GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways

The centrality of redox regulation and sensing of reactive oxygen species in abiotic and biotic stress acclimatization

During land plant evolution, the number of genes encoding for components of the thiol redox regulatory network and the generator systems of reactive oxygen species (ROS) expanded, tentatively indicating that they have a role in tailored environmental acclimatization. This hypothesis has been validated both experimentally and theoretically during the last few decades. Recent developments of dynamic redox-sensitive GFP (roGFP)-based in vivo sensors for H2O2 and the redox potential of the glutathione pool have paved the way for dissecting the kinetics changes that occur in these crucial parameters in response to environmental stressors. The versatile cellular redox sensory and response regulatory system monitors alterations in redox metabolism and controls the activity of redox target proteins, and thereby affects most, if not all, cellular processes ranging from transcription to translation and metabolism. This review uses examples to describe the role of the redox- and ROS-dependent regulatory network in realising the appropriate responses to diverse environmental stresses. The selected case studies concern different environmental challenges, namely excess excitation energy, the heavy metal cadmium and the metalloid arsenic, nitrogen or phosphate shortages as examples for nutrient deficiency, wounding, and nematode infestation. Each challenge affects the redox-regulatory and ROS network, but our present state of knowledge also points toward pressing questions that remain open in relation to the translation of redox regulation to environmental acclimatization.

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.

Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana

MOTIVATIONS

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

RESULTS

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

AVAILABILITY AND IMPLEMENTATION

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

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.

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

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

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

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

Recent advances in unraveling the mystery of combined nutrient stress in plants

Efficiently regulating growth to adapt to varying resource availability is crucial for organisms, including plants. In particular, the acquisition of essential nutrients is vital for plant development, as a shortage of just one nutrient can significantly decrease crop yield. However, plants constantly experience fluctuations in the presence of multiple essential mineral nutrients, leading to combined nutrient stress conditions. Unfortunately, our understanding of how plants perceive and respond to these multiple stresses remains limited. Unlocking this mystery could provide valuable insights and help enhance plant nutrition strategies. This review focuses specifically on the regulation of phosphorous homeostasis in plants, with a primary emphasis on recent studies that have shed light on the intricate interactions between phosphorous and other essential elements, such as nitrogen, iron, and zinc, as well as non-essential elements like aluminum and sodium. By summarizing and consolidating these findings, this review aims to contribute to a better understanding of how plants respond to and cope with combined nutrient stress.

Phosphorus/nitrogen sensing and signaling in diverse root-fungus symbioses

Establishing mutualistic relationships between plants and fungi is crucial for overcoming nutrient deficiencies in plants. This review highlights the intricate nutrient sensing and uptake mechanisms used by plants in response to phosphate and nitrogen starvation, as well as their interactions with plant immunity. The coordination of transport systems in both host plants and fungal partners ensures efficient nutrient uptake and assimilation, contributing to the long-term maintenance of these mutualistic associations. It is also essential to understand the distinct responses of fungal partners to external nutrient levels and forms, as they significantly impact the outcomes of symbiotic interactions. Our review also highlights the importance of evolutionarily younger and newly discovered root-fungus associations, such as endophytic associations, which offer potential benefits for improving plant nutrition. Mechanistic insights into the complex dynamics of phosphorus and nitrogen sensing within diverse root-fungus associations can facilitate the identification of molecular targets for engineering symbiotic systems and developing plant phenotypes with enhanced nutrient use efficiency. Ultimately, this knowledge can inform tailored fertilizer management practices to optimize plant nutrition.

Transcriptional survey of abiotic stress response in maize (Zea mays) in the level of gene co-expression network and differential gene correlation analysis

Abstract. Maize may be exposed to several abiotic stresses in the field. Therefore, identifying the tolerance mechanisms of natural field stress is mandatory. Gene expression data of maize upon abiotic stress were collected, and 560 differentially expressed genes (DEGs) were identified through meta-analysis. The most significant gene ontology terms in up-regulated genes were 'response to abiotic stress' and 'chitinase activity'. 'Phosphorelay signal transduction system' was the most significant enriched biological process in down-regulated DEGs. The co-expression analysis unveiled seven modules of DEGs, with a notable positive correlation between the modules and abiotic stress. Furthermore, the statistical significance was strikingly high for the turquoise, green and yellow modules. The turquoise group played a central role in orchestrating crucial adaptations in metabolic and stress response pathways in maize when exposed to abiotic stress. Within three up-regulated modules, Zm.7361.1.A1_at, Zm.10386.1.A1_a_at and Zm.10151.1.A1_at emerged as hub genes. These genes might introduce novel candidates implicated in stress tolerance mechanisms, warranting further comprehensive investigation and research. In parallel, the R package glmnet was applied to fit a logistic LASSO regression model on the DEGs profile to select candidate genes associated with abiotic responses in maize. The identified hub genes and LASSO regression genes were validated on an independent microarray dataset. Additionally, Differential Gene Correlation Analysis (DGCA) was performed on LASSO and hub genes to investigate the gene-gene regulatory relationship. The P value of DGCA of 16 pairwise gene comparisons was lower than 0.01, indicating a gene-gene significant change in correlation between control and abiotic stress. Integrated weighted gene correlation network analysis and logistic LASSO analysis revealed Zm.11185.1.S1_at, Zm.2331.1.S1_x_at and Zm.17003.1.S1_at. Notably, these 3 genes were identified in the 16 gene-pair comparisons. This finding highlights the notable significance of these genes in the abiotic stress response. Additional research into maize stress tolerance may focus on these three genes.

Melatonin activates the OsbZIP79-OsABI5 module that orchestrates nitrogen and ROS homeostasis to alleviate nitrogen-limitation stress in rice

Melatonin (Mel) has previously been reported to effectively alleviate nitrogen-limitation (N-L) stress and thus increase nitrogen-use efficiency (NUE) in several plants, but the underlying mechanism remains obscure. Here, we revealed that OsbZIP79 (BASIC LEUCINE ZIPPER 79) is transcriptionally activated under N-L conditions, and its expression is further enhanced by exogenous Mel. By the combined use of omics, genetics, and biological techniques, we revealed that the OsbZIP79-OsABI5 (ABSCISIC ACID INSENSITIVE 5) module stimulated regulation of reactive oxygen species (ROS) homeostasis and the uptake and metabolism of nitrogen under conditions of indoor nitrogen limitation (1/16 normal level). OsbZIP79 activated the transcription of OsABI5, and OsABI5 then bound to the promoters of target genes, including genes involved in ROS homeostasis and nitrogen metabolism, activating their transcription. This module was also indispensable for upregulation of several other genes involved in abscisic acid catabolism, nitrogen uptake, and assimilation under N-L and Mel treatment, although these genes were not directly transactivated by OsABI5. Field experiments demonstrated that Mel significantly improved rice growth under low nitrogen (L-N, half the normal level) by the same mechanism revealed in the nitrogen-limitation study. Mel application produced a 28.6% yield increase under L-N and thus similar increases in NUE. Also, two OsbZIP79-overexpression lines grown in L-N field plots had significantly higher NUE (+13.7% and +21.2%) than their wild types. Together, our data show that an OsbZIP79-OsABI5 module regulates the rice response to N insufficiency (N limitation or low N), which is important for increasing NUE in rice production.

Phase separation-based visualization of protein-protein interactions and kinase activities in plants

Protein activities depend heavily on protein complex formation and dynamic posttranslational modifications, such as phosphorylation. The dynamic nature of protein complex formation and posttranslational modifications is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to assay protein-protein interactions (PPIs) (separation of phases-based protein interaction reporter) and kinase activities (separation of phases-based activity reporter of kinase) in planta, based on phase separation. This technology enabled easy detection of inducible, binary and ternary PPIs among cytoplasmic and nuclear proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SNF1-related kinase 1 activity, allowing us to visualize tissue-specific, dynamic SnRK1 activity in stable transgenic Arabidopsis (Arabidopsis thaliana) plants. The SYMPL cloning toolbox provides a means to explore PPIs, phosphorylation, and other posttranslational modifications with unprecedented ease and sensitivity.

Nitrogen supply alleviates cold stress by increasing photosynthesis and nitrogen assimilation in maize seedlings

Cold stress inhibits the early growth of maize, leading to reduced productivity. Nitrogen (N) is an essential nutrient that stimulates maize growth and productivity, but the relationship between N availability and cold tolerance is poorly characterized. Therefore, we studied the acclimation of maize under combined cold stress and N treatments. Exposure to cold stress caused a decline in growth and N assimilation, but increased abscisic acid (ABA) and carbohydrate accumulation. The application of different N concentrations from the priming stage to the recovery period resulted in the following observations: (i) high N supply alleviated cold stress-dependent growth inhibition, as shown by increased biomass, chlorophyll and Rubisco content and PSII efficiency; (ii) cold stress-induced ABA accumulation was repressed under high N, presumably due to enhanced stomatal conductance; (iii) the mitigating effects of high N on cold stress could be due to the increased activities of N assimilation enzymes and improved redox homeostasis. After cold stress, the ability of maize seedlings to recover increased under high N treatment, indicating the potential role of high N in the cold stress tolerance of maize seedlings.

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

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

Derived Polymorphic Amplified Cleaved Sequence (dPACS) Assay

The derived polymorphic amplified cleaved sequence (dPACS) assay is a simple polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP)-based procedure for detecting known single-nucleotide polymorphisms (SNPs) and deletion-insertion polymorphisms (DIPs). It is relatively straightforward to carry out using basic and commonly available molecular biology kits. The method differs from other PCR-RFLP assays in that it employs 35-55 bp primer pairs that encompass the entire targeted DNA region except for a few diagnostic nucleotides being examined. In so doing, it allows for the introduction of nucleotide mismatches in one or both primers for differentiating wild from mutant sequences following polymerase chain reaction, restriction digestion and MetaPhor gel electrophoresis. Primer design and the selection of discriminating enzymes are achieved with the help of the dPACS 1.0 program. The method is exemplified here with the positive detection of serine 264-psbA, a key determinant for the effective binding of some photosystem II inhibitors to their target. A serine-to-glycine mutation at codon 264 of psbA causes resistance to serine-binding photosystem II herbicides in several grasses and broad-leaf weeds, including Amaranthus retroflexus, which is employed in this study.

Integration of reactive oxygen species and nutrient signalling to shape root system architecture

Yield losses due to nutrient deficiency are estimated as the primary cause of the yield gap worldwide. Understanding how plant roots perceive external nutrient status and elaborate morphological adaptations in response to it is necessary to develop reliable strategies to increase crop yield. In the last decade, reactive oxygen species (ROS) were shown to be key players of the mechanisms underlying root responses to nutrient limitation. ROS contribute in multiple ways to shape the root system in response to nutritional cues, both as direct effectors acting on cell wall architecture and as second messengers in signalling pathways. Here, we review the mutual interconnections existing between perception and signalling of the most common forms of the major macronutrients (nitrogen, phosphorus and potassium), and ROS in shaping plant root system architecture. We discuss recent advances in dissecting the integration of these elements and their impact on morphological traits of the root system, highlighting the functional ductility of ROS and enzymes implied in ROS metabolism, such as class III peroxidases.

The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells

The TARGET system allows for the rapid identification of direct regulated gene targets of transcription factors (TFs). It employs the transient transformation of plant protoplasts with inducible nuclear entry of the TF and subsequent transcriptomic and/or ChIP-seq analysis. The ability to separate direct TF-target gene regulatory interactions from indirect downstream responses and the significantly shorter amount of time required to perform the assay, compared to the generation of transgenics, make this plant cell-based approach a valuable tool for a higher throughput approach to identify the genome-wide targets of multiple TFs, to build validated transcriptional networks in plants. Here, we describe the use of the TARGET system in Arabidopsis seedling root protoplasts to map the gene regulatory network downstream of transcription factors-of-interest.

Nitrogen-inducible GLK1 modulates phosphate starvation response via the PHR1-dependent pathway

Phosphorus (P) is a limiting nutrient for plant growth and productivity. Thus, a deep understanding of the molecular mechanisms of plants' response to phosphate starvation is significant when breeding crops with higher phosphorus-use efficiency. Here, we found that GARP-type transcription factor GLK1 acted as a positive regulator for phosphate-starvation response (PSR) via the PHR1-dependent pathway in Arabidopsis thaliana. GLK1 increased the transcription activity of PHR1 through the direct physical interaction and regulated the multiple responses to inorganic orthophosphate (Pi) starvation. Nitrogen (N) is a key factor in the regulation of PSR. We also found that the N status controlled the function of the GLK1-PHR1 signaling module under Pi-deficient (LP) conditions by regulating the accumulation of GLK1 and PHR1. Ultimately, we showed that the presence of GLK1 effectively promoted the protein accumulation of PHR1 at low N concentrations, and this action was helpful to maintain the activation of PSR. According to these findings, we establish the working model for GLK1 in PSR and propose that GLK1 mediates the interaction between N and P by influencing the effect of N on PHR1 in Arabidopsis thaliana.

Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed

The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed.

LjNRT2.3 plays a hierarchical role in the control of high affinity transport system for root nitrate acquisition in Lotus japonicus

Nitrate is a key mineral nutrient required for plant growth and development. Plants have evolved sophisticated mechanisms to respond to changes of nutritional availability in the surrounding environment and the optimization of root nitrate acquisition under nitrogen starvation is crucial to cope with unfavoured condition of growth. In this study we present a general description of the regulatory transcriptional and spatial profile of expression of the Lotus japonicus nitrate transporter NRT2 family. Furthermore, we report a phenotypic characterization of two independent Ljnrt2.3 knock out mutants indicating the involvement of the LjNRT2.3 gene in the root nitrate acquisition and lateral root elongation pathways occurring in response to N starvation conditions. We also report an epistatic relationship between LjNRT2.3 and LjNRT2.1 suggesting a combined mode of action of these two genes in order to optimize the Lotus response to a prolonged N starvation.

GAF domain is essential for nitrate-dependent AtNLP7 function

Nitrate is an essential nutrient and an important signaling molecule in plants. However, the molecular mechanisms by which plants perceive nitrate deficiency signaling are still not well understood. Here we report that AtNLP7 protein transport from the nucleus to the cytoplasm in response to nitrate deficiency is dependent on the N-terminal GAF domain. With the deletion of the GAF domain, AtNLP7^ΔGAF always remains in the nucleus regardless of nitrate availability. AtNLP7 ^ΔGAF also shows reduced activation of nitrate-induced genes due to its impaired binding to the nitrate-responsive cis-element (NRE) as well as decreased growth like nlp7-1 mutant. In addition, AtNLP7^ΔGAF is unable to mediate the reduction of reactive oxygen species (ROS) accumulation upon nitrate treatment. Our investigation shows that the GAF domain of AtNLP7 plays a critical role in the sensing of nitrate deficiency signal and in the nitrate-triggered ROS signaling process.

Glutamate: A multifunctional amino acid in plants

Glutamate (Glu) is a versatile metabolite and a signaling molecule in plants. Glu biosynthesis is associated with the primary nitrogen assimilation pathway. The conversion between Glu and 2-oxoglutarate connects Glu metabolism to the tricarboxylic acid cycle, carbon metabolism, and energy production. Glu is the predominant amino donor for transamination reactions in the cell. In addition to protein synthesis, Glu is a building block for tetrapyrroles, glutathione, and folate. Glu is the precursor of γ-aminobutyric acid that plays an important role in balancing carbon/nitrogen metabolism and various cellular processes. Glu can conjugate to the major auxin indole 3-acetic acid (IAA), and IAA-Glu is destined for oxidative degradation. Glu also conjugates with isochorismate for the production of salicylic acid. Accumulating evidence indicates that Glu functions as a signaling molecule to regulate plant growth, development, and defense responses. The ligand-gated Glu receptor-like proteins (GLRs) mediate some of these responses. However, many of the Glu signaling events are GLR-independent. The receptor perceiving extracellular Glu as a danger signal is still unknown. In addition to GLRs, Glu may act on receptor-like kinases or receptor-like proteins to trigger immune responses. Glu metabolism and Glu signaling may entwine to regulate growth, development, and defense responses in plants.

Autophagic pathway contributes to low-nitrogen tolerance by optimizing nitrogen uptake and utilization in tomato

Autophagy is a primary process involved in the degradation and reuse of redundant or damaged cytoplasmic components in eukaryotes. Autophagy has been demonstrated to facilitate nutrient recycling and remobilization by delivering intracellular materials to the vacuole for degradation in plants under nutrient starvation. However, the role of autophagy in nitrogen (N) uptake and utilization remains unknown. Here, we report that the ATG6-dependent autophagic pathway regulates N utilization in tomato (Solanum lycopersicum) under low-nitrogen (LN) conditions. Autophagy-disrupted mutants exhibited weakened biomass production and N accumulation compared with wild-type (WT), while ATG6 overexpression promoted autophagy and biomass production under LN stress. The N content in atg6 mutants decreased while that in ATG6-overexpressing lines increased due to the control of N transporter gene expression in roots under LN conditions. Furthermore, ATG6-dependent autophagy enhanced N assimilation efficiency and protein production in leaves. Nitrate reductase and nitrite reductase activities and expression were compromised in atg6 mutants but were enhanced in ATG6-overexpressing plants under LN stress. Moreover, ATG6-dependent autophagy increased plant carbon fixation and photosynthetic capacity. The quantum yield of photosystem II, photosynthetic N use efficiency and photosynthetic protein accumulation were compromised in atg6 mutants but were restored in ATG6-overexpressing plants. A WT scion grafted onto atg6 mutant rootstock and an atg6 scion grafted onto WT rootstock both exhibited inhibited LN-induced autophagy and N uptake and utilization. Thus, ATG6-dependent autophagy regulates not only N uptake and utilization as well as carbon assimilation but also nutrient recycling and remobilization in tomato plants experiencing LN stress.

A guanosine tetraphosphate (ppGpp) mediated brake on photosynthesis is required for acclimation to nitrogen limitation in Arabidopsis

Guanosine pentaphosphate and tetraphosphate (together referred to as ppGpp) are hyperphosphorylated nucleotides found in bacteria and the chloroplasts of plants and algae. In plants and algae artificial ppGpp accumulation can inhibit chloroplast gene expression, and influence photosynthesis, nutrient remobilization, growth, and immunity. However, it is so far unknown whether ppGpp is required for abiotic stress acclimation in plants. Here, we demonstrate that ppGpp biosynthesis is necessary for acclimation to nitrogen starvation in Arabidopsis. We show that ppGpp is required for remodeling the photosynthetic electron transport chain to downregulate photosynthetic activity and for protection against oxidative stress. Furthermore, we demonstrate that ppGpp is required for coupling chloroplastic and nuclear gene expression during nitrogen starvation. Altogether, our work indicates that ppGpp is a pivotal regulator of chloroplast activity for stress acclimation in plants.

Adjusting plant nutrient acquisition to fluctuating availability: transcriptional co-regulation of the nitrate and phosphate deprivation responses in roots

This article comments on: Safi A, Medici A, Szponarski W, Martin F, Clement-Vidal A, Marshall-Colon A, Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G. 2021. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. Journal of Experimental Botany 72, 3881–3901.