The putative high-affinity nitrate transporter NRT2.1 represses lateral root initiation in response to nutritional cues

Signalling and regulation of plant development by carbon/nitrogen balance

The two most abundant macronutrients in plant cells are carbon (C) and nitrogen (N). Coordination of their cellular metabolism is a fundamental factor in guaranteeing the optimal growth and development of plants. N availability and assimilation profoundly affect plant gene expression and modulate root and stem architecture, thus affecting whole plant growth and crop yield. N status also affects C fixation, as it is an important component of the photosynthetic machinery in leaves. Reciprocally, increasing C supply promotes N uptake and assimilation. There is extensive knowledge of the different mechanisms that plants use for sensing and signalling their nutritional status to regulate the assimilation, metabolism and transport of C and N. However, the crosstalk between C and N pathways has received much less attention. Plant growth and development are greatly affected by suboptimal C/N balance, which can arise from nutrient deficiencies or/and environmental cues. Mechanisms that integrate and respond to changes in this specific nutritional balance have started to arise. This review will examine the specific responses to C/N imbalance in plants by focusing on the main inorganic and organic metabolites involved, how they are sensed and transported, and the interconnection between the early signalling components and hormonal networks that underlies plants' adaptive responses.

Wheat Tae-MIR1118 Constitutes a Functional Module With Calmodulin TaCaM2-1 and MYB Member TaMYB44 to Modulate Plant Low-N Stress Response

Distinct target genes are modulated by microRNA members and affect various biological processes associated with abiotic stress responses in plants. In this study, we characterized a functional module comprising miRNA/target and a downstream MYB transcription factor partner, Tae-MIR1118/TaCaM2/TaMYB44, in Triticum aestivum to mediate the plant low-nitrogen (N) stress response. Dual luciferase (LUC) assay and expression analysis indicated that TaCaM2 is regulated by Tae-MIR1118 through a posttranscriptional cleavage mechanism. Reporter LUC activity in N. benthamiana leaves co-transformed with effector CaMV35S::Tae-MIR1118 and reporter TaCaM2::LUC was significantly reduced, and the transcripts of Tae-MIR1118 and TaCaM2 in tissues exhibited converse expression patterns under varying N levels. Specifically, the transcripts of Tae-MIR1118 decreased, whereas those of TaCaM2 increased under low-N stress in a temporal-dependent manner. Yeast two-hybrid, bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays indicated that TaCaM2 interacted with the MYB transcription factor TaMYB44. Transgene analysis revealed the negative roles of Tae-MIR1118 and the positive functions of TaCaM2 and TaMYB44 in regulating plants for low-N stress adaptation by modulating glutamine synthetase activity, N uptake capacity, and root morphology. Yeast one-hybrid, transcriptional activation, and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-PCR) assays indicated that TaMYB44 could bind to the promoters of genes TaGS2.2, TaNRT2.1, and TaPIN4 and induce transcription of these stress-defensive genes. Knockdown of these three genes reduced GS activity, N accumulation, and root growth traits in plants subjected to N starvation. The yield in the wheat variety panel was highly correlated with the transcripts of Tae-MIR1118, TaCaM2, and TaMYB44 in plants cultured under N-deprived field conditions. A major haplotype of Tae-MIR1118, TaMIR1118-Hap1, enhanced the low-N stress tolerance of plants. Our findings indicate that the Tae-MIR1118/TaCaM2/TaMYB44 pathway primarily affects the low-N response of plants by modulating associated physiological processes.

The phytohormone brassinosteroid (BR) promotes early seedling development via auxin signaling pathway in rapeseed

The phytohormone brassinosteroid (BR) regulate various developmental and physiological processes in plants. However, the function of BR during early seedling development stage in rapeseed is largely unknown. To understand the effects of exogenous BR during early seedling development, the ZS11 and BR-INSENSITIVE (bin2) mutants were treated with BR before seed sowing and seed germination stage under 16/8 hours light/dark cycle. The phenotype results indicated that BR promotes only seedling establishment but not seed germination stage in ZS11, while no function in bin2 mutants. Since BRs play a crucial role in regulation of developmental transition between growth in the dark (skotomorphogenesis) and growth in the light (photomorphogenesis), the ZS11 and bin2 mutants were treated with BR under continuous light and dark. The BR treatment also showed the same functions as 16/8 hours light/dark cycle. To understand the function of BR on expression levels, the differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) between mock- and BR-treated seedlings were explored. A total of 234 significantly DEGs were identified between the mock- and BR-treated groups by transcriptomic analyses. These DEGs were markedly enriched in BR biosynthesis, pentose and glucuronate interconversions and plant hormone signal transduction pathways. Meanwhile, a total of 145 DEMs were identified through metabolomics analyses, with a significant enrichment in lipid substances. Interestingly, some genes and metabolites associated with auxin pathway were identified, which exhibited up-regulation in both DEGs and DEMs after BR treatment. Subsequently, functional enrichment analyses revealed that the majority of DEGs and DEMs were primarily enriched in ascorbate and aldehyde metabolism, arginine and proline metabolism, tryptophan metabolism (the main route for auxin synthesis) and cyanogenic amino acid metabolism. Furthermore, it was found that glutamate was up-regulated in nitrogen metabolism, glyoxylate and dicarboxylate metabolism, and arginine and proline metabolism pathways. These indicated that the glutamate signaling pathway was a key regulatory pathway for exogenous BR to induce seedling establishment. These evidence implied that exogenous BR treatment lead to up-regulation of auxin-related genes expression, then promoted seedling establishment in rapeseed.

The Arabidopsis PIP1;1 Aquaporin Represses Lateral Root Development and Nitrate Uptake Under Low Nitrate Availability

Nitrate (NO3 -) deficiency decreases root water uptake and root hydraulic conductance. This adaptive response is correlated with reduced abundance and activity of plasma membrane intrinsic protein (PIP) aquaporins. We therefore screened changes in the root architecture of a complete set of Arabidopsis pip loss-of-function mutants grown under NO3 - deficiency to systematically approach the impact of PIPs under these conditions. NO3 - deprivation led to attenuated responses of specific pip single mutants compared to the strongly altered LR parameters of wild-type plants. In particular, pip1;1 exhibited a lower relative reduction in LR length and LR density, revealing that PIP1;1 represses LR development when NO3 - is scarce. Indeed, PIP1;1 compromises root and shoot NO3 - accumulation during early developmental stages. A fluorescent VENUS-PIP1;1 fusion revealed that PIP1;1 is specifically repressed in the pericycle, endodermis and at the flanks of emerging LRs upon NO3 - deficiency. Thus, LR plasticity and NO3 - uptake are affected by an interactive mechanism involving aquaporins (PIP1;1) and nitrate accumulation during seedling development under NO3 --deficient conditions.

CPK28-mediated phosphorylation enhances nitrate transport activity of NRT2.1 during nitrogen deprivation

Nitrate (NO3 -) serves as the primary inorganic nitrogen source assimilated by most terrestrial plants. The acquisition of nitrate from the soil is facilitated by NITRATE TRANSPORTERS (NRTs), with NRT2.1 being the key high-affinity nitrate transporter. The activity of NRT2.1, which has multiple potential phosphorylation sites, is intricately regulated under various physiological conditions. Here, we discovered that CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28) positively regulates nitrate uptake under nitrogen deprivation conditions. We found CPK28 as the kinase targeted by immunoprecipitation followed by mass spectrometry and examined the in-planta phosphorylation status of NRT2.1 in cpk28 mutant plants by employing quantitative MS-based phosphoproteomics. Through a combination of in vitro phosphorylation experiment and immunoblotting using phospho-specific antibody, we successfully demonstrated that CPK28 specifically phosphorylates NRT2.1 at Ser21. Functional analysis conducted in Xenopus oocytes revealed that co-expression of CPK28 significantly enhanced high-affinity nitrate uptake of NRT2.1. Further investigation using transgenic plants showed that the phosphomimic variant NRT2.1S21E, but not the nonphosphorylatable variant NRT2.1S21A, fully restored high-affinity 15NO3 - uptake ability in both nrt2.1 and cpk28 mutant backgrounds. This study clarifies that the kinase activity of CPK28 is promoted during nitrogen deprivation conditions. These significant findings provide valuable insights into the intricate regulatory mechanisms that govern nitrate-demand adaptation.

Alleviation of drought stress in tomato by foliar application of seafood waste extract

To manage the adverse effects of garbage pollution and avoid using chemicals, a natural extract of seafood shells was obtained and explored for its beneficial role. Physical characterization highlighted that its active compounds correspond to chitin and its derivative, chitosan. The ability of the extracted biostimulant to foster tomato tolerance was tested on drought-stressed plants. Along with changes in morphological parameters, the accumulation of chlorophyll and carotenoids was improved. The biostimulant also mediates the accumulation of osmoprotectants and an increased leaf water content. Furthermore, the biostimulant effectively promotes tolerance by increasing drought-stress SIERF84 Transcription factor and decreasing both SIARF4 and SlWRKY81 transcript levels, which in turn, mediates stomatal closure. In addition, the up-regulation of key genes related to NO3- uptake (NTR1.1/2) and assimilation (NR) coupled with the downregulation of ammonium transporters' genes (AMT1.1/2), allowed the uptake of NO3- over NH4+ in the tolerant genotype which is likely to be associated with drought tolerance. Overall, the biostimulant was effective in alleviating water stress and showed similar effects to commercial chitosan. Besides the benefits of a circular economy framework, this biostimulant-based approach is innovative to promote a sustainable eco-agriculture, in the face of persistent water scarcity.

The clock-associated LUX ARRHYTHMO regulates high-affinity nitrate transport in Arabidopsis roots

The circadian clock organizes physiological processes in plants to occur at specific times of the day, optimizing efficient use of resources. Nitrate is a crucial inorganic nitrogen source for agricultural systems to sustain crop productivity. However, because nitrate fertilization has a negative impact on the environment, it is important to carefully manage nitrate levels. Understanding crop biological rhythms can lead to more ecologically friendly agricultural practices. Gating responses through the circadian clock could be a strategy to enhance root nitrate uptake and to limit nitrate runoff. In Arabidopsis, the NITRATE TRANSPORTER 2.1 (NRT2.1) gene encodes a key component of the high-affinity nitrate transporter system. Our study reveals that NRT2.1 exhibits a rhythmic expression pattern, with daytime increases and nighttime decreases. The NRT2.1 promoter activity remains rhythmic under constant light, indicating a circadian regulation. The clock-associated transcription factor LUX ARRHYTHMO (LUX) binds to the NRT2.1 promoter in vivo. Loss-of-function of LUX leads to increased NRT2.1 transcript levels and root nitrate uptake at dusk. This supports LUX acting as a transcriptional repressor and modulating NRT2.1 expression in a time-dependent manner. Furthermore, applying nitrate at different times of the day results in varying magnitudes of the transcriptional response in nitrate-regulated genes. We also demonstrate that a defect in the high-affinity nitrate transport system feeds back to the central oscillator by modifying the LUX promoter activity. In conclusion, this study uncovers a molecular pathway connecting the root nitrate uptake and circadian clock, with potential agro-chronobiological applications.

Recent advances in local and systemic nitrate signaling in Arabidopsisthaliana

Nitrate is the most abundant form of inorganic nitrogen in aerobic soils, serving both as a nutrient and a signaling molecule. Central to nitrate signaling in higher plants is the intricate balance between local and systemic signaling and response pathways. The interplay between local and systemic responses allows plants to regulate their global gene expression, metabolism, physiology, growth, and development under fluctuating nitrate availability. This review offers an overview of recent discoveries regarding new players on nitrate sensing and signaling, in local and systemic contexts in Arabidopsis thaliana. Additionally, it addresses unanswered questions that warrant further investigation for a better understanding of nitrate signaling and responses in plants.

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

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

Functional analyses of the NRT2 family of nitrate transporters in Arabidopsis

Nitrogen is an essential macronutrient for plant growth and development. Nitrate is the major form of nitrogen acquired by most crops and also serves as a vital signaling molecule. Nitrate is absorbed from the soil into root cells usually by the low-affinity NRT1 NO3 - transporters and high-affinity NRT2 NO3 - transporters, with NRT2s serving to absorb NO3 - under NO3 -limiting conditions. Seven NRT2 members have been identified in Arabidopsis, and they have been shown to be involved in various biological processes. In this review, we summarize the spatiotemporal expression patterns, localization, and biotic and abiotic responses of these transporters with a focus on recent advances in the current understanding of the functions of the seven AtNRT2 genes. This review offers beneficial insight into the mechanisms by which plants adapt to changing environmental conditions and provides a theoretical basis for crop research in the near future.

A comprehensive review of TGA transcription factors in plant growth, stress responses, and beyond

TGA transcription factors (TFs), belonging to the D clade of the basic region leucine zipper (bZIP) family, exhibit a specific ability to recognize and bind to regulatory elements with TGACG as the core recognition sequence, enabling the regulation of target gene expression and participation in various biological regulatory processes. In plant growth and development, TGA TFs influence organ traits and phenotypes, including initial root length and flowering time. They also play a vital role in responding to abiotic stresses like salt, drought, and cadmium exposure. Additionally, TGA TFs are involved in defending against potential biological stresses, such as fungal bacterial diseases and nematodes. Notably, TGA TFs are sensitive to the oxidative-reductive state within plants and participate in pathways that aid in the elimination of reactive oxygen species (ROS) generated during stressful conditions. TGA TFs also participate in multiple phytohormonal signaling pathways (ABA, SA, etc.). This review thoroughly examines the roles of TGA TFs in plant growth, development, and stress response. It also provides detailed insights into the mechanisms underlying their involvement in physiological and pathological processes, and their participation in plant hormone signaling. This multifaceted exploration distinguishes this review from others, offering a comprehensive understanding of TGA TFs.

Arabidopsis seedlings respond differentially to nutrient efficacy of three rock meals by regulating root architecture and endogenous auxin homeostasis

BACKGROUND

Plants show developmental plasticity with variations in environmental nutrients. Considering low-cost rock dust has been identified as a potential alternative to artificial fertilizers for more sustainable agriculture, the growth responses of Arabidopsis seedlings on three rock meals (basalt, granite, and marlstone) were examined for the different foraging behavior, biomass accumulation, and root architecture.

RESULTS

Compared to ½ MS medium, basalt and granite meal increased primary root length by 13% and 38%, respectively, but marlstone caused a 66% decrease, and they all drastically reduced initiation and elongation of lateral roots but lengthened root hairs. Simultaneous supply of organic nutrients and trace elements increased fresh weight due to the increased length of primary roots and root hairs. When nitrogen (N), phosphorus (P), and potassium (K) were supplied individually, N proved most effective in improving fresh weight of seedlings growing on basalt and granite, whereas K, followed by P, was most effective for those growing on marlstone. Unexpectedly, the addition of N to marlstone negatively affected seedling growth, which was associated with repressed auxin biosynthesis in roots.

CONCLUSIONS

Our data indicate that plants can recognize and adapt to complex mineral deficiency by adjusting hormonal homeostasis to achieve environmental sensitivity and developmental plasticity, which provide a basis for ecologically sound and sustainable strategies to maximize the use of natural resources and reduce the production of artificial fertilizers.

Comparative analysis of physiological traits and gene expression patterns in nitrogen deficiency among barley cultivars

BACKGROUND

Nitrogen is one of the most important mineral nutrients for plants and is absorbed by the root system mainly in the inorganic form (NH+4 and NO-3). Plants absorb nitrogen as a food source for growth, biomass production, and development. Nitrogen is mainly absorbed as nitrate, which is the most common source of nitrogen available to higher plants. One of the unique features of nitrate transport is that NO-3 is both a substrate for transport and an inducer of NO-3 transport systems in genes and at physiological levels.

METHODS

In the present study, morphological and physiological traits (chlorophyll a/b, total chlorophyll, and carotenoid, antioxidant enzymes, and protein content), correlation between traits and gene expression, and principle component analysis of traits among five barley cultivars were measured in response to nitrogen deficiency (ND). The starved plants were transferred to a nutrient solution containing 0.2 mM and 2 mM NO-3 up to 7 and 14 days after ND application and non-stressed conditions, respectively.

RESULTS

Gene expression analysis revealed that the 10 HvNRT2 genes were induced in the leaf and root tissues at 7 and 14 days after ND treatments in five barley cultivars. Expression of NRT2 genes by relative quantitative qRT-PCR analysis for 10 HvNRT2 genes were determined. Based on the gene expression, HvNRT2.1, HvNRT2.2, and HvNRT2.4 were strongly induced by NO-3, peaking at 7 and 14 days after ND treatment. In contrast, the HvNRT2.4 showed only moderate induction in both leaves and roots. From our results, the Reyhan cultivar showed a significant increase in root fresh weight (RFW), protein content, and antioxidant enzyme activity in roots at 7 and 14 days after ND treatment as compared to the non-stressed condition. A highly positive correlation was observed between root catalase (CATr) and HvNRT2.2/2.5/2.6 leaves.

CONCLUSION

The expression of HvNRT2.4 is increased during long-term nitrogen starvation, while the expression of HvNRT2.1 and HvNRT2.2 are transiently increased by ND. Based on physiological and morphological traits and molecular mechanisms, the Reyhan is considered a tolerant cultivar under ND condition.

Sailing in complex nutrient signaling networks: Where I am, where to go, and how to go?

To ensure survival and promote growth, sessile plants have developed intricate internal signaling networks tailored in diverse cells and organs with both shared and specialized functions that respond to various internal and external cues. A fascinating question arises: how can a plant cell or organ diagnose the spatial and temporal information it is experiencing to know "where I am," and then is able to make the accurate specific responses to decide "where to go" and "how to go," despite the absence of neuronal systems found in mammals. Drawing inspiration from recent comprehensive investigations into diverse nutrient signaling pathways in plants, this review focuses on the interactive nutrient signaling networks mediated by various nutrient sensors and transducers. We assess and illustrate examples of how cells and organs exhibit specific responses to changing spatial and temporal information within these interactive plant nutrient networks. In addition, we elucidate the underlying mechanisms by which plants employ posttranslational modification codes to integrate different upstream nutrient signals, thereby conferring response specificities to the signaling hub proteins. Furthermore, we discuss recent breakthrough studies that demonstrate the potential of modulating nutrient sensing and signaling as promising strategies to enhance crop yield, even with reduced fertilizer application.

Research Progress on the Effect of Nitrogen on Rapeseed between Seed Yield and Oil Content and Its Regulation Mechanism

Rapeseed (Brassica napus L.) is one of the most important oil crops in China. Improving the oil production of rapeseed is an important way to ensure the safety of edible oil in China. Oil production is an important index that reflects the quality of rapeseed and is determined by the oil content and yield. Applying nitrogen is an important way to ensure a strong and stable yield. However, the seed oil content has been shown to be reduced in most rapeseed varieties after nitrogen application. Thus, it is critical to screen elite germplasm resources with stable or improved oil content under high levels of nitrogen, and to investigate the molecular mechanisms of the regulation by nitrogen of oil accumulation. However, few studies on these aspects have been published. In this review, we analyze the effect of nitrogen on the growth and development of rapeseed, including photosynthetic assimilation, substance distribution, and the synthesis of lipids and proteins. In this process, the expression levels of genes related to nitrogen absorption, assimilation, and transport changed after nitrogen application, which enhanced the ability of carbon and nitrogen assimilation and increased biomass, thus leading to a higher yield. After a crop enters the reproductive growth phase, photosynthates in the body are transported to the developing seed for protein and lipid synthesis. However, protein synthesis precedes lipid synthesis, and a large number of photosynthates are consumed during protein synthesis, which weakens lipid synthesis. Moreover, we suggest several research directions, especially for exploring genes involved in lipid and protein accumulation under nitrogen regulation. In this study, we summarize the effects of nitrogen at both the physiological and molecular levels, aiming to reveal the mechanisms of nitrogen regulation in oil accumulation and, thereby, provide a theoretical basis for breeding varieties with a high oil content.

Alkalinity modulates a unique suite of genes to recalibrate growth and pH homeostasis

Alkaline soils pose a conglomerate of constraints to plants, restricting the growth and fitness of non-adapted species in habitats with low active proton concentrations. To thrive under such conditions, plants have to compensate for a potential increase in cytosolic pH and restricted softening of the cell wall to invigorate cell elongation in a proton-depleted environment. To discern mechanisms that aid in the adaptation to external pH, we grew plants on media with pH values ranging from 5.5 to 8.5. Growth was severely restricted above pH 6.5 and associated with decreasing chlorophyll levels at alkaline pH. Bicarbonate treatment worsened plant performance, suggesting effects that differ from those exerted by pH as such. Transcriptional profiling of roots subjected to short-term transfer from optimal (pH 5.5) to alkaline (pH 7.5) media unveiled a large set of differentially expressed genes that were partially congruent with genes affected by low pH, bicarbonate, and nitrate, but showed only a very small overlap with genes responsive to the availability of iron. Further analysis of selected genes disclosed pronounced responsiveness of their expression over a wide range of external pH values. Alkalinity altered the expression of various proton/anion co-transporters, possibly to recalibrate cellular proton homeostasis. Co-expression analysis of pH-responsive genes identified a module of genes encoding proteins with putative functions in the regulation of root growth, which appears to be conserved in plants subjected to low pH or bicarbonate. Our analysis provides an inventory of pH-sensitive genes and allows comprehensive insights into processes that are orchestrated by external pH.

Nitrate, Auxin and Cytokinin-A Trio to Tango

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

Biostimulant Properties of Protein Hydrolysates: Recent Advances and Future Challenges

Over the past decade, plant biostimulants have been increasingly used in agriculture as environment-friendly tools that improve the sustainability and resilience of crop production systems under environmental stresses. Protein hydrolysates (PHs) are a main category of biostimulants produced by chemical or enzymatic hydrolysis of proteins from animal or plant sources. Mostly composed of amino acids and peptides, PHs have a beneficial effect on multiple physiological processes, including photosynthetic activity, nutrient assimilation and translocation, and also quality parameters. They also seem to have hormone-like activities. Moreover, PHs enhance tolerance to abiotic stresses, notably through the stimulation of protective processes such as cell antioxidant activity and osmotic adjustment. Knowledge on their mode of action, however, is still piecemeal. The aims of this review are as follows: (i) Giving a comprehensive overview of current findings about the hypothetical mechanisms of action of PHs; (ii) Emphasizing the knowledge gaps that deserve to be urgently addressed with a view to efficiently improve the benefits of biostimulants for different plant crops in the context of climate change.

Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth

Plant root architecture flexibly adapts to changing nitrate (NO₃^-) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO₃^--mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO₃^- in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO₃^- availability. Under low-NO₃^- availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.

Exogenous sucrose promotes the growth of apple rootstocks under high nitrate supply by modulating carbon and nitrogen metabolism

Excessive nitrogen (N) supply often leads to an imbalance of carbon (C) and N metabolism and inhibits plant growth. Sucrose, an important source and signaling substance of C in plants, is closely linked to N metabolism. However, it is not clear whether exogenous sucrose can mitigate the inhibitory effect of high N on plant growth by regulating C and N metabolism. In this study, we investigated the effects of exogenous sucrose on the growth, N metabolism, and C assimilation in the apple rootstock M26 seedlings under normal (5 mM NO3－, NN) and high (30 mM NO3－, HN) NO3－ concentrations. Our results showed that high NO3－ supply reduced plant growth, photosynthesis, and chlorophyll fluorescence, but spraying with 1% sucrose (HN + 1% Sucrose) significantly alleviated this inhibition. Application of 1% sucrose increased sucrose and sorbitol contents as well as sucrose-phosphate synthase and sucrose synthase activities in the plants under HN treatment and promoted the distribution of 13C photoassimilation products to the root. In addition, spraying with 1% sucrose alleviated the inhibition of N metabolizing enzyme activities by high NO3－ supply, reduced NO3－ accumulation and N content, increased free amino acid content, and promoted 15N distribution to the aboveground parts. However, spraying with 1% sucrose under the NN treatment negatively affected plant photosynthesis and carbon assimilation. In conclusion, exogenous sucrose increased the C level in plants in the presence of excess N, promoted the balance of C and N metabolism, and alleviated the inhibitory effect of high N on the apple plant growth.

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.

The central role of GmGLP20.4 in root architecture modifications of soybean under low-nitrogen stress

KEY MESSAGE

The GmGLP20.4 candidate gene plays an important role to improve soybean root architecture under low-nitrogen stress. The results lay the foundation for breeding low-nitrogen-tolerant soybean. Roots are fundamentally important for plant growth and development, facilitating water and nutrient uptake. Various abiotic and biotic factors significantly affect the root system architecture, especially low nitrogen (LN), but the molecular mechanism remains unclear. In this study, we identified GmGLP20.4, a germin-like protein (ubiquitous plant glycoproteins belonging to the Cupin superfamily) crucial for lateral root development and highly induced by LN stress in lateral roots of soybean. GmGLP20.4 overexpression increased root biomass through development of an improved root system in soybean under LN, whereas a significant decrease in root biomass was observed in the gmglp20.4 knockout mutant. Overexpression of GmGLP20.4 improved plant growth and root architecture in transgenic tobacco (Nicotiana tabacum) under LN. Natural variation of the GT-1 cis-element in the promoter (T to A) of GmGLP20.4 was strongly associated with its expression level under LN, and significantly increased LN-sensitive variation (type A) was observed in wild soybean compared to that in elite cultivars. Thus, type A variation in the promoter of GmGLP20.4 may have been a site of artificial selection during domestication. The GmGT1-16g gene was highly expressed under LN and showed an expression pattern opposite to that of GmGLP20.4. A luciferase complementation imaging assay revealed that the GmGLP20.4 promoter specifically binds to GmGT1-16g. In conclusion, GmGLP20.4 is involved in soybean root development and the natural variation of its promoter will be useful in modern intercropping systems or to improve nitrogen-use efficiency.

Comparative Transcriptome Analysis of Two Peach Rootstocks Uncovers the Effect of Gene Differential Expression on Nitrogen Use Efficiency

Nitrogen is an important nutrient element that limits plant growth and yield formation, but excessive nitrogen has negative effects on plants and the environment. It is important to reveal the molecular mechanism of high NUE (nitrogen use efficiency) for breeding peach rootstock and variety with high NUE. In this study, two peach rootstocks, Shannong–1 (S) and Maotao (M), with different NUE were used as materials and treated with 0.1 mM KNO₃ for transcriptome sequencing together with the control group. From the results of comparison between groups, we found that the two rootstocks had different responses to KNO₃, and 2151 (KCL_S vs. KCL_M), 327 (KNO₃_S vs. KCL_S), 2200 (KNO₃_S vs. KNO₃_M) and 146 (KNO₃_M vs. KCL_M) differentially expressed genes (DEGs) were identified, respectively, which included multiple transcription factor families. These DEGs were enriched in many biological processes and signal transduction pathways, including nitrogen metabolism and plant hormone signal transduction. The function of PpNRT2.1, which showed up-regulated expression under KNO₃ treatment, was verified by heterologous expression in Arabidopsis. The plant height, SPAD (soil and plant analyzer development) of leaf and primary root length of the transgenic plants were increased compared with those of WT, indicating the roles of PpNRT2.1 in nitrogen metabolism. The study uncovered for the first time the different molecular regulatory pathways involved in nitrogen metabolism between two peach rootstocks and provided gene reserve for studying the molecular mechanism of nitrogen metabolism and theoretical basis for screening peach rootstock or variety with high NUE.

Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.

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.

Pisum sativum Response to Nitrate as Affected by Rhizobium leguminosarum-Derived Signals

Legumes are suitable for the development of sustainable agroecosystems because of their ability to use atmospheric N2 through symbiotic nitrogen fixation (SNF). However, a basic NO3− input is necessary before SNF takes place to ensure successful seedling establishment. Since Rhizobia not only induce nodulation but also affect root branching by stimulating the development of lateral roots, and NO3− as a signal also modulates root system architecture, we investigated whether Rhizobium-derived signals interfere in nitrate signaling. Here, we bring evidence that (i) Rhizobium-altered NO3−-mediated processes in pea expressions of major players in NO3− transport, sensing, and signaling were affected, and (ii) the characteristic limitation of root foraging and branching in response to NO3− supply was abolished. The number of tertiary roots per secondary root was higher in infected compared to uninfected peas, thus indicating that the Rhizobium effect allows for favorable management of trade-offs between nodules growth for nitrogen capture and root foraging for water and other nutrient uptake in pea. The outcome of this basic research can be used to produce molecular tools for breeding pea genotypes able to develop deep-foraging and branched root systems, and more competitive architectures and molecular levels for soil NO3− absorption during seedling establishment without jeopardizing nodulation.

Nitrate Uptake and Use Efficiency: Pros and Cons of Chloride Interference in the Vegetable Crops

Over the past five decades, nitrogen (N) fertilization has been an essential tool for boosting crop productivity in agricultural systems. To avoid N pollution while preserving the crop yields and profit margins for farmers, the scientific community is searching for eco-sustainable strategies aimed at increasing plants' nitrogen use efficiency (NUE). The present article provides a refined definition of the NUE based on the two important physiological factors (N-uptake and N-utilization efficiency). The diverse molecular and physiological mechanisms underlying the processes of N assimilation, translocation, transport, accumulation, and reallocation are revisited and critically discussed. The review concludes by examining the N uptake and NUE in tandem with chloride stress and eustress, the latter being a new approach toward enhancing productivity and functional quality of the horticultural crops, particularly facilitated by soilless cultivation.

Nitrogen Absorption Pattern Detection and Expression Analysis of Nitrate Transporters in Flowering Chinese Cabbage

Nitrate transporters (NRTs) play an important role in nitrate absorption and internal distribution in plant roots and other parts. Experiments were carried out to explore the sequences and expression characteristics of NRT genes, and their correlation with the N uptake in flowering Chinese cabbage. We have isolated three important BcNRTs (BcNRT1.1, BcNRT1.2, and BcNRT2.1) from flowering Chinese cabbage. Spatio-temporal expression analysis found that BcNRT1.1 and BcNRT2.1 were mainly expressed in roots, while BcNRT1.2 was more expressed in roots than in leaves during vegetative growth and was mainly expressed in leaves during reproductive growth. The NO3− uptake rate of the entire growth period was significantly correlated with BcNRT1.1 and BcNRT1.2 expression in roots. In addition, the total N content was increased with the increase in NO3− concentration in flowering Chinese cabbage. The NH4+ uptake was slightly induced by NH4+, but the total N content had no significant difference under the NH4+ concentration of 1–8 mmol/L. We also found that lower concentrations of NH4+ promoted the expression of BcNRT1.1 and BcNRT1.2 while inhibiting the expression of BcNRT2.1 in the roots of flowering Chinese cabbage. The amount of total N uptake in the treatment with 25/75 of NH4+/NO3− was significantly higher than that of the other two treatments (0/100 and 50/50). In the mixture of NH4+ and NO3−, total N uptake was significantly correlated with the BcNRT1.2 expression. We concluded that mixed nutrition with an NH4+/NO3− of 25/75 could significantly increase total nitrogen uptake in flowering Chinese cabbage, in which two members of the NRT1 subfamily (BcNRT1.1 and BcNRT1.2) might play a major regulatory role in it. This study is a beneficial attempt to dig deeper into the NRT genes resources and lays the foundation for the ultimate use of genetic improvement methods to increase the NUE with less nitrogen fertilizer in flowering Chinese cabbage.

New insights into the role of chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23 in nitrate signaling in Arabidopsis roots

Nitrate is an important source of nitrogen and also acts as a signaling molecule to trigger numerous physiological, growth, and developmental processes throughout the life of the plant. Many nitrate transporters, transcription factors, and protein kinases participate in the regulation of nitrate signaling. Here, we identified a gene encoding the chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23, which participates in nitrate signaling pathways. In Arabidopsis, overexpression of CmCIPK23 significantly decreased lateral root number and length and primary root length compared to the WT when grown on modified Murashige and Skoog medium with KNO₃ as the sole nitrogen source (modified MS). The expression of nitrate-responsive genes differed significantly between CmCIPK23-overexpressing Arabidopsis (CmCIPK23-OE) and the WT after nitrate treatment. Nitrate content was significantly lower in CmCIPK23-OE roots, which may have resulted from reduced nitrate uptake at high external nitrate concentrations (≥ 1 mM). Nitrate reductase activity and the expression of nitrate reductase and glutamine synthase genes were lower in CmCIPK23-OE roots. We also found that CmCIPK23 interacted with the transcription factor CmTGA1, whose Arabidopsis homolog regulates the nitrate response. We inferred that CmCIPK23 overexpression influences root development on modified MS medium, as well as root nitrate uptake and assimilation at high external nitrate supply. These findings offer new perspectives on the mechanisms by which the chrysanthemum CBL interacting protein kinase CmCIPK23 influences nitrate signaling.

Multi-Omic Investigation of Low-Nitrogen Conditional Resistance to Clubroot Reveals Brassica napus Genes Involved in Nitrate Assimilation

Nitrogen fertilization has been reported to influence the development of clubroot, a root disease of Brassicaceae species, caused by the obligate protist Plasmodiophora brassicae. Our previous works highlighted that low-nitrogen fertilization induced a strong reduction of clubroot symptoms in some oilseed rape genotypes. To further understand the underlying mechanisms, the response to P. brassicae infection was investigated in two genotypes "Yudal" and HD018 harboring sharply contrasted nitrogen-driven modulation of resistance toward P. brassicae. Targeted hormone and metabolic profiling, as well as RNA-seq analysis, were performed in inoculated and non-inoculated roots at 14 and 27 days post-inoculation, under high and low-nitrogen conditions. Clubroot infection triggered a large increase of SA concentration and an induction of the SA gene markers expression whatever the genotype and nitrogen conditions. Overall, metabolic profiles suggested that N-driven induction of resistance was independent of SA signaling, soluble carbohydrate and amino acid concentrations. Low-nitrogen-driven resistance in "Yudal" was associated with the transcriptional regulation of a small set of genes, among which the induction of NRT2- and NR-encoding genes. Altogether, our results indicate a possible role of nitrate transporters and auxin signaling in the crosstalk between plant nutrition and partial resistance to pathogens.

Exposure to high nitrogen triggered a genotype-dependent modulation of cell and root hydraulics, which can involve aquaporin regulation

Root nitrogen acquisition has been proposed to be regulated by mass flow, a process by which water flow brings nutrients to the root surface, depending on a concerted regulation of the root hydraulic properties and stomatal conductance. As aquaporins play an important role in regulating transcellular water flow, we aimed at evaluating the short-term effect of high nitrogen (HN) availability on the dynamics of hydraulic parameters at both the root and cell level and the regulation of aquaporins. The effect of short-term HN (8 mM NO₃ ^- ) treatment was investigated on 12 diverse 15-day-old maize genotypes. Root exposure to HN triggered a rapid (<4 h) increase in the root hydraulic conductivity (L_pr ) in seven genotypes while no L_pr variation was recorded for the others, allowing the separation of the genotypes into two groups (HN-responsive and HN-nonresponsive). A remarkable correlation between L_pr and the cortex cell hydraulic conductivity (L_pc ) was observed. However, while differences in gas exchange parameters were also observed, the variations were genotype-specific and not always correlated with the root hydraulic parameters. We then investigated whether HN-induced L_pr variations were linked to the activity and regulation of plasma membrane PIP aquaporins. While some changes in PIP mRNA levels were detected, this was not correlated with the protein levels. On the other hand, the rapid variation in L_pr observed in the B73 genotype was correlated with the PIP protein abundance in the plasma membrane, highlighting PIP posttranslational mechanisms in the short-term regulation of root hydraulic parameters in response to HN treatment.

Role of protein phosphatases in the regulation of nitrogen nutrition in plants

The reversible protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases regulate different biological processes and their response to environmental cues, including nitrogen (N) availability. Nitrate assimilation is under the strict control of phosphorylation-dephosphorylation mediated post-translational regulation. The protein phosphatase family with approximately 150 members in Arabidopsis and around 130 members in rice is a promising player in N uptake and assimilation pathways. Protein phosphatase 2A (PP2A) enhances the activation of nitrate reductase (NR) by deactivating SnRK1 and reduces the binding of inhibitory 14-3-3 proteins on NR. The functioning of nitrate transporter NPF6.3 is regulated by phosphorylation of CBL9 (Calcineurin B like protein 9) and CIPK23 (CBL interacting protein kinase 23) module. Phosphorylation by CIPK23 inhibits the activity of NPF6.3, whereas protein phosphatases (PP2C) enhance the NPF6.3-dependent nitrate sensing. PP2Cs and CIPK23 also regulate ammonium transporters (AMTs). Under either moderate ammonium supply or high N demand, CIPK23 is bound and inactivated by PP2Cs. Ammonium uptake is mediated by nonphosphorylated and active AMT1s. Whereas, under high ammonium availability, CIPK23 gets activated and phosphorylate AMT1;1 and AMT1;2 rendering them inactive. Recent reports suggest the critical role of protein phosphatases in regulating N use efficiency (NUE). In rice, PP2C9 regulates NUE by improving N uptake and assimilation. Comparative leaf proteome of wild type and PP2C9 over-expressing transgenic rice lines showed 30 differentially expressed proteins under low N level. These proteins are involved in photosynthesis, N metabolism, signalling, and defence.

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

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

Lateral root formation and nutrients: nitrogen in the spotlight

Lateral roots are important to forage for nutrients due to their ability to increase the uptake area of a root system. Hence, it comes as no surprise that lateral root formation is affected by nutrients or nutrient starvation, and as such contributes to the root system plasticity. Understanding the molecular mechanisms regulating root adaptation dynamics toward nutrient availability is useful to optimize plant nutrient use efficiency. There is at present a profound, though still evolving, knowledge on lateral root pathways. Here, we aimed to review the intersection with nutrient signaling pathways to give an update on the regulation of lateral root development by nutrients, with a particular focus on nitrogen. Remarkably, it is for most nutrients not clear how lateral root formation is controlled. Only for nitrogen, one of the most dominant nutrients in the control of lateral root formation, the crosstalk with multiple key signals determining lateral root development is clearly shown. In this update, we first present a general overview of the current knowledge of how nutrients affect lateral root formation, followed by a deeper discussion on how nitrogen signaling pathways act on different lateral root-mediating mechanisms for which multiple recent studies yield insights.

The positive effect of salinity on nitrate uptake in Suaeda salsa

Nitrate plays both nutritional and osmotic roles in the salt tolerance of halophytes. However, how halophytes take up NO₃^- under saline conditions is still not well understood. Seedlings of Suaeda salsa L. were treated with 0, 200 and 500 mM NaCl under 0.5 mM NO₃^--N with or without Na₃VO₄ (the inhibitor of plasma membrane H⁺-ATPase) for 24 h. Salinity treatment of 200 mM NaCl up-regulated the gene expression of nitrate transporter 2.1 (SsNRT2.1) in the roots, increased the root net influx of H⁺ and NO₃^- and ¹⁵NO₃^- accumulation in the leaves and roots. The expression of SsNRT2.1 at 200 mM NaCl with Na₃VO₄ was much higher than that without supplying Na₃VO₄, and the opposite trend was found in ¹⁵NO₃^- accumulation in the leaves and roots. Supplying Na₃VO₄ had no significant effect on the net H⁺ flux, but induced a net NO₃^- efflux in the roots at 200 mM NaCl. Salinity may directly activate the expression of SsNRT2.1 and promote NO₃^- uptake via the increment of pumping H⁺ by PM H⁺-ATPase in S. salsa, which may explain why certain halophytes can absorb and accumulate high concentration of NO₃^- under low NO₃^- and high salinity conditions.

Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.

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.

Expression of potential reference genes in response to macronutrient stress in rice and soybean

Given the complexity of nutrient stress responses and the availability of a few validated reference genes, we aimed to identify robust and stable reference genes for macronutrient stress in rice and soybean. Ten potential reference genes were evaluated using geNorm, NormFinder, BestKeeper, Comparative ΔCt method, and RefFinder algorithms under low and completely starved conditions of nitrogen (N), phosphorus (P), potassium (K), and sulphur (S). Results revealed distinct sets of reference gene pairs, showing stable expression under different experimental conditions. The gene pairs TIP41/UBC(9/10/18) and F-box/UBC10 were most stable in rice and soybean, respectively under N stress. Under P stress, UBC9/UBC10 in rice and F-Box/UBC10 in soybean were most stable. Similarly, TIP41/UBC10 in rice and RING FINGER/UBC9 in soybean were the best gene pairs under K stress while F-Box/TIP41 in rice and UBC9/UBC10 in soybean were the most stable gene pairs under S stress. These reference gene pairs were validated by quantifying the expression levels of high-affinity transporters like NRT2.1/NRT2.5, PT1, AKT1, and SULTR1 for N, P, K, and S stress, respectively. This study reiterates the importance of choosing reference genes based on crop species and the experimental conditions, in order to obtain concrete answers to missing links of gene regulation in response to macronutrient deficiencies.

The N uptake-associated physiological processes at late growth stage in wheat (Triticum aestivum) under N deprivation combined with deficit irrigation condition

Elucidating physiological mechanisms underlying the plant N uptake benefits breeding of high N use efficiency (NUE) crop cultivars. In this study, we investigated the growth and N uptake-associated processes in wheat under N deprivation and deficit irrigation, using two contrasting NUE cultivars. Compared with sufficient-N (SN), deficient-N (DN) treatment reduced plant biomass, N accumulation, and yields in two cultivars (high NUE Shinong 086 and N deprivation-sensitive Jimai 585), suggesting that N deprivation negatively regulates plant growth and N uptake. Shinong 086 was better on growth and N uptake-associated traits than Jimai 585 due to the improved root biomass across soil profile, which was consistent with the decrease of available N contents in soil layers. These results suggested that the improved root system architecture (RAS) enhances plant acquirement for soil N under N- and water-deprivation condition, contributing to the plant N uptake and yield formation capacities. Transcriptome investigation revealed that numerous genes were differentially expressed (DE) in the N-deprived Shinong 086 plants, which involve the regulation of complicate biochemical pathways. These results suggested that the modified RAS and N uptake in high NUE plants are accomplished underlying the regulation of numerous DE genes. TaWRKY20, a gene in ZFP transcription factor family, was functionally characterized for the role in mediating plant N uptake. Overexpression of it conferred plants improved growth and N uptake under DN due to its regulation on TaNRT2.1 and TaNRT2.2, two nitrate transporter genes. Our investigation provides insights in high NUE mechanisms in wheat under N deprivation.

Impacts of Reduced Nitrate Supply on Nitrogen Metabolism, Photosynthetic Light-Use Efficiency, and Nutritional Values of Edible Mesembryanthemum crystallinum

Mesembryanthemum crystallinum (common ice plant), as a nutritious ready-to-eat salad in Singapore, has become popular in recent years. However, basic data about the impacts of NO3 - supply on its NO3 - accumulation and nutritional quality are lacking. In this study, all plants were first grown indoor hydroponically in 10% artificial seawater (ASW) with modified full-strength Netherlands Standard Composition nutrient solution for 11 days, before transferring them to different reduced NO3 - solutions. All plants grew well and healthy after 7 days of treatment. However, plants grown with 3/4 N and 1/2 N were bigger with higher shoot and root fresh weight (FW), greater leaf number, and total leaf area (TLA) than those grown with full nitrogen (N), 1/4 N, and 0 N. Mesembryanthemum crystallinum grown with full N, 3/4 N, and 1/4 N had similar specific leaf area (SLA), while 0 N plants had significantly lower SLA. All plants had similar leaf succulence (LS). However, leaf water content (LWC) was lower, while leaf dry matter accumulation (LDMC) was higher in 0 N plants after 7 days of treatment. Compared with plants grown with full N, shoot NO3 - concentrations in 3/4 N, 1/2 N, and 1/4 N plants were constant or slightly increased during the treatments. For 0 N plants, shoot NO3 - concentration decreased significantly during the treatment compared with other plants. Shoot NO3 - accumulation was associated with nitrate reductase activity (NRA). For instance, after 7 days of treatment, shoot NO3 - concentration and NRA on a FW basis in 0 N plants were, respectively, 45 and 31% of full N plants. After transferring full N to 0 N for 7 days, all M. crystallinum had higher chlorophyll (Chl) content coupled with higher electron transport rate (ETR) and higher effective quantum yield of PSII, while full N plants had higher non-photochemical quenching (NPQ). The 0N plants had much higher concentrations of proline, total soluble sugar (TSS), and total ascorbic acid (ASC) than other plants. In conclusion, totally withdrawing NO3 - from the growth media prior to harvest could be one of the strategies to reduce shoot NO3 - concentration. Reduced NO3 - supply further enhanced nutritional values as concentrations of proline, TSS, and ASC were enhanced markedly in M. crystallinum plants after transferring them from full N to 0 N.

Interrelations of nutrient and water transporters in plants under abiotic stress

Environmental changes cause abiotic stress in plants, primarily through alterations in the uptake of the nutrients and water they require for their metabolism and growth and to maintain their cellular homeostasis. The plasma membranes of cells contain transporter proteins, encoded by their specific genes, responsible for the uptake of nutrients and water (aquaporins). However, their interregulation has rarely been taken into account. Therefore, in this review we identify how the plant genome responds to abiotic stresses such as nutrient deficiency, drought, salinity and low temperature, in relation to both nutrient transporters and aquaporins. Some general responses or regulation mechanisms can be observed under each abiotic stress such as the induction of plasma membrane transporter expression during macronutrient deficiency, the induction of tonoplast transporters and reduction of aquaporins during micronutrients deficiency. However, drought, salinity and low temperatures generally cause an increase in expression of nutrient transporters and aquaporins in tolerant plants. We propose that both types of transporters (nutrients and water) should be considered jointly in order to better understand plant tolerance of stresses.

Regulation of Lateral Root Development by Shoot-Sensed Far-Red Light via HY5 Is Nitrate-Dependent and Involves the NRT2.1 Nitrate Transporter

Plants are very effective in responding to environmental changes during competition for light and nutrients. Low Red:Far-Red (low R:FR)-mediated neighbor detection allows plants to compete successfully with other plants for available light. This above-ground signal can also reduce lateral root growth by inhibiting lateral root emergence, a process that might help the plant invest resources in shoot growth. Nitrate is an essential nutrient for plant growth and Arabidopsis thaliana responds to low nitrate conditions by enhancing nutrient uptake and reducing lateral and main root growth. There are indications that low R:FR signaling and low nitrate signaling can affect each other. It is unknown which response is prioritized when low R:FR light- and low nitrate signaling co-occur. We investigated the effect of low nitrate conditions on the low R:FR response of the A. thaliana root system in agar plate media, combined with the application of supplemental Far-Red (FR) light to the shoot. We observed that under low nitrate conditions main and lateral root growth was reduced, but more importantly, that the response of the root system to low R:FR was not present. Consistently, a loss-of-function mutant of a nitrate transporter gene NRT2.1 lacked low R:FR-induced lateral root reduction and its root growth was hypersensitive to low nitrate. ELONGATED HYPOCOTYL5 (HY5) plays an important role in the root response to low R:FR and we found that it was less sensitive to low nitrate conditions with regards to lateral root growth. In addition, we found that low R:FR increases NRT2.1 expression and that low nitrate enhances HY5 expression. HY5 also affects NRT2.1 expression, however, it depended on the presence of ammonium in which direction this effect was. Replacing part of the nitrogen source with ammonium also removed the effect of low R:FR on the root system, showing that changes in nitrogen sources can be crucial for root plasticity. Together our results show that nitrate signaling can repress low R:FR responses and that this involves signaling via HY5 and NRT2.1.

Plasma membrane calcineurin B-like calcium-ion sensor proteins function in regulating primary root growth and nitrate uptake by affecting global phosphorylation patterns and microdomain protein distribution

The collective function of calcineurin B-like (CBL) calcium ion (Ca²⁺ ) sensors and CBL-interacting protein kinases (CIPKs) in decoding plasma-membrane-initiated Ca²⁺ signals to convey developmental and adaptive responses to fluctuating nitrate availability remained to be determined. Here, we generated a cbl-quintuple mutant in Arabidopsis thaliana devoid of these Ca²⁺ sensors at the plasma membrane and performed comparative phenotyping, nitrate flux determination, phosphoproteome analyses, and studies of membrane domain protein distribution in response to low and high nitrate availability. We observed that CBL proteins exert multifaceted regulation of primary and lateral root growth and nitrate fluxes. Accordingly, we found that loss of plasma membrane Ca²⁺ sensor function simultaneously affected protein phosphorylation of numerous membrane proteins, including several nitrate transporters, proton pumps, and aquaporins, as well as their distribution within plasma membrane microdomains, and identified a specific phosphorylation and domain distribution pattern during distinct phases of low and high nitrate responses. Collectively, these analyses reveal a central and coordinative function of CBL-CIPK-mediated signaling in conveying plant adaptation to fluctuating nitrate availability and identify a crucial role of Ca²⁺ signaling in regulating the composition and dynamics of plasma membrane microdomains.

Role of Suaeda salsa SsNRT2.1 in nitrate uptake under low nitrate and high saline conditions

The global annual loss in agricultural production resulting from soil salinization is significant. Although nitrate (NO₃^-) is known to play both nutritional and osmotic roles in the salt tolerance of halophytes, it remains unclear how halophytes such as Suaeda salsa L. take up NO₃^- under saline conditions. In the present study, the gene of nitrate transporter 2.1 (SsNRT2.1) was cloned from S. salsa and its function was identified in both S. salsa and Arabidopsis thaliana under salinity and low NO₃^--N (0.5 mM NO₃^-) conditions. The results revealed that SsNRT2.1 expression and NO₃^- concentration in the roots of S. salsa were higher at 200 mM NaCl, compared with that at 0 and 500 mM NaCl after 24 h treatment. The Arabidopsis overexpression lines showed a higher NO₃^- content compared to the WT lines at 0 and 50 mM NaCl. A similar trend was observed in the root length. In conclusion, salinity promoted the SsNRT2.1 expression in S. salsa, suggesting that this gene may contribute to the efficient NO₃^- uptake in S. salsa under low NO₃^- and high salinity conditions. This trait may explain why S. salsa can tolerate high salinity and produce the highest biomass at about 200 mM NaCl.

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

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

PGPR Mediated Alterations in Root Traits: Way Toward Sustainable Crop Production

The above ground growth of the plant is highly dependent on the belowground root system. Rhizosphere is the zone of continuous interplay between plant roots and soil microbial communities. Plants, through root exudates, attract rhizosphere microorganisms to colonize the root surface and internal tissues. Many of these microorganisms known as plant growth promoting rhizobacteria (PGPR) improve plant growth through several direct and indirect mechanisms including biological nitrogen fixation, nutrient solubilization, and disease-control. Many PGPR, by producing phytohormones, volatile organic compounds, and secondary metabolites play important role in influencing the root architecture and growth, resulting in increased surface area for nutrient exchange and other rhizosphere effects. PGPR also improve resource use efficiency of the root system by improving the root system functioning at physiological levels. PGPR mediated root trait alterations can contribute to agroecosystem through improving crop stand, resource use efficiency, stress tolerance, soil structure etc. Thus, PGPR capable of modulating root traits can play important role in agricultural sustainability and root traits can be used as a primary criterion for the selection of potential PGPR strains. Available PGPR studies emphasize root morphological and physiological traits to assess the effect of PGPR. However, these traits can be influenced by various external factors and may give varying results. Therefore, it is important to understand the pathways and genes involved in plant root traits and the microbial signals/metabolites that can intercept and/or intersect these pathways for modulating root traits. The use of advanced tools and technologies can help to decipher the mechanisms involved in PGPR mediated determinants affecting the root traits. Further identification of PGPR based determinants/signaling molecules capable of regulating root trait genes and pathways can open up new avenues in PGPR research. The present review updates recent knowledge on the PGPR influence on root architecture and root functional traits and its benefits to the agro-ecosystem. Efforts have been made to understand the bacterial signals/determinants that can play regulatory role in the expression of root traits and their prospects in sustainable agriculture. The review will be helpful in providing future directions to the researchers working on PGPR and root system functioning.

Identification and characterization of the NPF, NRT2 and NRT3 in spinach

Nitrate transporters (NRTs) participate in nitrate uptake, transport and allocation within the plant. However, this gene family has not been studied thoroughly in spinach. This study provided the general information about spinach SoNRTs and their transcriptional and functional responses to different levels of nitrate supplies. Resultes showed that fifty-seven NPF (also known as NRT1), nine NRT2 and one NRT3 were identified in spinach homologous to characterized Arabidopsis NRT genes. Phylogenetic analysis organized the SoNRT family into three clades: NPF with three subclades, NRT2, and NRT3. The tested SoNRT genes showed the various expression profiles in relation to tissue specificity and nitrate supply, indicating their functional diversity in response to external nitrate supply. Among them, transgenic Arabidopsis plants overexpressing SoNPF30 showed improved biomass, decreased shoot nitrate contents but no significant difference of ¹⁵NO₃^- uptake rates when compared with those of the wild type in response to high N treatment. Under low N treatment, overexpressing of SoNRT3 significantly increased whole plant biomass, root nitrate contents and ¹⁵NO₃^- uptake rates. These demonstrated that SoNPF30 and SoNRT3 confer greater capacity for nitrate translocation or nitrate uptake, and could help to improve the ability of plant nitrogen utilization under those conditions. Our findings provide a valuable basis for future research on this family of genes in spinach.

Potassium: A key modulator for cell homeostasis

Potassium (K) is the most vital and abundant macro element for the overall growth of plants and its deficiency or, excess concentration results in many diseases in plants. It is involved in regulation of many crucial roles in plant development. Depending on soil-root interactions, complex soil dynamics often results in unpredictable availability of the elements. Based on the importance index, K is considered to be the second only to nitrogen for the overall growth of plants. More than 60 enzymes within the plant system depend on K for its activation, in which K act as a key regulator. K helps plants to resist several abiotic and biotic stresses in the environment. We have reviewed the research progress about K's role in plants covering various important considerations of K highlighting the effects of microbes on soil K⁺; K and its contribution to adsorbed dose in plants; the importance of K⁺ deficiency; physiological functions of K⁺ transporters and channels; and interference of abiotic stressor in the regulatory role of K. This review further highlights the scope of future research regarding K.

Genome-wide identification and expression analyses of nitrate transporter family genes in wild soybean (Glycine soja)

Nitrate transporters (NRTs) are important channel proteins facilitating cross-membrane movement of small molecules like NO3- which is a critical nutrient for all life. However, the classification and evolution of nitrate transporters in the legume plants are still elusive. In this study, we surveyed the wild soybean (G. soja) genomic databases and identified 120 GsNRT1 and 5 GsNRT2 encoding genes. Phylogenetic analyses show that GsNRT1 subfamily is consisted of eight clades (NPF1 to NPF8), while GsNRT2 subfamily has only one clade. Gene chromosomal location and evolutionary historic analyses indicate that GsNRT genes are unevenly distributed on 19 out of 20 G. soja chromosomes and segmental duplications may take a major part in the expansion of GsNRT family. Investigations of gene structure and protein motif compositions suggest that GsNRT family members are highly conserved in structures of both gene and protein levels. In addition, we analyzed the spatial expression patterns of representative GsNRT genes and their responses to exogenous nitrogen and carbon supplies and different abiotic stresses. The qRT-PCR data indicated that 16 selected GsNRT genes showed various expression levels in the roots, stems, leaves, and pods of young G. soja plants, and these genes were regulated by not only nitrogen and carbohydrate nutrients but also NaCl, NaHCO3, abscisic acid (ABA), and salicylic acid (SA). These results suggest that GsNRT genes may be involved in the regulation of plant growth, development, and adaptation to environmental stresses, and the study will shed light on functional dissection of plant nitrate transporter proteins in the future.