Nitrate transport: a key step in nitrate assimilation

Effects of temperature and nitrogen sources on physiological performance of the coccolithophore Emiliania huxleyi

Both temperature and nutrient levels are rising in worldwide ocean ecosystems, and they strongly influence biological responses of phytoplankton. However, few studies have addressed the interactive effects of temperature and nitrogen sources on physiological performance of the coccolithophore Emiliania huxleyi. In this study, we evaluated algal growth, photosynthesis and respiration, elemental composition, enzyme activity, and calcification under a matrix of two temperatures gradients (ambient temperature 20 °C and high temperature 24 °C) and two nitrogen sources (nitrate (NO3-) and ammonium (NH4+)). When the algae was cultured with NO3- medium, high temperature reduced algal photosynthesis and nitrate reductase activity, but it did not change other indicators significantly relative to ambient temperature. In addition, E. huxleyi preferred NO3- as the growth medium, whereas NH4+ had negative effects on physiological parameters. In the NH4+ medium, the growth rate, photosynthesis and photosynthetic rate, nitrate reductase activity, and particulate organic carbon and particulate organic nitrogen production rate of the algae decreased as temperature increased. Conversely, high temperature increased cellular particulate organic carbon, cellular particulate organic nitrogen, and particulate inorganic carbon levels. In summary, our findings indicate that the distribution and abundance of microalgae could be greatly affected under warming ocean temperature and different nutrient conditions.

Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes

Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.

Effects of Heat Stress on Plant-Nutrient Relations: An Update on Nutrient Uptake, Transport, and Assimilation

As a consequence of global climate change, the frequency, severity, and duration of heat stress are increasing, impacting plant growth, development, and reproduction. While several studies have focused on the physiological and molecular aspects of heat stress, there is growing concern that crop quality, particularly nutritional content and phytochemicals important for human health, is also negatively impacted. This comprehensive review aims to provide profound insights into the multifaceted effects of heat stress on plant-nutrient relationships, with a particular emphasis on tissue nutrient concentration, the pivotal nutrient-uptake proteins unique to both macro- and micronutrients, and the effects on dietary phytochemicals. Finally, we propose a new approach to investigate the response of plants to heat stress by exploring the possible role of plant peroxisomes in the context of heat stress and nutrient mobilization. Understanding these complex mechanisms is crucial for developing strategies to improve plant nutrition and resilience during heat stress.

A mechanistic mathematical model for describing and predicting the dynamics of high-affinity nitrate intake into roots of maize and other plant species

A fully mechanistic dynamical model for plant nitrate uptake is presented. Based on physiological and regulatory pathways and based on physical laws, we form a dynamic system mathematically described by seven differential equations. The model evidences the presence of a short-term positive feedback on the high-affinity nitrate uptake, triggered by the presence of nitrate around the roots, which induces its intaking. In the long run, this positive feedback is overridden by two long-term negative feedback loops which drastically reduces the nitrate uptake capacity. These two negative feedbacks are due to the generation of ammonium and amino acids, respectively, and inhibit the synthesis and the activity of high-affinity nitrate transporters. This model faithfully predicts the typical spiking behavior of the nitrate uptake, in which an initial strong increase of nitrate absorption capacity is followed by a drop, which regulates the absorption down to the initial value. The model outcome was compared with experimental data and they fit quite nicely. The model predicts that after the initial exposure of the roots with nitrate, the absorption of the anion strongly increases and that, on the contrary, the intensity of the absorption is limited in presence of ammonium around the roots.

Nitrate-responsive OsMADS27 promotes salt tolerance in rice

Salt stress is a major constraint on plant growth and yield. Nitrogen (N) fertilizers are known to alleviate salt stress. However, the underlying molecular mechanisms remain unclear. Here, we show that nitrate-dependent salt tolerance is mediated by OsMADS27 in rice. The expression of OsMADS27 is specifically induced by nitrate. The salt-inducible expression of OsMADS27 is also nitrate dependent. OsMADS27 knockout mutants are more sensitive to salt stress than the wild type, whereas OsMADS27 overexpression lines are more tolerant. Transcriptomic analyses revealed that OsMADS27 upregulates the expression of a number of known stress-responsive genes as well as those involved in ion homeostasis and antioxidation. We demonstrate that OsMADS27 directly binds to the promoters of OsHKT1.1 and OsSPL7 to regulate their expression. Notably, OsMADS27-mediated salt tolerance is nitrate dependent and positively correlated with nitrate concentration. Our results reveal the role of nitrate-responsive OsMADS27 and its downstream target genes in salt tolerance, providing a molecular mechanism for the enhancement of salt tolerance by nitrogen fertilizers in rice. OsMADS27 overexpression increased grain yield under salt stress in the presence of sufficient nitrate, suggesting that OsMADS27 is a promising candidate for the improvement of salt tolerance in rice.

Comparative Transcriptome Analysis of Two Peach Rootstocks Uncovers the Effect of Gene Differential Expression on Nitrogen Use Efficiency

Nitrogen is an important nutrient element that limits plant growth and yield formation, but excessive nitrogen has negative effects on plants and the environment. It is important to reveal the molecular mechanism of high NUE (nitrogen use efficiency) for breeding peach rootstock and variety with high NUE. In this study, two peach rootstocks, Shannong–1 (S) and Maotao (M), with different NUE were used as materials and treated with 0.1 mM KNO₃ for transcriptome sequencing together with the control group. From the results of comparison between groups, we found that the two rootstocks had different responses to KNO₃, and 2151 (KCL_S vs. KCL_M), 327 (KNO₃_S vs. KCL_S), 2200 (KNO₃_S vs. KNO₃_M) and 146 (KNO₃_M vs. KCL_M) differentially expressed genes (DEGs) were identified, respectively, which included multiple transcription factor families. These DEGs were enriched in many biological processes and signal transduction pathways, including nitrogen metabolism and plant hormone signal transduction. The function of PpNRT2.1, which showed up-regulated expression under KNO₃ treatment, was verified by heterologous expression in Arabidopsis. The plant height, SPAD (soil and plant analyzer development) of leaf and primary root length of the transgenic plants were increased compared with those of WT, indicating the roles of PpNRT2.1 in nitrogen metabolism. The study uncovered for the first time the different molecular regulatory pathways involved in nitrogen metabolism between two peach rootstocks and provided gene reserve for studying the molecular mechanism of nitrogen metabolism and theoretical basis for screening peach rootstock or variety with high NUE.

GAF domain is essential for nitrate-dependent AtNLP7 function

Nitrate is an essential nutrient and an important signaling molecule in plants. However, the molecular mechanisms by which plants perceive nitrate deficiency signaling are still not well understood. Here we report that AtNLP7 protein transport from the nucleus to the cytoplasm in response to nitrate deficiency is dependent on the N-terminal GAF domain. With the deletion of the GAF domain, AtNLP7^ΔGAF always remains in the nucleus regardless of nitrate availability. AtNLP7 ^ΔGAF also shows reduced activation of nitrate-induced genes due to its impaired binding to the nitrate-responsive cis-element (NRE) as well as decreased growth like nlp7-1 mutant. In addition, AtNLP7^ΔGAF is unable to mediate the reduction of reactive oxygen species (ROS) accumulation upon nitrate treatment. Our investigation shows that the GAF domain of AtNLP7 plays a critical role in the sensing of nitrate deficiency signal and in the nitrate-triggered ROS signaling process.

Aquatic Hyphomycete Taxonomic Relatedness Translates into Lower Genetic Divergence of the Nitrate Reductase Gene

Aquatic hyphomycetes are key microbial decomposers in freshwater that are capable of producing extracellular enzymes targeting complex molecules of leaf litter, thus, being crucial to nutrient cycling in these ecosystems. These fungi are also able to assimilate nutrients (e.g., nitrogen) from stream water, immobilizing these nutrients in the decomposing leaf litter and increasing its nutritional value for higher trophic levels. Evaluating the aquatic hyphomycete functional genetic diversity is, thus, pivotal to understanding the potential impacts of biodiversity loss on nutrient cycling in freshwater. In this work, the inter- and intraspecific taxonomic (ITS1-5.8S-ITS2 region) and functional (nitrate reductase gene) diversity of 40 aquatic hyphomycete strains, belonging to 23 species, was evaluated. A positive correlation was found between the taxonomic and nitrate reductase gene divergences. Interestingly, some cases challenged this trend: Dactylella cylindrospora (Orbiliomycetes) and Thelonectria rubi (Sordariomycetes), which were phylogenetically identical but highly divergent regarding the nitrate reductase gene; and Collembolispora barbata (incertae sedis) and Tetracladium apiense (Leotiomycetes), which exhibited moderate taxonomic divergence but no divergence in the nitrate reductase gene. Additionally, Tricladium chaetocladium (Leotiomycetes) strains were phylogenetically identical but displayed a degree of nitrate reductase gene divergence above the average for the interspecific level. Overall, both inter- and intraspecific functional diversity were observed among aquatic hyphomycetes.

Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont

Marine phytoplankton are major primary producers, and their growth is primarily limited by nitrogen in the oligotrophic ocean environment. The haptophyte Braarudosphaera bigelowii possesses a cyanobacterial endosymbiont (UCYN-A), which plays a major role in nitrogen fixation in the ocean. However, host-symbiont interactions are poorly understood because B. bigelowii was unculturable. In this study, we sequenced the complete genome of the B. bigelowii endosymbiont and showed that it was highly reductive and closely related to UCYN-A2 (an ecotype of UCYN-A). We succeeded in establishing B. bigelowii strains and performed microscopic observations. The detailed observations showed that the cyanobacterial endosymbiont was surrounded by a single host derived membrane and divided synchronously with the host cell division. The transcriptome of B. bigelowii revealed that B. bigelowii lacked the expression of many essential genes associated with the uptake of most nitrogen compounds, except ammonia. During cultivation, some of the strains completely lost the endosymbiont. Moreover, we did not find any evidence of endosymbiotic gene transfer from the endosymbiont to the host. These findings illustrate an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont.

Role for nitrate assimilatory genes in virulence of Ustilago maydis

Ustilago maydis can utilize nitrate as a sole source of nitrogen. This process is initiated by transporting nitrate from the extracellular environment into the cell by a nitrate transporter and followed by a two-step reduction of nitrate to ammonium via nitrate reductase and nitrite reductase enzymes, respectively. Here, we characterize the genes encoding nitrate transporter, um03849 and nitrite reductase, um03848 in U. maydis based on their roles in mating and virulence. The deletion mutants for um03848, um03849 or both genes were constructed in mating compatible haploid strains 1/2 and 2/9. In addition, CRISPR-Cas9 gene editing technique was used for um03849 gene to create INDEL mutations in U. maydis mating strains. For all the mutants, phenotypes such as growth ability, mating efficiency and pathogenesis were examined. The growth of all the mutants was diminished when grown in a medium with nitrate as the source of nitrogen. Although no clear effects on haploid filamentation or mating were observed for either single mutant, double Δum03848 Δum03849 mutants showed reduction in mating, but increased filamentation on low ammonium, particularly in the 1/2 background. With respect to pathogenesis on the host, all the mutants showed reduced degrees of disease symptoms. Further, when the deletion mutants were paired with wild type of opposite mating-type, reduced virulence was observed, in a manner specific to the genetic background of the mutant's progenitor. This background specific reduction of plant pathogenicity was correlated with differential expression of genes for the mating program in U. maydis.

The potential of foodwaste leachate as a phycoremediation substrate for microalgal CO2 fixation and biodiesel production

Foodwaste leachate (FWL) is often generated during foodwaste treatment processes. Owing to its high nutrient content, FWL has high potential for phycoremediation, a microalgal technology application for water treatment while acting as CO₂ fixation tank. Additionally, the end product of microalgal from phycoremediation can be potentially used for biodiesel production. Therefore, the phycoremediation has drawn a lot of attention in recent decades. This study evaluates the performance of microalgal foodwaste leachate treatment and the potential of utilizing FWL as medium for microalgal biodiesel production. Two microalgal species, Dunaliella tertiolecta and Cyanobacterium aponinum, were selected. For each species, two experimental levels of diluted FWL were used: 5 and 10% FWL. The partial inhibition growth model indicates that some inhibit factors such as ammonia; total suspended solids and oil and grease (O&G) content suppress the microalgal growth. Most of the nutrient such as nitrogen and phosphorus (> 80%) can be removed in the last day of phycoremediation by D. tertiolecta. C. aponinum also show considerable removal rate on total nitrogen ammonia and nitrate (> 60%). Biomass (0.4-0.5 g/L/day) of D. tertiolecta and C. aponinum can be produced though cultivated in diluted FWL. The bio-CO₂ fixation rates of the two species were 610.7 and 578.3 mg/L/day of D. tertiolecta and C. aponinum. The strains contain high content of saturated fatty acid such as C₁₆ and C₁₈ making them having potential for producing good quality biodiesel.

Role of Suaeda salsa SsNRT2.1 in nitrate uptake under low nitrate and high saline conditions

The global annual loss in agricultural production resulting from soil salinization is significant. Although nitrate (NO₃^-) is known to play both nutritional and osmotic roles in the salt tolerance of halophytes, it remains unclear how halophytes such as Suaeda salsa L. take up NO₃^- under saline conditions. In the present study, the gene of nitrate transporter 2.1 (SsNRT2.1) was cloned from S. salsa and its function was identified in both S. salsa and Arabidopsis thaliana under salinity and low NO₃^--N (0.5 mM NO₃^-) conditions. The results revealed that SsNRT2.1 expression and NO₃^- concentration in the roots of S. salsa were higher at 200 mM NaCl, compared with that at 0 and 500 mM NaCl after 24 h treatment. The Arabidopsis overexpression lines showed a higher NO₃^- content compared to the WT lines at 0 and 50 mM NaCl. A similar trend was observed in the root length. In conclusion, salinity promoted the SsNRT2.1 expression in S. salsa, suggesting that this gene may contribute to the efficient NO₃^- uptake in S. salsa under low NO₃^- and high salinity conditions. This trait may explain why S. salsa can tolerate high salinity and produce the highest biomass at about 200 mM NaCl.

Antagonistic Interaction between Phosphinothricin and Nepeta rtanjensis Essential Oil Affected Ammonium Metabolism and Antioxidant Defense of Arabidopsis Grown In Vitro

Phosphinothricin (PPT) is one of the most widely used herbicides. PTT targets glutamine synthetase (GS) activity in plants, and its phytotoxicity is ascribed to ammonium accumulation and reactive oxygen species bursts, which drives rapid lipid peroxidation of cell membranes. In agricultural fields, PPT is extensively sprayed on plant foliage; however, a portion of the herbicide reaches the soil. According to the present study, PPT absorbed via roots can be phytotoxic to Arabidopsis, inducing more adverse effects in roots than in shoots. Alterations in plant physiology caused by 10 days exposure to herbicide via roots are reflected through growth suppression, reduced chlorophyll content, perturbations in the sugar and organic acid metabolism, modifications in the activities and abundances of GS, catalase, peroxidase, and superoxide dismutase. Antagonistic interaction of Nepeta rtanjensis essential oil (NrEO) and PPT, emphasizes the existence of complex control mechanisms at the transcriptional and posttranslational level, which result in the mitigation of PPT-induced ammonium toxicity and in providing more efficient antioxidant defense of plants. Simultaneous application of the two agents in the field cannot be recommended; however, NrEO might be considered as the PPT post-treatment for reducing harmful effects of herbicide residues in the soil on non-target plants.

CaNRT2.1 Is Required for Nitrate but Not Nitrite Uptake in Chili Pepper Pathogen Colletotrichum acutatum

Chili peppers are an important food additive used in spicy cuisines worldwide. However, the yield and quality of chilis are threatened by anthracnose disease caused by Colletotrichum acutatum. Despite the impact of C. acutatum on chili production, the genes involved in fungal development and pathogenicity in this species have not been well characterized. In this study, through T-DNA insertional mutagenesis, we identified a mutant strain termed B7, which is defective for the growth of C. acutatum on a minimal nutrient medium. Our bioinformatics analysis revealed that a large fragment DNA (19.8 kb) is deleted from the B7 genome, thus resulting in the deletion of three genes, including CaGpiP1 encoding a glycosylphosphatidyl-inisotol (GPI)-anchored protein, CaNRT2.1 encoding a membrane-bound nitrate/nitrite transporter, and CaRQH1 encoding a RecQ helicase protein. In addition, T-DNA is inserted upstream of the CaHP1 gene encoding a hypothetical protein. Functional characterization of CaGpiP1, CaNRT2.1, and CaHP1 by targeted gene disruption and bioassays indicated that CaNRT2.1 is responsible for the growth-defective phenotype of B7. Both B7 and CaNRT2.1 mutant strains cannot utilize nitrate as nitrogen sources, thus restraining the fungal growth on a minimal nutrient medium. In addition to CaNRT2.1, our results showed that CaGpiP1 is a cell wall-associated GPI-anchored protein. However, after investigating the functions of CaGpiP1 and CaHP1 in fungal pathogenicity, growth, development and stress tolerance, we were unable to uncover the roles of these two genes in C. acutatum. Collectively, in this study, our results identify the growth-defective strain B7 via T-DNA insertion and reveal the critical role of CaNRT2.1 in nitrate transportation for the fungal growth of C. acutatum.

The Brassica napus GATA transcription factor BnA5.ZML1 is a stigma compatibility factor

Self-incompatibility (SI) is a genetic mechanism that rejects self-pollen and thus prevents inbreeding in some hermaphroditic angiosperms. In the Brassicaceae, SI involves a pollen-stigma recognition system controlled by a single locus known as the S locus, which consists of two highly polymorphic genes that encode S-locus cysteine-rich protein (SCR) and S-receptor kinase (SRK). When self-pollen lands on the stigma, the S-haplotype-specific interaction between SCR and SRK triggers SI. Here, we show that the GATA transcription factor BnA5.ZML1 suppresses SI responses in Brassica napus and is induced after compatible pollination. The loss-of-function mutant bna5.zml1 displays reduced self-compatibility. In contrast, overexpression of BnA5.ZML1 in self-incompatible stigmas leads to a partial breakdown of SI responses, suggesting that BnA5.ZML1 is a stigmatic compatibility factor. Furthermore, the expression levels of SRK and ARC1 are up-regulated in bna5.zml1 mutants, and they are down-regulated in BnA5.ZML1 overexpressing lines. SRK affects the cellular localization of BnA5.ZML1 through direct protein-protein interaction. Overall, our findings highlight the fundamental role of BnA5.ZML1 in SI responses in B. napus, establishing a direct interaction between BnA5.ZML1 and SRK in this process.

Characterization of the Nitrate Transporter gene family and functional identification of HvNRT2.1 in barley (Hordeum vulgare L.)

Nitrogen use efficiency (NUE) is the efficiency with which plants acquire and use nitrogen. Plants have high-affinity nitrate transport systems, which involve certain nitrate transporter (NRT) genes. However, limited data are available on the contribution of the NRT2/3 gene family in barley nitrate transport. In the present study, ten putative NRT2 and three putative NRT3 genes were identified using bioinformatics methods. All the HvNRT2/3 genes were located on chromosomes 3H, 5H, 6H or 7H. Remarkably, the presence of tandem repeats indicated that duplication events contributed to the expansion of the NRT2 gene family in barley. In addition, the HvNRT2/3 genes displayed various expression patterns at selected developmental stages and were induced in the roots by both low and high nitrogen levels. Furthermore, the overexpression of HvNRT2.1 improved the yield related traits in Arabidopsis. Taken together, the data generated in the present study will be useful for genome-wide analyses to determine the precise role of the HvNRT2/3 genes during barley development, with the ultimate goal of improving NUE and crop production.

Response of the photosynthetic activity and biomass of the phytoplankton community to increasing nutrients during cyanobacterial blooms in Meiliang Bay, Lake Taihu

Nutrient enrichment facilitates algal outbreaks in eutrophic shallow lakes. To further understand the influence of various inorganic nutrient forms on cyanobacterial blooms, a nitrate (NO₃ ), ammonium (NH₄ ), and orthophosphate (PO₄ ) amendment experiment was conducted in a large shallow lake of China (Lake Taihu) during summer. The results showed that the photosynthetic performance of phytoplankton responded more positively to phosphorus (P) than nitrogen (N), and NH₄ addition stimulated higher algal photosynthetic activities in P-enriched waters. Individual inorganic N or PO₄ addition significantly activated cyanobacteria and green algae. Meanwhile, the N plus P amendment promoted higher biomass of the planktonic microbial community, and the dual addition of NH₄  + PO₄ yielded the highest chlorophyll a concentration. NH₄ additions provisionally promoted higher green algae than cyanobacteria biomass in the beginning, while cyanobacteria dominated again with increasing NH₄ :PO₄ ratios. These results revealed that increasing ammonium would enhance the increase in phytoplankton biomass in advance and prolong the duration of algal blooms. Hence, based on the control of P loading, the reduction in external inorganic N focusing on ammonium sources (such as ammonia N fertilizer) at the watershed scale would help to alleviate eutrophication and cyanobacterial blooms over the long term in Lake Taihu. PRACTITIONER POINTS: Ammonium addition stimulated higher algal photosynthetic activities in P-enriched waters. Individual inorganic N or PO₄ addition significantly activated cyanobacteria and green algae. The dual addition of NH₄  + PO₄ yielded the highest chlorophyll a concentration. Increasing NH₄ would enhance the increase in phytoplankton biomass in advance and prolong the duration of cyanobacterial blooms.

Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean

Diatoms play important roles in primary production and carbon transportation in various environments. Large-scale diatom bloom occurs worldwide; however, metabolic responses of diatoms to environmental conditions have been little studied. Here, we targeted the Oyashio region of the western subarctic Pacific where diatoms bloom every spring and investigated metabolic response of major diatoms to bloom formation by comparing metatranscriptomes between two depths corresponding to different bloom phases. Thalassiosira nordenskioeldii and Chaetoceros debilis are two commonly occurring species at the study site. The gene expression profile was drastically different between the surface (late decline phase of the bloom; 10 m depth) and the subsurface chlorophyll maximum (SCM, initial decline phase of the bloom; 30 m depth); in particular, both species had high expression of genes for nitrate uptake at the surface, but for ammonia uptake at the SCM. Our culture experiments using T. nordenskioeldii imitating the environmental conditions showed that gene expression for nitrate and ammonia transporters was induced by nitrate addition and active cell division, respectively. These results indicate that the requirement for different nitrogen compounds is a major determinant of diatom species responses during bloom maturing.

Acute salt stress differentially modulates nitrate reductase expression in contrasting salt responsive rice cultivars

Salt stress response includes alteration in the activity of various important enzymes in plants. Nitrate reductase (NR) is one of the known enzyme affected by salt stress. In this study, contrasting salt responsive cultivars (CVS) (IR64-sensitive and CSR 36-tolerant) were considered to study the regulation of NR genes under salt stress conditions. Using Arabidopsis genes Nia1 and Nia2, three different NR genes were identified in rice and their expression study was conducted. Under stress condition, salt-sensitive CVS (IR64) showed a decrease in NR activity under in vitro and in vivo conditions, whereas tolerant CVS showed an increase in NR activity. Different trends for NR activity in contrasting genotype are explained by the variable number of GATA element in the upstream region of the NR gene. This variation of NR activity in contrasting CVS further co-relates with the transcript level of NR genes. The transcript level of three different NR genes also evidenced the effect of CREs in gene regulation. Promoter (1-kb upstream region) of different NR genes contained different abiotic stress-responsive CREs, which explain the differential behavior of these genes towards the abiotic stress. Overall, this study concludes the role of CREs in the regulation of NR gene and indicates the importance of transcriptional control of NR activity under stress condition. This is the first type of report that highlights the role of the regulatory mechanism of NR genes under salt stress condition.

iTRAQ-based quantitative proteomic and physiological analysis of the response to N deficiency and the compensation effect in rice

Background

The crop growth compensation effect is a naturally biological phenomenon, and nitrogen (N) is essential for crop growth and development, especially for yield formation. Little is known about the molecular mechanism of N deficiency and N compensation in rice. Thus, the N-sensitive stage of rice was selected to study N deficiency at the tillering stage and N compensation at the young panicle differentiation stage. In this study, a proteome analysis was performed to analyze leaf differentially expressed proteins (DEPs), and to investigate the leaf physiological characteristics and yield under N deficiency and after N compensation.

Results

The yield per plant presented an equivalent compensatory effect. The net photosynthetic rate, optimal/maximal quantum yield of photosystem II (Fv/Fm), soil and plant analyzer development (SPAD) value, and glutamic pyruvic transaminase (GPT) activity of T1 (N deficiency at the tillering stage, and N compensation at the young panicle differentiation stage) were lower than those of CK (N at different stages of growth by constant distribution) under N deficiency. However, after N compensation, the net photosynthetic rate, Fv/Fm, SPAD value and GPT activity were increased. Using an iTRAQ-based quantitative approach, a total of 1665 credible proteins were identified in the three 4-plex iTRAQ experiments. Bioinformatics analysis indicated that DEPs were enriched in photosynthesis, photosynthesis-antenna proteins, carbon metabolism and carbon fixation in the photosynthetic organism pathways. Moreover, the photosynthesis-responsive proteins of chlorophyll a-b binding protein, ribulose bisphosphate carboxylase small chain and phosphoglycerate kinase were significantly downregulated under N deficiency. After N compensation, chlorophyll a-b binding protein, NADH dehydrogenase subunit 5, NADH dehydrogenase subunit 7, and peroxidase proteins were significantly upregulated in rice leaves.

Conclusion

Through physiological and quantitative proteomic analysis, we concluded that a variety of metabolic pathway changes was induced by N deficiency and N compensation. GO and KEGG enrichment analysis revealed that DEPs were significantly associated with photosynthesis pathway-, energy metabolism pathway- and stress resistance-related proteins. The DEPs play an important role in the regulation of N deficiency and the compensation effect in rice.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6031-4) contains supplementary material, which is available to authorized users.

Nepetalactone-rich essential oil mitigates phosphinothricin-induced ammonium toxicity in Arabidopsis thaliana (L.) Heynh

Active ingredient of the commercial herbicide BASTA (B), phosphinothricin, acts as an inhibitor of glutamine synthetase (GS), a key enzyme in ammonium assimilation. The treatment with BASTA leads to an elevation of ammonium levels in plants and further to various physiological alterations, ammonium toxicity and lethality. Results of the present study emphasize the complexity underlying control mechanisms that determine BASTA interaction with essential oil (EO) from Nepeta rtanjensis (NrEO), bioherbicide inducing oxidative stress in target plants. Simultaneous application of NrEO and BASTA, two agents showing differential mode of action, suspends BASTA-induced ammonium toxicity in Arabidopsis thaliana plants. This is achieved through maintaining GS activity, which sustains a sub-toxic and/or sub-lethal ammonium concentration in tissues. As revealed by the present study, regulation of GS activity, as influenced by BASTA and NrEO, occurs at transcriptional, posttranscriptional, and/or posttranslational levels. Two genes encoding cytosolic GS, GLN1;1 and GLN1;3, are highlighted as the main isozymes in Arabidopsis shoots contributing to NrEO-induced overcoming of BASTA-generated ammonium toxicity. The effects of NrEO might be ascribed to its major component nepetalactone, but the contribution of minor EO components should not be neglected. Although of fundamental significance, the results of the present study suggest possible low efficiency of BASTA in plantations of medicinal/aromatic plants such as Nepeta species. Furthermore, these results highlight the possibility of using NrEO as a bioherbicide in BASTA-treated crop fields to mitigate the effect of BASTA residues in contaminated soils.

Ammonium Nitrogen Tolerant Chlorella Strain Screening and Its Damaging Effects on Photosynthesis

Nitrogen is an essential nutrient element. Ammonium nitrogen, one of the most common nitrogen sources, is found in various habitats, especially wastewater. However, excessive amounts of ammonium nitrogen can be toxic to phytoplankton, higher plants, fish, and other animals, and microorganisms. In this study, we explored the tolerance of green algae to ammonium nitrogen using 10 Chlorella strains. High concentrations of ammonium nitrogen directly inhibited the growth of Chlorella, but the degree of inhibition varied by strain. With the EC50 of 1.6 and 0.4 g L-1, FACHB-1563 and FACHB-1216, respectively had the highest and lowest tolerance to ammonium nitrogen among all strains tested, suggesting that FACHB-1563 could potentially be used to remove excess ammonium nitrogen from wastewater in bioremediation efforts. Two strains with the highest and lowest tolerance to ammonium nitrogen were selected to further explore the inhibitory effect of ammonium nitrogen on Chlorella. Analysis of chlorophyll fluorescence, oxygen evolution, and photosynthesis proteins via immunoblot showed that photosystem II (PSII) had been damaged when exposed to high levels of ammonium nitrogen, with the oxygen-evolving complex as the primary site, and electron transport fromQ A - to QB was subsequently inhibited by this treatment. A working model of ammonium nitrogen competition between N assimilation and PSII damage is proposed to elucidate that the assimilation rate of ammonium nitrogen by algae strains determines the tolerance of cells to ammonium nitrogen toxicity.

Elevated nitrogen metabolism and nitric oxide production are involved in Arabidopsis resistance to acid rain

Acid rain (AR) can induce great damages to plants and could be classified into different types according to the different SO₄^2-/NO₃^- ratio. However, the mechanism of plants' responding to different types of AR has not been elucidated clearly. Here, we found that nitric-rich simulated AR (N-SiAR) induced less leaves injury as lower necrosis percentage, better physiological parameters and reduced oxidative damage in the leaves of N-SiAR treated Arabidopsis thaliana compared with sulfate and nitrate mixed (SN-SiAR) or sulfuric-rich (S-SiAR) simulated AR treated ones. Of these three types of SiAR, N-SiAR treated Arabidopsis maintained the highest of nitrogen (N) content, nitrate reductase (NR) and nitrite reductase (NiR) activity as well as N metabolism related genes expression level. Nitric oxide (NO) content showed that N-SiAR treated seedlings had a higher NO level compared to SN-SiAR or S-SiAR treated ones. A series of NO production and elimination related reagents and three NO production-related mutants were used to further confirm the role of NO in regulating acid rain resistance in N-SiAR treated Arabidopsis seedlings. Taken together, we concluded that an elevated N metabolism and enhanced NO production are involved in the tolerance to different types of AR in Arabidopsis.

Knock-Down of CsNRT2.1, a Cucumber Nitrate Transporter, Reduces Nitrate Uptake, Root length, and Lateral Root Number at Low External Nitrate Concentration

Nitrogen (N) is a macronutrient that plays a crucial role in plant growth and development. Nitrate ( NO 3 - ) is the most abundant N source in aerobic soils. Plants have evolved two adaptive mechanisms such as up-regulation of the high-affinity transport system (HATS) and alteration of the root system architecture (RSA), allowing them to cope with the temporal and spatial variation of NO 3 - . However, little information is available regarding the nitrate transporter in cucumber, one of the most important fruit vegetables in the world. In this study we isolated a nitrate transporter named CsNRT2.1 from cucumber. Analysis of the expression profile of the CsNRT2.1 showed that CsNRT2.1 is a high affinity nitrate transporter which mainly located in mature roots. Subcellular localization analysis revealed that CsNRT2.1 is a plasma membrane transporter. In N-starved CsNRT2.1 knock-down plants, both of the constitutive HATS (cHATS) and inducible HATS (iHATS) were impaired under low external NO 3 - concentration. Furthermore, the CsNRT2.1 knock-down plants showed reduced root length and lateral root numbers. Together, our results demonstrated that CsNRT2.1 played a dual role in regulating the HATS and RSA to acquire NO 3 - effectively under N limitation.

Phylogenetic, expression and functional characterizations of the maize NLP transcription factor family reveal a role in nitrate assimilation and signaling

Although nitrate represents an important nitrogen (N) source for maize, a major crop of dryland areas, the molecular mechanisms of nitrate uptake and assimilation remain poorly understood. Here, we identified nine maize NIN-like protein (ZmNLP) genes and analyzed the function of one member, ZmNLP3.1, in nitrate nutrition and signaling. The NLP family genes were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that most ZmNLP genes had collinear relationships to the corresponding NLPs in rice, and that the expansion of the ZmNLP family resulted from segmental duplications in the maize genome. Quantitative PCR analysis revealed the expression of ZmNLP2.1, ZmNLP2.2, ZmNLP3.1, ZmNLP3.2, ZmNLP3.3, and ZmNLP3.4 was induced by nitrate in maize roots. The function of ZmNLP3.1 was investigated by overexpressing it in the Arabidopsis nlp7-1 mutant, which is defective in the AtNLP7 gene for nitrate signaling and assimilation. Ectopic expression of ZmNLP3.1 restored the N-deficient phenotypes of nlp7-1 under nitrate-replete conditions in terms of shoot biomass, root morphology and nitrate assimilation. Furthermore, the nitrate induction of NRT2.1, NIA1, and NiR1 gene expression was recovered in the 35S::ZmNLP3.1/nlp7-1 transgenic lines, indicating that ZmNLP3.1 plays essential roles in nitrate signaling. Taken together, these results suggest that ZmNLP3.1 plays an essential role in regulating nitrate signaling and assimilation processes, and represents a valuable candidate for developing transgenic maize cultivars with high N-use efficiency.

Emerging Trends in Epigenetic Regulation of Nutrient Deficiency Response in Plants

Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.

High-affinity nitrate/nitrite transporter genes (Nrt2) in Tisochrysis lutea: identification and expression analyses reveal some interesting specificities of Haptophyta microalgae

Microalgae have a diversity of industrial applications such as feed, food ingredients, depuration processes and energy. However, microalgal production costs could be substantially improved by controlling nutrient intake. Accordingly, a better understanding of microalgal nitrogen metabolism is essential. Using in silico analysis from transcriptomic data concerning the microalgae Tisochrysis lutea, four genes encoding putative high-affinity nitrate/nitrite transporters (TlNrt2) were identified. Unlike most of the land plants and microalgae, cloning of genomic sequences and their alignment with complementary DNA (cDNA) sequences did not reveal the presence of introns in all TlNrt2 genes. The deduced TlNRT2 protein sequences showed similarities to NRT2 proteins of other phyla such as land plants and green algae. However, some interesting specificities only known among Haptophyta were also revealed, especially an additional sequence of 100 amino acids forming an atypical extracellular loop located between transmembrane domains 9 and 10 and the function of which remains to be elucidated. Analyses of individual TlNrt2 gene expression with different nitrogen sources and concentrations were performed. TlNrt2.1 and TlNrt2.3 were strongly induced by low NO3 (-) concentration and repressed by NH4 (+) substrate and were classified as inducible genes. TlNrt2.2 was characterized by a constitutive pattern whatever the substrate. Finally, TlNrt2.4 displayed an atypical response that was not reported earlier in literature. Interestingly, expression of TlNrt2.4 was rather related to internal nitrogen quota level than external nitrogen concentration. This first study on nitrogen metabolism of T. lutea opens avenues for future investigations on the function of these genes and their implication for industrial applications.

Calix[4]pyrroles: versatile molecular containers with ion transport, recognition, and molecular switching functions

Calix[4]pyrroles function as “molecular containers” as illustrated by their ability to act as carriers for the through-membrane transport of ions and as “monomers” in the construction of aggregated supramolecular constructs.

Preferential utilization of intracellular nutrients supports microalgal growth under nutrient starvation: multi-nutrient mechanistic model and experimental validation

Microalgae are able to grow even under exhaustion of some key nutrients such as nitrogen and phosphorous. Here, we report a multi-nutrient mechanistic model to predict heterotrophic growth of Chlorella sp. FC2 IITG over two sequential phases of fermentation: nutrient sufficient condition to nutrient starved condition. The model assumes that the growth of the microorganism takes place via sequential utilization of extracellular nutrients (ECN) under nutrient replete condition followed by intracellular stored nutrients under exhaustion of limiting nutrients. Further, intracellular nutrient was assumed to be in three different forms: structural form of nutrient (SFN), readily utilizable nutrient (RUN) and non-readily utilizable nutrient (Non-RUN). After the exhaustion of ECN, microorganism switches to RUN followed by Non-RUN to continue its growth, which was experimentally validated by extracting intracellular nitrate and phosphate compounds. The model also incorporates variability in yield coefficients for nitrate and phosphate utilizations.

Nitrite transport activity of a novel HPP family protein conserved in cyanobacteria and chloroplasts

Some cyanobacterial genomes encode an integral membrane protein of the HPP family, which exhibited nitrite transport activity when expressed in the nitrite transport-less NA4 mutant of the cyanobacterium Synechococcus elongatus strain PCC 7942. AT5G62720 and AT3G47980 were found to encode Arabidopsis homologs of the cyanobacterial protein. The product of AT5G62720 was localized to the chloroplast envelope membrane and was shown to confer nitrite uptake activity on the NA4 mutant when expressed with an N-terminally truncated transit peptide or as a fusion with the N-terminal region of the cyanobacterial HPP family protein. Kinetic analyses showed that the Arabidopsis protein has much higher affinity for nitrite (K(m) = 13 µM) than the cyanobacterial protein (K(m) = 150 µM). Illuminated chloroplasts isolated from the mutant lines of AT5G62720 showed much lower activity of nitrite uptake than the chloroplasts isolated from the wild-type Col-0 plants, while the chloroplasts of the mutants of AT1G68570 (AtNPF3.1), the gene previously reported to encode a plastid nitrite transporter AtNitr1, showed wild-type levels of nitrite uptake activity. AT3G47980 was expressed in roots but not in shoots. It has a putative transit peptide similar to that of AT5G62720 and its fusion with the N-terminal region of the cyanobacterial HPP protein showed low but significant activity of nitrite transport in the cyanobacterial cell. Transcription of AT5G62720 (AtNITR2;1) and AT3G47980 (AtNITR2;2) was stimulated by nitrate under the control of the NIN-like proteins, suggesting that the HPP proteins represent nitrate-inducible components of the nitrite transport system of plastids.

Reducing the reliance on nitrogen fertilizer for wheat production

All crops require nitrogen (N) for the production of a photosynthetically active canopy, whose functionality will strongly influence yield. Cereal crops also require N for storage proteins in the grain, an important quality attribute. Optimal efficiency is achieved by the controlled remobilization of canopy-N to the developing grain during crop maturation. Whilst N will always be required for crop production, targeting efficient capture and use will optimise consumption of this valuable macronutrient. Efficient management of N through agronomic practice and use of appropriate germplasm are essential for sustainability of agricultural production. Both the economic demands of agriculture and the need to avoid negative environmental impacts of N-pollutants, such as nitrate in water courses or release of N-containing greenhouse gases, are important drivers to seek the most efficient use of this critical agronomic input. New cultivars optimised for traits relating to N-use efficiency rather than yield alone will be required. Targets for genetic improvement involve maximising capture, partitioning and remobilization in the canopy and to the grain, and yield per se. Whilst there is existing genetic diversity amongst modern cultivars, substantial improvements may require exploitation of a wider germplasm pool, utilizing land races and ancestral germplasm.

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Trends in yields, NUE and N fertilizer application are described.

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NUE terms are explained.

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Specific traits for improvement are listed.

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Existing variation is outlined.

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An overview for the scope for improvement is presented.

Induction of high-affinity NO3- uptake in grapevine roots is an active process correlated to the expression of specific members of the NRT2 and plasma membrane H+-ATPase gene families

The phenomenon of NO3- induction in plant roots has been characterised both in herbaceous and woody plants. Grapevine (Vitis vinifera L.) plants, hydroponically grown, showed an increase in NO3- uptake rate in response to anion treatment for different periods in the nutrient solution after 1 week of NO3- deprivation. The expression profile of the two high-affinity NO3- transporters VvNRT2.4A and VvNRT2.4B, and the gene encoding the accessory protein VvNAR2.2 exhibits a similar trend to that of the anion uptake. The induction, also involving the increase in activity and protein levels of plasma membrane H+-ATPase, is correlated with the expression profile of two (VvHA2 and VvHA4) out of eight putative plasma membrane H+-ATPase genes identified in grapevine genome.

High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis

Background

The cabbage, Brassica oleracea var. capitata L., has a distinguishable phenotype within the genus Brassica. Despite the economic and genetic importance of cabbage, there is little genomic data for cabbage, and most studies of Brassica are focused on other species or other B. oleracea subspecies. The lack of genomic data for cabbage, a non-model organism, hinders research on its molecular biology. Hence, the construction of reliable transcriptomic data based on high-throughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work.

Methodology/Principal Findings

We constructed cDNAs from total RNA isolated from the roots, leaves, flowers, seedlings, and calcium-limited seedling tissues of two cabbage genotypes: 102043 and 107140. We sequenced a total of six different samples using the Illumina HiSeq platform, producing 40.5 Gbp of sequence data comprising 401,454,986 short reads. We assembled 205,046 transcripts (≥ 200 bp) using the Velvet and Oases assembler and predicted 53,562 loci from the transcripts. We annotated 35,274 of the loci with 55,916 plant peptides in the Phytozome database. The average length of the annotated loci was 1,419 bp. We confirmed the reliability of the sequencing assembly using reverse-transcriptase PCR to identify tissue-specific gene candidates among the annotated loci.

Conclusion

Our study provides valuable transcriptome sequence data for B. oleracea var. capitata L., offering a new resource for studying B. oleracea and closely related species. Our transcriptomic sequences will enhance the quality of gene annotation and functional analysis of the cabbage genome and serve as a material basis for future genomic research on cabbage. The sequencing data from this study can be used to develop molecular markers and to identify the extreme differences among the phenotypes of different species in the genus Brassica.

Combined intracellular nitrate and NIT2 effects on storage carbohydrate metabolism in Chlamydomonas

Microalgae are receiving increasing attention as alternative production systems for renewable energy such as biofuel. The photosynthetic alga Chlamydomonas reinhardtii is widely recognized as the model system to study all aspects of algal physiology, including the molecular mechanisms underlying the accumulation of starch and triacylglycerol (TAG), which are the precursors of biofuel. All of these pathways not only require a carbon (C) supply but also are strongly dependent on a source of nitrogen (N) to sustain optimal growth rate and biomass production. In order to gain a better understanding of the regulation of C and N metabolisms and the accumulation of storage carbohydrates, the effect of different N sources (NH4NO3 and ) on primary metabolism using various mutants impaired in either NIA1, NIT2 or both loci was performed by metabolic analyses. The data demonstrated that, using NH4NO3, nia1 strain displayed the most striking phenotype, including an inhibition of growth, accumulation of intracellular nitrate, and strong starch and TAG accumulation. The measurements of the different C and N intermediate levels (amino, organic, and fatty acids), together with the determination of acetate and remaining in the medium, clearly excluded the hypothesis of a slower and acetate assimilation in this mutant in the presence of NH4NO3. The results provide evidence of the implication of intracellular nitrate and NIT2 in the control of C partitioning into different storage carbohydrates under mixotrophic conditions in Chlamydomonas. The underlying mechanisms and implications for strategies to increase biomass yield and storage product composition in oleaginous algae are discussed.

New insight into the strategy for nitrogen metabolism in plant cells

Nitrogen (N) is one of the most important mineral nutrients required by higher plants. Primary N absorbed by higher plants includes nitrate (NO3(-)), ammonium (NH4(+)), and organic N. Plants have developed several mechanisms for regulating their N metabolism in response to N availability and environmental conditions. Numerous transporters have been characterized and the mode of N movement within plants has been demonstrated. For further assimilation of N, various enzymes are involved in the key processes of NO3(-) or NH4(+) assimilation. N and carbon (C) metabolism are tightly coordinated in the fundamental biochemical pathway that permits plant growth. As N and C metabolism are the fundamental constituents of plant life, understanding N regulation is essential for growing plants and improving crop production. Regulation of N metabolism at the transcriptional and posttranscriptional levels provides important perceptions in the complex regulatory network of plants to adapt to changing N availability. In this chapter, recent advances in elucidating molecular mechanisms of N metabolism processes and regulation strategy, as well as interactions between C and N, are discussed. This review provides new insights into the strategy for studying N metabolism at the cellular level for optimum plant growth in different environments.

Genotypic differences in nitrate uptake, translocation and assimilation of two Chinese cabbage cultivars [Brassica campestris L. ssp. Chinensis (L.)]

A hydroponic trial was conducted to investigate genotypic differences in nitrate uptake, translocation and assimilation between low nitrate accumulator L18 and high accumulator H96 of Chinese cabbage [Brassica campestris L. ssp. Chinensis (L.)]. The results suggested that H96 could uptake more nitrate than L18 in the root but lower transport inside leaf cells and assimilation in the leaf. It was showed that root morphology parameters - length, surface area and volume of H96 were 18.0%, 31.6% and 46.5% higher than L18. Nitrate transporters NRT1.1 and NRT2.1 transcription levels were 41.6% and 269.6% higher than those of L18 respectively. NRT1.1 and NRT2.1 expression amount in leaf blade of two cultivars were opposite to in the root, L18 NRT1.1 and NRT2.1 expressions were 279.2% and 80.0% higher than H96. In addition, nitrate assimilation capacity of L18 was significantly higher than H96 in leaf. It was showed that Nitrate Reductase (NR; EC 1.7.1.1) activity and NIA expression level of L18 leaf were 234 0.4% and 105.4% higher than those of H96, Glutamine Synthetase (GS; EC 6.3.1.2) activity, Gln1 and Gln2 expression levels in the leaf blade of L18 were 43.9%, 331.5% and 124.8% higher than those of H96 respectively. Nitrate assimilation products-Glu, total amino acid, soluble protein content in the leaf of L18 were all significantly higher than those of H96. The results above suggested that nitrate accumulation differences were due to differential capacities to uptake, mechanisms for nitrate transport in leaves and assimilate nitrate. Comparing contribution of three aspects in nitrate accumulation, translocation and assimilation were contributed more in low nitrate concentration in the leaf blade.

The nitrate transporter NRT2.1 functions in the ethylene response to nitrate deficiency in Arabidopsis

The ethylene signalling pathway is closely associated with complex environmental stresses. Previous studies have reported impact of high nitrate (HN) availability on ethylene biosynthesis and regulation of ethylene on nitrate transporter 2.1 (NRT2.1) expression. However, molecular interaction between NRT2.1 transcript levels and the ethylene signalling pathway under nitrate deficiency is still elusive. Here, we report a low nitrate (LN) treatment-induced rapid burst of ethylene production and regulated expression of ethylene signalling components CTR1, EIN3 and EIL1 in wild-type Arabidopsis thaliana (Col-0) seedlings, and enhanced ethylene response reporter EBS:GUS activity in both Col-0 and the ethylene mutants ein3-1eil1-1 and ctr1-1. LN treatment also caused up-regulation of NRT2.1 expression, which was responsible for an enhanced high-affinity nitrate uptake. Comparison of ethylene production and EBS:GUS activity between nrt1.1, nrt2.1 mutants and Col-0 indicated that this up-regulation of NRT2.1 expression caused a positive effect on ethylene biosynthesis and signalling under LN treatment. On the other hand, ethylene down-regulated NRT2.1 expression and reduced the high-affinity nitrate uptake. Together, these findings uncover a negative feedback loop between NRT2.1 expression and ethylene biosynthesis and signalling under nitrate deficiency, which may contribute to finely tuning of plant nitrate acquisition during exploring dynamic soil conditions.

Nitrate signals determine the sensing of nitrogen through differential expression of genes involved in nitrogen uptake and assimilation in finger millet

In order to understand the molecular basis of high nitrogen use efficiency of finger millet, five genes (EcHNRT2, EcLNRT1, EcNADH-NR, EcGS, and EcFd-GOGAT) involved in nitrate uptake and assimilation were isolated using conserved primer approaches. Expression profiles of these five genes along with the previously isolated EcDof1 was studied under increased KNO3 concentrations (0.15 to 1,500 μM) for 2 h as well as at 1.5 μM for 24 h in the roots and shoots of 25 days old nitrogen deprived two contrasting finger millet genotypes (GE-3885 and GE-1437) differing in grain protein content (13.76 and 6.15 %, respectively). Time kinetics experiment revealed that, all the five genes except EcHNRT2 in the leaves of GE-3885 were induced within 30 min of nitrate exposure indicating that there might be a greater nitrogen deficit in leaves and therefore quick transportation of nitrate signals to the leaves. Exposing the plants to increasing nitrate concentrations for 2 h showed that in roots of GE-3885, NR was strongly induced while GS was repressed; however, the pattern was found to be reversed in leaves of GE-1437 indicating that in GE-3885, most of the nitrate might be reduced in the roots but assimilated in leaves and vice-versa. Furthermore, compared with the low-protein genotype, expression of HNRT2 was strongly induced in both roots and shoots of high-protein genotype at the least nitrate concentration supplied. This further indicates that GE-3885 is a quick sensor of nitrogen compared with the low-protein genotype. Furthermore, expression of EcDof1 was also found to overlap the expression of NR, GS, and GOGAT indicating that Dof1 probably regulates the expression of these genes under different conditions by sensing the nitrogen fluctuations around the root zone.

Arabidopsis NRT1.5 is another essential component in the regulation of nitrate reallocation and stress tolerance

Nitrate reallocation to plant roots occurs frequently under adverse conditions and was recently characterized to be actively regulated by Nitrate Transporter1.8 (NRT1.8) in Arabidopsis (Arabidopsis thaliana) and implicated as a common response to stresses. However, the underlying mechanisms remain largely to be determined. In this study, characterization of NRT1.5, a xylem nitrate-loading transporter, showed that the mRNA level of NRT1.5 is down-regulated by salt, drought, and cadmium treatments. Functional disruption of NRT1.5 enhanced tolerance to salt, drought, and cadmium stresses. Further analyses showed that nitrate, as well as Na(+) and Cd(2+) levels, were significantly increased in nrt1.5 roots. Important genes including Na(+)/H(+) exchanger1, Salt overly sensitive1, Pyrroline-5-carboxylate synthase1, Responsive to desiccation29A, Phytochelatin synthase1, and NRT1.8 in stress response pathways are steadily up-regulated in nrt1.5 mutant plants. Interestingly, altered accumulation of metabolites, including proline and malondialdehyde, was also observed in nrt1.5 plants. These data suggest that NRT1.5 is involved in nitrate allocation to roots and the consequent tolerance to several stresses, in a mechanism probably shared with NRT1.8.

BcNRT1, a plasma membrane-localized nitrate transporter from non-heading Chinese cabbage

A nitrate transporter, BcNRT1, was isolated from non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) cultivar 'Suzhouqing'. The full-length cDNA was obtained using the rapid amplification of cDNA ends technique and contains an open reading frame of 1,770 bp that predicts a protein of 589 acid residues that possesses 12 putative transmembrane domains. Using the GUS marker gene driven by the BcNRT1 promoter, we found BcNRT1 expression to be concentrated in primary and lateral root tips and in shoots of transgenic Arabidopsis plants. The YFP fused to BcNRT1 and transformed into cabbage protoplasts indicated that BcNRT1 was localized to the plasma membrane. The expression of BcNRT1 in roots was induced by exposure to 25 mM nitrate, and the BcNRT1 cRNA heterologously expressed in Xenopus laevis oocytes showed nitrate conductance when nitrate was included in the medium. Moreover, mutant chl1-5 plants harboring 35S::BcNRT1 showed sensitivity to chlorate treatment and exhibited restored nitrate uptake. In conclusion, the results indicate that BcNRT1 functions as a low affinity nitrate transporter in non-heading Chinese cabbage.

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.

Identification and analysis of differentially expressed genes in mountain cultivated ginseng and mountain wild ginseng

Ginseng is one of the most widely used herbal medicines in the world. Wild ginseng is thought to be more effective than cultivated ginseng in chemoprevention; however, little has been reported on the differences between wild and cultivated ginseng. In the present study we used suppressive subtractive hybridization to identify wild ginseng-specific genes. One of the clones isolated in this screen was the NRT2 gene (designated pNRT2), a high-affinity nitrate transporter. Real-time reverse transcription-polymerase chain reaction results showed that pNRT2 expression was significantly upregulated in wild ginseng compared with cultivated ginseng. However, pNRT2 mRNA levels were similar between mountain cultivated ginseng and mountain wild ginseng. Nitrate is an important nitrogen source for plant growth, and its soil levels can vary in wild environments; thus it is conceivable that pNRT2 expression is upregulated in wild ginseng and may be an important marker of wild ginseng.

NEMA, a functional-structural model of nitrogen economy within wheat culms after flowering. II. Evaluation and sensitivity analysis

BACKGROUND AND AIMS

Simulating nitrogen economy in crop plants requires formalizing the interactions between soil nitrogen availability, root nitrogen acquisition, distribution between vegetative organs and remobilization towards grains. This study evaluates and analyses the functional-structural and mechanistic model of nitrogen economy, NEMA (Nitrogen Economy Model within plant Architecture), developed for winter wheat (Triticum aestivum) after flowering.

METHODS

NEMA was calibrated for field plants under three nitrogen fertilization treatments at flowering. Model behaviour was investigated and sensitivity to parameter values was analysed.

KEY RESULTS

Nitrogen content of all photosynthetic organs and in particular nitrogen vertical distribution along the stem and remobilization patterns in response to fertilization were simulated accurately by the model, from Rubisco turnover modulated by light intercepted by the organ and a mobile nitrogen pool. This pool proved to be a reliable indicator of plant nitrogen status, allowing efficient regulation of nitrogen acquisition by roots, remobilization from vegetative organs and accumulation in grains in response to nitrogen treatments. In our simulations, root capacity to import carbon, rather than carbon availability, limited nitrogen acquisition and ultimately nitrogen accumulation in grains, while Rubisco turnover intensity mostly affected dry matter accumulation in grains.

CONCLUSIONS

NEMA enabled interpretation of several key patterns usually observed in field conditions and the identification of plausible processes limiting for grain yield, protein content and root nitrogen acquisition that could be targets for plant breeding; however, further understanding requires more mechanistic formalization of carbon metabolism. Its strong physiological basis and its realistic behaviour support its use to gain insights into nitrogen economy after flowering.

NEMA, a functional-structural model of nitrogen economy within wheat culms after flowering. I. Model description

BACKGROUND AND AIMS

Models simulating nitrogen use by plants are potentially efficient tools to optimize the use of fertilizers in agriculture. Most crop models assume that a target nitrogen concentration can be defined for plant tissues and formalize a demand for nitrogen, depending on the difference between the target and actual nitrogen concentrations. However, the teleonomic nature of the approach has been criticized. This paper proposes a mechanistic model of nitrogen economy, NEMA (Nitrogen Economy Model within plant Architecture), which links nitrogen fluxes to nitrogen concentration and physiological processes.

METHODS

A functional-structural approach is used: plant aerial parts are described in a botanically realistic way and physiological processes are expressed at the scale of each aerial organ or root compartment as a function of local conditions (light and resources).

KEY RESULTS

NEMA was developed for winter wheat (Triticum aestivum) after flowering. The model simulates the nitrogen (N) content of each photosynthetic organ as regulated by Rubisco turnover, which depends on intercepted light and a mobile N pool shared by all organs. This pool is enriched by N acquisition from the soil and N release from vegetative organs, and is depleted by grain uptake and protein synthesis in vegetative organs; NEMA accounts for the negative feedback from circulating N on N acquisition from the soil, which is supposed to follow the activities of nitrate transport systems. Organ N content and intercepted light determine dry matter production via photosynthesis, which is distributed between organs according to a demand-driven approach.

CONCLUSIONS

NEMA integrates the main feedbacks known to regulate plant N economy. Other novel features are the simulation of N for all photosynthetic tissues and the use of an explicit description of the plant that allows how the local environment of tissues regulates their N content to be taken into account. We believe this represents an appropriate frame for modelling nitrogen in functional-structural plant models. A companion paper will present model evaluation and analysis.

Predicting the physiological role of circadian metabolic regulation in the green alga Chlamydomonas reinhardtii

Although the number of reconstructed metabolic networks is steadily growing, experimental data integration into these networks is still challenging. Based on elementary flux mode analysis, we combine sequence information with metabolic pathway analysis and include, as a novel aspect, circadian regulation. While minimizing the need of assumptions, we are able to predict changes in the metabolic state and can hypothesise on the physiological role of circadian control in nitrogen metabolism of the green alga Chlamydomonas reinhardtii.

The essential role of anionic transport in plant cells: the pollen tube as a case study

Plasma membrane anion transporters play fundamental roles in plant cell biology, especially in stomatal closure and nutrition. Notwithstanding, a lot is still unknown about the specific function of these transporters, their specific localization, or molecular nature. Here the fundamental roles of anionic transport in plant cells are reviewed. Special attention will be paid to them in the control of pollen tube growth. Pollen tubes are extreme examples of cellular polarity as they grow exclusively in their apical extremity. Their unique cell biology has been extensively exploited for fundamental understanding of cellular growth and morphogenesis. Non-invasive methods have demonstrated that tube growth is governed by different ion fluxes, with different properties and distribution. Not much is known about the nature of the membrane transporters responsible for anionic transport and their regulation in the pollen tube. Recent data indicate the importance of chloride (Cl(-)) transfer across the plasma membrane for pollen germination and pollen tube growth. A general overview is presented of the well-known accumulated data in terms of biophysical and functional characterization, transcriptomics, and genomic description of pollen ionic transport, and the various controversies around the role of anionic fluxes during pollen tube germination, growth, and development. It is concluded that, like all other plant cells so far analysed, pollen tubes depend on anion fluxes for a number of fundamental homeostatic properties.