Nitrate in 2020: Thirty Years from Transport to Signaling Networks

Glutamate-related nitrogen metabolism regulates cold-adaptive synthesis of red pigment in polar fungus Geomyces sp. WNF-15A

The polar fungus Geomyces sp. WNF-15A produces high-quality red pigment (AGRP), but the cold-dependent characteristic of AGRP synthesis restricts its industrialization. This study employed transcriptome analysis to compare gene expression profiles of the wild-type strain with cold-independent mutants of scaffold1.t692 (Δ1-692) and scaffold2.t704 (Δ2-704). From the analysis, 23 candidate genes were identified and functionally characterized among 22,600 differentially expressed genes. Knockout and recovery of scaffold5.t61, scaffold7.t586, or scaffold7.t712 proved their regulatory functions in AGRP synthesis, among which scaffold5.t61 functioned as a transcription factor, while scaffold7.t586 and scaffold7.t712 were involved in the glutamate-related nitrogen metabolism. Exogenous addition of nitrate, glutamine, and glutamate, combined with transcriptional regulation studies, revealed the importance of glutamate metabolism for cold-adaptive synthesis of AGRP. Scaffold5.t61 responded to the cold environment and regulated the transcription of scaffold2.t704 and scaffold1.t692. It subsequently increased glutamate synthesis by regulating the key nitrogen metabolism genes of scaffold7.t586 and scaffold7.t712, ultimately resulting in cold-dependent synthesis of AGRP in Geomyces sp. WNF-15A. This study offers new insights into the mechanisms of cold adaptation in polar fungi and serves as a reference for the development of psychrophilic fungal resources.

Natural variation in ZmNRT2.5 modulates husk leaf width and promotes seed protein content in maize

The husk leaf of maize (Zea mays) encases the ear as a modified leaf and plays pivotal roles in protecting the ear from pathogen infection, translocating nutrition for grains and warranting grain yield. However, the natural genetic basis for variation in husk leaf width remains largely unexplored. Here, we performed a genome-wide association study for maize husk leaf width and identified a 3-bp InDel (insertion/deletion) in the coding region of the nitrate transporter gene ZmNRT2.5. This polymorphism altered the interaction strength of ZmNRT2.5 with another transporter, ZmNPF5, thereby contributing to variation in husk leaf width. We also isolated loss-of-function mutants in ZmNRT2.5, which exhibited a substantial decrease in husk leaf width relative to their controls. We demonstrate that ZmNRT2.5 facilitates the transport of nitrate from husk leaves to maize kernels in plants grown under low-nitrogen conditions, contributing to the accumulation of proteins in maize seeds. Together, our findings uncovered a key gene controlling maize husk leaf width and nitrate transport from husk leaves to kernels. Identification of the ZmNRT2.5 loci offers direct targets for improving the protein content of maize seeds via molecular-assisted maize breeding.

Resilient plants, sustainable future

The accelerated pace of climate change over the past several years should serve as a wake-up call for all scientists, farmers, and decision makers, as it severely threatens our food supply and could result in famine, migration, war, and an overall destabilization of our society. Rapid and significant changes are therefore needed in the way we conduct research on plant resilience, develop new crop varieties, and cultivate those crops in our agricultural systems. Here, we describe the main bottlenecks for these processes and outline a set of key recommendations on how to accelerate research in this critical area for our society.

Decoding Long-Distance Communication Under Mineral Stress: Advances in Vascular Signalling and Molecular Tools for Plant Resilience

Mineral nutrients are essential for plant growth, development and crop yield. Under mineral deficient conditions, plants rely on a sophisticated network of signalling pathways to coordinate their molecular, physiological, and morphological responses. Recent research has shown that long-distance signalling pathways play a pivotal role in maintaining mineral homeostasis and optimising growth. This review explores the intricate mechanisms of long-distance signalling under mineral deficiencies, emphasising its importance as a communication network between roots and shoots. Through the vascular tissues, plants transport an array of signalling molecules, including phytohormones, small RNAs, proteins, small peptides, and mobile mRNAs, to mediate systemic responses. Vascular tissues, particularly companion cells, are critical hubs for sensing and relaying mineral deficiency signals, leading to rapid changes in mineral uptake and optimised root morphology. We highlight the roles of key signalling molecules in regulating mineral acquisition and stress adaptation. Advances in molecular tools, including TRAP-Seq, heterografting, and single-cell RNA sequencing, have recently unveiled novel aspects of long-distance signalling and its regulatory components. These insights underscore the essential role of vascular-mediated communication in enabling plants to navigate heterogeneous mineral distribution environments and suggest new avenues for improving crop resilience and mineral use efficiency.

The E3 ubiquitin ligase BRG3 and the protein kinase MPK7 antagonistically regulate LBD36 turnover, a key node for integrating nitrate and gibberellin signaling in apple

Nitrate is the main source of nitrogen in plants. Nitrate stimulation causes changes in plant secondary metabolites, including anthocyanins. However, the molecular mechanism underlying how nitrate regulates anthocyanin biosynthesis remains unclear. In this study, we identified a nitrate response factor MdLBD36 in apple. This factor positively regulated nitrate deficiency-induced anthocyanin biosynthesis by promoting the transcriptional activity of MdABI5, an important regulator of anthocyanins, and directly activated MdABI5 expression. The E3 ubiquitin ligase MdBRG3 promoted the ubiquitinated degradation of MdLBD36 to reduce anthocyanin biosynthesis under nitrate-sufficient conditions. Nitrate deficiency-activated MdMPK7 maintained the stimulating effect of MdLBD36 on anthocyanin biosynthesis by counteracting the MdBRG3-mediated degradation of MdLBD36. Nitrate coordinated gibberellin (GA) signaling to regulate anthocyanin biosynthesis. The GA signaling repressor MdRGL2a contributed to MdLBD36-promoted anthocyanin biosynthesis by enhancing the MdLBD36-MdABI5 interaction and increasing the MdLBD36 transcriptional activation of MdABI5. In summary, our results elucidate the molecular framework of the coordinated regulation of the nitrate signaling response and anthocyanin biosynthesis by ubiquitination and phosphorylation. This study revealed the cross talk between nitrate and GA signaling in the regulation of anthocyanin biosynthesis and provides references for an in-depth exploration of the nitrate signal transduction pathway and its interactions with hormones.

The crosstalk between nitrate signaling and other signaling molecules in Arabidopsis thaliana

Nitrate signaling coordinates the expression of a broad range of genes involved in nitrate uptake, transport, and assimilation, playing a crucial role in plant growth and development. Notably, nitrate signaling interacts extensively with various messenger molecules, including phytohormones, calcium ions (Ca2+), reactive oxygen species (ROS), peptides, and sucrose. This crosstalk amplifies nitrate signaling and optimizes nutrient uptake, coordinating developmental processes and enhancing stress tolerance. Understanding the interactions between nitrate and these signaling molecules offers valuable insights into improving crop nutrient use efficiency (NUE), stress resilience, and agricultural sustainability. Using Arabidopsis thaliana as a model, this review consolidates current knowledge on nitrate signaling and its interplay with other signaling pathways that regulate plant development and adaptation. Finally, the review highlights potential genetic strategies for enhancing NUE, contributing to more sustainable agricultural practices.

Nitrate attenuates abscisic acid signaling via NIN-LIKE PROTEIN8 in Arabidopsis seed germination

Abscisic acid (ABA) suppresses Arabidopsis (Arabidopsis thaliana) seed germination and post-germinative growth. Nitrate stimulates seed germination, but whether it directly regulates ABA signaling and the associated underlying molecular mechanisms remain unknown. Here, we showed that nitrate alleviates the repressive effects of ABA on seed germination independently of the nitric oxide (NO) pathway. Moreover, nitrate attenuates ABA signaling activated by ABSCISIC ACID INSENSITIVE3 (ABI3) and ABI5, two critical transcriptional regulators of the ABA pathway. Mechanistic analyses demonstrated that ABI3 and ABI5 physically interact with the nitrate signaling-related core transcription factor NIN-LIKE PROTEIN 8 (NLP8). After ABA treatment, NLP8 suppresses ABA responses during seed germination without affecting ABA content. Notably, nitrate represses ABA signaling mainly through NLP8. Genetic analyses showed that NLP8 acts upstream of ABI3 and ABI5. Specifically, NLP8 inhibits the transcriptional functions of ABI3 and ABI5, as well as their ABA-induced accumulation. Additionally, NLP8 overexpression largely suppresses the ABA hypersensitivity of mutant plants exhibiting impaired NO biosynthesis or signaling. Collectively, our study reveals that nitrate counteracts the inhibitory effects of ABA signaling on seed germination and provides mechanistic insights into the NLP8-ABI3/ABI5 interactions and their antagonistic relationships in ABA signaling.

Interacting MeZFP29 and MebZIPW regulates MeNRT2.2 from cassava responding to nitrate signaling

KEY MESSAGE

Cassava is a significant tropical cash crop. MeZFP29 interacting with MebZIPW improves MeNRT2.2, encoding a high-affinity nitrate transporter, through binding to NREs under low nitrate and shows a nitrate-signaling-triggered regulation. Cassava (Manihot esculenta) is a globally significant tropical root crop and exhibits exceptional adaptability to native soil fertility. MeNRT2.2 encodes a high-affinity nitrate transporter in cassava and heterologous overexpression of MeNRT2.2 in Arabidopsis increases nitrate transportation and utilization under nitrogen scarcity. However, the responsive mechanism of MeNRT2.2 to nitrate remains unclear. In this study, we identified a nitrate-responsive fragment of 450 bp located upstream of the start codon of MeNRT2.2, and two potential regulators, MeZFP29 and MebZIPW, of MeNRT2.2. Two regulators specifically bound to nitrate-responsive cis-element (NRE), i.e., TGCATT and CAGATG, in the 450 bp fragment and together significantly stimulated promoter activity. Furthermore, we confirmed the interaction between two regulators in vivo and in vitro via Y2H, BiFC, Co-IP, and GST-pull-down assays. In addition, the distribution of MeZFP29 and its heterodimers (MeZFP&MebZIPW) are determined by nitrate signaling, i.e., in the cytoplasm and nucleus under nitrogen limitation, and predominantly in nucleus under sufficient nitrate. In contrast, MebZIPW consistently localizes to the cytoplasm and nucleus regardless of nitrate conditions. Moreover, overexpression of MeZFP29 in Arabidopsis enhanced growth and chlorophyll content, particularly, under low nitrate conditions, while MebZIPW did not. These findings not only confirm the regulation of MeZFP29 and MebZIPW on MeNRT2.2, but also illustrate the nitrate signaling-triggered promotion and feedback on MeNRT2.2. Our study provides a novel approach to enhancing nitrogen-use efficiency in cassava by modulating the regulators under moderate nitrogen levels as low as possible.

Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize

Nitrogen (N) is an essential macronutrient for plant development and, ultimately, yield. Identifying the genetic components and mechanisms underlying N use efficiency in maize (Zea mays L.) is thus of great importance. Nitrate (NO3-) is the preferred inorganic N source in maize. Here we performed a genome-wide association study of shoot NO3- accumulation in maize seedlings grown under low-NO3- conditions, identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait. ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity heterodimer with its closest paralogue, ZmFd9, in a NO3--sensitive manner. Although ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction limits their ability to associate with ZmNiRs and stimulate their activity. Knockout lines for ZmFd4 with decreased NO3- contents exhibit more efficient NO3- assimilation, and field experiments show consistently improved N utilization and grain yield under N-deficient conditions. Our work thus provides molecular and mechanistic insights into the natural variation in N utilization, instrumental for genetic improvement of yield in maize and, potentially, in other crops.

A Gln alteration influences leaf morphogenesis by mediating gibberellin levels in tobacco

Nitrogen is a critical nutrient for plant growth and development. While numerous studies have investigated the mechanisms by which nitrate and/or ammonium regulate plant growth, little is known about whether and how amino acids regulate plant leaf development. This study demonstrates that tobacco plants with altered expression levels of an amino acid transporter (LYSINE HISTIDINE TRANSPORTER1, NtLHT1, Ntab0818090) exhibit significant differences in leaf morphology. Knock-out mutants exhibit elongated and narrower leaves compared to wild-type plants, whereas overexpression (OE) lines display orbicular leaves. Additionally, mutant plants exhibit decreased nitrogen use efficiency (NUE) under half MS medium and delayed development under nitrogen-depleted conditions. Moreover, overexpression lines demonstrate better performance. Although the mutant does not show significant lower level of nitrate or total amino acid content in the developing leaves, its amino acid profile, particularly glutamine (Gln), is significantly altered. Supplementation with Gln in the growth medium, rather than glutamate, can restore the morphological differences observed in mutant leaves, suggesting a pivotal role of Gln in regulating leaf shape. To further elucidate the mechanisms underlying leaf shape regulation, we analyzed endogenous hormone levels and applied exogenous hormones to these lines. Our findings suggest that amino acids transported from source organs, particularly glutamine (Gln), play a key role in controlling leaf development and morphology through the modulation of multiple phytohormones, such as gibberellic acid (GA).

ACS2 and ACS6, especially ACS2 is involved in MPK6 evoked production of ethylene under Cd stress, which exacerbated Cd toxicity in Arabidopsis thaliana

As one of the heavy metal pollutants with strong biological toxicity, cadmium (Cd) is easily absorbed by plant roots, which seriously restricts the growth of plants, causes the quality of agricultural products to decline and threatens human health. Many complex signal transduction pathways are involved in the process of plant response to Cd stress. Among them, plant hormone ethylene is an important signal molecule for plant response to various environmental stresses, and its regulatory mechanism and signal transduction pathway in Cd stress response need to be further clarified. Here, we discovered that Cd stress induced a significant increment in ethylene production in Arabidopsis roots, and the amount of ethylene produced was positively correlated with the inhibition of Arabidopsis root growth and Cd accumulation. Simultaneously, Cd stress stimulated the detoxification mechanism within cells and promoted the expression of METAL TOLERANCE PROTEIN 3 (MTP3), IRON-REGULATED TRANSPORTER2 (IRT2), IRON REGULATED GENE 2 (IREG2) genes implicated in Cd vacuolar compartmentation. However, whether this is associated with ethylene signal transduction remains to be further explored. Further studies have revealed that the Cd induced ethylene burst is attributed to the up-regulation of the expression of 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE (ACS) genes that mediated by MITONGEN-ACTIVATED PROTEIN KINASE 6 (MAPK6) in Arabidopsis roots, and among them, ACS2 and ACS6, especially ACS2, are involved in MAPK6-induced ethylene production under Cd stress. The results of this study provide new ideas for understanding the signal transduction pathway of plant response to Cd stress.

Nitrogen at the crossroads of light: integration of light signalling and plant nitrogen metabolism

Plants have developed complex mechanisms to perceive, transduce, and respond to environmental signals, such as light, which are essential for acquiring and allocating resources, including nitrogen (N). This review delves into the complex interaction between light signals and N metabolism, emphasizing light-mediated regulation of N uptake and assimilation. Firstly, we examine the details of light-mediated regulation of N uptake and assimilation, focusing on the light-responsive activity of nitrate reductase (NR) and nitrate transporters. Secondly, we discuss the influence of light on N-dependent developmental plasticity, elucidating how N availability regulates crucial developmental transitions such as flowering time, shoot branching, and root growth, as well as how light modulates these processes. Additionally, we consider the molecular interaction between light and N signalling, focusing on photoreceptors and transcription factors such as HY5, which are necessary for N uptake and assimilation under varying light conditions. A recent understanding of the nitrate signalling and perception of low N is also highlighted. The in silico transcriptome analysis suggests a reprogramming of N signalling genes by shade, and identifies NLP7, bZIP1, CPK30, CBL1, LBD37, LBD38, and HRS1 as crucial molecular regulators integrating light-regulated N metabolism.

Maize2035: A decadal vision for intelligent maize breeding

Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet further increase in global maize production faces mounting challenges in a changing world. In this Perspective paper, we overview the historical successes of maize breeding that laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology approaches. A transition toward a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.

Illuminating anions in biology with genetically encoded fluorescent biosensors

Anions are critical to all life forms. Anions can be absorbed as nutrients or biosynthesized. Anions shape a spectrum of fundamental biological processes at the organismal, cellular, and subcellular scales. Genetically encoded fluorescent biosensors can capture anions in action across time and space dimensions with microscopy. The firsts of such technologies were reported more than 20 years for monoatomic chloride and polyatomic cAMP anions. However, the recent boom of anion biosensors illuminates the unknowns and opportunities that remain for toolmakers and end users to meet across the aisle to spur innovations in biosensor designs and applications for discovery anion biology. In this review, we will canvas progress made over the last three years for biologically relevant anions that are classified as halides, oxyanions, carboxylates, and nucleotides.

Nitrate activates an MKK3-dependent MAPK module via NLP transcription factors in Arabidopsis

Plant responses to nutrient availability are critical for plant development and yield. Nitrate, the major form of nitrogen in most soils, serves as both a nutrient and signaling molecule. Nitrate itself triggers rapid, major changes in gene expression, especially via nodule inception (NIN)-like protein (NLP) transcription factors, and stimulates protein phosphorylation. Mitogen-activated protein kinase (MAPK)-related genes are among the early nitrate-responsive genes; however, little is known about their roles in nitrate signaling pathways. Here, we show that nitrate resupply to nitrogen-depleted Arabidopsis (Arabidopsis thaliana) plants triggers, within minutes, an MAPK cascade that requires NLP-dependent transcriptional induction of mitogen-activated protein kinase kinase kinase 13 (MAP3K13) and MAP3K14 and that the MAPK cascade is composed of MKK3 and likely C-clade MAPKs (MPK1/2/7/14). Importantly, nitrate reductase-deficient mutants exhibited nitrate-induced MPK7 activities comparable to those observed in wild-type plants, indicating that nitrate itself is the signal that stimulates the cascade. We show that the modified expression of MAP3K13 and MAP3K14 affects nitrate-stimulated BT2 expression and modulates plant responses to nitrogen availability, such as nitrate uptake and senescence. Our finding that an MAPK cascade involving MAP3K13 and MAP3K14 functions in the complex regulatory network governing responses to nitrate availability will guide future strategies to optimize plant responses to nitrogen fertilization and nitrogen use efficiency.

Evolutionary dynamics of nitrate uptake, assimilation, and signalling in plants: adapting to a changing environment

Nitrogen (N) is a crucial macronutrient for plant growth, with nitrate as a primary inorganic N source for most plants. Beyond its role as a nutrient, nitrate also functions as a signalling molecule, influencing plant morphogenetic development. While nitrate utilization and signalling mechanisms have been extensively studied in model plants, the origin, evolution, and diversification of core components in nitrate uptake, assimilation, and signalling remain largely unexplored. In our investigation, we discovered that deep sea algae living in low nitrate conditions developed a high-affinity transport system (HATS) for nitrate uptake and a pathway of nitrate primary assimilation (NR-NiR-GS-GOGAT). In contrast, low-affinity transport systems (LATS) and the plastid GS originated from the ancestors of land and seed plants, respectively. These adaptations facilitated amino acid acquisition as plants conquered terrestrial environments. Furthermore, the intricate nitrate signalling, relying on NRT1.1 and NLP7, evolved stepwise, potentially establishing systematic regulation in bryophytes for self-regulation under complex terrestrial nitrate environments. As plants underwent terrestrialization, they underwent adaptive changes to thrive in dynamic nitrate environments, continually enhancing their nitrate uptake, assimilation, and signal transduction abilities.

Effect of elevated ammonium on biotic and abiotic stress defense responses and expression of related genes in cucumber (Cucumis sativus L.) plants

Ammonium (NH4+) enhances plant defense mechanisms but can be phytotoxic as the sole nitrogen source. To investigate the impact of a balanced NH4+ and NO3- ratio on plant defense parameters without adverse effects, cucumber plants (Cucumis sativus L.) were grown under control (14 mM NO3- + 2 mM NH4+) and elevated level of NH4+ (eNH4+, 8 mM NO3-+ 8 mM NH4+). Plants subjected to eNH4+ showed significantly increased shoot and root biomass by about 41% and 47%, respectively. Among the antioxidant enzymes studied, ascorbate peroxidase (EC 1.11.1.11) activity was increased up to 3.3 fold in eNH4+ compared with control plants, which was associated with enhanced resistance to paraquat. Upregulation of PATHOGENESIS RELATED PROTEIN 4 (PR4) and LIPOXYGENASE 1 (LOX1), accompanied by increased concentrations of salicylic acid and nitric oxide, conferred more excellent resistance of eNH4+ plants to powdery mildew infection. However, the expression levels of ACC OXIDASE 1 (ACO1) and RESPIRATORY BURST OXIDASE HOMOLOGS B (RBOHB) were lower in eNH4+ plants, which was consistent with decreased NADPH oxidase activity and lower leaf H2O2 levels. The biosynthesis of phenolics was enhanced, whereas the activities of polymerizing enzymes and lignin deposition were reduced by half in eNH4+ plants. Besides, a significant effect on plant biomass under salt or drought stress has not been observed between control and eNH4+ plants. These results showed that different defense pathways are distinctively affected by eNH4+ treatment, and the NH4+ to NO3- ratio may play a role in fine-tuning the plant defense response.

Genome-wide identification of high-affinity nitrate transporter 2 (NRT2) gene family under phytohormones and abiotic stresses in alfalfa (Medicago sativa)

The high-affinity nitrate transporter 2 (NRT2) protein plays an important role in nitrate uptake and transport in plants. In this study, the NRT2s gene family were systematically analyzed in alfalfa. We identified three MsNRT2 genes from the genomic database. They were named MsNRT2.1-2.3 based on their chromosomal location. The phylogenetic tree revealed that NRT2 proteins were categorized into two main subgroups, which were further confirmed by their gene structure and conserved motifs. Three MsNRT2 genes distributed on 2 chromosomes. Furthermore, we studied the expression patterns of MsNRT2 genes in six tissues based on RNA-sequencing data from the Short Read Archive (SRA) database of NCBI, and the results showed that MsNRT2 genes were widely expressed in six tissues. After leaves and roots were treated with drought, salt, abscisic acid (ABA) and salicylic acid (SA) for 0-48 h, and we used quantitative RT-PCR to analyze the expression levels of MsNRT2 genes and the results showed that most of the MsNRT2 genes responded to these stresses. However, there are specific genes that play a role under specific treatment conditions. This result provides a basis for further research on the target genes. In summary, MsNRT2s play an irreplaceable role in the growth, development and stress response of alfalfa, and this study provides valuable information and theoretical basis for future research on MsNRT2 function.

In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots

BACKGROUND

Nitrate (NO3-) is one of the two major forms of inorganic nitrogen absorbed by plant roots, and the tissue nitrate concentration in roots is considered important for optimizing developmental programs. Technologies to quantify the expression levels of nitrate transporters and assimilating enzymes at the cellular level have improved drastically in the past decade. However, a technological gap remains for detecting nitrate at a high spatial resolution. Using extraction-based methods, it is challenging to reliably estimate nitrate concentration from a small volume of cells (i.e., with high spatial resolution), since targeting a small or specific group of cells is physically difficult. Alternatively, nitrate detection with microelectrodes offers subcellular resolution with high cell specificity, but this method has some limitations on cell accessibility and detection speed. Finally, optical nitrate biosensors have very good (in-vivo) sensitivity (below 1 mM) and cellular-level spatial resolution, but require plant transformation, limiting their applicability. In this work, we apply Raman microspectroscopy for high-dynamic range in-vivo mapping of nitrate in different developmental zones of Arabidopsis thaliana roots in-situ.

RESULTS

As a proof of concept, we have used Raman microspectroscopy for in-vivo mapping of nitrate content in roots of Arabidopsis seedlings grown on agar media with different nitrate concentrations. Our results revealed that the root nitrate concentration increases gradually from the meristematic zone (~ 250 µm from the root cap) to the maturation zone (~ 3 mm from the root cap) in roots grown under typical growth conditions used for Arabidopsis, a trend that has not been previously reported. This trend was observed for plants grown in agar media with different nitrate concentrations (0.5-10 mM). These results were validated through destructive measurement of nitrate concentration.

CONCLUSIONS

We present a methodology based on Raman microspectroscopy for in-vivo label-free mapping of nitrate within small root tissue volumes in Arabidopsis. Measurements are done in-situ without additional sample preparation. Our measurements revealed nitrate concentration changes from lower to higher concentration from tip to mature root tissue. Accumulation of nitrate in the maturation zone tissue shows a saturation behavior. The presented Raman-based approach allows for in-situ non-destructive measurements of Raman-active compounds.

CEP signaling coordinates plant immunity with nitrogen status

Plant endogenous signaling peptides shape growth, development and adaptations to biotic and abiotic stress. Here, we identify C-TERMINALLY ENCODED PEPTIDEs (CEPs) as immune-modulatory phytocytokines in Arabidopsis thaliana. Our data reveals that CEPs induce immune outputs and are required to mount resistance against the leaf-infecting bacterial pathogen Pseudomonas syringae pv. tomato. We show that effective immunity requires CEP perception by tissue-specific CEP RECEPTOR 1 (CEPR1) and CEPR2. Moreover, we identify the related RECEPTOR-LIKE KINASE 7 (RLK7) as a CEP4-specific CEP receptor contributing to CEP-mediated immunity, suggesting a complex interplay of multiple CEP ligands and receptors in different tissues during biotic stress. CEPs have a known role in the regulation of root growth and systemic nitrogen (N)-demand signaling. We provide evidence that CEPs and their receptors promote immunity in an N status-dependent manner, suggesting a previously unknown molecular crosstalk between plant nutrition and cell surface immunity. We propose that CEPs and their receptors are central regulators for the adaptation of biotic stress responses to plant-available resources.

Genome-Wide Identification of NLP Gene Families and Haplotype Analysis of SiNLP2 in Foxtail Millet (Setaria italica)

Nitrogen is a critical factor in plant growth, development, and crop yield. NODULE-INCEPTION-like proteins (NLPs), which are plant-specific transcription factors, function as nitrate sensors and play a vital role in the nitrogen response of plants. However, the genome-wide identification of the NLP gene family, the elucidation of the underlying molecular mechanism governing nitrogen response, and haplotype mining remain elusive in millet. In this study, we identified seven members of the NLP gene family in the millet genome and systematically analyzed their physicochemical properties. Evolutionary tree analysis indicated that SiNLP members can be classified into three subgroups, with NLP members from the same species preferentially grouped together within each subgroup. Analysis of gene structure characteristics revealed that all SiNLP members contained 10 conserved motifs, as well as the RWP-RK and PB1 domains, indicating that these motifs and domains have been relatively conserved throughout evolution. Additionally, we identified a significant abundance of response elements related to hormones, stress, growth, and development within the promoter regions of SiNLP members, suggesting that these members are involved in regulating diverse physiological processes in millet. Transcriptome data under low-nitrogen conditions showed significant differences in the expression profiles of SiNLP2 and SiNLP4 compared to the other members. RNA-seq and qRT-PCR results demonstrated that SiNLP2 significantly responds to low-nitrogen stress. Notably, we found that SiNLP2 is involved in nitrogen pathways by regulating the expression of the SiNAR2.1A, SiNAR2.1B, SiNRT1.1, and SiNR2 genes. More importantly, we identified an elite haplotype, Hap2, of SiNLP2, which is gradually being utilized in the breeding process. Our study established a foundation for a comprehensive understanding of the SiNLP gene family and provided gene resources for variety improvement and marker-assisted selection breeding.

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.

PHR1 negatively regulates nitrate reductase activity by directly inhibiting the transcription of NIA1 in Arabidopsis

Nitrogen (N) and phosphorus (P), as indispensable mineral elements, both play pivotal roles in plant growth and development. Despite the intimate association between nitrate signaling and inorganic phosphate (Pi) signaling, the regulatory function of Pi in N metabolism remains poorly understood. In this study, we observed that Pi deficiency leads to a reduction in the activity of nitrate reductase (NR), an essential enzyme involved in N metabolism. Furthermore, PHOSPHATE STARVATION RESPONSE 1 (PHR1), a key regulator of Pi signaling, exerts a negative impact on both NR activity and the expression of its coding gene NIA1. Importantly, our analysis utilizing yeast one-hybrid (Y1H) and electrophoretic mobility shift assay (EMSA) techniques reveals the direct binding of PHR1 to the NIA1 promoter via the P1BS motifs. Subsequent transient transcription expression assay (TTEA) demonstrates PHR1 as a transcriptional suppressor of NIA1. In addition, it was also observed that the SPX (SYG1/Pho81/XPR1) proteins SPX1 and SPX4 can attenuate the transcriptional inhibition of NIA1 by PHR1. Collectively, these findings reveal a mechanism through which PHR1-mediated Pi signal governs N metabolism, thus offering evidence for the precise modulation of plant growth and development via N-P interaction.

Regulation of anthocyanin synthesis in red lettuce in plant factory conditions: A review

Anthocyanins, natural pigments known for their vibrant hues and beneficial properties, undergo intricate genetic control. However, red vegetables grown in plant factories frequently exhibit reduced anthocyanin synthesis compared to those in open fields due to factors like inadequate light, temperature, humidity, and nutrient availability. Comprehending these factors is essential for optimizing plant factory environments to enhance anthocyanin synthesis. This review insights the impact of physiological and genetic factors on the production of anthocyanins in red lettuce grown under controlled conditions. Further, we aim to gain a better understanding of the mechanisms involved in both synthesis and degradation of anthocyanins. Moreover, this review summarizes the identified regulators of anthocyanin synthesis in lettuce, addressing the gap in knowledge on controlling anthocyanin production in plant factories, with potential implications for various crops beyond red lettuce.

Plants Under Stress: Exploring Physiological and Molecular Responses to Nitrogen and Phosphorus Deficiency

Nitrogen (N) and phosphorus (P) are essential mineral macronutrients critical for plant structure and function. Both contribute to processes ranging from cellular integrity to signal transduction. Since plants require these nutrients in high concentrations, replenishing them in soil often involves chemical fertilizers. However, the main source of P, rock phosphate, is non-renewable and in decline. N, second only to carbon, oxygen, and hydrogen in plant requirements, is vital for synthesizing proteins, nucleic acids, and plant pigments. Although N is available to plants through biological fixation or fertilizer application, the frequent application of N is not a sustainable solution due to environmental concerns like groundwater contamination and eutrophication. Plants have developed sophisticated mechanisms to adapt to nutrient deficiencies, such as changes in root architecture, local signaling, and long-distance signaling through the phloem. A dual deficiency of N and P is common in the field. In addition to individual N and P deficiency responses, this review also highlights some of the most recent discoveries in the responses of plants to the combined N and P deficiencies. Understanding the molecular and physiological responses in plants to mineral deficiency will help implement strategies to produce plants with high mineral use efficiency, leading to the reduced application of fertilizers, decreased mineral runoff, and improved environment.

Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots

Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.

Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues

Plants growing at high densities can detect competitors through changes in the composition of light reflected by neighbours. In response to this far-red-enriched light, plants elicit adaptive shade avoidance responses for light capture, but these need to be balanced against other input signals, such as nutrient availability. Here, we investigated how Arabidopsis integrates shade and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived trans-zeatin (tZ) signal and the BEE1 transcription factor as an integrator of light and cytokinin signalling. Under nitrate-sufficient conditions, tZ promotes hypocotyl elongation specifically in the presence of supplemental far-red light. This occurs via PIF transcription factors-dependent inhibition of type-A ARRs cytokinin response inhibitors. Our data thus reveal how plants co-regulate responses to shade cues with root-derived information about nutrient availability, and how they restrict responses to this information to specific light conditions in the shoot.

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.

NRT2.1 mediates the reciprocal regulation of nitrate and NO/SNO in seedling leaves of Fraxinus mandshurica and Betula platyphylla

Nitric oxide (NO) and S-nitrosothiol (SNO) are signal molecules and the products of nitrogen metabolism. Nitrate (NO3-) is the main nitrogen source, and nitrate transporters (NRTs) are responsible for NO3- absorption or transport. However, the interactive effect between NO3-/NRT and NO/SNO in tree plants remains ambiguous. In the present study, 25 mmol L-1 NO3- and 1 mmol L-1 NO donor sodium nitroprusside (SNP) treatment that was conducted for 24 h enhanced NO/SNO and NO3- metabolism, whereas 2.5 mmol L-1 NO3- and 80 μmol L-1 N6022 (a compound that increases SNO content) treatment reduced them in seedling leaves of Fraxinus mandshurica and Betula platyphylla. Among the nine NRT family members examined, the gene expression level of NRT2.1 had a greater response to NO/SNO and NO3- treatment in the seedling leaves of F. mandshurica and B. platyphylla. Meanwhile, FmNRT2.1 mediated NO and SNO production in seedling leaves of F. mandshurica using Agrobacterium-mediated transient transformation. These findings shed light on the reciprocal regulation between NO3- and NO/SNO in seedlings of F. mandshurica and B. platyphylla, and NRT2.1 may act as a key regulatory hub.

Green control for inhibiting Rhizopus oryzae growth by stress factors in forage grass factory

The forage grass factory could break through the restrictions of land resources, region and climate to achieve efficient production throughout the year by accurate and intelligent management. However, due to its closed environment, mold outbreaks in the forage grass factory were severe, significantly affecting barley production. In this study, 9 contaminated barley tissues were collected and 45 strains were isolated in forage grass factory. After ITS sequencing, 45 strains were all identified as Rhizopus oryzae. Through stress factor assays, R. oryzae growth was seriously hindered by low concentration of sodium nitrate, high pH value and ozone water treatment. High pH and ozone water affected growth mainly by altering membrane integrity of R. oryzae. Sodium nitrate inhibited the growth of R. oryzae mainly by affecting the amount of sporulation. Low concentration of sodium nitrate and ozone water did not affect the growth of barley. High concentrations of sodium nitrate (100 mM) and pH values (8-8.5) inhibited barley growth. Among them, ozone water had the most obvious inhibition effect on R. oryzae. Large-scale ozone water treatment in the forage grass factory had also played a role in restoring barley production. Taken together, the green techonology to control mold disease and maintain the safety of forage through different physicochemical methods was selected, which was of considerable application value in animal husbandry.

Signaling function of NH4+ in the activation of Fe-deficiency response in cucumber (Cucumis sativus L.)

MAIN CONCLUSION

NH4+ is necessary for full functionality of reduction-based Fe deficiency response in plants. Nitrogen (N) is present in soil mainly as nitrate (NO3-) or ammonium (NH4+). Although the significance of a balanced supply of NO3- and NH4+ for optimal growth has been generally accepted, its importance for iron (Fe) acquisition has not been sufficiently investigated. In this work, hydroponically grown cucumber (Cucumis sativus L. cv. Maximus) plants were supplied with NO3- as the sole N source under -Fe conditions. Upon the appearance of chlorosis, plants were supplemented with 2 mM NH4Cl by roots or leaves. The NH4+ treatment increased leaf SPAD and the HCl-extractable Fe concentration while decreased root apoplastic Fe. A concomitant increase in the root concentration of nitric oxide and activity of FRO and its abolishment by an ethylene action inhibitor, indicated activation of the components of Strategy I in NH4+-treated plants. Ammonium-pretreated plants showed higher utilization capacity of sparingly soluble Fe(OH)3 and higher root release of H+, phenolics, and organic acids. The expression of the master regulator of Fe deficiency response (FIT) and its downstream genes (AHA1, FRO2, and IRT1) along with EIN3 and STOP1 was increased by NH4+ application. Temporal analyses and the employment of a split-root system enabled us to suggest that a permanent presence of NH4+ at concentrations lower than 2 mM is adequate to produce an unknown signal and causes a sustained upregulation of Fe deficiency-related genes, thus augmenting the Fe-acquisition machinery. The results indicate that NH4+ appears to be a widespread and previously underappreciated component of plant reduction-based Fe deficiency response.

Nitrate transporters and mechanisms of nitrate signal transduction in Arabidopsis and rice

Nitrate (NO3 -) is a significant inorganic nitrogen source in soil, playing a crucial role in influencing crop productivity. As sessile organisms, plants have evolved complex mechanisms for nitrate uptake and response to varying soil levels. Recent advancements have enhanced our understanding of nitrate uptake and signaling pathways. This mini-review offers a comparative analysis of nitrate uptake mechanisms in Arabidopsis and rice. It also examines nitrate signal transduction, highlighting the roles of AtNRT1.1 and AtNLP7 as nitrate receptors and elucidating the OsNRT1.1B-OsSPX4-OsNLP3 cascade. Additionally, it investigates nuclear transcriptional networks that regulate nitrate-responsive genes, controlled by various transcription factors (TFs) crucial for plant development. By integrating these findings, we highlight mechanisms that may help to enhance crop nitrogen utilization.

GmNLP1 and GmNLP4 activate nitrate-induced CLE peptides NIC1a/b to mediate nitrate-regulated root nodulation

Symbiotic nitrogen fixation is an energy-intensive process, to maintain the balance between growth and nitrogen fixation, high concentrations of nitrate inhibit root nodulation. However, the precise mechanism underlying the nitrate inhibition of nodulation in soybean remains elusive. In this study, CRISPR-Cas9-mediated knockout of GmNLP1 and GmNLP4 unveiled a notable nitrate-tolerant nodulation phenotype. GmNLP1b and GmNLP4a play a significant role in the nitrate-triggered inhibition of nodulation, as the expression of nitrate-responsive genes was largely suppressed in Gmnlp1b and Gmnlp4a mutants. Furthermore, we demonstrated that GmNLP1b and GmNLP4a can bind to the promoters of GmNIC1a and GmNIC1b and activate their expression. Manipulations targeting GmNIC1a and GmNIC1b through knockdown or overexpression strategies resulted in either increased or decreased nodule number in response to nitrate. Additionally, transgenic roots that constitutively express GmNIC1a or GmNIC1b rely on both NARK and hydroxyproline O-arabinosyltransferase RDN1 to prevent the inhibitory effects imposed by nitrate on nodulation. In conclusion, this study highlights the crucial role of the GmNLP1/4-GmNIC1a/b module in mediating high nitrate-induced inhibition of nodulation.

NIN-like proteins (NLPs) as crucial nitrate sensors: an overview of their roles in nitrogen signaling, symbiosis, abiotic stress, and beyond

Nitrogen is an essential macronutrient critical for plant growth and productivity. Plants have the capacity to uptake inorganic nitrate and ammonium, with nitrate playing a crucial role as a signaling molecule in various cellular processes. The availability of nitrate and the signaling pathways involved finely tune the processes of nitrate uptake and assimilation. NIN-like proteins (NLPs), a group of transcription factors belonging to the RWP-RK gene family, act as major nitrate sensors and are implicated in the primary nitrate response (PNR) within the nucleus of both non-leguminous and leguminous plants through their RWP-RK domains. In leguminous plants, NLPs are indispensable for the initiation and development of nitrogen-fixing nodules in symbiosis with rhizobia. Moreover, NLPs play pivotal roles in plant responses to abiotic stresses, including drought and cold. Recent studies have identified NLP homologs in oomycete pathogens, suggesting their potential involvement in pathogenesis and virulence. This review article delves into the conservation of RWP-RK genes, examining their significance and implications across different plant species. The focus lies on the role of NLPs as nitrate sensors, investigating their involvement in various processes, including rhizobial symbiosis in both leguminous and non-leguminous plants. Additionally, the multifaceted functions of NLPs in abiotic stress responses, developmental processes, and interactions with plant pathogens are explored. By comprehensively analyzing the role of NLPs in nitrate signaling and their broader implications for plant growth and development, this review sheds light on the intricate mechanisms underlying nitrogen sensing and signaling in various plant lineages.

Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana

MOTIVATIONS

Gene regulatory networks (GRNs) are traditionally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standards are often related and limited to a subset of genes. This lack of complete and independent evaluation calls for new criteria to robustly estimate the optimal intensity of prior data integration in the inference process.

RESULTS

We address this issue for two regression-based GRN inference models, a weighted random forest (weigthedRF) and a generalized linear model estimated under a weighted LASSO penalty with stability selection (weightedLASSO). These approaches are applied to data from the root response to nitrate induction in Arabidopsis thaliana. For each gene, we measure how the integration of transcription factor binding motifs influences model prediction. We propose a new approach, DIOgene, that uses model prediction error and a simulated null hypothesis in order to optimize data integration strength in a hypothesis-driven, gene-specific manner. This integration scheme reveals a strong diversity of optimal integration intensities between genes, and offers good performance in minimizing prediction error as well as retrieving experimental interactions. Experimental results show that DIOgene compares favorably against state-of-the-art approaches and allows to recover master regulators of nitrate induction.

AVAILABILITY AND IMPLEMENTATION

The R code and notebooks demonstrating the use of the proposed approaches are available in the repository https://github.com/OceaneCsn/integrative_GRN_N_induction.

Glutamine induces lateral root initiation, stress responses, and disease resistance in Arabidopsis

The production of glutamine (Gln) from NO3- and NH4+ requires ATP, reducing power, and carbon skeletons. Plants may redirect these resources to other physiological processes using Gln directly. However, feeding Gln as the sole nitrogen (N) source has complex effects on plants. Under optimal concentrations, Arabidopsis (Arabidopsis thaliana) seedlings grown on Gln have similar primary root lengths, more lateral roots, smaller leaves, and higher amounts of amino acids and proteins compared to those grown on NH4NO3. While high levels of Gln accumulate in Arabidopsis seedlings grown on Gln, the expression of GLUTAMINE SYNTHETASE1;1 (GLN1;1), GLN1;2, and GLN1;3 encoding cytosolic GS1 increases and expression of GLN2 encoding chloroplastic GS2 decreases. These results suggest that Gln has distinct effects on regulating GLN1 and GLN2 gene expression. Notably, Arabidopsis seedlings grown on Gln have an unexpected gene expression profile. Compared with NH4NO3, which activates growth-promoting genes, Gln preferentially induces stress- and defense-responsive genes. Consistent with the gene expression data, exogenous treatment with Gln enhances disease resistance in Arabidopsis. The induction of Gln-responsive genes, including PATHOGENESIS-RELATED1, SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1, WRKY54, and WALL ASSOCIATED KINASE1, is compromised in salicylic acid (SA) biosynthetic and signaling mutants under Gln treatments. Together, these results suggest that Gln may partly interact with the SA pathway to trigger plant immunity.

Transcriptomic Analysis Reveals the Effect of Urea on Metabolism of Nannochloropsis oceanica

The eukaryotic microalga Nannochloropsis oceanica represents a promising bioresource for the production of biofuels and pharmaceuticals. Urea, a crucial nutrient for the photosynthetic N. oceanica, stimulates the accumulation of substances such as lipids, which influence growth and physiology. However, the specific mechanisms by which N. oceanica responds and adapts to urea addition remain unknown. High-throughput mRNA sequencing and differential gene expression analysis under control and urea-added conditions revealed significant metabolic changes. This involved the differential expression of 2104 genes, with 1354 being upregulated and 750 downregulated, resulting in the reprogramming of crucial pathways such as carbon and nitrogen metabolism, photosynthesis, and lipid metabolism. The results specifically showed that genes associated with photosynthesis in N. oceanica were significantly downregulated, particularly those related to light-harvesting proteins. Interestingly, urea absorption and transport may depend not only on specialized transport channels such as urease but also on alternative transport channels such as the ABC transporter family and the CLC protein family. In addition, urea caused specific changes in carbon and lipid metabolism. Genes associated with the Calvin cycle and carbon concentration mechanisms were significantly upregulated. In lipid metabolism, the expression of genes associated with lipases and polyunsaturated fatty acid synthesis was highly activated. Furthermore, the expression of several genes involved in the tricarboxylic acid cycle and folate metabolism was enhanced, making important contributions to energy supply and the synthesis and modification of genes and macromolecules. Our observations indicate that N. oceanica actively and dynamically regulates the redistribution of carbon and nitrogen after urea addition, providing references for further research on the effects of urea on N. oceanica.

An Azospirillum brasilense chemoreceptor that mediates nitrate chemotaxis has conditional roles in the colonization of plant roots

Motile plant-associated bacteria use chemotaxis and dedicated chemoreceptors to navigate gradients in their surroundings and to colonize host plant surfaces. Here, we characterize a chemoreceptor that we named Tlp2 in the soil alphaproteobacterium Azospirillum brasilense. We show that the Tlp2 ligand-binding domain is related to the 4-helix bundle family and is conserved in chemoreceptors found in the genomes of many soil- and sediment-dwelling alphaproteobacteria. The promoter of tlp2 is regulated in an NtrC- and RpoN-dependent manner and is most upregulated under conditions of nitrogen fixation or in the presence of nitrate. Using fluorescently tagged Tlp2 (Tlp2-YFP), we show that this chemoreceptor is present in low abundance in chemotaxis-signaling clusters and is prone to degradation. We also obtained evidence that the presence of ammonium rapidly disrupts Tlp2-YFP localization. Behavioral experiments using a strain lacking Tlp2 and variants of Tlp2 lacking conserved arginine residues suggest that Tlp2 mediates chemotaxis in gradients of nitrate and nitrite, with the R159 residue being essential for Tlp2 function. We also provide evidence that Tlp2 is essential for root surface colonization of some plants (teff, red clover, and cowpea) but not others (wheat, sorghum, alfalfa, and pea). These results highlight the selective role of nitrate sensing and chemotaxis in plant root surface colonization and illustrate the relative contribution of chemoreceptors to chemotaxis and root surface colonization.IMPORTANCEBacterial chemotaxis mediates host-microbe associations, including the association of beneficial bacteria with the roots of host plants. Dedicated chemoreceptors specify sensory preferences during chemotaxis. Here, we show that a chemoreceptor mediating chemotaxis to nitrate is important in the beneficial soil bacterium colonization of some but not all plant hosts tested. Nitrate is the preferred nitrogen source for plant nutrition, and plants sense and tightly control nitrate transport, resulting in varying nitrate uptake rates depending on the plant and its physiological state. Nitrate is thus a limiting nutrient in the rhizosphere. Chemotaxis and dedicated chemoreceptors for nitrate likely provide motile bacteria with a competitive advantage to access this nutrient in the rhizosphere.

The beneficial rhizobacterium Bacillus velezensis SQR9 regulates plant nitrogen uptake via an endogenous signaling pathway

Nitrogen fertilizer is widely used in agriculture to boost crop yields. Plant growth-promoting rhizobacteria (PGPRs) can increase plant nitrogen use efficiency through nitrogen fixation and organic nitrogen mineralization. However, it is not known whether they can activate plant nitrogen uptake. In this study, we investigated the effects of volatile compounds (VCs) emitted by the PGPR strain Bacillus velezensis SQR9 on plant nitrogen uptake. Strain SQR9 VCs promoted nitrogen accumulation in both rice and Arabidopsis. In addition, isotope labeling experiments showed that strain SQR9 VCs promoted the absorption of nitrate and ammonium. Several key nitrogen-uptake genes were up-regulated by strain SQR9 VCs, such as AtNRT2.1 in Arabidopsis and OsNAR2.1, OsNRT2.3a, and OsAMT1 family members in rice, and the deletion of these genes compromised the promoting effect of strain SQR9 VCs on plant nitrogen absorption. Furthermore, calcium and the transcription factor NIN-LIKE PROTEIN 7 play an important role in nitrate uptake promoted by strain SQR9 VCs. Taken together, our results indicate that PGPRs can promote nitrogen uptake through regulating plant endogenous signaling and nitrogen transport pathways.

Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits

Na+ exclusion from above-ground tissues via the Na+-selective transporter HKT1;5 is a major salt-tolerance mechanism in crops. Using the expression genome-wide association study and yeast-one-hybrid screening, we identified TaSPL6-D, a transcriptional suppressor of TaHKT1;5-D in bread wheat. SPL6 also targeted HKT1;5 in rice and Brachypodium. A 47-bp insertion in the first exon of TaSPL6-D resulted in a truncated peptide, TaSPL6-DIn, disrupting TaHKT1;5-D repression exhibited by TaSPL6-DDel. Overexpressing TaSPL6-DDel, but not TaSPL6-DIn, led to inhibited TaHKT1;5-D expression and increased salt sensitivity. Knockout of TaSPL6-DDel in two wheat genotypes enhanced salinity tolerance, which was attenuated by a further TaHKT1;5-D knockdown. Spike development was preserved in Taspl6-dd mutants but not in Taspl6-aabbdd mutants. TaSPL6-DIn was mainly present in landraces, and molecular-assisted introduction of TaSPL6-DIn from a landrace into a leading wheat cultivar successfully improved yield on saline soils. The SPL6-HKT1;5 module offers a target for the molecular breeding of salt-tolerant crops.

Dof1.7 and NIGT1 transcription factors mediate multilayered transcriptional regulation for different expression patterns of NITRATE TRANSPORTER2 genes under nitrogen deficiency stress

Elucidating the mechanisms regulating nitrogen (N) deficiency responses in plants is of great agricultural importance. Previous studies revealed that decreased expression of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) transcriptional repressor genes upon N deficiency is involved in N deficiency-inducible gene expression in Arabidopsis thaliana. However, our knowledge of the mechanisms controlling N deficiency-induced changes in gene expression is still limited. Through the identification of Dof1.7 as a direct target of NIGT1 repressors and a novel N deficiency response-related transcriptional activator gene, we here show that NIGT1 and Dof1.7 transcription factors (TFs) differentially regulate N deficiency-inducible expression of three high-affinity nitrate transporter genes, NRT2.1, NRT2.4, and NRT2.5, which are responsible for most of the soil nitrate uptake activity of Arabidopsis plants under N-deficient conditions. Unlike NIGT1 repressors, which directly suppress NRT2.1, NRT2.4, and NRT2.5 under N-sufficient conditions, Dof1.7 directly activated only NRT2.5 but indirectly and moderately activated NRT2.1 and NRT2.4 under N-deficient conditions, probably by indirectly decreasing NIGT1 expression. Thus, Dof1.7 converted passive transcriptional activation into active and potent transcriptional activation, further differentially enhancing the expression of NRT2 genes. These findings clarify the mechanism underlying different expression patterns of NRT2 genes upon N deficiency, suggesting that time-dependent multilayered transcriptional regulation generates complicated expression patterns of N deficiency-inducible genes.

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.

Plant iron status regulates ammonium-use efficiency through protein N-glycosylation

Improving nitrogen-use efficiency is an important path toward enhancing crop yield and alleviating the environmental impacts of fertilizer use. Ammonium (NH4+) is the energetically preferred inorganic N source for plants. The interaction of NH4+ with other nutrients is a chief determinant of ammonium-use efficiency (AUE) and of the tipping point toward ammonium toxicity, but these interactions have remained ill-defined. Here, we report that iron (Fe) accumulation is a critical factor determining AUE and have identified a substance that can enhance AUE by manipulating Fe availability. Fe accumulation under NH4+ nutrition induces NH4+ efflux in the root system, reducing both growth and AUE in Arabidopsis (Arabidopsis thaliana). Low external availability of Fe and a low plant Fe status substantially enhance protein N-glycosylation through a Vitamin C1-independent pathway, thereby reducing NH4+ efflux to increase AUE during the vegetative stage in Arabidopsis under elevated NH4+ supply. We confirm the validity of the iron-ammonium interaction in the important crop species lettuce (Lactuca sativa). We further show that dolomite can act as an effective substrate to subdue Fe accumulation under NH4+ nutrition by reducing the expression of Low Phosphate Root 2 and acidification of the rhizosphere. Our findings present a strategy to improve AUE and reveal the underlying molecular-physiological mechanism.

Gene regulatory networks underlying sulfate deficiency responses in plants

Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.

Review: Nutrient-nutrient interactions governing underground plant adaptation strategies in a heterogeneous environment

Plant growth relies on the mineral nutrients present in the rhizosphere. The distribution of nutrients in soils varies depending on their mobility and capacity to bind with soil particles. Consequently, plants often encounter either low or high levels of nutrients in the rhizosphere. Plant roots are the essential organs that sense changes in soil mineral content, leading to the activation of signaling pathways associated with the adjustment of plant architecture and metabolic responses. During differential availability of minerals in the rhizosphere, plants trigger adaptation strategies such as cellular remobilization of minerals, secretion of organic molecules, and the attenuation or enhancement of root growth to balance nutrient uptake. The interdependency, availability, and uptake of minerals, such as phosphorus (P), iron (Fe), zinc (Zn), potassium (K), nitrogen (N) forms, nitrate (NO3-), and ammonium (NH4+), modulate the root architecture and metabolic functioning of plants. Here, we summarized the interactions of major nutrients (N, P, K, Fe, Zn) in shaping root architecture, physiological responses, genetic components involved, and address the current challenges associated with nutrient-nutrient interactions. Furthermore, we discuss the major gaps and opportunities in the field for developing plants with improved nutrient uptake and use efficiency for sustainable agriculture.

Nitrogen sensing and regulatory networks: it's about time and space

A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.

Integration of nitrate and abscisic acid signaling in plants

To meet the demands of the new Green Revolution and sustainable agriculture, it is important to develop crop varieties with improved yield, nitrogen use efficiency, and stress resistance. Nitrate is the major form of inorganic nitrogen available for plant growth in many well-aerated agricultural soils, and acts as a signaling molecule regulating plant development, growth, and stress responses. Abscisic acid (ABA), an important phytohormone, plays vital roles in integrating extrinsic and intrinsic responses and mediating plant growth and development in response to biotic and abiotic stresses. Therefore, elucidating the interplay between nitrate and ABA can contribute to crop breeding and sustainable agriculture. Here, we review studies that have investigated the interplay between nitrate and ABA in root growth modulation, nitrate and ABA transport processes, seed germination regulation, and drought responses. We also focus on nitrate and ABA interplay in several reported omics analyses with some important nodes in the crosstalk between nitrate and ABA. Through these insights, we proposed some research perspectives that could help to develop crop varieties adapted to a changing environment and to improve crop yield with high nitrogen use efficiency and strong stress resistance.

Small but mighty: Peptides regulating abiotic stress responses in plants

Throughout evolution, plants have developed strategies to confront and alleviate the detrimental impacts of abiotic stresses on their growth and development. The combat strategies involve intricate molecular networks and a spectrum of early and late stress-responsive pathways. Plant peptides, consisting of fewer than 100 amino acid residues, are at the forefront of these responses, serving as pivotal signalling molecules. These peptides, with roles similar to phytohormones, intricately regulate plant growth, development and facilitate essential cell-to-cell communications. Numerous studies underscore the significant role of these small peptides in coordinating diverse signalling events triggered by environmental challenges. Originating from the proteolytic processing of larger protein precursors or directly translated from small open reading frames, including microRNA (miRNA) encoded peptides from primary miRNA, these peptides exert their biological functions through binding with membrane-embedded receptor-like kinases. This interaction initiates downstream cellular signalling cascades, often involving major phytohormones or reactive oxygen species-mediated mechanisms. Despite these advances, the precise modes of action for numerous other small peptides remain to be fully elucidated. In this review, we delve into the dynamics of stress physiology, mainly focusing on the roles of major small signalling peptides, shedding light on their significance in the face of changing environmental conditions.

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).

Glutamine as sole nitrogen source prevents induction of nitrate transporter gene NRT2.4 and affects amino acid metabolism in Arabidopsis

Plants assimilate inorganic nitrogen (N) to glutamine. Glutamine is the most abundant amino acid in most plant species, the N-supplying precursor of all N-containing compounds in the cell and the first organic nitrogen molecule formed from inorganic nitrogen taken up by the roots. In addition to its role in plant nutrition, glutamine most likely also has a function as a signaling molecule in the regulation of nitrogen metabolism. We investigated whether glutamine influences the high-affinity transporter system for nitrate uptake. Therefore, we analyzed the expression of the nitrate transporter NRT2.4, which is inducible by N deficiency, in Arabidopsis thaliana grown under different nitrogen starvation scenarios, comparing nitrate or glutamine as the sole nitrogen source. Using the reporter line ProNRT2.4:GFP and two independent knockout lines, nrt2.4-1 and nrt2.4-2, we analyzed gene expression and amino acid profiles. We showed that the regulation of NRT2.4 expression depends on available nitrogen in general, for example on glutamine as a nitrogen source, and not specifically on nitrate. In contrast to high nitrate concentrations, amino acid profiles changed to an accumulation of amino acids containing more than one nitrogen during growth in high glutamine concentrations, indicating a switch to nitrogen storage metabolism. Furthermore, we demonstrated that the nrt2.4-2 line shows unexpected effects on NRT2.5 gene expression and the amino acids profile in shoots under high glutamine supply conditions compared to Arabidopsis wild type and nrt2.4-1, suggesting non-NRT2.4-related metabolic consequences in this knockout line.