Rice DUR3 mediates high-affinity urea transport and plays an effective role in improvement of urea acquisition and utilization when expressed in Arabidopsis

A Glutamate Receptor-Like Gene AtGLR25 With Its Unusual Splice Variant Has a Role in Mediating Glutamate-Elicited Changes in Arabidopsis Root Architecture

The occurrence of external L-glutamate at the Arabidopsis root tip triggers major changes in root architecture, but the mechanism of -L-Glu sensing is unknown. Members of the family of GLUTAMATE RECEPTOR-LIKE (GLR) proteins are known to act as amino acid-gated Ca2+-permeable channels and to have signalling roles in diverse plant processes. To investigate the possible role of GLRs in the root architectural response to L-Glu, we screened a collection of mutants with T-DNA insertions in each of the 20 AtGLR genes. Reduced sensitivity of root growth to L-Glu was found in mutants of one gene, GLR2.5. Interestingly, GLR2.5 was found to apparently produce four transcript variants encoding hypothetical proteins of 169-720 amino acids. One of these transcripts, GLR2.5c, encodes a truncated GLR protein lacking both the conserved amino-terminal domain and part of the ligand-binding domain. When a glr2.5 mutant was transformed with a construct constitutively expressing GLR2.5c, both L-Glu sensitivity of root growth and L-Glu-elicited Ca2+ currents in root tip protoplasts were restored. These results, along with homology modelling of the truncated ligand-binding domain of GLR2.5c, suggest that GLR2.5c has a regulatory or scaffolding role in heteromeric GLR complex(es) that may involve triggering the root architectural response to L-Glu.

Understanding fungal and plant active urea transport systems: Keys from Aspergillus nidulans and beyond

Urea is present in all ecosystems, as a result of the metabolism of different organisms and also of human activity, being the world's most common form of nitrogen fertilizer. Fungi and plants can use urea as a nitrogen source, taking it up from the environment through specialized active transport proteins. These proteins belong to a subfamily of urea/H+ symporters included in the Solute:Sodium Symporter (SSS) family of transporters. In this review we summarize the current knowledge on this group of transporters, based on our previous studies on Aspergillus nidulans UreA. We delve into its transcriptional and post-translational regulation, structure-function relationships, transport mechanism, and certain aspects of its biogenesis. Recent findings suggest that this urea transporter subfamily is more expanded than originally thought, with representatives found in organisms as diverse as Archaea and mollusks, which raises questions on evolutionary aspects. A. nidulans ureA knockout strains provide a valuable platform for expressing urea transporters from diverse sources, facilitating their characterization and functional analysis. In this context, given the close relationship between plant and fungal active urea transporters, this knowledge could serve to develop strategies to improve the efficiency of applied urea as fertilizer.

Transcriptomics combined with physiological analysis and metabolomics revealed the response of potato tuber formation to nitrogen

The absorption of the essential element nitrogen by plants affects various aspects of plant physiological activity, including gene expression, metabolite content and growth. However, the molecular mechanism underlying the potato tuberization response to nitrogen remains unclear. Potato plants were subjected to pot experiments under nitrogen deficiency, normal nitrogen levels and nitrogen sufficiency. A comprehensive analysis of the physiological responses, transcriptomic profiles, and metabolic pathways of potato stolons subjected to nitrogen stress was conducted. Transcriptomic analysis revealed 2756 differentially expressed genes (DEGs) associated with nitrogen stress. Metabolomic analysis identified a total of 600 differentially accumulated metabolites (DAMs). Further correlation analysis of the major DEGs and DAMs revealed that 9 key DEGs were associated with alpha-linolenic acid metabolism, 16 key DEGs with starch and sucrose metabolism, 7 key DEGs with nitrogen metabolism, and 16 key DEGs with ABC transporters. Nitrogen deficiency significantly increased the sucrose, GDP-glucose and L-glutamic acid levels and promoted stolon growth by increasing the expression of AMY (alpha-amylase), BE (1,4-alpha-glucan branching enzyme), SS (starch synthase), SPS (sucrose‒phosphate synthase) and AGPS (glucose‒1-phosphate adenylyltransferase). However, high nitrogen levels had the opposite effect. In addition, high nitrogen levels upregulated EG (endoglucanase), SUS (sucrose synthase) and GDH (glutamate dehydrogenase) and led to significant accumulation of 9-Hydroperoxy-10,12,15-octadecatrienoate (9(S)-HpOTrE), (13 S)-Hydroperoxyoctadeca-9,11,15-trienoate (13 (S)-HpOTrE) and L-glutamine, ultimately affecting the balance between plant growth and defense. Overall, our comprehensive study revealed the co-expressed genes and potential pathways related to potato tuber formation under different nitrogen conditions. These data provide a better understanding needed for improving potato tuber traits at the molecular and metabolic levels.

A multi-omics insight on the interplay between iron deficiency and N forms in tomato

Introduction

Nitrogen (N) and iron (Fe) are involved in several biochemical processes in living organisms, and their limited bioavailability is a strong constraint for plant growth and yield. This work investigated the interplay between Fe and N nutritional pathways in tomato plants kept under N and Fe deficiency and then resupplied with Fe and N (as nitrate, ammonium, or urea) through a physiological, metabolomics and gene expression study.

Results

After 24 hours of Fe resupply, the Fe concentration in Fe-deficient roots was dependent on the applied N form (following the pattern: nitrate > urea > ammonium > Fe-deficient control), and whereas in leaves of urea treated plants the Fe concentration was lower in comparison to the other N forms. Untargeted metabolomics pointed out distinctive modulations of plant metabolism in a treatment-dependent manner. Overall, N-containing metabolites were affected by the treatments in both leaves and roots, while N form significantly shaped the phytohormone profile. Moreover, the simultaneous application of Fe with N to Fe-deficient plants elicited secondary metabolites' accumulation, such as phenylpropanoids, depending on the applied N form (mainly by urea, followed by nitrate and ammonium). After 4 hours of treatment, ammonium- and urea-treated roots showed a reduction of enzymatic activity of Fe(III)-chelate reductase (FCR), compared to nitrate or N-depleted plants (maintained in Fe deficiency, where FCR was maintained at high levels). The response of nitrate-treated plants leads to the improvement of Fe concentration in tomato roots and the increase of Fe(II) transporter (IRT1) gene expression in tomato roots.

Conclusions

Our results strengthen and improve the understanding about the interaction between N and Fe nutritional pathways, thinning the current knowledge gap.

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.

Heat stress memory differentially regulates the expression of nitrogen transporter genes in the filamentous red alga 'Bangia' sp. ESS1

Introduction

To withstand high temperatures that would be lethal to a plant in the naïve state, land plants must establish heat stress memory. The acquisition of heat stress tolerance via heat stress memory in algae has only been observed in the red alga 'Bangia' sp. ESS1.

Methods

In this study, we further evaluated the intrinsic ability of this alga to establish heat stress memory by monitoring hydrogen peroxide (H2O2) production and examining the relationship between heat stress memory and the expression of genes encoding nitrogen transporters, since heat stress generally reduces nitrogen absorption. Next, genes encoding nitrogen transporters were selected from our unpublished transcriptome data of 'Bangia' sp. ESS1.

Results

We observed a reduction in H2O2 content when heat stress memory was established in the alga. In addition, six ammonium transporter genes, a single-copy nitrate transporter gene and two urea transporter genes were identified. Two of these nitrogen transporter genes were induced by heat stress but not by heat stress memory, two genes showed heat stress memory-dependent expression, and one gene was induced by both treatments. Heat stress memory therefore differentially regulated the expression of the nitrogen transporter genes by reducing heat stress-inducible gene expression and inducing heat stress memory-dependent gene expression.

Discussion

These findings point to the functional diversity of nitrogen transporter genes, which play different roles under various heat stress conditions. The characteristic effects of heat stress memory on the expression of individual nitrogen transporter genes might represent an indispensable strategy for reducing the threshold of sensitivity to recurrent high-temperature conditions and for maintaining nitrogen absorption under such conditions in 'Bangia' sp. ESS1.

Effects of Funneliformis mosseae on Growth and Photosynthetic Characteristics of Camellia oleifera under Different Nitrogen Forms

Nitrogen fertilizer increases agricultural yields but increases economic costs and causes a series of environmental problems. Arbuscular mycorrhizal fungi (AMF) have the potential to be used as biological fertilizer. However, the influence of nitrogen form on plant growth responsiveness to AMF inoculation is poorly understood. In this study, we investigated the effects of Funneliformis mosseae on growth, root morphology and photosynthetic characteristics of Camellia oleifera under different nitrogen forms during three harvest periods and clarified the most suitable nitrogen form for C. oleifera-AMF symbiosis. The results showed that urea, ammonium and nitrate nitrogen promoted plant growth and photosynthetic capacity, among which urea treatment had the highest value in all three harvests. No significant difference in plant growth parameters was observed between ammonium and nitrate nitrogen treatments in the first two harvests, while the plant height was significantly lower under ammonium nitrogen treatment than nitrate nitrogen treatment in the third harvest. Inoculation with F. mosseae in the presence of indigenous AMF could promote AMF colonization and plant growth at all three harvest times. Inoculation with F. mosseae significantly increased gas exchange parameters, the maximum photochemical efficiency (Fv/Fm) and the actual photochemical efficiency (ΦPSII). Inoculation with AMF increased the photochemical quenching coefficient (qP) better under urea treatment and improved the non-photochemical quenching coefficient (qN) better under ammonium nitrogen treatment. Principal component analysis showed that urea is the most beneficial nitrogen fertilizer for C. oleifera-AMF symbiosis. The results of this study provide a theoretical basis for the combination use of AMF and nitrogen fertilizer in agroforestry.

Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.

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.

The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites

The root-colonizing endophytic fungus Piriformospora indica promotes the root and shoot growth of its host plants. We show that the growth promotion of Arabidopsis thaliana leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote 15NO3- uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with 15N-labelled P. indica, more labels were detected in the leaves of N-starved host plants but not in plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as the expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host from the N limitation condition. P. indica alters the expression of transporter genes, which participate in the relocation of NO3-, NH4+ and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant's metabolomic adaptation against N limitation by delivering reduced N metabolites to the host, thus alleviating metabolic N starvation responses and reprogramming the expression of N metabolism-related genes.

Integrated transcriptomic analysis identifies coordinated responses to nitrogen and phosphate deficiency in rice

Nitrogen (N) and phosphorus (P) are two primary components of fertilizers for crop production. Coordinated acquisition and utilization of N and P are crucial for plants to achieve nutrient balance and optimal growth in a changing rhizospheric nutrient environment. However, little is known about how N and P signaling pathways are integrated. We performed transcriptomic analyses and physiological experiments to explore gene expression profiles and physiological homeostasis in the response of rice (Oryza sativa) to N and P deficiency. We revealed that N and P shortage inhibit rice growth and uptake of other nutrients. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) suggested that N and Pi deficiency stimulate specific different physiological reactions and also some same physiological processes in rice. We established the transcriptional regulatory network between N and P signaling pathways based on all DEGs. We determined that the transcript levels of 763 core genes changed under both N or P starvation conditions. Among these core genes, we focused on the transcription factor gene NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1) and show that its encoded protein is a positive regulator of P homeostasis and a negative regulator of N acquisition in rice. NIGT1 promoted Pi uptake but inhibited N absorption, induced the expression of Pi responsive genes PT2 and SPX1 and repressed the N responsive genes NLP1 and NRT2.1. These results provide new clues about the mechanisms underlying the interaction between plant N and P starvation responses.

Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice

Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.

Sustaining nitrogen dynamics: A critical aspect for improving salt tolerance in plants

In the current changing environment, salt stress has become a major concern for plant growth and food production worldwide. Understanding the mechanisms of how plants function in saline environments is critical for initiating efforts to mitigate the detrimental effects of salt stress. Agricultural productivity is linked to nutrient availability, and it is expected that the judicious metabolism of mineral nutrients has a positive impact on alleviating salt-induced losses in crop plants. Nitrogen (N) is a macronutrient that contributes significantly to sustainable agriculture by maintaining productivity and plant growth in both optimal and stressful environments. Significant progress has been made in comprehending the fundamental physiological and molecular mechanisms associated with N-mediated plant responses to salt stress. This review provided an (a) overview of N-sensing, transportation, and assimilation in plants; (b) assess the salt stress-mediated regulation of N dynamics and nitrogen use- efficiency; (c) critically appraise the role of N in plants exposed to salt stress. Furthermore, the existing but less explored crosstalk between N and phytohormones has been discussed that may be utilized to gain a better understanding of plant adaptive responses to salt stress. In addition, the shade of a small beam of light on the manipulation of N dynamics through genetic engineering with an aim of developing salt-tolerant plants is also highlighted.

Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter

Through a combination of comparative modeling, site-directed and classical random mutagenesis approaches, we previously identified critical residues for binding, recognition, and translocation of urea, and its inhibition by 2-thiourea and acetamide in the Aspergillus nidulans urea transporter, UreA. To deepen the structural characterization of UreA, we employed the artificial intelligence (AI) based AlphaFold2 (AF2) program. In this analysis, the resulting AF2 models lacked inward- and outward-facing cavities, suggesting a structural intermediate state of UreA. Moreover, the orientation of the W82, W84, N279, and T282 side chains showed a large variability, which in the case of W82 and W84, may operate as a gating mechanism in the ligand pathway. To test this hypothesis non-conservative and conservative substitutions of these amino acids were introduced, and binding and transport assessed for urea and its toxic analogue 2-thiourea, as well as binding of the structural analogue acetamide. As a result, residues W82, W84, N279, and T282 were implicated in substrate identification, selection, and translocation. Using molecular docking with Autodock Vina with flexible side chains, we corroborated the AF2 theoretical intermediate model, showing a remarkable correlation between docking scores and experimental affinities determined in wild-type and UreA mutants. The combination of AI-based modeling with classical docking, validated by comprehensive mutational analysis at the binding region, would suggest an unforeseen option to determine structural level details on a challenging family of proteins.

Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton

Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.

Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.)

BACKGROUND

Nitrogen (N) is a major element and fundamental constituent of grain yield. N fertilizer plays an essential role in the roots, shoots, and leaves of crop plants. Here, we obtained two N-sensitive potato cultivars.

RESULTS

The plants were cultivated in the pots using N-deficient and N-sufficient conditions. Crop height, leaf chlorophyll content, dry matter, and N-accumulation significantly decreased under N-deficient conditions. Furthermore, we performed a comprehensive analysis of the phenotype and transcriptome, GO terms, and KEGG pathways. We used WGCNA of co-expressed genes, and 116 differentially expressed hub genes involved in photosynthesis, nitrogen metabolism, and secondary metabolites to generate 23 modules. Among those modules, six NRT gene families, four pigment genes, two auxin-related genes, and two energy-related genes were selected for qRT-PCR validation.

CONCLUSIONS

Overall, our study demonstrates the co-expressed genes and potential pathways associated with N transport and accumulation in potato cultivars' roots, shoots, and leaves under N-deficient conditions. Therefore, this study provides new ideas to conduct further research on improving nitrogen use efficiency in potatoes.

Transcriptome and Proteomics Analysis of Wheat Seedling Roots Reveals That Increasing NH4 +/NO3 - Ratio Induced Root Lignification and Reduced Nitrogen Utilization

Wheat growth and nitrogen (N) uptake gradually decrease in response to high NH₄ ⁺/NO₃ ^- ratio. However, the mechanisms underlying the response of wheat seedling roots to changes in NH₄ ⁺/NO₃ ^- ratio remain unclear. In this study, we investigated wheat growth, transcriptome, and proteome profiles of roots in response to increasing NH₄ ⁺/NO₃ ^- ratios (N _a : 100/0; N _r1: 75/25, N _r2: 50/50, N _r3: 25/75, and N _n : 0/100). High NH₄ ⁺/NO₃ ^- ratio significantly reduced leaf relative chlorophyll content, Fv/Fm, and ΦII values. Both total root length and specific root length decreased with increasing NH₄ ⁺/NO₃ ^- ratios. Moreover, the rise in NH₄ ⁺/NO₃ ^- ratio significantly promoted O₂ ^- production. Furthermore, transcriptome sequencing and tandem mass tag-based quantitative proteome analyses identified 14,376 differentially expressed genes (DEGs) and 1,819 differentially expressed proteins (DEPs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that glutathione metabolism and phenylpropanoid biosynthesis were the main two shared enriched pathways across ratio comparisons. Upregulated DEGs and DEPs involving glutathione S-transferases may contribute to the prevention of oxidative stress. An increment in the NH₄ ⁺/NO₃ ^- ratio induced the expression of genes and proteins involved in lignin biosynthesis, which increased root lignin content. Additionally, phylogenetic tree analysis showed that both A0A3B6NPP6 and A0A3B6LM09 belong to the cinnamyl-alcohol dehydrogenase subfamily. Fifteen downregulated DEGs were identified as high-affinity nitrate transporters or nitrate transporters. Upregulated TraesCS3D02G344800 and TraesCS3A02G350800 were involved in ammonium transport. Downregulated A0A3B6Q9B3 is involved in nitrate transport, whereas A0A3B6PQS3 is a ferredoxin-nitrite reductase. This may explain why an increase in the NH₄ ⁺/NO₃ ^- ratio significantly reduced root NO₃ ^--N content but increased NH₄ ⁺-N content. Overall, these results demonstrated that increasing the NH₄ ⁺/NO₃ ^- ratio at the seedling stage induced the accumulation of reactive oxygen species, which in turn enhanced root glutathione metabolism and lignification, thereby resulting in increased root oxidative tolerance at the cost of reducing nitrate transport and utilization, which reduced leaf photosynthetic capacity and, ultimately, plant biomass accumulation.

Physiological and Molecular Investigation of Urea Uptake Dynamics in Cucumis sativus L. Plants Fertilized With Urea-Doped Amorphous Calcium Phosphate Nanoparticles

At present, the quest for innovative and sustainable fertilization approaches aiming to improve agricultural productivity represents one of the major challenges for research. In this context, nanoparticle-based fertilizers can indeed offer an interesting alternative with respect to traditional bulk fertilizers. Several pieces of evidence have already addressed the effectiveness of amorphous calcium phosphate-based nanoparticles as carriers for macronutrients, such as nitrogen (N), demonstrating increase in crop productivity and improvement in quality. Nevertheless, despite N being a fundamental nutrient for crop growth and productivity, very little research has been carried out to understand the physiological and molecular mechanisms underpinning N-based fertilizers supplied to plants via nanocarriers. For these reasons, this study aimed to investigate the responses of Cucumis sativus L. to amorphous calcium phosphate nanoparticles doped with urea (U-ACP). Urea uptake dynamics at root level have been investigated by monitoring both the urea acquisition rates and the modulation of urea transporter CsDUR3, whereas growth parameters, the accumulation of N in both root and shoots, and the general ionomic profile of both tissues have been determined to assess the potentiality of U-ACP as innovative fertilizers. The slow release of urea from nanoparticles and/or their chemical composition contributed to the upregulation of the urea uptake system for a longer period (up to 24 h after treatment) as compared to plants treated with bulk urea. This prolonged activation was mirrored by a higher accumulation of N in nanoparticle-treated plants (approximately threefold increase in the shoot of NP-treated plants compared to controls), even when the concentration of urea conveyed through nanoparticles was halved. In addition, besides impacting N nutrition, U-ACP also enhanced Ca and P concentration in cucumber tissues, thus having possible effects on plant growth and yield, and on the nutritional value of agricultural products.

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.

Characterization of physiological and molecular responses of Zea mays seedlings to different urea-ammonium ratios

Despite the wide use of urea and ammonium as N-fertilizers, no information is available about the proper ratio useful to maximize the efficiency of their acquisition by crops. Ionomic analyses of maize seedlings fed with five different mixes of urea and ammonium indicated that after 7 days of treatment, the elemental composition of plant tissues was more influenced by ammonium in the nutrient solution than by urea. Within 24 h, similar high affinity influx rates of ammonium were measured in ammonium-treated seedlings, independently from the amount of the cation present in the nutrient solution (from 0.5 to 2.0 mM N), and it was confirmed by the similar accumulation of ¹⁵N derived from ammonium source. After 7 days, some changes in ammonium acquisition occurred among treatments, with the highest ammonium uptake efficiency when the urea-to-ammonium ratio was 3:1. Gene expression analyses of enzymes and transporters involved in N nutrition highlight a preferential induction of the cytosolic N-assimilatory pathway (via GS, ASNS) when both urea and ammonium were supplied in conjunction, this response might explain the higher N-acquisition efficiency when both sources are applied. In conclusion, this study provides new insights on plant responses to mixes of N sources that maximize the N-uptake efficiency by crops and thus could allow to adapt agronomic practices in order to limit the economic and environmental impact of N-fertilization.

The function of high-affinity urea transporters in nitrogen-deficient conditions

Urea is the most used nitrogenous fertilizer worldwide and an important nitrogen-containing plant metabolite. Despite its major use as fertilizer, its direct uptake is limited due to the ubiquitous presence of bacterial urease, which leads to the formation of ammonium. In this review, we will focus mainly on the more recent research about the high-affinity urea transporter function in nitrogen-deficient conditions. The effective use of nitrogenous compounds is essential for plants to be able to deal with nitrogen-deficient conditions. Leaf senescence, either induced by development and/or by nitrogen deficiency, plays an important role in the efficient use of already assimilated nitrogen. Proteinaceous nitrogen is set free through catabolic reactions: the released amino acids from protein catabilization are in turn catabolized leading to an accumulation of ammonium and urea. The concentration and conversion to transportable forms of nitrogen, e.g. amino acids like glutamine and asparagine, are coordinated around the vascular tissue. Urea itself can be translocated directly over the phloem by a mechanism that involves DUR3, or it is converted by urease to ammonium and assimilated again into amino acids. The details of the high-affinity transporter function in this physiological context and the implications for crop yield are explained.

Chromosomal introgressions from Oryza meridionalis into domesticated rice Oryza sativa result in iron tolerance

Iron (Fe) toxicity is one of the most common mineral disorders affecting rice (Oryza sativa) production in flooded lowland fields. Oryza meridionalis is indigenous to northern Australia and grows in regions with Fe-rich soils, making it a candidate for use in adaptive breeding. With the aim of understanding tolerance mechanisms in rice, we screened a population of interspecific introgression lines from a cross between O. sativa and O. meridionalis for the identification of quantitative trait loci (QTLs) contributing to Fe-toxicity tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL was highly tolerant despite very high shoot Fe concentrations. Physiological, biochemical, ionomic, and transcriptomic analyses showed that the tolerance of the introgression lines could partly be explained by higher relative Fe retention in the leaf sheath and culm. We constructed the interspecific hybrid genome in silico for transcriptomic analysis and identified differentially regulated introgressed genes from O. meridionalis that could be involved in shoot-based Fe tolerance, such as metallothioneins, glutathione S-transferases, and transporters from the ABC and MFS families. This work demonstrates that introgressions of O. meridionalis into the O. sativa genome can confer increased tolerance to excess Fe.

The urea transporter DUR3 is differentially regulated by abiotic and biotic stresses in coffee plants

The high costs of N fertilizers in the coffee production emphasizes the need to optimize fertilization practices and improve nitrogen use efficiency. Urea is widespread in nature, characterizing itself as a significant source of nitrogen for the growth and development of several organisms. Thus, the characterization of genes involved in urea transport in coffee plants is an important research topic for the sustainable production of this valuable cash crop. In the current study, we evaluated the expression of the DUR3 gene under abiotic and biotic stresses in coffee plants. Here, we show that the expression of a high-affinity urea transporter gene (CaDUR3) was up-regulated by N starvation in leaves and roots of two out of three C. arabica cultivars examined. Moreover, the CaDUR3 gene was differentially expressed in coffee plants under different abiotic and biotic stresses. In plants of cv. IAPAR59, CaDUR3 showed an increased expression in leaves after exposure to water deficit and heat stress, while it was downregulated in plants under salinity. Upon infection with H. vastatrix (coffee rust), the CaDUR3 was markedly up-regulated at the beginning of the infection process in the disease susceptible Catuaí Vermelho 99 in comparison with the resistant cultivar. These results indicate that besides urea acquisition and N-remobilization, CaDUR3 gene may be closely involved in the response to various stresses.

Evidence that exogenous urea acts as a potent cue to alleviate ammonium-inhibition of root system growth of cotton plant (Gossypium hirsutum)

Many plants grown with low-millimolar concentration of NH₄ ⁺ as a sole nitrogen source develop NH₄ ⁺ -toxicity symptoms. To date, crucial molecular identities and a practical approach involved in the improvement of plant NH₄ ⁺ -tolerance remain largely unknown. By phenotyping of upland cotton grown on varied nitrogen forms, we came across a phenomenon that caused sub-millimolar concentrations of urea (e.g., up 50 μM) to repress the growth inhibition of roots and whole plant cultivated in a NH₄ ⁺ -containing nutrient solution. A growth-recovery assay revealed that the relief in NH₄ ⁺ -inhibited growth required only a short-term exposure (≧12 h) of the roots to urea, implying that urea could elicit an internal signaling and be involved in antagonizing NH₄ ⁺ -sensitivity. Intriguingly, split-root experiments demonstrated that low urea occurrence in one root-half could efficaciously stimulate not only supplied root but also the root-half grown in NH₄ ⁺ -solution without urea, indicating the existence of urea-triggered local and systemic long-distance signaling. In the split-root experiment we also observed high arginase activity, strong arginine reduction and remarkable upregulation of polyamine biosynthesis-related genes (ADC1/2, SPDS and SPMS). Therefore, we suggest that external urea might serve as an effective cue (signal molecule) in an arginine-/polyamine-related process for ameliorating NH₄ ⁺ -suppressed root growth, providing a novel aspect for deeper exploring and understanding plant NH₄ ⁺ -tolerance.

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

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

Phenotypical evidence of effective amelioration of ammonium-inhibited plant (root) growth by exogenous low urea

Ammonium and nitrate are major soil inorganic-nitrogen sources for plant growth, but many species cultivated with even low millimolar NH₄⁺ as a sole N form display a growth retardation. To date, critical biological components and applicable approaches involved in the effective enhancement of NH₄⁺ tolerance remain to be thoroughly explored. Here, we report phenotypical traits of urea-dependent improvement of NH₄⁺-suppressed plant/root growth. Urea at 0.1 mM was sufficient to remarkably stimulate NH₄⁺ (3 mM)-fed cotton growth, showing a 2.5∼4-fold increase in shoot- and root-biomass and total root-length, 20 % higher GS activity, 18 % less NH₄⁺-accumulation in roots, and a comparable plant total-N content compared to the control, implying a novel role for urea in cotton NH₄⁺detoxification. A similar phenomenon was observed in tobacco and rice. Moreover, comparisons between twelve NH₄⁺-grown Arabidopsis accessions revealed a great degree of natural variation in their root-growth response to low urea, with WAR and Blh-1 exhibiting the most significant increase in primary- and lateral-root length and numbers, and Sav-0 and Edi-0 being the most insensitive. Such phenotypical evidence suggests a common ability of plants to accommodate NH₄⁺-stress by responding to exogenous urea, providing a novel aspect for further understanding the process of urea-dependent plant NH₄⁺ tolerance.

Overexpression of exogenous biuret hydrolase in rice plants confers tolerance to biuret toxicity

Biuret, a common impurity in urea fertilizers, is toxic to plants, but little is known about the physiological mechanisms underlying its toxicity. Here, we analyzed biuret toxicity in rice (Oryza sativa) plants. We carried out uptake experiments using 15N-labelled biuret and demonstrated that biuret could reach sub millimolar concentrations in rice plants. We also demonstrated that the hydrolysis of biuret in plant cells could confer biuret tolerance to rice plants. This occurred because transgenic rice plants that overexpressed an exogenous biuret hydrolase cloned from a soil bacterium gained improved tolerance to biuret toxicity. Our results indicate that biuret toxicity is not an indirect toxicity caused by the presence of biuret outside the roots, and that biuret is not quickly metabolized in wild-type rice plants. Additionally, it was suggested that biuret was used as an additional nitrogen source in transgenic rice plants, because biuret hydrolase-overexpressing rice plants accumulated more biuret-derived N, as compared to wild-type rice.

Genetic regulation of water and nutrient transport in water stress tolerance in roots

Drought stress is one of the major abiotic factors affecting the growth and development of crops. The primary effect of drought is the alteration of water and nutrient uptake and transport by roots, related essentially with aquaporins and ion transporters of the plasma membrane. Therefore, the efficiency of water and nutrient transport across cell layers is a main factor in tolerance mechanisms. The regulation of this transport under water stress - in relation to the differing degrees of tolerance of crops and the effect of arbuscular mycorrhizae, together with signaling mechanisms - is reviewed here. Three different phases in the response to stress (immediate, short-term and long-term), involving different signals and levels of gene regulation, are highlighted.

Physiological and genome-wide RNA-sequencing analyses identify candidate genes in a nitrogen-use efficient potato cv. Kufri Gaurav

Nitrogen (N) is an important nutrient for plant growth. However, its excess application leads to environmental damage. Hence, improving nitrogen use efficiency (NUE) of plant is one of the plausible options to solve the problems. Aim of this study was to identify candidate genes involved in enhancing NUE in potato cv. Kufri Gaurav (N efficient). Plants were grown in aeroponic with two contrasting N regimes (low N: 0.75 mM, and high N: 7.5 mM). Higher NUE in Kufri Gaurav was observed in low N based on the parameters like NUE, NUpE (N uptake efficiency), NUtE (N utilization efficiency) and AgNUE (agronomic NUE). Further, global gene expression profiles in root, leaf and stolon tissues were analyzed by RNA-sequencing using Ion Proton™ System. Quality data (≥Q20) of 2.04-2.73 Gb per sample were mapped with the potato genome. Statistically significant (P ≤ 0.05) differentially expressed genes (DEGs) were identified such as 176 (up-regulated) and 30 (down-regulated) in leaves, 39 (up-regulated) and 105 (down-regulated) in roots, and 81 (up-regulated) and 694 (down-regulated) in stolons. The gene ontology (GO) terms like metabolic process, cellular process and catalytic activity were predominant. Our RT-qPCR analysis confirmed the gene expression profiles of RNA-seq. Overall, we identified candidate genes associated with improving NUE such as superoxide dismutase, GDSL esterase lipase, probable phosphatase 2C, high affinity nitrate transporters, sugar transporter, proline rich proteins, transcription factors (VQ motif, SPX domain, bHLH) etc. Our findings suggest that these candidate genes probably play crucial roles in enhancing NUE in potato.

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

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

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.

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

KEY MESSAGE

The "Green Super Rice" (GSR) project aims to fundamentally transform crop production techniques and promote the development of green agriculture based on functional genomics and breeding of GSR varieties by whole-genome breeding platforms. Rice (Oryza sativa L.) is one of the leading food crops of the world, and the safe production of rice plays a central role in ensuring food security. However, the conflicts between rice production and environmental resources are becoming increasingly acute. For this reason, scientists in China have proposed the concept of Green Super Rice for promoting resource-saving and environment-friendly rice production, while still achieving a yield increase and quality improvement. GSR is becoming one of the major goals for agricultural research and crop improvement worldwide, which aims to mine and use vital genes associated with superior agronomic traits such as high yield, good quality, nutrient efficiency, and resistance against insects and stresses; establish genomic breeding platforms to breed and apply GSR; and set up resource-saving and environment-friendly cultivation management systems. GSR has been introduced into eight African and eight Asian countries and has contributed significantly to rice cultivation and food security in these countries. This article mainly describes the GSR concept and recent research progress, as well as the significant achievements in GSR breeding and its application.

Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition

Excessive nitrogen fertilizer application causes severe environmental degradation and drives up agricultural production costs. Thus, improving crop nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture. Here, we characterized the roles of the MYB transcription factor OsMYB305 in nitrogen uptake and assimilation in rice. OsMYB305 encoded a transcriptional activator and its expression was induced by N deficiency in rice root. Under low-N condition, OsMYB305 overexpression significantly increased the tiller number, shoot dry weight and total N concentration. In the roots of OsMYB305-OE rice lines, the expression of OsNRT2.1, OsNRT2.2, OsNAR2.1, and OsNiR2 was up-regulated and 15NO3 - influx was significantly increased. In contrast, the expression of lignocellulose biosynthesis-related genes was repressed so that cellulose content decreased, and soluble sugar concentration increased. Certain intermediates in the glycolytic pathway and the tricarboxylic acid cycle were significantly altered and NADH-GOGAT, Pyr-K, and G6PDH were markedly elevated in the roots of OsMYB305-OE rice lines grown under low-N condition. Our results revealed that OsMYB305 overexpression suppressed cellulose biosynthesis under low-nitrogen condition, thereby freeing up carbohydrate for nitrate uptake and assimilation and enhancing rice growth. OsMYB305 is a potential molecular target for increasing NUE in rice.

Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress

Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60-86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ -2 log2 FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.

Novel Aspects of Nitrate Regulation in Arabidopsis

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

Molecular identification and functional characterization of GhAMT1.3 in ammonium transport with a high affinity from cotton (Gossypium hirsutum L.)

Ammonium (NH₄ ⁺ ) represents a primary nitrogen source for many plants, its effective transport into and between tissues and further assimilation in cells determine greatly plant nitrogen use efficiency. However, biological components involved in NH₄ ⁺ movement in woody plants are unclear. Here, we report kinetic evidence for cotton NH₄ ⁺ uptake and molecular identification of certain NH₄ ⁺ transporters (AMTs) from cotton (Gossypium hirustum). A substrate-influx assay using ¹⁵ N-isotope revealed that cotton possessed a high-affinity transport system with a K_m of 58 μM for NH₄ ⁺ . Sequence analysis showed that GhAMT1.1-1.3 encoded respectively a membrane protein containing 485, 509 or 499 amino acids. Heterologous functionality test demonstrated that GhAMT1.1-1.3 expression mediated NH₄ ⁺ permeation across the plasma membrane (PM) of yeast and/or Arabidopsis qko-mutant cells, allowing a growth restoration of both mutants on NH₄ ⁺ . Quantitative PCR measurement showed that GhAMT1.3 was expressed in roots and leaves and markedly up-regulated by N-starvation, repressed by NH₄ ⁺ resupply and regulated diurnally and age-dependently, suggesting that GhAMT1.3 should be a N-responsive gene. Importantly, GhAMT1.3 expression in Arabidopsis improved plant growth on NH₄ ⁺ and enhanced total nitrogen accumulation (∼50% more), conforming with the observation of 2-fold more NH₄ ⁺ absorption by GhAMT1.3-transformed qko plant roots during a 1-h root influx period. Together with its targeting to the PM and saturated transport kinetics with a K_m of 72 μM for NH₄ ⁺ , GhAMT1.3 is suggested to be a high-affinity NH₄ ⁺ permease that may play a significant role in cotton NH₄ ⁺ acquisition and utilization, adding a new member in the plant AMT family.

The urea transporter DUR3 contributes to rice production under nitrogen-deficient and field conditions

Nitrogen is one of the most important elements for plant growth, and urea is one of the most frequently used nitrogen fertilizers worldwide. Besides the exogenously-supplied urea to the soil, urea is endogenously synthesized during secondary nitrogen metabolism. Here, we investigated the contribution of a urea transporter, DUR3, to rice production using a reverse genetic approach combined with localization studies. Tos17 insertion lines for DUR3 showed a 50% yield reduction in hydroponic culture, and a 26.2% yield reduction in a paddy field, because of decreased grain filling. Because shoot biomass production and shoot total N was not reduced, insertion lines were disordered not only in nitrogen acquisition but also in nitrogen allocation. During seed development, DUR3 insertion lines accumulated nitrogen in leaves and could not sufficiently develop their panicles, although shoot and root dry weights were not significantly different from the wild-type. The urea concentration in old leaf harvested from DUR3 insertion lines was lower than that in wild-type. DUR3 promoter-dependent β-glucuronidase (GUS) activity was localized in vascular tissue and the midribs of old leaves. These results indicate that DUR3 contributes to nitrogen translocation and rice yield under nitrogen-deficient and field conditions.

Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions

Crop plants undergo morpho-physiological changes throughout the growth process in response to both the internal and the external environment, and that eventually determine the yield. The system-level adjustment of the morpho-physiological changes has remained largely unclear, however, especially in field conditions. Here, we reveal changes in nutrient status associated with tiller development and soil conditions based on the leaf transcriptome profile of rice (Oryza sativa) throughout the entire period of growth. We performed gene co-expression network analysis and identified three gene sets as indicators for monitoring the internal nitrogen and phosphorus status. Expression profiling reveals that the phosphorus starvation response is expressed during the tillering stage and is then switched off with the transition to nitrogen deficiency. Coincident with phosphorus status dynamics, the level of phosphate in the leaf is demonstrated to be low during the tillering stage and subsequently increases drastically. The phosphorus dynamics are genetically validated by analysing mutants with a defect in phosphorus homeostasis. Notably, we show that nitrogen limitation directly suppresses the phosphorus starvation response. Finally, the phosphorus starvation response is demonstrated to be activated in soil with a high phosphate retention capacity, without the visible phenotypes associated with phosphorus starvation. Our results reveal a growth stage- and soil condition-dependent reaction that requires phosphorus, which is expressed to promote the phosphorus uptake required for developing tillers and is directly adjusted by nitrogen status. A molecular framework for elucidating nutrient status dynamics under field conditions would provide insights into improving crop productivity.

Light exposure enhances urea absorption in the fluted giant clam, Tridacna squamosa, and up-regulates the protein abundance of a light-dependent urea active transporter, DUR3-like, in its ctenidium

Giant clams live in nutrient-poor reef waters of the Indo-Pacific and rely on symbiotic dinoflagellates (Symbiodinium spp., also known as zooxanthellae) for nutrients. As the symbionts are nitrogen deficient, the host clam has to absorb exogenous nitrogen and supply it to them. This study aimed to demonstrate light-enhanced urea absorption in the fluted giant clam, Tridacna squamosa, and to clone and characterize the urea active transporter DUR3-like from its ctenidium (gill). The results indicate that T. squamosa absorbs exogenous urea, and the rate of urea uptake in the light was significantly higher than that in darkness. The DUR3-like coding sequence obtained from its ctenidium comprised 2346 bp, encoding a protein of 782 amino acids and 87.0 kDa. DUR3-like was expressed strongly in the ctenidium, outer mantle and kidney. Twelve hours of exposure to light had no significant effect on the transcript level of ctenidial DUR3-like However, between 3 and 12 h of light exposure, DUR3-like protein abundance increased progressively in the ctenidium, and became significantly greater than that in the control at 12 h. DUR3-like had an apical localization in the epithelia of the ctenidial filaments and tertiary water channels. Taken together, these results indicate that DUR3-like might participate in light-enhanced urea absorption in the ctenidium of T. squamosa When made available to the symbiotic zooxanthellae that are known to possess urease, the absorbed urea can be metabolized to NH3 and CO2 to support amino acid synthesis and photosynthesis, respectively, during insolation.

Coding-Sequence Identification and Transcriptional Profiling of Nine AMTs and Four NRTs From Tobacco Revealed Their Differential Regulation by Developmental Stages, Nitrogen Nutrition, and Photoperiod

Although many members encoding different ammonium- and nitrate-transporters (AMTs, NRTs) were identified and functionally characterized from several plant species, little is known about molecular components for [Formula: see text]- and [Formula: see text] acquisition/transport in tobacco, which is often used as a plant model for biological studies besides its agricultural and industrial interest. We reported here the first molecular identification in tobacco (Nicotiana tabacum) of nine AMTs and four NRTs, which are respectively divided into four (AMT1/2/3/4) and two (NRT1/2) clusters and whose functionalities were preliminarily evidenced by heterologous functional-complementation in yeast or Arabidopsis. Tissue-specific transcriptional profiling by qPCR revealed that NtAMT1.1/NRT1.1 mRNA occurred widely in leaves, flower organs and roots; only NtAMT1.1/1.3/2.1NRT1.2/2.2 were strongly transcribed in the aged leaves, implying their dominant roles in N-remobilization from source/senescent tissues. N-dependent expression analysis showed a marked upregulation of NtAMT1.1 in the roots by N-starvation and resupply with N including [Formula: see text], suggesting a predominant action of NtAMT1.1 in [Formula: see text] uptake/transport whenever required. The obvious leaf-expression of other NtAMTs e.g., AMT1.2 responsive to N indicates a major place, where they may play transport roles associated with plant N-status and ([Formula: see text]-)N movement within aerial-parts. The preferentially root-specific transcription of NtNRT1.1/1.2/2.1 responsive to N argues their importance for root [Formula: see text] uptake and even sensing in root systems. Moreover, of all NtAMTs/NRTs, only NtAMT1.1/NRT1.1/1.2 showed their root-expression alteration in a typical diurnal-oscillation pattern, reflecting likely their significant roles in root N-acquisition regulated by internal N-demand influenced by diurnal-dependent assimilation and translocation of carbohydrates from shoots. This suggestion could be supported at least in part by sucrose- and MSX-affected transcriptional-regulation of NtNRT1.1/1.2. Thus, present data provide valuable molecular bases for the existence of AMTs/NRTs in tobacco, promoting a deeper understanding of their biological functions.

Phenotyping for Nitrogen Use Efficiency: Rice Genotypes Differ in N-Responsive Germination, Oxygen Consumption, Seed Urease Activities, Root Growth, Crop Duration, and Yield at Low N

The biological improvement of fertilizer nitrogen use efficiency (NUE) is hampered by the poor characterization of the phenotype and genotype for crop N response and NUE. In an attempt to identify phenotypic traits for N-response and NUE in the earliest stages of plant growth, we analyzed the N-responsive germination, respiration, urease activities, and root/shoot growth of 21 Indica genotypes of rice (Oryza sativa var. indica). We found that N delays germination from 0 to 12 h in a genotype-dependent and source-dependent manner, especially with urea and nitrate. We identified contrasting groups of fast germinating genotypes such as Aditya, Nidhi, and Swarnadhan, which were also least delayed by N and slow germinating genotypes such as Panvel 1, Triguna, and Vikramarya, which were also most delayed by N. Oxygen uptake measurements in the seeds of contrasting genotypes revealed that they were affected by N source in accordance with germination rates, especially with urea. Germinating seeds were found to have endogenous urease activity, indicating the need to explore genotypic differences in the effective urea uptake and metabolism, which remain unexplored so far. Urea was found to significantly inhibit early root growth in all genotypes but not shoot growth. Field evaluation of 15 of the above genotypes clearly showed that germination rates, crop duration, and yield are linked to NUE. Slow germinating genotypes had longer crop duration and higher yield even at lower N, indicating their higher NUE, relative to fast germinating or short duration genotypes. Moreover, longer duration genotypes suffered lesser yield losses at reduced N levels as compared to short duration genotypes, which is also a measure of their NUE. Together, these results indicate the potential of germination rates, crop duration, urea utilization and its effect on root growth in the development of novel phenotypic traits for screening genotypes and crop improvement for NUE, at least in rice.

Molecular identification of tobacco NtAMT1.3 that mediated ammonium root-influx with high affinity and improved plant growth on ammonium when overexpressed in Arabidopsis and tobacco

Although biological functions of ammonium (NH4+) transporters (AMTs) have been intensively studied in many plant species, little is known about molecular bases responsible for NH4+ movement in tobacco. Here, we reported the identification and functional characterization of a putative NH4+ transporter NtAMT1.3 from tobacco (Nicotiana tabacum). Analysis in silico showed that NtAMT1.3 encoded an integral membrane protein containing 464 amino acid residues and exhibiting 10 predicted transmembrane α-helices. Heterologous functionality study demonstrated that NtAMT1.3 expression facilitated NH4+ entry across plasma membrane of NH4+-uptake defective yeast and Arabidopsis qko mutant, allowing a restored growth of both yeast and Arabidopsis mutant on low NH4+. qPCR assay revealed that NtAMT1.3 was expressed in both roots and leaves and significantly up-regulated by nitrogen starvation and resupply of its putative substrate NH4+ and even nitrate, suggesting that NtAMT1.3 should represent a nitrogen-responsive gene. Critically, constitutive overexpression of NtAMT1.3 in tobacco per se improved obviously the growth of transgenic plants on NH4+ and enhanced leaf nitrogen (15% more) accumulation, consistent with observation of 35% more NH4+ uptake by the roots of transgenic lines in 20min root-influx test. Together with data showing its plasma membrane localization and saturated transport nature with Km of about 50μM for NH4+, we suggest that NtAMT1.3 acts an active NH4+ transporter that plays a significant role in NH4+ acquisition and utilization in tobacco.

The assembly of the plant urease activation complex and the essential role of the urease accessory protein G (UreG) in delivery of nickel to urease

Urease is a ubiquitous nickel metalloenzyme. In plants, its activation requires three urease accessory proteins (UAPs), UreD, UreF, and UreG. In bacteria, the UAPs interact with urease and facilitate activation, which involves the channeling of two nickel ions into the active site. So far this process has not been investigated in eukaryotes. Using affinity pulldowns of Strep-tagged UAPs from Arabidopsis and rice transiently expressed in planta, we demonstrate that a urease-UreD-UreF-UreG complex exists in plants and show its stepwise assembly. UreG is crucial for nickel delivery because UreG-dependent urease activation in vitro was observed only with UreG obtained from nickel-sufficient plants. This activation competence could not be generated in vitro by incubation of UreG with nickel, bicarbonate, and GTP. Compared with their bacterial orthologs, plant UreGs possess an N-terminal extension containing a His- and Asp/Glu-rich hypervariable region followed by a highly conserved sequence comprising two potential HXH metal-binding sites. Complementing the ureG-1 mutant of Arabidopsis with N-terminal deletion variants of UreG demonstrated that the hypervariable region has a minor impact on activation efficiency, whereas the conserved region up to the first HXH motif is highly beneficial and up to the second HXH motif strictly required for activation. We also show that urease reaches its full activity several days after nickel becomes available in the leaves, indicating that urease activation is limited by nickel accessibility in vivo Our data uncover the crucial role of UreG for nickel delivery during eukaryotic urease activation, inciting further investigations of the details of this process.

Physiological and molecular responses in tomato under different forms of N nutrition

Urea is the most common nitrogen (N) fertilizer in agriculture, due to its cheaper price and high N content. Although the reciprocal influence between NO₃^- and NH₄⁺ nutrition are well known, urea (U) interactions with these N-inorganic forms are poorly studied. Here, the responses of two tomato genotypes to ammonium nitrate (AN), U alone or in combination were investigated. Significant differences in root and shoot biomass between genotypes were observed. Under AN+U supply, Linosa showed higher biomass compared to UC82, exhibiting also higher values for many root architectural traits. Linosa showed higher Nitrogen Uptake (NUpE) and Utilization Efficiency (NUtE) compared to UC82, under AN+U nutrition. Interestingly, Linosa exhibited also a significantly higher DUR3 transcript abundance. These results underline the beneficial effect of AN+U nutrition, highlighting new molecular and physiological strategies for selecting crops that can be used for more sustainable agriculture. The data suggest that translocation and utilization (NUtE) might be a more important component of NUE than uptake (NUpE) in tomato. Genetic variation could be a source for useful NUE traits in tomato; further experiments are needed to dissect the NUtE components that confer a higher ability to utilize N in Linosa.

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.

Biological nitrification inhibition by rice root exudates and its relationship with nitrogen-use efficiency

Microbial nitrification in soils is a major contributor to nitrogen (N) loss in agricultural systems. Some plants can secrete organic substances that act as biological nitrification inhibitors (BNIs), and a small number of BNIs have been identified and characterized. However, virtually no research has focused on the important food crop, rice (Oryza sativa). Here, 19 rice varieties were explored for BNI potential on the key nitrifying bacterium Nitrosomonas europaea. Exudates from both indica and japonica genotypes were found to possess strong BNI potential. Older seedlings had higher BNI abilities than younger ones; Zhongjiu25 (ZJ25) and Wuyunjing7 (WYJ7) were the most effective genotypes among indica and japonica varieties, respectively. A new nitrification inhibitor, 1,9-decanediol, was identified, shown to block the ammonia monooxygenase (AMO) pathway of ammonia oxidation and to possess an 80% effective dose (ED₈₀ ) of 90 ng μl^-1 . Plant N-use efficiency (NUE) was determined using a ¹⁵ N-labeling method. Correlation analyses indicated that both BNI abilities and 1,9-decanediol amounts of root exudates were positively correlated with plant ammonium-use efficiency and ammonium preference. These findings provide important new insights into the plant-bacterial interactions involved in the soil N cycle, and improve our understanding of the BNI capacity of rice in the context of NUE.

CsNIP2;1 is a Plasma Membrane Transporter from Cucumis sativus that Facilitates Urea Uptake When Expressed in Saccharomyces cerevisiae and Arabidopsis thaliana

Urea is an important source of nitrogen (N) for the growth and development of plants. It occurs naturally in soils, is the major N source in agricultural fertilizers and is an important N metabolite in plants. Therefore, the identification and characterization of urea transporters in higher plants is important for the fundamental understanding of urea-based N nutrition in plants and for designing novel strategies for improving the N-use efficiency of urea based-fertilizers. Progress in this area, however, is hampered due to scarce knowledge of plant urea transporters. From what is known, urea uptake from the soil into plant roots is mediated by two types of transporters: the major intrinsic proteins (MIPs) and the DUR3 orthologs, mediating low- and high-affinity urea transport, respectively. Here we characterized a MIP family member from Cucumis sativus, CsNIP2;1, with regard to its contribution to urea transport. We show that CsNIP2;1 is a plasma membrane transporter that mediates pH-dependent urea uptake when expressed in yeast. We also found that ectopic expression of CsNIP2;1 improves growth of wild-type Arabidopsis thaliana and rescues growth and development of the atdur3-3 mutant on medium with urea as the sole N source. In addition, CsNIP2;1 is transcriptionally up-regulated by N deficiency, urea and NO3 (-). These data and results from the analyses of the pattern of CsNIP2;1 expression in A. thaliana and cucumber suggest that CsNIP2;1 might be involved in multiple steps of urea-based N nutrition, including urea uptake and internal transport during N remobilization throughout seed germination and N delivery to developing tissues.

Molecular and physiological interactions of urea and nitrate uptake in plants

While nitrate acquisition has been extensively studied, less information is available on transport systems of urea. Furthermore, the reciprocal influence of the two sources has not been clarified, so far. In this review, we will discuss recent developments on plant response to urea and nitrate nutrition. Experimental evidence suggests that, when urea and nitrate are available in the external solution, the induction of the uptake systems of each nitrogen (N) source is limited, while plant growth and N utilization is promoted. This physiological behavior might reflect cooperation among acquisition processes, where the activation of different N assimilatory pathways (cytosolic and plastidic pathways), allow a better control on the nutrient uptake. Based on physiological and molecular evidence, plants might increase (N) metabolism promoting a more efficient assimilation of taken-up nitrogen. The beneficial effect of urea and nitrate nutrition might contribute to develop new agronomical approaches to increase the (N) use efficiency in crops.

High and Low Affinity Urea Root Uptake: Involvement of NIP5;1

Urea is the most widespread nitrogen (N) fertilizer worldwide and is rapidly degraded in soil to ammonium by urease. Ammonium is either taken up by plant roots or is further processed to nitrate by soil microorganisms. However, urea can be taken up by roots and is further degraded to ammonium by plant urease for assimilation. When urea is supplied under sterile conditions, it acts as a poor N source for seedlings or adult Arabidopsis thaliana plants. Here, the gene expression of young seedlings exposed to urea and ammonium nitrate nutrition was compared. Several primary metabolism and transport genes, including those for nitrate and urea, were differentially expressed in seedlings. However, urease and most major intrinsic proteins were not differentially expressed, with the exception of NIP6;1, a urea-permeable channel, which was repressed. Furthermore, little overlap with the gene expression with ammonium as the sole N source was observed, confirming that pure urea nutrition is not associated with the ammonium toxicity syndrome in seedlings. The direct root uptake of urea was increased under boron deficiency, in both the high and low affinity range. This activity was entirely mediated by the NIP5;1 channel, which was confirmed to transport urea when expressed in oocytes. The uptake of urea in the high and low affinity range was also determined for maize and wheat roots. The urea uptake by maize roots was only about half that of wheat, but was not stimulated by boron deficiency or N deficiency in either species. This analysis identifies novel components of the urea uptake systems in plants, which may become agronomically relevant to urea uptake and utilization, as stabilized urea fertilizers become increasingly popular.

Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes

In an effort to better understand the diversity of genes coding for nitrogen (N) uptake and assimilation pathways among microalgae, we analyzed the transcriptomes of five phylogenetically diverse single celled algae originally isolated from the same high arctic marine region. The five photosynthetic flagellates (a pelagophyte, dictyochophyte, chrysoph-yte, cryptophyte and haptophyte) were grown on standard media and media with only urea or nitrate as a nitrogen source; cells were harvested during late exponential growth. Based on homolog protein sequences, transcriptomes of each alga were interrogated to retrieve genes potentially associated with nitrogen uptake and utilization pathways. We further investigated the phylogeny of poorly characterized genes and gene families that were identified. While the phylogeny of the active urea transporter (DUR3) was taxonomically coherent, those for the urea transporter superfamily, putative nitrilases and amidases indicated complex evolutionary histories, and preliminary evidence for horizontal gene transfers. All five algae expressed genes for ammonium assimilation and all but the chrysophyte expressed genes involved in nitrate utilization and the urea cycle. Among the four algae with nitrate transporter transcripts, we detected lower expression levels in three of these (the dictyochophyte, pelagophyte, and cryptophyte) grown in the urea only medium compared with cultures from the nitrate only media. The diversity of N pathway genes in the five algae, and their ability to grow using urea as a nitrogen source, suggest that these flagellates are able to use a variety of organic nitrogen sources, which would be an advantage in an inorganic nitrogen - limited environment, such as the Arctic Ocean.