Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate

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.

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.

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.

Reactive oxygen species (ROS) modulate nitrogen signaling using temporal transcriptome analysis in foxtail millet

Reactive oxygen species (ROS) is a chemically reactive chemical substance containing oxygen and a natural by-product of normal oxygen metabolism. Excessive ROS affect the growth process of crops, which will lead to the decrease of yield. Nitrogen, as a critical nutrient element in plants and plays a vital role in plant growth and crop production. Nitrate is the primary nitrogen source available to plants in agricultural soil and various natural environments. However, the molecular mechanism of ROS-nitrate crosstalk is still unclear. In this study, we used the foxtail millet (Setaria italica L.) as the material to figure it out. Here, we show that excessive NaCl inhibits nitrate-promoted plant growth and nitrogen use efficiency (NUE). NaCl induces ROS accumulation in roots, and ROS inhibits nitrate-induced gene expression in a short time. Surprisingly, low concentration ROS slight promotes and high concentration of ROS inhibits foxtail millet growth under long-term H2O2 treatment. These results may open a new perspective for further exploration of ROS-nitrate signaling pathway 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).

UMAMIT44 is a key player in glutamate export from Arabidopsis chloroplasts

Selective partitioning of amino acids among organelles, cells, tissues, and organs is essential for cellular metabolism and plant growth. Nitrogen assimilation into glutamine and glutamate and de novo biosynthesis of most protein amino acids occur in chloroplasts; therefore, various transport mechanisms must exist to accommodate their directional efflux from the stroma to the cytosol and feed the amino acids into the extraplastidial metabolic and long-distance transport pathways. Yet, Arabidopsis (Arabidopsis thaliana) transporters functioning in plastidial export of amino acids remained undiscovered. Here, USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTER 44 (UMAMIT44) was identified and shown to function in glutamate export from Arabidopsis chloroplasts. UMAMIT44 controls glutamate homeostasis within and outside of chloroplasts and influences nitrogen partitioning from leaves to sinks. Glutamate imbalances in chloroplasts and leaves of umamit44 mutants impact cellular redox state, nitrogen and carbon metabolism, and amino acid (AA) and sucrose supply of growing sinks, leading to negative effects on plant growth. Nonetheless, the mutant lines adjust to some extent by upregulating alternative pathways for glutamate synthesis outside the plastids and by mitigating oxidative stress through the production of other amino acids and antioxidants. Overall, this study establishes that the role of UMAMIT44 in glutamate export from chloroplasts is vital for controlling nitrogen availability within source leaf cells and for sink nutrition, with an impact on growth and seed yield.

Insights into molecular links and transcription networks integrating drought stress and nitrogen signaling

Drought and the availability of nitrate, the predominant source of nitrogen (N) in agriculture, are major factors limiting plant growth and crop productivity. The dissection of the transcriptional networks' components integrating droght stress and nitrate responses provides valuable insights into how plants effectively balance stress response with growth programs. Recent evidence in Arabidopsis thaliana indicates that transcription factors (TFs) involved in abscisic acid (ABA) signaling affect N metabolism and nitrate responses, and reciprocally, components of nitrate signaling might affect ABA and drought gene responses. Advances in understanding regulatory circuits of nitrate and drought crosstalk in plant tissues empower targeted genetic modifications to enhance plant development and stress resistance, critical traits for optimizing crop yield and promoting sustainable agriculture.

Finding Balance in Adversity: Nitrate Signaling as the Key to Plant Growth, Resilience, and Stress Response

To effectively adapt to changing environments, plants must maintain a delicate balance between growth and resistance or tolerance to various stresses. Nitrate, a significant inorganic nitrogen source in soils, not only acts as an essential nutrient but also functions as a critical signaling molecule that regulates multiple aspects of plant growth and development. In recent years, substantial advancements have been made in understanding nitrate sensing, calcium-dependent nitrate signal transmission, and nitrate-induced transcriptional cascades. Mounting evidence suggests that the primary response to nitrate is influenced by environmental conditions, while nitrate availability plays a pivotal role in stress tolerance responses. Therefore, this review aims to provide an overview of the transcriptional and post-transcriptional regulation of key components in the nitrate signaling pathway, namely, NRT1.1, NLP7, and CIPK23, under abiotic stresses. Additionally, we discuss the specificity of nitrate sensing and signaling as well as the involvement of epigenetic regulators. A comprehensive understanding of the integration between nitrate signaling transduction and abiotic stress responses is crucial for developing future crops with enhanced nitrogen-use efficiency and heightened resilience.

The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean

Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N2 fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N2 fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high nitrogen inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high nitrogen transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high nitrogen.

The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply

Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Whereas several transcriptional regulators of nitrate signaling have been identified, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN7 (NLP7), additional regulators are expected to fine-tune this pivotal physiological response. Here, we characterized Arabidopsis NLP2 as a top-tier transcriptional regulator of the early nitrate response gene regulatory network. NLP2 interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, DNA-binding motif, and some target genes with NLP7. Genetic, genomic, and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multitiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production.

Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response of Nitraria tangutorum to Increased Nitrogen

To identify genes that respond to increased nitrogen and assess the involvement of the chlorophyll metabolic pathway and associated regulatory mechanisms in these responses, Nitraria tangutorum seedlings were subjected to four nitrogen concentrations (N0, N6, N36, and N60: 0, 6, 36, and 60 mmol·L^-1 nitrogen, respectively). The N. tangutorum seedling leaf transcriptome was analyzed by high-throughput sequencing (Illumina HiSeq 4000), and 332,420 transcripts and 276,423 unigenes were identified. The numbers of differentially expressed genes (DEGs) were 4052 in N0 vs. N6, 6181 in N0 vs. N36, and 3937 in N0 vs. N60. Comparing N0 and N6, N0 and N36, and N0 and N60, we found 1101, 2222, and 1234 annotated DEGs in 113, 121, and 114 metabolic pathways, respectively, classified in the Kyoto Encyclopedia of Genes and Genomes database. Metabolic pathways with considerable accumulation were involved mainly in anthocyanin biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and amino acid metabolism. N36 increased δ-amino levulinic acid synthesis and upregulated expression of the magnesium chelatase H subunit, which promoted chlorophyll a synthesis. Hence, N36 stimulated chlorophyll synthesis rather than heme synthesis. These findings enrich our understanding of the N. tangutorum transcriptome and help us to research desert xerophytes' responses to increased nitrogen in the future.

Building High-Confidence Gene Regulatory Networks by Integrating Validated TF-Target Gene Interactions Using ConnecTF

Many methods are now available to identify or predict the target genes of transcription factors (TFs) in plants. These include experimental approaches such as in vivo or in vitro TF-target gene-binding assays and various methods for identifying regulated targets in mutants, transgenics, or isolated plant cells. In addition, computational approaches are used to infer TF-target gene interactions from the regulatory elements or gene expression changes across treatments. While each of these approaches has now been applied to a large number of TFs from many species, each method has its own limitations which necessitates that multiple data types are integrated to build the most accurate representation of the gene regulatory networks operating in plants. To make the analyses of TF-target interaction datasets available to the broader research community, we have developed the ConnecTF web platform ( https://connectf.org/ ). In this chapter, we describe how ConnecTF can be used to integrate validated and predicted TF-target gene interactions in order to dissect the regulatory role of TFs in developmental and stress response pathways. Using as our examples KN1 and RA1, two well-characterized maize TFs involved in developing floral tissue, we demonstrate how ConnecTF can be used to (1) compare the target genes between TFs, (2) identify direct vs. indirect targets by combining TF-binding and TF-regulation datasets, (3) chart and visualize network paths between TFs and their downstream targets, and (4) prune inferred user networks for high-confidence predicted interactions using validated TF-target gene data. Finally, we provide instructions for setting up a private version of ConnecTF that enables research groups to store and analyze their own TF-target gene interaction datasets.

Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry

The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. Additionally, leveraging next-generation sequencing (NGS) platforms efforts have been undertaken to evaluate the effects of chromatin accessibility, histone modifications, or even transcription factor binding sites. We have shown that Fluorescence-Activated Nuclear Sorting (FANS) is an effective means to characterize the transcriptomes of nuclei from different tissues. In light of our own technical and experimental developments, we extend this effort to combine FACS/FANS with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) for profiling individual cell types according to their chromatin and transcriptional states.

Synergistic effects of nitrogen metabolites on auxin regulating plant growth and development

Nitrogen is one of the important nutrients required for plant growth and development. There is increasing evidences that almost all types of nitrogen metabolites affect, at least to some extent, auxin content and/or signaling in plants, which in turn affects seed germination, plant root elongation, gravitropism, leaf expansion and floral transition. This opinion focuses on the roles of nitrogen metabolites, NO 3 - , NH 4 + , tryptophan and NO and their synergistic effects with auxin on plant growth and development. Nitrate reductase (NR) converts nitrate into nitrite, and was roughly positive-correlated with the root auxin level, suggesting a crosstalk between nitrate signaling and auxin signaling. Abscisic Acid Responsive Element Binding Factor 3 (AFB3) and Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) are also the key enzymes involved in nitrogen metabolite-regulated auxin biosynthesis. Recent advances in the crosstalk among NO 3 - , NH 4 + , tryptophan and NO in regulation to NR, AFB3 and TAA1 are also summarized.

Watermelon responds to organic fertilizer by enhancing root-associated acid phosphatase activity to improve organic phosphorus utilization

Organic fertilizer is commonly used to increase crop yields and improve soil quality. However, it is unclear whether crops adapt to organic fertilizer by regulating metabolic pathways that are involved in nutrient utilization. In this study, we focused on the organic phosphorus (P_o) in organic fertilizer and, using watermelon, investigated changes in gene expression and metabolic pathways in response to organic fertilizer and the combination of chemical fertilizer and organic fertilizer (chemical fertilizer 70% and organic fertilizer 30%, based on phosphorus supply). Purple acid phosphatase (PAP) gene expression was upregulated in leaves and roots of watermelon grown in organic fertilizer alone and in the combination of chemical/organic fertilizer, resulting in enhanced phosphatase activity in roots. When the ratio of chemical to organic fertilizer was 85/15, root-associated acid phosphatase (APase) activity increased over chemical fertilizer alone. This formulation also resulted in increased inorganic phosphate (P_i) concentration in roots and leaves, and the upregulation of the secretory APase genes ClaPAP10/12/15/26, and ClaPAP18 in roots. In conclusion, watermelon responds to organic fertilizer by upregulating expression of secretory ClaPAP genes, subsequently enhancing root-associated APase activity further improving the hydrolysis of phosphomonoesters, and ultimately facilitating P_o utilization by roots. The mechanisms of P utilization by roots comprise the enhancement of APase and phytase activity, absorption of small P_o molecules, uptake of P_i, and the increase of lateral root number when organic fertilizer is applied to the plants. These findings help to establish the mechanisms by which plants respond to organic fertilizer by regulating metabolic pathways at the transcriptional level.

Metabolome and RNA-seq Analysis of Responses to Nitrogen Deprivation and Resupply in Tea Plant (Camellia sinensis) Roots

Nitrogen (N) is an important contributor in regulating plant growth and development as well as secondary metabolites synthesis, so as to promote the formation of tea quality and flavor. Theanine, polyphenols, and caffeine are important secondary metabolites in tea plant. In this study, the responses of Camellia sinensis roots to N deprivation and resupply were investigated by metabolome and RNA-seq analysis. N deficiency induced content increase for most amino acids (AAs) and reduction for the remaining AAs, polyphenols, and caffeine. After N recovery, the decreased AAs and polyphenols showed a varying degree of recovery in content, but caffeine did not. Meanwhile, theanine increased in content, but its related synthetic genes were down-regulated, probably due to coordination of the whole N starvation regulatory network. Flavonoids-related pathways were relatively active following N stress according to KEGG enrichment analysis. Gene co-expression analysis revealed TCS2, AMT1;1, TAT2, TS, and GOGAT as key genes, and TFs like MYB, bHLH, and NAC were also actively involved in N stress responses in C. sinensis roots. These findings facilitate the understanding of the molecular mechanism of N regulation in tea roots and provide genetic reference for improving N use efficiency in tea plant.