The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches

A holistic view of nitrogen acquisition in plants

Nitrogen (N) is the mineral nutrient required in the greatest amount and its availability is a major factor limiting growth and development of plants. As sessile organisms, plants have evolved different strategies to adapt to changes in the availability and distribution of N in soils. These strategies include mechanisms that act at different levels of biological organization from the molecular to the ecosystem level. At the molecular level, plants can adjust their capacity to acquire different forms of N in a range of concentrations by modulating the expression and function of genes in different N uptake systems. Modulation of plant growth and development, most notably changes in the root system architecture, can also greatly impact plant N acquisition in the soil. At the organism and ecosystem levels, plants establish associations with diverse microorganisms to ensure adequate nutrition and N supply. These different adaptive mechanisms have been traditionally discussed separately in the literature. To understand plant N nutrition in the environment, an integrated view of all pathways contributing to plant N acquisition is required. Towards this goal, in this review the different mechanisms that plants utilize to maintain an adequate N supply are summarized and integrated.

Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency

Development of genetic varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Generally, NUE can be divided into two parts. First, assimilation efficiency involves nitrogen (N) uptake and assimilation and second utilization efficiency involves N remobilization. Understanding the mechanisms regulating these processes is crucial for the improvement of NUE in crop plants. One important approach is to develop an understanding of the plant response to different N regimes, especially to N limitation, using various methods including transcription profiling, analysing mutants defective in their normal response to N limitation, and studying plants that show better growth under N-limiting conditions. One can then attempt to improve NUE in crop plants using the knowledge gained from these studies. There are several potential genetic and molecular approaches for the improvement of crop NUE discussed in this review. Increased knowledge of how plants respond to different N levels as well as to other environmental conditions is required to achieve this.

Uncoupling phosphate deficiency from its major effects on growth and transcriptome via PHO1 expression in Arabidopsis

Inorganic phosphate (Pi) is one of the most limiting nutrients for plant growth in both natural and agricultural contexts. Pi-deficiency leads to a strong decrease in shoot growth, and triggers extensive changes at the developmental, biochemical and gene expression levels that are presumably aimed at improving the acquisition of this nutrient and sustaining growth. The Arabidopsis thaliana PHO1 gene has previously been shown to participate in the transport of Pi from roots to shoots, and the null pho1 mutant has all the hallmarks associated with shoot Pi deficiency. We show here that A. thaliana plants with a reduced expression of PHO1 in roots have shoot growth similar to Pi-sufficient plants, despite leaves being strongly Pi deficient. Furthermore, the gene expression profile normally triggered by Pi deficiency is suppressed in plants with low PHO1 expression. At comparable levels of shoot Pi supply, the wild type reduces shoot growth but maintains adequate shoot vacuolar Pi content, whereas the PHO1 underexpressor maintains maximal growth with strongly depleted Pi reserves. Expression of the Oryza sativa (rice) PHO1 ortholog in the pho1 null mutant also leads to plants that maintain normal growth and suppression of the Pi-deficiency response, despite the low shoot Pi. These data show that it is possible to unlink low shoot Pi content with the responses normally associated with Pi deficiency through the modulation of PHO1 expression or activity. These data also show that reduced shoot growth is not a direct consequence of Pi deficiency, but is more likely to be a result of extensive gene expression reprogramming triggered by Pi deficiency.

Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana

Nitrogen (N) is an essential macronutrient for plants. In nature, N cycles between different inorganic and organic forms some of which can serve as nutrients for plants. The inorganic N forms nitrate and ammonium are the most important sources of N for plants. However, plants can also uptake and use organic N forms such as amino acids and urea. Besides their nutritional role, nitrate and other forms of N can also act as signals that regulate the expression of hundreds of genes causing modulation of plant metabolism, physiology, growth, and development. Although many genes and processes affected by changes in external or internal N have been identified, the molecular mechanisms involved in N sensing and signaling are still poorly understood. Classic reverse and forward genetics and more recently the advent of genomic and systems approaches have helped to characterize some of the components of the signaling pathways directing Arabidopsis responses to N. Here, we provide an update on recent advances to identify the components involved in N sensing and signaling in Arabidopsis and their importance for the plant response to N.

Anion channels/transporters in plants: from molecular bases to regulatory networks

Anion channels/transporters are key to a wide spectrum of physiological functions in plants, such as osmoregulation, cell signaling, plant nutrition and compartmentalization of metabolites, and metal tolerance. The recent identification of gene families encoding some of these transport systems opened the way for gene expression studies, structure-function analyses of the corresponding proteins, and functional genomics approaches toward further understanding of their integrated roles in planta. This review, based on a few selected examples, illustrates that the members of a given gene family exhibit a diversity of substrate specificity, regulation, and intracellular localization, and are involved in a wide range of physiological functions. It also shows that post-translational modifications of transport proteins play a key role in the regulation of anion transport activity. Key questions arising from the increasing complexity of networks controlling anion transport in plant cells (the existence of redundancy, cross talk, and coordination between various pathways and compartments) are also addressed.

Integration of nitrogen and potassium signaling

Sensing and responding to soil nutrient fluctuations are vital for the survival of higher plants. Over the past few years, great progress has been made in our understanding of nitrogen and potassium signaling. Key components of the signaling pathways including sensors, kinases, miRNA, ubiquitin ligases, and transcriptional factors. These components mediate the transcriptional responses, root-architecture changes, and uptake-activity modulation induced by nitrate, ammonium, and potassium in the soil solution. Integration of these responses allows plants to compete for limited nutrients and to survive under nutrient deficiency or toxic nutrient excess. A future challenge is to extend the present fragmented sets of data to a comprehensive signaling network. Then, such knowledge and the accompanying molecular tools can be applied to improve the efficiency of nutrient utilization in crops.

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

Background

Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified.

Results

Here we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes and functions needed to prepare plants to use or reduce nitrate. A state-space model inferred from this microarray time-series data successfully predicts gene behavior in unlearnt conditions.

Conclusions

The experiments and methods allow us to propose a temporal working model for nitrate-driven gene networks. This network model is tested both in silico and experimentally. For example, the over-expression of a predicted gene hub encoding a transcription factor induced early in the cascade indeed leads to the modification of the kinetic nitrate response of sentinel genes such as NIR, NIA2, and NRT1.1, and several other transcription factors. The potential nitrate/hormone connections implicated by this time-series data are also evaluated.

Auxin transport in maize roots in response to localized nitrate supply

background and aims: Roots typically respond to localized nitrate by enhancing lateral-root growth. Polar auxin transport has important roles in lateral-root formation and growth; however, it is a matter of debate whether or how auxin plays a role in the localized response of lateral roots to nitrate.

METHODS

Treating maize (Zea mays) in a split-root system, auxin levels were quantified directly and polar transport was assayed by the movement of [(3)H]IAA. The effects of exogenous auxin and polar auxin transport inhibitors were also examined.

KEY RESULTS

Auxin levels in roots decreased more in the nitrate-fed compartment than in the nitrate-free compartment and nitrate treatment appeared to inhibit shoot-to-root auxin transport. However, exogenous application of IAA only partially reduced the stimulatory effect of localized nitrate, and auxin level in the roots was similarly reduced by local applications of ammonium that did not stimulate lateral-root growth.

CONCLUSIONS

It is concluded that local applications of nitrate reduced shoot-to-root auxin transport and decreased auxin concentration in roots to a level more suitable for lateral-root growth. However, alteration of root auxin level alone is not sufficient to stimulate lateral-root growth.

Control of root architecture and nodulation by the LATD/NIP transporter

The Medicago truncatula LATD/NIP gene is essential for the development of lateral and primary root and nitrogen-fixing nodule meristems as well as for rhizobial invasion of nodules. LATD/NIP encodes a member of the NRT1(PTR1) nitrate and di-and tri-peptide transporter family, suggesting that its function is to transport one of these or another compound(s). Because latd/nip mutants can have their lateral and primary root defects rescued by ABA, ABA is a potential substrate for transport. LATD/NIP expression in the root meristem was demonstrated to be regulated by auxin, cytokinin and abscisic acid, but not by nitrate. LATD/NIP's potential function and its role in coordinating root architecture and nodule formation are discussed.

Ammonium triggers lateral root branching in Arabidopsis in an AMMONIUM TRANSPORTER1;3-dependent manner

Root development is strongly affected by the plant's nutritional status and the external availability of nutrients. Employing split-root systems, we show here that local ammonium supply to Arabidopsis thaliana plants increases lateral root initiation and higher-order lateral root branching, whereas the elongation of lateral roots is stimulated mainly by nitrate. Ammonium-stimulated lateral root number or density decreased after ammonium or Gln supply to a separate root fraction and did not correlate with cumulative uptake of (15)N-labeled ammonium, suggesting that lateral root branching was not purely due to a nutritional effect but most likely is a response to a sensing event. Ammonium-induced lateral root branching was almost absent in a quadruple AMMONIUM TRANSPORTER (qko, the amt1;1 amt1;2 amt1;3 amt2;1 mutant) insertion line and significantly lower in the amt1;3-1 mutant than in the wild type. Reconstitution of AMT1;3 expression in the amt1;3-1 or in the qko background restored higher-order lateral root development. By contrast, AMT1;1, which shares similar transport properties with AMT1;3, did not confer significant higher-order lateral root proliferation. These results show that ammonium is complementary to nitrate in shaping lateral root development and that stimulation of lateral root branching by ammonium occurs in an AMT1;3-dependent manner.

Characterization of a developmental root response caused by external ammonium supply in Lotus japonicus

Plants respond to changes of nutrient availability in the soil by modulating their root system developmental plan. This response is mediated by systemic changes of the nutritional status and/or by local perception of specific signals. The effect of nitrate on Arabidopsis (Arabidopsis thaliana) root development represents a paradigm of these responses, and nitrate transporters are involved both in local and systemic control. Ammonium (NH(4)(+)) represents an important nitrogen (N) source for plants, although toxicity symptoms are often associated with high NH(4)(+) concentration when this is present as the only N source. The reason for these effects is still controversial, and mechanisms associating ammonium supply and plant developmental programs are completely unknown. We determined in Lotus japonicus the range of ammonium concentration that significantly inhibits the elongation of primary and lateral roots without affecting the biomass of the shoot. The comparison of the growth phenotypes in different N conditions indicated the specificity of the ammonium effect, suggesting that this was not mediated by assimilatory negative feedback mechanisms. In the range of inhibitory NH(4)(+) conditions, only the LjAMT1;3 gene, among the members of the LjAMT1 family, showed a strong increased transcription that was reflected by an enlarged topology of expression. Remarkably, the short-root phenotype was phenocopied in transgenic lines by LjAMT1;3 overexpression independently of ammonium supply, and the same phenotype was not induced by another AMT1 member. These data describe a new plant mechanism to cope with environmental changes, giving preliminary information on putative actors involved in this specific ammonium-induced response.

Multiple regulatory elements in the Arabidopsis NIA1 promoter act synergistically to form a nitrate enhancer

To accommodate fluctuating nutrient levels in the soil, plants modulate their metabolism and root development via signaling mechanisms that rapidly reprogram the plant transcriptome. In the case of nitrate, over 1,000 genes are induced or repressed within minutes of nitrate exposure. To identify cis-regulatory elements that mediate these responses, an enhancer screen was performed in transgenic Arabidopsis (Arabidopsis thaliana) plants. A 1.8-kb promoter fragment from the nitrate reductase gene NIA1 was identified that acts as a nitrate enhancer when fused to a 35S minimal promoter. Enhancer activity was localized to a 180-bp fragment, and this activity could be enhanced by the addition of a 131-bp fragment from the nitrite reductase promoter. A promoter construct containing the 180- and 131-bp fragments was also induced by nitrite and repressed by ammonium, indicating that it was responsive to multiple nitrogen signals. To identify specific regulatory elements within the 180-bp NIA1 fragment, a transient expression system using agroinfiltration of Nicotiana benthamiana was developed. Deletion analysis identified three elements corresponding to predicted binding motifs for homeodomain/E-box, Myb, and Alfin1 transcription factors. A fully active promoter showing nitrate and nitrite enhancer activity equivalent to that of the wild-type 180-bp fragment could be built from these three elements if the spacing between the homeodomain/E-box and Myb-Alfin1 sites was equivalent to that of the native promoter. These findings were validated in transgenic Arabidopsis plants and identify a cis-regulatory module containing three elements that comprise a nitrate enhancer in the NIA1 promoter.

Root growth inhibition by NH(4)(+) in Arabidopsis is mediated by the root tip and is linked to NH(4)(+) efflux and GMPase activity

Root growth in higher plants is sensitive to excess ammonium (NH(4)(+)). Our study shows that contact of NH(4)(+) with the primary root tip is both necessary and sufficient to the development of arrested root growth under NH(4)(+) nutrition in Arabidopsis. We show that cell elongation and not cell division is the principal target in the NH(4)(+) inhibition of primary root growth. Mutant and expression analyses using DR5:GUS revealed that the growth inhibition is furthermore independent of auxin and ethylene signalling. NH(4)(+) fluxes along the primary root, measured using the Scanning Ion-selective Electrode Technique, revealed a significant stimulation of NH(4)(+) efflux at the elongation zone following treatment with elevated NH(4)(+), coincident with the inhibition of root elongation. Stimulation of NH(4)(+) efflux and inhibition of cell expansion were significantly more pronounced in the NH(4)(+)-hypersensitive mutant vtc1-1, deficient in the enzyme GDP-mannose pyrophosphorylase (GMPase). We conclude that both restricted transmembrane NH(4)(+) fluxes and proper functioning of GMPase in roots are critical to minimizing the severity of the NH(4)(+) toxicity response in Arabidopsis.

Nitrate contra auxin: nutrient sensing by roots

In a new study published in this issue of Developmental Cell, Krouk et al. reveal a surprising mechanism by which plant root systems adapt their architecture for soil exploitation. The dual transporter NRT1.1 uses both nitrate and the plant hormone auxin as substrates, enabling soil nitrate availability to regulate auxin-driven lateral root development.

Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants

Nitrate is both a nitrogen source for higher plants and a signal molecule regulating their development. In Arabidopsis, the NRT1.1 nitrate transporter is crucial for nitrate signaling governing root growth, and has been proposed to act as a nitrate sensor. However, the sensing mechanism is unknown. Herein we show that NRT1.1 not only transports nitrate but also facilitates uptake of the phytohormone auxin. Moreover, nitrate inhibits NRT1.1-dependent auxin uptake, suggesting that transduction of nitrate signal by NRT1.1 is associated with a modification of auxin transport. Among other effects, auxin stimulates lateral root development. Mutation of NRT1.1 enhances both auxin accumulation in lateral roots and growth of these roots at low, but not high, nitrate concentration. Thus, we propose that NRT1.1 represses lateral root growth at low nitrate availability by promoting basipetal auxin transport out of these roots. This defines a mechanism connecting nutrient and hormone signaling during organ development.

A putative transporter is essential for integrating nutrient and hormone signaling with lateral root growth and nodule development in Medicago truncatula

Legume root architecture involves not only elaboration of the root system by the formation of lateral roots but also the formation of symbiotic root nodules in association with nitrogen-fixing soil rhizobia. The Medicago truncatula LATD/NIP gene plays an essential role in the development of both primary and lateral roots as well as nodule development. We have cloned the LATD/NIP gene and show that it encodes a member of the NRT1(PTR) transporter family. LATD/NIP is expressed throughout the plant. pLATD/NIP-GFP promoter-reporter fusions in transgenic roots establish the spatial expression of LATD/NIP in primary root, lateral root and nodule meristems and the surrounding cells. Expression of LATD/NIP is regulated by hormones, in particular by abscisic acid which has been previously shown to rescue the primary and lateral root meristem arrest of latd mutants. latd mutants respond normally to ammonium but have defects in responses of the root architecture to nitrate. Taken together, these results suggest that LATD/NIP may encode a nitrate transporter or transporter of another compound.

The dynamics of root meristem distribution in the soil

Plants must develop efficient root architectures to secure access to nutrients and water in soil. This is achieved during plant development through a series of expansion and branching processes, mostly in the proximity of root apical meristems, where the plant senses the environment and explores immediate regions of the soil. We have developed a new approach to study the dynamics of root meristem distribution in soil, using the relationship between the increase in root length density and the root meristem density. Initiated at the seed, the location of root meristems in barley seedlings was shown to propagate, wave-like, through the soil, leaving behind a permanent network of roots for the plant to acquire water and nutrients. Data from observations on barley roots were used to construct mathematical models to describe the density of root meristems in space. These models suggested that the morphology of the waves of meristems was a function of specific root developmental processes. The waves of meristems observed in root systems of barley seedlings exploring the soil might represent a more general and fundamental aspect of plant rooting strategies for securing soil resources.

Adaptation of Medicago truncatula to nitrogen limitation is modulated via local and systemic nodule developmental responses

Adaptation of Medicago truncatula to local nitrogen (N) limitation was investigated to provide new insights into local and systemic N signaling. The split-root technique allowed a characterization of the local and systemic responses of NO(3)(-) or N(2)-fed plants to localized N limitation. (15)N and (13)C labeling were used to monitor plant nutrition. Plants expressing pMtENOD11-GUS and the sunn-2 hypernodulating mutant were used to unravel mechanisms involved in these responses. Unlike NO(3)(-)-fed plants, N(2)-fixing plants lacked the ability to compensate rapidly for a localized N limitation by up-regulating the N(2)-fixation activity of roots supplied elsewhere with N. However they displayed a long-term response via a growth stimulation of pre-existing nodules, and the generation of new nodules, likely through a decreased abortion rate of early nodulation events. Both these responses involve systemic signaling. The latter response is abolished in the sunn mutant, but the mutation does not prevent the first response. Local but also systemic regulatory mechanisms related to plant N status regulate de novo nodule development in Mt, and SUNN is required for this systemic regulation. By contrast, the stimulation of nodule growth triggered by systemic N signaling does not involve SUNN, indicating SUNN-independent signaling.

Mild salinity stimulates a stress-induced morphogenic response in Arabidopsis thaliana roots

Plant roots exhibit remarkable developmental plasticity in response to local soil conditions. It is shown here that mild salt stress stimulates a stress-induced morphogenic response (SIMR) in Arabidopsis thaliana roots characteristic of several other abiotic stresses: the proliferation of lateral roots (LRs) with a concomitant reduction in LR and primary root length. The LR proliferation component of the salt SIMR is dramatically enhanced by the transfer of seedlings from a low to a high NO3- medium, thereby compensating for the decreased LR length and maintaining overall LR surface area. Increased LR proliferation is specific to salt stress (osmotic stress alone has no stimulatory effect) and is due to the progression of more LR primordia from the pre-emergence to the emergence stage, in salt-stressed plants. In salt-stressed seedlings, greater numbers of LR primordia exhibit expression of a reporter gene driven by the auxin-sensitive DR5 promoter than in unstressed seedlings. Moreover, in the auxin transporter mutant aux1-7, the LR proliferation component of the salt SIMR is completely abrogated. The results suggest that salt stress promotes auxin accumulation in developing primordia thereby preventing their developmental arrest at the pre-emergence stage. Examination of ABA and ethylene mutants revealed that ABA synthesis and a factor involved in the ethylene signalling network also regulate the LR proliferation component of the salt SIMR.

Nitrate responses of Arabidopsis cho1 mutants: obvious only when excess nitrate is supplied

We reported a loss-of-function of an Arabidopsis double AP2 transcription factor CHOTTO1 (CHO1) gene results in the altered responses to high concentrations of nitrate (approximately 50 mM). Nitrate up to 10 mM promotes growth of the wildtype seedling, but inhibits it under higher concentrations. The cho1 seedlings responded to nitrate up to 10 mM similarly to the wildtype, but the inhibitory effect of excess nitrate is less prominent in the mutants. This phenotype is restricted to the cotyledons, and growth of the hypocotyl and roots of the cho1 mutants is inhibited by excess nitrate. The cho1 mutations caused the upregulation of two nitrate transporter genes, AtNRT1.4 and At1g52190. Altered nitrate distribution and storage may explain the phenotypes of the cho1 mutants.

Ethylene is involved in nitrate-dependent root growth and branching in Arabidopsis thaliana

*Here, we investigated the role of ethylene in high nitrate-induced change in root development in Arabidopsis thaliana using wild types and mutants defective in ethylene signaling (etr1, ein2) and nitrate transporters (chl1, nrt2.1). *The length and number of visible lateral roots (LRs) were reduced upon exposure of wild-type seedlings grown on low (0.1 mM) to high nitrate concentration (10 mM). There was a rapid burst of ethylene production upon exposure to high nitrate concentration. *Ethylene synthesis antagonists, cobalt (Co(2+)) and aminoethoxyvinylglycine (AVG), mitigated the inhibitory effect of high nitrate concentration on lateral root growth. The etr1-3 and ein2-1 mutants exhibited less reductions in LR length and number than wild-type plants in response to high nitrate concentration. Expression of nitrate transporters AtNRT1.1 and AtNRT2.1 was upregulated and downregulated in response to high nitrate concentration, respectively. A similar upregulation and downregulation of AtNRT1.1 and AtNRT2.1 was observed by ethylene synthesis precursor aminocyclopropane carboxylic acid (ACC) and AVG in low and high nitrate concentration, respectively. Expression of AtNRT1.1 and AtNRT2.1 became insensitive to high nitrate concentration in etr1-3 and ein2-1 plants. *These findings highlight the regulatory role that ethylene plays in high nitrate concentration-regulated LR development by modulating nitrate transporters.

Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis

Nitrogen (N) and nitrate (NO(3)(-)) per se regulate many aspects of plant metabolism, growth, and development. N/NO(3)(-) also suppresses parts of secondary metabolism, including anthocyanin synthesis. Molecular components for this repression are unknown. We report that three N/NO(3)(-)-induced members of the LATERAL ORGAN BOUNDARY DOMAIN (LBD) gene family of transcription factors (LBD37, LBD38, and LBD39) act as negative regulators of anthocyanin biosynthesis in Arabidopsis thaliana. Overexpression of each of the three genes in the absence of N/NO(3)(-) strongly suppresses the key regulators of anthocyanin synthesis PAP1 and PAP2, genes in the anthocyanin-specific part of flavonoid synthesis, as well as cyanidin- but not quercetin- or kaempferol-glycoside production. Conversely, lbd37, lbd38, or lbd39 mutants accumulate anthocyanins when grown in N/NO(3)(-)-sufficient conditions and show constitutive expression of anthocyanin biosynthetic genes. The LBD genes also repress many other known N-responsive genes, including key genes required for NO(3)(-) uptake and assimilation, resulting in altered NO(3)(-) content, nitrate reductase activity/activation, protein, amino acid, and starch levels, and N-related growth phenotypes. The results identify LBD37 and its two close homologs as novel repressors of anthocyanin biosynthesis and N availability signals in general. They also show that, besides being developmental regulators, LBD genes fulfill roles in metabolic regulation.

A toggle switch in plant nitrate uptake

In plants, the uptake of nitrate from the soil is a critical process controlled by complex regulatory networks that target nitrate transporters in the roots. In this issue, Ho et al. (2009) show that phosphorylation of the CHL1 nitrate transporter allows the plant root to sense and respond to different nitrate concentrations in the soil.

A genetic screen for nitrate regulatory mutants captures the nitrate transporter gene NRT1.1

Nitrate regulatory mutants (nrg) of Arabidopsis (Arabidopsis thaliana) were sought using a genetic screen that employed a nitrate-inducible promoter fused to the yellow fluorescent protein marker gene YFP. A mutation was identified that impaired nitrate induction, and it was localized to the nitrate regulatory gene NLP7, demonstrating the validity of this screen. A second, independent mutation (nrg1) mapped to a region containing the NRT1.1 (CHL1) nitrate transporter gene on chromosome 1. Sequence analysis of NRT1.1 in the mutant revealed a nonsense mutation that truncated the NRT1.1 protein at amino acid 301. The nrg1 mutation disrupted nitrate regulation of several endogenous genes as induction of three nitrate-responsive genes (NIA1, NiR, and NRT2.1) was dramatically reduced in roots of the mutant after 2-h treatment using nitrate concentrations from 0.25 to 20 mm. Another nrt1.1 mutant (deletion mutant chl1-5) showed a similar phenotype. The loss of nitrate induction in the two nrt1.1 mutants (nrg1 and chl1-5) was not explained by reduced nitrate uptake and was reversed by nitrogen deprivation. Microarray analysis showed that nitrate induction of 111 genes was reduced and of three genes increased 2-fold or more in the nrg1 mutant. Genes involved in nitrate assimilation, energy metabolism, and pentose-phosphate pathway were most affected. These results strongly support the model that NRT1.1 acts as a nitrate regulator or sensor in Arabidopsis.

Dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants

Genetic analyses of plant symbiotic mutants has led to the identification of key genes involved in Rhizobium-legume communication as well as in development and function of nitrogen fixing root nodules. However, the impact of these genes in coordinating the transcriptional programs of nodule development has only been studied in limited and isolated studies. Here, we present an integrated genome-wide analysis of transcriptome landscapes in Lotus japonicus wild-type and symbiotic mutant plants. Encompassing five different organs, five stages of the sequentially developed determinate Lotus root nodules, and eight mutants impaired at different stages of the symbiotic interaction, our data set integrates an unprecedented combination of organ- or tissue-specific profiles with mutant transcript profiles. In total, 38 different conditions sampled under the same well-defined growth regimes were included. This comprehensive analysis unravelled new and unexpected patterns of transcriptional regulation during symbiosis and organ development. Contrary to expectations, none of the previously characterized nodulins were among the 37 genes specifically expressed in nodules. Another surprise was the extensive transcriptional response in whole root compared to the susceptible root zone where the cellular response is most pronounced. A large number of transcripts predicted to encode transcriptional regulators, receptors and proteins involved in signal transduction, as well as many genes with unknown function, were found to be regulated during nodule organogenesis and rhizobial infection. Combining wild type and mutant profiles of these transcripts demonstrates the activation of a complex genetic program that delineates symbiotic nitrogen fixation. The complete data set was organized into an indexed expression directory that is accessible from a resource database, and here we present selected examples of biological questions that can be addressed with this comprehensive and powerful gene expression data set.

A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"

BACKGROUND

Nitrate-induced reprogramming of the transcriptome has recently been shown to be highly context dependent. Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO3- signaling.

RESULTS

Biclustering was used to identify a set of genes that are N-responsive across a range of Nitrogen (N)-treatment backgrounds (i.e. nitrogen treatments under different growth conditions) using a meta-dataset of 76 Affymetrix ATH1 chips from 5 different laboratories. Twenty-one biclusters were found to be N-responsive across subsets of this meta-dataset. N-bicluster 9 (126 genes) was selected for further analysis, as it was shown to be reproducibly responsive to NO3- as a signal, across a wide-variety of background conditions and datasets. N-bicluster 9 genes were then used as "seed" to identify putative cross-talk mechanisms between nitrate and hormone signaling. For this, the 126 nitrate-regulated genes in N-bicluster 9 were biclustered over a meta-dataset of 278 ATH1 chips spanning a variety of hormone treatments. This analysis divided the bicluster 9 genes into two classes: i) genes controlled by NO3- only vs. ii) genes controlled by both NO3- and hormones. The genes in the latter group showed a NO3- response that is significantly enhanced, compared to the former. In silico analysis identified two Cis-Regulatory Elements candidates (CRE) (E2F, HSE) potentially involved the interplay between NO3- and hormonal signals.

CONCLUSION

This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development.

Root uptake regulation: a central process for NPS homeostasis in plants

Homeostasis of nitrogen, phosphorus and sulfur in growing plants requires a sustained intake of these elements into root cells. Under most situations, the adjustment of root N, P or S acquisition to the nutrient demand of the plant is hampered by the limiting and fluctuating availability of these elements in the soil. To cope with this constraint, higher plants modulate their root uptake capacity to compensate for the changes in external concentrations of the N, P or S sources. This adaptive response relies on both physiological and morphological changes in the root system, triggered by nutrient-specific sensing and signalling pathways. The underlying molecular mechanisms now begin to be elucidated. Key root membrane transport proteins have been identified, as well as molecular regulators that control root uptake systems or root system architecture in response to N, P or S availability. Significant but yet poorly understood interactions with carbon or hormone signalling have been unravelled, opening new routes for integrating the mechanisms of nutrient homeostasis into the whole plant.

Freeways in the plant: transporters for N, P and S and their regulation

This review focuses on plant acquisition and transport of the inorganic forms of nitrogen, phosphorus and sulfur. Families of membrane transporters have been identified and several members are well characterised. Although some families are large, specific members may be expressed in a particular membrane or cell type, or at certain times during development. Therefore, each transporter can have specific activities and the concept of functional redundancy is questionable. Structurally related proteins can mediate all transport steps within the plant, including uptake from the soil. Although transport mechanisms and membrane locations may be different, a picture is emerging that suggests sequence homology can be a reasonable indicator of the nutrient that is transported by each protein.

Nitrate and glutamate as environmental cues for behavioural responses in plant roots

As roots explore the soil, they encounter a complex and fluctuating environment in which the different edaphic resources (water and nutrients) are heterogeneously distributed in space and time. Many plant species are able to respond to this heterogeneity by modifying their root system development, such that they colonize the most resource-rich patches of soil. The complexities of these responses, and their dependence on the implied ability to perceive and integrate multiple external signals, would seem to amply justify the term 'behaviour'. This review will consider the types of behaviour that are elicited in roots of Arabidopsis thaliana by exposure to variations in the external concentrations and distribution of two different N compounds, nitrate and glutamate. Molecular genetic studies have revealed an intricate N regulatory network at the root tip that is responsible for orchestrating changes in root growth rate and root architecture to accommodate variations in the extrinsic and intrinsic supply of N. The review will discuss what is known of the genetic basis for these responses and speculate on their physiological and ecological significance.

A modular concept of plant foraging behaviour: the interplay between local responses and systemic control

In this paper we examined the notion that plant foraging for resources in heterogeneous environments must involve: (1) plasticity at the level of individual modules in reaction to localized environmental signals; and (2) the potential for modification of these responses either by the signals received from connected modules that may be exposed to different conditions, or by the signals reflecting the overall resource status of the plant. A conceptual model is presented to illustrate how plant foraging behaviour is achieved through these processes acting in concert, from the signal reception through signal transduction to morphological or physiological response. Evidence to support the concept is reviewed, using selective root placement under nutritionally heterogeneous conditions and elongation responses of stems and petioles to shade as examples. We discussed how the adoption of this model can promote understanding of the ecological significance of foraging behaviour. We also identified a need to widen the experimental repertoires of both molecular physiology and ecology in order to increase our insight into both the regulation and functioning of foraging responses, and their relationship with the patterns of environmental heterogeneity under which plants have evolved.

Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation in Arabidopsis

We have established a simple soil-based experimental system that allows a small and sustained restriction of growth of Arabidopsis by low nitrogen (N). Plants were grown in a large volume of a peat-vermiculite mix that contained very low levels of inorganic N. As a control, inorganic N was added in solid form to the peat-vermiculite mix, or plants were grown in conventional nutrient-rich solids. The low N growth regime led to a sustained 20% decrease of the relative growth rate over a period of 2 weeks, resulting in a two- to threefold decrease in biomass in 35- to 40-day-old plants. Plants in the low N regime contained lower levels of nitrate, lower nitrate reductase activity, lower levels of malate, fumarate and other organic acids and slightly higher levels of starch, as expected from published studies of N-limited plants. However, their rosette protein content was unaltered, and total and many individual amino acid levels increased compared with N-replete plants. This metabolic phenotype reveals that Arabidopsis responds adaptively to low N by decreasing the rate of growth, while maintaining the overall protein content, and maintaining or even increasing the levels of many amino acids.

Plant hormones and nutrient signaling

Plants count on a wide variety of metabolic, physiological, and developmental responses to adapt their growth to variations in mineral nutrient availability. To react to such variations plants have evolved complex sensing and signaling mechanisms that allow them to monitor the external and internal concentration of each of these nutrients, both in absolute terms and also relatively to the status of other nutrients. Recent evidence has shown that hormones participate in the control of these regulatory networks. Conversely, mineral nutrient conditions influence hormone biosynthesis, further supporting close interrelation between hormonal stimuli and nutritional homeostasis. In this review, we summarize these evidences and analyze possible transcriptional correlations between hormonal and nutritional responses, as a means to further characterize the role of hormones in the response of plants to limiting nutrients in soil.

EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture

The root system is essential for the growth and development of plants. In addition to anchoring the plant in the ground, it is the site of uptake of water and minerals from the soil. Plant root systems show an astonishing plasticity in their architecture, which allows for optimal exploitation of diverse soil structures and conditions. The signalling pathways that enable plants to sense and respond to changes in soil conditions, in particular nutrient supply, are a topic of intensive research, and root system architecture (RSA) is an important and obvious phenotypic output. At present, the quantitative description of RSA is labour intensive and time consuming, even using the currently available software, and the lack of a fast RSA measuring tool hampers forward and quantitative genetics studies. Here, we describe EZ-Rhizo: a Windows-integrated and semi-automated computer program designed to detect and quantify multiple RSA parameters from plants growing on a solid support medium. The method is non-invasive, enabling the user to follow RSA development over time. We have successfully applied EZ-Rhizo to evaluate natural variation in RSA across 23 Arabidopsis thaliana accessions, and have identified new RSA determinants as a basis for future quantitative trait locus (QTL) analysis.

The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis

Nitrate is an essential nutrient, and is involved in many adaptive responses of plants, such as localized proliferation of roots, flowering or stomatal movements. How such nitrate-specific mechanisms are regulated at the molecular level is poorly understood. Although the Arabidopsis ANR1 transcription factor appears to control stimulation of lateral root elongation in response to nitrate, no regulators of nitrate assimilation have so far been identified in higher plants. Legume-specific symbiotic nitrogen fixation is under the control of the putative transcription factor, NIN, in Lotus japonicus. Recently, the algal homologue NIT2 was found to regulate nitrate assimilation. Here we report that Arabidopsis thaliana NIN-like protein 7 (NLP7) knockout mutants constitutively show several features of nitrogen-starved plants, and that they are tolerant to drought stress. We show that nlp7 mutants are impaired in transduction of the nitrate signal, and that the NLP7 expression pattern is consistent with a function of NLP7 in the sensing of nitrogen. Translational fusions with GFP showed a nuclear localization for the NLP7 putative transcription factor. We propose NLP7 as an important element of the nitrate signal transduction pathway and as a new regulatory protein specific for nitrogen assimilation in non-nodulating plants.

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.

Nitrate control of root hydraulic properties in plants: translating local information to whole plant response

The sessile lifestyle of plants constrains their ability to acquire mobile nutrients such as nitrate. Whereas proliferation of roots might help in the longer term, nitrate-rich patches can shift rapidly with mass flow of water in the soil. A mechanism that allows roots to follow and capture this source of mobile nitrogen would be highly desirable. Here, we report that variation in nitrate concentration around roots induces an immediate alteration of root hydraulic properties such that water is preferentially absorbed from the nitrate-rich patch. Further, we show that this coupling between nitrate availability and water acquisition results from changes in cell membrane hydraulic properties and is directly related to intracellular nitrate concentrations. Split-root experiments in which nitrate was applied to a portion of the root system showed that the response is both localized and reversible, resulting in rapid changes in water uptake to the portions of the roots exposed to the nitrate-rich patch. At the same time, water uptake by roots not supplied with nitrate was reduced. We believe that the increase in root hydraulic conductance in one part causes a decline of water uptake in the other part due to a collapse in the water potential gradient driving uptake. The translation of local information, in this case nitrate concentration, into a hydraulic signal that can be transmitted rapidly throughout the plant and thus coordinate responses at the whole plant level, represents an unexpected, higher level physiological interaction that precedes the level of gene expression.

Nitrate control of root hydraulic properties in plants: translating local information to whole plant response

The sessile lifestyle of plants constrains their ability to acquire mobile nutrients such as nitrate. Whereas proliferation of roots might help in the longer term, nitrate-rich patches can shift rapidly with mass flow of water in the soil. A mechanism that allows roots to follow and capture this source of mobile nitrogen would be highly desirable. Here, we report that variation in nitrate concentration around roots induces an immediate alteration of root hydraulic properties such that water is preferentially absorbed from the nitrate-rich patch. Further, we show that this coupling between nitrate availability and water acquisition results from changes in cell membrane hydraulic properties and is directly related to intracellular nitrate concentrations. Split-root experiments in which nitrate was applied to a portion of the root system showed that the response is both localized and reversible, resulting in rapid changes in water uptake to the portions of the roots exposed to the nitrate-rich patch. At the same time, water uptake by roots not supplied with nitrate was reduced. We believe that the increase in root hydraulic conductance in one part causes a decline of water uptake in the other part due to a collapse in the water potential gradient driving uptake. The translation of local information, in this case nitrate concentration, into a hydraulic signal that can be transmitted rapidly throughout the plant and thus coordinate responses at the whole plant level, represents an unexpected, higher level physiological interaction that precedes the level of gene expression.

Functional characterization of the Arabidopsis thaliana nitrate transporter CHL1 in the yeast Hansenula polymorpha

CHL1 (AtNRT1.1) is a dual-affinity nitrate transporter of Arabidopsis thaliana, in which phosphorylation at Thr 101 switches CHL1 from low to high nitrate affinity. CHL1 expressed in a Hansenula polymorpha high-affinity nitrate-transporter deficient mutant (Deltaynt1) restores nitrate uptake and growth. These events take place at nitrate concentrations as low as 500 microM, suggesting that CHL1 has a high-affinity for nitrate in yeast. Accordingly, CHL1 expressed in H. polymorpha presents a K(m) for nitrate of about 125 microM. The absence of nitrate, the CHL1 gene inducer, showed the high turnover rate of CHL1 expressed in yeast, which is counteracted by nitrate CHL1 induction. Furthermore, H. polymorpha strains expressing CHL1 become sensitive to 250 microM chlorate, as expected for CHL1 high-affinity behaviour. Given that CHL1 presented high affinity by nitrate, we study the role of CHL1 Thr101 in yeast. Strains producing CHL1Thr101Ala, unable to undergo phosphorylation, and CHL1Thr101Asp, where CHL1 phosphorylation is constitutively mimicked, were used. Yeast strains expressing CHL1Thr101Ala, CHL1Thr101Asp and CHL1 at the same rate showed that Deltaynt1CHL1Thr101Ala is strikingly unable to transport nitrate and contains a very low amount of CHL1 protein; however, Deltaynt1CHL1Thr101Asp restores nitrate uptake and growth, although no significant changes in nitrate affinity were observed. Our results show that CHL1-Thr101 is involved in regulating the levels of CHL1 expressed in yeast and suggest that the phosphorylation of this residue could be involved in targeting this nitrate transporter to the plasma membrane. The functional expression of CHL1 in H. polymorpha reveals that this yeast is a suitable tool for evaluating the real nitrate transport capacity of plant putative nitrate transporters belonging to different families and study their regulation and structure function relationship.

Mutation of the Arabidopsis NRT1.5 nitrate transporter causes defective root-to-shoot nitrate transport

Little is known about the molecular and regulatory mechanisms of long-distance nitrate transport in higher plants. NRT1.5 is one of the 53 Arabidopsis thaliana nitrate transporter NRT1 (Peptide Transporter PTR) genes, of which two members, NRT1.1 (CHL1 for Chlorate resistant 1) and NRT1.2, have been shown to be involved in nitrate uptake. Functional analysis of cRNA-injected Xenopus laevis oocytes showed that NRT1.5 is a low-affinity, pH-dependent bidirectional nitrate transporter. Subcellular localization in plant protoplasts and in planta promoter-beta-glucuronidase analysis, as well as in situ hybridization, showed that NRT1.5 is located in the plasma membrane and is expressed in root pericycle cells close to the xylem. Knockdown or knockout mutations of NRT1.5 reduced the amount of nitrate transported from the root to the shoot, suggesting that NRT1.5 participates in root xylem loading of nitrate. However, root-to-shoot nitrate transport was not completely eliminated in the NRT1.5 knockout mutant, and reduction of NRT1.5 in the nrt1.1 background did not affect root-to-shoot nitrate transport. These data suggest that, in addition to that involving NRT1.5, another mechanism is responsible for xylem loading of nitrate. Further analyses of the nrt1.5 mutants revealed a regulatory loop between nitrate and potassium at the xylem transport step.

Nitrate signalling mediated by the NRT1.1 nitrate transporter antagonises L-glutamate-induced changes in root architecture

Arabidopsis root architecture is highly responsive to changes in the nitrogen supply. External NO(3)(-) stimulates lateral root growth via a signalling pathway involving the ANR1 MADS box transcription factor, while the presence of exogenous l-glutamate (Glu) at the primary root tip slows primary root growth and stimulates root branching. We have found that NO(3)(-), in conjunction with Glu, has a hitherto unrecognized role in regulating the growth of primary roots. Nitrate was able to stimulate primary root growth, both directly and by antagonising the inhibitory effect of Glu. Each response depended on direct contact between the primary root tip and the NO(3)(-), and was not elicited by an alternative N source (NH(4)(+)). The chl1-5 mutant, which is defective in the NRT1.1 (CHL1) NO(3)(-) transporter, was insensitive to NO(3)(-) antagonism of Glu signalling, while an anr1 mutant retained its sensitivity. Sensitivity to NO(3)(-) was restored in a chl1-5 mutant constitutively expressing NRT1.1. However, expression in chl1-5 of a transport-competent but non-phosphorylatable form of NRT1.1 not only failed to restore NO(3)(-) sensitivity but also had a dominant-negative effect on Glu sensitivity. Our results indicate the existence of a NO(3)(-) signalling pathway at the primary root tip that can antagonise the root's response to Glu, and they further suggest that NRT1.1 has a direct NO(3)(-) sensing role in this pathway. We discuss how the observed signalling interactions between NO(3)(-) and Glu could provide a mechanism for modulating root architecture in response to changes in the relative abundance of organic and inorganic N.

Elongation changes of exploratory and root hair systems induced by aminocyclopropane carboxylic acid and aminoethoxyvinylglycine affect nitrate uptake and BnNrt2.1 and BnNrt1.1 transporter gene expression in oilseed rape

Ethylene is a plant hormone that plays a major role in the elongation of both exploratory and root hair systems. Here, we demonstrate in Brassica napus seedlings that treatments with the ethylene precursor, aminocyclopropane carboxylic acid (ACC) and the ethylene biosynthesis inhibitor, aminoethoxyvinylglycine (AVG), cause modification of the dynamic processes of primary root and root hair elongation in a dose-dependent way. Moreover, restoration of root elongation in AVG-treated seedlings by 1 mm l-glutamate suggested that high concentrations of AVG affect root elongation through nonoverlapping ethylene metabolic pathway involving pyridoxal 5'-P-dependent enzymes of nitrate (N) metabolism. In this respect, treatments with high concentrations of ACC and AVG (10 mum) over 5 d revealed significant differences in relationships between root growth architecture and N uptake capacities. Indeed, if these treatments decreased severely the elongation of the exploratory root system (primary root and lateral roots) they had opposing effects on the root hair system. Although ACC increased the length and number of root hairs, the rate of N uptake and the transcript level of the N transporter BnNrt2.1 were markedly reduced. In contrast, the decrease in root hair length and number in AVG-treated seedlings was overcompensated by an increase of N uptake and BnNrt2.1 gene expression. These root architectural changes demonstrated that BnNrt2.1 expression levels were more correlated to the changes of the exploratory root system than the changes of the root hair system. The difference between treatments in N transporters BnNrt1.1 and BnNrt2.1 gene expression is discussed with regard to presumed transport functions of BnNrt1.1 in relation to root elongation.

Cytosolic nitrate ion homeostasis: could it have a role in sensing nitrogen status?

BACKGROUND AND AIMS

question of whether homeostasis occurs for some nutrients and, if so, what are the consequences for how plants sense their nutrient status. Particularly for nitrate, this controversy has focused on the methods used and the cellular pools which they measure. Cytoplasm and cytosol have been distinguished and it has been suggested that two ranges of nitrate values can be separated depending on whether the method separates the pools found in organelles.

SCOPE

The present study defines homeostasis of nutrient ions and discusses how whole organ averaging techniques can hide important cellular differences that can help to explain some of the discrepancies between results reported by various methods. These results are considered in relation to a possible role in signalling nutrient status, and have relevance to other averaging techniques such as the use of 'omics' technologies.

Root branching responses to phosphate and nitrate

Plant roots favour colonization of nutrient-rich zones in soil. Molecular genetic evidences demonstrate that roots sense and respond to local and global concentrations of inorganic phosphate and nitrate, in a fashion that depends on the shoot nutrient status. Recent investigations in Arabidopsis highlighted the role of the root tip in phosphate sensing and attributed to already known proteins (multicopper oxidases and nitrate transporters) new and unexpected functions in the root growth response to phosphate or nitrate.

Cell-specific nitrogen responses mediate developmental plasticity

The organs of multicellular species consist of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change. Some cell-specific responses to changes in environmental conditions are known, but the scale of cell-specific responses within an entire organ as it perceives an environmental flux has not been well characterized in plants or any other multicellular organism. Here, we use cellular profiling of five Arabidopsis root cell types in response to an influx of a critical resource, nitrogen, to uncover a vast and predominantly cell-specific response. We show that cell-specific profiling increases sensitivity several-fold, revealing highly localized regulation of transcripts that were largely hidden from previous global analyses. The cell-specific data revealed responses that suggested a coordinated developmental response in distinct cell types or tissues. One example is the cell-specific regulation of a transcriptional circuit that we showed mediates lateral root outgrowth in response to nitrogen via microRNA167, linking small RNAs to nitrogen responses. Together, these results reveal a previously cryptic component of cell-specific responses to nitrogen. Thus, the results make an important advance in our understanding of how multicellular organisms cope with environmental change at the cell level.

Roots, nitrogen transformations, and ecosystem services

This review considers some of the mechanistic processes that involve roots in the soil nitrogen (N) cycle, and their implications for the ecological functions that retain N within ecosystems: 1) root signaling pathways for N transport systems, and feedback inhibition, especially for NO(3)(-) uptake; 2) dependence on the mycorrhizal and Rhizobium/legume symbioses and their tradeoffs for N acquisition; 3) soil factors that influence the supply of NH(4)(+) and NO(3)(-) to roots and soil microbes; and 4) rhizosphere processes that increase N cycling and retention, such as priming effects and interactions with the soil food web. By integrating information on these plant-microbe-soil N processes across scales and disciplinary boundaries, we propose ideas for better manipulating ecological functions and processes by which the environment provides for human needs, i.e., ecosystem services. Emphasis is placed on agricultural systems, effects of N deposition in natural ecosystems, and ecosystem responses to elevated CO(2) concentrations. This shows the need for multiscale approaches to increase human dependence on a biologically based N supply.