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

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

Extraction and labeling methods for microarrays using small amounts of plant tissue

Procedures were developed to maximize the yield of high-quality RNA from small amounts of plant biomass for microarrays. Two disruption techniques (bead milling and pestle and mortar) were compared for the yield and the quality of RNA extracted from 1-week-old Arabidopsis thaliana seedlings (approximately 0.5–30 mg total biomass). The pestle and mortar method of extraction showed enhanced RNA quality at the smaller biomass samples compared with the bead milling technique, although the quality in the bead milling could be improved with additional cooling steps. The RNA extracted from the pestle and mortar technique was further tested to determine if the small quantity of RNA (500 ng–7 μg) was appropriate for microarray analyses. A new method of low-quantity RNA labeling for microarrays (NuGEN Technologies, Inc.) was used on five 7-day-old seedlings (approximately 2.5 mg fresh weight total) of Arabidopsis that were grown in the dark and exposed to 1 h of red light or continued dark. Microarray analyses were performed on a small plant sample (five seedlings; approximately 2.5 mg) using these methods and compared with extractions performed with larger biomass samples (approximately 500 roots). Many well-known light-regulated genes between the small plant samples and the larger biomass samples overlapped in expression changes, and the relative expression levels of selected genes were confirmed with quantitative real-time polymerase chain reaction, suggesting that these methods can be used for plant experiments where the biomass is extremely limited (i.e. spaceflight studies).     

Heterosis of biomass production in Arabidopsis. Establishment during early development

Heterosis has been widely used in agriculture to increase yield and to broaden adaptability of hybrid varieties and is applied to an increasing number of crop species. We performed a systematic survey of the extent and degree of heterosis for dry biomass in 63 Arabidopsis accessions crossed to three reference lines (Col-0, C24, and Nd). We detected a high heritability (69%) for biomass production in Arabidopsis. Among the 169 crosses analyzed, 29 exhibited significant mid-parent-heterosis for shoot biomass. Furthermore, we analyzed two divergent accessions, C24 and Col-0, the F(1) hybrids of which were shown to exhibit hybrid vigor, in more detail. In the combination Col-0/C24, heterosis for biomass was enhanced at higher light intensities; we found 51% to 66% mid-parent-heterosis at low and intermediate light intensities (60 and 120 micromol m(-2) s(-1)), and 161% at high light intensity (240 micromol m(-2) s(-1)). While at the low and intermediate light intensities relative growth rates of the hybrids were higher only in the early developmental phase (0-15 d after sowing [DAS]), at high light intensity the hybrids showed increased relative growth rates over the entire vegetative phase (until 25 DAS). An important finding was the early onset of heterosis for biomass; in the cross Col-0/C24, differences between parental and hybrid lines in leaf size and dry shoot mass could be detected as early as 10 DAS. The widespread occurrence of heterosis in the model plant Arabidopsis opens the possibility to investigate the genetic basis of this phenomenon using the tools of genetical genomics.     

Natural variation of the root morphological response to nitrate supply in Arabidopsis thaliana

Nitrogen fertilization increases crop yield but excessive nitrate use can be a major environmental problem due to soil leaching or greenhouse gas emission. Root traits have been seldom considered as selection criteria to improve Nitrogen Use Efficiency of crops, due to the difficulty of measuring root traits under field conditions. Nonetheless, learning about mechanisms of lateral root (LR) growth stimulation or repression by nitrate availability could help to redesign root system architecture (RSA), a strategy aimed at developing plants with a dense and profound root system and with higher N uptake efficiency. Here, we explored the genetic diversity provided by natural populations of the model species Arabidopsis thaliana to identify potentially adaptive differences in biomass production and root morphology in response to nitrate availability. A core collection of 24 accessions that maximizes the genetic diversity within the species and Col-0 (the reference accession) were grown vertically on agar medium at moderate (N+) nitrate level for 6 days and then transferred to the same condition or to low (N?) nitrate concentration for 7 days. There was a major nutritional effect on the shoot biomass and root to shoot biomass ratio. The variation of the root biomass and RSA traits (primary root length, LRs number, LR mean length, total LRs length and LR densities) was primarily genetically determined. Differences in RSA traits between accessions were somewhat more pronounced at N?. Some accessions produced almost no visible LRs (Pyl-1, N13) at N?, while other produced up to a dozen (Kn-0). Taken together our data illustrate that natural variation exists within Arabidopsis for the studied traits. The identification of RSA ideotypes in the N response will facilitate further analysis of quantitative traits for root morphology.     

Primary structure, genomic organization and heterologous expression of a glucose transporter from Arabidopsis thaliana.

Both genomic and full length cDNA clones of an Arabidopsis thaliana sugar carrier, STP1, have been obtained using a cDNA clone of the H+/hexose cotransporter from the green alga Chlorella kessleri as hybridization probe. The peptide predicted from these sequences in 522 amino acids long and has a molecular weight of 57,518 kd. This higher plant sugar carrier contains 12 putative transmembrane segments and is highly homologous to the H+/hexose cotransporter from Chlorella, with an overall identity in the amino acid sequence of 47.1%. It is also homologous to the human HepG2 glucose transporter (28.4%), and other sugar carriers from man, rat, yeast and Escherichia coli. The definite proof for the function of the STP1 protein as a hexose transporter and data on its substrate specificity were obtained by heterologous expression in the fission yeast Schizosaccharomyces pombe. Transformed yeast cells transport D-glucose with a 100-fold lower KM value than control cells. Moreover only the transformed cells were able to accumulate the non-metabolizable D-glucose analogue 3-O-methyl-D-glucose, indicating that the Arabidopsis carrier catalyses an energy dependent, active uptake of hexoses. Expression of STP1 mRNA is low in heterotrophic tissues like roots or flowers. High levels of expression are found in leaves.     

The Arabidopsis nitrate transporter NRT2.4 plays a double role in roots and shoots of nitrogen-starved plants

Plants have evolved a variety of mechanisms to adapt to N starvation. NITRATE TRANSPORTER2.4 (NRT2.4) is one of seven NRT2 family genes in Arabidopsis thaliana, and NRT2.4 expression is induced under N starvation. Green fluorescent protein and β-glucuronidase reporter analyses revealed that NRT2.4 is a plasma membrane transporter expressed in the epidermis of lateral roots and in or close to the shoot phloem. The spatiotemporal expression pattern of NRT2.4 in roots is complementary with that of the major high-affinity nitrate transporter NTR2.1. Functional analysis in Xenopus laevis oocytes and in planta showed that NRT2.4 is a nitrate transporter functioning in the high-affinity range. In N-starved nrt2.4 mutants, nitrate uptake under low external supply and nitrate content in shoot phloem exudates was decreased. In the absence of NRT2.1 and NRT2.2, loss of function of NRT2.4 (triple mutants) has an impact on biomass production under low nitrate supply. Together, our results demonstrate that NRT2.4 is a nitrate transporter that has a role in both roots and shoots under N starvation.     

Characterization of Xanthophyll Pigments,Photosynthetic Performance,Photon Energy Dissipation,Reactive Oxygen Species Generation and Carbon Isotope Discrimination during Artemisinin-Induced Stress in Arabidopsis thaliana

Artemisinin, a potent antimalarial drug, is phytotoxic to many crops and weeds. The effects of artemisinin on stress markers, including fluorescence parameters, photosystem II photochemistry, photon energy dissipation, lipid peroxidation, reactive oxygen species generation and carbon isotope discrimination in Arabidopsis thaliana were studied. Arabidopsis ecotype Columbia (Col-0) seedlings were grown in perlite and watered with 50% Hoagland nutrient solution. Adult plants of Arabidopsis were treated with artemisinin at 0, 40, 80, 160 μM for one week. Artemisinin, in the range 40–160 μM, decreased the fresh biomass, chl a, b and leaf mineral contents. Photosynthetic efficiency, yield and electron transport rate in Arabidopsis were also reduced following exposure to 80 and 160 μM artemisinin. The Φ_NPQ and NPQ were less than control. Artemisinin treatment caused an increase in root oxidizability and lipid peroxidation (MDA contents) of Arabidopsis. Calcium and nitrogen contents decreased after 80 and 160 μM artemisinin treatment compared to control. δ¹³C values were less negative following treatment with artemisinin as compared to the control. Artemisinin also decreased leaf protein contents in Arabidopsis. Taken together, these data suggest that artemisinin inhibits many physiological and biochemical processes in Arabidopsis.     

Variation of enzyme activities and metabolite levels in 24 Arabidopsis accessions growing in carbon-limited conditions

Our understanding of the interaction of carbon (C) metabolism with nitrogen (N) metabolism and growth is based mainly on studies of responses to environmental treatments, and studies of mutants and transformants. Here, we investigate which metabolic parameters vary and which parameters change in a coordinated manner in 24 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions, grown in C-limited conditions. The accessions were grown in short days, moderate light, and high nitrate, and analyzed for rosette biomass, levels of structural components (protein, chlorophyll), total phenols and major metabolic intermediates (sugars, starch, nitrate, amino acids), and the activities of seven representative enzymes from central C and N metabolism. The largest variation was found for plant weight, reducing sugars, starch at the end of the night, and several enzyme activities. High levels of one sugar correlated with high levels of other sugars and starch, and a trend to increased amino acids, slightly lower nitrate, and higher protein. The activities of enzymes at the interface of C and N metabolism correlated with each other, but were unrelated to carbohydrates, amino acid levels, and total protein. Rosette weight was unrelated or showed a weak negative trend to sugar and amino acid contents at the end of the day in most of the accessions, and was negatively correlated with starch at the end of the night. Rosette weight was positively correlated with several enzyme activities. We propose that growth is not related to the absolute levels of starch, sugars, and amino acids; instead, it is related to flux, which is indicated by the enzymatic capacity to use these central resources.     

Characterization of a two-component high-affinity nitrate uptake system in Arabidopsis. Physiology and protein-protein interaction

The identification of a family of NAR2-type genes in higher plants showed that there was a homolog in Arabidopsis (Arabidopsis thaliana), AtNAR2.1. These genes encode part of a two-component nitrate high-affinity transport system (HATS). As the Arabidopsis NRT2 gene family of nitrate transporters has been characterized, we tested the idea that AtNAR2.1 and AtNRT2.1 are partners in a two-component HATS. Results using the yeast split-ubiquitin system and Xenopus oocyte expression showed that the two proteins interacted to give a functional HATS. The growth and nitrogen (N) physiology of two Arabidopsis gene knockout mutants, atnrt2.1-1 and atnar2.1-1, one for each partner protein, were compared. Both types of plants had lost HATS activity at 0.2 mm nitrate, but the effect was more severe in atnar2.1-1 plants. The relationship between plant N status and nitrate transporter expression revealed a pattern that was characteristic of N deficiency that was again stronger in atnar2.1-1. Plants resulting from a cross between both mutants (atnrt2.1-1 x atnar2.1-1) showed a phenotype like that of the atnar2.1-1 mutant when grown in 0.5 mm nitrate. Lateral root assays also revealed growth differences between the two mutants, confirming that atnar2.1-1 had a stronger phenotype. To show that the impaired HATS did not result from the decreased expression of AtNRT2.1, we tested if constitutive root expression of a tobacco (Nicotiana plumbaginifolia) gene, NpNRT2.1, previously been shown to complement atnrt2.1-1, can restore HATS to the atnar2.1-1 mutant. These plants did not recover wild-type nitrate HATS. Taken together, these results show that AtNAR2.1 is essential for HATS of nitrate in Arabidopsis.     

Chloroplast biogenesis by Arabidopsis seedlings is impaired in the presence of exogenous glucose

Seedlings of Arabidopsis thaliana (L.) Heynh. fail to become green when germinated and grown on media containing high concentrations of glucose (Glc). Although previous studies have shown that sugar concentration affects chlorophyll levels and photosynthetic gene expression, the possibility that sugar concentration might affect actual chloroplast biogenesis has received little attention. Therefore, experiments were conducted to determine whether germination and growth on Glc impairs development of mature chloroplasts from the proplastids found in plant embryos. To monitor chloroplast biogenesis, the levels of a chloroplast-specific fatty acid, hexadecatrienoic (16:3) fatty acid, were measured in Arabidopsis seedlings grown on media containing different concentrations of Glc. These experiments indicate that moderate concentrations of Glc delay accumulation of 16:3. The effects of Glc on 16:3 levels are not solely due to osmotic stress, as equi-molar and even twice equi-molar concentrations of sorbitol do not exert comparable effects. Seedlings grown on concentrations of Glc high enough to prevent greening accumulate almost no 16:3, even after 22 days of growth under continuous light conditions. The lack of 16:3, a major structural component of chloroplast membranes, suggests that seedlings do not develop mature chloroplasts when grown in the presence of high concentrations of exogenous Glc. Further support for this hypothesis is provided by electron microscopy studies revealing that seedlings grown on high concentrations of Glc lack identifiable chloroplasts. Although Glc has been reported to inhibit chloroplast development in unicellular organisms, similar studies on intact higher plants have been lacking.     

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.     

Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose,trehalose-6-phosphate,iron, and sulfate metabolism

The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 microm nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism.     

Influence of aluminium on biomass, nutrients, soluble carbohydrates and phenols in beech (Fagus sylvatica)

The effects of aluminium on biomass, nutrients and soluble carbohydrates and phenols were studied in beech ( Fagus sylvatica L.) seedlings. After germination, seedlings with cotyledons and the buds of the first leaf-pair developed, were preconditioned for two weeks and then grown for 31 days in nutrient solutions containing 0.1, 0.5, 1.0 or 2.0 m M A1C1₃. Aluminium did not affect the dry weights of roots but at Al concentrations ≥ 1.0 m M the development of the terminal shoot above the first leaf pair, was reduced by 80% or more. The concentrations of most nutrients (P, Ca, Mg, Zn, Cu) in the plant tissues decreased strongly even at the lowest Al levels, but K increased in the shoots. The tissue concentration of N was not affected of Al. but the distribution between the organs was changed to a higher content of N in the roots. At ≥1.0 m M Al the concentrations of starch in both the shoots and the roots were significantly increased, and at ≥ 0.5 m M the roots contained more of total phenols than untreated seedlings. The elevated concentrations and contents of starch and phenols in the seedlings may partly be related to the reduced shoot growth. The observed effects of Al were marked already at Al levels found in soil waters from beech forests in southern Sweden.     

Disposal of metal treated Salvinia biomass in soil and its effect on growth and photosynthetic efficiency of wheat

Phytoremediation technologies generate huge quantities of biomass, the disposal of which is a serious concern. Wastewater samples collected from electroplating industries were treated with Salvinia biomass. The effect of application of metal loaded Salvinia plant biomass in soil on growth and physiological indices of 10-day-old seedlings of Triticum aestivum was evaluated. Controls (A) consisted of soil supplemented with untreated plant biomass. Seed germination, seedling height, total chlorophyll, glucose and protein levels, photosynthetic efficiency (Fv/Fm), photochemical quenching (qP), non-photochemical quenching (qn), quantum yield (Y), and electron transport rate (ETR) were not significantly affected in seedlings raised in soils supplemented with metal loaded biomass from most of the samples (B-F) in comparison to control. However, significant decline was noted in total chlorophyll, glucose, and quantum yield in plants grown in soil supplemented with biomass from sample E. Among elemental levels, C(%) remained largely unaffected, N(%) showed slight enhancement but a decrease in H(%) was noted in plants grown in soil supplemented with biomass from sample E. Our results, therefore, suggest that metal accumulated Salvinia biomass obtained after phytoremediation of heavy metal contaminated wastewater can be supplemented in soil. Further studies are required to assess long-term effects of disposal of metal loaded Salvinia plant biomass in soil.