NRT1.1 Dual-Affinity Nitrate Transport/Signalling and its Roles in Plant Abiotic Stress Resistance

Arabidopsis Ankyrin-Repeat Protein Kinase ANK-PK2 Negatively Regulates Salt Tolerance by Mediating Degradation of the Sugar Transporter Protein STP11

Soluble sugars provide energy sources required for plant growth and development. They also act as osmoprotectants to improve the salt tolerance of plants. However, molecular mechanism underlying the negative regulation of soluble sugar accumulation in plants under salt stress conditions remains unknown. In this study, we investigated the functions of ankyrin-repeat kinase 2 (ANK-PK2) that regulates soluble sugar content in Arabidopsis under salt stress. ANK-PK2 interacts with and phosphorylates the sugar transporter protein 11 (STP11) under salt stress. Phosphorylated STP11 is easier to degrade, and its glucose-transporting ability and soluble sugar accumulation are inhibited. The ank-pk2 mutant exhibited increased salt tolerance. The salt-sensitive phenotype of the mutant stp11 was recovered through a dephosphorylation mutation that changed Thr227 in STP11 to Ala227. Our results revealed a novel molecular mechanism underlying salt stress adaptation in Arabidopsis, which ANK-PK2 negatively regulates salt tolerance by phosphorylating and subsequently decreasing the transport activity of STP11 to balance the cellular soluble sugar content in Arabidopsis.

Functional and Molecular Characterization of Plant Nitrate Transporters Belonging to NPF (NRT1/PTR) 6 Subfamily

Plant nitrate transporters in the NPF (NRT1) family are characterized by multifunctionality and their involvement in a number of physiological processes. The proteins in this family have been identified in many monocotyledonous and dicotyledonous species: a bioinformatic analysis predicts from 20 to 139 members in the plant genomes sequenced so far, including mosses. Plant NPFs are phylogenetically related to proton-coupled oligopeptide transporters, which are evolutionally conserved in all kingdoms of life apart from Archaea. The phylogenetic analysis of the plant NPF family is based on the amino acid sequences present in databases; an analysis identified a separate NPF6 clade (subfamily) with the first plant nitrate transporters studied at the molecular level. The available information proves that proteins of the NPF6 clade play key roles not only in the supply of nitrate and its allocation within different parts of plants but also in the transport of chloride, amino acids, ammonium, and plant hormones such as auxins and ABA. Moreover, members of the NPF6 family participate in the perception of nitrate and ammonium, signaling, plant responses to different abiotic stresses, and the development of tolerance to these stresses and contribute to the structure of the root-soil microbiome composition. The available information allows us to conclude that NPF6 genes are among the promising targets for engineering/editing to increase the productivity of crops and their tolerance to stresses. The present review summarizes the available published data and our own results on members of the NPF6 clade of nitrate transporters, especially under salinity; we outline their molecular, structural, and functional characteristics and suggest potential lines for future research.

Local signal from Trichoderma afroharzianum T22 induces host transcriptome and endophytic microbiome leading to growth promotion in sorghum

Trichoderma, a highly abundant soil fungus, may benefit plants, yet it remains understudied in sorghum (Sorghum bicolor). In this study, sorghum plants were grown for 5 weeks in pots of soil with or without inoculation of T. afroharzianum T22. Inoculation with T. afroharzianum T22 significantly increased growth parameters and nutrient levels, demonstrating its beneficial role in sorghum. A split-root assay demonstrated that T. afroharzianum T22 is essential in both compartments of the pot for promoting plant growth, suggesting that local signals from this fungus drive symbiotic benefits in sorghum. RNA-seq analysis revealed that inoculation with T. afroharzianum T22 induced genes responsible for mineral transport (such as nitrate and aquaporin transporters), auxin response, sugar assimilation (hexokinase), and disease resistance (thaumatin) in sorghum roots. Microbial community analysis further unveiled the positive role of T. afroharzianum T22 in enriching Penicillium and Streptomyces while reducing disease-causing Fusarium in the roots. The microbial consortium, consisting of enriched microbiomes from bacterial and fungal communities, showed disrupted morphological features in plants inoculated with T. afroharzianum T22 in the absence of Streptomyces griseus. However, this disruption was not observed in the absence of Penicillium chrysogenum. These results indicate that S. griseus acts as a helper microbe in close association with T. afroharzianum T22 in the sorghum endosphere. This study provides the first comprehensive explanation of how T. afroharzianum T22 modulates host molecular determinants and endophytic helper microbes, thereby collectively promoting sorghum growth. These findings may facilitate the formulation of synthetic microbial inoculants dominated by T. afroharzianum T22 to enhance growth and stress resilience in sorghum and similar crops.

Screening Key Genes Related to Nitrogen Use Efficiency in Cucumber Through Weighted Gene Co-Expression Network Analysis

Cucumber (Cucumis sativus L.) is a crucial vegetable crop, requiring significant nitrogen fertilizer inputs. However, excessive nitrogen application not only impairs growth but also poses severe environmental risks. Thus, enhancing nitrogen use efficiency (NUE) in cucumber is imperative. For the identification of genes associated with NUE in cucumber, roots of high NUE and low NUE lines were analyzed under high nitrogen conditions. Using transcriptome sequencing through WGCNA, a total of 15,180 genes were categorized into 35 co-expression modules, with 5 modules being highly correlated with NUE. Based on differential expression within the five modules and the results of GO and KEGG enrichment analyses, 25 genes were identified as potentially related to NUE. Among these, CsaV4_1G002492 (GLR22), CsaV4_2G003460 (GLR35), CsaV4_3G000307 (NRT1.1), and CsaV4_7G001709 (UPS2) were homologous to genes in Arabidopsis known to directly participate in NUE related process. These four genes were chosen as key genes for further analysis. qRT-PCR analysis revealed that CsaV4_3G000307 and CsaV4_7G001709 were more active during the early stages of the high nitrogen treatment in the high NUE line. Conversely, CsaV4_1G002492 and CsaV4_2G003460 were more active in the low NUE line. Using transcriptomic analysis, a frameshift INDEL mutation was observed in CsaV4_3G000307 in the low NUE line, which impacted the compactness of the protein structure, potentially altering its function. Analysis of protein interactions of these four key genes predicted some potential interaction networks. This research offers critical insights into the genetic factors influencing NUE in cucumber, presenting potential targets for genetic modification or breeding programs.

Role of SbNRT1.1B in cadmium accumulation is attributed to nitrate uptake and glutathione-dependent phytochelatins biosynthesis

Phytoremediation of cadmium (Cd)-polluted soil by using sweet sorghum displays a tremendous potential as it is a fast-growing, high biomass and Cd tolerant energy plant. Previous study has demonstrated SbNRT1.1B expression change is in accordance with enhanced Cd accumulation by external nitrate supply in sweet sorghum. Nevertheless, underlying mechanism of SbNRT1.1B response to Cd stress is still elusive. SbNRT1.1B exhibited a positive response to Cd stress in sweet sorghum. Overexpressing SbNRT1.1B increased primary root length, shoot fresh weight, nitrate and chlorophyll concentrations compared with Col-0 under Cd stress, while complementary SbNRT1.1B rescued these decreased values in mutant chl1-5. Cd concentrations in overexpressing SbNRT1.1B, complementary SbNRT1.1B and Col-0 lines were 3.2-4.1, 2.5-3.1 and 1.2-2.1 folds of that in chl1-5. Consistent with Cd concentrations, non-protein thiol (NPT), reduced glutathione (GSH) and phytochelatins (PCs) concentrations as well as the related genes expression levels showed the same trends under Cd stress. GSH biosynthesis inhibitor failed to reverse the patterns of GSH-dependent PCs concentrations changes in different lines, suggesting that SbNRT1.1B plays an upstream role in GSH-dependent PCs biosynthesis under Cd treatment. Altogether, SbNRT1.1B enhances nitrate concentrations contributing to increased chlorophyll concentrations and GSH-dependent PCs metabolites biosynthesis, thereby improving growth and Cd concentrations in plants.

Microplastic exposure inhibits nitrate uptake and assimilation in wheat plants

Microplastic (MP) contamination in soil severely impairs plant growth. However, mechanisms underlying the effects of MPs on plant nutrient uptake remain largely unknown. In this study, we revealed that NO3- content was significantly decreased in shoots and roots of wheat plants exposed to high concentrations (50-100 mg L-1) of MPs (1 μm and 0.1 μm; type: polystyrene) in the hydroponic solution. Isotope labeling experiments demonstrated that MP exposure led to a significant inhibition of NO3- uptake in wheat roots. Further analysis indicated that the presence of MPs markedly inhibited root growth and caused oxidative damage to the roots. Additionally, superoxide dismutase and peroxidase activities in wheat roots decreased under all MP treatments, whereas catalase and ascorbate peroxidase activities significantly increased under the 100 mg L-1 MP treatment. The transcription levels of most nitrate transporters (NRTs) in roots were significantly downregulated by MP exposure. Furthermore, exposure to MPs distinctly suppressed the activity of nitrate reductase (NR) and nitrite reductase (NiR), as well as the expression levels of their coding genes in wheat shoots. These findings indicate that a decline in root uptake area and root vitality, as well as in the expression of NRTs, NR, and NiR genes caused by MP exposure may have adverse effects on NO3- uptake and assimilation, consequently impairing normal growth of plants.

Contrasting Alleles of OsNRT1.1b Fostering Potential in Improving Nitrogen Use Efficiency in Rice

Nitrogen use efficiency (NUE) is important for the growth and development of rice and is significant in reducing the costs of rice production. OsNRT1.1b is involved in nitrate assimilation, and the alleles at position 21,759,092 on chromosome 10 clearly separate indica (Pathum Thani 1 (PTT1) and Homcholasit (HCS)) and japonica (Azucena and Leum Pua (LP)) rice varieties. Rice morphological and physiological traits were collected at three nitrogen levels (N0 = 0 kg ha-1, N7 = 43.75 kg ha-1, and N14 = 87.5 kg ha-1). Leaf and tiller numbers in PTT1 and HCS at N7 and N14 were two to three times higher than those at N0. At harvest, the biomass yield in PTT1 was the highest, while the total grain number in HCS was the maximum. The leaf widths and total chlorophyll contents (SPAD units) of Azucena and LP increased with nitrogen application as well as photosynthetic pigment parameters; for example, plant senescence reflectance indices (PSRIs), structure-insensitive pigment indices (SIPIs), and modified chlorophyll absorption ratio indices (MCARIs) were highly related in the japonica varieties. PTT1 and HCS, both carrying the A allele at OsNRT1.1b, had better NUE than Azucena and LP with the G allele. HCS, overall, had better NUE than PTT1. The translation to grain yield of assimilates was remarkable in PTT1 and HCS compared with Azucena and LP. In addition, HCS converted biomass for a 75% higher yield than PTT1. The ability of HCS to produce high yields was achieved even at N7 nitrogen fertilization, manifesting efficient use of nitrogen.

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.

Chitosan microparticles mitigate nitrogen deficiency in tomato plants

Nitrogen (N) deficiency is one of the most prevalent nutrient deficiencies in plants, and has a significant impact on crop yields. In this work we aimed to develop and evaluate innovative strategies to mitigate N deficiency. We studied the effect of supplementing tomato plants grown under suboptimal N nutrition with chitosan microparticles (CS-MPs) during short- and long-term periods. We observed that the supplementation with CS-MPs prevented the reduction of aerial biomass and the elongation of lateral roots (LR) triggered by N deficiency in tomato plantlets. In addition, levels of nitrates, amino acids and chlorophyll, which decreased drastically upon N deficiency, were either partial or totally restored upon CS-MPs addition to N deficient media. Finally, we showed that CS-MPs treatments increased nitric oxide (NO) levels in root tips and caused the up-regulation of genes involved in N metabolism. Altogether, we suggest that CS-MPs enhance the growth and development of tomato plants under N deficiency through the induction of biochemical and transcriptional responses that lead to increased N metabolism. We propose treatments with CS-MPs as an efficient practice focused to mitigate the nutritional deficiencies in N impoverished soils.

Exploring glycine root uptake dynamics in phosphorus and iron deficient tomato plants during the initial stages of plant development

BACKGROUND

Phosphorus (P) and iron (Fe) deficiencies are relevant plants nutritional disorders, prompting responses such as increased root exudation to aid nutrient uptake, albeit at an energy cost. Reacquiring and reusing exudates could represent an efficient energy and nitrogen saving strategy. Hence, we investigated the impact of plant development, Fe and P deficiencies on this process. Tomato seedlings were grown hydroponically for 3 weeks in Control, -Fe, and -P conditions and sampled twice a week. We used Isotope Ratio Mass-Spectrometry to measure δ13C in roots and shoots after a 2-h exposure to 13C-labeled glycine (0, 50, or 500 μmol L-1). Plant physiology was assessed with an InfraRed Gas Analyzer and ionome with an Inductively Coupled Plasma Mass-Spectrometry.

RESULTS

Glycine uptake varied with concentration, suggesting an involvement of root transporters with different substrate affinities. The uptake decreased over time, with -Fe and -P showing significantly higher values as compared to the Control. This highlights its importance during germination and in nutrient-deficient plants. Translocation to shoots declined over time in -P and Control but increased in -Fe plants, suggesting a role of Gly in the Fe xylem transport.

CONCLUSIONS

Root exudates, i.e. glycine, acquisition and their subsequent shoot translocation depend on Fe and P deficiency. The present findings highlight the importance of this adaptation to nutrient deficiencies, that can potentially enhance plants fitness. A thorough comprehension of this trait holds potential significance for selecting cultivars that can better withstand abiotic stresses.

Nutrient levels control root growth responses to high ambient temperature in plants

Global warming will lead to significantly increased temperatures on earth. Plants respond to high ambient temperature with altered developmental and growth programs, termed thermomorphogenesis. Here we show that thermomorphogenesis is conserved in Arabidopsis, soybean, and rice and that it is linked to a decrease in the levels of the two macronutrients nitrogen and phosphorus. We also find that low external levels of these nutrients abolish root growth responses to high ambient temperature. We show that in Arabidopsis, this suppression is due to the function of the transcription factor ELONGATED HYPOCOTYL 5 (HY5) and its transcriptional regulation of the transceptor NITRATE TRANSPORTER 1.1 (NRT1.1). Soybean and Rice homologs of these genes are expressed consistently with a conserved role in regulating temperature responses in a nitrogen and phosphorus level dependent manner. Overall, our data show that root thermomorphogenesis is a conserved feature in species of the two major groups of angiosperms, monocots and dicots, that it leads to a reduction of nutrient levels in the plant, and that it is dependent on environmental nitrogen and phosphorus supply, a regulatory process mediated by the HY5-NRT1.1 module.

Excessive iron deposition in root apoplast is involved in growth arrest of roots in response to low pH

The rhizotoxicity of protons (H+) in acidic soils is a fundamental constraint that results in serious yield losses. However, the mechanisms underlying H+-mediated inhibition of root growth are poorly understood. In this study, we revealed that H+-induced root growth inhibition in Arabidopsis depends considerably on excessive iron deposition in the root apoplast. Reducing such aberrant iron deposition by decreasing the iron supply or disrupting the ferroxidases LOW PHOSPHATE ROOT 1 (LPR) and LPR2 attenuates the inhibitory effect of H+ on primary root growth efficiently. Further analysis showed that excessive iron deposition triggers a burst of highly reactive oxygen species, consequently impairing normal root development. Our study uncovered a valuable strategy for improving the ability of plants to tolerate H+ toxicity by manipulating iron availability.

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

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

Ion and lipid orchestration of secondary active transport

Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.

Molecular switches in plant stress adaptation

Climate change poses a significant threat to the global ecosystem, prompting plants to use various adaptive mechanisms via molecular switches to combat biotic and abiotic stress factors. These switches activate stress-induced pathways by altering their configuration between stable states. In this review, we investigated the regulation of molecular switches in different plant species in response to stress, including the stress-regulated response of multiple switches in Arabidopsis thaliana. We also discussed techniques for developing stress-resilient crops using molecular switches through advanced biotechnological tools. The literature search, conducted using databases such as PubMed, Google Scholar, Web of Science, and SCOPUS, utilized keywords such as molecular switch, plant adaptation, biotic and abiotic stresses, transcription factors, Arabidopsis thaliana, and crop improvement. Recent studies have shown that a single molecular switch can regulate multiple stress networks, and multiple switches can regulate a single stress condition. This multifactorial understanding provides clarity to the switch regulatory network and highlights the interrelationships of different molecular switches. Advanced breeding techniques, along with genomic and biotechnological tools, have paved the way for further research on molecular switches in crop improvement. The use of synthetic biology in molecular switches will lead to a better understanding of plant stress biology and potentially bring forth a new era of stress-resilient, climate-smart crops worldwide.

Genome-Wide Identification of the NRT1 Family Members and Their Expression under Low-Nitrate Conditions in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Nitrate transporters (NRTs) actively take up and transform nitrate (N) to form a large family with many members and distinct functions in plant growth and development. However, few studies have identified them in the context of low nitrate concentrations in Chinese cabbage (Brassica rapa L. ssp. Pekinensis), an important vegetable in China. This study focuses on the identification and analysis of the nitrate transporter 1 (NRT1) gene family as well as various aspects, including its phylogenic distribution, chromosomal position, gene structure, conserved motifs, and duplication pattern. Using bioinformatics methods, we identified and analyzed 84 BrNRT1 genes distributed on ten chromosomes. Furthermore, we conducted an analysis of the expression profile of the NRT1 gene in various tissues of Chinese cabbage exposed to varying nitrate concentrations. A phylogenetic analysis revealed that BrNRT1s members are distributed in six distinct groups. Based on an analysis of gene structure and conserved motifs, it can be inferred that BrNRT1 exhibits a generally conserved structural pattern. The promoters of BrNRT1 were discovered to contain moosefs (MFS) elements, suggesting their potential role in the regulation of NO3- transport across the cell membrane in Chinese cabbage. A transcriptome study and a subsequent RT-qPCR analysis revealed that the expression patterns of some BrNRT1 genes were distinct to specific tissues. This observation implies these genes may contribute to nitrate uptake and transport in various tissues or organs. The results offer fundamental insights into investigating the NRT1 gene family in Chinese cabbage. These results provide basic information for future research on the functional characterization of NRT1 genes in Chinese cabbage and the elucidation of the molecular mechanisms underlying low nitrogen tolerance in Chinese cabbage.

Arabidopsis ecotype Ct-1, with its altered nitrate sensing ability, exhibits enhanced growth under low nitrate conditions in comparison to Col-0

To address the urgent need for sustainable solutions to the increased use of nitrogen fertilizers in agriculture, it is imperative to acquire an in-depth comprehension of the intricate interplay between plants and nitrogen. In this context, our research aimed to elucidate the molecular mechanism behind NO3- sensing/signaling in plants, which can enhance nitrogen utilization efficiency. Previous reports have revealed that the density and quantity of root hairs exhibit responsive behavior to varying levels of NO3-, while the precise molecular mechanisms governing these changes remain elusive. To further investigate this phenomenon, we specifically selected the Ct-1 ecotype, which manifested a greater abundance of root hairs compared to the Col-0 ecotype under conditions of low NO3-. Our investigations unveiled that the dissimilarities in the amino acid sequence of NRT1.1, a transceptor responsible for regulating nitrate signaling and transport, accounted for the observed variation in root hair numbers. These results suggest that NRT1.1 represents a promising target for gene editing technology, offering potential applications in enhancing the efficiency of nitrogen utilization in agricultural crops.

Molecular Cloning, Expression and Transport Activity of SaNPF6.3/SaNRT1.1, a Novel Protein of the Low-Affinity Nitrate Transporter Family from the Euhalophyte Suaeda altissima (L.) Pall

The SaNPF6.3 gene, a putative ortholog of the dual-affinity nitrate (NO3-) transporter gene AtNPF6.3/AtNRT1.1 from Arabidopsis thaliana, was cloned from the euhalophyte Suaeda altissima. The nitrate transporting activity of SaNPF6.3 was studied by heterologous expression of the gene in the yeast Hansenula (Ogataea) polymorpha mutant strain Δynt1 lacking the original nitrate transporter. Expression of SaNPF6.3 in Δynt1 cells rescued their ability to grow on the selective medium in the presence of nitrate and absorb nitrate from this medium. Confocal laser microscopy of the yeast cells expressing the fused protein GFP-SaNPF6.3 revealed GFP (green fluorescent protein) fluorescence localized predominantly in the cytoplasm and/or vacuoles. Apparently, in the heterologous expression system used, only a relatively small fraction of the GFP-SaNPF6.3 reached the plasma membrane of yeast cells. In S. altissima plants grown in media with either low (0.5 mM) or high (15 mM) NO3-; concentrations, SaNPF6.3 was expressed at various ontogenetic stages in different organs, with the highest expression levels in roots, pointing to an important role of SaNPF6.3 in nitrate uptake. SaNPF6.3 expression was induced in roots of nitrate-deprived plants in response to raising the nitrate concentration in the medium and was suppressed when the plants were transferred from sufficient nitrate to the lower concentration. When NaCl concentration in the nutrient solution was elevated, the SaNPF6.3 transcript abundance in the roots increased at the low nitrate concentration and decreased at the high one. We also determined nitrate and chloride concentrations in the xylem sap excreted by detached S. altissima roots as a function of their concentrations in the root medium. Based on a linear increase in Cl- concentrations in the xylem exudate as the external Cl- concentration increased and the results of SaNPF6.3 expression experiments, we hypothesize that SaNPF6.3 is involved in chloride transport along with nitrate transport in S. altissima plants.

Understanding signaling pathways governing the polar development of root hairs in low-temperature, nutrient-deficient environments

Plants exposed to freezing and above-freezing low temperatures must employ a variety of strategies to minimize fitness loss. There is a considerable knowledge gap regarding how mild low temperatures (around 10 °C) affect plant growth and developmental processes, even though the majority of the molecular mechanisms that plants use to adapt to extremely low temperatures are well understood. Root hairs (RH) have become a useful model system for studying how plants regulate their growth in response to both cell-intrinsic cues and environmental inputs. Here, we'll focus on recent advances in the molecular mechanisms underpinning Arabidopsis thaliana RH growth at mild low temperatures and how these discoveries may influence our understanding of nutrient sensing mechanisms by the roots. This highlights how intricately linked mechanisms are necessary for plant development to take place under specific circumstances and to produce a coherent response, even at the level of a single RH cell.

Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction

Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.

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

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

Identification and Functional Characterization of MdNRT1.1 in Nitrogen Utilization and Abiotic Stress Tolerance in Malus domestica

Nitrate is one of the main sources of nitrogen for plant growth. Nitrate transporters (NRTs) participate in nitrate uptake and transport, and they are involved in abiotic stress tolerance. Previous studies have shown that NRT1.1 has a dual role in nitrate uptake and utilization; however, little is known about the function of MdNRT1.1 in regulating apple growth and nitrate uptake. In this study, apple MdNRT1.1, a homolog of Arabidopsis NRT1.1, was cloned and functionally identified. Nitrate treatment induced an increased transcript level of MdNRT1.1, and overexpression of MdNRT1.1 promoted root development and nitrogen utilization. Ectopic expression of MdNRT1.1 in Arabidopsis repressed tolerance to drought, salt, and ABA stresses. Overall, this study identified a nitrate transporter, MdNRT1.1, in apples and revealed how MdNRT1.1 regulates nitrate utilization and abiotic stress tolerance.

Nitric Oxide Regulates Seed Germination by Integrating Multiple Signalling Pathways

Seed germination is of great significance for plant development and crop yield. Recently, nitric oxide (NO) has been shown to not only serve as an important nitrogen source during seed development but also to participate in a variety of stress responses in plants to high salt, drought, and high temperature. In addition, NO can affect the process of seed germination by integrating multiple signaling pathways. However, due to the instability of NO gas activity, the network mechanism for its fine regulation of seed germination remains unclear. Therefore, this review aims to summarize the complex anabolic processes of NO in plants, to analyze the interaction mechanisms between NO-triggered signaling pathways and different plant hormones such as abscisic acid (ABA) and gibberellic acid (GA), ethylene (ET) and reactive oxygen species (ROS) signaling molecules, and to discuss the physiological responses and molecular mechanisms of seeds during the involvement of NO in abiotic stress, so as to provide a reference for solving the problems of seed dormancy release and improving plant stress tolerance.

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins perform an essential role in regulating plant nitrate absorption and distribution and in improving plant nitrogen use efficiency. In this study, cucumber (Cucumis sativus L.) NPF genes were comprehensively analyzed at the whole genome level, and 54 NPF genes were found to be unevenly distributed on seven chromosomes in the cucumber genome. The phylogenetic analysis showed that these genes could be divided into eight subfamilies. We renamed all CsNPF genes according to the international nomenclature, based on their homology with AtNPF genes. By surveying the expression profiles of CsNPF genes in various tissues, we found that CsNPF6.4 was specifically expressed in roots, indicating that CsNPF6.4 may play a role in N absorption; CsNPF6.3 was highly expressed in petioles, which may be related to NO₃^- storage in petioles; and CsNPF2.8 was highly expressed in fruits, which may promote NO₃^- transport to the embryos. We further examined their expression patterns under different abiotic stress and nitrogen conditions, and found that CsNPF7.2 and CsNPF7.3 responded to salt, cold, and low nitrogen stress. Taken together, our study lays a foundation for further exploration of the molecular and physiological functions of cucumber nitrate transporters.

PuHox52 promotes coordinated uptake of nitrate, phosphate, and iron under nitrogen deficiency in Populus ussuriensis

It is of great importance to better understand how trees regulate nitrogen (N) uptake under N deficiency conditions which severely challenge afforestation practices, yet the underlying molecular mechanisms have not been well elucidated. Here, we functionally characterized PuHox52, a Populus ussuriensis HD-ZIP transcription factor, whose overexpression greatly enhanced nutrient uptake and plant growth under N deficiency. We first conducted an RNA sequencing experiment to obtain root transcriptome using PuHox52-overexpression lines of P. ussuriensis under low N treatment. We then performed multiple genetic and phenotypic analyses to identify key target genes of PuHox52 and validated how they acted against N deficiency under PuHox52 regulation. PuHox52 was specifically induced in roots by N deficiency, and overexpression of PuHox52 promoted N uptake, plant growth, and root development. We demonstrated that several nitrate-responsive genes (PuNRT1.1, PuNRT2.4, PuCLC-b, PuNIA2, PuNIR1, and PuNLP1), phosphate-responsive genes (PuPHL1A and PuPHL1B), and an iron transporter gene (PuIRT1) were substantiated to be direct targets of PuHox52. Among them, PuNRT1.1, PuPHL1A/B, and PuIRT1 were upregulated to relatively higher levels during PuHox52-mediated responses against N deficiency in PuHox52-overexpression lines compared to WT. Our study revealed a novel regulatory mechanism underlying root adaption to N deficiency where PuHox52 modulated a coordinated uptake of nitrate, phosphate, and iron through 'PuHox52-PuNRT1.1', 'PuHox52-PuPHL1A/PuPHL1B', and 'PuHox52-PuIRT1' regulatory relationships in poplar roots.

Insights on Phytohormonal Crosstalk in Plant Response to Nitrogen Stress: A Focus on Plant Root Growth and Development

Nitrogen (N) is a vital mineral component that can restrict the growth and development of plants if supplied inappropriately. In order to benefit their growth and development, plants have complex physiological and structural responses to changes in their nitrogen supply. As higher plants have multiple organs with varying functions and nutritional requirements, they coordinate their responses at the whole-plant level based on local and long-distance signaling pathways. It has been suggested that phytohormones are signaling substances in such pathways. The nitrogen signaling pathway is closely associated with phytohormones such as auxin (AUX), abscisic acid (ABA), cytokinins (CKs), ethylene (ETH), brassinosteroid (BR), strigolactones (SLs), jasmonic acid (JA), and salicylic acid (SA). Recent research has shed light on how nitrogen and phytohormones interact to modulate physiology and morphology. This review provides a summary of the research on how phytohormone signaling affects root system architecture (RSA) in response to nitrogen availability. Overall, this review contributes to identifying recent developments in the interaction between phytohormones and N, as well as serving as a foundation for further study.

Flexible response and rapid recovery strategies of the plateau forage Poa crymophila to cold and drought

Cold and drought stress are the two most severe abiotic stresses in alpine regions. Poa crymophila is widely grown in the Qinghai-Tibet Plateau with strong tolerance. Here, by profiling gene expression patterns and metabolomics-associated transcriptomics co-expression network, the acclimation of Poa crymophila to the two stresses was characterized. (1) The genes and metabolites with stress tolerance were induced by cold and drought, while those related with growth were inhibited, and most of them were restored faster after stresses disappeared. In particular, the genes for the photosynthesis system had strong resilience. (2) Additionally, cold and drought activated hypoxia and UV-B adaptation genes, indicating long-term life on the plateau could produce special adaptations. (3) Phenolamines, polyamines, and amino acids, especially N',N″,N'″-p-coumaroyl-cinnamoyl-caffeoyl spermidine, putrescine, and arginine, play key roles in harsh environments. Flexible response and quick recovery are strategies for adaptation to drought and cold in P. crymophila, accounting for its robust tolerance and resilience. In this study, we presented a comprehensive stress response profile of P. crymophila and provided many candidate genes or metabolites for future forage improvement.

Structural and functional analysis of stress-inducible genes and their promoters selected from young oil palm (Elaeis guineensis) under salt stress

Background

Soil salinity is a problem in more than 100 countries across all continents. It is one of the abiotic stress that threatens agriculture the most, negatively affecting crops and reducing productivity. Transcriptomics is a technology applied to characterize the transcriptome in a cell, tissue, or organism at a given time via RNA-Seq, also known as full-transcriptome shotgun sequencing. This technology allows the identification of most genes expressed at a particular stage, and different isoforms are separated and transcript expression levels measured. Once determined by this technology, the expression profile of a gene must undergo validation by another, such as quantitative real-time PCR (qRT-PCR). This study aimed to select, annotate, and validate stress-inducible genes—and their promoters—differentially expressed in the leaves of oil palm (Elaeis guineensis) plants under saline stress.

Results

The transcriptome analysis led to the selection of 14 genes that underwent structural and functional annotation, besides having their expression validated using the qRT-PCR technique. When compared, the RNA-Seq and qRT-PCR profiles of those genes resulted in some inconsistencies. The structural and functional annotation analysis of proteins coded by the selected genes showed that some of them are orthologs of genes reported as conferring resistance to salinity in other species. There were those coding for proteins related to the transport of salt into and out of cells, transcriptional regulatory activity, and opening and closing of stomata. The annotation analysis performed on the promoter sequence revealed 22 distinct types of cis-acting elements, and 14 of them are known to be involved in abiotic stress.

Conclusion

This study has helped validate the process of an accurate selection of genes responsive to salt stress with a specific and predefined expression profile and their promoter sequence. Its results also can be used in molecular-genetics-assisted breeding programs. In addition, using the identified genes is a window of opportunity for strategies trying to relieve the damages arising from the salt stress in many glycophyte crops with economic importance.

Inhibition of shoot-expressed NRT1.1 improves reutilization of apoplastic iron under iron-deficient conditions

Iron deficiency is a major constraint for plant growth in calcareous soils. The interplay between NO₃ ^- and Fe nutrition affects plant performance under Fe-deficient conditions. However, how NO₃ ^- negatively regulates Fe nutrition at the molecular level in plants remains elusive. Here, we showed that the key nitrate transporter NRT1.1 in Arabidopsis plants, especially in the shoots, was markedly downregulated at post-translational levels by Fe deficiency. However, loss of NRT1.1 function alleviated Fe deficiency chlorosis, suggesting that downregulation of NRT1.1 by Fe deficiency favors plant tolerance to Fe deficiency. Further analysis showed that although disruption of NRT1.1 did not alter Fe levels in both the shoots and roots, it improved the reutilization of apoplastic Fe in shoots but not in roots. In addition, disruption of NRT1.1 prevented Fe deficiency-induced apoplastic alkalization in shoots by inhibiting apoplastic H⁺ depletion via NO₃ ^- uptake. In vitro analysis showed that reduced pH facilitates release of cell wall-bound Fe. Thus, foliar spray with an acidic buffer promoted the reutilization of Fe in the leaf apoplast to enhance plant tolerance to Fe deficiency, while the opposite was true for the foliar spray with a neutral buffer. Thus, downregulation of the shoot-part function of NRT1.1 prevents apoplastic alkalization to ensure the reutilization of apoplastic Fe under Fe-deficient conditions. Our findings may provide a basis for elucidating the link between N and Fe nutrition in plants and insight to scrutinize the relevance of shoot-expressed NRT1.1 to the plant response to stress.

Nitrogen in plants: from nutrition to the modulation of abiotic stress adaptation

Nitrogen is one of the most important nutrient for plant growth and development; it is strongly associated with a variety of abiotic stress responses. As sessile organisms, plants have evolved to develop efficient strategies to manage N to support growth when exposed to a diverse range of stressors. This review summarizes the recent progress in the field of plant nitrate (NO3-) and ammonium (NH4+) uptake, which are the two major forms of N that are absorbed by plants. We explore the intricate relationship between NO3-/NH4+ and abiotic stress responses in plants, focusing on stresses from nutrient deficiencies, unfavorable pH, ions, and drought. Although many molecular details remain unclear, research has revealed a number of core signaling regulators that are associated with N-mediated abiotic stress responses. An in-depth understanding and exploration of the molecular processes that underpin the interactions between N and abiotic stresses is useful in the design of effective strategies to improve crop growth, development, and productivity.

Nitrogen use efficiency (NUE): elucidated mechanisms, mapped genes and gene networks in maize (Zea mays L.)

Nitrogen, the vital primary plant growth nutrient at deficit soil conditions, drastically affects the growth and yield of a crop. Over the years, excess use of inorganic nitrogenous fertilizers resulted in pollution, eutrophication and thereby demanding the reduction in the use of chemical fertilizers. Being a C₄ plant with fibrous root system and high NUE, maize can be deployed to be the best candidate for better N uptake and utilization in nitrogen deficient soils. The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits. Adoption of single cross maize hybrids as well as inherent property of high NUE has helped maize cultivars to achieve the highest growth rate among the cereals during last decade. Further, considering the high cost of nitrogenous fertilizers, adverse effects on soil health and environmental impact, maize improvement demands better utilization of existing genetic variation for NUE via introgression of novel allelic combinations in existing cultivars. Marker assisted breeding efforts need to be supplemented with introgression of genes/QTLs related to NUE in ruling varieties and thereby enhancing the overall productivity of maize in a sustainable manner. To achieve this, we need mapped genes and network of interacting genes and proteins to be elucidated. Identified genes may be used in screening ideal maize genotypes in terms of better physiological functionality exhibiting high NUE. Future genome editing may help in developing lines with increased productivity under low N conditions in an environment of optimum agronomic practices.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01113-z.

Regulation of Nitrate (NO3) Transporters and Glutamate Synthase-Encoding Genes under Drought Stress in Arabidopsis: The Regulatory Role of AtbZIP62 Transcription Factor

Nitrogen (N) is an essential macronutrient, which contributes substantially to the growth and development of plants. In the soil, nitrate (NO3) is the predominant form of N available to the plant and its acquisition by the plant involves several NO3 transporters; however, the mechanism underlying their involvement in the adaptive response under abiotic stress is poorly understood. Initially, we performed an in silico analysis to identify potential binding sites for the basic leucine zipper 62 transcription factor (AtbZIP62 TF) in the promoter of the target genes, and constructed their protein-protein interaction networks. Rather than AtbZIP62, results revealed the presence of cis-regulatory elements specific to two other bZIP TFs, AtbZIP18 and 69. A recent report showed that AtbZIP62 TF negatively regulated AtbZIP18 and AtbZIP69. Therefore, we investigated the transcriptional regulation of AtNPF6.2/NRT1.4 (low-affinity NO3 transporter), AtNPF6.3/NRT1.1 (dual-affinity NO3 transporter), AtNRT2.1 and AtNRT2.2 (high-affinity NO3 transporters), and AtGLU1 and AtGLU2 (both encoding glutamate synthase) in response to drought stress in Col-0. From the perspective of exploring the transcriptional interplay of the target genes with AtbZIP62 TF, we measured their expression by qPCR in the atbzip62 (lacking the AtbZIP62 gene) under the same conditions. Our recent study revealed that AtbZIP62 TF positively regulates the expression of AtPYD1 (Pyrimidine 1, a key gene of the de novo pyrimidine biosynthesis pathway know to share a common substrate with the N metabolic pathway). For this reason, we included the atpyd1-2 mutant in the study. Our findings revealed that the expression of AtNPF6.2/NRT1.4, AtNPF6.3/NRT1.1 and AtNRT2.2 was similarly regulated in atzbip62 and atpyd1-2 but differentially regulated between the mutant lines and Col-0. Meanwhile, the expression pattern of AtNRT2.1 in atbzip62 was similar to that observed in Col-0 but was suppressed in atpyd1-2. The breakthrough is that AtNRT2.2 had the highest expression level in Col-0, while being suppressed in atbzip62 and atpyd1-2. Furthermore, the transcript accumulation of AtGLU1 and AtGLU2 showed differential regulation patterns between Col-0 and atbzip62, and atpyd1-2. Therefore, results suggest that of all tested NO3 transporters, AtNRT2.2 is thought to play a preponderant role in contributing to NO3 transport events under the regulatory influence of AtbZIP62 TF in response to drought stress.