Nitrate regulation of metabolism and growth

Enhanced nitrogen and phosphorus removal from eutrophic lake water by Ipomoea aquatica with low-energy ion implantation

Ipomoea aquatica with low-energy N+ ion implantation was used for the removal of both nitrogen and phosphorus from the eutrophic Chaohu Lake, China. The biomass growth, nitrate reductase and peroxidase activities of the implanted I. aquatica were found to be higher than those of I. aquatica without ion implantation. Higher NO3-N and PO4-P removal efficiencies were obtained for the I. aquatica irradiation at 25 keV, 3.9 x 10(16) N+ ions/cm(2) and 20 keV 5.2 x 10(16) N+ ions/cm(2), respectively (p < 0.05). Moreover, the nitrogen and phosphorus contents in the plant biomass with ion implantation were also greater than those of the controls. I. aquatica with ion implantation was directly responsible for 51-68% N removal and 54-71% P removal in the three experiments. The results further confirm that the ion implantation could enhance the growth potential of I. aquatica in real eutrophic water and increase its nutrient removal efficiency. Thus, the low-energy ion implantation for aquatic plants could be considered as an approach for in situ phytoremediation and bioremediation of eutrophic waters.

Nitrate supply induces changes in polyamine content and ethylene production in wheat plants grown with ammonium

In order to explore the mechanisms of nitrate's beneficial effect on ammonium-grown plants, we investigated the effects of nitrate on free and conjugated polyamine plant content and ethylene biosynthesis in wheat (Triticum aestivum L.) plants grown with ammonium nutrition. Two different doses of nitrate (100 microM and 5 mM) were supplied to ammonium-fed plants, in order to determine whether the effects of nitrate require significant doses (nutritional character), or can be promoted by very low doses (pseudo-hormonal character). Our results showed that nitrate's effects on putrescine, spermidine and spermine contents of ammonium-grown plants tended to follow the pattern associated with strict nitrate nutrition. Both low (100 microM) and high (5 mM) nitrate doses caused a rapid and significant increase in free spermidine content in roots and shoots, which was well correlated with reduced root ethylene production. In shoots, this increase in free spermidine was correlated with changes in the conjugation pattern, while in roots these changes appear to be due to alternative mechanisms. On the other hand, no clear relationship between the supply of a lower dose of nitrate (100 microM) and a reduction of free putrescine content was observed. With higher doses of nitrate (5 mM) we observed a reduction of free putrescine content that was well correlated with increases in its conjugated forms. In conclusion, nitrate's effects on putrescine, spermidine and spermine contents of ammonium-fed plants tended to follow the pattern associated with strict nitrate nutrition, corroborating its beneficial effect.

Redundant roles of photoreceptors and cytokinins in regulating photosynthetic acclimation to canopy density

The regulation of photosynthetic acclimation to canopy density was investigated in tobacco canopies and in tobacco and Arabidopsis plants with part of their foliage experimentally shaded. Both species acclimated to canopy light gradients and partial shading by allocating photosynthetic capacity to leaves in high light and adjusting chloroplast organization to the local light conditions. An investigation was carried out to determine whether signalling mediated by photoreceptors, sugars, cytokinin, and nitrate is involved in and necessary for proper photosynthetic acclimation. No evidence was found for a role for sugars, or for nitrate. The distribution of cytokinins in tobacco stands of contrasting density could be explained in part by irradiance-dependent delivery of cytokinins through the transpiration stream. Functional studies using a comprehensive selection of Arabidopsis mutants and transgenics showed that normal wild-type responses to partial shading were retained when signalling mediated by photoreceptors or cytokinins was disrupted. This indicates that these pathways probably operate in a redundant manner. However, the reduction of the chlorophyll a/b ratio in response to local shade was completely absent in the Arabidopsis Ws-2 accession mutated in PHYTOCHROME D and in the triple phyAphyCphyD mutant. Moreover, cytokinin receptor mutants also showed a reduced response, suggesting a previously unrecognized function of phyD and cytokinins.

AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response

Nitrate, the major nitrogen source for most plants, is not only a nutrient but also a signaling molecule. For almost two decades, it has been known that nitrate can rapidly induce transcriptional expression of several nitrate-related genes, a process that is referred to as the primary nitrate response. However, little is known about how plants actually sense nitrate and how the signal is transmitted in this pathway. In this study, a calcineurin B-like (CBL) -interacting protein kinase (CIPK) gene, CIPK8, was found to be involved in early nitrate signaling. CIPK8 expression was rapidly induced by nitrate. Analysis of two independent knockout mutants and a complemented line showed that CIPK8 positively regulates the nitrate-induced expression of primary nitrate response genes, including nitrate transporter genes and genes required for assimilation. Kinetic analysis of nitrate induction levels of these genes in wild-type plants indicated that there are two response phases: a high-affinity phase with a K(m) of approximately 30 mum and a low-affinity phase with a K(m) of approximately 0.9 mm. As cipk8 mutants were defective mainly in the low-affinity response, the high-affinity and low-affinity nitrate signaling systems are proposed to be genetically distinct, with CIPK8 involved in the low-affinity system. In addition, CIPK8 was found to be involved in long-term nitrate-modulated primary root growth and nitrate-modulated expression of a vacuolar malate transporter. Taken together, our results indicate that CBL-CIPK networks are responsible not only for stress responses and potassium shortage, but also for nitrate sensing.

Nitrate induction of root hydraulic conductivity in maize is not correlated with aquaporin expression

Some plant species can increase the mass flow of water from the soil to the root surface in response to the appearance of nitrate in the rhizosphere by increasing root hydraulic conductivity. Such behavior can be seen as a powerful strategy to facilitate the uptake of nitrate in the patchy and dynamically changing soil environment. Despite the significance of such behavior, little is known about the dynamics and mechanism of this phenomenon. Here we examine root hydraulic response of nitrate starved Zea mays (L.) plants after a sudden exposure to 5 mM NO(3)(-) solution. In all cases the treatment resulted in a significant increase in pressure-induced (pressure gradient approximately 0.2 MPa) flow across the root system by approximately 50% within 4 h. Changes in osmotic gradient across the root were approximately 0.016 MPa (or 8.5%) and thus the results could only be explained by a true change in root hydraulic conductance. Anoxia treatment significantly reduced the effect of nitrate on xylem root hydraulic conductivity indicating an important role for aquaporins in this process. Despite a 1 h delay in the hydraulic response to nitrate treatment, we did not detect any change in the expression of six ZmPIP1 and seven ZmPIP2 genes, strongly suggesting that NO(3)(-) ions regulate root hydraulics at the protein level. Treatments with sodium tungstate (nitrate reductase inhibitor) aimed at resolving the information pathway regulating root hydraulic properties resulted in unexpected findings. Although this treatment blocked nitrate reductase activity and eliminated the nitrate-induced hydraulic response, it also produced changes in gene expression and nitrate uptake levels, precluding us from suggesting that nitrate acts on root hydraulic properties via the products of nitrate reductase.

A systems view of nitrogen nutrient and metabolite responses in Arabidopsis

Nitrogen (N) is an essential macronutrient available to plants mainly as nitrate in agricultural soils. Besides its role as a nutrient, inorganic and organic N sources play key roles as signals that control genome-wide gene expression in Arabidopsis and other plant species. Genomics approaches have provided us with thousands of genes whose expression is modulated in response to N treatments in Arabidopsis. Recently, systems approaches have been utilized to map the complex molecular network that plants utilize to integrate metabolic, cellular, and developmental processes to successfully adapt to changing N availability. The challenge now is to understand the molecular mechanisms underlying N regulation of gene networks and bridge the gap between N sensing, signaling, and downstream physiological and developmental changes. We discuss recent advances in this direction.

Light-induced degradation of storage starch in turions of Spirodela polyrhiza depends on nitrate

Light induces both the germination of turions of the duckweed Spirodela polyrhiza and the degradation of the reserve starch stored in the turions. The germination photoresponse requires nitrate, and we show here that nitrate is also needed for the light-induced degradation of the turion starch. Ammonium cannot substitute for nitrate in this regard, and nitrate thus acts specifically as signal to promote starch degradation in the turions. Irradiation with continuous red light leads to starch degradation via auto-phosphorylation of starch-associated glucan, water dikinase (GWD), phosphorylation of the turion starch and enhanced binding of alpha-amylase to starch granules. The present study shows that all of these processes require the presence of nitrate, and that nitrate exerts its effect on starch degradation at a point between the absorption of light by phytochrome and the auto-phosphorylation of the GWD. Nitrate acts to coordinate carbon and nitrogen metabolism in germinating turions: starch will only be broken down when sufficient nitrogen is present to ensure appropriate utilization of the released carbohydrate. These data constitute the first report of control over the initiation of reserve starch degradation by nitrate.

Comparative genomic and physiological analysis of nutrient response to NH4+, NH4+:NO3- and NO3- in barley seedlings

Long-term differences in photosynthesis, respiration and growth of plants receiving distinct nitrogen (N) sources imply that N metabolism generates signals that regulate metabolism and development. The molecular basis of these signals remains unclear. Here we studied the gene expression profiles of barley (Hordeum vulgare L. cv. Graphic) seedlings fertilized either with ammonium (NH4+), with ammonium and nitrate (NH4+:NO3-), or with nitrate (NO3-) only. Our transcriptome analysis after 48 h of growth in these N sources showed major changes in the expression of genes involved in N metabolism (nitrate reductase), signalling (protein kinases and protein phosphatases), photosynthesis (chlorophyll a/b-binding protein and a PsbQ domain), where increases in NO3- as compared with NH4+ were observed. Moreover, NH4+ assimilation induced genes participating in C and sugars metabolism (phosphoglycerate kinase, glucosyltranferase and galactokinase), respiration (cytochrome c oxidase), protein fate (heat shock proteins) and development (MTN3-like protein). These changes in gene expression could well explain the long-term growth depression observed in NH4+ plants. Even if a few genes participating in protein fate (proteases) and development (OsNAC5) were upregulated in NH4+ as compared with NH4+:NO3-, the general pattern of expression was quite similar between these two N sources. Taken together, these results indicated that other downstream mechanisms should be involved in the synergetic long-term response of NH4+:NO3-.

Altering young tomato plant growth by nitrate and CO2 preserves the proportionate relation linking long-term organic-nitrogen accumulation to intercepted radiation

* A previously published model of crop nitrogen (N) status based on intercepted photosynthetically active radiation (R(i), mol per plant) suggested that plant organic N accumulation is related to R(i) by a constant ratio, defined hereafter as the radiation use efficiency for N (NRUE). The aim of this paper was to compare the effects of N nutrition and CO2 enrichment on NRUE and RUE (radiation use efficiency for biomass accumulation). * In three unrelated glasshouse experiments, tomato plants (Solanum lycopersicum) grown in hydroponics were fed for 28 d (exponential growth) with full solutions containing constant NO3(-) concentrations ([NO3(-)]) ranging from 0.05 to 15 mol m(-3), both under ambient or CO2-enriched (1000 microl l(-1)) air. * Each experiment comprised five harvests. Low [NO3(-)] (< 0.3 mol m(-3)) limited growth via leaf area (LA) restriction and decreased light interception. CO2 enrichment enhanced dry weight and LA. RUE was not affected by [NO3(-)], but increased under CO2-enriched air. By contrast, NRUE was not affected by [NO3(-)] or CO2 enrichment. * It is suggested that the radiation efficiency for organic N acquisition (NRUE) did not depend on C or N nutrition for young plants grown under unstressed conditions.

Expression of two maize putative nitrate transporters in response to nitrate and sugar availability

A full-length cDNA encoding a putative high-affinity nitrate transporter (ZmNrt2.2) from maize was isolated and characterised, together with another previously identified transporter (ZmNrt2.1), in terms of phylogenesis, protein structure prediction and regulation of transcript accumulation in response to nitrate and sugar availability. The expression of both genes was evaluated by quantitative and semi-quantitative RT-PCR in response to nitrate and sugar supply and the in planta localisation of mRNA was studied by in situ hybridisation. Data obtained suggested similar genetic evolution and identical transmembrane structure prediction between the two deduced proteins, and differences in both regulation of their expression and mRNA localisation in response to nitrate, leading us to hypothesise a principal role for ZmNRT2.1 in the influx activity and the major involvement of ZmNRT2.2 in the xylem loading process. Our data suggest opposing sugar regulation by ZmNrt2.1 and ZmNrt2.2 transcription in the presence or absence of nitrate and the existence of both hexokinase-dependent and hexokinase-independent transduction mechanisms for the regulation of ZmNrt2.1 and ZmNrt2.2 expression by sugars.

The Arabidopsis halophytic relative Thellungiella halophila tolerates nitrogen-limiting conditions by maintaining growth, nitrogen uptake, and assimilation

A comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low (15)NO(3)(-) supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance.

Nitrogen deficiency inhibits leaf blade growth in Lolium perenne by increasing cell cycle duration and decreasing mitotic and post-mitotic growth rates

Nitrogen deficiency severely inhibits leaf growth. This response was analysed at the cellular level by growing Lolium perenne L. under 7.5 mM (high) or 1 mM (low) nitrate supply, and performing a kinematic analysis to assess the effect of nitrogen status on cell proliferation and cell growth in the leaf blade epidermis. Low nitrogen supply reduced leaf elongation rate (LER) by 43% through a similar decrease in the cell production rate and final cell length. The former was entirely because of a decreased average cell division rate (0.023 versus 0.032 h(-1)) and thus longer cell cycle duration (30 versus 22 h). Nitrogen status did not affect the number of division cycles of the initial cell's progeny (5.7), and accordingly the meristematic cell number (53). Meristematic cell length was unaffected by nitrogen deficiency, implying that the division and mitotic growth rates were equally impaired. The shorter mature cell length arose from a considerably reduced post-mitotic growth rate (0.033 versus 0.049 h(-1)). But, nitrogen stress did not affect the position where elongation stopped, and increased cell elongation duration. In conclusion, nitrogen deficiency limited leaf growth by increasing the cell cycle duration and decreasing mitotic and post-mitotic elongation rates, delaying cell maturation.

Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula

Legumes can acquire nitrogen (N) from NO(3)(-), NH(4)(+), and N(2) (through symbiosis with Rhizobium bacteria); however, the mechanisms by which uptake and assimilation of these N forms are coordinately regulated to match the N demand of the plant are currently unknown. Here, we find by use of the split-root approach in Medicago truncatula plants that NO(3)(-) uptake, NH(4)(+) uptake, and N(2) fixation are under general control by systemic signaling of plant N status. Indeed, irrespective of the nature of the N source, N acquisition by one side of the root system is repressed by high N supply to the other side. Transcriptome analysis facilitated the identification of over 3,000 genes that were regulated by systemic signaling of the plant N status. However, detailed scrutiny of the data revealed that the observation of differential gene expression was highly dependent on the N source. Localized N starvation results, in the unstarved roots of the same plant, in a strong compensatory up-regulation of NO(3)(-) uptake but not of either NH(4)(+) uptake or N(2) fixation. This indicates that the three N acquisition pathways do not always respond similarly to a change in plant N status. When taken together, these data indicate that although systemic signals of N status control root N acquisition, the regulatory gene networks targeted by these signals, as well as the functional response of the N acquisition systems, are predominantly determined by the nature of the N source.

Nitrite acts as a transcriptome signal at micromolar concentrations in Arabidopsis roots

Nitrate serves as a potent signal to control gene expression in plants and algae, but little is known about the signaling role of nitrite, the direct product of nitrate reduction. Analysis of several nitrate-induced genes showed that nitrite increases mRNA levels as rapidly as nitrate in nitrogen-starved Arabidopsis (Arabidopsis thaliana) roots. Both nitrite and nitrate induction are apparent at concentrations as low as 100 nm. The response at low nitrite concentrations was not due to contaminating nitrate, which was present at <1% of the nitrite concentration. High levels of ammonium (20 mm) in the growth medium suppressed induction of several genes by nitrate, but had varied effects on the nitrite response. Transcriptome analysis using 250 or 5 microm nitrate or nitrite showed that over one-half of the nitrate-induced genes, which included genes involved in nitrate and ammonium assimilation, energy production, and carbon and nitrogen metabolism responded equivalently to nitrite; however, the nitrite response was more robust and there were many genes that responded specifically to nitrite. Thus, nitrite can serve as a signal as well as if not better than nitrate.

Cytokinins and auxin communicate nitrogen availability as long-distance signal molecules in pineapple (Ananas comosus)

This work aimed at identifying a possible role of phytohormones in long-distance (root-shoot) signaling under nitrogen deficiency. Three-months old pineapple plants were transferred from Murashige and Skoog (MS) medium to nitrogen-free MS (-N). During the first 24h on -N, 20 plants were harvested every 4h. After 30 days in -N, the remaining plants were transferred back to regular MS (+N) and 20 plants harvested every 4h for the first 24h. Following the harvests, endogenous levels of nitrate (NO(3)(-)), indole-3-acetic acid (IAA), isopentenyladenine (iP), isopentenyladenine riboside (iPR), zeatin (Z) and zeatin riboside (ZR) were analyzed in roots and leaves. In N-starved plants, the NO(3)(-) level dropped by 20% in roots between the first (4h) and the second harvest (8h). In leaves a reduction of 20% was found 4h later. Accumulation of IAA peaked in leaves at 16h. In roots, the accumulation of IAA only started at 16h while the leaf content was already in decline, which suggests that the hormone might have traveled from the leaves to the roots, communicating N-shortage. The contents of the four cytokinins were generally low in both, shoot and roots, and remained almost unchanged during the 24h of analysis. After N re-supply, roots showed a NO(3)(-) peak at 8h whereas the foliar concentration increased 4h later. Hormone levels in roots climaxed at 8h, this coinciding with the highest NO(3)(-) concentration. In leaf tissue, a dramatic accumulation was only observed for Z and ZR, and the peak was seen 4h later than in roots, suggesting that Z-type cytokinins might have traveled from the roots to the leaves. These findings provide evidence that there is a signaling pathway for N availability in pineapple plants, communicated upwards through cytokinins (N-supplemented plants) and downwards through auxin (N-starved plants).

Canopy light gradient perception by cytokinin

We have recently identified cytokinin as an important xylem-carried signal involved in the photosynthetic acclimation of plants to light gradients in dense canopies. Lower leaves become shaded in a dense canopy and consequently have reduced transpiration rates. our measurements have shown that this results in a reduced delivery of cytokinins carried in the transpiration stream to shaded leaves, as compared to light-exposed leaves. Cytokinins are involved in the regulation of photosynthetic acclimation to the light gradient by stimulating the expression of photosynthetic enzymes in light-exposed leaves. In shaded leaves, the low delivery rate of cytokinin leads to reduced photosynthetic capacity and ultimately senescence. We show evidence for this role of cytokinin, as part of a complex of signaling pathways where other regulatory mechanisms are also involved. A model is presented depicting the regulation of photosynthetic acclimation by cytokinin delivery to leaves dependent on the irradiance they receive.

Identification of a 150 bp cis-acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant

The Arabidopsis thaliana AtNRT2.1 gene, which encodes a NO(3)(-) transporter involved in high-affinity uptake by the roots, is a molecular target of several mechanisms responsible for the regulation of root NO(3)(-) acquisition by the N status of the plant. All levels of AtNRT2.1 expression (promoter activity, transcript level, protein accumulation, transport activity) are coordinately up-regulated in the presence of NO(3)(-), and repressed by downstream N metabolites. Transgenic plants expressing the GUS reporter gene under the control of upstream sequences of AtNRT2.1 have been studied to identify elements targeted by these two regulatory mechanisms. A 150 bp sequence located upstream of the TATA box that is required for both stimulation by NO(3)(-) and repression by N metabolites of the promoter has been identified. This sequence is able to confer these two regulations to a minimal promoter. Split-root experiments indicate that the stimulation of the chimaeric promoter by NO(3)(-) occurs only at the local level, whereas its repression by N metabolites is mediated by a systemic signal spread to the whole plant. The activity of the cis-acting 150 bp element is also regulated by sucrose supply to the roots, suggesting a possible interaction between N and C signalling within this short region. Accordingly, multiple motifs potentially involved in regulations by N and/or C status are identified within this sequence by bioinformatic approaches. This is the first report of such a cis-acting element in higher plants.

Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis

BACKGROUND

A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and identifying N-responsive genes in order to manipulate their expression, thus enabling plants to use N more efficiently. No studies have yet delineated these responses at the transcriptional level when plants are grown under chronic N stress and the understanding of regulatory elements involved in N response is very limited.

RESULTS

To further our understanding of the response of plants to varying N levels, a growth system was developed where N was the growth-limiting factor. An Arabidopsis whole genome microarray was used to evaluate global gene expression under different N conditions. Differentially expressed genes under mild or severe chronic N stress were identified. Mild N stress triggered only a small set of genes significantly different at the transcriptional level, which are largely involved in various stress responses. Plant responses were much more pronounced under severe N stress, involving a large number of genes in many different biological processes. Differentially expressed genes were also identified in response to short- and long-term N availability increases. Putative N regulatory elements were determined along with several previously known motifs involved in the responses to N and carbon availability as well as plant stress.

CONCLUSION

Differentially expressed genes identified provide additional insights into the coordination of the complex N responses of plants and the components of the N response mechanism. Putative N regulatory elements were identified to reveal possible new components of the regulatory network for plant N responses. A better understanding of the complex regulatory network for plant N responses will help lead to strategies to improve N use efficiency.

Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis

BACKGROUND

A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and identifying N-responsive genes in order to manipulate their expression, thus enabling plants to use N more efficiently. No studies have yet delineated these responses at the transcriptional level when plants are grown under chronic N stress and the understanding of regulatory elements involved in N response is very limited.

RESULTS

To further our understanding of the response of plants to varying N levels, a growth system was developed where N was the growth-limiting factor. An Arabidopsis whole genome microarray was used to evaluate global gene expression under different N conditions. Differentially expressed genes under mild or severe chronic N stress were identified. Mild N stress triggered only a small set of genes significantly different at the transcriptional level, which are largely involved in various stress responses. Plant responses were much more pronounced under severe N stress, involving a large number of genes in many different biological processes. Differentially expressed genes were also identified in response to short- and long-term N availability increases. Putative N regulatory elements were determined along with several previously known motifs involved in the responses to N and carbon availability as well as plant stress.

CONCLUSION

Differentially expressed genes identified provide additional insights into the coordination of the complex N responses of plants and the components of the N response mechanism. Putative N regulatory elements were identified to reveal possible new components of the regulatory network for plant N responses. A better understanding of the complex regulatory network for plant N responses will help lead to strategies to improve N use efficiency.

Regulation of root nitrate uptake at the NRT2.1 protein level in Arabidopsis thaliana

In Arabidopsis the NRT2.1 gene encodes a main component of the root high-affinity nitrate uptake system (HATS). Its regulation has been thoroughly studied showing a strong correlation between NRT2.1 expression and HATS activity. Despite its central role in plant nutrition, nothing is known concerning localization and regulation of NRT2.1 at the protein level. By combining a green fluorescent protein fusion strategy and an immunological approach, we show that NRT2.1 is mainly localized in the plasma membrane of root cortical and epidermal cells, and that several forms of the protein seems to co-exist in cell membranes (the monomer and at least one higher molecular weight complex). The monomer is the most abundant form of NRT2.1, and seems to be the one involved in NO(3)(-) transport. It strictly requires the NAR2.1 protein to be expressed and addressed at the plasma membrane. No rapid changes in NRT2.1 abundance were observed in response to light, sucrose, or nitrogen treatments that strongly affect both NRT2.1 mRNA level and HATS activity. This suggests the occurrence of post-translational regulatory mechanisms. One such mechanism could correspond to the cleavage of NRT2.1 C terminus, which results in the presence of both intact and truncated proteins in the plasma membrane.

Effects of agricultural production systems and their components on protein profiles of potato tubers

A range of studies have compared the level of nutritionally relevant compounds in crops from organic and nonorganic farming systems, but there is very limited information on the effect of farming systems and their key components on the protein composition of plants. We addressed this gap by quantifying the effects of different farming systems and key components of such systems on the protein profiles of potato tubers. Tuber samples were produced in the Nafferton factorial systems study, a group of long-term, replicated factorial field experiments designed to identify and quantify the effect of fertility management methods, crop protection practices and rotational designs used in organic, low input and conventional production systems. Protein profiles were determined by 2-DE and subsequent protein identification by HPLC-ESI-MS/MS. Principal component analysis of 2-DE data showed that only fertility management practices (organic matter vs. mineral fertiliser based) had a significant effect on protein composition. Quantitative differences were detected in 160 of the 1100 tuber proteins separated by 2-DE. Proteins identified by MS are involved in protein synthesis and turnover, carbon and energy metabolism and defence responses, suggesting that organic fertilisation leads to an increased stress response in potato tubers.

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis and indicate that regulation by carbon/nitrogen metabolites occurs at multiple levels.

Background

Carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana. Here, we use multinetwork analysis of microarray data to identify molecular networks regulated by C and N in the Arabidopsis root system.

Results

We used the Arabidopsis whole genome Affymetrix gene chip to explore global gene expression responses in plants exposed transiently to a matrix of C and N treatments. We used ANOVA analysis to define quantitative models of regulation for all detected genes. Our results suggest that about half of the Arabidopsis transcriptome is regulated by C, N or CN interactions. We found ample evidence for interactions between C and N that include genes involved in metabolic pathways, protein degradation and auxin signaling. To provide a global, yet detailed, view of how the cell molecular network is adjusted in response to the CN treatments, we constructed a qualitative multinetwork model of the Arabidopsis metabolic and regulatory molecular network, including 6,176 genes, 1,459 metabolites and 230,900 interactions among them. We integrated the quantitative models of CN gene regulation with the wiring diagram in the multinetwork, and identified specific interacting genes in biological modules that respond to C, N or CN treatments.

Conclusion

Our results indicate that CN regulation occurs at multiple levels, including potential post-transcriptional control by microRNAs. The network analysis of our systematic dataset of CN treatments indicates that CN sensing is a mechanism that coordinates the global and coordinated regulation of specific sets of molecular machines in the plant cell.

Comparative effect of Al, Se, and Mo toxicity on NO3(-) assimilation in sunflower (Helianthus annuus L.) plants

Here, we study the effect caused by three trace elements--Al, Se, and Mo--applied at the same concentration (100 microM) and in their oxyanionic forms--NaAl(OH)(4), Na(2)SeO(4), and Na(2)MoO(4)--on NO(3)(-) assimilation (NO(3)(-), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamate synthase (GOGAT) activities, and concentrations of amino acids and proteins) in sunflower (Helianthus annuus L. var. Kasol) plants. The most harmful element for sunflower plants proved to be selenate, followed by aluminate. On the contrary, the application of molybdate had no negative effect on the growth of this plant, suggesting the possibility of using sunflower for the phytoremediation of this metal, mainly in agricultural zones used for grazing where the excess of this element can provoke problems of molybdenosis in ruminants (particularly in cattle). In addition, we found that the alteration of NO(3)(-) assimilation by SeO(4)(2-) and Al(OH)(4)(-) directly influences the growth and development of plants, foliar inhibition of NR activity by SeO(4)(2-) being more harmful than the decrease in foliar availability of NO(3)(-) provoked by Al(OH)(4)(-).

Cytokinin import rate as a signal for photosynthetic acclimation to canopy light gradients

Plants growing in dense canopies are exposed to vertical light gradients and show photosynthetic acclimation at the whole-plant level, resulting in efficient photosynthetic carbon gain. We studied the role of cytokinins transported through the transpiration stream as one of probably multiple signals for photosynthetic acclimation to light gradients using both tobacco (Nicotiana tabacum) and Arabidopsis (Arabidopsis thaliana). We show that substantial variation in leaf transpiration parallels the light gradient in tobacco canopies and experimental reduction of the transpiration rate of a leaf, independent of light, is sufficient to reduce photosynthetic capacity in both species, as well as transcript levels of the small subunit of Rubisco (rbcS) gene in Arabidopsis. Mass spectrometric analysis of xylem sap collected from intact, transpiring tobacco plants revealed that shaded leaves import less cytokinin than leaves exposed to high light. In Arabidopsis, reduced transpiration rate of a leaf in the light is associated with lower cytokinin concentrations, including the bioactive trans-zeatin and trans-zeatin riboside, as well as reduced expression of the cytokinin-responsive genes ARR7 and ARR16. External application of cytokinin to shaded leaves rescued multiple shade effects, including rbcS transcript levels in both species, as did locally induced cytokinin overproduction in transgenic tobacco plants. From these data, we conclude that light gradients over the foliage of a plant result in reduced cytokinin activity in shaded leaves as a consequence of reduced import through the xylem and that cytokinin is involved in the regulation of whole-plant photosynthetic acclimation to light gradients in canopies.

A mutation in NLA, which encodes a RING-type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation

Abundant nitrogen is required for the optimal growth and development of plants, while numerous biotic and abiotic factors that consume soil nitrogen frequently create a nitrogen limitation growth condition. To cope with this, plants have evolved a suite of adaptive responses to nitrogen limitation. However, the molecular mechanism governing the adaptability of plants to nitrogen limitation is totally unknown because no reported mutant defines this trait. Here we isolated an Arabidopsis mutant, nla (nitrogen limitation adaptation), and identified the NLA gene as an essential component in this molecular mechanism. Supplied with insufficient inorganic nitrogen (nitrate or ammonium), the nla mutant failed to develop the essential adaptive responses to nitrogen limitation, but senesced much earlier and more rapidly than did the wild type. Under other stress conditions including low phosphorus nutrient, drought and high temperature, the nla mutant did not show this early senescence phenotype, but closely resembled the wild type in growth and development. Map-based cloning of NLA revealed that this gene encodes a RING-type ubiquitin ligase, and nla is a deletion mutation which does not code for the RING domain in the NLA protein. The NLA protein is localized to the nuclear speckles, where this protein interacts with the Arabidopsis ubiquitin conjugase 8 (AtUBC8). In the nla mutant, the deletion of the RING domain from NLA altered its subcellular localization, disrupted the interaction between NLA and AtUBC8 and caused the early senescence phenotype induced by low inorganic nitrogen. All the results indicate that NLA is a positive regulator for the development of the adaptability of Arabidopsis to nitrogen limitation.

Nitrogen deficiency in Arabidopsis affects galactolipid composition and gene expression and results in accumulation of fatty acid phytyl esters

Nitrogen is an essential nutrient for plants because it represents a major constituent of numerous cellular compounds, including proteins, amino acids, nucleic acids and lipids. While N deprivation is known to have severe consequences for primary carbon metabolism, the effect on chloroplast lipid metabolism has not been analysed in higher plants. Nitrogen limitation in Arabidopsis led to a decrease in the chloroplast galactolipid monogalactosyldiacylglycerol (MGDG) and a concomitant increase in digalactosyldiacylglycerol (DGDG), which correlated with an elevated expression of the DGDG synthase genes DGD1 and DGD2. The amounts of triacylglycerol and free fatty acids increased during N deprivation. Furthermore, phytyl esters accumulated containing medium-chain fatty acids (12:0, 14:0) and a large amount of hexadecatrienoic acid (16:3). Fatty acid phytyl esters were localized to chloroplasts, in particular to thylakoids and plastoglobules. Different polyunsaturated acyl groups were found in phytyl esters accumulating in Arabidopsis lipid mutants and in other plants, including 16:3 and 18:3 species. Therefore N deficiency in higher plants results in a co-ordinated breakdown of galactolipids and chlorophyll with deposition of specific fatty acid phytyl esters in thylakoids and plastoglobules of chloroplasts.

Nitrogen assimilation studies using 15N in soybean plants treated with imazethapyr, an inhibitor of branched-chain amino acid biosynthesis

The pattern of nitrogen assimilation in soybean plants treated with a herbicide that inhibits branched-chain amino acid biosynthesis was evaluated by (15)N isotopic analysis. The herbicide imazethapyr caused a strong decrease in nitrate uptake by roots, partly due to a reduced stomatal conductance. The inhibition of (15)N uptake was accompanied by a decrease in the (15)N content in the plant and, concomitantly, an inhibition of translocation to the shoot. Imazethapyr inhibited nitrate reductase activity in leaves and roots. Among all parameters studied, "de novo" synthesis of proteins was the first parameter of the N assimilation metabolism affected by the herbicide. These results show that this class of herbicides totally damages N metabolism and indicates a regulatory effect on N uptake and translocation that would be mediated by the increase in free amino acid pool provoked by the inhibition of branched-chain amino acid biosynthesis.

Regulation of the high-affinity NO3- uptake system by NRT1.1-mediated NO3- demand signaling in Arabidopsis

The NRT2.1 gene of Arabidopsis thaliana encodes a major component of the root high-affinity NO(3)(-) transport system (HATS) that plays a crucial role in NO(3)(-) uptake by the plant. Although NRT2.1 was known to be induced by NO(3)(-) and feedback repressed by reduced nitrogen (N) metabolites, NRT2.1 is surprisingly up-regulated when NO(3)(-) concentration decreases to a low level (<0.5 mm) in media containing a high concentration of NH(4)(+) or Gln (>or=1 mm). The NRT3.1 gene, encoding another key component of the HATS, displays the same response pattern. This revealed that both NRT2.1 and NRT3.1 are coordinately down-regulated by high external NO(3)(-) availability through a mechanism independent from that involving N metabolites. We show here that repression of both genes by high NO(3)(-) is specifically mediated by the NRT1.1 NO(3)(-) transporter. This mechanism warrants that either NRT1.1 or NRT2.1 is active in taking up NO(3)(-) in the presence of a reduced N source. Under low NO(3)(-)/high NH(4)(+) provision, NRT1.1-mediated repression of NRT2.1/NRT3.1 is relieved, which allows reactivation of the HATS. Analysis of atnrt2.1 mutants showed that this constitutes a crucial adaptive response against NH(4)(+) toxicity because NO(3)(-) taken up by the HATS in this situation prevents the detrimental effects of pure NH(4)(+) nutrition. It is thus hypothesized that NRT1.1-mediated regulation of NRT2.1/NRT3.1 is a mechanism aiming to satisfy a specific NO(3)(-) demand of the plant in relation to the various specific roles that NO(3)(-) plays, in addition to being a N source. A new model is proposed for regulation of the HATS, involving both feedback repression by N metabolites and NRT1.1-mediated repression by high NO(3)(-).

Interactions between nitrogen and cytokinin in the regulation of metabolism and development

Inorganic nitrogen is a substrate for nitrogen assimilation and also functions as a signal triggering widespread changes in gene expression that modulate metabolism and development. To integrate the actions of the nitrogen signal at the whole plant level, plants use multiple signaling routes that communicate internal and external nitrogen status. One route depends on nitrate itself and one uses cytokinin as a messenger. Recent genome-wide research has shown that the nitrate-specific signal regulates a wide variety of metabolic processes including nitrogen and carbon metabolism, and cytokinin biosynthesis. Cytokinin-mediated signaling is related to the control of development, protein synthesis and acquisition of macronutrients. The coordination and interaction of both regulatory pathways is important for normal plant growth under variable nitrogen supply conditions.

Characterization and functional analysis of phosphoenolpyruvate carboxylase kinase genes in rice

Phosphoenolpyruvate carboxylase (PEPC), a key enzyme of primary metabolism of higher plants, is regulated by reversible phosphorylation, which is catalyzed by PEPC kinase (PPCK). Rice has three functional PPCK genes, OsPPCK1, OsPPCK2 and OsPPCK3, all of which have an intron close to the 3' end of the coding region. A novel control mechanism was found for expression of OsPPCK2, namely alternative transcription initiation, and two different transcripts were detected. The four different transcripts of the OsPPCK genes showed different expression patterns. While OsPPCK1 and OsPPCK3 were highly expressed in roots and at low levels in other organs, the two OsPPCK2 transcripts were expressed in all organs. OsPPCK3 was expressed mostly at night, while the long OsPPCK2 transcripts were present in the leaves only in the daytime. Nitrate supplementation of leaves selectively induced expression of both OsPPCK2 transcripts, while phosphate starvation only induced the shorter one. Such diverse expression patterns of OsPPCK genes suggest the importance and variety of strict activity regulation of PEPC in rice. From the correlation between gene expression and the phosphorylation level of PEPC, which was monitored as that of the maize PEPC expressed in transgenic rice plants, it was concluded that the short OsPPCK2 transcripts were expressed in rice leaf mesophyll cells upon nitrogen supplementation and phosphate starvation, whereas OsPPCK3 participated in the nocturnal phosphorylation of PEPC in these cells. Expression of PPCK proteins in rice leaves was detected by immunoblotting using a specific antiserum, and the expression of two different OsPPCK2 proteins derived from alternative transcription initiation was confirmed.

Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control

Sucrose starvation of Arabidopsis (Arabidopsis thaliana) cell culture was used to identify translationally regulated genes by DNA microarray analysis. Cells were starved by subculture without sucrose, and total and polysomal RNA was extracted between 6 and 48 h. Probes were derived from both RNA populations and used to screen oligonucleotide microarrays. Out of 25,607 screened genes, 224 were found to be differentially accumulated in polysomal RNA following starvation and 21 were found to be invariant in polysomal RNA while their total RNA abundance was modified. Most of the mRNA appears to be translationally repressed (183/245 genes), which is consistent with a general decrease in metabolic activities during starvation. The parallel transcriptional analysis identifies 268 regulated genes. Comparison of transcriptional and translational gene lists highlights the importance of translational regulation (mostly repression) affecting genes involved in cell cycle and cell growth, these being overrepresented in translationally regulated genes, providing a molecular framework for the arrest of cell proliferation following starvation. Starvation-induced translational control also affects chromatin regulation genes, such as the HD1 histone deacetylase, and the level of histone H4 acetylation was found to increase during starvation. This suggests that regulation of the global nuclear transcriptional activity might be linked to cytoplasmic translational regulations.

Regulation of secondary metabolism by the carbon-nitrogen status in tobacco: nitrate inhibits large sectors of phenylpropanoid metabolism

Interactions between nitrogen and carbon metabolism modulate many aspects of the metabolism, physiology and development of plants. This paper investigates the contribution of nitrate and nitrogen metabolism to the regulation of phenylpropanoid and nicotine synthesis. Wild-type tobacco was grown on 12 or 0.2 mm nitrate and compared with a nitrate reductase-deficient mutant [Nia30(145)] growing on 12 mm nitrate. Nitrate-deficient wild-type plants accumulate high levels of a range of phenylpropanoids including chlorogenic acid, contain high levels of rutin, are highly lignified, but contain less nicotine than nitrogen-replete wild-type tobacco. Nia30(145) resembles nitrate-deficient wild-type plants with respect to the levels of amino acids, but accumulates large amounts of nitrate. The levels of phenylpropanoids, rutin and lignin resemble those in nitrogen-replete wild-type plants, whereas the level of nicotine resembles that in nitrate-deficient wild-type plants. Expression arrays and real time RT-PCR revealed that a set of genes required for phenylpropanoid metabolism including PAL, 4CL and HQT are induced in nitrogen-deficient wild-type plants but not in Nia30(145). It is concluded that nitrogen deficiency leads to a marked shift from the nitrogen-containing alkaloid nicotine to carbon-rich phenylpropanoids. The stimulation of phenylpropanoid metabolism is triggered by changes of nitrate, rather than downstream nitrogen metabolites, and is mediated by induction of a set of enzymes in the early steps of the phenylpropanoid biosynthetic pathway.

Lead toxicity in Brassica pekinensis Rupr.: effect on nitrate assimilation and growth

Lead is a major heavy-metal contaminant in the environment that has various anthropogenic and natural sources. To study the phytotoxic effects of Pb on the popular vegetable Chinese cabbage (Brassica pekinensis Rupr.) via depression of nitrogen assimilation, pot culture experiments with three concentrations of treatment with Pb (0, 4, and 8 mmol/kg dry soil) were carried out. Our results demonstrated adverse effects of Pb on nitrogen assimilation and plant growth. The addition of Pb in the soil resulted in elevated accumulation of Pb in the shoots of the plants: Pb concentrations of 14.3, 202.3, and 418.2 mg/kg (DW) in the shoots were detected with the 0, 4, and 8 mmol/kg treatments, respectively. Compared to the control, Pb exposure (4 and 8 mmol/kg) significantly decreased shoot nitrate content (71% and 80% of the control), nitrate reductase activity (104% and 49% of the control), and free amino acid content (81% and 82% of the control), indicating decreased nitrogen assimilation in the plants. The effect of Pb also was shown by the progressive decline in shoot biomass with increasing Pb concentration in plant shoots and in the soil. However, at the treatment levels used in this study, lead did not induce visible toxic symptoms. The lowest-concentration Pb treatment (4 mmol/kg) stimulated chlorophyll b content but did not influence chlorophyll a content. The results suggested that the toxicity of Pb to the plants occurred at least partly via depression of nitrogen assimilation.

Impact of nitrate supply in C and N assimilation in the parasitic plant Striga hermonthica (Del.) Benth (Scrophulariaceae) and its host Sorghum bicolor L

The threshold of tolerance for nitrate of the parasitic weed Striga hermonthica (Del.) Benth and the host plant Sorghum bicolor L. was determined by estimating the impact of increasing nitrate loads on plant growth and various parameters of C and N assimilation. Nitrate supply improved chlorophyll (Chl) content and photosystem II (PSII) photochemistry of infected S. bicolor that, in comparison to S. hermonthica, displayed a low imbalance between C and N assimilation when nitrate was supplied up to 1500 mg N per plant. Indeed, nitrate supplies increased strongly the leaf N:C ratio of the parasite. The higher nitrate load induced strong accumulation of nitrate, nitrite and ammonium, and consequently the death of S. hermonthica. Nevertheless, lower nitrate loads (up to 500 mg N per S. bicolor in this study) promoted leaf expansion, PSII photochemistry and N metabolism of S. hermonthica mature (M) plants, as attested by the significant rise in soluble protein and free amino-acid contents. Following these N supplies, the nitrate tolerance of S. hermonthica was correlated with an increase in PSII activity and a high incorporation of N excess into asparagine. This confirmed the central role of asparagine in the N metabolism of S. hermonthica, although this detoxification pathway was insufficient to limit ammonium accumulation under higher nitrate loads.

Expression and transcriptional regulation of amino acid transporters in plants

Recent studies have shown that there are more than 50 amino acid transporter genes in the Arabidopsis genome. This abundance of amino acid transporters implies that they play a multitude of fundamental roles in plant growth and development. Current research on the expression and regulation (i.e., tissue-specific expression and regulation of expression in response to nutrient and environmental changes) of these genes has provided useful information about the functional significance of plant amino acid transport systems.

Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray

Development of crop varieties with high nitrogen use efficiency (NUE) is imperative for sustainable agriculture. Understanding how plant genes respond to low N stress is essential for formulating approaches to manipulating genes for improving NUE. In this study we analyzed the expression profiles of an indica rice cultivar Minghui 63 at seedling stage at 20 min, 1 and 2 h after low N stress with the normal N as the control, using a microarray of 11,494 rice ESTs representing 10,422 unique genes. While no significant difference was detected in the leaf tissue, a total of 471 ESTs were detected as responsive to low N stress in the root tissue with 115 ESTs showing up-regulation and 358 ESTs showing down-regulation. The analysis of expression profiles after low N stress identified following patterns: (1) the genes involved in photosynthesis and energy metabolism were down-regulated rapidly; (2) many of the genes involved in early responses to biotic and abiotic stresses were up-regulated while many other stress responsive genes were down-regulated; (3) regulatory genes including transcription factors and ones involved in signal transduction were both up- and down-regulated; and (4) the genes known to be involved in N uptake and assimilation showed little response to the low N stress. The challenges for future studies are to characterize the functional roles of the low N stress responsive genes in N metabolisms, including the large number of genes presently with unknown functions.

Three maize leaf ferredoxin:NADPH oxidoreductases vary in subchloroplast location, expression, and interaction with ferredoxin

In higher plants, ferredoxin (Fd):NADPH oxidoreductase (FNR) catalyzes reduction of NADP+ in the final step of linear photosynthetic electron transport and is also implicated in cyclic electron flow. We have identified three leaf FNR isoenzymes (LFNR1, LFNR2, and LFNR3) in maize (Zea mays) chloroplasts at approximately equivalent concentrations. Fractionation of chloroplasts showed that, while LFNR3 is an exclusively soluble enzyme, LFNR1 is only found at the thylakoid membrane and LFNR2 has a dual location. LFNR1 and LFNR2 were found to associate with the cytochrome b6f complex following its partial purification. We cloned LFNR3 and produced all three isoenzymes as stable, soluble proteins. Measurement of Fd reduction ability showed no significant differences between these recombinant enzymes. Column chromatography revealed variation between the interaction mechanisms of LFNR1 and LFNR2 with Fd, as detected by differential dependence on specific intermolecular salt bridges and variable sensitivity of interactions to changes in pH. A comparison of LFNR transcripts in leaves of plants grown on variable nitrogen regimes revealed that LFNR1 and LFNR2 transcripts are relatively more abundant under conditions of high demand for NADPH. These results are discussed in terms of the functional differentiation of maize LFNR isoenzymes.

Nutritional regulation of ANR1 and other root-expressed MADS-box genes in Arabidopsis thaliana

The ANR1 MADS-box gene in Arabidopsis thaliana (L.) Heynh. has previously been identified as a key regulator of lateral root growth in response to signals from external nitrate (NO3(-)). We have used quantitative real-time PCR to investigate the responsiveness of ANR1 and 11 other root-expressed MADS-box genes to fluctuations in the supply of N, P and S. ANR1 expression in roots of hydroponically grown Arabidopsis plants was specifically regulated by changes in the N supply, being induced by N deprivation and rapidly repressed by N re-supply. This pattern of N responsiveness differs from the NO3(-)-inducibility of ANR1 previously observed in Arabidopsis root cultures [H.M. Zhang and B.G. Forde (1998) Science 279:407-409]. Seven of the other MADS-box genes responded to N in a manner similar to ANR1, but less strongly, while four (AGL12, AGL17, AGL18 and AGL79) were unaffected. Six of the N-regulated genes (ANR1, AGL14, AGL16, AGL19, SOC1 and AGL21) belong to just two clades within the type II MADS-box lineage, while the other two (AGL26 and AGL56) belong to the poorly characterized type I lineage. Only SOC1 was additionally found to respond to changes in the P and S supply, suggesting a possible role in a general response to nutrient stress. Studies with an ANR1 transposon-insertion mutant provided no evidence for regulatory interactions between ANR1 and the other root-expressed MADS-box genes. The implications of the current data for our understanding of the role of ANR1 and other MADS box genes in the nutritional regulation of lateral root growth are discussed.

A model for the circadian oscillations in expression and activity of nitrate reductase in higher plants

BACKGROUND AND AIMS

Nitrate is the major nitrogen source for many plants. The first step of the nitrate assimilation pathway is the reduction of nitrate to nitrite, catalysed by nitrate reductase (NR). Circadian oscillations in expression and activity of NR have been demonstrated in many plant species. The pathway by which this circadian behaviour is regulated remains to be elucidated. In this study, based on recent experimental observations, a mathematical model is proposed to explain the origin of diurnal and circadian oscillations in NR gene expression and enzyme activity.

METHODS

The dynamic model is based on the feedback interconnections between NR and its substrate, nitrate. In the model, NR activity is regulated at the transcriptional level, in response to the balance between nitrate influx and reduction, and at the post-translational levels in response to signals from carbon assimilation. Conditions for the model system to generate self-sustained circadian oscillations are investigated by numerical simulations.

KEY RESULTS AND CONCLUSIONS

Under light/dark cycles, the simulation results are in agreement with the observed diurnal pattern of changes in leaf nitrate concentration, NR transcript level and NR activity. Within a range of kinetic parameter values, circadian oscillation behaviour persists even under constant light, with periods of approx. 24 h. These simulation results suggest that sustained circadian oscillations can originate from the feedback interactions between NR and its substrate, nitrate, without the need to postulate the existence of an endogenous 'circadian clock'.

Plant N capture from pulses: effects of pulse size, growth rate, and other soil resources

In arid ecosystems, the ability to rapidly capture nitrogen (N) from brief pulses is expected to influence plant growth, survival, and competitive ability. Theory and data suggest that N capture from pulses should depend on plant growth rate and availability of other limiting resources. Theory also predicts trade-offs in plant stress tolerance and ability to capture N from different size pulses. We injected K15NO3, to simulate small and large N pulses at three different times during the growing season into soil around the co-dominant Great Basin species Sarcobatus vermiculatus, Chrysothamnus nauseosus ssp. consimilis, and Distichlis spicata. Soils were amended with water and P in a partial factorial design. As predicted, all study species showed a comparable decline in N capture from large pulses through the season as growth rates slowed. Surprisingly, however, water and P availability differentially influenced the ability of these species to capture N from pulses. Distichlis N capture increased up to tenfold with water addition while Chrysothamnus N capture increased up to threefold with P addition. Sarcobatus N capture was not affected by water or P availability. Opposite to our prediction, Sarcobatus, the most stress tolerant species, captured less N from small pulses but more N from large pulses relative to the other species. These observations suggest that variation in N pulse timing and size can interact with variable soil water and P supply to determine how N is partitioned among co-existing Great Basin species.

Light-dark changes in cytosolic nitrate pools depend on nitrate reductase activity in Arabidopsis leaf cells

Several different cellular processes determine the size of the metabolically available nitrate pool in the cytoplasm. These processes include not only ion fluxes across the plasma membrane and tonoplast but also assimilation by the activity of nitrate reductase (NR). In roots, the maintenance of cytosolic nitrate activity during periods of nitrate starvation and resupply (M. van der Leij, S.J. Smith, A.J. Miller [1998] Planta 205: 64-72; R.-G. Zhen, H.-W. Koyro, R.A. Leigh, A.D. Tomos, A.J. Miller [1991] Planta 185: 356-361) suggests that this pool is regulated. Under nitrate-replete conditions vacuolar nitrate is a membrane-bound store that can release nitrate to the cytoplasm; after depletion of cytosolic nitrate, tonoplast transporters would serve to restore this pool. To study the role of assimilation, specifically the activity of NR in regulating the size of the cytosolic nitrate pool, we have compared wild-type and mutant plants. In leaf mesophyll cells, light-to-dark transitions increase cytosolic nitrate activity (1.5-2.8 mm), and these changes were reversed by dark-to-light transitions. Such changes were not observed in nia1nia2 NR-deficient plants indicating that this change in cytosolic nitrate activity was dependent on the presence of functional NR. Furthermore, in the dark, the steady-state cytosolic nitrate activities were not statistically different between the two types of plant, indicating that NR has little role in determining resting levels of nitrate. Epidermal cells of both wild type and NR mutants had cytosolic nitrate activities that were not significantly different from mesophyll cells in the dark and were unaltered by dark-to-light transitions. We propose that the NR-dependent changes in cytosolic nitrate provide a cellular mechanism for the diurnal changes in vacuolar nitrate storage, and the results are discussed in terms of the possible signaling role of cytosolic nitrate.

Effects of nitric oxide on growth of maize seedling leaves in the presence or absence of ultraviolet-B radiation

The leaves of maize seedlings were used to measure leaf biomass including leaf length, width and weight, and to examine the relationship between nitric oxide (NO) synthase activity in microsomes and cytosol to the exo- and endo-beta-glucanase activity during growth. It was found that ultraviolet-B radiation (UV-B radiation) strongly induced nitric oxide synthase (NOS) activity but caused both a decrease of leaf biomass and exo- or endo-beta-glucanase activity. In contrast, the NOS inhibitor and NO donor largely decreased the activity of NOS in non-irradiated seedlings. The inhibitor also reduced exo- and endo-beta-glucanase activity and leaf biomass while the donor increased the enzyme activity and leaf biomass under normal conditions. Alternatively, under ultraviolet-B, the additional inhibitor of NOS and NO donor appeared to compromise the effects of ultraviolet-B on glucanase activity and leaf biomass, making the relationship between NOS activity and glucanase activity negatively correlated. This suggests that the changes of NOS activity showed a positive correlation to glucanase activity and leaf biomass in the absence of ultraviolet-B, but a negative correlation to ultraviolet-B irradiation and NO donor treatment alone. It is assumed that exo- and endogenous NO is responsible for the up-regulation of regular growth and development without ultraviolet-B. Under UV-B radiation, however, it might function as a signaling molecule of ultraviolet-B inhibiting leaf growth of maize seedlings to carry out stress-signaling transduction.

Cytokinin biosynthesis and regulation

Most natural cytokinins (CKs) are adenine derivatives that carry an isoprene-derived side chain at the N6-terminus. Structural variation at the isoprenoid side chain alters their biological activity and stability. The first step of de novo synthesis of CKs is catalyzed by adenosine phosphate-isopentenyltransferase (IPT), which produces isopentenyladenine nucleotide. In higher plants, trans-zeatin (tZ), a major CK, is formed by subsequent hydroxylation, which is catalyzed by a cytochrome P450 monooxygenase (P450), CYP735A1 or CYP735A2. Biochemical characterization of IPTs revealed that the substrate specificities differ between Agrobacterium and higher plants. Agrobacterium IPTs have the ability to produce tZ-type species directly by use of hydroxymethylbutenyl diphosphate as the side chain donor. Analyses of expression patterns of genes for CK metabolic enzymes suggest that CK biosynthesis and homeostasis are finely controlled by internal and external environmental factors such as phytohormones and inorganic nitrogen sources. This regulatory system appears important in linking nutrient signals and morphogenetic responses.

Metabolic profiling reveals altered nitrogen nutrient regimes have diverse effects on the metabolism of hydroponically-grown tomato (Solanum lycopersicum) plants

The role of inorganic nitrogen assimilation in the production of amino acids is one of the most important biochemical processes in plants. For this reason, a detailed broad-range characterization of the metabolic response of tomato (Solanum lycopersicum) leaves to the alteration of nitrate level was performed. Tomato plants were grown hydroponically in liquid culture under three different nitrate regimes: saturated (8 mM NO3-), replete (4 mM NO3-) and deficient (0.4 mM NO3-). All treatments were performed under varied light intensity, with leaf samples being collected after 7, 14, and 21 d. In addition, the short-term response (after 1, 24, 48, and 94 h) to varying nutrient status was evaluated at the higher light intensity. GC-MS analysis of the levels of amino acids, tricarboxylic acid cycle intermediates, sugars, sugar alcohols, and representative compounds of secondary metabolism revealed substantial changes under the various growth regimes applied. The data presented here suggest that nitrate nutrition has wide-ranging effects on plant leaf metabolism with nitrate deficiency resulting in decreases in many amino and organic acids and increases in the level of several carbohydrates and phosphoesters, as well as a handful of secondary metabolites. These results are compared with previously reported transcript profiles of altered nitrogen regimes and discussed within the context of current models of carbon nitrogen interaction.

Transcript profiling in the chl1-5 mutant of Arabidopsis reveals a role of the nitrate transporter NRT1.1 in the regulation of another nitrate transporter, NRT2.1

Arabidopsis thaliana mutants deficient for the NRT1.1 NO(3)(-) transporter display complex phenotypes, including lowered NO(3)(-) uptake, altered development of nascent organs, and reduced stomatal opening. To obtain further insight at the molecular level on the multiple physiological functions of NRT1.1, we performed large-scale transcript profiling by serial analysis of gene expression in the roots of the chl1-5 deletion mutant of NRT1.1 and of the Columbia wild type. Several hundred genes were differentially expressed between the two genotypes, when plants were grown on NH(4)NO(3) as N source. Among these genes, the N satiety-repressed NRT2.1 gene, encoding a major component of the root high-affinity NO(3)(-) transport system (HATS), was found to be strongly derepressed in the chl1-5 mutant (as well as in other NRT1.1 mutants). This was associated with a marked stimulation of the NO(3)(-) HATS activity in the mutant, suggesting adaptive response to a possible N limitation resulting from NRT1.1 mutation. However, derepression of NRT2.1 in NH(4)NO(3)-fed chl1-5 plants could not be attributed to lowered production of N metabolites. Rather, the results show that normal regulation of NRT2.1 expression is strongly altered in the chl1-5 mutant, where this gene is no more repressible by high N provision to the plant. This indicates that NRT1.1 plays an unexpected but important role in the regulation of both NRT2.1 expression and NO(3)(-) HATS activity. Overexpression of NRT2.1 was also found in wild-type plants supplied with 1 mM NH(4)(+) plus 0.1 mM NO(3)(-), a situation where NRT1.1 is likely to mediate very low NO(3)(-) transport. Thus, we suggest that it is the lack of NRT1.1 activity, rather than the absence of this transporter, that derepresses NRT2.1 expression in the presence of NH(4)(+). Two hypotheses are discussed to explain these results: (1) NRT2.1 is upregulated by a NO(3)(-) demand signaling, indirectly triggered by lack of NRT1.1-mediated uptake, which overrides feedback repression by N metabolites, and (2) NRT1.1 plays a more direct signaling role, and its transport activity generates an unknown signal required for NRT2.1 repression by N metabolites. Both mechanisms would warrant that either NRT1.1 or NRT2.1 ensure significant NO(3)(-) uptake in the presence of NH(4)(+) in the external medium, which is crucial to prevent the detrimental effects of pure NH(4)(+) nutrition.

Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis

A nitrate reductase (NR)-null mutant of Arabidopsis was constructed that had a deletion of the major NR gene NIA2 and an insertion in the NIA1 NR gene. This mutant had no detectable NR activity and could not use nitrate as the sole nitrogen source. Starch mobilization was not induced by nitrate in this mutant but was induced by ammonium, indicating that nitrate was not the signal for this process. Microarray analysis of gene expression revealed that 595 genes responded to nitrate (5 mm nitrate for 2 h) in both wild-type and mutant plants. This group of genes was overrepresented most significantly in the functional categories of energy, metabolism, and glycolysis and gluconeogenesis. Because the nitrate response of these genes was NR independent, nitrate and not a downstream metabolite served as the signal. The microarray analysis also revealed that shoots can be as responsive to nitrate as roots, yet there was substantial organ specificity to the nitrate response.