Ammonium-dependent respiratory increase is dependent on the cytochrome pathway in Arabidopsis thaliana shoots

Alternative Oxidase Alleviates Mitochondrial Oxidative Stress during Limited Nitrate Reduction in Arabidopsis thaliana

The conversion of nitrate to ammonium, i.e., nitrate reduction, is a major consumer of reductants in plants. Previous studies have reported that the mitochondrial alternative oxidase (AOX) is upregulated under limited nitrate reduction conditions, including no/low nitrate or when ammonium is the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Thus, upregulated AOX under limited nitrate reduction may dissipate excessive reductants and thereby attenuate oxidative stress. Nevertheless, so far there is no firm evidence for this hypothesis due to the lack of experimental systems to analyze the direct relationship between nitrate reduction and AOX. We therefore developed a novel culturing system for A. thaliana that manipulates shoot activities of nitrate reduction and AOX separately without causing N starvation, ammonium toxicity, or lack of nitrate signal. Using shoots processed with this system, we examined genome-wide gene expression and growth to better understand the relationship between AOX and nitrate reduction. The results showed that, only when nitrate reduction was limited, AOX deficiency significantly upregulated genes involved in mitochondrial oxidative stress, reductant shuttles, and non-phosphorylating bypasses of the respiratory chain, and inhibited growth. Thus, we conclude that AOX alleviates mitochondrial oxidative stress and sustains plant growth under limited nitrate reduction.

Integrated comparative transcriptome and physiological analysis reveals the metabolic responses underlying genotype variations in NH4+ tolerance

Several mechanisms have been proposed to explain NH4 + toxicity. However, the core information about the biochemical regulation of plants in response to NH4 + toxicity is still lacking. In this study, the tissue NH4 + concentration is an important factor contributing to variations in plant growth even under nitrate nutrition and NH4 + tolerance under ammonium nutrition. Furthermore, NH4 + led to the reprogramming of the transcriptional profile, as genes related to trehalose-6-phosphate and zeatin biosynthesis were downregulated, whereas genes related to nitrogen metabolism, camalexin, stilbenoid and phenylpropanoid biosynthesis were upregulated. Further analysis revealed that a large number of genes, which enriched in phenylpropanoid and stilbenoid biosynthesis, were uniquely upregulated in the NH4 +- tolerant ecotype Or-1. These results suggested that the NH4 +-tolerant ecotype showed a more intense response to NH4 + by activating defense processes and pathways. Importantly, the tolerant ecotype had a higher 15NH4 + uptake and nitrogen utilization efficiency, but lower NH4 +, indicating the tolerant ecotype maintained a low NH4 + level, mainly by promoting NH4 + assimilation rather than inhibiting NH4 + uptake. The carbon and nitrogen metabolism analysis revealed that the tolerant ecotype had a stronger carbon skeleton production capacity with higher levels of hexokinase, pyruvate kinase, and glutamate dehydrogenase activity to assimilate free NH4 +, Taken together, the results revealed the core mechanisms utilized by plants in response to NH4 +, which are consequently of ecological and agricultural importance.

Nitrogen sources differentially affect respiration, growth, and carbon allocation in Andean and Lowland ecotypes of Chenopodium quinoa Willd

Chenopodium quinoa Willd. is a native species that originated in the High Andes plateau (Altiplano) and its cultivation spread out to the south of Chile. Because of the different edaphoclimatic characteristics of both regions, soils from Altiplano accumulated higher levels of nitrate (NO3-) than in the south of Chile, where soils favor ammonium (NH₄ ⁺) accumulation. To elucidate whether C. quinoa ecotypes differ in several physiological and biochemical parameters related to their capacity to assimilate NO3- and NH₄ ⁺, juvenile plants of Socaire (from Altiplano) and Faro (from Lowland/South of Chile) were grown under different sources of N (NO3- or NH₄ ⁺). Measurements of photosynthesis and foliar oxygen-isotope fractionation were carried out, together with biochemical analyses, as proxies for the analysis of plant performance or sensitivity to NH₄ ⁺. Overall, while NH₄ ⁺ reduced the growth of Socaire, it induced higher biomass productivity and increased protein synthesis, oxygen consumption, and cytochrome oxidase activity in Faro. We discussed that ATP yield from respiration in Faro could promote protein production from assimilated NH₄ ⁺ to benefit its growth. The characterization of this differential sensitivity of both quinoa ecotypes for NH₄ ⁺ contributes to a better understanding of nutritional aspects driving plant primary productivity.

Does energy cost constitute the primary cause of ammonium toxicity in plants?

Nitrate (NO₃^-) and ammonium (NH₄⁺) are the main nitrogen (N) sources and key determinants for plant growth and development. In recent decades, NH₄⁺, which is a double-sided N compound, has attracted considerable amounts of attention from researchers. Elucidating the mechanisms of NH₄⁺ toxicity and exploring the means to overcome this toxicity are necessary to improve agricultural sustainability. In this review, we discuss the current knowledge concerning the energy consumption and production underlying NH₄⁺ metabolism and toxicity in plants, such as N uptake; assimilation; cellular pH homeostasis; and functions of the plasma membrane (PM), vacuolar H⁺-ATPase and H⁺-pyrophosphatase (H⁺-PPase). We also discuss whether the overconsumption of energy is the primary cause of NH₄⁺ toxicity or constitutes a fundamental strategy for plants to adapt to high-NH₄⁺ stress. In addition, the effects of regulators on energy production and consumption and other physiological processes are listed for evaluating the possibility of high energy costs associated with NH₄⁺ toxicity. This review is helpful for exploring the tolerance mechanisms and for developing NH₄⁺-tolerant varieties as well as agronomic techniques to alleviate the effects of NH₄⁺ stress in the field.

Nitrate alleviates ammonium toxicity in wheat (Triticum aestivum L.) by regulating tricarboxylic acid cycle and reducing rhizospheric acidification and oxidative damage

Ammonium (NH₄⁺) is one of the most important nutrients required by plants. However, a high concentration of NH₄⁺ as the sole nitrogen source suppresses plant growth. Although nitrate (NO₃^-) can alleviate NH₄⁺ toxicity, the mechanisms underlying this ability have not been fully elucidated. In this study, wheat plants were cultivated in hydroponic solution with 7.5 mM NO₃^- (control), 7.5 mM NH₄⁺ (sole ammonium, SA) or 7.5 mM NH₄⁺ plus 1.0 mM NO₃^- (ammonium and nitrate, AN). The results showed that compared with the control, the SA treatment significantly decreased root growth, protein content and the concentrations of most intermediates and the activity of enzymes from the tricarboxylic acid (TCA) cycle. Moreover, increased the activity of plasma membrane H⁺-ATPase and the rate of H⁺ efflux along roots, caused solution acidification, and increased the activity of mitochondrial respiratory chain complexes I-IV and the contents of protein-bound carbonyls and malondialdehyde in roots. SA treatment induced ultrastructure disruption and reduced the viability of root cells. Compared with the SA treatment, the AN treatment increased root growth, protein content, the concentrations of most intermediates and the activity of enzymes from the TCA cycle. Furthermore, AN treatment decreased the rate of H⁺ efflux, retarded medium acidification, decreased protein carbonylation and lipid peroxidation in roots and relieved ultrastructure disruption and increased the viability of root cells. Taken together, these results indicate that NO₃^--dependent alleviation of NH₄⁺ toxicity in wheat seedlings is closely associated with physiological processes that mediate TCA cycle, relieve rhizospheric acidification and decrease the production of ROS and oxidative damage.

Manganese toxicity disrupts indole acetic acid homeostasis and suppresses the CO2 assimilation reaction in rice leaves

Despite the essentiality of Mn in terrestrial plants, its excessive accumulation in plant tissues can cause growth defects, known as Mn toxicity. Mn toxicity can be classified into apoplastic and symplastic types depending on its onset. Symplastic Mn toxicity is hypothesised to be more critical for growth defects. However, details of the relationship between growth defects and symplastic Mn toxicity remain elusive. In this study, we aimed to elucidate the molecular mechanisms underlying symplastic Mn toxicity in rice plants. We found that under excess Mn conditions, CO₂ assimilation was inhibited by stomatal closure, and both carbon anabolic and catabolic activities were decreased. In addition to stomatal dysfunction, stomatal and leaf anatomical development were also altered by excess Mn accumulation. Furthermore, indole acetic acid (IAA) concentration was decreased, and auxin-responsive gene expression analyses showed IAA-deficient symptoms in leaves due to excess Mn accumulation. These results suggest that excessive Mn accumulation causes IAA deficiency, and low IAA concentrations suppress plant growth by suppressing stomatal opening and leaf anatomical development for efficient CO₂ assimilation in leaves.

Excessive ammonium assimilation by plastidic glutamine synthetase causes ammonium toxicity in Arabidopsis thaliana

Plants use nitrate, ammonium, and organic nitrogen in the soil as nitrogen sources. Since the elevated CO₂ environment predicted for the near future will reduce nitrate utilization by C₃ species, ammonium is attracting great interest. However, abundant ammonium nutrition impairs growth, i.e., ammonium toxicity, the primary cause of which remains to be determined. Here, we show that ammonium assimilation by GLUTAMINE SYNTHETASE 2 (GLN2) localized in the plastid rather than ammonium accumulation is a primary cause for toxicity, which challenges the textbook knowledge. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress-responsive genes. Application of an alkaline ammonia solution to the ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress.

NRT1.1-centered nitrate signaling in plants

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.

In Vivo Metabolic Regulation of Alternative Oxidase under Nutrient Deficiency-Interaction with Arbuscular Mycorrhizal Fungi and Rhizobium Bacteria

The interaction of the alternative oxidase (AOX) pathway with nutrient metabolism is important for understanding how respiration modulates ATP synthesis and carbon economy in plants under nutrient deficiency. Although AOX activity reduces the energy yield of respiration, this enzymatic activity is upregulated under stress conditions to maintain the functioning of primary metabolism. The in vivo metabolic regulation of AOX activity by phosphorus (P) and nitrogen (N) and during plant symbioses with Arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria is still not fully understood. We highlight several findings and open questions concerning the in vivo regulation of AOX activity and its impact on plant metabolism during P deficiency and symbiosis with AMF. We also highlight the need for the identification of which metabolic regulatory factors of AOX activity are related to N availability and nitrogen-fixing legume-rhizobia symbiosis in order to improve our understanding of N assimilation and biological nitrogen fixation.

Tolerant mechanisms to O2 deficiency under submergence conditions in plants

Wetland plants can tolerate long-term strict hypoxia and anoxic conditions and the subsequent re-oxidative stress compared to terrestrial plants. During O2 deficiency, both wetland and terrestrial plants use NAD(P)+ and ATP that are produced during ethanol fermentation, sucrose degradation, and major amino acid metabolisms. The oxidation of NADH by non-phosphorylating pathways in the mitochondrial respiratory chain is common in both terrestrial and wetland plants. As the wetland plants enhance and combine these traits especially in their roots, they can survive under long-term hypoxic and anoxic stresses. Wetland plants show two contrasting strategies, low O2 escape and low O2 quiescence strategies (LOES and LOQS, respectively). Differences between two strategies are ascribed to the different signaling networks related to phytohormones. During O2 deficiency, LOES-type plants show several unique traits such as shoot elongation, aerenchyma formation and leaf acclimation, whereas the LOQS-type plants cease their growth and save carbohydrate reserves. Many wetland plants utilize NH4+ as the nitrogen (N) source without NH4+-dependent respiratory increase, leading to efficient respiratory O2 consumption in roots. In contrast, some wetland plants with high O2 supply system efficiently use NO3- from the soil where nitrification occurs. The differences in the N utilization strategies relate to the different systems of anaerobic ATP production, the NO2--driven ATP production and fermentation. The different N utilization strategies are functionally related to the hypoxia or anoxia tolerance in the wetland plants.

Efficient Photosynthetic Functioning of Arabidopsis thaliana Through Electron Dissipation in Chloroplasts and Electron Export to Mitochondria Under Ammonium Nutrition

An improvement in photosynthetic rate promotes the growth of crop plants. The sink-regulation of photosynthesis is crucial in optimizing nitrogen fixation and integrating it with carbon balance. Studies on these processes are essential in understanding growth inhibition in plants with ammonium ( NH 4 + ) syndrome. Hence, we sought to investigate the effects of using nitrogen sources with different states of reduction (during assimilation of NO 3 - versus NH 4 + ) on the photosynthetic performance of Arabidopsis thaliana. Our results demonstrated that photosynthetic functioning during long-term NH 4 + nutrition was not disturbed and that no indication of photoinhibition of PSII was detected, revealing the robustness of the photosynthetic apparatus during stressful conditions. Based on our findings, we propose multiple strategies to sustain photosynthetic activity during limited reductant utilization for NH 4 + assimilation. One mechanism to prevent chloroplast electron transport chain overreduction during NH 4 + nutrition is for cyclic electron flow together with plastid terminal oxidase activity. Moreover, redox state in chloroplasts was optimized by a dedicated type II NAD(P)H dehydrogenase. In order to reduce the amount of energy that reaches the photosynthetic reaction centers and to facilitate photosynthetic protection during NH 4 + nutrition, non-photochemical quenching (NPQ) and ample xanthophyll cycle pigments efficiently dissipate excess excitation. Additionally, high redox load may be dissipated in other metabolic reactions outside of chloroplasts due to the direct export of nucleotides through the malate/oxaloacetate valve. Mitochondrial alternative pathways can downstream support the overreduction of chloroplasts. This mechanism correlated with the improved growth of A. thaliana with the overexpression of the alternative oxidase 1a (AOX1a) during NH 4 + nutrition. Most remarkably, our findings demonstrated the capacity of chloroplasts to tolerate NH 4 + syndrome instead of providing redox poise to the cells.

Exploring the Relationship between Crassulacean Acid Metabolism (CAM) and Mineral Nutrition with a Special Focus on Nitrogen

Crassulacean acid metabolism (CAM) is characterized by nocturnal CO2 uptake and concentration, reduced photorespiration, and increased water-use efficiency (WUE) when compared to C3 and C4 plants. Plants can perform different types of CAM and the magnitude and duration of CAM expression can change based upon several abiotic conditions, including nutrient availability. Here, we summarize the abiotic factors that are associated with an increase in CAM expression with an emphasis on the relationship between CAM photosynthesis and nutrient availability, with particular focus on nitrogen, phosphorus, potassium, and calcium. Additionally, we examine nitrogen uptake and assimilation as this macronutrient has received the greatest amount of attention in studies using CAM species. We also discuss the preference of CAM species for different organic and inorganic sources of nitrogen, including nitrate, ammonium, glutamine, and urea. Lastly, we make recommendations for future research areas to better understand the relationship between macronutrients and CAM and how their interaction might improve nutrient and water-use efficiency in order to increase the growth and yield of CAM plants, especially CAM crops that may become increasingly important as global climate change continues.

The Arabidopsis AMOT1/EIN3 gene plays an important role in the amelioration of ammonium toxicity

Ammonium (NH4+) toxicity inhibits shoot growth in Arabidopsis, but the underlying mechanisms remain poorly characterized. Here, we show that a novel Arabidopsis mutant, ammonium tolerance 1 (amot1), exhibits enhanced shoot growth tolerance to NH4+. Molecular cloning revealed that amot1 is a new allele of EIN3, a key regulator of ethylene responses. The amot1 mutant and the allelic ein3-1 mutants show greater NH4+ tolerance than the wild type. Moreover, transgenic plants overexpressing EIN3 (EIN3ox) are more sensitive to NH4+ toxicity The ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) increases shoot sensitivity to NH4+, whereas the ethylene perception inhibitor Ag+ decreases sensitivity. NH4+ induces ACC and ethylene accumulation. Furthermore, ethylene-insensitive mutants such as etr1-3 and ein3eil1 display enhanced NH4+ tolerance. In contrast, the ethylene overproduction mutant eto1-1 exhibits decreased ammonium tolerance. AMOT1/EIN3 positively regulates shoot ROS accumulation, leading to oxidative stress under NH4+ stress, a trait that may be related to increased expression of peroxidase-encoding genes. These findings demonstrate the role of AMOT1/EIN3 in NH4+ tolerance and confirm the strong link between NH4+ toxicity symptoms and the accumulation of hydrogen peroxide.

New Insights on Arabidopsis thaliana Root Adaption to Ammonium Nutrition by the Use of a Quantitative Proteomic Approach

Nitrogen is an essential element for plant nutrition. Nitrate and ammonium are the two major inorganic nitrogen forms available for plant growth. Plant preference for one or the other form depends on the interplay between plant genetic background and environmental variables. Ammonium-based fertilization has been shown less environmentally harmful compared to nitrate fertilization, because of reducing, among others, nitrate leaching and nitrous oxide emissions. However, ammonium nutrition may become a stressful situation for a wide range of plant species when the ion is present at high concentrations. Although studied for long time, there is still an important lack of knowledge to explain plant tolerance or sensitivity towards ammonium nutrition. In this context, we performed a comparative proteomic study in roots of Arabidopsis thaliana plants grown under exclusive ammonium or nitrate supply. We identified and quantified 68 proteins with differential abundance between both conditions. These proteins revealed new potential important players on root response to ammonium nutrition, such as H⁺-consuming metabolic pathways to regulate pH homeostasis and specific secondary metabolic pathways like brassinosteroid and glucosinolate biosynthetic pathways.

Short-term ammonium supply induces cellular defence to prevent oxidative stress in Arabidopsis leaves

Plants can assimilate nitrogen from soil pools of both ammonium and nitrate, and the relative levels of these two nitrogen sources are highly variable in soil. Long-term ammonium nutrition is known to cause damage to Arabidopsis that has been linked to mitochondrial oxidative stress. Using hydroponic cultures, we analysed the consequences of rapid shifts between nitrate and ammonium nutrition. This did not induce growth retardation, showing that Arabidopsis can compensate for the changes in redox metabolism associated with the variations in nitrogen redox status. During the first 3 h of ammonium treatment, we observed distinct transient shifts in reactive oxygen species (ROS), low-mass antioxidants, ROS-scavenging enzymes, and mitochondrial alternative electron transport pathways, indicating rapid but temporally separated changes in chloroplastic, mitochondrial and cytosolic ROS metabolism. The fast induction of antioxidant defences significantly lowered intracellular H₂ O₂ levels, and thus protected Arabidopsis leaves from oxidative stress. On the other hand elevated extracellular ROS production in response to ammonium supply may be involved in signalling. The response pattern displays an intricate plasticity of Arabidopsis redox metabolism to minimise stress in responses to nutrient changes.

Interactions between nitrate and ammonium in their uptake, allocation, assimilation, and signaling in plants

Nitrogen (N) availability is a major factor determining plant growth and productivity. Plants acquire inorganic N from the soil, mainly in the form of nitrate and ammonium. To date, researchers have focused on these N sources, and demonstrated that plants exhibit elaborate responses at both physiological and morphological levels. Mixtures of nitrate and ammonium are beneficial in terms of plant growth, as compared to nitrate or ammonium alone, and therefore synergistic responses to both N sources are predicted at different steps ranging from acquisition to assimilation. In this review, we summarize interactions between nitrate and ammonium with respect to uptake, allocation, assimilation, and signaling. Given that cultivated land often contains both nitrate and ammonium, a better understanding of the synergism between these N sources should help to identify targets with the potential to improve crop productivity.

A Functional Approach towards Understanding the Role of the Mitochondrial Respiratory Chain in an Endomycorrhizal Symbiosis

Arbuscular mycorrhizal fungi (AMF) are crucial components of fertile soils, able to provide several ecosystem services for crop production. Current economic, social and legislative contexts should drive the so-called "second green revolution" by better exploiting these beneficial microorganisms. Many challenges still need to be overcome to better understand the mycorrhizal symbiosis, among which (i) the biotrophic nature of AMF, constraining their production, while (ii) phosphate acts as a limiting factor for the optimal mycorrhizal inoculum application and effectiveness. Organism fitness and adaptation to the changing environment can be driven by the modulation of mitochondrial respiratory chain, strongly connected to the phosphorus processing. Nevertheless, the role of the respiratory function in mycorrhiza remains largely unexplored. We hypothesized that the two mitochondrial respiratory chain components, alternative oxidase (AOX) and cytochrome oxidase (COX), are involved in specific mycorrhizal behavior. For this, a complex approach was developed. At the pre-symbiotic phase (axenic conditions), we studied phenotypic responses of Rhizoglomus irregulare spores with two AOX and COX inhibitors [respectively, salicylhydroxamic acid (SHAM) and potassium cyanide (KCN)] and two growth regulators (abscisic acid - ABA and gibberellic acid - Ga3). At the symbiotic phase, we analyzed phenotypic and transcriptomic (genes involved in respiration, transport, and fermentation) responses in Solanum tuberosum/Rhizoglomus irregulare biosystem (glasshouse conditions): we monitored the effects driven by ABA, and explored the modulations induced by SHAM and KCN under five phosphorus concentrations. KCN and SHAM inhibited in vitro spore germination while ABA and Ga3 induced differential spore germination and hyphal patterns. ABA promoted mycorrhizal colonization, strong arbuscule intensity and positive mycorrhizal growth dependency (MGD). In ABA treated plants, R. irregulare induced down-regulation of StAOX gene isoforms and up-regulation of genes involved in plant COX pathway. In all phosphorus (P) concentrations, blocking AOX or COX induced opposite mycorrhizal patterns in planta: KCN induced higher Arum-type arbuscule density, positive MGD but lower root colonization compared to SHAM, which favored Paris-type formation and negative MGD. Following our results and current state-of-the-art knowledge, we discuss metabolic functions linked to respiration that may occur within mycorrhizal behavior. We highlight potential connections between AOX pathways and fermentation, and we propose new research and mycorrhizal application perspectives.

Alternative oxidase and plant stress tolerance

Alternative oxidase (AOX) is one of the terminal oxidases of the plant mitochondrial electron transport chain. AOX acts as a means to relax the highly coupled and tensed electron transport process in mitochondria thus providing and maintaining the much needed metabolic homeostasis by directly reducing oxygen to water. In the process AOX also act as facilitator for signaling molecules conveying the metabolic status of mitochondria to the nucleus and thus able to influence nuclear gene expression. Since AOX indirectly, is able to control the synthesis of important signaling molecules like hydrogen peroxide, superoxide, nitric oxide, thus it is also helping in stress signaling. AOX mediated signaling and metabolic activities are very much important for plant stress response. This include both biotic (fungal, bacterial, viral, etc.) and abiotic (drought, salinity, cold, heavy metal, etc.) stresses. The review provides a gist of regulation and functioning of AOX.

Overcoming ammonium toxicity

Ammonia (ammonium ion under physiological conditions) is one of the key nitrogen sources in cellular amino acid biosynthesis. It is continuously produced in living organisms by a number of biochemical processes, but its accumulation in cells leads to tissue damage. Current knowledge suggests that a few enzymes and transporters are responsible for maintaining the delicate balance of ammonium fluxes in plant tissues. In this study we analyze the data in the scientific literature and the publicly available information on the dozens of biochemical reactions in which endogenous ammonium is produced or consumed, the enzymes that catalyze them, and the enzyme and transporter mutants listed in plant metabolic and genetic databases (Plant Metabolic Network, TAIR, and Genevestigator). Our compiled data show a surprisingly high number of little-studied reactions that might influence cellular ammonium concentrations. The role of ammonium in apoptosis, its relation to oxidative stress, and alterations in ammonium metabolism induced by environmental stress need to be explored in order to develop methods to manage ammonium toxicity.

High CO2 triggers preferential root growth of Arabidopsis thaliana via two distinct systems under low pH and low N stresses

Biomass allocation between shoots and roots is an important strategy used by plants to optimize growth in various environments. Root to shoot mass ratios typically increase in response to high CO2, a trend particularly evident under abiotic stress. We investigated this preferential root growth (PRG) in Arabidopsis thaliana plants cultivated under low pH/high CO2 or low nitrogen (N)/high CO2 conditions. Previous studies have suggested that changes in plant hormone, carbon (C) and N status may be related to PRG. We therefore examined the mechanisms underlying PRG by genetically modifying cytokinin (CK) levels, C and N status, and sugar signaling, performing sugar application experiments and determining primary metabolites, plant hormones and expression of related genes. Both low pH/high CO2 and low N/high CO2 stresses induced increases in lateral root (LR) number and led to high C/N ratios; however, under low pH/high CO2 conditions, large quantities of C were accumulated, whereas under low N/high CO2 conditions, N was severely depleted. Analyses of a CK-deficient mutant and a starchless mutant, in conjunction with sugar application experiments, revealed that these stresses induce PRG via different mechanisms. Metabolite and hormone profile analysis indicated that under low pH/high CO2 conditions, excess C accumulation may enhance LR number through the dual actions of increased auxin and decreased CKs.

Long-term ammonium nutrition of Arabidopsis increases the extrachloroplastic NAD(P)H/NAD(P)(+) ratio and mitochondrial reactive oxygen species level in leaves but does not impair photosynthetic capacity

Ammonium nutrition has been suggested to be associated with alterations in the oxidation-reduction state of leaf cells. Herein, we show that ammonium nutrition in Arabidopsis thaliana increases leaf NAD(P)H/NAD(P)(+) ratio, reactive oxygen species content and accumulation of biomolecules oxidized by free radicals. We used the method of rapid fractionation of protoplasts to analyse which cellular compartments were over-reduced under ammonium supply and revealed that observed changes in NAD(P)H/NAD(P)(+) ratio involved only the extrachloroplastic fraction. We also showed that ammonium nutrition changes mitochondrial electron transport chain activity, increasing mitochondrial reactive oxygen species production. Our results indicate that the functional impairment associated with ammonium nutrition is mainly associated with redox reactions outside the chloroplast.

The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a complex response to changes in nitrogen supply

The extent to which individual plants utilise nitrate and ammonium, the two principal nitrogen sources in the rhizosphere, is variable and many species require a balance between the two forms for optimal growth. The effects of nitrate and ammonium on gene expression, enzyme activity and metabolite composition have been documented extensively with the aim of understanding the way in which plant cells respond to the different forms of nitrogen, but ultimately the impact of these changes on the organisation and operation of the central metabolic network can only be addressed by analysing the fluxes supported by the network. Accordingly steady-state metabolic flux analysis was used to define the metabolic phenotype of a heterotrophic Arabidopsis thaliana cell culture grown in Murashige and Skoog and ammonium-free media, treatments that influenced growth and biomass composition. Fluxes through the central metabolic network were deduced from the redistribution of label into metabolic intermediates and end products observed when cells were labelled with [1-(13) C]-, [2-(13) C]- or [(13) C6 ]glucose, in tandem with (14) C-measurements of the net accumulation of biomass. Analysis of the flux maps showed that: (i) flux through the oxidative pentose phosphate pathway varied independently of the reductant demand for biosynthesis, (ii) non-plastidic processes made a significant and variable contribution to the provision of reducing power for the plastid, and (iii) the inclusion of ammonium in the growth medium increased cell maintenance costs, in agreement with the futile cycling model of ammonium toxicity. These conclusions highlight the complexity of the metabolic response to a change in nitrogen nutrition.

Alternative oxidase: a mitochondrial respiratory pathway to maintain metabolic and signaling homeostasis during abiotic and biotic stress in plants

Alternative oxidase (AOX) is a non-energy conserving terminal oxidase in the plant mitochondrial electron transport chain. While respiratory carbon oxidation pathways, electron transport, and ATP turnover are tightly coupled processes, AOX provides a means to relax this coupling, thus providing a degree of metabolic homeostasis to carbon and energy metabolism. Beside their role in primary metabolism, plant mitochondria also act as "signaling organelles", able to influence processes such as nuclear gene expression. AOX activity can control the level of potential mitochondrial signaling molecules such as superoxide, nitric oxide and important redox couples. In this way, AOX also provides a degree of signaling homeostasis to the organelle. Evidence suggests that AOX function in metabolic and signaling homeostasis is particularly important during stress. These include abiotic stresses such as low temperature, drought, and nutrient deficiency, as well as biotic stresses such as bacterial infection. This review provides an introduction to the genetic and biochemical control of AOX respiration, as well as providing generalized examples of how AOX activity can provide metabolic and signaling homeostasis. This review also examines abiotic and biotic stresses in which AOX respiration has been critically evaluated, and considers the overall role of AOX in growth and stress tolerance.

The role of mitochondria in leaf nitrogen metabolism

For optimal plant growth and development, cellular nitrogen (N) metabolism must be closely coordinated with other metabolic pathways, and mitochondria are thought to play a central role in this process. Recent studies using genetically modified plants have provided insight into the role of mitochondria in N metabolism. Mitochondrial metabolism is linked with N assimilation by amino acid, carbon (C) and redox metabolism. Mitochondria are not only an important source of C skeletons for N incorporation, they also produce other necessary metabolites and energy used in N remobilization processes. Nitric oxide of mitochondrial origin regulates respiration and influences primary N metabolism. Here, we discuss the changes in mitochondrial metabolism during ammonium or nitrate nutrition and under low N conditions. We also describe the involvement of mitochondria in the redistribution of N during senescence. The aim of this review was to demonstrate the role of mitochondria as an integration point of N cellular metabolism.

A field-compatible method for measuring alternative respiratory pathway activities in vivo using stable O₂ isotopes

Plants can alter rates of electron transport through the alternative oxidase (AOX) pathway in response to environmental cues, thus modulating respiratory efficiency, but the (18)O discrimination method necessary for measuring electron partitioning in vivo has been restricted to laboratory settings. To overcome this limitation, we developed a field-compatible analytical method. Series of plant tissue subsamples were incubated in 12 mL septum-capped vials for 0.5-4 h before aliquots of incubation air were injected into 3.7 mL evacuated storage vials. Vials were stored for up to 10 months before analysis by mass spectrometry. Measurements were corrected for unavoidable contamination. Additional mathematical tools were developed for detecting and addressing non-linearity (whether intrinsic or due to contamination) in the data used to estimate discrimination values. Initial contamination in the storage vials was 0.03 ± 0.01 atm; storing the gas samples at -17 °C eliminated further contamination effects over 10 months. Discrimination values obtained using our offline incubation and computation method replicated previously reported results over a range of 10-31‰, with precision generally better than ±0.5‰. Our method enables large-scale investigations of plant alternative respiration along natural environmental gradients under field conditions.

Nitrate sensing and signaling in plants

Nitrate (NO(3)(-)) is a major nutrient for plants, taken up by their roots from the soil. Plants are able to sense NO(3)(-) in their environment, allowing them to quickly respond to the dramatic fluctuations of its availability. Significant advances have been made during the recent period concerning the molecular mechanisms of NO(3)(-) sensing and signaling in the model plant Arabidopsis thaliana. The striking action of NO(3)(-) as a signal regulating genome expression has been unraveled. Note worthily, NO(3)(-) sensing systems have been identified. These correspond to membrane transporters also ensuring the uptake of NO(3)(-) into root cells, thus generalizing the nutrient 'transceptor' (transporter/receptor) concept defined in yeast. Furthermore, components of the downstream transduction cascades, such as transcription factors or kinases, have also been isolated. A breakthrough arising from this improved knowledge is a better understanding of the integration of NO(3)(-) and hormone signaling pathways, that explains the extraordinary developmental plasticity of plants in response to NO(3)(-).

Evidence for a nitrate-independent function of the nitrate sensor NRT1.1 in Arabidopsis thaliana

NRT1.1 is a putative nitrate sensor and is involved in many nitrate-dependent responses. On the other hand, a nitrate-independent function of NRT1.1 has been implied, but the clear-cut evidence is unknown. We found that NRT1.1 mutants showed enhanced tolerance to concentrated ammonium as sole N source in Arabidopsis thaliana. This unique phenotype was not observed in mutants of NLP7, which has been suggested to play a role in the nitrate-dependent signaling pathway. Our real-time PCR analysis, and evidence from a literature survey revealed that several genes relevant to the aliphatic glucosinolate-biosynthetic pathway were regulated via a nitrate-independent signal from NRT1.1. When taken together, the present study strongly suggests the existence of a nitrate-independent function of NRT1.1.

The cytosolic glutamine synthetase GLN1;2 plays a role in the control of plant growth and ammonium homeostasis in Arabidopsis rosettes when nitrate supply is not limiting

Glutamine synthetase (EC 6.3.1.2) is a key enzyme of ammonium assimilation and recycling in plants where it catalyses the synthesis of glutamine from ammonium and glutamate. In Arabidopsis, five GLN1 genes encode GS1 isoforms. GLN1;2 is the most highly expressed in leaves and is over-expressed in roots by ammonium supply and in rosettes by ample nitrate supply compared with limiting nitrate supply. It is shown here that the GLN1;2 promoter is mainly active in the minor veins of leaves and flowers and, to a lower extent, in the parenchyma of mature leaves. Cytoimmunochemistry reveals that the GLN1;2 protein is present in the companion cells. The role of GLN1;2 was determined by examining the physiology of gln1;2 knockout mutants. Mutants displayed lower glutamine synthetase activity, higher ammonium concentration, and reduced rosette biomass compared with the wild type (WT) under ample nitrate supply only. No difference between mutant and WT can be detected under limiting nitrate conditions. Despite total amino acid concentration was increased in the old leaves of mutants at high nitrate, no significant difference in nitrogen remobilization can be detected using (15)N tracing. Growing plants in vitro with ammonium or nitrate as the sole nitrogen source allowed us to confirm that GLN1;2 is induced by ammonium in roots and to observe that gln1;2 mutants displayed, under such conditions, longer root hair and smaller rosette phenotypes in ammonium. Altogether the results suggest that GLN1;2 is essential for nitrogen assimilation under ample nitrate supply and for ammonium detoxification.

Integrative response of plant mitochondrial electron transport chain to nitrogen source

Nitrogen (N) availability is widely known as a determinant of plant growth and respiration rate. However, less attention has been paid to the effect of the type of N source (nitrate, nitrite or ammonium) on the respiratory system. This review summarizes the latest findings on this topic, with an emphasis on the effect of ammonium and nitric oxide (NO) on the respiratory system, and the physiological role of alternative oxidase (AOX). First, concentrated ammonium has been found to increase plant respiration rate (ammonium-dependent respiratory increase, ARI). We will introduce two hypotheses to explain ARI, futile ammonium cycling and excess reducing equivalents, and verify the validity of each hypothesis. We suggest that these two hypotheses are not necessarily mutually exclusive. Second, gene expression of AOX is suppressed when N is predominately available as nitrate instead of ammonium. We will discuss possible signaling pathways leading to this expression pattern. Third, while AOX expression is induced by NO, AOX activity itself is insensitive to NO. In contrast, activity of cytochrome c oxidase (COX) is sensitive to NO. We outline the NO production pathway, focusing on nitrite-dependent NO production, and discuss the physiological significance of the fact that AOX activity is insensitive to NO. Finally, this review aims to build an integrated scheme of the respiratory response to the type of N source, considering leaves in high light conditions or hypoxic roots.