Characterization and Expression of KT/HAK/KUP Transporter Family Genes in Willow under Potassium Deficiency, Drought, and Salt Stresses

Investigation of two-pore K+ (TPK) channels in Triticum aestivum L. suggests their role in stress response

Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.

Genome wide identification, structural characterization and phylogenetic analysis of High-Affinity potassium (HAK) ion transporters in common bean (Phaseolus vulgaris L.)

BACKGROUND

High-Affinity Potassium ions represent one of the most important and large group of potassium transporters. Although HAK genes have been studied in a variety of plant species, yet, remain unexplored in common bean.

RESULTS

In the current study, 20 HAK genes were identified in common bean genome. Super-family "K_trans" domain was found in all PvHAK genes. Signals for localization of PvHAK proteins were detected in cell membrane. Fifty three HAKs genes, across diverse plant species, were divided into 5 groups based on sequential homology. Twelve pairs of orthologs genes were found in various plant species. PvHAKs genes were distributed unequally on 7 chromosomes with maximum number (7) mapped on chromosome 2 while only 1 PvHAK found on each chromosome 1, 4, and 6. Tandem gene duplication was witnessed in 2 paralog pairs while 1 pair exhibited segmental gene duplication. Five groups were made in PvHAK gene family based on Phylogeny. Maximum PvHAKs (10) were detected in Group-V while group-II composed of only 1 PvHAK gene. Variation was witnessed in number and size of motifs, and structure of PvHAKs associated with different groups. Light and hormone responsive elements contributed 57 and 24% share, respectively, to cis regulatory elements. qRT-PCR based results revealed significant increase in expression of all 4 PvHAK genes under low-potassium stress.

CONCLUSION

The current study provides valuable information for further functional characterization and uncovering the molecular mechanism associated with Potassium transportation in plants.

Genome-wide characterization of SINA E3 ubiquitin ligase family members and their expression profiles in response to various abiotic stresses and hormones in kiwifruit

SINA (Seven in absentia) proteins in the subtype of E3 ubiquitin ligase family have important functions in regulating the growth and development as well as in response to abiotic and biotic stresses in plants. However, the characteristics and possible functions of SINA family proteins in kiwifruit are not studied. In this research, a total number of 11 AcSINA genes in the kiwifruit genome were identified. Chromosome location and multiple sequence alignment analyses indicated that they were unevenly distributed on 10 chromosomes and all contained the typical N-terminal RING domain and C-terminal SINA domain. Phylogenetic, gene structure and collinear relationship analyses revealed that they were highly conserved with the same gene structure, and have gone through segmental duplication events. Expression pattern analyses demonstrated that all AcSINAs were ubiquitously expressed in roots, stems and leaves, and were responsive to different abiotic and plant hormone treatments with overlapped but distinct expression patterns. Further yeast two-hybrid and Arabidopsis transformation analyses demonstrated most AcSINAs interacted with itself or other AcSINA members to form homo- or heterodimers, and ectopic expression of AcSINA2 in Arabidopsis led to hypersensitive growth phenotype of transgenic seedlings to ABA treatment. Our results reveal that AcSINAs take part in the response to various abiotic stresses and hormones, and provide important information for the functional elucidation of AcSINAs in vine fruit plants.

Differential response of nano zinc sulphate with other conventional sources of Zn in mitigating salinity stress in rice grown on saline-sodic soil

Salinization causes the degradation of the soil and threatening the global food security but the application of essential micronutrients like zinc (Zn), improve the plant growth by stabilizing the plant cell and root development. Keeping in view the above-mentioned scenario, an experiment was conducted to compare the efficiency of conventional Zn fertilizers like zinc sulphate (ZnSO₄), zinc ethylene diamine tetra acetic acid (Zn-EDTA) and advance nano Zn fertilizers such as zinc sulphate nanoparticles (ZnSO₄NPs), and zinc oxide nanoparticles (ZnONPs) (applied at the rate of 5 and 10 mg/kg) in saline-sodic soil. Results revealed that the maximum plant height (67%), spike length (72%), root length (162%), number of tillers (71%), paddy weight (100%), shoot dry weight (158%), and root dry weight (119%) was found in ZnSO₄NPs applied at the rate of 10 mg/kg (ZnSO₄NPs-10) as compared to salt-affected control (SAC). Similarly, the plants physiological attributes like chlorophyll contents (91%), photosynthesis rate (113%), transpiration rate (106%), stomatal conductance (56%) and internal CO₂ (11%) were increased by the application of ZnSO₄NPs-10, as compared to SAC. The maximum Zn concentration in root (153%), shoot (205%) and paddy (167%) found in ZnSO₄NPs-10, as compared to control. In the body of rice plants, other nutrients like phosphorus and potassium were also increased by the application of ZnSO₄NPs-10 and soil chemical attributes such as sodium and sodium adsorption ratio were decreased. The current experiment concluded that the application of ZnSO₄NPs at the rate of 10 mg/kg in salt-affected paddy soil increased the growth, physiology, up take of essential nutrients and yield of rice by balancing the cationic ratio under salt stress.

Transcriptome analysis of sweet potato responses to potassium deficiency

Background

As one of three essential nutrients, potassium is regarded as a main limiting factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of seven major food crops grown worldwide, and is both a nutrient-rich food and a bioenergy crop. It is a typical ‘K-favoring’ crop, and the level of potassium ion (K⁺) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K⁺ conditions. Here, we analyzed the transcriptomic profiles of sweet potato roots in response to K⁺ deficiency to determine the effect of low-K⁺ stress on this economically important crop.

Results

The roots of sweet potato seedlings with or without K⁺ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K⁺ groups. Among the DEGs, 336 were upregulated and 223 were downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. Further analysis revealed previously unknow genes involved in low-K⁺ stress, which could be investigated further to improve low K⁺ tolerance in plants. Confirmation of RNA-sequencing results using qRT-PCR displayed a high level of consistency between the two experiments. Analysis showed that many auxin-, ethylene- and jasmonic acid-related genes respond to K⁺ deficiency, suggesting that these hormones have important roles in K⁺ nutrient signaling in sweet potato.

Conclusions

According to the transcriptome data of sweet potato, various DEGs showed transcriptional changes in response to low-K⁺ stress. However, the expression level of some kinases, transporters, transcription factors (TFs), hormone-related genes, and plant defense-related genes changed significantly, suggesting that they have important roles during K⁺ deficiency. Thus, this study identifies potential genes for genetic improvement of responses to low-K⁺ stress and provides valuable insight into the molecular mechanisms regulating low K⁺ tolerance in sweet potato. Further research is required to clarify the function of these DEGs under low-K⁺ stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08870-5.

Genome-wide identification and multiple abiotic stress transcript profiling of potassium transport gene homologs in Sorghum bicolor

Potassium (K⁺) is the most abundant cation that plays a crucial role in various cellular processes in plants. Plants have developed an efficient mechanism for the acquisition of K⁺ when grown in K⁺ deficient or saline soils. A total of 47 K⁺ transport gene homologs (27 HAKs, 4 HKTs, 2 KEAs, 9 AKTs, 2 KATs, 2 TPCs, and 1 VDPC) have been identified in Sorghum bicolor. Of 47 homologs, 33 were identified as K⁺ transporters and the remaining 14 as K⁺ channels. Chromosome 2 has been found as the hotspot of K⁺ transporters with 9 genes. Phylogenetic analysis revealed the conservation of sorghum K⁺ transport genes akin to Oryza sativa. Analysis of regulatory elements indicates the key roles that K⁺ transport genes play under different biotic and abiotic stress conditions. Digital expression data of different developmental stages disclosed that expressions were higher in milk, flowering, and tillering stages. Expression levels of the genes SbHAK27 and SbKEA2 were higher during milk, SbHAK17, SbHAK11, SbHAK18, and SbHAK7 during flowering, SbHAK18, SbHAK10, and 23 other gene expressions were elevated during tillering inferring the important role that K⁺ transport genes play during plant growth and development. Differential transcript expression was observed in different tissues like root, stem, and leaf under abiotic stresses such as salt, drought, heat, and cold stresses. Collectively, the in-depth genome-wide analysis and differential transcript profiling of K⁺ transport genes elucidate their role in ion homeostasis and stress tolerance mechanisms.

Evaluation of salt tolerance of oat cultivars and the mechanism of adaptation to salinity

Soil salinity is a threat to agricultural production worldwide. Oat (Avena sativa L.) is an irreplaceable crop in areas with fragile ecological conditions. However, there is a lack of research on salt tolerance evaluation of oat germplasm resources. Therefore, the purpose of this work was to evaluate the salt tolerance of oat cultivars and investigate the mechanism of salt-tolerant oat cultivars' adaptation to salinity. Salt tolerance of 100 oat cultivars was evaluated, and then two salt-tolerant cultivars and two salt-sensitive cultivars were used to compare their physiological responses and expression patterns of Na⁺- and K⁺-transport-related genes under salinity. Principal component analysis and membership function analysis had good predictability for salt tolerance evaluation of oat and other crops. The 100 oat cultivars were clustered into three categories, with three salt tolerance levels. Under saline condition, salt-tolerant cultivars maintained higher growth rate, leaf cell membrane integrity, and osmotic adjustment capability via enhancing the activities of antioxidant enzymes and accumulating more osmotic regulators. Furthermore, salt-tolerant cultivars had stronger capability to restrict root Na ⁺ uptake through reducing AsAKT1 and AsHKT2;1 expression, exclude more Na⁺ from root through increasing AsSOS1 expression, compartmentalize more Na ⁺ into root vacuoles through increasing AsNHX1 and AsVATP-P1 expression, and absorb more K⁺ through increasing AsKUP1 expression, compared with salt-sensitive cultivars. The evaluation procedure developed in this work can be applied for screening cereal crop cultivars with higher salt tolerance, and the elucidated mechanism of oat adaptation to salinity lays a foundation for identifying more functional genes related to salt tolerance.

Genomic & structural diversity and functional role of potassium (K+) transport proteins in plants

Potassium (K⁺) is an essential macronutrient for plant growth and productivity. It is the most abundant cation in plants and is involved in various cellular processes. Variable K⁺ availability is sensed by plant roots, consequently K⁺ transport proteins are activated to optimize K⁺ uptake. In addition to K⁺ uptake and translocation these proteins are involved in other important physiological processes like transmembrane voltage regulation, polar auxin transport, maintenance of Na⁺/K⁺ ratio and stomata movement during abiotic stress responses. K⁺ transport proteins display tremendous genomic and structural diversity in plants. Their key structural features, such as transmembrane domains, N-terminal domains, C-terminal domains and loops determine their ability of K⁺ uptake and transport and thus, provide functional diversity. Most K⁺ transporters are regulated at transcriptional and post-translational levels. Genetic manipulation of key K⁺ transporters/channels could be a prominent strategy for improving K⁺ utilization efficiency (KUE) in plants. This review discusses the genomic and structural diversity of various K⁺ transport proteins in plants. Also, an update on the function of K⁺ transport proteins and their regulatory mechanism in response to variable K⁺ availability, in improving KUE, biotic and abiotic stresses is provided.

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses

Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants' dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil to numerous parts of plants. In this study, we have identified 39 genes encoding putative K+ transport-related genes in Vigna radiata. Chromosomal mapping of these genes indicated an uneven distribution across eight out of 11 chromosomes. Comparative phylogenetic analysis of different plant species, i.e., V. radiata, Glycine max, Cicer arietinum, Oryza sativa, and Arabidopsis thaliana, showed their strong conservation in different plant species. Evolutionary analysis of these genes suggests that gene duplication is a major route of expansion for this family in V. radiata. Comprehensive promoter analysis identified several abiotic stresses related to cis-elements in the promoter regions of these genes, suggesting their role in abiotic stress tolerance. Our additional analyses indicated that abiotic stresses adversely affected the chlorophyll concentration, carotenoids, catalase, total soluble protein concentration, and the activities of superoxide and peroxidase in V. radiata. It also disturbs the ionic balance by decreasing the uptake of K+ content and increasing the uptake of Na+. Expression analysis from high-throughput sequencing data and quantitative real-time PCR experiments revealed that several K+ transport genes were expressed in different tissues (seed, flower, and pod) and in abiotic stress-responsive manners. A highly significant variation of expression was observed for VrHKT (1.1 and 1.2), VrKAT (1 and 2) VrAKT1.1, VrAKT2, VrSKOR, VrKEA5, VrTPK3, and VrKUP/HAK/KT (4, 5, and 8.1) in response to drought, heat or salinity stress. It reflected their potential roles in plant growth, development, or stress adaptations. The present study gives an in-depth understanding of K+ transport system genes in V. radiata and will serve as a basis for a functional analysis of these genes.

Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio

We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.

Identification and characterization of HAK/KUP/KT potassium transporter gene family in barley and their expression under abiotic stress

BACKGROUND

HAK/KUP/KT (High-affinity K⁺ transporters/K⁺ uptake permeases/K⁺ transporters) is the largest potassium transporter family in plants, and plays pivotal roles in K⁺ uptake and transport, as well as biotic and abiotic stress responses. However, our understanding of the gene family in barley (Hordeum vulgare L.) is quite limited.

RESULTS

In the present study, we identified 27 barley HAK/KUP/KT genes (hereafter called HvHAKs) through a genome-wide analysis. These HvHAKs were unevenly distributed on seven chromosomes, and could be phylogenetically classified into four clusters. All HvHAK protein sequences possessed the conserved motifs and domains. However, the substantial difference existed among HAK members in cis-acting elements and tissue expression patterns. Wheat had the most orthologous genes to barley HAKs, followed by Brachypodium distachyon, rice and maize. In addition, six barley HAK genes were selected to investigate their expression profiling in response to three abiotic stresses by qRT-PCR, and their expression levels were all up-regulated under salt, hyperosmotic and potassium deficiency treatments.

CONCLUSION

Twenty seven HAK genes (HvHAKs) were identified in barley, and they differ in tissue expression patterns and responses to salt stress, drought stress and potassium deficiency.

Isolation and Functional Determination of SKOR Potassium Channel in Purple Osier Willow, Salix purpurea

Potassium (K⁺) plays key roles in plant growth and development. However, molecular mechanism studies of K⁺ nutrition in forest plants are largely rare. In plants, SKOR gene encodes for the outward rectifying Shaker-type K⁺ channel that is responsible for the long-distance transportation of K⁺ through xylem in roots. In this study, we determined a Shaker-type K⁺ channel gene in purple osier (Salix purpurea), designated as SpuSKOR, and determined its function using a patch clamp electrophysiological system. SpuSKOR was closely clustered with poplar PtrSKOR in the phylogenetic tree. Quantitative real-time PCR (qRT-PCR) analyses demonstrated that SpuSKOR was predominantly expressed in roots, and expression decreased under K⁺ depletion conditions. Patch clamp analysis via HEK293-T cells demonstrated that the activity of the SpuSKOR channel was activated when the cell membrane voltage reached at -10 mV, and the channel activity was enhanced along with the increase of membrane voltage. Outward currents were recorded and induced in response to the decrease of external K⁺ concentration. Our results indicate that SpuSKOR is a typical voltage dependent outwardly rectifying K⁺ channel in purple osier. This study provides theoretical basis for revealing the mechanism of K⁺ transport and distribution in woody plants.

Genome-wide characterization and expression analysis of HAK K+ transport family in Ipomoea

The potassium transporter high-affinity K⁺ transporter/K⁺ uptake permease/K⁺ transporter (HAK/KUP/KT) family plays a vital role in potassium uptake, and potassium ion (K⁺)-mediated environmental stress. In the present study, we identified 22 IbHAK/KUP/KT (HAK) genes in sweet potato [Ipomoea batata (L.) Lam] and the same number of HAK genes from sweet potato wild relative Ipomoea trifida. Phylogeny analysis indicated that the HAKs can be divided into five clades. Chromosomal distribution and genome synteny analyses revealed two tandem-duplicated gene pairs IbHAK16/17 and IbHAK17/18 on chromosomes 13 and eight segmental-duplicated gene pairs on chromosomes 1, 3, 5, 8, 10, 12, 14 among the IbHAK gene family. Eleven orthologous HAK gene pairs between I. batata and I. trifida were involved in the duplication of genomic blocks based on comparative genomic analysis. The Ka/Ks ratios of these IbHAK genes ranged from 0.02 to 0.55(< 1), further indicated that purifying selection was the primary force driving the evolution of HAKs in Ipomoea. A heat map based on RNA-seq data showed that 13 HAKs in Xushu32 (a K⁺-tolerant sweet potato genotype) and 10 HAKs in Ningzi1 (a K⁺-sensitive sweet potato genotype) in response to K⁺ deficiency stress. Quantitative real-time PCR (qRT-PCR) analysis revealed IbHAK2, -3, -8, -10, -11, -18, -19, and -21 were induced in both Xushu32 and Ningzi1 under low K⁺ stress. Compared with other IbHAK genes, IbHAK8 showed more strongly upregulation after exposure to drought and salt stress. Furthermore, co-expression analysis showed that only IbHAK8 of 22 IbHAK genes involved in network interactions with 30 genes related to abiotic and biotic stresses. Taken together, these results are helpful for further functional studies on IbHAK and molecular breeding of sweet potato.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02552-3.

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

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

Regulation of AtKUP2 Expression by bHLH and WRKY Transcription Factors Helps to Confer Increased Salt Tolerance to Arabidopsis thaliana Plants

Potassium transporters play an essential role in maintaining cellular ion homeostasis, turgor pressure, and pH, which are critical for adaptation under salt stress. We identified a salt responsive Avicennia officinalis KUP/HAK/KT transporter family gene, AoKUP2, which has high sequence similarity to its Arabidopsis ortholog AtKUP2. These genes were functionally characterized in mutant yeast cells and Arabidopsis plants. Both AoKUP2 and AtKUP2 were induced by salt stress, and AtKUP2 was primarily induced in roots. Subcellular localization revealed that AoKUP2 and AtKUP2 are localized to the plasma membrane and mitochondria. Expression of AtKUP2 and AoKUP2 in Saccharomyces cerevisiae mutant strain (BY4741 trk1Δ::loxP trk2Δ::loxP) helped to rescue the growth defect of the mutant under different NaCl and K⁺ concentrations. Furthermore, constitutive expression of AoKUP2 and AtKUP2 conferred enhanced salt tolerance in Arabidopsis indicated by higher germination rate, better survival, and increased root and shoot length compared to the untreated controls. Analysis of Na⁺ and K⁺ contents in the shoots and roots showed that ectopic expression lines accumulated less Na⁺ and more K⁺ than the WT. Two stress-responsive transcription factors, bHLH122 and WRKY33, were identified as direct regulators of AtKUP2 expression. Our results suggest that AtKUP2 plays a key role in enhancing salt stress tolerance by maintaining cellular ion homeostasis.