditions could be due to the genetic differences in a diverse set of genes influencing N uptake through the regulation of root architecture.

Silencing the Oryza sativa plasma membrane H+-ATPase isoform OsA2 affects grain yield and shoot growth and decreases nitrogen concentration

The plasma membrane (PM) H⁺-ATPase (EC 3.6.1.3.) is a key component involved in nutrient uptake. There are 10 PM H⁺-ATPase isoforms in the rice genome (OsA1-OsA10), and OsA2 is highly responsive to nitrate (NO₃^-). We investigated the role that the OsA2 isoform plays in the total N and growth of rice (Oryza sativa). By the use of artificial microRNA, mutant osa2 rice lines presented ∼70 % downregulated levels of OsA2. Three osa2 lines and control plants (transformed with an empty IRS154 vector and named IRS) were cultivated in the greenhouse to evaluate grain and shoot production. For hydroponic experiments, the same lines were grown in Hoagland solution under two different NO₃^- levels for 30 days - 0.2 mM NO₃^--N (low N) or 2.0 mM NO₃^--N (sufficient N) - or were grown for three days without NO₃^- (starvation) after 27 days under 2.0 mM NO₃^--N. In the greenhouse experiments, compared with the IRS plants, the osa2 lines had lower shoot fresh weights, grain yields and SPAD values. Moreover, compared with the IRS plants, the three osa2 lines grown hydroponically under low NO₃^- levels had lower N concentration and net flux of NO₃^-. PM H⁺-ATPase activity was lower in the osa2 mutants than in the IRS plants. The relatively low N concentration in the osa2 lines was not due to lower expression of OsNRT2.1, OsNRT2.2, or OsNAR2.1. These results indicate that the specific PM H⁺-ATPase isoform OsA2 affects the net flux of NO₃^-, N concentration, and grain yield.

Getting more bark for your buck: nitrogen economy of deciduous forest trees

This article comments on:

Li G, Lin R, Egekwu C, Blakeslee J, Lin J, Pettengill E, Murphy AS, Peer WA, Islam N, Babst BA, Gao F, Komarov S, Tai Y-C, Coleman GD. 2020. Seasonal nitrogen remobilization and the role of auxin transport in poplar trees. Journal of Experimental Botany 71, 4512–4530.

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.

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.

OsNAR2.2 plays a vital role in the root growth and development by promoting nitrate uptake and signaling in rice

Plants in soil faces great fluctuations of external mineral nutrient availability, and they have developed sophisticated nutrient sensing systems to regulate their physiological responses to prevent nutrient deficiency. However, complete knowledge of the regulatory system is required to maximize inorganic nitrogen (N) uptake and utilization. In this study, we report a partner protein for high-affinity nitrate transport, OsNAR2.2. OsNAR2.2 was involved in the root growth in a nitrate-dependent manner in rice, and this process was closely associated with auxin. Expression analysis showed that OsNAR2.2 responded to nitrate and various plant hormone signals. Knockdown of OsNAR2.2 by T-DNA insertion not only significantly repressed the primary root elongation, but also severely reduced the number of lateral root and adventitious root. Further research indicated that the size of meristematic zone and epidermal cell length of mature zone in the primary root tip were remarkably reduced, and the formation of lateral root primordial was constrained in osnar2.2 mutant. Interestingly, the repression of root growth in osnar2.2 mutant was observed when NO₃^- but not NH₄⁺ was used as N source in the medium. The NO₃^- content in osnar2.2 root was significantly reduced under NO₃^- conditions, in comparison with that of wild type. Meanwhile, the free IAA accumulation as well as the expression of auxin biosynthesis and transport genes was altered in osnar2.2 root, suggesting there might be a crosslink between the nitrate and auxin signaling. Together, OsNAR2.2 plays a vital role in rice root growth and development in a nitrate-dependent manner, which might be associated with auxin signaling.

Ammonium acts systemically while nitrate exerts an additional local effect on Medicago truncatula nodules

Symbiotic nitrogen fixation (SNF) has a high energetic cost for legume plants; legumes thus reduce SNF when soil N is available. The present study aimed to increase our understanding regarding the impacts of the two principal forms of available N in soils (ammonium and nitrate) on SNF. We continuously measured the SNF of Medicago truncatula under controlled conditions. This permitted nodule sampling for comparative transcriptome profiling at points connected to the nodules' reaction following ammonium or nitrate applications. The N component of both ions systemically induced a rhythmic pattern of SNF, while the activity in control plants remained constant. This rhythmic activity reduced the per-day SNF. The nitrate ion had additional local effects; the more pronounced were a strong downregulation of leghaemoglobin, nodule cysteine-rich (NCR) peptides and nodule-enhanced nicotianamine synthase (neNAS). The neNAS has proven to be of importance for nodule functioning. Although other physiological impacts of nitrate on nodules were observed (e.g. nitrosylation of leghaemoglobin), the main effect was a rapid ion-specific and organ-specific change in gene expression levels. Contrastingly, during the first hours after ammonium applications, the transcriptome remained virtually unaffected. Therefore, nitrate-induced genes could be key for increasing the nitrate tolerance of SNF.

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

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

Nitrate Induction of Primary Root Growth Requires Cytokinin Signaling in Arabidopsis thaliana

Nitrate can act as a potent signal to control growth and development in plants. In this study, we show that nitrate is able to stimulate primary root growth via increased meristem activity and cytokinin signaling. Cytokinin perception and biosynthesis mutants displayed shorter roots as compared with wild-type plants when grown with nitrate as the only nitrogen source. Histological analysis of the root tip revealed decreased cell division and elongation in the cytokinin receptor double mutant ahk2/ahk4 as compared with wild-type plants under a sufficient nitrate regime. Interestingly, a nitrate-dependent root growth arrest was observed between days 5 and 6 after sowing. Wild-type plants were able to recover from this growth arrest, while cytokinin signaling or biosynthesis mutants were not. Transcriptome analysis revealed significant changes in gene expression after, but not before, this transition in contrasting genotypes and nitrate regimes. We identified genes involved in both cell division and elongation as potentially important for primary root growth in response to nitrate. Our results provide evidence linking nitrate and cytokinin signaling for the control of primary root growth in Arabidopsis thaliana.

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.

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.

Role of auxin homeostasis and response in nitrogen limitation and dark stimulation of adventitious root formation in petunia cuttings

BACKGROUND AND AIMS

Adventitious root (AR) formation in Petunia hybrida is inhibited by low nitrogen fertilization of stock plants but promoted by dark incubation of cuttings before planting. We investigated whether the plant hormone auxin is involved in nitrogen- and dark-mediated AR formation.

METHODS

Concentrations of indole-3-acetic acid (IAA) and RNA accumulation of genes controlling auxin homeostasis and function were monitored in the stem base in response to high versus low nitrogen supply to stock plants and to temporal dark vs. light exposure of cuttings by use of GC-MS/MS, a petunia-specific microarray and quantitative RT-PCR. Auxin source capacity, polar auxin transport in cuttings and auxin concentration in the rooting zone were manipulated to investigate the functional contribution of auxin homeostasis and response to the effects of nitrogen fertilization and dark exposure on rooting.

KEY RESULTS

The nitrogen content of cuttings had only a marginal effect on IAA concentration in the stem base. Dark incubation enhanced the accumulation of IAA in the stem base during AR induction independent of nitrogen level. Early IAA accumulation in the dark depended on the upper shoot as an auxin source and was enhanced after apical IAA supply. Dark exposure stimulated RNA accumulation of auxin-related genes. In particular, expression of Ph-PIN1 and of genes controlling auxin signalling, including Ph-IAA14, Ph-ARF8, Ph-ARF10 and Ph-SAUR14, was enhanced, while the latter four were repressed in nitrogen-limited cuttings, particularly in the dark. Dark stimulation of rooting depended on polar auxin transport. Basal auxin application partially substituted the effect of dark exposure on rooting, whereas the auxin response of AR formation was strongly depressed by nitrogen limitation.

CONCLUSIONS

Increased auxin delivery from the upper shoot and enhanced auxin signalling in the stem base contribute to dark-stimulated AR formation, while nitrogen limitation inhibits AR formation downstream of the auxin signal.

TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture

Developmental processes that control root system architecture are critical for soil exploration by plants, allowing for uptake of water and nutrients. Conversion of the auxin precursor indole-3-butyric acid (IBA) to active auxin (indole-3-acetic acid; IAA) modulates lateral root formation. However, mechanisms governing IBA-to-IAA conversion have yet to be elucidated. We identified TRANSPORTER OF IBA1 (TOB1) as a vacuolar IBA transporter that limits lateral root formation. Moreover, TOB1, which is transcriptionally regulated by the phytohormone cytokinin, is necessary for the ability of cytokinin to exert inhibitory effects on lateral root production. The increased production of lateral roots in tob1 mutants, TOB1 transport of IBA into the vacuole, and cytokinin-regulated TOB1 expression provide a mechanism linking cytokinin signaling and IBA contribution to the auxin pool to tune root system architecture.

CmTCP20 Plays a Key Role in Nitrate and Auxin Signaling-Regulated Lateral Root Development in Chrysanthemum

Lateral root (LR) formation and development play a vital role in plant development by permitting the establishment of branched root systems. It is well known that nutrient availability controls LR development. Moreover, LR development is fine-tuned by a myriad of hormonal signals. Many transcription factors (TFs) participate in LR development. Here, we discuss the TFs involved in the nitrate and auxin signaling pathways and how these function in the regulation of LR formation and development in chrysanthemum. AtTCP20 is a plant-specific TF, which can modulate LR development in response to nitrate. The roles of CmTCP20 in LR development were identified by overexpression in chrysanthemum and heterologous expression in Arabidopsis. Overexpression of CmTCP20 significantly increased the number and average length of LRs compared with the wild type in chrysanthemum and Arabidopsis. We also found that CmTCP20 positively influenced auxin accumulation in the LRs at least partly by improving auxin biosynthesis, transport and response, thereby promoting LR development. Moreover, we found that CmTCP20 interacts with an auxin response factor, CmARF8, which also can be induced by nitrate and combined to proximal sites in the upstream promoter region of CmCYCB1;1 to positively regulate the cell cycle. The CmTCP20-CmARF8 heterodimer links nitrate and auxin signaling and converts cell-cycle signals to regulate LR initiation and growth.

Determination of the [15N]-Nitrate/[14N]-Nitrate Ratio in Plant Feeding Studies by GC⁻MS

Feeding experiments with stable isotopes are helpful tools for investigation of metabolic fluxes and biochemical pathways. For assessing nitrogen metabolism, the heavier nitrogen isotope, [¹⁵N], has been frequently used. In plants, it is usually applied in form of [¹⁵N]-nitrate, which is assimilated mainly in leaves. Thus, methods for quantification of the [¹⁵N]-nitrate/[¹⁴N]-nitrate ratio in leaves are useful for the planning and evaluation of feeding and pulse–chase experiments. Here we describe a simple and sensitive method for determining the [¹⁵N]-nitrate to [¹⁴N]-nitrate ratio in leaves. Leaf discs (8 mm diameter, approximately 10 mg fresh weight) were sufficient for analysis, allowing a single leaf to be sampled multiple times. Nitrate was extracted with hot water and derivatized with mesitylene in the presence of sulfuric acid to nitromesitylene. The derivatization product was analyzed by gas chromatography–mass spectrometry with electron ionization. Separation of the derivatized samples required only 6 min. The method shows excellent repeatability with intraday and interday standard deviations of less than 0.9 mol%. Using the method, we show that [¹⁵N]-nitrate declines in leaves of hydroponically grown Crassocephalum crepidioides, an African orphan crop, with a biological half-life of 4.5 days after transfer to medium containing [¹⁴N]-nitrate as the sole nitrogen source.

NRT1.1 Regulates Nitrate Allocation and Cadmium Tolerance in Arabidopsis

Abiotic stress induces nitrate (NO3 -) allocation to roots, which increases stress tolerance in plants. NRT1.1 is broadly involved in abiotic stress tolerance in plants, but the relationship between NRT1.1 and NO3 - allocation under stress conditions is unclear. In this study, we found that Arabidopsis wild-type Col-0 was more cadmium (Cd2+)-tolerant than the nrt1.1 mutant at 20 μM CdCl2. Cd2+ exposure repressed NRT1.5 but upregulated NRT1.8 in roots of Col-0 plants, resulting in increased NO3 - allocation to roots and higher [NO3 -] root-to-shoot (R:S) ratios. Interestingly, NITRATE REGULATORY GENE2 (NRG2) was upregulated by Cd2+ stress in Col-0 but not in nrt1.1. Under Cd2+ stress, nrg2 and nrg2-3chl1-13 mutants exhibited similar phenotypes and NO3 - allocation patterns as observed in the nrt1.1 mutant, but overexpression of NRG2 in Col-0 and nrt1.1 increased the [NO3 -] R:S ratio and restored Cd2+ stress tolerance. Our results indicated that NRT1.1 and NRG2 regulated Cd2+ stress-induced NO3 - allocation to roots and that NRG2 functioned downstream of NRT1.1. Cd2+ uptake did not differ between Col-0 and nrt1.1, but Cd2+ allocation to roots was higher in Col-0 than in nrt1.1. Stressed Col-0 plants increased Cd2+ and NO3 - allocation to root vacuoles, which reduced their cytosolic allocation and transport to the shoots. Our results suggest that NRT1.1 regulates NO3 - allocation to roots by coordinating Cd2+ accumulation in root vacuoles, which facilitates Cd2+ detoxification.

An Update on the Signals Controlling Shoot Branching

Many new questions on the regulation of shoot branching have been raised in recent years, prompting a review and reassessment of the role of each signal involved. Sugars and their signaling networks have been attributed a major role in the early events of axillary bud outgrowth, whereas cytokinin appears to play a critical role in the modulation of this process in response to the environment. Perception of the recently discovered hormone strigolactone is now quite well understood, while the downstream targets remain largely unknown. Recent literature has highlighted that auxin export from a bud is important for its subsequent growth.

A novel function of N-signaling in plants with special reference to Trichoderma interaction influencing plant growth, nitrogen use efficiency, and cross talk with plant hormones

Trichoderma spp. is considered as a plant growth promoter and biocontrol fungal agents. They colonize on the surface of root in most of the agriculture crops. They secrete different secondary metabolites and enzymes which promote different physiological processes as well as protect plants from various environmental stresses. This is part of their vital functions. They are widely exploited as a biocontrol agent and plant growth promoter in agricultural fields. Colonization of Trichoderma with roots can enhance nutrient acquisition from surrounding soil to root and can substantially increase nitrogen use efficiency (NUE) in crops and linked with activation of plant signaling cascade. Among Trichoderma species, only some Trichoderma species were well characterized which help in the uptake of nitrogen-containing compound (especially nitrate form) and induced nitric oxide (NO) in plants. Both nitrate and NO are known as a signaling agent, involved in plant growth and development and disease resistance. Activation of these signaling molecules may crosstalk with other signaling molecule (Ca²⁺) and phytohormone (auxin, gibberellins, cytokinin and ethylene). This ability of Trichoderma is important to agriculture not only for increased plant growth but also to control plant diseases. Recently, Trichoderma strains have been shown to encompass the ability to regulate transcripts level of high-affinity nitrate transporters and probably it was positively regulated by NO. This review aims to focus the usage of Trichoderma strains on crops by their abilities to regulate transcript levels, probably through activation of plant N signaling transduction that improve plant health.

OsMADS27 regulates the root development in a NO3--Dependent manner and modulates the salt tolerance in rice (Oryza sativa L.)

OsMADS27 is one of the ANR1-like homologues in rice, whreas its functions in plant growth and development as well as the abiotic stress responses remain unclear. Here we investigated the roles of OsMADS27 in the root development in response to NO₃- availability. Constitutive expression of OsMADS27 significantly inhibited the elongation of primary root (PR), but enhanced lateral root (LR) formation in a NO₃--dependent manner. Furthermore, OsMADS27 overexpression promoted NO₃- accumulation as well as the expression of NO₃- transporter genes. ABA is reported to play an important role in mediating the effects of NO₃- on the root development, thus it is supposed that OsMADS27 might regulate the root growth and development by ABA pathway. The root growth and development in OsMADS27 overexpression lines was shown to be more sensitive to exogenous ABA than wild type. Moreover, under NO₃- conditions, higher levels of ABA accumulates in OsMADS27 overexpression plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays showed that OsMADS27 physically interacts with ABA-INSENSITIVE5 (OsABI5) via DELLA protein OsSLR1. More importantly, OsMADS27 overexpression could enhance the salt tolerance. Taken together, our findings suggested that OsMADS27 is an important regulator controlling the root system development and adaption to osmotic stress in rice.

Auxins and Cytokinins-The Role of Subcellular Organization on Homeostasis

Plant hormones are master regulators of plant growth and development. Better knowledge of their spatial signaling and homeostasis (transport and metabolism) on the lowest structural levels (cellular and subcellular) is therefore crucial to a better understanding of developmental processes in plants. Recent progress in phytohormone analysis at the cellular and subcellular levels has greatly improved the effectiveness of isolation protocols and the sensitivity of analytical methods. This review is mainly focused on homeostasis of two plant hormone groups, auxins and cytokinins. It will summarize and discuss their tissue- and cell-type specific distributions at the cellular and subcellular levels.