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Nitrogen (N) is one of the key mineral nutrients for plants and its availability has a major impact on their growth and development. Most often N resources are limiting and plants have evolved various strategies to modulate their root uptake capacity to compensate for both spatial and temporal changes in N availability in soil. The main N sources for terrestrial plants in soils of temperate regions are in decreasing order of abundance, nitrate, ammonium and amino acids. N uptake systems combine, for these different N forms, high- and low-affinity transporters belonging to multige families. Expression and activity of most uptake systems are regulated locally by the concentration of their substrate, and by a systemic feedback control exerted by whole-plant signals of N status, giving rise to a complex combinatory network. Besides modulation of the capacity of transport systems, plants are also able to modulate their growth and development to maintain N homeostasis. In particular, root system architecture is highly plastic and its changes can greatly impact N acquisition from soil. In this review, we aim at detailing recent advances in the identification of molecular mechanisms responsible for physiological and developmental responses of root N acquisition to changes in N availability. These mechanisms are now unravelled at an increasing rate, especially in the model plant Arabidopsis thaliana L.. Within the past decade, most root membrane transport proteins that determine N acquisition have been identified. More recently, molecular regulators in nitrate or ammonium sensing and signalling have been isolated, revealing common regulatory genes for transport system and root development, as well as a strong connection between N and hormone signalling pathways. Deciphering the complexity of the regulatory networks that control N uptake, metabolism and plant development will help understanding adaptation of plants to sub-optimal N availability and fluctuating environments. It will also provide solutions for addressing the major issues of pollution and economical costs related to N fertilizer use that threaten agricultural and ecological sustainability.

The elevation of atmospheric CO 2 leads to a decline in plant mineral content, which might pose a significant threat to food security in coming decades. Although few genes have been identified for the negative effect of elevated CO 2 on plant mineral composition, several studies suggest the existence of genetic factors. Here, we performed a large-scale study to explore genetic diversity of plant ionome responses to elevated CO 2 , using six hundred Arabidopsis thaliana accessions, representing geographical distributions ranging from worldwide to regional and local environments. We show that growth under elevated CO 2 leads to a global decrease of ionome content, whatever the geographic distribution of the population. We observed a high range of genetic diversity, ranging from the most negative effect to resilience or even to a benefit in response to elevated CO 2 . Using genome-wide association mapping, we identified a large set of genes associated with this response, and we demonstrated that the function of one of these genes is involved in the negative effect of elevated CO 2 on plant mineral composition. This resource will contribute to understand the mechanisms underlying the effect of elevated CO 2 on plant mineral nutrition, and could help towards the development of crops adapted to a high-CO 2 world.

Localized proliferation of lateral roots in NO₃⁻-rich patches is a striking example of the nutrient-induced plasticity of root development. In Arabidopsis, NO₃⁻ stimulation of lateral root elongation is apparently under the control of a NO₃⁻-signaling pathway involving the ANR1 transcription factor. ANR1 is thought to transduce the NO₃⁻ signal internally, but the upstream NO₃⁻ sensing system is unknown. Here, we show that mutants of the NRT1.1 nitrate transporter display a strongly decreased root colonization of NO₃⁻-rich patches, resulting from reduced lateral root elongation. This phenotype is not due to lower specific NO₃⁻ uptake activity in the mutants and is not suppressed when the NO₃⁻-rich patch is supplemented with an alternative N source but is associated with dramatically decreased ANR1 expression. These results show that NRT1.1 promotes localized root proliferation independently of any nutritional effect and indicate a role in the ANR1-dependent NO₃⁻ signaling pathway, either as a NO₃⁻ sensor or as a facilitator of NO₃⁻ influx into NO₃⁻-sensing cells. Consistent with this model, the NRT1.1 and ANR1 promoters both directed reporter gene expression in root primordia and root tips. The inability of NRT1.1-deficient mutants to promote increased lateral root proliferation in the NO₃⁻-rich zone impairs the efficient acquisition of NO₃⁻ and leads to slower plant growth. We conclude that NRT1.1, which is localized at the forefront of soil exploration by the roots, is a key component of the NO₃⁻-sensing system that enables the plant to detect and exploit NO₃⁻-rich soil patches.

In natural environments, nitrogen (N) concentration in the soil fluctuates greatly and is often limiting for plant growth and development. The ability of plants to respond to changes in N availability is therefore essential for adaptation. The response of plants to N variations consists in particular of adjusting root N uptake systems and root architecture. To do so, plants integrate local sensing and signaling of external N availability with systemic sensing and signaling of their internal N status, in order to tune the functional and structural properties of the root system in accordance with the N demand for growth of the whole plant. Transcriptional regulation of gene expression is one of the most important processes plants use to adapt the properties of the root system in response to local and long-distance N pathways. This review focuses on the mechanisms that give rise to transcriptional responses in Arabidopsis roots under N fluctuations, with an emphasis on those associated with the regulation of nitrate uptake and transport systems. We discuss the putative long-distance signals triggering the gene expression responses, as well as the molecular players that locally induce transcriptional changes. We also highlight several observations revealing the importance of adopting an integrative approach in the regulation of N signaling.

In Arabidopsis (Arabidopsis thaliana), the NRT2.1 gene codes for the main component of the root nitrate (NO₃⁻) high-affinity transport system (HATS). Due to the strong correlation generally found between high-affinity root NO₃⁻ influx and NRT2.1 mRNA level, it has been postulated that transcriptional regulation of NRT2.1 is a key mechanism for modulation of the HATS activity. However, this hypothesis has never been demonstrated, and is challenged by studies suggesting the occurrence of posttranscriptional regulation at the NRT2.1 protein level. To unambiguously clarify the respective roles of transcriptional and posttranscriptional regulations of NRT2.1, we generated transgenic lines expressing a functional 35S::NRT2.1 transgene in an atnrt2.1 mutant background. Despite a high and constitutive NRT2.1 transcript accumulation in the roots, the HATS activity was still down-regulated in the 35S::NRT2.1 transformants in response to repressive nitrogen or dark treatments that strongly reduce NRT2.1 transcription and NO₃⁻ HATS activity in the wild type. In some treatments, this was associated with a decline of NRT2.1 protein abundance, indicating posttranscriptional regulation of NRT2.1. However, in other instances, NRT2.1 protein level remained constant. Changes in abundance of NAR2.1, a partner protein of NRT2.1, closely followed those of NRT2.1, and thus could not explain the close-to-normal regulation of the HATS in the 35S::NRT2.1 transformants. Even if in certain conditions the transcriptional regulation of NRT2.1 contributes to a limited extent to the control of the HATS, we conclude from this study that posttranscriptional regulation of NRT2.1 and/or NAR2.1 plays a predominant role in the control of the NO₃⁻ HATS in Arabidopsis.

Up-regulation of the high-affinity transport system (HATS) for NO₃⁻ and stimulation of lateral root (LR) growth are two important adaptive responses of the root system to nitrogen limitation. Up-regulation of the NO₃⁻ HATS by nitrogen starvation is suppressed in the atnrt2.1-1 mutant of Arabidopsis (Arabidopsis thaliana), deleted for both NRT2.1 and NRT2.2 nitrate transporter genes. We then used this mutant to determine whether lack of HATS stimulation affected the response of the root system architecture (RSA) to low NO₃⁻ availability. In Wassilewskija (Ws) wild-type plants, transfer from high to low NO₃⁻ medium resulted in contrasting responses of RSA, depending on the level of nitrogen limitation. Moderate nitrogen limitation (transfer from 10 mM to 1 or 0.5 mM NO₃⁻) mostly led to an increase in the number of visible laterals, while severe nitrogen stress (transfer from 10 mM to 0.1 or 0.05 mM NO₃⁻) promoted mean LR length. The RSA response of the atnrt2.1-1 mutant to low NO₃⁻ was markedly different. After transfer from 10 to 0.5 mM NO₃⁻, the stimulated appearance of LRs was abolished in atnrt2.1-1 plants, whereas the increase in mean LR length was much more pronounced than in Ws. These modifications of RSA mimicked those of Ws plants subjected to severe nitrogen stress and could be fully explained by the lowered NO₃⁻ uptake measured in the mutant. This suggests that the uptake rate of NO₃⁻, rather than its external concentration, is the key factor triggering the observed changes in RSA. However, the mutation of NRT2.1 was also found to inhibit initiation of LR primordia in plants subjected to nitrogen limitation independently of the rate of NO₃⁻ uptake by the whole root system and even of the presence of added NO₃⁻ in the external medium. This indicates a direct stimulatory role for NRT2.1 in this particular step of LR development. Thus, it is concluded that NRT2.1 has a key dual function in coordinating root development with external NO₃⁻ availability, both indirectly through its role as a major NO₃⁻ uptake system that determines the nitrogen uptake-dependent RSA responses, and directly through a specific action on LR initiation under nitrogen-limited conditions.

For microorganisms and plants, nitrate and ammonium are the main nitrogen sources and they are also important signaling molecules controlling several aspects of metabolism and development. Over the past decade, numerous studies revealed that nitrogen transporters are strongly regulated at the transcriptional level. However, more and more reports are now showing that nitrate and ammonium transporters are also subjected to post-translational regulations in response to nitrogen availability. Phosphorylation is so far the most well studied post-translational modification for these transporters and it affects both the regulation of nitrogen uptake and nitrogen sensing. For example, in Arabidopsis thaliana, phosphorylation was shown to activate the sensing function of the root nitrate transporter NRT1.1 and to switch the transport affinity. Also, for ammonium transporters, a phosphorylation-dependent activation/inactivation mechanism was elucidated in recent years in both plants and microorganisms. However, despite the fact that these regulatory mechanisms are starting to be thoroughly described, the signaling pathways involved and their action on nitrogen transporters remain largely unknown. In this review, we highlight the inorganic nitrogen transporters regulated at the post-translational level and we compare the known mechanisms in plants and microorganisms. We then discuss how these mechanisms could contribute to the regulation of nitrogen uptake and/or nitrogen sensing.

Plant scientists and farmers are facing major challenges in providing food and nutritional security for a growing population, while preserving natural resources and biodiversity. Moreover, this should be done while adapting agriculture to climate change and by reducing its carbon footprint. To address these challenges, there is an urgent need to breed crops that are more resilient to suboptimal environments. Huge progress has recently been made in understanding the physiological, genetic and molecular bases of plant nutrition and environmental responses, paving the way towards a more sustainable agriculture. In this review, we present an overview of these progresses and strategies that could be developed to increase plant nutrient use efficiency and tolerance to abiotic stresses. As illustrated by many examples, they already led to promising achievements and crop improvements. Here, we focus on nitrogen and phosphate uptake and use efficiency and on adaptation to drought, salinity and heat stress. These examples first show the necessity of deepening our physiological and molecular understanding of plant environmental responses. In particular, more attention should be paid to investigate stress combinations and stress recovery and acclimation that have been largely neglected to date. It will be necessary to extend these approaches from model plants to crops, to unravel the relevant molecular targets of biotechnological or genetic strategies directly in these species. Similarly, sustained efforts should be done for further exploring the genetic resources available in these species, as well as in wild species adapted to unfavourable environments. Finally, technological developments will be required to breed crops that are more resilient and efficient. This especially relates to the development of multiscale phenotyping under field conditions and a wide range of environments, and use of modelling and big data management to handle the huge amount of information provided by the new molecular, genetic and phenotyping techniques. In this review we propose prospects to improve crop resilience and sustainability of crop production. We identified major challenges (blue) for future crop production and propose opportunities (green) to address them with the aim to prepare a roadmap for the development of improved crops in the frame of the CropBooster‐P project.

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)(-).

Revealing the over-represented functions in a particular gene list is a particular important post-genomic challenge. Genome-wide investigations generate gene lists from which meaningful information has to be extracted. This information is key to orient in planta investigations and to define the biological significance of genome-wide reprogramming. Here we describe the development and use of the GeneCloud algorithm, which retrieves the over-represented semantic terms in the description of a gene list.