Deciphering the molecular basis of ammonium uptake and transport in maritime pine

Analysis of the AMT gene family in chili pepper and the effects of arbuscular mycorrhizal colonization on the expression patterns of CaAMT2 genes

BACKGROUND

Ammonium (NH₄⁺) is a key nitrogen source supporting plant growth and development. Proteins in the ammonium transporter (AMT) family mediate the movement of NH₄⁺ across the cell membrane. Although several studies have examined AMT genes in various plant species, few studies of the AMT gene family have been conducted in chili pepper.

RESULTS

Here, a total of eight AMT genes were identified in chili pepper, and their exon/intron structures, phylogenetic relationships, and expression patterns in response to arbuscular mycorrhizal (AM) colonization were explored. Synteny analyses among chili pepper, tomato, eggplant, soybean, and Medicago revealed that the CaAMT2;1, CaAMT2.4, and CaAMT3;1 have undergone an expansion prior to the divergence of Solanaceae and Leguminosae. The expression of six AMT2 genes was either up-regulated or down-regulated in response to AM colonization. The expression of CaAMT2;1/2;2/2;3 and SlAMT2;1/2;2/2;3 was significantly up-regulated in AM fungi-inoculated roots. A 1,112-bp CaAMT2;1 promoter fragment and a 1,400-bp CaAMT2;2 promoter fragment drove the expression of the β-glucuronidase gene in the cortex of AM roots. Evaluation of AM colonization under different NH₄⁺ concentrations revealed that a sufficient, but not excessive, supply of NH₄⁺ promotes the growth of chili pepper and the colonization of AM. Furthermore, we demonstrated that CaAMT2;2 overexpression could mediate NH₄⁺ uptake in tomato plants.

CONCLUSION

In sum, our results provide new insights into the evolutionary relationships and functional divergence of chili pepper AMT genes. We also identified putative AMT genes expressed in AM symbiotic roots.

Epitranscriptome changes triggered by ammonium nutrition regulate the proteome response of maritime pine roots

Epitranscriptome constitutes a gene expression checkpoint in all living organisms. Nitrogen is an essential element for plant growth and development that influences gene expression at different levels such as epigenome, transcriptome, proteome, and metabolome. Therefore, our hypothesis is that changes in the epitranscriptome may regulate nitrogen metabolism. In this study, epitranscriptomic modifications caused by ammonium nutrition were monitored in maritime pine roots using Oxford Nanopore Technology. Transcriptomic responses mainly affected transcripts involved in nitrogen and carbon metabolism, defense, hormone synthesis/signaling, and translation. Global detection of epitranscriptomic marks was performed to evaluate this posttranscriptional mechanism in un/treated seedlings. Increased N⁶-methyladenosine (m⁶A) deposition in the 3'-UTR was observed in response to ammonium, which seems to be correlated with poly(A) lengths and changes in the relative abundance of the corresponding proteins. The results showed that m⁶A deposition and its dynamics seem to be important regulators of translation under ammonium nutrition. These findings suggest that protein translation is finely regulated through epitranscriptomic marks likely by changes in mRNA poly(A) length, transcript abundance and ribosome protein composition. An integration of multiomics data suggests that the epitranscriptome modulates responses to nutritional, developmental and environmental changes through buffering, filtering, and focusing the final products of gene expression.

Nitrogen Acquisition and Transport in the Ectomycorrhizal Symbiosis-Insights from the Interaction between an Oak Tree and Pisolithus tinctorius

In temperate forests, the roots of various tree species are colonized by ectomycorrhizal fungi, which have a key role in the nitrogen nutrition of their hosts. However, not much is known about the molecular mechanisms related to nitrogen metabolism in ectomycorrhizal plants. This study aimed to evaluate the nitrogen metabolic response of oak plants when inoculated with the ectomycorrhizal fungus Pisolithus tinctorius. The expression of candidate genes encoding proteins involved in nitrogen uptake and assimilation was investigated in ectomycorrhizal roots. We found that three oak ammonium transporters were over-expressed in root tissues after inoculation, while the expression of amino acid transporters was not modified, suggesting that inorganic nitrogen is the main form of nitrogen transferred by the symbiotic fungus into the roots of the host plant. Analysis by heterologous complementation of a yeast mutant defective in ammonium uptake and GFP subcellular protein localization clearly confirmed that two of these genes encode functional ammonium transporters. Structural similarities between the proteins encoded by these ectomycorrhizal upregulated ammonium transporters, and a well-characterized ammonium transporter from E. coli, suggest a similar transport mechanism, involving deprotonation of NH4+, followed by diffusion of uncharged NH3 into the cytosol. This view is supported by the lack of induction of NH4+ detoxifying mechanisms, such as the GS/GOGAT pathway, in the oak mycorrhizal roots.

Genome-Wide Identification and Expression Analysis of AMT and NRT Gene Family in Pecan (Carya illinoinensis) Seedlings Revealed a Preference for NH4+-N

Nitrogen (N) is a major limiting factor for plant growth and crop production. The use of N fertilizer in forestry production is increasing each year, but the loss is substantial. Mastering the regulatory mechanisms of N uptake and transport is a key way to improve plant nitrogen use efficiency (NUE). However, this has rarely been studied in pecans. In this study, 10 AMT and 69 NRT gene family members were identified and systematically analyzed from the whole pecan genome using a bioinformatics approach, and the expression patterns of AMT and NRT genes and the uptake characteristics of NH₄⁺ and NO₃⁻ in pecan were analyzed by aeroponic cultivation at varying NH₄⁺/NO₃⁻ ratios (0/0, 0/100,25/75, 50/50, 75/25,100/0 as CK, T1, T2, T3, T4, and T5). The results showed that gene duplication was the main reason for the amplification of the AMT and NRT gene families in pecan, both of which experienced purifying selection. Based on qRT-PCR results, CiAMTs were primarily expressed in roots, and CiNRTs were majorly expressed in leaves, which were consistent with the distribution of pecan NH₄⁺ and NO₃⁻ concentrations in the organs. The expression levels of CiAMTs and CiNRTs were mainly significantly upregulated under N deficiency and T4 treatment. Meanwhile, T4 treatment significantly increased the NH₄⁺, NO₃⁻, and NO₂⁻ concentrations as well as the Vmax and Km values of NH₄⁺ and NO₃⁻ in pecans, and Vmax/Km indicated that pecan seedlings preferred to absorb NH₄⁺. In summary, considering the single N source of T5, we suggested that the NH₄⁺/NO₃⁻ ratio of 75:25 was more beneficial to improve the NUE of pecan, thus increasing pecan yield, which provides a theoretical basis for promoting the scale development of pecan and provides a basis for further identification of the functions of AMT and NRT genes in the N uptake and transport process of pecan.

Melatonin and dopamine mediate the regulation of nitrogen uptake and metabolism at low ammonium levels in Malus hupehensis

In plants, ammonium (NH₄⁺) is the main nitrogen source and acts as a physiological and morphological response signaling molecule. Melatonin and dopamine are associated with plant responses to abiotic stress. However, previous studies have rarely focused on nutrient stress, and the roles of melatonin and dopamine in the uptake and metabolism of nitrogen in plants remain unclear. In this study, we investigated the regulatory effects of melatonin and dopamine on nitrogen utilization efficiency in apple seedlings under two NH₄⁺ concentrations (2 and 0.1 mM) by measuring plant growth, root system architecture, ¹⁵NH₄⁺ content, and related enzyme activity and gene expression. Under low nitrogen supply, apple seedling growth slowed and showed marked reductions in biomass accumulation, chlorophyll content, and nutrient uptake. However, both melatonin and dopamine significantly improved plant growth, chlorophyll content, and root development and enhanced antioxidant enzyme activity. Exogenous application of melatonin or dopamine also promoted the absorption and accumulation of ¹⁵NH₄⁺ and enhanced nitrogen metabolism-related enzyme activity. At the molecular level, melatonin and dopamine significantly increased the expression levels of nitrogen metabolism genes and transporter genes. Overall, these results suggest that melatonin and dopamine can relieve nutrient stress caused by low concentrations of NH₄⁺ through regulating the absorption and metabolism of nitrogen.

Effects of arbuscular mycorrhizal fungi on the nitrogen distribution in endangered Torreya jackii under nitrogen limitation

Arbuscular mycorrhizal fungi regulated the distribution of nitrogen in the leaves, thereby facilitating the adaptation of the endangered plant Torreya jackii to a low-nitrogen environment. Rhizophagus irregularis was inoculated into sterilized soil to investigate its impact on the distribution ratio of leaf nitrogen in cell wall proteins, cell membrane proteins, water-soluble proteins, and photosynthetic systems which includes the carboxylation system (P_C), energy metabolism (P_B), and light-harvesting system in the endangered species Torreya jackii. The results showed that R. irregularis reduced the specific leaf weight and the distribution ratio of nitrogen in cell wall proteins in the leaves of T. jackii, whereas it enhanced the distribution ratio of nitrogen in cell membrane proteins and water-soluble proteins. R. irregularis enabled more nitrogen uptake for growth by decreasing the distribution of nitrogen to the structural substances. At low-nitrogen levels, inoculation with R. irregularis improved the plant height (18.78 ~ 36.04%), shoot dry weight (50.53 ~ 64.33%), total dry weight (42.86 ~ 52.82%), maximal net photosynthetic rate (P_max) (16.83 ~ 20.11%), photosynthetic nitrogen use efficiency (PNUE) (40.01 ~ 43.14%), P_C (33.56 ~ 38.59%) and P_B (29.08 ~ 34.02%). However, it did not substantially affect the leaf nitrogen content per unit area or the leaf nitrogen content per unit mass. Moreover, P_max exhibited a significant positive correlation with P_C and P_B, and all three parameters showed a significant positive correlation with the PNUE, thereby revealing that R. irregularis increased the photosynthetic capacity and PNUE of T. jackii through boosting P_C and P_B.

Function and Regulation of Ammonium Transporters in Plants

Ammonium transporter (AMT)-mediated acquisition of ammonium nitrogen from soils is essential for the nitrogen demand of plants, especially for those plants growing in flooded or acidic soils where ammonium is dominant. Recent advances show that AMTs additionally participate in many other physiological processes such as transporting ammonium from symbiotic fungi to plants, transporting ammonium from roots to shoots, transferring ammonium in leaves and reproductive organs, or facilitating resistance to plant diseases via ammonium transport. Besides being a transporter, several AMTs are required for the root development upon ammonium exposure. To avoid the adverse effects of inadequate or excessive intake of ammonium nitrogen on plant growth and development, activities of AMTs are fine-tuned not only at the transcriptional level by the participation of at least four transcription factors, but also at protein level by phosphorylation, pH, endocytosis, and heterotrimerization. Despite these progresses, it is worth noting that stronger growth inhibition, not facilitation, unfortunately occurs when AMT overexpression lines are exposed to optimal or slightly excessive ammonium. This implies that a long road remains towards overcoming potential limiting factors and achieving AMT-facilitated yield increase to accomplish the goal of persistent yield increase under the present high nitrogen input mode in agriculture.

Nitrogen Metabolism and Biomass Production in Forest Trees

Low nitrogen (N) availability is a major limiting factor for tree growth and development. N uptake, assimilation, storage and remobilization are key processes in the economy of this essential nutrient, and its efficient metabolic use largely determines vascular development, tree productivity and biomass production. Recently, advances have been made that improve our knowledge about the molecular regulation of acquisition, assimilation and internal recycling of N in forest trees. In poplar, a model tree widely used for molecular and functional studies, the biosynthesis of glutamine plays a central role in N metabolism, influencing multiple pathways both in primary and secondary metabolism. Moreover, the molecular regulation of glutamine biosynthesis is particularly relevant for accumulation of N reserves during dormancy and in N remobilization that takes place at the onset of the next growing season. The characterization of transgenic poplars overexpressing structural and regulatory genes involved in glutamine biosynthesis has provided insights into how glutamine metabolism may influence the N economy and biomass production in forest trees. Here, a general overview of this research topic is outlined, recent progress are analyzed and challenges for future research are discussed.

Identification and characterization of two ammonium transporter genes in flowering Chinese cabbage (Brassica campestris)

Ammonium transporters (AMTs), which include AMT1 and AMT2 subfamilies, have been identified and partially characterized in many plants. In this study, two AMT2-type genes from Brassica campestris, namely BcAMT2 and BcAMT2like, were identified and characterized. BcAMT2 and BcAMT2like are 2666 bp and 2952 bp, encode proteins of 490 and 489 amino acids, respectively, and contain five exons and four introns. Transient expression of these proteins labelled with green fluorescence protein in onion epidermal cells indicated that both are located on the plasma membrane. When expressing BcAMT2 or BcAMT2like, the mutant yeast strain 31019b could grow on medium containing 2 mM ammonium as the only nitrogen source when expressing BcAMT2 or BcAMT2like, indicating that both are functional AMT genes. Quantitative PCR results showed that BcAMT2 and BcAMT2like were expressed in all tissues, but they displayed different expression patterns in the reproductive stages. BcAMT2s transcript levels in leaves were positively correlated with ammonium concentration and external pH. Moreover, the expression BcAMT2s responded to diurnal change. Furthermore, the uncharged form of ammonium, i.e., ammonia, might also be transported by BcAMT2s. These results provide new insights into the molecular mechanisms underlying ammonium absorption and transportation by the AMT2 subfamily in B. campestris.

Source and sink mechanisms of nitrogen transport and use

Contents Summary 35 I. Introduction 35 II. Nitrogen acquisition and assimilation 36 III. Root-to-shoot transport of nitrogen 38 IV. Nitrogen storage pools in vegetative tissues 39 V. Nitrogen transport from source leaf to sink 40 VI. Nitrogen import into sinks 42 VII. Relationship between source and sink nitrogen transport processes and metabolism 43 VIII. Regulation of nitrogen transport 43 IX. Strategies for crop improvement 44 X. Conclusions 46 Acknowledgements 47 References 47 SUMMARY: Nitrogen is an essential nutrient for plant growth. World-wide, large quantities of nitrogenous fertilizer are applied to ensure maximum crop productivity. However, nitrogen fertilizer application is expensive and negatively affects the environment, and subsequently human health. A strategy to address this problem is the development of crops that are efficient in acquiring and using nitrogen and that can achieve high seed yields with reduced nitrogen input. This review integrates the current knowledge regarding inorganic and organic nitrogen management at the whole-plant level, spanning from nitrogen uptake to remobilization and utilization in source and sink organs. Plant partitioning and transient storage of inorganic and organic nitrogen forms are evaluated, as is how they affect nitrogen availability, metabolism and mobilization. Essential functions of nitrogen transporters in source and sink organs and their importance in regulating nitrogen movement in support of metabolism, and vegetative and reproductive growth are assessed. Finally, we discuss recent advances in plant engineering, demonstrating that nitrogen transporters are effective targets to improve crop productivity and nitrogen use efficiency. While inorganic and organic nitrogen transporters were examined separately in these studies, they provide valuable clues about how to successfully combine approaches for future crop engineering.

Molecular fundamentals of nitrogen uptake and transport in trees

Nitrogen (N) is frequently a limiting factor for tree growth and development. Because N availability is extremely low in forest soils, trees have evolved mechanisms to acquire and transport this essential nutrient along with biotic interactions to guarantee its strict economy. Here we review recent advances in the molecular basis of tree N nutrition. The molecular characteristics, regulation, and biological significance of membrane proteins involved in the uptake and transport of N are addressed. The regulation of N uptake and transport in mycorrhized roots and transcriptome-wide studies of N nutrition are also outlined. Finally, several areas of future research are suggested.

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza

Soil nutrient acquisition and exchanges through symbiotic plant-fungus interactions in the rhizosphere are key features for the current agricultural and environmental challenges. Improved crop yield and plant mineral nutrition through a fungal symbiont has been widely described. In return, the host plant supplies carbon substrates to its fungal partner. We review here recent progress on molecular players of membrane transport involved in nutritional exchanges between mycorrhizal plants and fungi. We cover the transportome, from the transport proteins involved in sugar fluxes from plants towards fungi, to the uptake from the soil and exchange of nitrogen, phosphate, potassium, sulfate, and water. Together, these advances in the comprehension of the mycorrhizal transportome will help in developing the future engineering of new agro-ecological systems.