Gene characterization and transcription analysis of two new ammonium transporters in pear rootstock (Pyrus betulaefolia)

Genome-Wide Analysis of Sweet Potato Ammonium Transporter (AMT): Influence on Nitrogen Utilization, Storage Root Development and Yield

Ammonium, as a major inorganic source of nitrogen (N) for sweet potato N utilization and growth, is specifically transported by ammonium transporters (AMTs). However, the activities of AMT family members in sweet potatoes have not been analyzed. In the present study, the sweet potato cultivar 'Pushu 32', which is planted in a large area in China, was used in field experiments at the Agricultural Base of Hainan University (20°06' N, 110°33' E) in 2021, and Sanya Nanfan Research Institute of Hainan University (18°30' N, 109°60' E) in 2022. Four N levels were tested: 0, 60, 120, and 180 kg ha-1. The results are as follows. Twelve IbAMT genes were identified in the sweet potato genome, which were classified into three distinct subgroups based on phylogeny; the same subgroup genes had similar properties and structures. IbAMT1.3 and IbAMT1.5 were mostly expressed in the storage roots under N deficiency. Compared with the NN and HN groups, IbAMT1.3 and IbAMT1.5 expressions, N content in storage roots, N uptake efficiency at the canopy closure, N fertilization contribution rates, number of storage roots per plant, storage root weight, and yield were all increased in the MN group. Furthermore, there was a significant positive correlation between the expressions of IbAMT1.3 and IbAMT1.5 with N content in the storage roots of sweet potato. In a word, IbAMT1.3 and IbAMT1.5 may regulate N utilization, affect the development of the storage root. and determine the yield of sweet potato. The results provide valuable insights into the AMT gene family's role in the use of N and effects on storage root development and yield in sweet potatoes.

Nitrogen transport and assimilation in tea plant (Camellia sinensis): a review

Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.

Genome-Wide Identification and Expression Analysis of AMT Gene Family in Apple (Malus domestica Borkh.)

Ammonium is one of the prevalent nitrogen sources for growth and development of higher plants. Ammonium acquisition from soil is facilitated by ammonium transporters (AMTs), which are plasma membrane proteins that exclusively transport ammonium/ammonia. However, the functional characteristics and molecular mechanisms of AMTs in apple remain unclear. In this work, 15 putative AMT genes were identified and classified into four clusters (AMT1–AMT4) in apple. According to expression analysis, these AMTs had varying expressions in roots, leaves, stems, flowers and fruits. Some of them were strongly affected by diurnal cycles. AMT genes showed multiple transcript patterns to N regimes and were quite responsive to osmotic stress. In addition, phosphorylation analysis revealed that there were some conserved phosphorylation residues within the C-terminal of AMT proteins. Furthermore, detailed research was conducted on AMT1;2 functioning by heterologous expression in yeast. The present study is expected to provide basic bioinformatic information and expression profiles for the apple AMT family and to lay a basis for exploring the functional roles and regulation mechanisms of AMTs in apple.

Physiological, biochemical, and molecular aspects of grafting in fruit trees

Grafting is a widely used practice for asexual propagation of fruit trees. Many physiological, biochemical, and molecular changes occur upon grafting that can influence important horticultural traits. This technology has many advantages, including avoidance of juvenility, modifying the scion architecture, improving productivity, adapting scion cultivars to unfavourable environmental conditions, and developing traits in resistance to insect pests, bacterial and fungal diseases. A limitation of grafting is scion-rootstock incompatibility. It may be caused by many factors, including insufficient genetic proximity, physiological or biochemical factors, lignification at the graft union, poor graft architecture, insufficient cell recognition between union tissues, and metabolic differences in the scion and the rootstock. Plant hormones, like auxin, ethylene (ET), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) orchestrate several crucial physiological and biochemical processes happening at the site of the graft union. Additionally, epigenetic changes at the union affect chromatin architecture by DNA methylation, histone modification, and the action of small RNA molecules. The mechanism triggering these effects likely is affected by hormonal crosstalk, protein and small molecules movement, nutrients uptake, and transport in the grafted trees. This review provides an overview of the basis of physiological, biochemical, and molecular aspects of fruit tree grafting between scion and rootstock.

Genome-wide identification, characterization, and expression analysis of the ammonium transporter gene family in tea plants (Camellia sinensis L.)

As a preferred nitrogen form, ammonium (NH₄ ⁺ ) transport via specific transporters is particularly important for the growth and development of tea plants (Camellia sinensis L.). However, our understanding of the functions of the AMT family in tea plants is limited. We identified and named 16 putative AMT genes according to phylogenetic analysis. All CsAMT genes were divided into three groups, distributed on 12 chromosomes with only one segmental duplication repetition. The CsAMT genes showed different expression levels in different organs, and most of them were expressed mainly in the apical buds and roots. Complementation analysis of yeast mutants showed that CsAMTs restored the uptake of NH₄ ⁺ . This study provides insights into the genome-wide distribution and spatial expression of AMT genes in tea plants.

Cloning and Functional Determination of Ammonium Transporter PpeAMT3;4 in Peach

Ammonium (NH₄⁺) plays key roles in plant growth, development, fruit quality, and yield. In plants, NH₄⁺ uptake and transport are facilitated by NH₄⁺ transporters (AMT). However, molecular mechanisms and physiological functions of type-II AMT (AMT2) transporters in fruit trees are still unclear, especially in peach. In this study, we cloned and characterized an AMT2 family gene from peach, PpeAMT3;4, and determined its function in yeast mutant. Expression analysis showed that PpeAMT3;4 was majorly expressed in peach roots and significantly decreased by NH₄⁺ excess but had no response to NH₄⁺ deficiency. Functional determination and ¹⁵nitrogen-labeled NH₄⁺ uptake assay in yeast cells implied that PpeAMT3;4 was a typical high-affinity transporter, with a K_m value of 86.3 μM, that can uptake external NH₄⁺ in yeast cells. This study provides gene resources to uncover the biological function of AMT2 transporters and reveals molecular basis for NH₄⁺ uptake and nitrogen (N) nutrition mechanisms in fruit trees.

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.

De novo assembly of a wild pear (Pyrus betuleafolia) genome

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.

Molecular identification and functional characterization of GhAMT1.3 in ammonium transport with a high affinity from cotton (Gossypium hirsutum L.)

Ammonium (NH₄ ⁺ ) represents a primary nitrogen source for many plants, its effective transport into and between tissues and further assimilation in cells determine greatly plant nitrogen use efficiency. However, biological components involved in NH₄ ⁺ movement in woody plants are unclear. Here, we report kinetic evidence for cotton NH₄ ⁺ uptake and molecular identification of certain NH₄ ⁺ transporters (AMTs) from cotton (Gossypium hirustum). A substrate-influx assay using ¹⁵ N-isotope revealed that cotton possessed a high-affinity transport system with a K_m of 58 μM for NH₄ ⁺ . Sequence analysis showed that GhAMT1.1-1.3 encoded respectively a membrane protein containing 485, 509 or 499 amino acids. Heterologous functionality test demonstrated that GhAMT1.1-1.3 expression mediated NH₄ ⁺ permeation across the plasma membrane (PM) of yeast and/or Arabidopsis qko-mutant cells, allowing a growth restoration of both mutants on NH₄ ⁺ . Quantitative PCR measurement showed that GhAMT1.3 was expressed in roots and leaves and markedly up-regulated by N-starvation, repressed by NH₄ ⁺ resupply and regulated diurnally and age-dependently, suggesting that GhAMT1.3 should be a N-responsive gene. Importantly, GhAMT1.3 expression in Arabidopsis improved plant growth on NH₄ ⁺ and enhanced total nitrogen accumulation (∼50% more), conforming with the observation of 2-fold more NH₄ ⁺ absorption by GhAMT1.3-transformed qko plant roots during a 1-h root influx period. Together with its targeting to the PM and saturated transport kinetics with a K_m of 72 μM for NH₄ ⁺ , GhAMT1.3 is suggested to be a high-affinity NH₄ ⁺ permease that may play a significant role in cotton NH₄ ⁺ acquisition and utilization, adding a new member in the plant AMT family.

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.

Molecular identification of tobacco NtAMT1.3 that mediated ammonium root-influx with high affinity and improved plant growth on ammonium when overexpressed in Arabidopsis and tobacco

Although biological functions of ammonium (NH4+) transporters (AMTs) have been intensively studied in many plant species, little is known about molecular bases responsible for NH4+ movement in tobacco. Here, we reported the identification and functional characterization of a putative NH4+ transporter NtAMT1.3 from tobacco (Nicotiana tabacum). Analysis in silico showed that NtAMT1.3 encoded an integral membrane protein containing 464 amino acid residues and exhibiting 10 predicted transmembrane α-helices. Heterologous functionality study demonstrated that NtAMT1.3 expression facilitated NH4+ entry across plasma membrane of NH4+-uptake defective yeast and Arabidopsis qko mutant, allowing a restored growth of both yeast and Arabidopsis mutant on low NH4+. qPCR assay revealed that NtAMT1.3 was expressed in both roots and leaves and significantly up-regulated by nitrogen starvation and resupply of its putative substrate NH4+ and even nitrate, suggesting that NtAMT1.3 should represent a nitrogen-responsive gene. Critically, constitutive overexpression of NtAMT1.3 in tobacco per se improved obviously the growth of transgenic plants on NH4+ and enhanced leaf nitrogen (15% more) accumulation, consistent with observation of 35% more NH4+ uptake by the roots of transgenic lines in 20min root-influx test. Together with data showing its plasma membrane localization and saturated transport nature with Km of about 50μM for NH4+, we suggest that NtAMT1.3 acts an active NH4+ transporter that plays a significant role in NH4+ acquisition and utilization in tobacco.

The AMT1 family genes from Malus robusta display differential transcription features and ammonium transport abilities

Ammonium is an important nitrogen sources for plant growth. In this study, we report on the gene characterization of the ammonium transporter AMT1 subfamily in the apple rootstock Malus robusta Rehd. Thirteen AMT genes were comprehensively evaluated from the apple genome (version 1.0). Then the gene features and expression patterns of five AMT1 members from M. robusta were analyzed. These genes fell into four clusters in the AMT phylogenetic tree: clade I (MrAMT1;1 and MrAMT1;3), clade II (MrAMT1;4), clade III (MrAMT1;2), and clade IV (MrAMT1;5). All the AMT1s, apart from MrAMT1;4, were expressed in vegetative organs and strongly responded to nitrogen concentration changes. For example, MrAMT1;2 and MrAMT1;3 had high transcript accumulation levels in the leaves and roots, respectively. Finally, the functions of these AMT1s were studied in detail by heterologous expression in yeast. These genes allowed strain 31019b to assimilate nitrogen, but their ¹⁵NH₄⁺ uptake kinetics varied. These results revealed the functional roles of AMT1 during ammonium absorption in the AMT-defective mutant yeast system.

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.

Grafting: A Technique to Modify Ion Accumulation in Horticultural Crops

Grafting is a centuries-old technique used in plants to obtain economic benefits. Grafting increases nutrient uptake and utilization efficiency in a number of plant species, including fruits, vegetables, and ornamentals. Selected rootstocks of the same species or close relatives are utilized in grafting. Rootstocks absorb more water and ions than self-rooted plants and transport these water and ions to the aboveground scion. Ion uptake is regulated by a complex communication mechanism between the scion and rootstock. Sugars, hormones, and miRNAs function as long-distance signaling molecules and regulate ion uptake and ion homeostasis by affecting the activity of ion transporters. This review summarizes available information on the effect of rootstock on nutrient uptake and utilization and the mechanisms involved. Information on specific nutrient-efficient rootstocks for different crops of commercial importance is also provided. Several other important approaches, such as interstocking (during double grafting), inarching, use of plant-growth-promoting rhizobacteria, use of arbuscular mycorrhizal fungi, use of plant growth substances (e.g., auxin and melatonin), and use of genetically engineered rootstocks and scions (transgrafting), are highlighted; these approaches can be combined with grafting to enhance nutrient uptake and utilization in commercially important plant species. Whether the rootstock and scion affect each other's soil microbiota and their effect on the nutrient absorption of rootstocks remain largely unknown. Similarly, the physiological and molecular bases of grafting, crease formation, and incompatibility are not fully identified and require investigation. Grafting in horticultural crops can help reveal the basic biology of grafting, the reasons for incompatibility, sensing, and signaling of nutrients, ion uptake and transport, and the mechanism of heavy metal accumulation and restriction in rootstocks. Ion transporter and miRNA-regulated nutrient studies have focused on model and non-grafted plants, and information on grafted plants is limited. Such information will improve the development of nutrient-efficient rootstocks.