Nitric oxide signaling in health and disease.

The surprising discovery that the diatomic gas nitric oxide (NO) is generated by mammalian cells and serves to regulate a multitude of physiological processes has continued to fascinate biologists for almost four decades. The biochemistry of NO is complex, and novel insights into the control of NO biosynthesis and mechanisms of signal transduction are continuously emerging. NO is a key regulator of cardiovascular function, metabolism, neurotransmission, immunity, and more, and aberrant NO signaling is a central feature of many major disorders including cardiovascular disease, diabetes, and cancer. Here, we discuss the basics of NO biology emphasizing recent advances in the field including novel means of increasing NO bioactivity with therapeutic and nutritional implications.

Dynamic Nutrient Signaling Networks in Plants.

Nutrients are vital to life through intertwined sensing, signaling, and metabolic processes. Emerging research focuses on how distinct nutrient signaling networks integrate and coordinate gene expression, metabolism, growth, and survival. We review the multifaceted roles of sugars, nitrate, and phosphate as essential plant nutrients in controlling complex molecular and cellular mechanisms of dynamic signaling networks. Key advances in central sugar and energy signaling mechanisms mediated by the evolutionarily conserved master regulators HEXOKINASE1 (HXK1), TARGET OF RAPAMYCIN (TOR), and SNF1-RELATED PROTEIN KINASE1 (SNRK1) are discussed. Significant progress in primary nitrate sensing, calcium signaling, transcriptome analysis, and root-shoot communication to shape plant biomass and architecture are elaborated. Discoveries on intracellular and extracellular phosphate signaling and the intimate connections with nitrate and sugar signaling are examined. This review highlights the dynamic nutrient, energy, growth, and stress signaling networks that orchestrate systemwide transcriptional, translational, and metabolic reprogramming, modulate growth and developmental programs, and respond to environmental cues.

Geological evidence of extensive N-fixation by volcanic lightning during very large explosive eruptions.

Most of the nitrogen (N) accessible for life is trapped in dinitrogen (N2), the most stable atmospheric molecule. In order to be metabolized by living organisms, N2 has to be converted into biologically assimilable forms, so-called fixed N. Nowadays, nearly all the N-fixation is achieved through biological and anthropogenic processes. However, in early prebiotic environments of the Earth, N-fixation must have occurred via natural abiotic processes. One of the most invoked processes is electrical discharges, including from thunderstorms and lightning associated with volcanic eruptions. Despite the frequent occurrence of volcanic lightning during explosive eruptions and convincing laboratory experimentation, no evidence of substantial N-fixation has been found in any geological archive. Here, we report on the discovery of a significant amount of nitrate in volcanic deposits from Neogene caldera-forming eruptions, which are well correlated with the concentrations of species directly emitted by volcanoes (sulfur, chlorine). The multi-isotopic composition (δ18O, Δ17O) of the nitrates reveals that they originate from the atmospheric oxidation of nitrogen oxides formed by volcanic lightning. According to these first geological volcanic nitrate archive, we estimate that, on average, about 60 Tg of N can be fixed during a large explosive event. Our findings hint at a unique role potentially played by subaerial explosive eruptions in supplying essential ingredients for the emergence of life on Earth.

Allosteric regulation of nitrate transporter NRT via the signaling protein PII.

Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in which the widespread signaling protein PII acts as a major regulatory hub. In cyanobacteria, PII was proposed to regulate the nitrate uptake by an ABC (ATP-binding cassette)-type nitrate transporter NrtABCD, in which the nucleotide-binding domain of NrtC is fused with a C-terminal regulatory domain (CRD). Here, we solved three cryoelectron microscopy structures of NrtBCD, bound to nitrate, ATP, and PII, respectively. Structural and biochemical analyses enable us to identify the key residues that form a hydrophobic and a hydrophilic cavity along the substrate translocation channel. The core structure of PII, but not the canonical T-loop, binds to NrtC and stabilizes the CRD, making it visible in the complex structure, narrows the substrate translocation channel in NrtB, and ultimately locks NrtBCD at an inhibited inward-facing conformation. Based on these results and previous reports, we propose a putative transport cycle driven by NrtABCD, which is allosterically inhibited by PII in response to the cellular level of 2-oxoglutarate. Our findings provide a distinct regulatory mechanism of ABC transporter via asymmetrically binding to a signaling protein.

Reversed I1Cu4 single-atom sites for superior neutral ammonia electrosynthesis with nitrate.

Electrochemical ammonia (NH3) synthesis from nitrate reduction (NITRR) offers an appealing solution for addressing environmental concerns and the energy crisis. However, most of the developed electrocatalysts reduce NO3- to NH3 via a hydrogen (H*)-mediated reduction mechanism, which suffers from undesired H*-H* dimerization to H2, resulting in unsatisfactory NH3 yields. Herein, we demonstrate that reversed I1Cu4 single-atom sites, prepared by anchoring iodine single atoms on the Cu surface, realized superior NITRR with a superior ammonia yield rate of 4.36 mg h-1 cm-2 and a Faradaic efficiency of 98.5% under neutral conditions via a proton-coupled electron transfer (PCET) mechanism, far beyond those of traditional Cu sites (NH3 yield rate of 0.082 mg h-1 cm-2 and Faradaic efficiency of 36.5%) and most of H*-mediated NITRR electrocatalysts. Theoretical calculations revealed that I single atoms can regulate the local electronic structures of adjacent Cu sites in favor of stronger O-end-bidentate NO3- adsorption with dual electron transfer channels and suppress the H* formation from the H2O dissociation, thus switching the NITRR mechanism from H*-mediated reduction to PCET. By integrating the monolithic I1Cu4 single-atom electrode into a flow-through device for continuous NITRR and in situ ammonia recovery, an industrial-level current density of 1 A cm-2 was achieved along with a NH3 yield rate of 69.4 mg h-1 cm-2. This study offers reversed single-atom sites for electrochemical ammonia synthesis with nitrate wastewater and sheds light on the importance of switching catalytic mechanisms in improving the performance of electrochemical reactions.

A Multiplex Enzymatic Machinery for Cellular Protein S-nitrosylation.

S-nitrosylation, the oxidative modification of Cys residues by nitric oxide (NO) to form S-nitrosothiols (SNOs), modifies all main classes of proteins and provides a fundamental redox-based cellular signaling mechanism. However, in contrast to other post-translational protein modifications, S-nitrosylation is generally considered to be non-enzymatic, involving multiple chemical routes. We report here that endogenous protein S-nitrosylation in the model organism E. coli depends principally upon the enzymatic activity of the hybrid cluster protein Hcp, employing NO produced by nitrate reductase. Anaerobiosis on nitrate induces both Hcp and nitrate reductase, thereby resulting in the S-nitrosylation-dependent assembly of a large interactome including enzymes that generate NO (NO synthase), synthesize SNO-proteins (SNO synthase), and propagate SNO-based signaling (trans-nitrosylases) to regulate cell motility and metabolism. Thus, protein S-nitrosylation by NO in E. coli is essentially enzymatic, and the potential generality of the multiplex enzymatic mechanism that we describe may support a re-conceptualization of NO-based cellular signaling.

The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation.

As a crucial nitrogen source, nitrate (NO3-) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3- availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3- conditions. lonr2 is defective in the high-affinity NO3- transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3--induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3- levels. These results reveal a mechanism by which NRT2.1 in response to NO3- limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3- availability.

Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific.

Our understanding of ocean-cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air-sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.

Constructing molecule-metal relay catalysis over heterophase metallene for high-performance rechargeable zinc-nitrate/ethanol batteries.

Zinc-nitrate batteries can integrate energy supply, ammonia electrosynthesis, and sewage disposal into one electrochemical device. However, current zinc-nitrate batteries still severely suffer from the limited energy density and poor rechargeability. Here, we report the synthesis of tetraphenylporphyrin (tpp)-modified heterophase (amorphous/crystalline) rhodium-copper alloy metallenes (RhCu M-tpp). Using RhCu M-tpp as a bifunctional catalyst for nitrate reduction reaction (NO3RR) and ethanol oxidation reaction in neutral solution, a highly rechargeable and low-overpotential zinc-nitrate/ethanol battery is successfully constructed, which exhibits outstanding energy density of 117364.6 Wh kg-1cat, superior rate capability, excellent cycling stability of ~400 cycles, and potential ammonium acetate production. Ex/in situ experimental studies and theoretical calculations reveal that there is a molecule-metal relay catalysis in NO3RR over RhCu M-tpp that significantly facilitates the ammonia selectivity and reaction kinetics via a low energy barrier pathway. This work provides an effective design strategy of multifunctional metal-based catalysts toward the high-performance zinc-based hybrid energy systems.

Atomic coordination environment engineering of bimetallic alloy nanostructures for efficient ammonia electrosynthesis from nitrate.

Electrochemical nitrate reduction reaction (NO3RR) to ammonia has been regarded as a promising strategy to balance the global nitrogen cycle. However, it still suffers from poor Faradaic efficiency (FE) and limited yield rate for ammonia production on heterogeneous electrocatalysts, especially in neutral solutions. Herein, we report one-pot synthesis of ultrathin nanosheet-assembled RuFe nanoflowers with low-coordinated Ru sites to enhance NO3RR performances in neutral electrolyte. Significantly, RuFe nanoflowers exhibit outstanding ammonia FE of 92.9% and yield rate of 38.68 mg h-1 mgcat-1 (64.47 mg h-1 mgRu-1) at -0.30 and -0.65 V (vs. reversible hydrogen electrode), respectively. Experimental studies and theoretical calculations reveal that RuFe nanoflowers with low-coordinated Ru sites are highly electroactive with an increased d-band center to guarantee efficient electron transfer, leading to low energy barriers of nitrate reduction. The demonstration of rechargeable zinc-nitrate batteries with large-specific capacity using RuFe nanoflowers indicates their great potential in next-generation electrochemical energy systems.

The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency.

Nitrate distribution in soils is often heterogeneous. Plants have adapted to this by modifying their root system architecture (RSA). Previous studies showed that NITRATE-TRANSPORTER1.1 (NRT1.1), which also transports auxin, helps inhibit lateral root primordia (LRP) emergence in nitrate-poor patches, by preferentially transporting auxin away from the LRP. In this study, we identified the regulatory system for this response involving the transcription factor (TF), SENSITIVE-TO-PROTON-RHIZOTOXICITY1 (STOP1), which is accumulated in the nuclei of LRP cells under nitrate deficiency and directly regulates Arabidopsis NRT1.1 expression. Mutations in STOP1 mimic the root phenotype of the loss-of-function NRT1.1 mutant under nitrate deficiency, compared to wild-type plants, including increased LR growth and higher DR5promoter activity (i.e., higher LRP auxin signaling/activity). Nitrate deficiency-induced LR growth inhibition was almost completely reversed when STOP1 and the TF, TEOSINTE-BRANCHED1,-CYCLOIDEA,-PCF-DOMAIN-FAMILY-PROTEIN20 (TCP20), a known activator of NRT1.1 expression, were both mutated. Thus, the STOP1-TCP20 system is required for activation of NRT1.1 expression under nitrate deficiency, leading to reduced LR growth in nitrate-poor regions. We found this STOP1-mediated system is more active as growth media becomes more acidic, which correlates with reductions in soil nitrate as the soil pH becomes more acidic. STOP1 has been shown to be involved in RSA modifications in response to phosphate deficiency and increased potassium uptake, hence, our findings indicate that root growth regulation in response to low availability of the major fertilizer nutrients, nitrogen, phosphorus and potassium, all involve STOP1, which may allow plants to maintain appropriate root growth under the complex and varying soil distribution of nutrients.

Promoting the efficiency and selectivity of NO3--to-NH3 reduction on Cu-O-Ti active sites via preferential glycol oxidation with holes.

The combined reductive and oxidative reaction is the essence of a solar-driven photoredox system. Unfortunately, most of these efforts focus on the specific half-reactions, and the key roles of complete photoredox reactions have been overlooked. Taking the nitrate reduction reaction (NO3-RR) as a typical multiple-electrons involved process, the selective reduction of the NO3- into ammonia (NH3) synthesis with high efficiency is still a grand challenge. Herein, a rational oxidative half-reaction is tailored to achieve the selective conversion of NO3- to NH3 on Cu-O-Ti active sites. Through the coupled NO3-RR with glycol oxidation reaction system, a superior NH3 photosynthesis rate of 16.04 ± 0.40 mmol gcat-1 h-1 with NO3- conversion ratio of 100% and almost 100% of NH3 selectivity is reached on Cu-O-Ti bimetallic oxide cluster-anchored TiO2 nanosheets (CuOx@TNS) catalyst. A combination of comprehensive in situ characterizations and theoretical calculations reveals the molecular mechanism of the synergistic interaction between NO3-RR and glycol oxidation pair on CuOx@TNS. The introduction of glycol accelerates the h+ consumption for the formation of alkoxy (•R) radicals to avoid the production of •OH radicals. The construction of Cu-O-Ti sites facilitates the preferential oxidation of glycol with h+ and enhances the production of e- to participate in NO3-RR. The efficiency and selectivity of NO3--to-NH3 synthesis are thus highly promoted on Cu-O-Ti active sites with the accelerated glycol oxidative half-reaction. This work upgrades the conventional half photocatalysis into a complete photoredox system, demonstrating the tremendous potential for the precise regulation of reaction pathway and product selectivity.

Free-standing membrane incorporating single-atom catalysts for ultrafast electroreduction of low-concentration nitrate.

The release of wastewaters containing relatively low levels of nitrate (NO3-) results in sufficient contamination to induce harmful algal blooms and to elevate drinking water NO3- concentrations to potentially hazardous levels. In particular, the facile triggering of algal blooms by ultra-low concentrations of NO3- necessitates the development of efficient methods for NO3- destruction. However, promising electrochemical methods suffer from weak mass transport under low reactant concentrations, resulting in long treatment times (on the order of hours) for complete NO3- destruction. In this study, we present flow-through electrofiltration via an electrified membrane incorporating nonprecious metal single-atom catalysts for NO3- reduction activity enhancement and selectivity modification, achieving near-complete removal of ultra-low concentration NO3- (10 mg-N L-1) with a residence time of only a few seconds (10 s). By anchoring Cu single atoms supported on N-doped carbon in a carbon nanotube interwoven framework, we fabricate a free-standing carbonaceous membrane featuring high conductivity, permeability, and flexibility. The membrane achieves over 97% NO3- removal with high N2 selectivity of 86% in a single-pass electrofiltration, which is a significant improvement over flow-by operation (30% NO3- removal with 7% N2 selectivity). This high NO3- reduction performance is attributed to the greater adsorption and transport of nitric oxide under high molecular collision frequency coupled with a balanced supply of atomic hydrogen through H2 dissociation during electrofiltration. Overall, our findings provide a paradigm of applying a flow-through electrified membrane incorporating single-atom catalysts to improve the rate and selectivity of NO3- reduction for efficient water purification.

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.

Nitrate alleviates ammonium toxicity in Brassica napus by coordinating rhizosphere and cell pH and ammonium assimilation.

In natural and agricultural situations, ammonium ( NH 4 + ) is a preferred nitrogen (N) source for plants, but excessive amounts can be hazardous to them, known as NH 4 + toxicity. Nitrate ( NO 3 - ) has long been recognized to reduce NH 4 + toxicity. However, little is known about Brassica napus, a major oil crop that is sensitive to high NH 4 + . Here, we found that NO 3 - can mitigate NH 4 + toxicity by balancing rhizosphere and intracellular pH and accelerating ammonium assimilation in B. napus. NO 3 - increased the uptake of NO 3 - and NH 4 + under high NH 4 + circumstances by triggering the expression of NO 3 - and NH 4 + transporters, while NO 3 - and H+ efflux from the cytoplasm to the apoplast was enhanced by promoting the expression of NO 3 - efflux transporters and genes encoding plasma membrane H+ -ATPase. In addition, NO 3 - increased pH in the cytosol, vacuole, and rhizosphere, and down-regulated genes induced by acid stress. Root glutamine synthetase (GS) activity was elevated by NO 3 - under high NH 4 + conditions to enhance the assimilation of NH 4 + into amino acids, thereby reducing NH 4 + accumulation and translocation to shoot in rapeseed. In addition, root GS activity was highly dependent on the environmental pH. NO 3 - might induce metabolites involved in amino acid biosynthesis and malate metabolism in the tricarboxylic acid cycle, and inhibit phenylpropanoid metabolism to mitigate NH 4 + toxicity. Collectively, our results indicate that NO 3 - balances both rhizosphere and intracellular pH via effective NO 3 - transmembrane cycling, accelerates NH 4 + assimilation, and up-regulates malate metabolism to mitigate NH 4 + toxicity in oilseed rape.

Melatonin confers tolerance to nitrogen deficiency through regulating MdHY5 in apple plants.

Nitrogen (N) is an essential nutrient for crop growth and development, significantly influencing both yield and quality. Melatonin (MT), a known enhancer of abiotic stress tolerance, has been extensively studied. However, its relationship with nutrient stress, particularly N deficiency, and the underlying regulatory mechanisms of MT on N absorption remain unclear. In this study, exogenous MT treatment was found to improve the tolerance of apple plants to N deficiency. Apple plants overexpressing the MT biosynthetic gene N-acetylserotonin methyltransferase 9 (MdASMT9) were used to further investigate the effects of endogenous MT on low-N stress. Overexpression of MdASMT9 improved the light harvesting and heat transfer capability of apple plants, thereby mitigating the detrimental effects of N deficiency on the photosynthetic system. Proteomic and physiological data analyses indicated that MdASMT9 overexpression enhanced the trichloroacetic acid cycle and positively modulated amino acid metabolism to counteract N-deficiency stress. Additionally, both exogenous and endogenous MT promoted the transcription of MdHY5, which in turn bound to the MdNRT2.1 and MdNRT2.4 promoters and activated their expression. Notably, MT-mediated promotion of MdNRT2.1 and MdNRT2.4 expression through regulating MdHY5, ultimately enhancing N absorption. Taken together, these findings shed light on the association between MdASMT9-mediated MT biosynthesis and N absorption in apple plants under N-deficiency conditions.

MtNPF6.5 mediates chloride uptake and nitrate preference in Medicago roots.

The preference for nitrate over chloride through regulation of transporters is a fundamental feature of plant ion homeostasis. We show that Medicago truncatula MtNPF6.5, an ortholog of Arabidopsis thaliana AtNPF6.3/NRT1.1, can mediate nitrate and chloride uptake in Xenopus oocytes but is chloride selective and that its close homologue, MtNPF6.7, can transport nitrate and chloride but is nitrate selective. The MtNPF6.5 mutant showed greatly reduced chloride content relative to wild type, and MtNPF6.5 expression was repressed by high chloride, indicating a primary role for MtNPF6.5 in root chloride uptake. MtNPF6.5 and MtNPF6.7 were repressed and induced by nitrate, respectively, and these responses required the transcription factor MtNLP1. Moreover, loss of MtNLP1 prevented the rapid switch from chloride to nitrate as the main anion in nitrate-starved plants after nitrate provision, providing insight into the underlying mechanism for nitrate preference. Sequence analysis revealed three sub-types of AtNPF6.3 orthologs based on their predicted substrate-binding residues: A (chloride selective), B (nitrate selective), and C (legume specific). The absence of B-type AtNPF6.3 homologues in early diverged plant lineages suggests that they evolved from a chloride-selective MtNPF6.5-like protein.

A cyclical marker system enables indefinite series of oligonucleotide-directed gene editing in Chlamydomonas reinhardtii.

CRISPR/Cas9 gene editing in the model green alga Chlamydomonas reinhardtii relies on the use of selective marker genes to enrich for non-selectable target mutations. This becomes challenging when many sequential modifications are required in a single cell line, as useful markers are limited. Here, we demonstrate a cyclical selection process which only requires a single marker gene to identify an almost infinite sequential series of CRISPR-based target gene modifications. We used the NIA1 (Nit1, NR; nitrate reductase) gene as the selectable marker in this study. In the forward stage of the cycle, a stop codon was engineered into the NIA1 gene at the CRISPR target location. Cells retaining the wild-type NIA1 gene were killed by chlorate, while NIA1 knockout mutants survived. In the reverse phase of the cycle, the stop codon engineered into the NIA1 gene during the forward phase was edited back to the wild-type sequence. Using nitrate as the sole nitrogen source, only the reverted wild-type cells survived. By using CRISPR to specifically deactivate and reactivate the NIA1 gene, a marker system was established that flipped back and forth between chlorate- and auxotrophic (nitrate)-based selection. This provided a scarless cyclical marker system that enabled an indefinite series of CRISPR edits in other, non-selectable genes. We demonstrate that this 'Sequential CRISPR via Recycling Endogenous Auxotrophic Markers (SCREAM)' technology enables an essentially limitless series of genetic modifications to be introduced into a single cell lineage of C. reinhardtii in a fast and efficient manner to complete complex genetic engineering.

Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses.

Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.

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

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.