AAP1 transports uncharged amino acids into roots of Arabidopsis

HSCA2 G87D point mutation enhances Arabidopsis proline tolerance via boosting mitochondrial Fe-S cluster assembly

As a mitochondrial HSP70 chaperone, HSCA2 orchestrates iron-sulfur (Fe-S) cluster assembly through dynamic interactions with scaffold protein ISU1, facilitating Fe-S cluster transfer to recipient proteins critical for electron transport chain (ETC) function. However, its regulatory roles in plant development and stress adaptation remain elusive. This study investigated the potential stress resistance function and molecular mechanisms of a novel G87D mutation in Arabidopsis HSCA2 (HSCA2m). We found that HSCA2m mutant exhibited increased resistance to high proline levels without altering proline uptake capacity. Under proline treatment, HSCA2m seedlings displayed lower malondialdehyde (MDA) and reactive oxygen species (ROS) levels, and higher superoxide dismutase (SOD) activity, indicating reduced stress damage. Molecular characterization revealed the induction of mitochondrial stress-related marker genes AOX1a and AT12CYS-2 in HSCA2m was suppressed. Strikingly, the G87D substitution enhanced intrinsic ATPase activity without disrupting ISU1 binding, while promoting HSCA2 transcript up-regulation under proline stress. Additionally, HSCA2m demonstrated increased tolerance to higher Fe2+ concentrations. These findings suggested that this mutation might enhance the supply of Fe-S clusters to Fe-S proteins, thereby mitigating proline-induced mitochondrial stress. Transgenic Arabidopsis overexpressing HSCA2m, but not HSCA2, showed enhanced proline resistance, highlighting the potential of HSCA2m as an elite allele for improving plant stress tolerance.

Developmental landscape and asymmetric gene expression in the leaf vasculature of Brassica rapa revealed by single-cell transcriptome

Leaf vasculature not only acts as a channel for nutrients and signaling information but also influences leaf morphology. It consists of several distinct cell types with specialized functions. Cell type-specific characterizations based on single-cell RNA sequencing technology could aid in understanding the identities of vascular tissues and their roles in leaf morphogenesis in Brassica rapa. Here, we generated a single-cell transcriptome landscape of the Chinese cabbage leaf vasculature. A total of 12 cell clusters covering seven known cell types were identified. Different vascular cell types were characterized by distinct identities. The xylem parenchyma and companion cells exhibited an active expression pattern of amino acid metabolism genes. Tracheary elements and sieve elements were enriched in many genes related to cell wall biosynthesis, and the phloem parenchyma was enriched in many sugar transporter-encoding genes. Pseudo-time analyses revealed the developmental trajectories of the xylem and phloem and the potential roles of auxin and ethylene in xylem development. Furthermore, we identified key candidate regulators along the differentiation trajectory of the sieve elements and companion cells. Most of the homoeologous genes in the syntenic triads from the three subgenomes showed asymmetric gene expression patterns in different vascular cell types. Collectively, our study revealed that Chinese cabbage leaf vasculature cells had highly heterogeneous transcriptomes, providing new insights into the complex processes of leaf vasculature development in B. rapa leafy vegetables and other Brassica crops.

Root Exudation: An In-Depth Experimental Guide

Plants exude a wide variety of compounds into the rhizosphere, modulating soil functioning and diversity. The number of studies investigating exudation has exponentially increased over the past decades. Yet, the high inter-study variability of the results is slowing down our understanding of root-soil interactions. This variability is partly due to the absence of harmonized methodologies to collect and characterize exudation. Here, we discuss how various experimental aspects influence exudation profiles by performing a literature review, and we suggest best practices for different experimental setups. We discuss state-of-the-art of spatially resolved exudate collection, collection in controlled versus field conditions and plant growth setups ranging from hydroponics to soil. We highlight the importance of preparing experimental blanks, in situ versus ex situ exudate collection, various collection media and timing of collection, exudate storage and processing and analytical considerations. We summarize best practices for experimental setup and reporting of parameters in an easily accessible table format to facilitate discussion of best practices in the field. An increased standardization in the field together with the systematic studies suggested will improve our knowledge of how plant exudation shapes interactions with organisms in soil.

Enhanced AtAAP1 endocytosis is correlated with calcium induced-proline hyper-sensitivity in Arabidopsis

The calcium (Ca2+) could enhance the toxicity of exogenous proline and the production of reactive oxygen species (ROS). However, the molecular mechanism underlying calcium-enhanced proline toxicity (CEPT) is still elusive. Here, we find that CEPT depends on the presence of the amino acid permease 1 in Arabidopsis (AtAAP1), since CEPT was significantly attenuated in ataap1 mutant than in wild-type plants. Notably, the role of AtAAP1 in CEPT is not related to its primary function as an amino acid transporter, neither was the expression of AtAAP1 affected under calcium or proline treatment. Further analysis revealed that treatment with 15 mM calcium, but not with proline, significantly induced the endocytosis of AtAAP1 protein through both clathrin and membrane micro-domain pathways, which was not blocked by translation inhibitor cycloheximide. After being internalized into cells, AtAAP1 protein go through the early endosome and late endosome, as evidenced by the co-localization of AtAAP1-GFP with the markers for the early (TGN) or late endosome (PVC). These results suggested that internalized AtAAP1 protein was not destined for degradation in vacuole, because the AtAAP1-GFP were not co-localized with the marker of PVC/vacuole. Collectively, our results indicated that Ca2+ can promote the endocytosis of AtAAP1, playing a role in relaying a signal of high amino acid levels in the surrounding environment.

Genome-wide identification of the AAT gene family in quinoa and analysis of its expression pattern under abiotic stresses

BACKGROUND

Plant amino acid transporters play an important role in the absorption of soil amino acids by roots, the transport of amino acids between xylem and phloem, plant growth and development, and response to abiotic stress.

RESULT

In this study, we identified 147 AAT genes in the quinoa genome sequence and categorized them into 12 subfamilies on the basis of their similarity and phylogenetic relationships with AAT found in Arabidopsis thaliana. Interestingly, these AAT genes are not evenly distributed on the quinoa chromosomes. Instead, most of these genes are centrally located on the outer edges of the chromosome arms. After performing motif analysis and gene structure analysis, we observed the consistent presence of similar motifs and intron-exon distribution patterns among subfamilies. Tissue expression analysis revealed that CqAAT gene was less expressed in fruits and more expressed in roots, stems, leaves and flowers. Meanwhile, expression analysis under four adversities of high temperature, low temperature, waterlogging, and drought and different treatments of nitrogen, phosphorus, and potash fertilizers found that two genes of the CqGAT subfamily, AUR62031750 and AUR62023955 were up-regulated expressed under abiotic stresses.

CONCLUSIONS

In summary, there is a significant differentiation in the tissue expression and stress expression of the CqAAT gene, indicating that CqAATs play a role in regulating growth and development under abiotic stress.

Combined analysis of proteomics and metabolism reveals critical roles of oxidoreductase activity in mushrooms stimulated by wolfberry and sea buckthorn substrates

Background

Cultivating edible fungi, particularly Lentinula edodes, efficiently transforms agroforestry byproducts into valuable products. However, the mechanism of the promotive effects of those substrates was largely unknown. This study used wolfberry (WB) and sea buckthorn (SBK) substrates to investigate mushroom fruiting bodies' physiological, proteomics, and metabolism profiling.

Results

Results show that compared to apple wood (AW), the crude protein and fatty acids were substantially enhanced by both WB and SBK treatment. We identified 1409 and 1190 upregulated and downregulated differentially abundant proteins (DAPs) for the SBK versus AW group and observed 929 overlapped DAPs with upregulation patterns. Of these DAPs, carbohydrates and oxidoreductase activity pathways were significantly enriched. Moreover, the enhanced expression of nine genes by WB and SBK was confirmed by qPCR. Metabolism suggests that 66 differentially abundant metabolites overlapped in the list of two comparison groups (WB versus AW and SBK versus AW).

Conclusion

Collectively, we summarized that both WB and SBK stimulate glucose degradation, enhance the expression of gene-related oxidoreductase activity, and promote protein biosynthesis by coordinating with amino acid metabolism. This study highlights the importance of oxidoreductase activity in promoting nutritional value in mushroom fruiting bodies induced by WB and SBK substrates.

Amino acid transporter GmAAP6-like contributes to seed quality and responds to jasmonic acid pathway under MSX toxicity stress

Amino acid transporters participate in the transport and distribution of amino acids in plants and are vital for plant growth and development. Despite their importance, few works have investigated the functions of amino acid permeases (AAP) amino acid transporters in soybean. In this study, we re-identified the AAP family genes in soybean using a new public genome database and cloned a soybean AAP gene renamed GmAAP6-like. Growth and uptake studies using treatments with single toxic amino acid analogs or single amino acids as a sole nitrogen source indicated that GmAAP6-like is involved in the selective transport of neutral and alkaline amino acids but is not sensitive to high concentrations of acidic amino acids. Overexpression of GmAAP6-like resulted in enhanced resistance to the toxic Glu analog, MSX, by significantly inducing jasmonic acid biosynthesis and signal transduction. We further evaluated the contribution of GmAAP6-like overexpression to seed quality and yield, and the tolerance of transgenic Arabidopsis seedlings to nitrogen deficiency. This study revealed the gene function of GmAAP6-like, improving the understanding of the functions and mechanisms of AAP family genes in soybeans.

Genome-Wide Identification and Expression Analysis of Amino Acid/Auxin Permease (AAAP) Genes in Grapes (Vitis vinifera L.) Under Abiotic Stress and During Development

Amino acids in wine grapes function as precursors for various secondary metabolites and play a vital role in plant growth, development, and stress resistance. The amino acid/auxin permease (AAAP) genes encode a large family of transporters; however, the identification and function of the AAAP gene family in grapes remain limited. Consequently, we conducted a comprehensive bioinformatics analysis of all AAAP genes in grapes, encompassing genome sequence analysis, conserved protein domain identification, chromosomal localization, phylogenetic relationship analysis, and gene expression profiling. This study identified 60 VvAAAP genes, distributed on 14 chromosomes and classified into eight subfamilies. Microarray and transcriptome data revealed that most VvAAAP genes decrease during development, but VvAAAP7 and VvAAAP33 gradually increase. VvAAAP23 and VvAAAP46 exhibited significantly higher expression levels, while VvAAAP30 demonstrated lower expression when subjected to salt and drought stress. VvAAAP genes exhibited diverse expression patterns, suggesting that the AAAP gene family possesses both diversity and specific functions in grapes. Furthermore, the expression patterns of VvAAAP genes analyzed by RT-qPCR facilitate further investigation into the biological functions of individual genes in different tissues. These findings provide valuable insights into the continued analysis of the AAAP gene family's functions in grapes.

Effects of two amino acid transporter-like genes on potato growth

Amino acid transporters are membrane proteins that mediate amino acid transport across the plasma membrane. They play a significant role in plant growth and development. The amino acid permease (AAP) subfamily belongs to the activating transcription factor family, which is one of the main amino acid transporter families. Potato AAP genes were identified through simple bioinformatics, and the functions of StAAP1 and StAAP8 were verified by plant subcellular localization and potato transgenic technology. In this study, eight AAP-like genes in potato were separated into two subgroups based on the differences in the number of pore-lining residues. To identify the locations where the genes were expressed, we built green fluorescent protein expression vectors for two genes, StAAP1 and StAAP8, and found that these two genes were expressed on the plasma membrane. Meanwhile, we constructed overexpression vectors for these two genes to construct transgenic plants. By observing the phenotype of the transgenic plants, we concluded that StAAP1 and StAAP8 promoted leaf growth and increased leaf area and StAAP1 elongated the potato tubers. Overall, these two genes did not significantly affect tuber weight or number. However, the assessment of amino acid content in potato tubers showed that StAAP8 overexpression increased the content of amino acids, and some of these amino acids were related to protein synthesis. Therefore, StAAP8 overexpression may promote the accumulation of plant amino acids. Studies have shown that there are some differences in the functions of different transcription factor members. The studied AAP8 gene plays a role in amino acid transport and protein accumulation in potato tubers, which provides support for subsequent research on potato tuber nutrition.

Research progress on the function and regulatory pathways of amino acid permeases in fungi

Nitrogen sources are pivotal for the formation of fungal mycelia and the biosynthesis of metabolites, playing a crucial role in the growth and development of fungi. Amino acids are integral to protein construction, constitute an essential nitrogen source for fungi. Fungi actively uptake amino acids from their surroundings, a process that necessitates the involvement of amino acid permeases (AAPs) located on the plasma membrane. By sensing the intracellular demand for amino acids and their extracellular availability, fungi activate or suppress relevant pathways to precisely regulate the genes encoding these transporters. This review aims to illustrate the function of fungal AAPs on uptake of amino acids and the effect of AAPs on fungal growth, development and virulence. Additionally, the complex mechanisms to regulate expression of aaps are elucidated in mainly Saccharomyces cerevisiae, including the Ssy1-Ptr3-Ssy5 (SPS) pathway, the Nitrogen Catabolite Repression (NCR) pathway, and the General Amino Acid Control (GAAC) pathway. However, the physiological roles of AAPs and their regulatory mechanisms in other species, particularly pathogenic fungi, merit further exploration. Gaining insights into these aspects could reveal how AAPs facilitate fungal adaptation and survival under diverse stress conditions, shedding light on their potential impact on fungal biology and pathogenicity.

Amino acid permease OsAAP12 negatively regulates rice tillers and grain yield by transporting specific amino acids to affect nitrogen and cytokinin pathways

Amino acids are necessary nutrients for the growth of Oryza sativa (rice), which can be mediated by amino acid transporter; however, our understanding of these transporters is still limited. This study found that the expression levels of amino acid permease gene OsAAP12 differed between indica and japonica rice. Altered expression of OsAAP12 negatively regulated tillering and yield in transgenic rice lines. Subcellular localization revealed that OsAAP12 was primarily localized to the plasma membrane. Moreover, it was indicated that OsAAP12 transported polar neutral amino acids asparagine (Asn), threonine (Thr), and serine (Ser) through experiments involving yeast heterologous complementation, fluorescence amino acid uptake, and amino acid content determination. Additionally, exogenous application of amino acids Asn, Thr, and Ser suppressed axillary buds outgrowth in OsAAP12 overexpression lines compared with wild-type ZH11. Conversely, the opposite trend was observed in CRISPR mutant lines. RNA-seq analysis showed that the expression patterns of genes involved in the nitrogen and cytokinin pathways were generally altered in OsAAP12 modified lines. Hormone assays indicated that OsAAP12 mutant lines accumulated cytokinins in the basal part of rice, whereas overexpression lines had the opposite effect. In summary, CRISPR mutant of OsAAP12 boosted rice tillering and grain yield by coordinating the content of amino acids and cytokinins, which has potential application value in high-yield rice breeding.

Amino acids biosynthesis in root hair development: a mini-review

Metabolic factors are essential for developmental biology of an organism. In plants, roots fulfill important functions, in part due to the development of specific epidermal cells, called hair cells that form root hairs (RHs) responsible for water and mineral uptake. RH development consists in (a) patterning processes involved in formation of hair and non-hair cells developed from trichoblasts and atrichoblasts; (b) RH initiation; and (c) apical (tip) growth of the RH. Here we review how these processes depend on pools of different amino acids and what is known about RH phenotypes of mutants disrupted in amino acid biosynthesis. This analysis shows that some amino acids, particularly aromatic ones, are required for RH apical (tip) growth, and that not much is known about the role of amino acids at earlier stages of RH formation. We also address the role of amino acids in rhizosphere, inhibitory and stimulating effects of amino acids on RH growth, amino acids as N source in plant nutrition, and amino acid transporters and their expression in the RHs. Amino acids form conjugates with auxin, a hormone essential for RH growth, and respective genes are overviewed. Finally, we outline missing links and envision some perspectives in the field.

Integrated transcriptome and metabolism unravel critical roles of carbon metabolism and oxidoreductase in mushroom with Korshinsk peashrub substrates

Edible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despite the widespread use of KP, the molecular mechanisms underlying its regulation of mushroom development remain largely unknown. In this study, we conducted a combined analysis of transcriptome and metabolism of mushroom fruiting bodies cultivated on KP substrates compared to those on apple wood sawdust (AWS) substrate. Our aim was to identify key metabolic pathways and genes that respond to the effects of KP substrates on mushrooms. The results revealed that KP induced at least a 1.5-fold increase in protein and fat content relative to AWS, with 15% increase in polysaccharide and total sugar content in mushroom fruiting bodies. There are 1196 differentially expressed genes (DEGs) between mushrooms treated with KP relative to AWS. Bioinformatic analysis show significant enrichments in amino acid metabolic process, oxidase activity, malic enzyme activity and carbon metabolism among the 698 up-regulated DEGs induced by KP against AWS. Additionally, pathways associated with organic acid transport and methane metabolism were significantly enriched among the 498 down-regulated DEGs. Metabolomic analysis identified 439 differentially abundant metabolites (DAMs) in mushrooms treated with KP compared to AWS. Consistent with the transcriptome data, KEGG analysis on metabolomic dataset suggested significant enrichments in carbon metabolism, alanine, aspartate and glutamate metabolism among the up-regulated DAMs by KP. In particular, some DAMs were enhanced by 1.5-fold, including D-glutamine, L-glutamate, glucose and pyruvate in mushroom samples treated with KP relative to AWS. Targeted metabolomic analysis confirmed the contents of DAMs related to glutamate metabolism and energy metabolism. In conclusion, our findings suggest that reprogrammed carbon metabolism and oxidoreductase pathways act critical roles in the enhanced response of mushroom to KP substrates.

Exploring glycine root uptake dynamics in phosphorus and iron deficient tomato plants during the initial stages of plant development

BACKGROUND

Phosphorus (P) and iron (Fe) deficiencies are relevant plants nutritional disorders, prompting responses such as increased root exudation to aid nutrient uptake, albeit at an energy cost. Reacquiring and reusing exudates could represent an efficient energy and nitrogen saving strategy. Hence, we investigated the impact of plant development, Fe and P deficiencies on this process. Tomato seedlings were grown hydroponically for 3 weeks in Control, -Fe, and -P conditions and sampled twice a week. We used Isotope Ratio Mass-Spectrometry to measure δ13C in roots and shoots after a 2-h exposure to 13C-labeled glycine (0, 50, or 500 μmol L-1). Plant physiology was assessed with an InfraRed Gas Analyzer and ionome with an Inductively Coupled Plasma Mass-Spectrometry.

RESULTS

Glycine uptake varied with concentration, suggesting an involvement of root transporters with different substrate affinities. The uptake decreased over time, with -Fe and -P showing significantly higher values as compared to the Control. This highlights its importance during germination and in nutrient-deficient plants. Translocation to shoots declined over time in -P and Control but increased in -Fe plants, suggesting a role of Gly in the Fe xylem transport.

CONCLUSIONS

Root exudates, i.e. glycine, acquisition and their subsequent shoot translocation depend on Fe and P deficiency. The present findings highlight the importance of this adaptation to nutrient deficiencies, that can potentially enhance plants fitness. A thorough comprehension of this trait holds potential significance for selecting cultivars that can better withstand abiotic stresses.

Natural variation in SSW1 coordinates seed growth and nitrogen use efficiency in Arabidopsis

Seed size is controlled not only by intrinsic genetic factors but also by external environmental signals. Here, we report a major quantitative trait locus (QTL) gene for seed size and weight on chromosome 1 (SSW1) in Arabidopsis, and we found SSW1 acts maternally to positively regulate seed size. Natural variation in SSW1 contains three types of alleles. The SSW1Cvi allele produces larger seeds with more amino acid and storage protein contents than the SSW1Ler allele. SSW1Cvi displays higher capacity for amino acid transport than SSW1Ler due to the differences in transport efficiency. Under low nitrogen supply, the SSW1Cvi allele exhibits increased seed yield and nitrogen use efficiency (NUE). Locations of natural variation alleles of SSW1 are associated with local soil nitrogen contents, suggesting that SSW1 might contribute to geographical adaptation in Arabidopsis. Thus, our findings reveal a mechanism that coordinates seed growth and NUE, suggesting a potential target for improving seed yield and NUE in crops.

Blocking of amino acid transporter OsAAP7 promoted tillering and yield by determining basic and neutral amino acids accumulation in rice

BACKGROUND

Amino acids are not only the main form of N in rice, but also are vital for its growth and development. These processes are facilitated by amino acid transporters within the plant. Despite their significance, only a few AAP amino acid transporters have been reported.

RESULTS

In this study, we observed that there were differences in the expression of amino acid transporter OsAAP7 among 521 wild cultivated rice varieties, and it directly negatively correlated with tillering and grain yield per plant. We revealed that OsAAP7 protein was localized to the endoplasmic reticulum and had absorption and transport affinity for amino acids such as phenylalanine (Phe), lysine (Lys), leucine (Leu), and arginine (Arg) using subcellular localization, yeast substrate testing, fluorescent amino acid uptake, and amino acid content determination. Further hydroponic studies showed that exogenous application of amino acids Phe, Lys and Arg inhibited the growth of axillary buds in the overexpression lines, and promoted the elongation of axillary buds in the mutant lines. Finally, RNA-seq analysis showed that the expression patterns of genes related to nitrogen, auxin and cytokinin pathways were changed in axillary buds of OsAAP7 transgenic plants.

CONCLUSIONS

This study revealed the gene function of OsAAP7, and found that blocking of amino acid transporter OsAAP7 with CRISPR/Cas9 technology promoted tillering and yield by determining basic and neutral amino acids accumulation in rice.

OsNAC74 affects grain protein content and various biological traits by regulating OsAAP6 expression in rice

The grain protein content is an important quality trait in cereals, and the expression level of the OsAAP6 can significantly affect the grain protein content in rice. Through site-directed mutagenesis, we found that the position from -7 to -12 bp upstream of the transcription start site of the OsAAP6 was the functional variation site. By using the yeast single hybrid test, point-to-point in yeast, and the local surface plasmon resonance test, the OsNAC74 was screened and verified to be a regulator upstream of OsAAP6. The OsNAC74 is a constitutively expressed gene whose product is located on the cell membrane. The OsAAP6 and the genes related to the seed storage in the Osnac74 mutants were downregulated, and grain protein content was significantly reduced. In addition, OsNAC74 had a significant impact on quality traits such as grain chalkiness and gel consistency in rice. Although the Osnac74 mutant seeds were relatively small, the individual plant yield was not decreased. Therefore, OsNAC74 is an important regulatory factor with multiple biological functions. This study provides important information for the later use of OsNAC74 gene for molecular design and breeding in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01433-w.

Phenylalanine in motion: A tale of an essential molecule with many faces

Phenylalanine has a unique role in plants as a source of a wide range of specialized metabolites, named phenylpropanoids that contribute to the adjustment of plants to changing developmental and environmental conditions. The profile of these metabolites differs between plants and plant organs. Some of the prominent phenylpropanoids include anthocyanins, phenolic acids, flavonoids, tannins, stilbenes, lignins, glucosinolates and benzenoid phenylpropanoid volatiles. Phenylalanine biosynthesis, leading to increased phenylpropanoid levels, is induced under stress. However, high availability of phenylalanine in plants under non-stressed conditions can be achieved either by genetically engineering plants to overproduce phenylalanine, or by external treatment of whole plants or detached plant organs with phenylalanine solutions. The objective of this review is to portray the many effects that increased phenylalanine availability has in plants under non-stressed conditions, focusing mainly on external applications. These applications include spraying and drenching whole plants with phenylalanine solutions, postharvest treatments by dipping fruit and cut flower stems, and addition of phenylalanine to cell suspensions. The results of these treatments include increased fragrance in flowers, increased aroma and pigmentation in fruit, increased production of health promoting metabolites in plant cell cultures, and increased resistance of plants, pre- and post-harvest, to a wide variety of pathogens. These effects suggest that plants can very efficiently uptake phenylalanine from their roots, leaves, flowers and fruits, translocate it from one organ to the other and between cell compartments, and metabolize it into phenylpropanoids. The mechanisms by which Phe treatment increases plant resistance to pathogens reveal new roles of phenylpropanoids in induction of genes related to the plant immune system. The simplicity of treatments with phenylalanine open many possibilities for industrial use. Many of the phenylalanine-treatment effects on increased resistance to plant pathogens have also been successful in commercial field trials.

Genome-Wide Analysis of the Amino Acid Permeases Gene Family in Wheat and TaAAP1 Enhanced Salt Tolerance by Accumulating Ethylene

Amino acid permeases (AAPs) are proteins of the integral membrane that play important roles in plant growth, development, and responses to various stresses. The molecular functions of several AAPs were characterized in Arabidopsis and rice, but there is still limited information on wheat. Here, we identified 51 AAP genes (TaAAPs) in the wheat genome, classified into six groups based on phylogenetic and protein structures. The chromosome location and gene duplication analysis showed that gene duplication events played a crucial role in the expansion of the TaAAPs gene family. Collinearity relationship analysis revealed several orthologous AAPs between wheat and other species. Moreover, cis-element analysis of promoter regions and transcriptome data suggested that the TaAAPs can respond to salt stress. A TaAAP1 gene was selected and transformed in wheat. Overexpressing TaAAP1 enhanced salt tolerance by increasing the expression of ethylene synthesis genes (TaACS6/TaACS7/TaACS8) and accumulating more ethylene. The present study provides an overview of the AAP family in the wheat genome as well as information on systematics, phylogenetics, and gene duplication, and shows that overexpressing TaAAP1 enhances salt tolerance by regulating ethylene production. These results serve as a theoretical foundation for further functional studies on TaAAPs in the future.

d-Amino acids in biological systems

Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.

Genetic regulation of nitrogen use efficiency in Gossypium spp

Cotton (Gossypium spp.) is the most important fibre crop, with desirable characteristics preferred for textile production. Cotton fibre output relies heavily on nitrate as the most important source of inorganic nitrogen (N). However, nitrogen dynamics in extreme environments limit plant growth and lead to yield loss and pollution. Therefore, nitrogen use efficiency (NUE), which involves the utilisation of the 'right rate', 'right source', 'right time', and 'right place' (4Rs), is key for efficient N management. Recent omics techniques have genetically improved NUE in crops. We herein highlight the mechanisms of N uptake and assimilation in the vegetative and reproductive branches of the cotton plant while considering the known and unknown regulatory factors. The phylogenetic relationships among N transporters in four Gossypium spp. have been reviewed. Further, the N regulatory genes that participate in xylem transport and phloem loading are also discussed. In addition, the functions of microRNAs and transcription factors in modulating the expression of target N regulatory genes are highlighted. Overall, this review provides a detailed perspective on the complex N regulatory mechanism in cotton, which would accelerate the research toward improving NUE in crops.

Disruption of the amino acid transporter CsAAP2 inhibits auxin-mediated root development in cucumber

Amino acid transporters are the principal mediators of organic nitrogen distribution within plants and are essential for plant growth and development. Despite this importance, relatively few amino acid transporter genes have been explored and elucidated in cucumber (Cucumis sativus). Here, a total of 86 amino acid transporter genes were identified in the cucumber genome. We further identified Amino Acid Permease (AAP) subfamily members that exhibited distinct expression patterns in different tissues. We found that the CsAAP2 as a candidate gene encoding a functional amino acid transporter is highly expressed in cucumber root vascular cells. CsAAP2 knockout lines exhibited arrested development of root meristem, which then caused the delayed initiation of lateral root and the inhibition of root elongation. What is more, the shoot growth of aap2 mutants was strongly retarded due to defects in cucumber root development. Moreover, aap2 mutants exhibited higher concentrations of amino acids and lignin in roots. We found that the mutant roots had a stronger ability to acidize medium. Furthermore, in the aap2 mutants, polar auxin transport was disrupted in the root tip, leading to high auxin levels in roots. Interestingly, slightly alkaline media rescued their severely reduced root growth by stimulating auxin pathway.

Signaling pathways underlying nitrogen transport and metabolism in plants

Nitrogen (N) is an essential macronutrient required for plant growth and crop production. However, N in soil is usually insufficient for plant growth. Thus, chemical N fertilizer has been extensively used to increase crop production. Due to negative effects of N rich fertilizer on the environment, improving N usage has been a major issue in the field of plant science to achieve sustainable production of crops. For that reason, many efforts have been made to elucidate how plants regulate N uptake and utilization according to their surrounding habitat over the last 30 years. Here, we provide recent advances focusing on regulation of N uptake, allocation of N by N transporting system, and signaling pathway controlling N responses in plants. [BMB Reports 2023; 56(2): 56-64].

Genome-Wide Analysis of the AAAP Gene Family in Populus and Functional Analysis of PsAAAP21 in Root Growth and Amino Acid Transport

The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability.

CsAAP7.2 is involved in the uptake of amino acids from soil and the long-distance transport of theanine in tea plants (Camellia sinensis L.)

Tea plant roots can uptake both inorganic nitrogen (NH4+ and NO3-) and organic nitrogen (amino acids) from the soil. These amino acids are subsequently assimilated into theanine and transported to young shoots through the xylem. Our previous study showed that CsLHT1 and CsLHT6 transporters take up amino acids from the soil, and CsAAPs participate in the transport of theanine. However, whether other amino acid transporters are involved in this process remains unknown. In this study, we identified two new CsAAPs homologous to CsAAP7, named CsAAP7.1 and CsAAP7.2. Heterologous expression of CsAAP7.1 and CsAAP7.2 in the yeast mutant 22Δ10α showed that CsAAP7.2 had the capacity to transport theanine and other amino acids, whereas CsAAP7.1 had no transport activity. Transient expression of the CsAAP7.2-GFP fusion protein in tobacco leaf epidermal cells confirmed its localization to the endoplasmic reticulum. Tissue-specific analysis showed that CsAAP7.2 was highly expressed in roots and stems. In addition, CsAAP7.2 overexpression lines were more sensitive to high concentrations of theanine due to the high accumulation of theanine in seedlings. Taken together, these findings suggested that CsAAP7.2 plays an important role in the uptake of amino acids from soil and the long-distance transport of theanine. These results provide valuable tools for nitrogen nutrition studies and enrich our understanding of theanine transport in tea plants.

Comprehensive genomic characterization of cotton cationic amino acid transporter genes reveals that GhCAT10D regulates salt tolerance

BACKGROUND

The cationic amino acid transporters (CAT) play indispensable roles in maintaining metabolic functions, such as synthesis of proteins and nitric oxide (NO), biosynthesis of polyamine, and flow of amino acids, by mediating the bidirectional transport of cationic amino acids in plant cells.

RESULTS

In this study, we performed a genome-wide and comprehensive study of 79 CAT genes in four species of cotton. Localization of genes revealed that CAT genes reside on the plasma membrane. Seventy-nine CAT genes were grouped into 7 subfamilies by phylogenetic analysis. Structure analysis of genes showed that CAT genes from the same subgroup have similar genetic structure and exon number. RNA-seq and real-time PCR indicated that the expression of most GhCAT genes were induced by salt, drought, cold and heat stresses. Cis-elements analysis of GhCAT promoters showed that the GhCAT genes promoters mainly contained plant hormones responsive elements and abiotic stress elements, which indicated that GhCAT genes may play key roles in response to abiotic stress. Moreover, we also conducted gene interaction network of the GhCAT proteins. Silencing GhCAT10D expression decreased the resistance of cotton to salt stress because of a decrease in the accumulation of NO and proline.

CONCLUSION

Our results indicated that CAT genes might be related with salt tolerance in cotton and lay a foundation for further study on the regulation mechanism of CAT genes in cationic amino acids transporting and distribution responsing to abiotic stress.

Transcriptome Analysis Reveals Critical Genes and Pathways in Carbon Metabolism and Ribosome Biogenesis in Poplar Fertilized with Glutamine

Exogenous Gln as a single N source has been shown to exert similar roles to the inorganic N in poplar 'Nanlin895' in terms of growth performance, yet the underlying molecular mechanism remains unclear. Herein, transcriptome analyses of both shoots (L) and roots (R) of poplar 'Nanlin895' fertilized with Gln (G) or the inorganic N (control, C) were performed. Compared with the control, 3109 differentially expressed genes (DEGs) and 5071 DEGs were detected in the GL and GR libraries, respectively. In the shoots, Gln treatment resulted in downregulation of a large number of ribosomal genes but significant induction of many starch and sucrose metabolism genes, demonstrating that poplars tend to distribute more energy to sugar metabolism rather than ribosome biosynthesis when fertilized with Gln-N. By contrast, in the roots, most of the DEGs were annotated to carbon metabolism, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis, suggesting that apart from N metabolism, exogenous Gln has an important role in regulating the redistribution of carbon resources and secondary metabolites. Therefore, it can be proposed that the promotion impact of Gln on poplar growth and photosynthesis may result from the improvement of both carbon and N allocation, accompanied by an efficient energy switch for growth and stress responses.

Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production

The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.

To have or not to have: expression of amino acid transporters during pathogen infection

The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.

Isotopic and Spectroscopic Investigation of Mercury Accumulation in Houttuynia cordata Colonizing Historically Contaminated Soil

Houttuynia cordata Thunb (H. cordata) is a native vegetable colonizing mercury (Hg) mining sites in the southwest of China; it can accumulate high Hg concentrations in the rhizomes and roots (edible sections), and thus consumption of H. cordata represents an important Hg exposure source to human. Here, we studied the spatial distribution, chemical speciation, and stable isotope compositions of Hg in the soil-H. cordata system at the Wuchuan Hg mining region in China, aiming to provide essential knowledge for assessing Hg risks and managing the transfer of Hg from soils to plants and agricultural systems. Mercury was mainly compartmentalized in the outlayer (periderm) of the underground tissues, with little Hg being translocated to the vascular bundle of the stem. Mercury presented as Hg-thiolates (94% ± 8%), with minor fractional amount of nanoparticulate β-HgS (β-HgS_NP, 15% ± 4%), in the roots and rhizomes. Analysis of Hg stable isotope ratios showed that cysteine-extractable soil Hg pool (δ²⁰²Hg_cys), root and rhizome Hg (δ²⁰²Hg_root, δ²⁰²Hg_rhizome) were isotopically lighter than Hg in the bulk soils. A significant positive correlation between δ²⁰²Hg_cys and δ²⁰²Hg_root was observed, suggesting that cysteine-extractable soil Hg pool was an important Hg source to H. cordata. The slightly positive Δ¹⁹⁹Hg value in the plant (Δ¹⁹⁹Hg_root = 0.07 ± 0.07‰, 2SD, n = 21; Δ¹⁹⁹Hg_rhizome = 0.06 ± 0.06‰, 2SD, n = 22) indicated that minor Hg was sourced from the surface water. Our results are important to assess the risks of Hg in H. cordata, and to develop sustainable methods to manage the transfer of Hg from soils to agricultural systems.

CsATG101 Delays Growth and Accelerates Senescence Response to Low Nitrogen Stress in Arabidopsis thaliana

For tea plants, nitrogen (N) is a foundational element and large quantities of N are required during periods of roundly vigorous growth. However, the fluctuation of N in the tea garden could not always meet the dynamic demand of the tea plants. Autophagy, an intracellular degradation process for materials recycling in eukaryotes, plays an important role in nutrient remobilization upon stressful conditions and leaf senescence. Studies have proven that numerous autophagy-related genes (ATGs) are involved in N utilization efficiency in Arabidopsis thaliana and other species. Here, we identified an ATG gene, CsATG101, and characterized the potential functions in response to N in A. thaliana. The expression patterns of CsATG101 in four categories of aging gradient leaves among 24 tea cultivars indicated that autophagy mainly occurred in mature leaves at a relatively high level. Further, the in planta heterologous expression of CsATG101 in A. thaliana was employed to investigate the response of CsATG101 to low N stress. The results illustrated a delayed transition from vegetative to reproductive growth under normal N conditions, while premature senescence under N deficient conditions in transgenic plants vs. the wild type. The expression profiles of 12 AtATGs confirmed the autophagy process, especially in mature leaves of transgenic plants. Also, the relatively high expression levels for AtAAP1, AtLHT1, AtGLN1;1, and AtNIA1 in mature leaves illustrated that the mature leaves act as the source leaves in transgenic plants. Altogether, the findings demonstrated that CsATG101 is a candidate gene for improving annual fresh tea leaves yield under both deficient and sufficient N conditions via the autophagy process.

Effect of ACGT motif in spatiotemporal regulation of AtAVT6D, which improves tolerance to osmotic stress and nitrogen-starvation

Plasma membrane-localized AtAVT6D importing aspartic acid can be targeted to develop plants with enhanced osmotic and nitrogen-starvation tolerance. AtAVT6D promoter can be exploited as a stress-inducible promoter for genetic improvements to raise stress-resilient crops. The AtAVT6 family of amino acid transporters in Arabidopsis thaliana has been predicted to export amino acids like aspartate and glutamate. However, the functional characterization of these amino acid transporters in plants remains unexplored. The present study investigates the expression patterns of AtAVT6 genes in different tissues and under various abiotic stress conditions using quantitative Real-time PCR. The expression analysis demonstrated that the member AtAVT6D was significantly induced in response to phytohormone ABA and stresses like osmotic and drought. The tissue-specific expression analysis showed that AtAVT6D was strongly expressed in the siliques. Taking together these results, we can speculate that AtAVT6D might play a vital role in silique development and abiotic stress tolerance. Further, subcellular localization study showed AtAVT6D was localized to the plasma membrane. The heterologous expression of AtAVT6D in yeast cells conferred significant tolerance to nitrogen-deficient and osmotic stress conditions. The Xenopus oocyte studies revealed that AtAVT6D is involved in the uptake of Aspartic acid. While overexpression of AtAVT6D resulted in smaller siliques in Arabidopsis thaliana. Additionally, transient expression studies were performed with the full-length AtAVT6D promoter and its deletion constructs to study the effect of ACGT-N₂₄-ACGT motifs on the reporter gene expression in response to abiotic stresses and ABA treatment. The fluorometric GUS analyses revealed that the promoter deletion construct-2 (Pro.C2) possessing a single copy of ACGT-N₂₄-ACGT motif directed the strongest GUS expression under all the abiotic conditions tested. These results suggest that Pro.C2 can be used as a stress-inducible promoter to drive a significant transgene expression.

Identification, Phylogenetic and Expression Analyses of the AAAP Gene Family in Liriodendron chinense Reveal Their Putative Functions in Response to Organ and Multiple Abiotic Stresses

In this study, 52 AAAP genes were identified in the L. chinense genome and divided into eight subgroups based on phylogenetic relationships, gene structure, and conserved motif. A total of 48 LcAAAP genes were located on the 14 chromosomes, and the remaining four genes were mapped in the contigs. Multispecies phylogenetic tree and codon usage bias analysis show that the LcAAAP gene family is closer to the AAAP of Amborella trichopoda, indicating that the LcAAAP gene family is relatively primitive in angiosperms. Gene duplication events revealed six pairs of segmental duplications and one pair of tandem duplications, in which many paralogous genes diverged in function before monocotyledonous and dicotyledonous plants differentiation and were strongly purification selected. Gene expression pattern analysis showed that the LcAAAP gene plays a certain role in the development of Liriodendron nectary and somatic embryogenesis. Low temperature, drought, and heat stresses may activate some WRKY/MYB transcription factors to positively regulate the expression of LcAAAP genes to achieve long-distance transport of amino acids in plants to resist the unfavorable external environment. In addition, the GAT and PorT subgroups could involve gamma-aminobutyric acid (GABA) transport under aluminum poisoning. These findings could lay a solid foundation for further study of the biological role of LcAAAP and improvement of the stress resistance of Liriodendron.

Organic nitrogen enhances nitrogen nutrition and early growth of Pinus sylvestris seedlings

Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris L. seedlings' biomass growth and allocation, transpiration and N uptake in response to additions of organic N (the amino acid arginine) or inorganic N (ammonium nitrate). We also monitored in situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings' nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium.

Plant nitrogen nutrition: The roles of arbuscular mycorrhizal fungi

Nitrogen (N) is the most abundant mineral nutrient required by plants, and crop productivity depends heavily on N fertilization in many soils. Production and application of N fertilizers consume huge amounts of energy and substantially increase the costs of agricultural production. Excess N compounds released from agricultural systems are also detrimental to the environment. Thus, increasing plant N uptake efficiency is essential for the development of sustainable agriculture. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most terrestrial plants that facilitate plant nutrient uptake and increase host resistance to diverse environmental stresses. AM association is an endosymbiotic process that relies on the differentiation of both host plant roots and AM fungi to create novel contact interfaces within the cells of plant roots. AM plants have two pathways for nutrient uptake: either direct uptake via the root hairs and root epidermis, or indirectly through AM fungal hyphae into root cortical cells. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake processes, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungi-root interface have been identified. Here, we mainly summarize the recent advances in N uptake, assimilation, and translocation in AM symbiosis, and also discuss how N interplays with C and P in modulating AM development, as well as the synergies between AM fungi and soil microbial communities in N uptake.

Tissue specific expression of UMAMIT amino acid transporters in wheat

Wheat grain protein content and composition are important for its end-use quality. Protein synthesis during the grain filling phase is supported by the amino acids remobilized from the vegetative tissue, the process in which both amino acid importers and exporters are expected to be involved. Previous studies identified amino acid importers that might function in the amino acid remobilization in wheat. However, the amino acid exporters involved in this process have been unexplored so far. In this study, we have curated the Usually Multiple Amino acids Move In and out Transporter (UMAMIT) family of transporters in wheat. As expected, the majority of UMAMITs were found as triads in the A, B, and D genomes of wheat. Expression analysis using publicly available data sets identified groups of TaUMAMITs expressed in root, leaf, spike, stem and grain tissues, many of which were temporarily regulated. Strong expression of TaUMAMITs was detected in the late senescing leaves and transfer cells in grains, both of which are the expected site of apoplastic amino acid transport during grain filling. Biochemical characterization of selected TaUMAMITs revealed that TaUMAMIT17 shows a strong amino acid export activity and might play a role in amino acid transfer to the grains.

Exogenous Cysteine Improves Mercury Uptake and Tolerance in Arabidopsis by Regulating the Expression of Heavy Metal Chelators and Antioxidative Enzymes

Cysteine (Cys) is an essential amino acid component of the major heavy metal chelators, such as glutathione (GSH), metallothioneins (MTs), and phytochelatins (PCs), which are involved in the pathways of mercury (Hg) tolerance in plants. However, the mechanism through which Cys facilitates Hg tolerance in plants remains largely unclear. In this study, we investigated the effects of exogenous Cys on Hg uptake in the seedlings, roots, and shoots of Arabidopsis throughout 6 and 36 h of Hg exposure and on the regulation of Hg detoxification by heavy metal chelators and antioxidative enzymes. The results showed that exogenous Cys significantly improved Hg tolerance during the germination and seedling growth stages in Arabidopsis. Exogenous Cys significantly promoted Hg uptake in Arabidopsis roots by upregulating the expression of the Cys transporter gene AtLHT1, resulting in increased Hg accumulation in the roots and seedlings. In Arabidopsis seedlings, exogenous Cys further increased the Hg-induced glutathione synthase (GS1 and GS2) transcript levels, and the Hg and Hg + Cys treatments greatly upregulated MT3 expression after 36 h exposure. In the roots, MT3 was also significantly upregulated by treatment of 36 h of Hg or Hg + Cys. Notably, in the shoots, MT2a expression was rapidly induced (10-fold) in Hg presence and further markedly increased (20-fold) by exogenous Cys. Moreover, in the seedlings, exogenous Cys upregulated the transcripts of all superoxide dismutase (CuSOD1, CuSOD2, MnSOD1, FeSOD1, FeSOD2, and FeSOD3) within 6 h and subsequently increased the Hg-induced GR1 and GR2 transcript levels at 36 h, all of which could eliminate the promotion of reactive oxygen species production and cell damage caused by Hg. Additionally, exogenous Cys upregulated all the antioxidative genes rapidly in the roots and subsequently increased the expression of CuSOD1, CuSOD2, and MnSOD1 in the shoots. These results indicate that exogenous Cys regulates the transcript levels of heavy metal chelators and antioxidative enzymes differently in a time- and organ-specific manner under Hg stress. Taken together, our study elucidates the positive functional roles of exogenous Cys in the Hg uptake and tolerance mechanisms of Arabidopsis.

Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops

The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.

Low-molecular-weight ligands in plants: role in metal homeostasis and hyperaccumulation

Mineral nutrition is one of the key factors determining plant productivity. In plants, metal homeostasis is achieved through the functioning of a complex system governing metal uptake, translocation, distribution, and sequestration, leading to the maintenance of a regulated delivery of micronutrients to metal-requiring processes as well as detoxification of excess or non-essential metals. Low-molecular-weight ligands, such as nicotianamine, histidine, phytochelatins, phytosiderophores, and organic acids, play an important role in metal transport and detoxification in plants. Nicotianamine and histidine are also involved in metal hyperaccumulation, which determines the ability of some plant species to accumulate a large amount of metals in their shoots. In this review we extensively summarize and discuss the current knowledge of the main pathways for the biosynthesis of these ligands, their involvement in metal uptake, radial and long-distance transport, as well as metal influx, isolation and sequestration in plant tissues and cell compartments. It is analyzed how diverse endogenous ligand levels in plants can determine their different tolerance to metal toxic effects. This review focuses on recent advances in understanding the physiological role of these compounds in metal homeostasis, which is an essential task of modern ionomics and plant physiology. It is of key importance in studying the influence of metal deficiency or excess on various physiological processes, which is a prerequisite to the improvement of micronutrient uptake efficiency and crop productivity and to the development of a variety of applications in phytoremediation, phytomining, biofortification, and nutritional crop safety.

Genome-Wide Analysis of AAT Genes and Their Expression Profiling during Fiber Development in Cotton

Amino acid transporters (AATs) are a kind of membrane proteins that mediate the transport of amino acids across cell membranes in higher plants. The AAT proteins are involved in regulating plant cell growth and various developmental processes. However, the biological function of this gene family in cotton fiber development is not clear. In this study, 190, 190, 101, and 94 full-length AAT genes were identified from Gossypiumhirsutum, G. barbadense, G. arboreum, and G. raimondii. A total of 575 AAT genes from the four cotton species were divided into two subfamilies and 12 clades based on phylogenetic analysis. The AAT genes in the four cotton species were distributed on all the chromosomes. All GhAAT genes contain multiple exons, and each GhAAT protein has multiple conserved motifs. Transcriptional profiling and RT qPCR analysis showed that four GhATT genes tend to express specifically at the fiber initiation stage. Eight genes tend to express specifically at the fiber elongation and maturity stage, and four genes tend to express specifically at the fiber initiation and elongation stages. Our results provide a solid basis for further elucidating the biological function of AAT genes related to cotton fiber development and offer valuable genetic resources for crop improvement in the future.

Light Intensity Modulates the Effect of Phosphate Limitation on Carbohydrates, Amino Acids, and Catechins in Tea Plants (Camellia sinensis L.)

Metabolites are major contributors to the quality of tea that are regulated by various abiotic stresses. Light intensity and phosphorus (P) supply affect the metabolism of tea plants. However, how these two factors interact and mediate the metabolite levels in tea plants are not fully understood. The present study investigated the consequences of different light intensity and P regimes on the metabolism of carbohydrates, amino acids, and flavonoids in the Fengqing tea cultivar. The leaves and young shoots were subjected to untargeted metabolomics analysis by two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOF/MS), ultra-performance liquid chromatography-quadrupole-TOF/MS (UPLC-Q-TOF/MS), and targeted analysis by high-performance liquid chromatography (HPLC) along with quantification of gene expression by quantitative real time-PCR (qRT-PCR). The results from young shoots showed that amino acids, pentose phosphate, and flavonol glycosides pathways were enhanced in response to decreasing light intensities and P deficiency. The expression of the genes hexokinase 1, ribose 5-phosphate isomerase A (RPIA), glutamate synthetase 1 (GS1), prolyl 4-hydroxylase (P4H), and arginase was induced by P limitation, thereafter affecting carbohydrates and amino acids metabolism, where shading modulated the responses of transcripts and corresponding metabolites caused by P deficiency. P deprivation repressed the expression of Pi transport, stress, sensing, and signaling (SPX2) and induced bidirectional sugar transporter (SWEET3) and amino acid permeases (AAP) which ultimately caused an increase in the amino acids: glutamate (Glu), proline (Pro), and arginine (Arg) under shading but decreased catechins [epicatechingallate (ECG) and Gallic acid, GA] content in young shoots.

Rice amino acid transporter-like 6 (OsATL6) is involved in amino acid homeostasis by modulating the vacuolar storage of glutamine in roots

Glutamine is a product of ammonium (NH₄⁺ ) assimilation catalyzed by glutamine synthetase (GS) and glutamate synthase (GOGAT). The growth of NH₄⁺ -preferring paddy rice (Oryza sativa L.) depends on root NH₄⁺ assimilation and the subsequent root-to-shoot allocation of glutamine; however, little is known about the mechanism of glutamine storage in roots. Here, using transcriptome and reverse genetics analyses, we show that the rice amino acid transporter-like 6 (OsATL6) protein exports glutamine to the root vacuoles under NH₄⁺ -replete conditions. OsATL6 was expressed, along with OsGS1;2 and OsNADH-GOGAT1, in wild-type (WT) roots fed with sufficient NH₄ Cl, and was induced by glutamine treatment. We generated two independent Tos17 retrotransposon insertion mutants showing reduced OsATL6 expression to determine the function of OsATL6. Compared with segregants lacking the Tos17 insertion, the OsATL6 knock-down mutant seedlings exhibited lower root glutamine content but higher glutamine concentration in the xylem sap and greater shoot growth under NH₄⁺ -replete conditions. The transient expression of monomeric red fluorescent protein-fused OsATL6 in onion epidermal cells confirmed the tonoplast localization of OsATL6. When OsATL6 was expressed in Xenopus laevis oocytes, glutamine efflux from the cell into the acidic bath solution increased. Under sufficient NH₄⁺ supply, OsATL6 transiently accumulated in sclerenchyma and pericycle cells, which are located adjacent to the Casparian strip, thus obstructing the apoplastic solute path, and in vascular parenchyma cells of WT roots before the peak accumulation of GS1;2 and NADH-GOGAT1 occurred. These findings suggest that OsATL6 temporarily stores excess glutamine, produced by NH₄⁺ assimilation, in root vacuoles before it can be translocated to the shoot.

The tea plant CsLHT1 and CsLHT6 transporters take up amino acids, as a nitrogen source, from the soil of organic tea plantations

Organic tea is more popular than conventional tea that originates from fertilized plants. Amino acids inorganic soils constitute a substantial pool nitrogen (N) available for plants. However, the amino-acid contents in soils of tea plantations and how tea plants take up these amino acids remain largely unknown. In this study, we show that the amino-acid content in the soil of an organic tea plantation is significantly higher than that of a conventional tea plantation. Glutamate, alanine, valine, and leucine were the most abundant amino acids in the soil of this tea plantation. When ¹⁵N-glutamate was fed to tea plants, it was efficiently absorbed and significantly increased the contents of other amino acids in the roots. We cloned seven CsLHT genes encoding amino-acid transporters and found that the expression of CsLHT1, CsLHT2, and CsLHT6 in the roots significantly increased upon glutamate feeding. Moreover, the expression of CsLHT1 or CsLHT6 in a yeast amino-acid uptake-defective mutant, 22∆10α, enabled growth on media with amino acids constituting the sole N source. Amino-acid uptake assays indicated that CsLHT1 and CsLHT6 are H⁺-dependent high- and low-affinity amino-acid transporters, respectively. We further demonstrated that CsLHT1 and CsLHT6 are highly expressed in the roots and are localized to the plasma membrane. Moreover, overexpression of CsLHT1 and CsLHT6 in Arabidopsis significantly improved the uptake of exogenously supplied ¹⁵N-glutamate and ¹⁵N-glutamine. Taken together, our findings are consistent with the involvement of CsLHT1 and CsLHT6 in amino-acid uptake from the soil, which is particularly important for tea plants grown inorganic tea plantations.

Amino acid transporter (AAT) gene family in foxtail millet (Setaria italica L.): widespread family expansion, functional differentiation, roles in quality formation and response to abiotic stresses

Background

Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response.

Results

A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted.

Conclusion

This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07779-9.

Identification, systematic evolution and expression analyses of the AAAP gene family in Capsicum annuum

BACKGROUND

The amino acid/auxin permease (AAAP) family represents a class of proteins that transport amino acids across cell membranes. Members of this family are widely distributed in different organisms and participate in processes such as growth and development and the stress response in plants. However, a systematic comprehensive analysis of AAAP genes of the pepper (Capsicum annuum) genome has not been reported.

RESULTS

In this study, we performed systematic bioinformatics analyses to identify AAAP family genes in the C. annuum 'Zunla-1' genome to determine gene number, distribution, structure, duplications and expression patterns in different tissues and stress. A total of 53 CaAAAP genes were identified in the 'Zunla-1' pepper genome and could be divided into eight subgroups. Significant differences in gene structure and protein conserved domains were observed among the subgroups. In addition to CaGAT1, CaATL4, and CaVAAT1, the remaining CaAAAP genes were unevenly distributed on 11 of 12 chromosomes. In total, 33.96% (18/53) of the CaAAAP genes were a result of duplication events, including three pairs of genes due to segmental duplication and 12 tandem duplication events. Analyses of evolutionary patterns showed that segmental duplication of AAAPs in pepper occurred before tandem duplication. The expression profiling of the CaAAAP by transcriptomic data analysis showed distinct expression patterns in various tissues and response to different stress treatment, which further suggest that the function of CaAAAP genes has been differentiated.

CONCLUSIONS

This study of CaAAAP genes provides a theoretical basis for exploring the roles of AAAP family members in C. annuum.

Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective

Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H⁺-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.

The Amino Acid Transporter OsAAP4 Contributes to Rice Tillering and Grain Yield by Regulating Neutral Amino Acid Allocation through Two Splicing Variants

BACKGROUND

Amino acids, which are transported by amino acid transporters, are the major forms of organic nitrogen utilized by higher plants. Among the 19 Amino Acid Permease transporters (AAPs) in rice, only a small number of these genes have been reported to influence rice growth and development. However, whether other OsAAPs are responsible for rice growth and development is unclear.

RESULTS

In this study, we demonstrate that OsAAP4 promoter sequences are divergent between Indica and Japonica, with higher expression in the former, which produces more tillers and higher grain yield than does Japonica. Overexpression of two different splicing variants of OsAAP4 in Japonica ZH11 significantly increased rice tillering and grain yield as result of enhancing the neutral amino acid concentrations of Val, Pro, Thr and Leu. OsAAP4 RNA interference (RNAi) and mutant lines displayed opposite trends compared with overexpresing (OE) lines. In addition, exogenous Val or Pro at 0.5 mM significantly promoted the bud outgrowth of lines overexpressing an OsAAP4a splicing variant compared with ZH11, and exogenous Val or Pro at 2.0 mM significantly enhanced the bud outgrowth of lines overexpressing splicing variant OsAAP4b compared with ZH11. Of note, the results of a protoplast amino acid-uptake assay showed that Val or Pro at different concentrations was specifically transported and accumulated in these overexpressing lines. Transcriptome analysis further demonstrated that OsAAP4 may affect nitrogen transport and metabolism, and auxin, cytokinin signaling in regulating rice tillering.

CONCLUSION

Our results suggested that OsAAP4 contributes to rice tiller and grain yield by regulating neutral amino acid allocation through two different splicing variants and that OsAAP4 might have potential applications in rice breeding.

SSR1 is involved in maintaining the function of mitochondria electron transport chain and iron homeostasis upon proline treatment in Arabidopsis

Although increasing intracellular proline under stressed condition could help the plants survive, treating plant with high level of proline under normal condition could be inhibitory to plant growth. Among other possible mechanisms, proline-induced mitochondrial reactive oxygen species (ROS) production due to electron overflow in mitochondria electron transport chain (mETC) caused by elevated proline degradation may contribute to the proline toxicity. However, direct evidences are still elusive. Here, we reported a functional characterization of SSR1, encoding a protein localized in mitochondria matrix, in maintaining the function of mETC through analyzing the proline hypersensitive phenotype of an Arabidopsis mutant ssr1-1 with a truncated SSR1 protein. Our analysis demonstrated that upon proline treatment, there were higher mitochondrial ROS, lower ATP content, reduced activity of mETC complex I and II, and reduced iron content in ssr1-1, in comparison to the wild type. Therefore, SSR1 is involved in maintaining normal capacity of mETC in transporting electrons in a way that related to iron homeostasis. Our results also supported that normal mETC activity is required for alleviating the proline toxicity.

The growth of Arabidopsis primary root is repressed by several and diverse amino acids through auxin-dependent and independent mechanisms and MPK6 kinase activity

Amino acids serve as structural monomers for protein synthesis and are considered important biostimulants for plants. In this report, the effects of all 20-L amino acids in Arabidopsis primary root growth were evaluated. 15 amino acids inhibited growth, being l-leucine (l-Leu), l-lysine (l-Lys), l-tryptophan (l-Trp), and l-glutamate (l-Glu) the most active, which repressed both cell division and elongation in primary roots. Comparisons of DR5:GFP expression and growth of WT Arabidopsis seedlings and several auxin response mutants including slr, axr1 and axr2 single mutants, arf7/arf19 double mutant and tir1/afb2/afb3 triple mutant, treated with inhibitory concentrations of l-Glu, l-Leu, l-Lys and l-Trp revealed gene-dependent, specific changes in auxin response. In addition, l- isomers of Glu, Leu and Lys, but not l-Trp diminished the GFP fluorescence of pPIN1::PIN1:GFP, pPIN2::PIN2:GFP, pPIN3::PIN3:GFP and pPIN7::PIN7:GFP constructs in root tips. MPK6 activity in roots was enhanced by amino acid treatment, being greater in response to l-Trp while mpk6 mutants supported cell division and elongation at high doses of l-Glu, l-Leu, l-Lys and l-Trp. We conclude that independently of their auxin modulating properties, amino acids signals converge in MPK6 to alter the Arabidopsis primary root growth.