Maize NPF6 Proteins Are Homologs of Arabidopsis CHL1 That Are Selective for Both Nitrate and Chloride

NRT1.1s in plants: functions beyond nitrate transport

Arabidopsis AtNRT1.1 (CHL1/AtNPF6.3) is the first nitrate transporter identified in plants and was initially found to play a role in nitrate uptake and transport. AtNRT1.1 also displays auxin transport activity and mediates nitrate-modulated root development, suggesting that it has transport capacity for multiple substrates. Subsequent work revealed that AtNRT1.1 can respond to environmental nitrate fluctuations by altering its nitrate transport activity, modulated by phosphorylation, leading to the critical finding that AtNRT1.1 acts as a transceptor for nitrate sensing. Recent studies have revealed how OsNRT1.1B, the functional homologue of AtNRT1.1 in rice, mediates nitrate signal transduction from the plasma membrane to the nucleus, and how OsNRT1.1B integrates the nitrate and phosphate signaling networks. OsNRT1.1B has also been shown to be involved in regulating the root microbiota to facilitate organic nitrogen mineralization in soil, thus mediating plant-microbe interactions. Furthermore, the divergent functions of OsNRT1.1A and OsNRT1.1B in regulating nitrogen use in rice suggest that the function of NRT1.1 is still far from fully understood. In this review, we focus on the most recent progress on the molecular mechanisms of NRT1.1s in plants, with the aim of providing an up-to-date view of the versatile functions of NRT1.1 in nitrogen utilization in plants.

Phylogeny and gene expression of the complete NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Triticum aestivum

NPF genes encode membrane transporters involved in the transport of a large variety of substrates including nitrate and peptides. The NPF gene family has been described for many plants, but the whole NPF gene family for wheat has not been completely identified. The release of the wheat reference genome has enabled the identification of the entire wheat NPF gene family. A systematic analysis of the whole wheat NPF gene family was performed, including responses of specific gene expression to development and nitrogen supply. A total of 331 NPF genes (113 homoeologous groups) have been identified in wheat. The chromosomal location of the NPF genes is unevenly distributed, with predominant occurrence in the long arms of the chromosomes. The phylogenetic analysis indicated that wheat NPF genes are closely clustered with Arabidopsis, Brachypodium, and rice orthologues, and subdivided into eight subfamilies. The expression profiles of wheat NPF genes were examined using RNA-seq data, and a subset of 44 NPF genes (homoeologous groups) with contrasting expression responses to nitrogen and/or development in different tissues were identified. The systematic identification of gene composition, chromosomal locations, evolutionary relationships, and expression profiles contributes to a better understanding of the roles of the wheat NPF genes and lays the foundation for further functional analysis in wheat.

Plant nitrogen uptake and assimilation: regulation of cellular pH homeostasis

The enzymatic controlled metabolic processes in cells occur at their optimized pH ranges, therefore cellular pH homeostasis is fundamental for life. In plants, the nitrogen (N) source for uptake and assimilation, mainly in the forms of nitrate (NO3-) and ammonium (NH4+) quantitatively dominates the anion and cation equilibrium and the pH balance in cells. Here we review ionic and pH homeostasis in plant cells and regulation by N source from the rhizosphere to extra- and intracellular pH regulation for short- and long-distance N distribution and during N assimilation. In the process of N transport across membranes for uptake and compartmentation, both proton pumps and proton-coupled N transporters are essential, and their proton-binding sites may sense changes of apoplastic or intracellular pH. In addition, during N assimilation, carbon skeletons are required to synthesize amino acids, thus the combination of NO3- or NH4+ transport and assimilation results in different net charge and numbers of protons in plant cells. Efficient maintenance of N-controlled cellular pH homeostasis may improve N uptake and use efficiency, as well as enhance the resistance to abiotic stresses.

Effect of Seedling Nitrogen Condition on Subsequent Vegetative Growth Stages and Its Relationship to the Expression of Nitrogen Transporter Genes in Rice

Nitrogen (N) deficiency is one of the most common problems in soils, limiting crop growth and production. However, the effects of N limitation in seedlings on vegetative growth remain poorly understood. Here, we show that N limitation in rice seedlings restricted vegetative growth but not yield. Aboveground parts were affected mainly during the period of tillering, but belowground parts were sensitive throughout vegetative growth, especially during panicle development. At the tillering stage, N-limited plants had a significantly lower N content in shoots, but not in roots. On the other hand, N content in roots during the panicle development stage was significantly lower in N-limited plants. This distinct response was driven by significant changes in expression of N transporter genes during growth. Under N limitation, N translocation from roots to shoots was greatly sped up by systemic expression of N transporter genes to obtain balanced growth. N limitation during the seedling stage did not reduce any yield components. We conclude that the N condition during the seedling stage affects physiological responses such as N translocation through the expression of N transporter genes.

Chloride Improves Nitrate Utilization and NUE in Plants

Chloride (Cl-) has traditionally been considered harmful to agriculture because of its toxic effects in saline soils and its antagonistic interaction with nitrate (NO3 -), which impairs NO3 - nutrition. It has been largely believed that Cl- antagonizes NO3 - uptake and accumulation in higher plants, reducing crop yield. However, we have recently uncovered that Cl- has new beneficial macronutrient, functions that improve plant growth, tissue water balance, plant water relations, photosynthetic performance, and water-use efficiency. The increased plant biomass indicates in turn that Cl- may also improve nitrogen use efficiency (NUE). Considering that N availability is a bottleneck for the plant growth, the excessive NO3 - fertilization frequently used in agriculture becomes a major environmental concern worldwide, causing excessive leaf NO3 - accumulation in crops like vegetables and, consequently, a potential risk to human health. New farming practices aimed to enhance plant NUE by reducing NO3 - fertilization should promote a healthier and more sustainable agriculture. Given the strong interaction between Cl- and NO3 - homeostasis in plants, we have verified if indeed Cl- affects NO3 - accumulation and NUE in plants. For the first time to our knowledge, we provide a direct demonstration which shows that Cl-, contrary to impairing of NO3 - nutrition, facilitates NO3 - utilization and improves NUE in plants. This is largely due to Cl- improvement of the N-NO3 - utilization efficiency (NUTE), having little or moderate effect on N-NO3 - uptake efficiency (NUPE) when NO3 - is used as the sole N source. Clear positive correlations between leaf Cl- content vs. NUE/NUTE or plant growth have been established at both intra- and interspecies levels. Optimal NO3 - vs. Cl- ratios become a useful tool to increase crop yield and quality, agricultural sustainability and reducing the negative ecological impact of NO3 - on the environment and on human health.

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.

The Role of Gibberellins in Regulation of Nitrogen Uptake and Physiological Traits in Maize Responding to Nitrogen Availability

Modified gibberellin (GA) signaling leads to semi-dwarfism with low nitrogen (N) use efficiency (NUE) in crops. An understanding of GA-mediated N uptake is essential for the development of crops with improved NUE. The function of GA in modulating N uptake capacity and nitrate (NO3-) transporters (NRTs) was analyzed in the GA synthesis-deficient mutant zmga3ox grown under low (LN) and sufficient (SN) N conditions. LN significantly suppressed the production of GA1, GA3, and GA4, and the zmga3ox plants showed more sensitivity in shoots as well as LN stress. Moreover, the higher anthocyanin accumulation and the decrease of chlorophyll content were also recorded. The net NO3- fluxes and 15N content were decreased in zmga3ox plants under both LN and SN conditions. Exogenous GA3 could restore the NO3- uptake in zmga3ox plants, but uniconazole repressed NO3- uptake. Moreover, the transcript levels of ZmNRT2.1/2.2 were downregulated in zmga3ox plants, while the GA3 application enhanced the expression level. Furthermore, the RNA-seq analyses identified several transcription factors that are involved in the GA-mediated transcriptional operation of NRTs related genes. These findings revealed that GAs influenced N uptake involved in the transcriptional regulation of NRTs and physiological responses in maize responding to nitrogen supply.

Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake

Plants are inherently dynamic. Dynamics minimize stress while enabling plants to flexibly acquire resources. Three examples are presented for plants tolerating saline soil: transport of sodium chloride (NaCl), water and macronutrients is nonuniform along a branched root; water and NaCl redistribute between shoot and soil at night-time; and ATP for salt exclusion is much lower in thinner branch roots than main roots, quantified using a biophysical model and geometry from anatomy. Noninvasive phenotyping and precision agriculture technologies can be used together to harness plant dynamics, but analytical methods are needed. A plant advancing in time through a soil and atmosphere space is proposed as a framework for dynamic data and their relationship to crop improvement.

Energy costs of salt tolerance in crop plants

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H⁺ -ATPase also is a critical component. One proposed leak, that of Na⁺ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na⁺ and Cl^- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.

Transcriptomic Profiling Identifies Candidate Genes Involved in the Salt Tolerance of the Xerophyte Pugionium cornutum

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl⁻) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could also maintain cell membrane stability due to its prominent ROS-scavenging ability and exhibits efficient carbon assimilation capacity under salt stress. Then, the candidate genes associated with the important physiological traits of the salt tolerance of P. cornutum were identified through transcriptomic analysis. The results showed that after 50 mM NaCl treatment for 6 or 24 h, multiple genes encoding proteins facilitating Cl⁻ accumulation and NO₃⁻ homeostasis, as well as the transport of other major inorganic osmoticums, were significantly upregulated in roots and shoots, which should be favorable for enhancing osmotic adjustment capacity and maintaining the uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which might be beneficial for mitigating salt-induced oxidative damage to the cells. Meanwhile, many genes encoding components of the photosynthetic electron transport pathway and carbon fixation enzymes were significantly upregulated in shoots, possibly resulting in high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes that probably regulate the abovementioned processes were found. This work lays a preliminary foundation for clarifying the molecular mechanism underlying the adaptation of xerophytes to harsh environments.

Roles of membrane transporters: connecting the dots from sequence to phenotype

BACKGROUND

Plant membrane transporters are involved in diverse cellular processes underpinning plant physiology, such as nutrient acquisition, hormone movement, resource allocation, exclusion or sequestration of various solutes from cells and tissues, and environmental and developmental signalling. A comprehensive characterization of transporter function is therefore key to understanding and improving plant performance.

SCOPE AND CONCLUSIONS

In this review, we focus on the complexities involved in characterizing transporter function and the impact that this has on current genomic annotations. Specific examples are provided that demonstrate why sequence homology alone cannot be relied upon to annotate and classify transporter function, and to show how even single amino acid residue variations can influence transporter activity and specificity. Misleading nomenclature of transporters is often a source of confusion in transporter characterization, especially for people new to or outside the field. Here, to aid researchers dealing with interpretation of large data sets that include transporter proteins, we provide examples of transporters that have been assigned names that misrepresent their cellular functions. Finally, we discuss the challenges in connecting transporter function at the molecular level with physiological data, and propose a solution through the creation of new databases. Further fundamental in-depth research on specific transport (and other) proteins is still required; without it, significant deficiencies in large-scale data sets and systems biology approaches will persist. Reliable characterization of transporter function requires integration of data at multiple levels, from amino acid residue sequence annotation to more in-depth biochemical, structural and physiological studies.

Chloride as a Beneficial Macronutrient in Higher Plants: New Roles and Regulation

Chloride (Cl-) has traditionally been considered a micronutrient largely excluded by plants due to its ubiquity and abundance in nature, its antagonism with nitrate (NO3-), and its toxicity when accumulated at high concentrations. In recent years, there has been a paradigm shift in this regard since Cl- has gone from being considered a harmful ion, accidentally absorbed through NO3- transporters, to being considered a beneficial macronutrient whose transport is finely regulated by plants. As a beneficial macronutrient, Cl- determines increased fresh and dry biomass, greater leaf expansion, increased elongation of leaf and root cells, improved water relations, higher mesophyll diffusion to CO2, and better water- and nitrogen-use efficiency. While optimal growth of plants requires the synchronic supply of both Cl- and NO3- molecules, the NO3-/Cl- plant selectivity varies between species and varieties, and in the same plant it can be modified by environmental cues such as water deficit or salinity. Recently, new genes encoding transporters mediating Cl- influx (ZmNPF6.4 and ZmNPF6.6), Cl- efflux (AtSLAH3 and AtSLAH1), and Cl- compartmentalization (AtDTX33, AtDTX35, AtALMT4, and GsCLC2) have been identified and characterized. These transporters have proven to be highly relevant for nutrition, long-distance transport and compartmentalization of Cl-, as well as for cell turgor regulation and stress tolerance in plants.

Tissue and nitrogen-linked expression profiles of ammonium and nitrate transporters in maize

BACKGROUND

In order to grow, plants rely on soil nutrients which can vary both spatially and temporally depending on the environment, the soil type or the microbial activity. An essential nutrient is nitrogen, which is mainly accessible as nitrate and ammonium. Many studies have investigated transport genes for these ions in Arabidopsis thaliana and recently in crop species, including Maize, Rice and Barley. However, in most crop species, an understanding of the participants in nitrate and ammonium transport across the soil plant continuum remains undefined.

RESULTS

We have mapped a non-exhaustive set of putative nitrate and ammonium transporters in maize. The selected transporters were defined based on previous studies comparing nitrate transport pathways conserved between Arabidopsis and Zea mays (Plett D et. al, PLOS ONE 5:e15289, 2010). We also selected genes from published studies (Gu R et. al, Plant and Cell Physiology, 54:1515-1524, 2013, Garnett T et. al, New Phytol 198:82-94, 2013, Garnett T et. al, Frontiers in Plant Sci 6, 2015, Dechorgnat J et. al, Front Plant Sci 9:531, 2018). To analyse these genes, the plants were grown in a semi-hydroponic system to carefully control nitrogen delivery and then harvested at both vegetative and reproductive stages. The expression patterns of 26 putative nitrogen transporters were then tested. Six putative genes were found not expressed in our conditions. Transcripts of 20 other genes were detected at both the vegetative and reproductive stages of maize development. We observed the expression of nitrogen transporters in all organs tested: roots, young leaves, old leaves, silks, cobs, tassels and husk leaves. We also followed the gene expression response to nitrogen starvation and resupply and uncovered mainly three expression patterns: (i) genes unresponsiveness to nitrogen supply; (ii) genes showing an increase of expression after nitrogen starvation; (iii) genes showing a decrease of expression after nitrogen starvation.

CONCLUSIONS

These data allowed the mapping of putative nitrogen transporters in maize at both the vegetative and reproductive stages of development. No growth-dependent expression was seen in our conditions. We found that nitrogen transporter genes were expressed in all the organs tested and in many cases were regulated by the availability of nitrogen supplied to the plant. The gene expression patterns in relation to organ specificity and nitrogen availability denote a speciality of nitrate and ammonium transporter genes and their probable function depending on the plant organ and the environment.

Friend or Foe? Chloride Patterning in Halophytes

In this opinion article, we challenge the traditional view that breeding for reduced Cl^- uptake would benefit plant salinity tolerance. A negative correlation between shoot Cl^- concentration and plant biomass does not hold for halophytes - naturally salt tolerant species. We argue that, under physiologically relevant conditions, Cl^- uptake requires plants to invest metabolic energy, and that the poor selectivity of Cl^--transporting proteins may explain the reported negative correlation between Cl^- accumulation and crop salinity tolerance. We propose a new paradigm: salinity tolerance could be achieved by improving the selectivity of some of the broadly selective anion-transporting proteins (e.g., for NO₃^->Cl^-), alongside tight control of Cl^- uptake, rather than targeting traits mediating its efflux from the root.

Engineering Strategies to Boost Crop Productivity by Cutting Respiratory Carbon Loss

Roughly half the carbon that crop plants fix by photosynthesis is subsequently lost by respiration. Nonessential respiratory activity leading to unnecessary CO2 release is unlikely to have been minimized by natural selection or crop breeding, and cutting this large loss could complement and reinforce the currently dominant yield-enhancement strategy of increasing carbon fixation. Until now, however, respiratory carbon losses have generally been overlooked by metabolic engineers and synthetic biologists because specific target genes have been elusive. We argue that recent advances are at last pinpointing individual enzyme and transporter genes that can be engineered to (1) slow unnecessary protein turnover, (2) replace, relocate, or reschedule metabolic activities, (3) suppress futile cycles, and (4) make ion transport more efficient, all of which can reduce respiratory costs. We identify a set of engineering strategies to reduce respiratory carbon loss that are now feasible and model how implementing these strategies singly or in tandem could lead to substantial gains in crop productivity.

Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice

Nitrogen (N) is a major driving force for crop yield improvement, but application of high levels of N delays flowering, prolonging maturation and thus increasing the risk of yield losses. Therefore, traits that enable utilization of high levels of N without delaying maturation will be highly desirable for crop breeding. Here, we show that OsNRT1.1A (OsNPF6.3), a member of the rice (Oryza sativa) nitrate transporter 1/peptide transporter family, is involved in regulating N utilization and flowering, providing a target to produce high yield and early maturation simultaneously. OsNRT.1A has functionally diverged from previously reported NRT1.1 genes in plants and functions in upregulating the expression of N utilization-related genes not only for nitrate but also for ammonium, as well as flowering-related genes. Relative to the wild type, osnrt1.1a mutants exhibited reduced N utilization and late flowering. By contrast, overexpression of OsNRT1.1A in rice greatly improved N utilization and grain yield, and maturation time was also significantly shortened. These effects were further confirmed in different rice backgrounds and also in Arabidopsis thaliana Our study paves a path for the use of a single gene to dramatically increase yield and shorten maturation time for crops, outcomes that promise to substantially increase world food security.

Root Ideotype Influences Nitrogen Transport and Assimilation in Maize

Maize (Zea mays, L.) yield is strongly influenced by external nitrogen inputs and their availability in the soil solution. Overuse of nitrogen-fertilizers can have detrimental ecological consequences through increased nitrogen pollution of water and the release of the potent greenhouse gas, nitrous oxide. To improve yield and overall nitrogen use efficiency (NUE), a deeper understanding of nitrogen uptake and utilization is required. This study examines the performance of two contrasting maize inbred lines, B73 and F44. F44 was selected in Florida on predominantly sandy acidic soils subject to nitrate leaching while B73 was selected in Iowa on rich mollisol soils. Transcriptional, enzymatic and nitrogen transport analytical tools were used to identify differences in their N absorption and utilization capabilities. Our results show that B73 and F44 differ significantly in their genetic, enzymatic, and biochemical root nitrogen transport and assimilatory pathways. The phenotypes show a strong genetic relationship linked to nitrogen form, where B73 showed a greater capacity for ammonium transport and assimilation whereas F44 preferred nitrate. The contrasting phenotypes are typified by differences in root system architecture (RSA) developed in the presence of both nitrate and ammonium. F44 crown roots were longer, had a higher surface area and volume with a greater lateral root number and density than B73. In contrast, B73 roots (primary, seminal, and crown) were more abundant but lacked the defining features of the F44 crown roots. An F1 hybrid between B73 and F44 mirrored the B73 nitrogen specificity and root architecture phenotypes, indicating complete dominance of the B73 inbred. This study highlights the important link between RSA and nitrogen management and why both variables need to be tested together when defining NUE improvements in any selection program.

Unraveling the Functional Role of NPF6 Transporters

The nitrate transporter 1/peptide transporter (NPF) family represents a growing list of putative nitrate permeable transport proteins expressed within multiple cell types and tissues across a diverse range of plant species. Their designation as nitrate permeable and/or selective transporters is slowly being defined as more genes are characterized and their functional activities tested both in planta and in vitro. The most notable of the NPF family has been the Arabidopsis thaliana homolog, AtNPF6.3, previously known as AtNRT1.1 or CHL1. AtNPF6.3 has traditionally been characterized as a dual-affinity nitrate transporter contributing to root nitrate uptake in Arabidopsis. It has also been identified as a nitrate sensor which regulates the expression of high-affinity nitrate transport proteins NRT2s and lateral root development as a part of the primary nitrate response in plants. The sensor function of AtNPF6.3 has also been attributed to its auxin transport activity. Other homologs of AtNPF6.3 are now being described highlighting the variability in their functional capabilities (alternative substrates and kinetics) linking to structural aspects of the proteins. This review focusses on NPF6.3-like transport proteins and the knowledge that has been gained since their initial discovery over two decades ago. The review will investigate from a structural point of view how NPF6.3-like proteins may transport nitrate as well as other ions and what can be learned from structural uniqueness about predicted activities in plants.