The many changes in environmental conditions mean that plants have a wide range of responses that enable them to adapt constantly. Among the molecular players involved, glutaredoxins (GRXs), small proteins associated with redox metabolism, have emerged in recent years as key elements. While classes I and II of this family of regulators are clearly associated with redox pathways, class III GRXs, which are specific to plants, appear to be involved in signaling pathways without clear redox activity. GRXs are central to a variety of responses to the environment, and their role in regulating root function and development has recently been the subject of numerous studies. Scope. The aim of this review is to describe the role of GRXs in the regulation of root function and development in response to the environment. After describing the biochemical functions of GRXs according to their class and their specific features in plants, we aim to illustrate how class II and III GRXs are involved in the mechanisms by which plants adapt to the environment, and in particular in the regulation of root traits. Although their involvement has been described in the response to multiple environmental variations, we also illustrate that many members of class III have a specific and critical role in root nitrate signaling. We conclude that GRXs are emerging as major players in the response to environmental variations. The development of a sub-family specific to plants, and their biochemical divergence, currently make them regulators of particular interest for understanding plant adaptation to climate constraints.

The Arabidopsis nitrate transceptor NRT1.1/NPF6.3/CHL1 regulates physiological responses to nitrate. Several studies have reported that Arabidopsis plants lacking NRT1.1 show enhanced shoot growth under toxic levels of ammonium without nitrate, suggesting a nitrate-independent function for NRT1.1. To further investigate this nitrate-independent function and its impact on ammonium tolerance, we conducted genetic analysis, tissue-specific expression analysis, and transcriptome analysis using various NRT1.1-related lines. Transgenic plants expressing either nonphosphomimic or phosphomimic mutants of NRT1.1 exhibited similar ammonium tolerance to the wild-type. The chl1-9 mutant, in which NRT1.1 with the P492L substitution is localized intracellularly rather than at the plasma membrane and fails to transport nitrate, showed significantly improved ammonium tolerance. Confocal imaging revealed that the NRT1.1-GFP signal was detected in the plasma membrane of various tissues, including cotyledon pavement cells, hypocotyl epidermal cells, mesophyll cells, root cap cells, and epidermal cells near root tips. In early seedlings, the absence of functional NRT1.1 altered the expression of genes associated with aliphatic glucosinolate biosynthesis, ethylene signaling, and low pH stress. Genes predicted to encode products localized to the extracellular space were enriched among those differentially expressed due to NRT1.1 deficiency. Our data suggest that in the absence of nitrate, plasma membrane-targeted NRT1.1 reduces ammonium tolerance irrespective of its phosphorylation state with alterations of gene expression associated with stress and senescence.

The elevation of CO2 in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO2 on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO2, nitrate, and iron. We demonstrated that elevated CO2 has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO2 negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO2. This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO2. Our approach identified key features and regulators of the plant response to elevated CO2, with the objective of developing crops resilient to climate change.

The elevation of atmospheric CO2 concentration has a strong impact on the physiology of C3 plants, far beyond photosynthesis and C metabolism. In particular, it reduces the concentrations of most mineral nutrients in plant tissues, posing major threats on crop quality, nutrient cycles, and carbon sinks in terrestrial agro-ecosystems. The causes of the detrimental effect of high CO2 levels on plant mineral status are not understood. We provide an update on the main hypotheses and review the increasing evidence that, for nitrogen, this detrimental effect is associated with direct inhibition of key mechanisms of nitrogen uptake and assimilation. We also mention promising strategies for identifying genotypes that will maintain robust nutrient status in a future high-CO2 world.

Carbon storage in soils is one of the most promising strategies for mitigating greenhouse gas emissions and the associated climate change. In this context, how plant root systems respond to the elevation of the atmospheric CO2 concentration is of crucial importance because these organs are the main source of C input into the soils. It is expected that root growth will be stimulated by elevated CO2 as a consequence of enhanced photosynthesis, and that this will favour belowground C sequestration. In add-ition, larger root systems with optimized architecture are also expected to improve water and nutrient acquisition by plants, and to indirectly stimulate photosynthetic CO2 capture. This review critically examines the evidence supporting these expectations from a molecular physiology perspective. We illustrate the strong but highly variable effects of elevated CO2 on root system size and architecture, and provide an update on the signal-ling mechanisms that may trigger these effects. This highlights the lack of knowledge on the physiological and genetic bases of the root growth and development response to ele-vated CO2, but shows that candidate genes and genetic resources are largely available to fill this gap.

There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.

In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule in plant growth, development, and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). Here we show that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing the cell wall remodeling required for overlying tissue separation during LRP emergence. NRT1.1-mediated repression of both TAR2 and LAX3 is suppressed at high nitrate availability, resulting in nitrate induction of the TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously expected in regulating the nitrate response of root system architecture.

Plants need efficient nitrate (NO3-) sensing systems and sophisticated signaling pathways to develop a wide range of adaptive responses to external fluctuations of NO3- supply. In Arabidopsis thaliana, numerous molecular regulators have been identified to participate in signaling pathways that respond specifically to NO3-. In contrast, only a single NO3- sensing system has been described to date, relying on the NRT1.1 (NPF6.3/CHL1) NO3- transceptor. NRT1.1 governs a wide range of responses to NO3-, from fast reprogramming of genome expression (the primary nitrate response) to longer-term developmental changes (effects on lateral root development). NRT1.1 appears to be at the center of a complex network of signaling pathways, involving numerous molecular players acting downstream and/or upstream of it. Interestingly, some of these regulators are involved in crosstalk with the signaling pathways of other nutrients, such as inorganic phosphate or potassium. Although NRT1.1-mediated NO3- sensing and signaling has mostly been documented in Arabidopsis, recent evidence indicates that similar mechanisms involving NRT1.1 orthologues are operative in rice. This review aims to delineate how the NRT1.1 sensing system and the downstream/upstream transduction cascades are integrated to control both the expression of NO3--responsive genes and the induced plasticity of root development.

One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or age. Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to improve our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping accuracy was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.

Excessive nitrogen supply leads to reactive oxygen species accumulation and requires the function of major transcriptional regulators to maintain physiological balance. Reactive oxygen species (ROS) can accumulate in cells at excessive levels, leading to unbalanced redox states and to potential oxidative stress, which can have damaging effects on the molecular components of plant cells. Several environmental conditions have been described as causing an elevation of ROS production in plants. Consequently, activation of detoxification responses is necessary to maintain ROS homeostasis at physiological levels. Misregulation of detoxification systems during oxidative stress can ultimately cause growth retardation and developmental defects. Here, we demonstrate that Arabidopsis (Arabidopsis thaliana) plants grown in a high nitrogen (N) environment express a set of genes involved in detoxification of ROS that maintain ROS at physiological levels. We show that the chromatin factor HIGH NITROGEN INSENSITIVE9 (HNI9) is an important mediator of this response and is required for the expression of detoxification genes. Mutation in HNI9 leads to elevated ROS levels and ROS-dependent phenotypic defects under high but not low N provision. In addition, we identify ELONGATED HYPOCOTYL5 as a major transcription factor required for activation of the detoxification program under high N. Our results demonstrate the requirement of a balance between N metabolism and ROS production, and our work establishes major regulators required to control ROS homeostasis under conditions of excess N.

Reactive oxygen species (ROS) can accumulate in cells at excessive levels, leading to unbalanced redox states and to potential oxidative stress, which can have damaging effects on the molecular components of plant cells. Several environmental conditions have been described as causing an elevation of ROS production in plants. Consequently, activation of detoxification responses is necessary to maintain ROS homeostasis at physiological levels. Misregulation of detoxification systems during oxidative stress can ultimately cause growth retardation and developmental defects. Here, we demonstrate that Arabidopsis (Arabidopsis thaliana) plants grown in a high nitrogen (N) environment express a set of genes involved in detoxification of ROS that maintain ROS at physiological levels. We show that the chromatin factor HIGH NITROGEN INSENSITIVE9 (HNI9) is an important mediator of this response and is required for the expression of detoxification genes. Mutation in HNI9 leads to elevated ROS levels and ROS-dependent phenotypic defects under high but not low N provision. In addition, we identify ELONGATED HYPOCOTYL5 as a major transcription factor required for activation of the detoxification program under high N. Our results demonstrate the requirement of a balance between N metabolism and ROS production, and our work establishes major regulators required to control ROS homeostasis under conditions of excess N.

The plant cell is tightly regulated by factors that integrate cues and environmental signals adapt plant growth to changing conditions. Under 43 drought, cell division in young leaves is blocked by an active mechanism, reducing 44 the evaporative surface and conserving energy resources. The molecular function of 45 cyclin-dependent kinase-inhibitory proteins (CKIs) in regulating the cell cycle has 46 already been well studied, but little is known about their involvement in cell cycle 47 regulation under adverse growth conditions. In this study, we show that the transcript 48 of the CKI gene SIAMESE-RELATED1 ( SMR1 ) is quickly induced under moderate 49 drought in young Arabidopsis thaliana leaves. Functional characterization further 50 revealed that SMR1 inhibits cell division and affects meristem activity, thereby 51 restricting the growth of leaves and roots. Moreover, we demonstrate that SMR1 is a 52 short-lived protein that is degraded by the 26S proteasome after being ubiquitinated 53 by a Cullin-RING E3 ubiquitin ligase. Consequently, overexpression of a more stable 54 variant of the SMR1 protein leads to a much stronger phenotype than 55 overexpression of the native SMR1. Under moderate drought, both the SMR1 56 transcript and SMR1 protein accumulate. Despite this induction, smr1 mutants do not 57 show overall tolerance to drought stress but do show less growth inhibition of young 58 leaves under drought. Surprisingly, the growth-repressive hormone ethylene 59 promotes SMR1 induction, but the classical drought hormone abscisic acid does not. 60 61 62 63 64 65 66

One sentence summary Excessive N nutrition leads to ROS accumulation, and requires the function of major transcriptional regulators to maintain plants under physiological conditions. Author contributions An.M. and A.G. conceived research plans and supervised the experiments; F.B, Am.M., J.B., L.L., L.B. and An.M performed most of the experiments; F.B, Am.M., J.B., G.K., L.L., L.B. and An.M analyzed the data; An.M. wrote the article with contributions of all the authors. Competing interests The authors declare no competing financial interests. Summary Reactive Oxygen Species (ROS) can accumulate in cells at excessive levels, leading to unbalanced redox status and to a potential oxidative stress, which can have damaging effects to the molecular components of plant cells. Several environmental conditions have been described as causing an elevation of ROS production in plants. Consequently, this requires the expression of detoxification responses in order to maintain ROS homeostasis at physiological levels. In case of mis-regulation of the detoxification systems, oxidative stress can lead ultimately to growth retardation and developmental defects. Here, we demonstrate that Arabidopsis plants growing under high nitrogen environment have to express a set of genes involved in detoxification of ROS in order to maintain ROS at physiological levels. We show that the chromatin factor HNI9 is an important actor of this response, required for the expression of these detoxification genes. Mutation in HNI9 leads to elevated ROS levels, and to ROS-dependent phenotypic defects under high but not low N provision. In addition, we identify HY5 as one of the major transcription factors also required for the expression of this detoxification program under high N condition. Our results demonstrate the requirement of a balance between N nutrition and ROS production, and identified the first major regulators required to control ROS homeostasis under excessive N nutrition.

The plant cell cycle is tightly regulated by factors that integrate endogenous cues and environmental signals to adapt plant growth to changing conditions. Under drought, cell division in young leaves is blocked by an active mechanism, reducing the evaporative surface and conserving energy resources. The molecular function of cyclin-dependent kinase-inhibitory proteins (CKIs) in regulating the cell cycle has already been well studied, but little is known about their involvement in cell cycle regulation under adverse growth conditions. In this study, we show that the transcript of the CKI gene SIAMESE-RELATED1 (SMR1) is quickly induced under moderate drought in young Arabidopsis (Arabidopsis thaliana) leaves. Functional characterization further revealed that SMR1 inhibits cell division and affects meristem activity, thereby restricting the growth of leaves and roots. Moreover, we demonstrate that SMR1 is a short-lived protein that is degraded by the 26S proteasome after being ubiquitinated by a Cullin-RING E3 ubiquitin ligase. Consequently, overexpression of a more stable variant of the SMR1 protein leads to a much stronger phenotype than overexpression of the native SMR1. Under moderate drought, both the SMR1 transcript and SMR1 protein accumulate. Despite this induction, smr1 mutants do not show overall tolerance to drought stress but do show less growth inhibition of young leaves under drought. Surprisingly, the growth-repressive hormone ethylene promotes SMR1 induction, but the classical drought hormone abscisic acid does not.

The CDK inhibitory protein SMR1 is regulated by protein turnover under favorable conditions and is induced by ethylene to fine-tune cell cycle arrest under drought. The plant cell cycle is tightly regulated by factors that integrate endogenous cues and environmental signals to adapt plant growth to changing conditions. Under drought, cell division in young leaves is blocked by an active mechanism, reducing the evaporative surface and conserving energy resources. The molecular function of cyclin-dependent kinase-inhibitory proteins (CKIs) in regulating the cell cycle has already been well studied, but little is known about their involvement in cell cycle regulation under adverse growth conditions. In this study, we show that the transcript of the CKI gene SIAMESE-RELATED1 (SMR1) is quickly induced under moderate drought in young Arabidopsis (Arabidopsis thaliana) leaves. Functional characterization further revealed that SMR1 inhibits cell division and affects meristem activity, thereby restricting the growth of leaves and roots. Moreover, we demonstrate that SMR1 is a short-lived protein that is degraded by the 26S proteasome after being ubiquitinated by a Cullin-RING E3 ubiquitin ligase. Consequently, overexpression of a more stable variant of the SMR1 protein leads to a much stronger phenotype than overexpression of the native SMR1. Under moderate drought, both the SMR1 transcript and SMR1 protein accumulate. Despite this induction, smr1 mutants do not show overall tolerance to drought stress but do show less growth inhibition of young leaves under drought. Surprisingly, the growth-repressive hormone ethylene promotes SMR1 induction, but the classical drought hormone abscisic acid does not.

Whether environmentally induced changes in phenotypes can be heritable is a topic with revived interest, in part because of observations in plants that heritable trait variation can occur without DNA sequence mutations. This other system of inheritance, called transgenerational epigenetics, typically involves differences in DNA methylation that are stable across multiple generations. However, it remains unknown if such a system responds to environmental changes and if it could therefore provide a rapid way for plants to generate adaptive heritable phenotypic variation. Here, we used a well-controlled phenotyping platform and whole-genome bisulfite sequencing to investigate potential heritable effects of mild drought applied over two successive generations in Arabidopsis thaliana . Plastic phenotypic responses were observed in plants exposed to drought. After an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects, and irrespective of whether they were grown in control conditions or under water deficit. Moreover, while mild drought induced changes to the DNA methylome of exposed plants, DNA methylation variants were not inherited. These findings add to the growing body of evidence indicating that transgenerational epigenetics is not a common response of plants to environmental changes.

Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3-) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3- through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3- To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3- stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3- mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue.

Although nitrate stimulates NRT1-1 transcription in all root tissues, it represses protein accumulation in lateral primordial, explaining that NRT1-1 controls lateral root development only in low nitrate medium. Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3−) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3− through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3−. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3− stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3− mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue.

Plant growth control has become a major focus due to economic reasons and results from a balance of cell proliferation in meristems and cell elongation that occurs during differentiation. Research on plant cell proliferation over the last two decades has revealed that the basic cell-cycle machinery is conserved between human and plants, although specificities exist. While many regulatory circuits control each step of the cell cycle, the ubiquitin proteasome system (UPS) appears in fungi and metazoans as a major player. In particular, the UPS promotes irreversible proteolysis of a set of regulatory proteins absolutely required for cell-cycle phase transitions. Not unexpectedly, work over the last decade has brought the UPS to the forefront of plant cell-cycle research. In this review, we will summarize our knowledge of the function of the UPS in the mitotic cycle and in endoreduplication, and also in meiosis in higher plants.