Integration of nitrogen and potassium signaling

From White to Reddish-Brown: The Anthocyanin Journey in Stropharia rugosoannulata Driven by Auxin and Genetic Regulators

Stropharia rugosoannulata, or wine-cap Stropharia, is a well-known edible mushroom cultivated globally. The pileipellis color is a crucial quality attribute of S. rugosoannulata, exhibiting significant variation throughout its developmental stages. However, the pigment types and regulatory mechanisms behind color variation remain unclear. The metabolome analysis found that the anthocyanin biosynthesis pathway was significantly enriched and anthocyanins accumulated steadily in fruiting bodies during three developmental stages. The pileipellis pigment was extracted, and HPLC-MS confirmed the presence of anthocyanins. Notably, significant differences in anthocyanin content were observed among the various colored varieties. Thus, anthocyanins contribute to the pileipellis color of S. rugosoannulata. Through further investigation, this study elucidated, for the first time, the relationship between the "SrNFYA-SrDRF2" regulatory module and anthocyanin accumulation. Combined multiomics assays and HPLC analysis revealed that auxin functions as a signaling molecule that regulates the accumulation of anthocyanins in the pileipellis. Subsequently, the hub gene of anthranilate synthase for auxin synthesis was identified as SrTRP1, and the transcription factor SrMYB1 was verified as a regulator of SrTRP1, influencing auxin accumulation. These findings provide a valuable resource for the targeted enhancement of the quality of S. rugosoannulata.

Peculiarity of the early metabolomic response in tomato after urea, ammonium or nitrate supply

Nitrogen (N) is the nutrient most applied in agriculture as fertilizer (as nitrate, Nit; ammonium, A; and/or urea, U, forms) and its availability strongly constrains the crop growth and yield. To investigate the early response (24 h) of N-deficient tomato plants to these three N forms, a physiological and molecular study was performed. In comparison to N-deficient plants, significant changes in the transcriptional, metabolomic and ionomic profiles were observed. As a probable consequence of N mobility in plants, a wide metabolic modulation occurred in old leaves rather than in young leaves. The metabolic profile of U and A-treated plants was more similar than Nit-treated plant profile, which in turn presented the lowest metabolic modulation with respect to N-deficient condition. Urea and A forms induced some changes at the biosynthesis of secondary metabolites, amino acids and phytohormones. Interestingly, a specific up-regulation by U and down-regulation by A of carbon synthesis occurred in roots. Along with the gene expression, data suggest that the specific N form influences the activation of metabolic pathways for its assimilation (cytosolic GS/AS and/or plastidial GS/GOGAT cycle). Urea induced an up-concentration of Cu and Mn in leaves and Zn in whole plant. This study highlights a metabolic reprogramming depending on the N form applied, and it also provide evidence of a direct relationship between urea nutrition and Zn concentration. The understanding of the metabolic pathways activated by the different N forms represents a milestone in improving the efficiency of urea fertilization in crops.

Population epigenetics: DNA methylation in the plant omics era

DNA methylation plays an important role in many biological processes. The mechanisms underlying the establishment and maintenance of DNA methylation are well understood thanks to decades of research using DNA methylation mutants, primarily in Arabidopsis (Arabidopsis thaliana) accession Col-0. Recent genome-wide association studies (GWASs) using the methylomes of natural accessions have uncovered a complex and distinct genetic basis of variation in DNA methylation at the population level. Sequencing following bisulfite treatment has served as an excellent method for quantifying DNA methylation. Unlike studies focusing on specific accessions with reference genomes, population-scale methylome research often requires an additional round of sequencing beyond obtaining genome assemblies or genetic variations from whole-genome sequencing data, which can be cost prohibitive. Here, we provide an overview of recently developed bisulfite-free methods for quantifying methylation and cost-effective approaches for the simultaneous detection of genetic and epigenetic information. We also discuss the plasticity of DNA methylation in a specific Arabidopsis accession, the contribution of DNA methylation to plant adaptation, and the genetic determinants of variation in DNA methylation in natural populations. The recently developed technology and knowledge will greatly benefit future studies in population epigenomes.

TOR in plants: Multidimensional regulators of plant growth and signaling pathways

Target Of Rapamycin (TOR) represents a ubiquitous kinase complex that has emerged as a central regulator of cell growth and metabolism in nearly all eukaryotic organisms. TOR is an evolutionarily conserved protein kinase, functioning as a central signaling hub that integrates diverse internal and external cues to regulate a multitude of biological processes. These processes collectively exert significant influence on plant growth, development, nutrient assimilation, photosynthesis, fruit ripening, and interactions with microorganisms. Within the plant domain, the TOR complex comprises three integral components: TOR, RAPTOR, and LST8. This comprehensive review provides insights into various facets of the TOR protein, encompassing its origin, structure, function, and the regulatory and signaling pathways operative in photosynthetic organisms. Additionally, we explore future perspectives related to this pivotal protein kinase.

Can nutrients act as signals under abiotic stress?

Plant cells are in constant communication to coordinate development processes and environmental reactions. Under stressful conditions, such communication allows the plant cells to adjust their activities and development. This is due to intercellular signaling events which involve several components. In plant development, cell-to-cell signaling is ensured by mobile signals hormones, hydrogen peroxide (H2O2), nitric oxide (NO), or hydrogen sulfide (H2S), as well as several transcription factors and small RNAs. Mineral nutrients, including macro and microelements, are determinant factors for plant growth and development and are, currently, recognized as potential signal molecules. This review aims to highlight the role of nutrients, particularly calcium, potassium, magnesium, nitrogen, phosphorus, and iron as signaling components with special attention to the mechanism of response against stress conditions.

Nitrogen-potassium balance improves leaf photosynthetic capacity by regulating leaf nitrogen allocation in apple

Nitrogen (N) and potassium (K) are two important mineral nutrients in regulating leaf photosynthesis. However, the influence of N and K interaction on photosynthesis is still not fully understood. Using a hydroponics approach, we studied the effects of different N and K conditions on the physiological characteristics, N allocation and photosynthetic capacity of apple rootstock M9T337. The results showed that high N and low K conditions significantly reduced K content in roots and leaves, resulting in N/K imbalance, and allocated more N in leaves to non-photosynthetic N. Low K conditions increased biochemical limitation (BL), mesophyll limitation (MCL), and stomatal limitation (SL). By setting different N supplies, lowering N levels under low K conditions increased the proportion of water-soluble protein N (Nw) and sodium dodecyl sulfate-soluble proteins (Ns) by balancing N/K and increased the proportion of carboxylation N and electron transfer N. This increased the maximum carboxylation rate and mesophyll conductance, which reduced MCL and BL and alleviated the low K limitation of photosynthesis in apple rootstocks. In general, our results provide new insights into the regulation of photosynthetic capacity by N/K balance, which is conducive to the coordinated supply of N and K nutrients.

Why do plants blush when they are hungry?

Foliar anthocyanins, as well as other secondary metabolites, accumulate transiently under nutritional stress. A misconception that only nitrogen or phosphorus deficiency induces leaf purpling/reddening has led to overuse of fertilizers that burden the environment. Here, we emphasize that several other nutritional imbalances induce anthocyanin accumulation, and nutrient-specific differences in this response have been reported for some deficiencies. A range of ecophysiological functions have been attributed to anthocyanins. We discuss the proposed functions and signalling pathways that elicit anthocyanin synthesis in nutrient-stressed leaves. Knowledge from the fields of genetics, molecular biology, ecophysiology and plant nutrition is combined to deduce how and why anthocyanins accumulate under nutritional stress. Future research to fully understand the mechanisms and nuances of foliar anthocyanin accumulation in nutrient-stressed crops could be utilized to allow these leaf pigments to act as bioindicators for demand-oriented application of fertilizers. This would benefit the environment, being timely due to the increasing impact of the climate crisis on crop performance.

Genetic regulation of nitrogen use efficiency in Gossypium spp

Cotton (Gossypium spp.) is the most important fibre crop, with desirable characteristics preferred for textile production. Cotton fibre output relies heavily on nitrate as the most important source of inorganic nitrogen (N). However, nitrogen dynamics in extreme environments limit plant growth and lead to yield loss and pollution. Therefore, nitrogen use efficiency (NUE), which involves the utilisation of the 'right rate', 'right source', 'right time', and 'right place' (4Rs), is key for efficient N management. Recent omics techniques have genetically improved NUE in crops. We herein highlight the mechanisms of N uptake and assimilation in the vegetative and reproductive branches of the cotton plant while considering the known and unknown regulatory factors. The phylogenetic relationships among N transporters in four Gossypium spp. have been reviewed. Further, the N regulatory genes that participate in xylem transport and phloem loading are also discussed. In addition, the functions of microRNAs and transcription factors in modulating the expression of target N regulatory genes are highlighted. Overall, this review provides a detailed perspective on the complex N regulatory mechanism in cotton, which would accelerate the research toward improving NUE in crops.

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.

Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice

Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.

Optimum Nitrogen Application Acclimatizes Root Morpho-Physiological Traits and Yield Potential in Rice under Subtropical Conditions

Nitrogen (N) is a highly essential macronutrient for plant root growth and grain yield (GY). To assess the relationship among N, root traits, and the yield of boro (dry season irrigated) rice, a pot experiment was performed in the Department of Agronomy, Bangladesh Agricultural University, Mymensingh, Bangladesh, during the boro rice season of 2020-2021. Three boro rice varieties, namely BRRI dhan29, Hira-2, and Binadhan-10, were planted at four N doses: 0 kg ha^-1 (N₀), 70 kg ha^-1 (N₇₀), 140 kg ha^-1 (N₁₄₀), and 210 kg ha^-1 (N₂₁₀). The experiment was conducted following a completely randomized design with three replicates. The varieties were evaluated for root number (RN), root length (RL), root volume (RV), root porosity (RP), leaf area index (LAI), total dry matter (TDM), and yield. The results indicated that the Binadhan-10, Hira-2, and BRRI dhan29 varieties produced better root characteristics under at the N₁₄₀ and N₂₁₀ levels. A substantial positive association was noticed between the grain yield and the root traits, except for root porosity. Based on the root traits and growth dynamics, Binadhan-10 performed the best at the N₁₄₀ level and produced the highest grain yield (26.96 g pot^-1), followed by Hira-2 (26.35 g pot^-1) and BRRI dhan29 (25.90 g pot^-1).

Transcriptome analysis of sweet potato responses to potassium deficiency

Background

As one of three essential nutrients, potassium is regarded as a main limiting factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of seven major food crops grown worldwide, and is both a nutrient-rich food and a bioenergy crop. It is a typical ‘K-favoring’ crop, and the level of potassium ion (K⁺) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K⁺ conditions. Here, we analyzed the transcriptomic profiles of sweet potato roots in response to K⁺ deficiency to determine the effect of low-K⁺ stress on this economically important crop.

Results

The roots of sweet potato seedlings with or without K⁺ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K⁺ groups. Among the DEGs, 336 were upregulated and 223 were downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. Further analysis revealed previously unknow genes involved in low-K⁺ stress, which could be investigated further to improve low K⁺ tolerance in plants. Confirmation of RNA-sequencing results using qRT-PCR displayed a high level of consistency between the two experiments. Analysis showed that many auxin-, ethylene- and jasmonic acid-related genes respond to K⁺ deficiency, suggesting that these hormones have important roles in K⁺ nutrient signaling in sweet potato.

Conclusions

According to the transcriptome data of sweet potato, various DEGs showed transcriptional changes in response to low-K⁺ stress. However, the expression level of some kinases, transporters, transcription factors (TFs), hormone-related genes, and plant defense-related genes changed significantly, suggesting that they have important roles during K⁺ deficiency. Thus, this study identifies potential genes for genetic improvement of responses to low-K⁺ stress and provides valuable insight into the molecular mechanisms regulating low K⁺ tolerance in sweet potato. Further research is required to clarify the function of these DEGs under low-K⁺ stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08870-5.

Multiple Facets of Nitrogen: From Atmospheric Gas to Indispensable Agricultural Input

Nitrogen (N) is a gas and the fifth most abundant element naturally found in the atmosphere. N's role in agriculture and plant metabolism has been widely investigated for decades, and extensive information regarding this subject is available. However, the advent of sequencing technology and the advances in plant biotechnology, coupled with the growing interest in functional genomics-related studies and the various environmental challenges, have paved novel paths to rediscovering the fundamentals of N and its dynamics in physiological and biological processes, as well as biochemical reactions under both normal and stress conditions. This work provides a comprehensive review on multiple facets of N and N-containing compounds in plants disseminated in the literature to better appreciate N in its multiple dimensions. Here, some of the ancient but fundamental aspects of N are revived and the advances in our understanding of N in the metabolism of plants is portrayed. It is established that N is indispensable for achieving high plant productivity and fitness. However, the use of N-rich fertilizers in relatively higher amounts negatively affects the environment. Therefore, a paradigm shift is important to shape to the future use of N-rich fertilizers in crop production and their contribution to the current global greenhouse gases (GHGs) budget would help tackle current global environmental challenges toward a sustainable agriculture.

The apple GARP family gene MdHHO3 regulates the nitrate response and leaf senescence

The regulation of plant gene expression by nitrate is a complex regulatory process. Here, we identified 90 GARP family genes in apples by genome-wide analysis. As a member of the GARP gene family, the expression of MdHHO3 (Malus domestica HYPERSENSITIVITY TO LOW PHOSPHATE-ELICITED PRIMARY ROOT SHORTENING1 HOMOLOG 3) is upregulated under N (nitrogen) supply. The results of DNA-binding site analysis and electrophoretic mobility shift assays (EMSA) showed that MdHHO3 binds to the motif-containing GAATC. Furthermore, MdHHO3 binds to its promoter sequence and inhibits its activity. In addition, the overexpression of MdHHO3 in apple calli resulted in less accumulation of nitrate in 35S:MdHHO3-GFP calli and downregulated the expression of the nitrate transport-related genes but upregulated the expression of the nitrate assimilation-related genes. Similarly, the expression of the nitrate transport-related genes was downregulated and the expression of the nitrate assimilation-related genes was upregulated in MdHHO3 overexpression Arabidopsis and tobacco plants. Interaction experiments showed that MdHHO3 could bind to the promoter MdNRT2.1 (NITRATE TRANSPORTER 2.1) and negatively regulate its expression. Moreover, the exposure of MdHHO3-overexpressing Arabidopsis and tobacco to nitrate deficiency resulted in an early senescence phenotype as compared to the WT plants. These results show that MdHHO3 can not only negatively regulate nitrate accumulation in response to nitrate but also promote early leaf senescence under nitrate deficiency. This information may be useful to further reveal the mechanism of the nitrate response and demonstrates that nitrate deficiency induces leaf senescence in apples.

Roles of TOR signaling in nutrient deprivation and abiotic stress

In living organisms, nutrient, energy, and environmental stimuli sensing and signaling are considered as the most primordial regulatory networks governing growth and development. Target of Rapamycin (TOR) is a diversified Serine/Threonine protein kinase existing in all eukaryotes that regulates distinct salient growth and developmental signaling pathways. TOR signaling acts as a central hub in plants that allows a variety of nutrients, energy, hormones, and environmental stimuli to be integrated. TOR is activated by several nutrients and promotes energy-consuming processes such as cell division, protein translation, mRNA translation and ribosome biogenesis. We summarized the recent findings on the TOR function in regulating the dynamic networks of nutrients, including sugar, sulfur, nitrogen, carbon, phosphorus, potassium, and amino acids. TOR's role in abiotic stress was discussed, in which TOR orchestrating stress signaling, including heat, cold, salt, and osmotic stress, to regulate transcriptional and metabolic reprogramming, as well as growth and development. The interconnections between TOR and SnRK1 kinase were discussed in controlling nutrient deprivation and abiotic stress.

Improving Crop Nitrogen Use Efficiency Toward Sustainable Green Revolution

The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.

Nitrogen Absorption Pattern Detection and Expression Analysis of Nitrate Transporters in Flowering Chinese Cabbage

Nitrate transporters (NRTs) play an important role in nitrate absorption and internal distribution in plant roots and other parts. Experiments were carried out to explore the sequences and expression characteristics of NRT genes, and their correlation with the N uptake in flowering Chinese cabbage. We have isolated three important BcNRTs (BcNRT1.1, BcNRT1.2, and BcNRT2.1) from flowering Chinese cabbage. Spatio-temporal expression analysis found that BcNRT1.1 and BcNRT2.1 were mainly expressed in roots, while BcNRT1.2 was more expressed in roots than in leaves during vegetative growth and was mainly expressed in leaves during reproductive growth. The NO3− uptake rate of the entire growth period was significantly correlated with BcNRT1.1 and BcNRT1.2 expression in roots. In addition, the total N content was increased with the increase in NO3− concentration in flowering Chinese cabbage. The NH4+ uptake was slightly induced by NH4+, but the total N content had no significant difference under the NH4+ concentration of 1–8 mmol/L. We also found that lower concentrations of NH4+ promoted the expression of BcNRT1.1 and BcNRT1.2 while inhibiting the expression of BcNRT2.1 in the roots of flowering Chinese cabbage. The amount of total N uptake in the treatment with 25/75 of NH4+/NO3− was significantly higher than that of the other two treatments (0/100 and 50/50). In the mixture of NH4+ and NO3−, total N uptake was significantly correlated with the BcNRT1.2 expression. We concluded that mixed nutrition with an NH4+/NO3− of 25/75 could significantly increase total nitrogen uptake in flowering Chinese cabbage, in which two members of the NRT1 subfamily (BcNRT1.1 and BcNRT1.2) might play a major regulatory role in it. This study is a beneficial attempt to dig deeper into the NRT genes resources and lays the foundation for the ultimate use of genetic improvement methods to increase the NUE with less nitrogen fertilizer in flowering Chinese cabbage.

The CBL1/9-CIPK23-AKT1 complex is essential for low potassium response in cassava

Cassava is a food crop and an important energy crop worldwide. However, its yield and quality are easily affected by low K+ stress, and the molecular mechanism of potassium channel is unknown in cassava. Herein, we revealed that calcineurin B-like 1/9 (MeCBL1/9)-CBL-interacting protein kinase 23 (MeCIPK23)-K+ TRANSPORTER1 (MeAKT1) complex plays an important role in low potassium response in cassava. Firstly, this study verified the in vivo role of MeAKT1 in K+ uptake in yeast. Secondly, we found that MeCBL1, MeCBL9, MeCIPK23 and MeAKT1 are involved in the absorption of K+ in cassava, and MeCBL1/9-CIPK23 complex is essential for MeAKT1-mediated K+ uptake. Moreover, MeCBL1/9-MeCIPK23-MeAKT1 showed different expression in different cassava varieties contrasting in the resistance to low K+ stress. Taken together, this study provides new insights into further improvement of K+ uptake in cassava.

Identification of QTLs associated with potassium use efficiency and underlying candidate genes by whole-genome resequencing of two parental lines in Brassica napus

Breeding crops that acquire and/or utilize potassium (K) more effectively could reduce the use of K fertilizers. Sixteen traits affecting K use efficiency (KUE) at the seedling stage were investigated in a B. napus double haploid population grown at an optimal K supply (OK) and a low K supply (LK) in a hydroponic culture system. In total, 50 and 62 QTLs associated with these traits were identified at OK and LK, respectively. A total of 25 orthologues of 23 Arabidopsis genes regulating K transport were identified in the confidence intervals of nine QTLs impacting shoot dry weight at LK, and 22 of these showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in roots at LK between the two parental lines. This study provided insights to the genetic basis of KUE in B. napus, which will accelerate the breeding of K-efficient rapeseed cultivars by marker-assisted selection.

Ammonium Accumulation Caused by Reduced Tonoplast V-ATPase Activity in Arabidopsis thaliana

Plant vacuoles are unique compartments that play a critical role in plant growth and development. The vacuolar H⁺-ATPase (V-ATPase), together with the vacuolar H⁺-pyrophosphatase (V-PPase), generates the proton motive force that regulates multiple cell functions and impacts all aspects of plant life. We investigated the effect of V-ATPase activity in the vacuole on plant growth and development. We used an Arabidopsisthaliana (L.) Heynh. double mutant, vha-a2 vha-a3, which lacks two tonoplast-localized isoforms of the membrane-integral V-ATPase subunit VHA-a. The mutant is viable but exhibits impaired growth and leaf chlorosis. Nitrate assimilation led to excessive ammonium accumulation in the shoot and lower nitrogen uptake, which exacerbated growth retardation of vha-a2 vha-a3. Ion homeostasis was disturbed in plants with missing VHA-a2 and VHA-a3 genes, which might be related to limited growth. The reduced growth and excessive ammonium accumulation of the double mutant was alleviated by potassium supplementation. Our results demonstrate that plants lacking the two tonoplast-localized subunits of V-ATPase can be viable, although with defective growth caused by multiple factors, which can be alleviated by adding potassium. This study provided a new insight into the relationship between V-ATPase, growth, and ammonium accumulation, and revealed the role of potassium in mitigating ammonium toxicity.

Potassium: A key modulator for cell homeostasis

Potassium (K) is the most vital and abundant macro element for the overall growth of plants and its deficiency or, excess concentration results in many diseases in plants. It is involved in regulation of many crucial roles in plant development. Depending on soil-root interactions, complex soil dynamics often results in unpredictable availability of the elements. Based on the importance index, K is considered to be the second only to nitrogen for the overall growth of plants. More than 60 enzymes within the plant system depend on K for its activation, in which K act as a key regulator. K helps plants to resist several abiotic and biotic stresses in the environment. We have reviewed the research progress about K's role in plants covering various important considerations of K highlighting the effects of microbes on soil K⁺; K and its contribution to adsorbed dose in plants; the importance of K⁺ deficiency; physiological functions of K⁺ transporters and channels; and interference of abiotic stressor in the regulatory role of K. This review further highlights the scope of future research regarding K.

Target of rapamycin regulates potassium uptake in Arabidopsis and potato

Potassium (K) is an essential inorganic nutrient needed by plants for their growth and development. The conserved target of rapamycin (TOR) kinase, a well-known nutrition signaling integrator, has crucial roles in regulating growth and development in all eukaryotes. Emerging evidence suggests that TOR is a core regulator of nutrient absorption and utilization in plants. However, it is still unclear whether there is a causative link between the TOR pathway and potassium absorption. Here, we show that the expression of some potassium transporters and channels was regulated by TOR, and the suppression of TOR activity significantly affected potassium uptake in Arabidopsis and potato. Furthermore, we discovered that a Type 2A phosphatase-associated protein of 46 kDa (TAP46), a direct TOR downstream effector, could interact with CBL-interacting protein kinase 23 (CIPK23) in Arabidopsis and potato. In Arabidopsis, the K⁺ channel AKT1 conducting K⁺ uptake was significantly regulated by Calcineurin B-like Calcium Sensor Protein 1/9 (CBL1/9)-CIPK23 modules. We found that the cbl1cbl9, cipk23 (lks1-2 and lks1-3), and akt1 mutants were more hyposensitive to the TOR inhibitor than the wild-type, and the TOR inhibitor induced the downregulation of K⁺ uptake rate in the wild-type more than in these mutants. In addition, the overexpression of CIPK23 could effectively restore the defects in growth and potassium uptake induced by the TOR inhibitors. Thus, our work reveals a link between TOR signaling and CIPK23 and provides new insight into the regulation of potassium uptake in plants.

Nitrogen form plays an important role in the growth of moso bamboo (Phyllostachys edulis) seedlings

Background

This study aimed to gain an understanding of the growth response of Phyllostachys edulis (moso bamboo) seedlings to nitrogen (N) and potassium (K) to benefit nutrient management practices and the design of proper fertilizer in nursery cultivation.

Methods

An orthogonal array L₈(4×2⁴) was used to study the effects of N forms (NH₄⁺, NO₃⁻), N concentrations (8, 32 mmol/L), and K⁺concentrations (0, 0.5, 1.5, 3 mmol/L) on seedling height, leaf number, chlorophyll content (SPAD value), biomass, root systems, and N content of P. edulis seedlings. Plants were grown in vermiculite under controlled greenhouse conditions.

Results

Our study showed that N form played a significant role in the overall performance of P. edulis seedlings, followed by the effect of N and K⁺ concentrations. Among the N forms, NH₄⁺ significantly improved the growth of P. edulis seedlings compared with NO₃⁻. Seedling height, leaf number, chlorophyll SPAD value, biomass, and root system architecture (root length, root surface area, root volume, and root tips) were greater with 8 mmol/L of NH₄⁺ treatments than with 32 mmol/L of NH₄⁺treatments, whereas root diameter and N content of P. edulis seedlings were higher with 32 mmol/L of NH₄⁺ than with 8 mmol/L of NH₄⁺. K displayed inconsistent effects on the growth of P. edulis seedlings. Specifically, seedling height, leaf number, biomass and root volume increased when the K⁺ concentration was increased from 0 to 0.5 mmol/L, followed by a decrease when the K⁺ concentration was further increased from 0.5 to 3 mmol/L. Root average diameter of the seedlings was the highest with a K⁺ concentration of 1.5 mmol/L, and K had some inhibitory effects on the chlorophyll SPAD value of the seedlings. P. edulis seedlings performed well with 8 mmol/L NH₄⁺and further tolerated a higher concentration of both NH₄⁺ and NO₃⁻, although excessive N could inhibit seedling growth. A lower concertation of K (≤ 0.5 mmol/L) promoted seedling growth and increasing K⁺ concentration in the nutrient solution did not alleviate the inhibitory effect of high N on the growth of P. edulis seedlings. Therefore, NH₄⁺nitrogen as the main form of N fertilizer, together with a low concertation of K⁺, should be supplied in the cultivation and nutrient management practices of moso bamboo.

Signaling pathways underlying nitrogen-dependent changes in root system architecture: from model to crop species

Among all essential mineral elements, nitrogen (N) is required in the largest amounts and thus is often a limiting factor for plant growth. N is taken up by plant roots in the form of water-soluble nitrate, ammonium, and, depending on abundance, low-molecular weight organic N. In soils, the availability and composition of these N forms can vary over space and time, which exposes roots to various local N signals that regulate root system architecture in combination with systemic signals reflecting the N nutritional status of the shoot. Uncovering the molecular mechanisms underlying N-dependent signaling provides great potential to optimize root system architecture for the sake of higher N uptake efficiency in crop breeding. In this review, we summarize prominent signaling mechanisms and their underlying molecular players that derive from external N forms or the internal N nutritional status and modulate root development including root hair formation and gravitropism. We also compare the current state of knowledge of these pathways between Arabidopsis and graminaceous plant species.

Coordinated Transport of Nitrate, Potassium, and Sodium

Potassium (K+) and nitrogen (N) are essential nutrients, and their absorption and distribution within the plant must be coordinated for optimal growth and development. Potassium is involved in charge balance of inorganic and organic anions and macromolecules, control of membrane electrical potential, pH homeostasis and the regulation of cell osmotic pressure, whereas nitrogen is an essential component of amino acids, proteins, and nucleic acids. Nitrate (NO3 -) is often the primary nitrogen source, but it also serves as a signaling molecule to the plant. Nitrate regulates root architecture, stimulates shoot growth, delays flowering, regulates abscisic acid-independent stomata opening, and relieves seed dormancy. Plants can sense K+/NO3 - levels in soils and adjust accordingly the uptake and root-to-shoot transport to balance the distribution of these ions between organs. On the other hand, in small amounts sodium (Na+) is categorized as a "beneficial element" for plants, mainly as a "cheap" osmolyte. However, at high concentrations in the soil, Na+ can inhibit various physiological processes impairing plant growth. Hence, plants have developed specific mechanisms to transport, sense, and respond to a variety of Na+ conditions. Sodium is taken up by many K+ transporters, and a large proportion of Na+ ions accumulated in shoots appear to be loaded into the xylem by systems that show nitrate dependence. Thus, an adequate supply of mineral nutrients is paramount to reduce the noxious effects of salts and to sustain crop productivity under salt stress. In this review, we will focus on recent research unraveling the mechanisms that coordinate the K+-NO3 -; Na+-NO3 -, and K+-Na+ transports, and the regulators controlling their uptake and allocation.

Emerging concepts of potassium homeostasis in plants

Potassium (K+) is an essential cation in all organisms that influences crop production and ecosystem stability. Although most soils are rich in K minerals, relatively little K+ is present in forms that are available to plants. Moreover, leaching and run-off from the upper soil layers contribute to K+ deficiencies in agricultural soils. Hence, the demand for K fertilizer is increasing worldwide. K+ regulates multiple processes in cells and organs, with K+ deficiency resulting in decreased plant growth and productivity. Here, we discuss the complexity of the reactive oxygen species-calcium-hormone signalling network that is responsible for the sensing of K+ deficiency in plants, together with genetic approaches using K+ transporters that have been used to increase K+ use efficiency (KUE) in plants, particularly under environmental stress conditions such as salinity and heavy metal contamination. Publicly available rice transcriptome data are used to demonstrate the two-way relationship between K+ and nitrogen nutrition, highlighting how each nutrient can regulate the uptake and root to shoot translocation of the other. Future research directions are discussed in terms of this relationship, as well as prospects for molecular approaches for the generation of improved varieties and the implementation of new agronomic practices. An increased knowledge of the systems that sense and take up K+, and their regulation, will not only improve current understanding of plant K+ homeostasis but also facilitate new research and the implementation of measures to improve plant KUE for sustainable food production.

Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots

Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO₃^-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO₃^- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO₃^- treatments. NO₃^--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO₃^- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

High External K+ Concentrations Impair Pi Nutrition, Induce the Phosphate Starvation Response, and Reduce Arsenic Toxicity in Arabidopsis Plants

Potassium (K⁺) and phosphorous (Pi) are two of the most important nutrients required by plants and there is an interest in studying how they are acquired. Most studies have focused on the characterization of the mechanisms involved in K⁺ and Pi uptake and their distribution within the plants, as well as the regulatory mechanisms involved. Evidence is emerging which points to interactions in the nutrition of different nutrients and to the existence of crosstalk in the signaling cascades regulating their acquisition. However, the interaction between K⁺ and Pi has been scarcely studied. Here we show that high concentrations of K⁺ in the external solution inhibit Pi uptake and impair Pi nutrition in Arabidopsis plants, resulting in the induction of phosphate starvation response (PSR) and the upregulation of genes encoding root phosphate uptake systems. The high K⁺-induced PSR depends on the PHR1 and PHL1 transcription factors that are key pieces of Pi signaling in Arabidopsis. Importantly, high K⁺ reduces arsenic accumulation in plants and its toxic effects. The results presented may help to design strategies to reduce Pi deficiency as well as the accumulation of arsenic in crops.

The Arabidopsis AtUNC-93 Acts as a Positive Regulator of Abiotic Stress Tolerance and Plant Growth via Modulation of ABA Signaling and K+ Homeostasis

Potassium (K⁺) is one of the essential macronutrients required for plant growth and development, and the maintenance of cellular K⁺ homeostasis is important for plants to adapt to abiotic stresses and growth. However, the mechanism involved has not been understood clearly. In this study, we demonstrated that AtUNC-93 plays a crucial role in this process under the control of abscisic acid (ABA). AtUNC-93 was localized to the plasma membrane and mainly expressed in the vascular tissues in Arabidopsis thaliana. The atunc-93 mutants showed typical K⁺-deficient symptoms under low-K⁺ conditions. The K⁺ contents of atunc-93 mutants were significantly reduced in shoots but not in roots under either low-K⁺ or normal conditions compared with wild type plants, whereas the AtUNC-93-overexpressing lines still maintained relatively higher K⁺ contents in shoots under low-K⁺ conditions, suggesting that AtUNC-93 positively regulates K⁺ translocation from roots to shoots. The atunc-93 plants exhibited dwarf phenotypes due to reduced cell expansion, while AtUNC-93-overexpressing plants had larger bodies because of increased cell expansion. After abiotic stress and ABA treatments, the atunc-93 mutants was more sensitive to salt, drought, osmotic, heat stress and ABA than wild type plants, while the AtUNC-93-overexpressing lines showed enhanced tolerance to these stresses and insensitive phenotype to ABA. Furthermore, alterations in the AtUNC-93 expression changed expression of many ABA-responsive and stress-related genes. Our findings reveal that AtUNC-93 functions as a positive regulator of abiotic stress tolerance and plant growth by maintaining K⁺ homeostasis through ABA signaling pathway in Arabidopsis.

A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis

Nitrate is a nutrient signal that triggers complex regulation of transcriptional networks to modulate nutrient-dependent growth and development in plants. This includes time- and nitrate concentration-dependent regulation of nitrate-related gene expression. However, the underlying mechanisms remain poorly understood. Here we identify NIGT1 transcriptional repressors as negative regulators of the ArabidopsisNRT2.1 nitrate transporter gene, and show antagonistic regulation by NLP primary transcription factors for nitrate signalling and the NLP-NIGT1 transcriptional cascade-mediated repression. This antagonistic regulation provides a resolution to the complexity of nitrate-induced transcriptional regulations. Genome-wide analysis reveals that this mechanism is applicable to NRT2.1 and other genes involved in nitrate assimilation, hormone biosynthesis and transcription. Furthermore, the PHR1 master regulator of the phosphorus-starvation response also directly promotes expression of NIGT1 family genes, leading to reductions in nitrate uptake. NIGT1 repressors thus act in two transcriptional cascades, forming a direct link between phosphorus and nitrogen nutritional regulation.

Plants respond to nutrients by modulating gene expression. Here, the authors show that nitrate suppresses NRT2.1 nitrate transporter expression via NIGT1 transcriptional repressors and that phosphate starvation enhances this pathway via PHR1, thus linking phosphorus and nitrogen signalling.

The nitrogen-potassium intersection: membranes, metabolism, and mechanism

Nitrogen (N) and potassium (K) are the two most abundantly acquired mineral elements by plants, and their acquisition pathways interact in complex ways. Here, we review pivotal interactions with respect to root acquisition, storage, translocation and metabolism, between the K⁺ ion and the two major N sources, ammonium (NH₄⁺ ) and nitrate (NO₃^- ). The intersections between N and K physiology are explored at a number of organizational levels, from molecular-genetic processes, to compartmentation, to whole plant physiology, and discussed in the context of both N-K cooperation and antagonism. Nutritional regulation and optimization of plant growth, yield, metabolism and water-use efficiency are also discussed.

NO3- , PO43- and SO42- deprivation reduced LKT1-mediated low-affinity K+ uptake and SKOR-mediated K+ translocation in tomato and Arabidopsis plants

Regulation of essential macronutrients acquisition by plants in response to their availability is a key process for plant adaptation to changing environments. Here we show in tomato and Arabidopsis plants that when they are subjected to NO₃^- , PO₄^3- and SO₄^2- deprivation, low-affinity K⁺ uptake and K⁺ translocation to the shoot are reduced. In parallel, these nutritional deficiencies produce reductions in the messenger levels of the genes encoding the main systems for low-affinity K⁺ uptake and K⁺ translocation, i.e. AKT1 and SKOR in Arabidopsis and LKT1 and the tomato homolog of SKOR, SlSKOR in tomato, respectively. The results suggest that the shortage of one nutrient produces a general downregulation of the acquisition of other nutrients. In the case of K⁺ nutrient, one of the mechanisms for such a response resides in the transcriptional repression of the genes encoding the systems for K⁺ uptake and translocation.

Two spatially and temporally distinct Ca2+ signals convey Arabidopsis thaliana responses to K+ deficiency

In plants, potassium (K⁺ ) homeostasis is tightly regulated and established against a concentration gradient to the environment. Despite the identification of Ca²⁺ -regulated kinases as modulators of K⁺ channels, the immediate signaling and adaptation mechanisms of plants to low-K⁺ conditions are only partially understood. To assess the occurrence and role of Ca²⁺ signals in Arabidopsis thaliana roots, we employed ratiometric analyses of Ca²⁺ dynamics in plants expressing the Ca²⁺ reporter YC3.6 in combination with patch-clamp analyses of root cells and two-electrode voltage clamp (TEVC) analyses in Xenopus laevis oocytes. K⁺ deficiency triggers two successive and distinct Ca²⁺ signals in roots exhibiting spatial and temporal specificity. A transient primary Ca²⁺ signature arose within 1 min in the postmeristematic stelar tissue of the elongation zone, while a secondary Ca²⁺ response occurred after several hours as sustained Ca²⁺ elevation in defined tissues of the elongation and root hair differentiation zones. Patch-clamp and TEVC analyses revealed Ca²⁺ dependence of the activation of the K⁺ channel AKT1 by the CBL1-CIPK23 Ca²⁺ sensor-kinase complex. Together, these findings identify a critical role of cell group-specific Ca²⁺ signaling in low K⁺ responses and indicate an essential and direct role of Ca²⁺ signals for AKT1 K⁺ channel activation in roots.

Structured plant metabolomics for the simultaneous exploration of multiple factors

Multiple factors act simultaneously on plants to establish complex interaction networks involving nutrients, elicitors and metabolites. Metabolomics offers a better understanding of complex biological systems, but evaluating the simultaneous impact of different parameters on metabolic pathways that have many components is a challenging task. We therefore developed a novel approach that combines experimental design, untargeted metabolic profiling based on multiple chromatography systems and ionization modes, and multiblock data analysis, facilitating the systematic analysis of metabolic changes in plants caused by different factors acting at the same time. Using this method, target geraniol compounds produced in transgenic tobacco cell cultures were grouped into clusters based on their response to different factors. We hypothesized that our novel approach may provide more robust data for process optimization in plant cell cultures producing any target secondary metabolite, based on the simultaneous exploration of multiple factors rather than varying one factor each time. The suitability of our approach was verified by confirming several previously reported examples of elicitor-metabolite crosstalk. However, unravelling all factor-metabolite networks remains challenging because it requires the identification of all biochemically significant metabolites in the metabolomics dataset.

Anionic metabolite biosynthesis enhanced by potassium under dark, anaerobic conditions in cyanobacteria

Potassium (K(+)) is an essential macronutrient for all living organisms including cyanobacteria. Cyanobacteria are a group of bacteria performing oxygenic photosynthesis, widely studied in basic and applied sciences. The primary metabolism of the unicellular cyanobacterium Synechocystis sp. PCC 6803 is altered by environmental conditions, and it excretes organic acids and hydrogen under dark, anaerobic conditions. Here we demonstrated that K(+) widely changes the primary carbon metabolism of this cyanobacterium. Succinate and lactate excretion from the cells incubated under dark, anaerobic conditions was enhanced in the presence of K(+), while hydrogen production was repressed. The addition of K(+) and the genetic manipulation of acetate kinase AckA and an RNA polymerase sigma factor SigE additively increased succinate and lactate production to 141.0 and 217.6 mg/L, which are 11 and 46 times, compared to the wild-type strain without K(+), respectively. Intracellular levels of 2-oxoglutarate, succinate, fumarate, and malate increased by K(+) under dark, anaerobic conditions. This study provides the evidence of the considerable effect of K(+) on the biosynthesis of anionic metabolites in a unicellular cyanobacterium.

Nitrate Transport, Sensing, and Responses in Plants

Nitrogen (N) is an essential macronutrient that affects plant growth and development. N is an important component of chlorophyll, amino acids, nucleic acids, and secondary metabolites. Nitrate is one of the most abundant N sources in the soil. Because nitrate and other N nutrients are often limiting, plants have developed sophisticated mechanisms to ensure adequate supply of nutrients in a variable environment. Nitrate is absorbed in the root and mobilized to other organs by nitrate transporters. Nitrate sensing activates signaling pathways that impinge upon molecular, metabolic, physiological, and developmental responses locally and at the whole plant level. With the advent of genomics technologies and genetic tools, important advances in our understanding of nitrate and other N nutrient responses have been achieved in the past decade. Furthermore, techniques that take advantage of natural polymorphisms present in divergent individuals from a single species have been essential in uncovering new components. However, there are still gaps in our understanding of how nitrate signaling affects biological processes in plants. Moreover, we still lack an integrated view of how all the regulatory factors identified interact or crosstalk to orchestrate the myriad N responses plants typically exhibit. In this review, we provide an updated overview of mechanisms by which nitrate is sensed and transported throughout the plant. We discuss signaling components and how nitrate sensing crosstalks with hormonal pathways for developmental responses locally and globally in the plant. Understanding how nitrate impacts on plant metabolism, physiology, and growth and development in plants is key to improving crops for sustainable agriculture.

Arabidopsis NRT1.5 Mediates the Suppression of Nitrate Starvation-Induced Leaf Senescence by Modulating Foliar Potassium Level

Nitrogen deficiency induces leaf senescence. However, whether or how nitrate might affect this process remains to be investigated. Here, we report an interesting finding that nitrate-instead of nitrogen-starvation induced early leaf senescence in nrt1.5 mutant, and present genetic and physiological data demonstrating that nitrate starvation-induced leaf senescence is suppressed by NRT1.5. NRT1.5 suppresses the senescence process dependent on its function from roots, but not the nitrate transport function. Further analyses using nrt1.5 single and nia1 nia2 nrt1.5-4 triple mutant showed a negative correlation between nitrate concentration and senescence rate in leaves. Moreover, when exposed to nitrate starvation, foliar potassium level decreased in nrt1.5, but adding potassium could essentially restore the early leaf senescence phenotype of nrt1.5 plants. Nitrate starvation also downregulated the expression of HAK5, RAP2.11, and ANN1 in nrt1.5 roots, and appeared to alter potassium level in xylem sap from nrt1.5. These data suggest that NRT1.5 likely perceives nitrate starvation-derived signals to prevent leaf senescence by facilitating foliar potassium accumulation.

Comparison between Arabidopsis and Rice for Main Pathways of K(+) and Na(+) Uptake by Roots

K(+) is an essential macronutrient for plants. It is acquired by specific uptake systems located in roots. Although the concentrations of K(+) in the soil solution are widely variable, K(+) nutrition is secured by uptake systems that exhibit different affinities for K(+). Two main systems have been described for root K(+) uptake in several species: the high-affinity HAK5-like transporter and the inward-rectifier AKT1-like channel. Other unidentified systems may be also involved in root K(+) uptake, although they only seem to operate when K(+) is not limiting. The use of knock-out lines has allowed demonstrating their role in root K(+) uptake in Arabidopsis and rice. Plant adaptation to the different K(+) supplies relies on the finely tuned regulation of these systems. Low K(+)-induced transcriptional up-regulation of the genes encoding HAK5-like transporters occurs through a signal cascade that includes changes in the membrane potential of root cells and increases in ethylene and reactive oxygen species concentrations. Activation of AKT1 channels occurs through phosphorylation by the CIPK23/CBL1 complex. Recently, activation of the Arabidopsis HAK5 by the same complex has been reported, pointing to CIPK23/CBL as a central regulator of the plant's adaptation to low K(+). Na(+) is not an essential plant nutrient but it may be beneficial for some plants. At low concentrations, Na(+) improves growth, especially under K(+) deficiency. Thus, high-affinity Na(+) uptake systems have been described that belong to the HKT and HAK families of transporters. At high concentrations, typical of saline environments, Na(+) accumulates in plant tissues at high concentrations, producing alterations that include toxicity, water deficit and K(+) deficiency. Data concerning pathways for Na(+) uptake into roots under saline conditions are still scarce, although several possibilities have been proposed. The apoplast is a significant pathway for Na(+) uptake in rice grown under salinity conditions, but in other plant species different mechanisms involving non-selective cation channels or transporters are under discussion.

Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice

BACKGROUND

Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes has never been fully explored especially in rice. Coexpression network analysis is a useful tool to elucidate the functional relationships of genes based on common expression. Therefore, we performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions. Moreover, we conducted a large scale coexpression analysis by integrating the data with previously generated gene expression profiles of organs and tissues at different developmental stages to obtain a global view of gene networks associated with plant response to nutrient deficiency.

RESULTS

We statistically identified 5400 differentially expressed genes under the nutrient deficiency treatments. Subsequent coexpression analysis resulted in the extraction of 6 modules (groups of highly interconnected genes) with distinct gene expression signatures. Three of these modules comprise mostly of downregulated genes under N deficiency associated with distinct functions such as development of immature organs, protein biosynthesis and photosynthesis in chloroplast of green tissues, and fundamental cellular processes in all organs and tissues. Furthermore, we identified one module containing upregulated genes under N and K deficiency conditions, and a number of genes encoding protein kinase, kinase-like domain containing protein and nutrient transporters. This module might be particularly involved in adaptation to nutrient deficiency via phosphorylation-mediated signal transduction and/or post-transcriptional regulation.

CONCLUSIONS

Our study demonstrated that large scale coexpression analysis is an efficient approach in characterizing the nutrient response genes based on biological functions and could provide new insights in understanding plant response to nutrient deficiency.

Two short sequences in OsNAR2.1 promoter are necessary for fully activating the nitrate induced gene expression in rice roots

Nitrate is an essential nitrogen source and serves as a signal to control growth and gene expression in plants. In rice, OsNAR2.1 is an essential partner of multiple OsNRT2 nitrate transporters for nitrate uptake over low and high concentration range. Previously, we have reported that -311 bp upstream fragment from the translational start site in the promoter of OsNAR2.1 gene is the nitrate responsive region. To identify the cis-acting DNA elements necessary for nitrate induced gene expression, we detected the expression of beta-glucuronidase (GUS) reporter in the transgenic rice driven by the OsNAR2.1 promoter with different lengths and site mutations of the 311 bp region. We found that -129 to -1 bp region is necessary for the nitrate-induced full activation of OsNAR2.1. Besides, the site mutations showed that the 20 bp fragment between -191 and -172 bp contains an enhancer binding site necessary to fully drive the OsNAR2.1 expression. Part of the 20 bp fragment is commonly presented in the sequences of different promoters of both the nitrate induced NAR2 genes and nitrite reductase NIR1 genes from various higher plants. These findings thus reveal the presence of conserved cis-acting element for mediating nitrate responses in plants.

An RNA-seq screen of the Drosophila antenna identifies a transporter necessary for ammonia detection

Many insect vectors of disease detect their hosts through olfactory cues, and thus it is of great interest to understand better how odors are encoded. However, little is known about the molecular underpinnings that support the unique function of coeloconic sensilla, an ancient and conserved class of sensilla that detect amines and acids, including components of human odor that are cues for many insect vectors. Here, we generate antennal transcriptome databases both for wild type Drosophila and for a mutant that lacks coeloconic sensilla. We use these resources to identify genes whose expression is highly enriched in coeloconic sensilla, including many genes not previously implicated in olfaction. Among them, we identify an ammonium transporter gene that is essential for ammonia responses in a class of coeloconic olfactory receptor neurons (ORNs), but is not required for responses to other odorants. Surprisingly, the transporter is not expressed in ORNs, but rather in neighboring auxiliary cells. Thus, our data reveal an unexpected non-cell autonomous role for a component that is essential to the olfactory response to ammonia. The defective response observed in a Drosophila mutant of this gene is rescued by its Anopheles ortholog, and orthologs are found in virtually all insect species examined, suggesting that its role is conserved. Taken together, our results provide a quantitative analysis of gene expression in the primary olfactory organ of Drosophila, identify molecular components of an ancient class of olfactory sensilla, and reveal that auxiliary cells, and not simply ORNs, play an essential role in the coding of an odor that is a critical host cue for many insect vectors of human disease.

Olfaction underlies the attraction of insect pests and vectors of disease to their plant and human hosts. In the genetic model insect Drosophila, the neuronal basis of odor coding has been extensively analyzed in the antenna, its major olfactory organ, but the molecular basis of odor coding has not. Additionally, there has been little analysis of any olfactory cells other than neurons. We have undertaken a comprehensive and quantitative analysis of gene expression in the Drosophila antenna. This analysis revealed a surprisingly broad dynamic range of odor receptor and odor binding protein expression, and unexpected expression of taste receptor genes. Further analysis identified 250 genes that are expressed at reduced levels in a mutant lacking an evolutionarily ancient class of sensilla, antennal hairs housing neurons that respond to human odors. One of these genes, a transporter, is expressed in non-neuronal cells but is essential to the response of a neuron to ammonia, a key cue for insect vectors of disease. A mutation in this transporter can be rescued by its mosquito homolog. While many studies of sensory coding consider the neural circuit in isolation, our analysis reveals an essential role for an auxiliary cell.

A low K+ signal is required for functional high-affinity K+ uptake through HAK5 transporters

The high-affinity K(+) transporter HAK5 is a key system for root K(+) uptake and, under very low external K(+), the only one capable of supplying K(+) to the plant. Functional HAK5-mediated K(+) uptake should be tightly regulated for plant adaptation to different environmental conditions. Thus, it has been described that the gene encoding the transporter is transcriptionally regulated, being highly induced under K(+) limitation. Here we show that environmental conditions, such as the lack of K(+), NO(3)(-) or P, that induced a hyperpolarization of the plasma membrane of root cells, induce HAK5 transcription. However, only the deprivation of K(+) produces functional HAK5-mediated K(+) uptake in the root. These results suggest on the one hand the existence of a posttranscriptional regulation of HAK5 elicited by the low K(+) signal and on the other that HAK5 may be involved in yet-unknown functions related to NO(3)(-) and P deficiencies. These results have been obtained here with Solanum lycopersicum (cv. Micro-Tom) as well as Arabidopsis thaliana plants, suggesting that the posttranscriptional regulation of high-affinity HAK transporters take place in all plant species.

Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots

Nitrate acts as a potent signal to control global gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly after nitrate treatments in roots. Global gene expression analysis revealed 97% of the genes with altered expression in tga1 tga4 double mutant plants respond to nitrate treatments, indicating that these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. We found TGA1 and TGA4 regulate the expression of nitrate transporter genes NRT2.1 and NRT2.2. Specific binding of TGA1 to its cognate DNA sequence on NRT2.1 and NRT2.2 promoters was confirmed by chromatin immunoprecipitation assays. The tga1 tga4 double mutant plants exhibit nitrate-dependent lateral and primary root phenotypes. Lateral root initiation is affected in both tga1 tga4 and nrt1.2 nrt2.2 double mutants, suggesting TGA1 and TGA4 regulate lateral root development at least partly via NRT2.1 and NRT2.2. Additional root phenotypes of tga1 tga4 double mutants indicate that these transcription factors play an important role in root developmental responses to nitrate. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots.

Nitrogen control of developmental phase transitions in Arabidopsis thaliana

Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition.

Identification and characterization of improved nitrogen efficiency in interspecific hybridized new-type Brassica napus

BACKGROUND AND AIMS

Oilseed rape (Brassica napus) is an important oil crop worldwide. The aim of this study was to identify the variation in nitrogen (N) efficiency of new-type B. napus (genome A(r)A(r)C(c)C(c)) genotypes, and to characterize some critical physiological and molecular mechanisms in response to N limitation.

METHODS

Two genotypes with contrasting N efficiency (D4-15 and D1-1) were identified from 150 new-type B. napus lines, and hydroponic and pot experiments were conducted. Root morphology, plant biomass, N uptake parameters and seed yield of D4-15 and D1-1 were investigated. Two traditional B. napus (genome A(n)A(n)C(n)C(n)) genotypes, QY10 and NY7, were also cultivated. Introgression of exotic genomic components in D4-15 and D1-1 was evaluated with molecular markers.

KEY RESULTS

Large genetic variation existed among traits contributing to the N efficiency of new-type B. napus. Under low N levels at the seedling stage, the N-efficient new-type D4-15 showed higher values than the N-inefficient D1-1 line and the traditional B. napus QY10 and NY7 genotypes with respect to several traits, including root and shoot biomass, root morphology, N accumulation, N utilization efficiency (NutE), N uptake efficiency (NupE), activities of nitrate reductase (NR) and glutamine synthetase (GS), and expression levels of N transporter genes and genes that are involved in N assimilation. Higher yield was produced by the N-efficient D4-15 line compared with the N-inefficient D1-1 at maturity. More exotic genome components were introgressed into the genome of D4-15 (64·97 %) compared with D1-1 (32·23 %).

CONCLUSIONS

The N-efficient new-type B. napus identified in this research had higher N efficiency (and tolerance to low-N stress) than traditional B. napus cultivars, and thus could have important potential for use in breeding N-efficient B. napus cultivars in the field.

Strategies for improving potassium use efficiency in plants

Potassium is a macronutrient that is crucial for healthy plant growth. Potassium availability, however, is often limited in agricultural fields and thus crop yields and quality are reduced. Therefore, improving the efficiency of potassium uptake and transport, as well as its utilization, in plants is important for agricultural sustainability. This review summarizes the current knowledge on the molecular mechanisms involved in potassium uptake and transport in plants, and the molecular response of plants to different levels of potassium availability. Based on this information, four strategies for improving potassium use efficiency in plants are proposed; 1) increased root volume, 2) increasing efficiency of potassium uptake from the soil and translocation in planta, 3) increasing mobility of potassium in soil, and 4) molecular breeding new varieties with greater potassium efficiency through marker assisted selection which will require identification and utilization of potassium associated quantitative trait loci.

Chrysanthemum CmNAR2 interacts with CmNRT2 in the control of nitrate uptake

Nitrate transporters are an important component of plant growth and development. Chrysanthemum morifolium is an important ornamental species, for which a sufficient supply of nitrogenous fertilizer is required to maintain economic yields. In this study, the full-length cDNA of the nitrate transporter genes CmNRT2 and CmNAR2 were isolated. CmNRT2 transcript accumulation was inducible by both nitrate and ammonium, but the latter ion down-regulated the transcript accumulation of CmNAR2. CmNRT2 might be a plasma membrane localized protein, while CmNAR2 was distributed throughout the cell. CmNAR2 was shown to interact with CmNRT2 by in vitro and in vivo assays. Arabidopsis thaliana plants heterologously expressing CmNRT2 showed an increased rate of nitrate influx, while this trait was unaltered in plants expressing CmNAR2. Double transformants (CmNRT2 plus CmNAR2) exhibited an enhanced rate of nitrate influx into the root. Our data indicated that the interaction of CmNAR2 with CmNRT2 contributed to the uptake of nitrate.

Analysis of the Root System Architecture of Arabidopsis Provides a Quantitative Readout of Crosstalk between Nutritional Signals

As plant roots forage the soil for food and water, they translate a multifactorial input of environmental stimuli into a multifactorial developmental output that manifests itself as root system architecture (RSA). Our current understanding of the underlying regulatory network is limited because root responses have traditionally been studied separately for individual nutrient deficiencies. In this study, we quantified 13 RSA parameters of Arabidopsis thaliana in 32 binary combinations of N, P, K, S, and light. Analysis of variance showed that each RSA parameter was determined by a typical pattern of environmental signals and their interactions. P caused the most important single-nutrient effects, while N-effects were strongly light dependent. Effects of K and S occurred mostly through nutrient interactions in paired or multiple combinations. Several RSA parameters were selected for further analysis through mutant phenotyping, which revealed combinations of transporters, receptors, and kinases acting as signaling modules in K-N interactions. Furthermore, nutrient response profiles of individual RSA features across NPK combinations could be assigned to transcriptionally coregulated clusters of nutrient-responsive genes in the roots and to ionome patterns in the shoots. The obtained data set provides a quantitative basis for understanding how plants integrate multiple nutritional stimuli into complex developmental programs.

ABA control of plant macroelement membrane transport systems in response to water deficit and high salinity

Plant growth and productivity are adversely affected by various abiotic stressors and plants develop a wide range of adaptive mechanisms to cope with these adverse conditions, including adjustment of growth and development brought about by changes in stomatal activity. Membrane ion transport systems are involved in the maintenance of cellular homeostasis during exposure to stress and ion transport activity is regulated by phosphorylation/dephosphorylation networks that respond to stress conditions. The phytohormone abscisic acid (ABA), which is produced rapidly in response to drought and salinity stress, plays a critical role in the regulation of stress responses and induces a series of signaling cascades. ABA signaling involves an ABA receptor complex, consisting of an ABA receptor family, phosphatases and kinases: these proteins play a central role in regulating a variety of diverse responses to drought stress, including the activities of membrane-localized factors, such as ion transporters. In this review, recent research on signal transduction networks that regulate the function ofmembrane transport systems in response to stress, especially water deficit and high salinity, is summarized and discussed. The signal transduction networks covered in this review have central roles in mitigating the effect of stress by maintaining plant homeostasis through the control of membrane transport systems.