NIN-like protein 7 transcription factor is a plant nitrate sensor

Overexpression of AtbZIP69 in transgenic wheat confers tolerance to nitrogen and drought stress

MAIN CONCLUSION

AtbZIP69 overexpression in wheat significantly enhanced drought and low nitrogen tolerance by modulating ABA synthesis, antioxidant activity, nitrogen allocation, and transporter gene expression, boosting yield. In this study, we generated wheat plants with improved low nitrogen (LN) and drought tolerance by introducing AtbZIP69, a gene encoding a basic leucine zipper domain transcription factor, into the wheat cultivar Shi 4056. AtbZIP69 localized to the nucleus and activated transcription. A greenhouse study further revealed that, compared to wild type (WT) wheat, AtbZIP69 transgenic wheat exhibited significantly increased drought and LN stress tolerance. Under drought stress, the H2O2 concentration in transgenic lines decreased, whereas SOD activity and proline content increased, resulting in remarkably enhanced drought resistance. Furthermore, drought stress boosted the expression of critical abscisic acid (ABA) synthesis enzymes as well as the ABA content of transgenic plants, implying that this gene may improve wheat's drought resistance by promoting ABA production. Additionally, during a two-year field test, the yield and the number of spikes of transgenic wheat were significantly higher than those of WT wheat under LN conditions. Mechanistically, the overexpression of AtbZIP69 altered nitrogen distribution by allocating more nitrogen to grains under LN conditions. In addition, the expression of genes encoding nitrogen transporter proteins was higher in AtbZIP69 transgenic wheat than in WT wheat under LN conditions. These findings suggest that the insertion of AtbZIP69 opens up new opportunities for wheat stress resistance breeding.

Carbon and nitrogen signaling regulate FLOWERING LOCUS C and impact flowering time in Arabidopsis

The timing of flowering in plants is modulated by both carbon (C) and nitrogen (N) signaling pathways. In a previous study, we established a pivotal role of the sucrose-signaling trehalose 6-phosphate pathway in regulating flowering under N-limited short-day conditions. In this work, we show that both wild-type Arabidopsis (Arabidopsis thaliana) plants grown under N-limited conditions and knock-down plants of TREHALOSE PHOSPHATE SYNTHASE 1 induce FLOWERING LOCUS C (FLC) expression, a well-known floral repressor associated with vernalization. When exposed to an extended period of cold, a flc mutant fails to respond to N availability and flowers at the same time under N-limited and full-nutrition conditions. Our data suggest that SUCROSE NON-FERMENTING 1 RELATED KINASE 1-dependent trehalose 6-phosphate-mediated C signaling and a mechanism downstream of N signaling (likely involving NIN-LIKE PROTEIN 7) impact the expression of FLC. Collectively, our data underscore the existence of a multi-factor regulatory system in which the C and N signaling pathways jointly govern the regulation of flowering in plants.

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.

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.

A Microplate-Based Expression Monitoring System for Arabidopsis NITRATE TRANSPORTER2.1 Using the Luciferase Reporter

Gene expression analysis is a fundamental technique to elucidate the regulatory mechanisms of genes of interest or to reveal the patterns of plant response to environmental stimuli. Traditionally, gene expression analyses have required RNA extraction, followed by cDNA synthesis and qPCR analyses. However, this conventional method is costly and time-consuming, limiting the amount of data collected. The protocol outlined in this study, which utilizes a chemiluminescence system, offers a cost-effective and rapid method for assessing the expression of Arabidopsis (Arabidopsis thaliana) genes, exemplified by analyzing the nitrate-inducible expression of a major nitrate transporter gene, nitrate transporter 2.1 (NRT2.1). A reporter construct, containing the NRT2.1 promoter fused to the firefly luciferase gene, was introduced into wild-type and mutant Arabidopsis plants. Seeds obtained from the transgenic lines were grown for 3 days in 96-well microplates containing a nitrate-free nutrient solution. After 3 days, the nutrient solution was replaced with a fresh batch, which was supplemented with luciferin potassium. One hour later, nitrate was added at various concentrations, and the temporal expression pattern of NRT2.1 was analyzed by monitoring the chemiluminescence signals. This method allowed for the cost-effective, quantitative, and high-throughput analysis of NRT2.1 expression over time under the effects of various nutrient conditions and genetic backgrounds. Key features • Small-scale and immediate assessment of NRT2.1 promoter activity using 3-day-old Arabidopsis seedlings expressing the firefly luciferase gene under the control of the Arabidopsis NRT2.1 promoter. • Comparison of various Arabidopsis genotypes and nutrient conditions using 96-well microplates. • Quantitative assessment of the temporal changes in gene expression levels. Graphical overview Graphical summary of the microplate-based NRT2.1 expression monitoring system in planta. Note: The steps within gray square brackets are part of a general protocol and are not included in this manuscript.

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.

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.

Genetic and molecular mechanisms underlying nitrogen use efficiency in maize

Nitrogen (N) is vital for crop growth and yield, impacting food quality. However, excessive use of N fertilizers leads to high agricultural costs and environmental challenges. This review offers a thorough synthesis of the genetic and molecular regulation of N uptake, assimilation, and remobilization in maize, emphasizing the role of key genes and metabolic pathways in enhancing N use efficiency (NUE). We summarize the genetic regulators of N transports for nitrate (NO3-) and ammonium (NH4+) that contribute to efficient N uptake and transportation. We further discuss the molecular mechanisms by which root system development adapts to N distribution and how N influences root system development and growth. Given the advancements in high-throughput microbiome studies, we delve into the impact of rhizosphere microorganisms on NUE and the complex plant-microbe interactions that regulate maize NUE. Additionally, we conclude with intricate regulatory mechanisms of N assimilation and remobilization in maize, involving key enzymes, transcription factors, and amino acid transporters. We also scrutinize the known N signaling perception and transduction mechanisms in maize. This review underscores the challenges in improving maize NUE and advocates for an integrative research approach that leverages genetic diversity and synthetic biology, paving the way for sustainable agriculture.

High-nitrogen-induced γ-aminobutyric acid triggers host immunity and pathogen oxidative stress tolerance in tomato and Ralstonia solanacearum interaction

Soil nitrogen (N) significantly influences the interaction between plants and pathogens, yet its impact on host defenses and pathogen strategies via alterations in plant metabolism remains unclear. Through metabolic and genetic studies, this research demonstrates that high-N-input exacerbates tomato bacterial wilt by altering γ-aminobutyric acid (GABA) metabolism of host plants. Under high-N conditions, the nitrate sensor NIN-like protein 7 (SlNLP7) promotes the glutamate decarboxylase 2/4 (SlGAD2/4) transcription and GABA synthesis by directly binding to the promoters of SlGAD2/4. The tomato plants with enhanced GABA levels showed stronger immune responses but remained susceptible to Ralstonia solanacearum. This led to the discovery that GABA produced by the host actually heightens the pathogen's virulence. We identified the R. solanacearum LysR-type transcriptional regulator OxyR protein, which senses host-derived GABA and, upon interaction, triggers a response involving protein dimerization that enhances the pathogen's oxidative stress tolerance by activating the expression of catalase (katE/katGa). These findings reveal GABA's dual role in activating host immunity and enhancing pathogen tolerance to oxidative stress, highlighting the complex relationship between tomato plants and R. solanacearum, influenced by soil N status.

VrNIN1 interacts with VrNNC1 to regulate root nodulation in mungbean

Node Inception (NIN) plays a crucial role in legume symbiosis by participating in both infection and nodule formation processes. However, its specific function in mungbean (Vigna radiata) remains poorly understood. This study aimed to functionally characterize the VrNIN1 gene in mungbean through an enhanced hairy root transformation approach. Examination of proVrNIN1: GUS hairy roots via GUS staining indicated the expression of VrNIN1 in later root promodia, nodule primordia, and nodules. Phenotypic evaluation revealed that overexpression or silencing of VrNIN1 led to a significant reduction in nodule numbers in hairy roots compared to controls. Additionally, interaction between VrNIN1 and VrNNC1 was confirmed through yeast two-hybrid, luciferase complementation and Co-immunoprecipitation assays. VrNNC1 expression was observed in the vascular bundle and cortex of roots and root nodules, where it notably suppressed nodule formation in transgenic hairy roots. Furthermore, gene expression analysis demonstrated the involvement of VrNIN1 and VrNNC1 in regulating root nodulation by modulating the expression of VrRIC1 and VrEDOD40. This study not only optimized the genetic transformation system for hairy roots in mungbean, but also provided mechanistic insights into the regulatory role of VrNIN1 in root nodule symbiosis in mungbean.

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.

OsNLP3 enhances grain weight and reduces grain chalkiness in rice

Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.

Phosphorus acquisition, translocation, and redistribution in maize

Phosphorus (P) is an essential nutrient for crop growth, making it important for maintaining food security as the global population continues to increase. Plants acquire P primarily via the uptake of inorganic phosphate (Pi) in soil through their roots. Pi, which is usually sequestered in soils, is not easily absorbed by plants and represses plant growth. Plants have developed a series of mechanisms to cope with P deficiency. Moreover, P fertilizer applications are critical for maximizing crop yield. Maize is a major cereal crop cultivated worldwide. Increasing its P-use efficiency is important for optimizing maize production. Over the past two decades, considerable progresses have been achieved in research aimed at adapting maize varieties to changes in environmental P supply. Here, we present an overview of the morphological, physiological, and molecular mechanisms involved in P acquisition, translocation, and redistribution in maize and combine the advances in Arabidopsis and rice, to better elucidate the progress of P nutrition. Additionally, we summarize the correlation between P and abiotic stress responses. Clarifying the mechanisms relevant to improving P absorption and use in maize can guide future research on sustainable agriculture.

NIN-LIKE PROTEIN3.2 inhibits repressor Aux/IAA14 expression and enhances root biomass in maize seedlings under low nitrogen

Plants generally enhance their root growth in the form of greater biomass and/or root length to boost nutrient uptake in response to short-term low nitrogen (LN). However, the underlying mechanisms of short-term LN-mediated root growth remain largely elusive. Our genome-wide association study, haplotype analysis, and phenotyping of transgenic plants showed that the crucial nitrate signaling component NIN-LIKE PROTEIN3.2 (ZmNLP3.2), a positive regulator of root biomass, is associated with natural variations in root biomass of maize (Zea mays L.) seedlings under LN. The monocot-specific gene AUXIN/INDOLE-3-ACETIC ACID14 (ZmAux/IAA14) exhibited opposite expression patterns to ZmNLP3.2 in ZmNLP3.2 knockout and overexpression lines, suggesting that ZmNLP3.2 hampers ZmAux/IAA14 transcription. Importantly, ZmAux/IAA14 knockout seedlings showed a greater root dry weight (RDW), whereas ZmAux/IAA14 overexpression reduced RDW under LN compared with wild-type plants, indicating that ZmAux/IAA14 negatively regulates the RDW of LN-grown seedlings. Moreover, in vitro and vivo assays indicated that AUXIN RESPONSE FACTOR19 (ZmARF19) binds to and transcriptionally activates ZmAux/IAA14, which was weakened by the ZmNLP3.2-ZmARF19 interaction. The zmnlp3.2 ZmAux/IAA14-OE seedlings exhibited further reduced RDW compared with ZmAux/IAA14 overexpression lines when subjected to LN treatment, corroborating the ZmNLP3.2-ZmAux/IAA14 interaction. Thus, our study reveals a ZmNLP3.2-ZmARF19-ZmAux/IAA14 module regulating root biomass in response to nitrogen limitation in maize.

Conserved cis-elements enable NODULES WITH ACTIVATED DEFENSE1 regulation by NODULE INCEPTION during nodulation

Symbiotic nitrogen fixation within nitrogen-fixing clade (NFC) plants is thought to have arisen from a single gain followed by massive losses in the genomes of ancestral non-nodulating plants. However, molecular evidence supporting this model is limited. Here, we confirm through bioinformatic analysis that NODULES WITH ACTIVATED DEFENSE1 (NAD1) is present only in NFC plants and is thus an NFC-specific gene. Moreover, NAD1 was specifically expressed in nodules. We identified three conserved nodulation-associated cis-regulatory elements (NACE1-3) in the promoter of LjNAD1 from Lotus japonicus that are required for its nodule specific expression. A survey of NFC plants revealed that NACE1 and NACE2 are specific to the Fabales and Papilionoideae, respectively, while NACE3 is present in all NFC plants. Moreover, we found that nodule inception (NIN) directly binds to all three NACEs to activate NAD1 expression. Mutation of L. japonicus LjNAD1 resulted in the formation of abnormal symbiosomes with enlarged symbiosome space and frequent breakdown of bacteroids in nodules, resembling phenotypes reported for Medicago truncatula Mtnad1 and Mtnin mutants. These data point to NIN-NAD1 as an important module regulating rhizobial accommodation in nodules. The regulation of NAD1 by NIN in the NFC ancestor represent an important evolutionary adaptation for nodulation.

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.

Precise counter anion modulation of the self-assembly behavior-endowed ultrasensitive and specific dual-mode visualization of nitrate

Pt(II) polypyridine complex-based probe exhibits promising performance in anion detection by the change of the absorption and emission properties based on supramolecular self-assembly. However, whether one can develop a modulation strategy of the counter anion to boost the detection sensitivity and anti-interference capability of the Pt(II) complex-based probe remains a big challenge. Here, an effective modulation strategy was proposed by precisely regulating the interaction energy through adjusting the type of the counter anions, and a series of probes have been synthesized by counter anion (X = Cl-, ClO4-, PF6-) exchange in [Pt(tpy)Cl]·X (tpy=2,2':6',2''-terpyridine), and thus the colorimetric-luminescence dual-mode detection toward nitrate was achieved. The optimal [Pt(tpy)Cl]·Cl probe shows superior nitrate detection performance including a limit of detection (LOD) (8.68 nM), rapid response (<0.5 s), an excellent selectivity and anti-interference capability even facing 14 common anions. Moreover, a polyvinyl alcohol (PVA) sponge-based sensing chip loaded with the probe enables the ultra-sensitive detection of nitrate particles with an ultralow detection limit of 7.6 pg, and it was further integrated into a detection pen for the accurate recognition of nitrate particles in real scenarios. The proposed counter-anion modulation strategy is expected to start a new frontier for the exploration of novel Pt(II) complex-based probes.

Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis

Understanding plant responses to individual stresses does not mean that we understand real-world situations, where stresses usually combine and interact. These interactions arise at different levels, from stress exposure to the molecular networks of the stress response. Here, we built an in-depth multiomic description of plant responses to mild water (W) and nitrogen (N) limitations, either individually or combined, among 5 genetically different Arabidopsis (Arabidopsis thaliana) accessions. We highlight the different dynamics in stress response through integrative traits such as rosette growth and the physiological status of the plants. We also used transcriptomic and metabolomic profiling during a stage when the plant response was stabilized to determine the wide diversity in stress-induced changes among accessions, highlighting the limited reality of a "universal" stress response. The main effect of the W × N interaction was an attenuation of the N-deficiency syndrome when combined with mild drought, but to a variable extent depending on the accession. Other traits subject to W × N interactions are often accession specific. Multiomic analyses identified a subset of transcript-metabolite clusters that are critical to stress responses but essentially variable according to the genotype factor. Including intraspecific diversity in our descriptions of plant stress response places our findings in perspective.

Systems genetic analysis of lignin biosynthesis in Populus tremula

The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural 'SwAsp' population of aspen (Populus tremula) trees. We analyzed gene expression by RNA sequencing (RNA-seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis-GC-MS in mature wood of 268 trees from 99 genotypes. Abundant variation was observed for lignin content and composition, and genome-wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top-ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co-expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin-biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL-CoA O-METHYLTRANSFERASE 3. PHENYLALANINE AMMONIA LYASE 3 was co-expressed with HOMEOBOX PROTEIN 5 (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees. The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability.

Nitrate and ammonium, the yin and yang of nitrogen uptake: a time-course transcriptomic study in rice

Nitrogen is an essential nutrient for plants and a major determinant of plant growth and crop yield. Plants acquire nitrogen mainly in the form of nitrate and ammonium. Both nitrogen sources affect plant responses and signaling pathways in a different way, but these signaling pathways interact, complicating the study of nitrogen responses. Extensive transcriptome analyses and the construction of gene regulatory networks, mainly in response to nitrate, have significantly advanced our understanding of nitrogen signaling and responses in model plants and crops. In this study, we aimed to generate a more comprehensive gene regulatory network for the major crop, rice, by incorporating the interactions between ammonium and nitrate. To achieve this, we assessed transcriptome changes in rice roots and shoots over an extensive time course under single or combined applications of the two nitrogen sources. This dataset enabled us to construct a holistic co-expression network and identify potential key regulators of nitrogen responses. Next to known transcription factors, we identified multiple new candidates, including the transcription factors OsRLI and OsEIL1, which we demonstrated to induce the primary nitrate-responsive genes OsNRT1.1b and OsNIR1. Our network thus serves as a valuable resource to obtain novel insights in nitrogen signaling.

Pupylation-Based Proximity-Tagging of FERONIA-Interacting Proteins in Arabidopsis

The plasma membrane-localized receptor kinase FERONIA (FER) plays critical roles in a remarkable variety of biological processes throughout the life cycle of Arabidopsis thaliana. Revealing the molecular connections of FER that underlie these processes starts with identifying the proteins that interact with FER. We applied pupylation-based interaction tagging (PUP-IT) to survey cellular proteins in proximity to FER, encompassing weak and transient interactions that can be difficult to capture for membrane proteins. We reproducibly identified 581, 115, and 736 specific FER-interacting protein candidates in protoplasts, seedlings, and flowers, respectively. We also confirmed 14 previously characterized FER-interacting proteins. Protoplast transient gene expression expedited the testing of new gene constructs for PUP-IT analyses and the validation of candidate proteins. We verified the proximity labeling of five selected candidates that were not previously characterized as FER-interacting proteins. The PUP-IT method could be a valuable tool to survey and validate protein-protein interactions for targets of interest in diverse subcellular compartments in plants.

RNA-seq reveals the gene expression in patterns in Populus × euramericana 'Neva' plantation under different precision water and fertilizer-intensive management

BACKGROUND

Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored.

RESULTS

Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar.

CONCLUSION

Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.

New molecular components that regulate the transcriptional hub in root hairs: coupling environmental signals with endogenous hormones to coordinate growth

Root hairs have become an important model system for studying plant growth, and in particular how plants modulate their growth in response to cell-intrinsic and environmental stimuli. In this review, we discuss recent advances in our understanding of the molecular mechanisms underlying the growth of Arabidopsis root hairs in the interface between responses to environmental cues (e.g. nutrients such as nitrates and phosphate, and microorganisms) and hormonal stimuli (e.g. auxin). Growth of root hairs is under the control of several transcription factors that are also under strong regulation at different levels. We highlight recent new discoveries along these transcriptional pathways that might have the potential to increase our capacity to enhance nutrient uptake by the roots in the context of abiotic stresses. We use the text-mining capacities of the PlantConnectome database to generate an up-to-date view of root hairs growth within these complex biological contexts.

A practical guide to the discovery of biomolecules with biostimulant activity

The growing demand for sustainable solutions in agriculture, which are critical for crop productivity and food quality in the face of climate change and the need to reduce agrochemical usage, has brought biostimulants into the spotlight as valuable tools for regenerative agriculture. With their diverse biological activities, biostimulants can contribute to crop growth, nutrient use efficiency, and abiotic stress resilience, as well as to the restoration of soil health. Biomolecules include humic substances, protein lysates, phenolics, and carbohydrates have undergone thorough investigation because of their demonstrated biostimulant activities. Here, we review the process of the discovery and development of extract-based biostimulants, and propose a practical step-by-step pipeline that starts with initial identification of biomolecules, followed by extraction and isolation, determination of bioactivity, identification of active compound(s), elucidation of mechanisms, formulation, and assessment of effectiveness. The different steps generate a roadmap that aims to expedite the transfer of interdisciplinary knowledge from laboratory-scale studies to pilot-scale production in practical scenarios that are aligned with the prevailing regulatory frameworks.

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.

Zinc mediates control of nitrogen fixation via transcription factor filamentation

Plants adapt to fluctuating environmental conditions by adjusting their metabolism and gene expression to maintain fitness1. In legumes, nitrogen homeostasis is maintained by balancing nitrogen acquired from soil resources with nitrogen fixation by symbiotic bacteria in root nodules2-8. Here we show that zinc, an essential plant micronutrient, acts as an intracellular second messenger that connects environmental changes to transcription factor control of metabolic activity in root nodules. We identify a transcriptional regulator, FIXATION UNDER NITRATE (FUN), which acts as a sensor, with zinc controlling the transition between an inactive filamentous megastructure and an active transcriptional regulator. Lower zinc concentrations in the nodule, which we show occur in response to higher levels of soil nitrate, dissociates the filament and activates FUN. FUN then directly targets multiple pathways to initiate breakdown of the nodule. The zinc-dependent filamentation mechanism thus establishes a concentration readout to adapt nodule function to the environmental nitrogen conditions. In a wider perspective, these results have implications for understanding the roles of metal ions in integration of environmental signals with plant development and optimizing delivery of fixed nitrogen in legume crops.

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.

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.

Sensing and regulation of C and N metabolism - novel features and mechanisms of the TOR and SnRK1 signaling pathways

Carbon (C) and nitrogen (N) metabolisms are tightly integrated to allow proper plant growth and development. Photosynthesis is dependent on N invested in chlorophylls, enzymes, and structural components of the photosynthetic machinery, while N uptake and assimilation rely on ATP, reducing equivalents, and C-skeletons provided by photosynthesis. The direct connection between N availability and photosynthetic efficiency allows the synthesis of precursors for all metabolites and building blocks in plants. Thus, the capacity to sense and respond to sudden changes in C and N availability is crucial for plant survival and is mediated by complex yet efficient signaling pathways such as TARGET OF RAPAMYCIN (TOR) and SUCROSE-NON-FERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1). In this review, we present recent advances in mechanisms involved in sensing C and N status as well as identifying current gaps in our understanding. We finally attempt to provide new perspectives and hypotheses on the interconnection of diverse signaling pathways that will allow us to understand the integration and orchestration of the major players governing the regulation of the CN balance.

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.

Genome-Wide Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum

Apomixis is a common reproductive characteristic of Zanthoxylum plants, and RWP-RKs are plant-specific transcription factors known to regulate embryonic development. However, the genome-wide analysis and function prediction of RWP-RK family genes in Z. armatum are unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z. armatum, among which 15 genes belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed a close phylogenetic relationship between Z. armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of the embryonic development of Z. armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Results of a real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study is expected to improve our understanding of ZaRWP-RK transcription factors and provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z. armatum.

Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

The NODULE-INCEPTION-like protein (NLP) family is a plant-specific transcription factor (TF) family involved in nitrate transport and assimilation in plants, which are essential for improving plant nitrogen use efficiency. Currently, the molecular nature and evolutionary trajectory of NLP genes in the C4 model crop foxtail millet are unknown. Therefore, we performed a comprehensive analysis of NLP and molecular evolution in foxtail millet by scanning the genomes of foxtail millet and representative species of the plant kingdom. We identified seven NLP genes in the foxtail millet genome, all of which are individually and separately distributed on different chromosomes. They were not structurally identical to each other and were mainly expressed on root tissues. We unearthed two key genes (Si5G004100.1 and Si6G248300.1) with a variety of excellent characteristics. Regarding its molecular evolution, we found that NLP genes in Gramineae mainly underwent dispersed duplication, but maize NLP genes were mainly generated via WGD events. Other factors such as base mutations and natural selection have combined to promote the evolution of NLP genes. Intriguingly, the family in plants showed a gradual expansion during evolution with more duplications than losses, contrary to most gene families. In conclusion, this study advances the use of NLP genetic resources and the understanding of molecular evolution in cereals.

Nitrate Signaling and Its Role in Regulating Flowering Time in Arabidopsis thaliana

Plant growth is coordinated with the availability of nutrients that ensure its development. Nitrate is a major source of nitrogen (N), an essential macronutrient for plant growth. It also acts as a signaling molecule to modulate gene expression, metabolism, and a variety of physiological processes. Recently, it has become evident that the calcium signal appears to be part of the nitrate signaling pathway. New key players have been discovered and described in Arabidopsis thaliana (Arabidopsis). In addition, knowledge of the molecular mechanisms of how N signaling affects growth and development, such as the nitrate control of the flowering process, is increasing rapidly. Here, we review recent advances in the identification of new components involved in nitrate signal transduction, summarize newly identified mechanisms of nitrate signaling-modulated flowering time in Arabidopsis, and suggest emerging concepts and existing open questions that will hopefully be informative for further discoveries.

Genome-wide identification of nitrate transporter 1/peptide transporter family (NPF) induced by arbuscular mycorrhiza in the maize genome

The Transporter 1/Peptide Transporter Family (NPF) is essential for the uptake and transport of nitrate nitrogen. Significant increases in nitrogen have been increasingly reported for many mycorrhizal plants, but there are few reports on maize. Here, we have identified the maize NPF family and screened for arbuscular mycorrhiza fungi (AMF) induced NPFs. In this study, a systematic analysis of the maize NPF gene family was performed. A total of 82 NPF genes were identified in maize. ZmNPF4.5 was strongly induced by AMF in both low and high nitrogen. Lotus japonicus hairy root-induced transformation experiments showed that ZmNPF4.5 promoter-driven GUS activity was restricted to cells containing tufts. Yeast backfill experiments indicate that ZmNPF4.5 functions in nitrate uptake. Therefore, we speculate that ZmNPF4.5 is a key gene for nitrate-nitrogen uptake in maize through the mycorrhizal pathway. This is a reference value for further exploring the acquisition of nitrate-nitrogen by maize through AMF pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01464-3.

Redox regulation in primary nitrate response: Nitric oxide in the spotlight

Nitrogen (N) is the main macronutrient of plants that determines growth and productivity. Nitrate is the major source form of N in soils and its uptake and assimilatory pathway has been extensively studied. The early events that occur after the perception of nitrate is known as primary nitrate response (PNR). In this review, new findings on the redox signal that impacts PNR are discussed. We will focus on the novel role of Nitric Oxide (NO) as a signal molecule and the mechanisms that are involved to control NO homeostasis during PNR. Moreover, the role of Reactive Oxygen Species (ROS) and the possible interplay with NO in the PNR are discussed. The sources of NO during PNR will be analyzed as well as the regulation of its intracellular levels. Furthermore, we explored the relevance of the direct action of NO through the S-nitrosation of the transcription factor NLP7, one of the master regulators in the nitrate signaling cascade. This review gives rise to an interesting field with new actors to mark future research directions. This allows us to increase the knowledge of the physiological and molecular fine-tuned modulation during nitrate signaling processes in plants. The discussion of new experimental data will stimulate efforts to further refine our understanding of the redox regulation of nitrate signaling.

Microbe-dependent and independent nitrogen and phosphate acquisition and regulation in plants

Nitrogen (N) and phosphorus (P) are the most important macronutrients required for plant growth and development. To cope with the limited and uneven distribution of N and P in complicated soil environments, plants have evolved intricate molecular strategies to improve nutrient acquisition that involve adaptive root development, production of root exudates, and the assistance of microbes. Recently, great advances have been made in understanding the regulation of N and P uptake and utilization and how plants balance the direct uptake of nutrients from the soil with the nutrient acquisition from beneficial microbes such as arbuscular mycorrhiza. Here, we summarize the major advances in these areas and highlight plant responses to changes in nutrient availability in the external environment through local and systemic signals.

Reviewing impacts of biotic and abiotic stresses on the regulation of phosphate homeostasis in plants

Adapting to varying phosphate levels in the environment is vital for plant growth. The PHR1 phosphate starvation response transcription factor family, along with SPX inhibitors, plays a pivotal role in plant phosphate responses. However, this regulatory hub intricately links with diverse biotic and abiotic signaling pathways, as outlined in this review. Understanding these intricate networks is crucial, not only on a fundamental level but also for practical applications, such as enhancing sustainable agriculture and optimizing fertilizer efficiency. This comprehensive review explores the multifaceted connections between phosphate homeostasis and environmental stressors, including various biotic factors, such as symbiotic mycorrhizal associations and beneficial root-colonizing fungi. The complex coordination between phosphate starvation responses and the immune system are explored, and the relationship between phosphate and nitrate regulation in agriculture are discussed. Overall, this review highlights the complex interactions governing phosphate homeostasis in plants, emphasizing its importance for sustainable agriculture and nutrient management to contribute to environmental conservation.

Enough is enough: feedback control of specialized metabolism

Recent advances in our understanding of plant metabolism have highlighted the significance of specialized metabolites in the regulation of gene expression associated with biosynthetic networks. This opinion article focuses on the molecular mechanisms of small-molecule-mediated feedback regulation at the transcriptional level and its potential modes of action, including metabolite signal perception, the nature of the sensor, and the signaling transduction mechanisms leading to transcriptional and post-transcriptional regulation, based on evidence available from plants and other kingdoms of life. We also discuss the challenges associated with identifying the occurrences, effects, and localization of small molecule-protein interactions. Further understanding of small-molecule-controlled metabolic fluxes will enable rational design of transcriptional regulation systems in metabolic engineering to produce high-value specialized metabolites.

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.

Role of GARP family transcription factors in the regulatory network for nitrogen and phosphorus acquisition

The GARP (Golden2, ARR-B, Psr1) family proteins with a conserved DNA-binding domain, called the B-motif, are plant-specific transcription factors involved in the regulation of various physiological processes. The GARP family proteins are divided into members that function as monomeric transcription factors, and members that function as transcription factors in the dimeric form, owing to the presence of a coiled-coil dimerization domain. Recent studies revealed that the dimer-forming GARP family members, which are further divided into the PHR1 and NIGT1 subfamilies, play critical roles in the regulation of phosphorus (P) and nitrogen (N) acquisition. In this review, we present a general overview of the GARP family proteins and discuss how several members of the PHR1 and NIGT1 subfamilies are involved in the coordinated acquisition of P and N in response to changes in environmental nutrient conditions, while mainly focusing on the recent findings that enhance our knowledge of the roles of PHR1 and NIGT1 in phosphate starvation signaling and nitrate signaling.

Phytohormones in a universe of regulatory metabolites: lessons from jasmonate

Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite-protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.

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.

Transceptor NRT1.1 and receptor-kinase QSK1 complex controls PM H+-ATPase activity under low nitrate

NRT1.1, a nitrate transceptor, plays an important role in nitrate binding, sensing, and nitrate-dependent lateral root (LR) morphology. However, little is known about NRT1.1-mediated nitrate signaling transduction through plasma membrane (PM)-localized proteins. Through in-depth phosphoproteome profiling using membranes of Arabidopsis roots, we identified receptor kinase QSK1 and plasma membrane H+-ATPase AHA2 as potential downstream components of NRT1.1 signaling in a mild low-nitrate (LN)-dependent manner. QSK1, as a functional kinase and molecular link, physically interacts with NRT1.1 and AHA2 at LN and specifically phosphorylates AHA2 at S899. Importantly, we found that LN, not high nitrate (HN), induces formation of the NRT1.1-QSK1-AHA2 complex in order to repress the proton efflux into the apoplast by increased phosphorylation of AHA2 at S899. Loss of either NRT1.1 or QSK1 thus results in a higher T947/S899 phosphorylation ratio on AHA2, leading to enhanced pump activity and longer LRs under LN. Our results uncover a regulatory mechanism in which NRT1.1, under LN conditions, promotes coreceptor QSK1 phosphorylation and enhances the NRT1.1-QSK1 complex formation to transduce LN sensing to the PM H+-ATPase AHA2, controlling the phosphorylation ratio of activating and inhibitory phosphorylation sites on AHA2. This then results in altered proton pump activity, apoplast acidification, and regulation of NRT1.1-mediated LR growth.

The LRR receptor-like kinase ALR1 is a plant aluminum ion sensor

Plant survival requires an ability to adapt to differing concentrations of nutrient and toxic soil ions, yet ion sensors and associated signaling pathways are mostly unknown. Aluminum (Al) ions are highly phytotoxic, and cause severe crop yield loss and forest decline on acidic soils which represent ∼30% of land areas worldwide. Here we found an Arabidopsis mutant hypersensitive to Al. The gene encoding a leucine-rich-repeat receptor-like kinase, was named Al Resistance1 (ALR1). Al ions binding to ALR1 cytoplasmic domain recruits BAK1 co-receptor kinase and promotes ALR1-dependent phosphorylation of the NADPH oxidase RbohD, thereby enhancing reactive oxygen species (ROS) generation. ROS in turn oxidatively modify the RAE1 F-box protein to inhibit RAE1-dependent proteolysis of the central regulator STOP1, thus activating organic acid anion secretion to detoxify Al. These findings establish ALR1 as an Al ion receptor that confers resistance through an integrated Al-triggered signaling pathway, providing novel insights into ion-sensing mechanisms in living organisms, and enabling future molecular breeding of acid-soil-tolerant crops and trees, with huge potential for enhancing both global food security and forest restoration.