Phylogenetic relationships within cation transporter families of Arabidopsis

Genome-wide survey of KT/HAK/KUP genes in the genus Citrullus and analysis of their involvement in K+-deficiency and drought stress responses in between C. lanatus and C. amarus

BACKGROUND

The KT/HAK/KUP is the largest K+ transporter family in plants, playing crucial roles in K+ absorption, transport, and defense against environmental stress. Sweet watermelon is an economically significant horticultural crop belonging to the genus Citrullus, with a high demand for K+ during its growth process. However, a comprehensive analysis of the KT/HAK/KUP gene family in watermelon has not been reported.

RESULTS

14 KT/HAK/KUP genes were identified in the genomes of each of seven Citrullus species. These KT/HAK/KUPs in watermelon were unevenly distributed across seven chromosomes. Segmental duplication is the primary driving force behind the expansion of the KT/HAK/KUP family, subjected to purifying selection during domestication (Ka/Ks < 1), and all KT/HAK/KUPs exhibit conserved motifs and could be phylogenetically classified into four groups. The promoters of KT/HAK/KUPs contain numerous cis-regulatory elements related to plant growth and development, phytohormone response, and stress response. Under K+ deficiency, the growth of watermelon seedlings was significantly inhibited, with cultivated watermelon experiencing greater impacts (canopy width, redox enzyme activity) compared to the wild type. All KT/HAK/KUPs in C. lanatus and C. amarus exhibit specific expression responses to K+-deficiency and drought stress by qRT-PCR. Notably, ClG42_07g0120700/CaPI482276_07g014010 were predominantly expressed in roots and were further induced by K+-deficiency and drought stress. Additionally, the K+ transport capacity of ClG42_07g0120700 under low K+ stress was confirmed by yeast functional complementation assay.

CONCLUSIONS

KT/HAK/KUP genes in watermelon were systematically identified and analyzed at the pangenome level and provide a foundation for understanding the classification and functions of the KT/HAK/KUPs in watermelon plants.

Understanding the salinity resilience and productivity of halophytes in saline environments

The escalating salinity levels in cultivable soil pose a significant threat to agricultural productivity and, consequently, human sustenance. This problem is being exacerbated by natural processes and human activities, coinciding with a period of rapid population growth. Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. Evolution has created many close halophyte relatives of our major glycophytic crops, such as Puccinellia tenuiflora (relative of barley and wheat), Oryza coarctata (relative of rice) and Glycine soja (relative of soybean). There are also some halophytes have been subjected to semi-domestication and are considered as minor crops, such as Chenopodium quinoa. In this paper, we examine the prevailing comprehension of robust salinity resilience in halophytes. We summarize the existing strategies and technologies that equip researchers with the means to enhance the salt tolerance capabilities of primary crops and investigate the genetic makeup of halophytes.

Molecular evolution and functional diversification of metal tolerance protein families in cereals plants and function of maize MTP protein

Plants employ metal tolerance proteins (MTPs) to confer tolerance by sequestering excess ions into vacuoles. MTPs belong to the cation diffusion facilitator (CDF) family, which facilitates the transport of divalent transition metal cations. In this study, we conducted a comprehensive analysis of the MTP gene families across 21 plant species, including maize (Zea mays). A total of 247 MTP genes were identified within these plant genomes and categorized into distinct subgroups, namely Zn-CDF, Mn-CDF, and Fe/Zn-CDF, based on phylogenetic analyses. This investigation encompassed the characterization of genomic distribution, gene structures, cis-regulatory elements, collinearity relationships, and gene ontology functions associated with MTPs. Transcriptomic analyses unveiled stress-specific expression patterns of MTP genes under various abiotic stresses. Moreover, quantitative RT-PCR assays were employed to assess maize MTP gene responses to diverse heavy metal stress conditions. Functional validation of metal tolerance roles was achieved through heterologous expression in yeast. This integrated evolutionary scrutiny of MTP families in cereals furnishes a valuable framework for the elucidation of MTP functions in subsequent studies. Notably, the prioritized MTP gene ZmMTP6 emerged as a positive regulator of plant Cd tolerance, thereby offering a pivotal genetic asset for the development of Cd-tolerant crops, particularly maize cultivars.

Genome-Wide Identification and Expression Analysis of SlNRAMP Genes in Tomato under Nutrient Deficiency and Cadmium Stress during Arbuscular Mycorrhizal Symbiosis

Arbuscular mycorrhizal (AM) fungi are well known for enhancing phosphorus uptake in plants; however, their regulating roles in cation transporting gene family, such as natural resistance-associated macrophage protein (NRAMP), are still limited. Here, we performed bioinformatics analysis and quantitative expression assays of tomato SlNRAMP 1 to 5 genes under nutrient deficiency and cadmium (Cd) stress in response to AM symbiosis. These five SlNRAMP members are mainly located in the plasma or vacuolar membrane and can be divided into two subfamilies. Cis-element analysis revealed several motifs involved in phytohormonal and abiotic regulation in their promoters. SlNRAMP2 was downregulated by iron deficiency, while SlNRAMP1, SlNRAMP3, SlNRAMP4, and SlNRAMP5 responded positively to copper-, zinc-, and manganese-deficient conditions. AM colonization reduced Cd accumulation and expression of SlNRAMP3 but enhanced SlNRAMP1, SlNRAMP2, and SlNRMAP4 in plants under Cd stress. These findings provide valuable genetic information for improving tomato resilience to nutrient deficiency and heavy metal stress by developing AM symbiosis.

Chemical and biological study of flavonoid-related plant pigment: current findings and beyond

Flavonoids are polyphenolic plant constituents. Anthocyanins are flavonoid pigments found in higher plants that show a wide variety of colors ranging from red through purple to blue. The blue color of the flowers is mostly attributed to anthocyanins. However, only a few types of anthocyanidin, chromophore of anthocyanin, exist in nature, and the extracted pigments are unstable with the color fading away. Therefore, the wide range and stable nature of colors in flowers have remained a mystery for more than a century. The mechanism underlying anthocyanin-induced flower coloration was studied using an interdisciplinary method involving chemistry and biology. Furthermore, the chemical studies on flavonoid pigments in various edible plants, synthetic and biosynthetic studies on anthocyanins were conducted. The results of these studies have been outlined in this review.

Genome-Wide Identification of the Cation/Proton Antiporter (CPA) Gene Family and Functional Analysis of AtrNHX8 under Salt Stress

Amaranthus tricolor is an important vegetable, and its quality is affected by salt stress. Cation/proton antiporters (CPA) contribute to plant development and tolerance to salt stress. In this study, 35 CPA genes were identified from a genome database for A. tricolor, including 9 NHX, 5 KEA, and 21 CPA2 genes. Furthermore, in A. tricolor, the expression levels of most AtrNHX genes were higher at a low salinity level (50 or 100 mM NaCl) than in the control or 200 mM NaCl treatment. Levels of most AtrNHX genes were elevated in the stem. Moreover, AtrNHX8 was homologous to AtNHX4, which is involved in the regulation of sodium homeostasis and salt stress response. After AtrNHX8 overexpression in Arabidopsis thaliana, seed germination was better, and the flowering time was earlier than that of wild-type plants. Additionally, the overexpression of AtrNHX8 in A. thaliana improved salt tolerance. These results reveal the roles of AtrNHX genes under salt stress and provide valuable information on this gene family in amaranth.

Genome-Wide Identification of OsZIPs in Rice and Gene Expression Analysis under Manganese and Selenium Stress

Zinc (Zn)- and iron (Fe)-regulating transport-like proteins (ZIPs) are a class of proteins crucial for metal uptake and transport in plants, particularly for Zn and Fe absorption and distribution. These proteins ensure the balance of trace elements essential for plant growth, development, and metabolic activities. However, the role of the rice (Oryza sativa) OsZIP gene family in manganese (Mn) and selenium (Se) transport remains underexplored. This research conducted an all-sided analysis of the rice OsZIPs and identified 16 OsZIP sequences. Phylogenetic analysis categorized the OsZIPs predominantly within the three subfamilies. The expression levels of OsZIPs in rice root and leaf subjected to Mn and Se toxicity stress were examined through quantitative real-time PCR (qRT-PCR). The findings revealed significant differential expression of many OsZIPs under these conditions, indicating a potential regulating effect in the response of rice to Mn and Se toxicity. This work lays a foundation for further functional studies of OsZIPs, enhancing our understanding of the response mechanisms of rice to Mn and Se toxicity and their roles in growth, development, and environmental adaptation.

The Uptake, Transfer, and Detoxification of Cadmium in Plants and Its Exogenous Effects

Cadmium (Cd) exerts a toxic influence on numerous crucial growth and development processes in plants, notably affecting seed germination rate, transpiration rate, chlorophyll content, and biomass. While considerable advances in Cd uptake and detoxification of plants have been made, the mechanisms by which plants adapt to and tolerate Cd toxicity remain elusive. This review focuses on the relationship between Cd and plants and the prospects for phytoremediation of Cd pollution. We highlight the following issues: (1) the present state of Cd pollution and its associated hazards, encompassing the sources and distribution of Cd and the risks posed to human health; (2) the mechanisms underlying the uptake and transport of Cd, including the physiological processes associated with the uptake, translocation, and detoxification of Cd, as well as the pertinent gene families implicated in these processes; (3) the detrimental effects of Cd on plants and the mechanisms of detoxification, such as the activation of resistance genes, root chelation, vacuolar compartmentalization, the activation of antioxidant systems and the generation of non-enzymatic antioxidants; (4) the practical application of phytoremediation and the impact of incorporating exogenous substances on the Cd tolerance of plants.

Genome-wide identification and evolutionary analysis of the NRAMP gene family in the AC genomes of Brassica species

BACKGROUND

Brassica napus, a hybrid resulting from the crossing of Brassica rapa and Brassica oleracea, is one of the most important oil crops. Despite its significance, B. napus productivity faces substantial challenges due to heavy metal stress, especially in response to cadmium (Cd), which poses a significant threat among heavy metals. Natural resistance-associated macrophage proteins (NRAMPs) play pivotal roles in Cd uptake and transport within plants. However, our understanding of the role of BnNRAMPs in B. napus is limited. Thus, this study aimed to conduct genome-wide identification and bioinformatics analysis of three Brassica species: B. napus, B. rapa, and B. oleracea.

RESULTS

A total of 37 NRAMPs were identified across the three Brassica species and classified into two distinct subfamilies based on evolutionary relationships. Conservative motif analysis revealed that motif 6 and motif 8 might significantly contribute to the differentiation between subfamily I and subfamily II within Brassica species. Evolutionary analyses and chromosome mapping revealed a reduction in the NRAMP gene family during B. napus evolutionary history, resulting in the loss of an orthologous gene derived from BoNRAMP3.2. Cis-acting element analysis suggested potential regulation of the NRAMP gene family by specific plant hormones, such as abscisic acid (ABA) and methyl jasmonate (MeJA). However, gene expression pattern analyses under hormonal or stress treatments indicated limited responsiveness of the NRAMP gene family to these treatments, warranting further experimental validation. Under Cd stress in B. napus, expression pattern analysis of the NRAMP gene family revealed a decrease in the expression levels of most BnNRAMP genes with increasing Cd concentrations. Notably, BnNRAMP5.1/5.2 exhibited a unique response pattern, being stimulated at low Cd concentrations and inhibited at high Cd concentrations, suggesting potential response mechanisms distinct from those of other NRAMP genes.

CONCLUSIONS

In summary, this study indicates complex molecular dynamics within the NRAMP gene family under Cd stress, suggesting potential applications in enhancing plant resilience, particularly against Cd. The findings also offer valuable insights for further understanding the functionality and regulatory mechanisms of the NRAMP gene family.

Genome-wide identification and expression analysis of the HAK/KUP/KT gene family in Moso bamboo

The K+ uptake permease/high-affinity K+/K+ transporter (KUP/HAK/KT) family is the most prominent group of potassium (K+) transporters, playing a key role in K+ uptake, transport, plant growth and development, and stress tolerance. However, the presence and functions of the KUP/HAK/KT family in Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau), the fastest-growing plant, have not been studied. In this study, we identified 41 KUP/HAK/KT genes (PeHAKs) distributed across 18 chromosomal scaffolds of the Moso bamboo genome. PeHAK is a typical membrane protein with a conserved structural domain and motifs. Phylogenetic tree analysis classified PeHAKs into four distinct clusters, while collinearity analysis revealed gene duplications resulting from purifying selection, including both tandem and segmental duplications. Enrichment analysis of promoter cis-acting elements suggested their plausible role in abiotic stress response and hormone induction. Transcriptomic data and STEM analyses indicated that PeHAKs were involved in tissue and organ development, rapid growth, and responded to different abiotic stress conditions. Subcellular localization analysis demonstrated that PeHAKs are predominantly expressed at the cell membrane. In-situ PCR experiments confirmed that PeHAK was mainly expressed in the lateral root primordia. Furthermore, the involvement of PeHAKs in potassium ion transport was confirmed by studying the potassium ion transport properties of a yeast mutant. Additionally, through homology modeling, we revealed the structural properties of HAK as a transmembrane protein associated with potassium ion transport. This research provides a solid basis for understanding the classification, characterization, and functional analysis of the PeHAK family in Moso bamboo.

Positive Regulatory Roles of Manihot esculenta HAK5 under K+ Deficiency or High Salt Stress

HAK/KUP/KT family members have been identified as playing key roles in K+ uptake and salt tolerance in numerous higher plants. However, their functions in cassava (Manihot esculenta Cantz) remain unknown. In this study, a gene encoding for a high-affinity potassium transporter (MeHAK5) was isolated from cassava and its function was investigated. Subcellular localization analysis showed that MeHAK5 is a plasma membrane-localized transporter. RT-PCR and RT-qPCR indicated that MeHAK5 is predominantly expressed in cassava roots, where it is upregulated by low potassium or high salt; in particular, its highest expression levels separately increased by 2.2 and 2.9 times after 50 µM KCl and 150 mM NaCl treatments. When heterologously expressed in yeast, MeHAK5 mediated K+ uptake within the cells of the yeast strain CY162 and rescued the salt-sensitive phenotype of AXT3K yeast. MeHAK5 overexpression in transgenic Arabidopsis plants exhibited improved growth and increased shoot K+ content under low potassium conditions. Under salt stress, MeHAK5 transgenic Arabidopsis plants accumulated more K+ in the shoots and roots and had reduced Na+ content in the shoots. As a result, MeHAK5 transgenic Arabidopsis demonstrated a more salt-tolerant phenotype. These results suggest that MeHAK5 functions as a high-affinity K+ transporter under K+ starvation conditions, improving K+/Na+ homeostasis and thereby functioning as a positive regulator of salt stress tolerance in transgenic Arabidopsis. Therefore, MeHAK5 may be a suitable candidate gene for improving K+ utilization efficiency and salt tolerance.

Physiological, transcriptome and gene functional analysis provide novel sights into cadmium accumulation and tolerance mechanisms in kenaf

Kenaf is considered to have great potential for remediation of heavy metals in ecosystems. However, studies on molecular mechanisms of root Cd accumulation and tolerance are still inadequate. In this study, two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd stress. This study showed that 200 µmol/L CdCl2 treatment triggered the reactive oxygen species (ROS) explosion and membrane lipid peroxidation. Compared with the Cd-sensitive cultivar 'Z', the Cd-tolerant cultivar 'F' was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid (AsA) and glutathione (GSH). The root cell wall of 'F' exhibited higher polysaccharide contents under Cd treatment, providing more Cd-binding sites. There were 3,439 differentially expressed genes (DEGs) that were co-regulated by Cd treatment in two cultivars. Phenylpropanoid biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation analysis. DEGs associated with pectin, cellulose, and hemi-cellulose metabolism were involved in Cd chelation of root cell wall; V-ATPases, ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd; PDR1 was responsible for Cd efflux; the organic acid transporters contributed to the absorption of Cd in soil. These genes might have played key roles in kenaf Cd tolerance and Cd accumulation. Moreover, HcZIP2 was identified to be involved in Cd uptake and transport in kenaf. Our findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.

Genome-wide identification, expression and function analysis of the MTP gene family in tulip (Tulipa gesneriana)

Currently, soil heavy metal contamination is a severe issue, particularly with Cd pollution. The metal tolerance protein (MTP) proteins, as plant divalent cation transporters, play a crucial role in the transport and tolerance of heavy metals in plants. This study conducted comprehensive identification and characterization of the MTP gene family in the tulip. A total of 11 TgMTP genes were identified and phylogenetically classified into three subfamilies. Conserved motif and gene structure analyses unveiled commonalities and variations among subfamily members. Expression profiling demonstrated several TgMTPs were markedly upregulated under Cd exposure, including the TgMTP7.1. Heterologous expression in yeast validated that TgMTP7.1 could ameliorate Cd sensitivity and enhance its tolerance. These results provide primary insights into the MTP gene family in tulip. Phylogenetic relationships and functional analyses establish a framework for elucidating the transporters and molecular mechanisms governing Cd accumulation and distribution in tulip. Key TgMTPs identified, exemplified by TgMTP7.1, may illuminate molecular breeding efforts aimed at developing Cd-tolerant cultivars for the remediation of soil Cd contamination.

Molecular characterization of genes involved in tolerance of cadmium in Triticum aestivum (L.) under Cd stress

The NRAMPs (natural resistance-associated macrophage proteins) are major transporters for the absorption and transport of metals like Pb, Zn, Mn, Fe, and Cd in plants. While NRAMP gene family members have been extensively studied as metal transporters in model and other plants, little information has been reported on their role in Triticum aestivum, particularly in response to Cd stress. Current study reported 13 NRAMP candidates in the genome of T. aestivum. Phylogenetic analysis divided these into three clades. Motif and gene structure study showed that members in the same clades shared the same location and pattern, which further supported the phylogenetic analysis. The analysis of cis-acting elements in promoter sequences of NRAMP genes in wheat identified stress-responsive transcription factor binding sites. Multiple sequence alignment identified the conservation of important residues. Based on RNA-seq and qRT-PCR analysis, Cd stress-responsive variations of TaNRAMP gene expression were reported. This study provides comprehensive data to understand the TaNRAMP gene family, its features, and its expression, which will be a helpful framework for functional research.

K+ and pH homeostasis in plant cells is controlled by a synchronized K+ /H+ antiport at the plasma and vacuolar membrane

Stomatal movement involves ion transport across the plasma membrane (PM) and vacuolar membrane (VM) of guard cells. However, the coupling mechanisms of ion transporters in both membranes and their interplay with Ca2+ and pH changes are largely unclear. Here, we investigated transporter networks in tobacco guard cells and mesophyll cells using multiparametric live-cell ion imaging and computational simulations. K+ and anion fluxes at both, PM and VM, affected H+ and Ca2+ , as changes in extracellular KCl or KNO3 concentrations were accompanied by cytosolic and vacuolar pH shifts and changes in [Ca2+ ]cyt and the membrane potential. At both membranes, the K+ transporter networks mediated an antiport of K+ and H+ . By contrast, net transport of anions was accompanied by parallel H+ transport, with differences in transport capacity for chloride and nitrate. Guard and mesophyll cells exhibited similarities in K+ /H+ transport but cell type-specific differences in [H+ ]cyt and pH-dependent [Ca2+ ]cyt signals. Computational cell biology models explained mechanistically the properties of transporter networks and the coupling of transport across the PM and VM. Our integrated approach indicates fundamental principles of coupled ion transport at membrane sandwiches to control H+ /K+ homeostasis and points to transceptor-like Ca2+ /H+ -based ion signaling in plant cells.

Calcium Signaling and the Response to Heat Shock in Crop Plants

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca2+), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca2+ is detected by Ca2+-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca2+ in plant cells increases rapidly, making Ca2+ signals the earliest response to HS. In this review, we discuss the crucial role of Ca2+ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR).

Genome-wide identification and expression analysis of the glutamate receptor gene family in sweet potato and its two diploid relatives

Plant glutamate receptor (GLR) homologs are crucial calcium channels that play an important role in plant development, signal transduction, and response to biotic and abiotic stresses. However, the GLR gene family has not yet been thoroughly and systematically studied in sweet potato. In this study, a total of 37 GLR genes were identified in the cultivated hexaploid sweet potato (Ipomoea batatas), and 32 GLR genes were discovered in each of the two diploid relatives (Ipomoea trifida and Ipomoea triloba) for the first time. Based on their evolutionary relationships to those of Arabidopsis, these GLRs were split into five subgroups. We then conducted comprehensive analysis to explore their physiological properties, protein interaction networks, promoter cis-elements, chromosomal placement, gene structure, and expression patterns. The results indicate that the homologous GLRs of the cultivated hexaploid sweet potato and its two relatives are different. These variations are reflected in their functions related to plant growth, hormonal crosstalk, development of tuberous roots, resistance to root rot, and responses to abiotic stress factors, all of which are governed by specific individual GLR genes. This study offers a comprehensive analysis of GLR genes in sweet potato and its two diploid relatives. It also provides a theoretical basis for future research into their regulatory mechanisms, significantly influencing the field of molecular breeding in sweet potatoes.

Sensing and regulation of plant extracellular pH

In plants, pH determines nutrient acquisition and sensing, and triggers responses to osmotic stress, whereas pH homeostasis protects the cellular machinery. Extracellular pH (pHe) controls the chemistry and rheology of the cell wall to adjust its elasticity and regulate cell expansion in space and time. Plasma membrane (PM)-localized proton pumps, cell-wall components, and cell wall-remodeling enzymes jointly maintain pHe homeostasis. To adapt to their environment and modulate growth and development, plant cells must sense subtle changes in pHe caused by the environment or neighboring cells. Accumulating evidence indicates that PM-localized cell-surface peptide-receptor pairs sense pHe. We highlight recent advances in understanding how plants perceive and maintain pHe, and discuss future perspectives.

Genome-Wide Analysis of Cation/Proton Antiporter Family in Soybean (Glycine max) and Functional Analysis of GmCHX20a on Salt Response

Monovalent cation proton antiporters (CPAs) play crucial roles in ion and pH homeostasis, which is essential for plant development and environmental adaptation, including salt tolerance. Here, 68 CPA genes were identified in soybean, phylogenetically dividing into 11 Na+/H+ exchangers (NHXs), 12 K+ efflux antiporters (KEAs), and 45 cation/H+ exchangers (CHXs). The GmCPA genes are unevenly distributed across the 20 chromosomes and might expand largely due to segmental duplication in soybean. The GmCPA family underwent purifying selection rather than neutral or positive selections. The cis-element analysis and the publicly available transcriptome data indicated that GmCPAs are involved in development and various environmental adaptations, especially for salt tolerance. Based on the RNA-seq data, twelve of the chosen GmCPA genes were confirmed for their differentially expression under salt or osmotic stresses using qRT-PCR. Among them, GmCHX20a was selected due to its high induction under salt stress for the exploration of its biological function on salt responses by ectopic expressing in Arabidopsis. The results suggest that the overexpression of GmCHX20a increases the sensitivity to salt stress by altering the redox system. Overall, this study provides comprehensive insights into the CPA family in soybean and has the potential to supply new candidate genes to develop salt-tolerant soybean varieties.

Identification of the High-Affinity Potassium Transporter Gene Family (HKT) in Brassica U-Triangle Species and Its Potential Roles in Abiotic Stress in Brassica napus L

Members of the high-affinity potassium transporter (HKT) protein family regulate the uptake and homeostasis of sodium and potassium ions, but little research describes their roles in response to abiotic stresses in rapeseed (Brassica napus L.). In this study, we identified and characterized a total of 36 HKT genes from the species comprising the triangle of U model (U-triangle species): B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. We analyzed the phylogenetic relationships, gene structures, motif compositions, and chromosomal distributions of the HKT family members of rapeseed. Based on their phylogenetic relationships and assemblage of functional domains, we classified the HKT members into four subgroups, HKT1;1 to HKT1;4. Analysis of the nonsynonymous substitutions (Ka), synonymous substitutions (Ks), and the Ka/Ks ratios of HKT gene pairs suggested that these genes have experienced strong purifying selective pressure after duplication, with their evolutionary relationships supporting the U-triangle theory. Furthermore, the expression profiles of BnaHKT genes varies among potassium, phytohormone and heavy-metal treatment. Their repression provides resistance to heavy-metal stress, possibly by limiting uptake. Our results systematically reveal the characteristics of HKT family proteins and their encoding genes in six Brassica species and lay a foundation for further exploration of the role of HKT family genes in heavy-metal tolerance.

Genome-Wide Identification and Characterization of the HAK Gene Family in Quinoa (Chenopodium quinoa Willd.) and Their Expression Profiles under Saline and Alkaline Conditions

The high-affinity K+ transporter (HAK) family, the most prominent potassium transporter family in plants, which involves K+ transport, plays crucial roles in plant responses to abiotic stresses. However, the HAK gene family remains to be characterized in quinoa (Chenopodium quinoa Willd.). We explored HAKs in quinoa, identifying 30 members (CqHAK1-CqHAK30) in four clusters phylogenetically. Uneven distribution was observed across 18 chromosomes. Furthermore, we investigated the proteins' evolutionary relationships, physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of the CqHAKs family members. Transcription data analysis showed that CqHAKs have diverse expression patterns among different tissues and in response to abiotic stresses, including drought, heat, low phosphorus, and salt. The expressional changes of CqHAKs in roots were more sensitive in response to abiotic stress than that in shoot apices. Quantitative RT-PCR analysis revealed that under high saline condition, CqHAK1, CqHAK13, CqHAK19, and CqHAK20 were dramatically induced in leaves; under alkaline condition, CqHAK1, CqHAK13, CqHAK19, and CqHAK20 were dramatically induced in leaves, and CqHAK6, CqHAK9, CqHAK13, CqHAK23, and CqHAK29 were significantly induced in roots. Our results establish a foundation for further investigation of the functions of HAKs in quinoa. It is the first study to identify the HAK gene family in quinoa, which provides potential targets for further functional study and contributes to improving the salt and alkali tolerance in quinoa.

Bioinformatic analysis of wheat defensin gene family and function verification of candidate genes

Plant defensins are widely distributed in the leaves, fruits, roots, stems, seeds, and tubers. Research shows that defensin in plants play a significant role in physiological metabolism, growth and development. Plant defensins can kill and suppress a variety of pathogenic bacteria. In this study, we understand the phylogenetic relationships, protein characterization, chromosomal localization, promoter and gene structural features of the TaPDFs family through sequence alignment and conserved protein structural domain analysis. A total of 73 PDF gene members in wheat, 15 PDF genes in maize, and 11 PDF genes in rice were identified. A total of 35, 65, and 34 PDF gene members were identified in the genomes of Ae. tauschii, T. urartu, and T. dicoccoides, respectively. TaPDF4.9 and TaPDF2.15 were constructed into pART27 vector with YFP by homologous recombination for subcellular localization analysis. Subcellular localization results showed that TaPDF4.9 and TaPDF2.15 were basically located in the cell membrane and cytoplasm, and TaPDF4.9 was also located in the nucleus. TaPDF4.9 and TaPDF2.15 could inhibit the infection of Phytophthora infestans strain '88069'. The results suggest that TaPDFs may be able to improve disease resistance. The study of wheat defensins will be beneficial for improving wheat yield and provides a theoretical basis for research on resistance to wheat diseases.

Xylem K+ loading modulates K+ and Cs+ absorption and distribution in Arabidopsis under K+-limited conditions

Potassium (K+) is an essential macronutrient for plant growth. The transcriptional regulation of K+ transporter genes is one of the key mechanisms by which plants respond to K+ deficiency. Among the HAK/KUP/KT transporter family, HAK5, a high-affinity K+ transporter, is essential for root K+ uptake under low external K+ conditions. HAK5 expression in the root is highly induced by low external K+ concentration. While the molecular mechanisms of HAK5 regulation have been extensively studied, it remains unclear how plants sense and coordinates K+ uptake and translocation in response to changing environmental conditions. Using skor mutants, which have a defect in root-to-shoot K+ translocation, we have been able to determine how the internal K+ status affects the expression of HAK5. In skor mutant roots, under K+ deficiency, HAK5 expression was lower than in wild-type although the K+ concentration in roots was not significantly different. These results reveal that HAK5 is not only regulated by external K+ conditions but it is also regulated by internal K+ levels, which is in agreement with recent findings. Additionally, HAK5 plays a major role in the uptake of Cs+ in roots. Therefore, studying Cs+ in roots and having more detailed information about its uptake and translocation in the plant would be valuable. Radioactive tracing experiments revealed not only a reduction in the uptake of 137Cs+ and 42K+in skor mutants compared to wild-type but also a different distribution of 137Cs+ and 42K+ in tissues. In order to gain insight into the translocation, accumulation, and repartitioning of both K+ and Cs+ in plants, long-term treatment and split root experiments were conducted with the stable isotopes 133Cs+ and 85Rb+. Finally, our findings show that the K+ distribution in plant tissues regulates root uptake of K+ and Cs+ similarly, depending on HAK5; however, the translocation and accumulation of the two elements are different.

Function identification and characterization of Oryza sativa ZRT and IRT-like proteins computationally for nutrition and biofortification in rice

Zinc plays a very critical role and function in all organisms. Its deficiency can cause a serious issue. In Oryza sativa, the ZRT/IRT transporter-like proteins play a role in the zinc metal uptake and transport. Few OsZIPs genes have been validated and characterized for their biological functions and most of OsZIPs are not well physiologically, biochemically and phenotypically characterized. In the current study, they analyzed for their function through subcellular localization, phylogenetic analysis, homology modeling, expression analysis, protein-protein interaction (PPI) network prediction, and prediction of their binding sites. Hierarchical clustering of OsZIP genes based on different anatomical parts and developmental stages also orthologs prediction was identified. The presence of SNPs, SSRs, ESTs, FSTs, MPSS, and SAGE tags were analyzed for useful development of markers. SNPs were identified in all OsZIPs genes and each gene was further classified based on their number and position in the 3'UTR and 5'UTR regions of the gene-specific sequences. Binding clusters and their location on the protein sequences were predicted. We found Changing in residues number and position which were due to partial overlapping and sequence alignment, but they share the same mechanism of binding and transporting Zinc. A wide range of CRISPR Cas9 gRNAs was designed based on single nucleotide polymorphism (SNP) for each OsZIP transporter gene for well-function identification and characterization with genome-wide association studies. Hence this study would provide useful information, understanding, and predicting molecular insights for the future studies that will help for improvement of nutritional quality of rice varieties.Communicated by Ramaswamy H. Sarma.

Plastid KEA-type cation/H+ antiporters are required for vacuolar protein trafficking in Arabidopsis

Arabidopsis plastid antiporters KEA1 and KEA2 are critical for plastid development, photosynthetic efficiency, and plant development. Here, we show that KEA1 and KEA2 are involved in vacuolar protein trafficking. Genetic analyses found that the kea1 kea2 mutants had short siliques, small seeds, and short seedlings. Molecular and biochemical assays showed that seed storage proteins were missorted out of the cell and the precursor proteins were accumulated in kea1 kea2. Protein storage vacuoles (PSVs) were smaller in kea1 kea2. Further analyses showed that endosomal trafficking in kea1 kea2 was compromised. Vacuolar sorting receptor 1 (VSR1) subcellular localizations, VSR-cargo interactions, and p24 distribution on the endoplasmic reticulum (ER) and Golgi apparatus were affected in kea1 kea2. Moreover, plastid stromule growth was reduced and plastid association with the endomembrane compartments was disrupted in kea1 kea2. Stromule growth was regulated by the cellular pH and K+ homeostasis maintained by KEA1 and KEA2. The organellar pH along the trafficking pathway was altered in kea1 kea2. Overall, KEA1 and KEA2 regulate vacuolar trafficking by controlling the function of plastid stromules via adjusting pH and K+ homeostasis.

Genome-Wide Exploration and Expression Analysis of the CNGC Gene Family in Eggplant (Solanum melongena L.) under Cold Stress, with Functional Characterization of SmCNGC1a

Eggplant (Solanum melongena L.) is an important economic crop, and to date, there has been no genome-wide identification and analysis of the cyclic nucleotide-gated channel (CNGC) gene family in eggplant. In this study, we identified the CNGC gene family in eggplant, and the results showed that 29 SmCNGC genes were classified into five groups, unevenly distributed across the 12 chromosomes of eggplant. The gene structure and motif analysis indicated that the SmCNGC family proteins may exhibit apparent preferences during evolution. Furthermore, our study revealed the presence of numerous light-responsive elements, hormone-responsive elements, and transcription factor binding sites in the promoter regions of SmCNGC genes, suggesting their significant role in environmental adaptability regulation. Finally, we analyzed the expression patterns of all SmCNGC genes under cold stress and found that SmCNGC1a was significantly upregulated under cold stress. Subcellular localization experiments indicated that this gene is located on the plasma membrane. Subsequently, its importance in the low-temperature response of eggplant was validated through virus-induced gene silencing (VIGS), and its protein interactome was predicted. In summary, our study provides a comprehensive understanding of the function and regulatory mechanisms of the CNGC gene family in eggplant, laying an important foundation for further research on cold adaptation in eggplant.

Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus

BACKGROUND

Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown.

METHODS

Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses.

RESULTS

Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency.

CONCLUSIONS

Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.

Halotolerance mechanisms in salt‑tolerant cyanobacteria

Cyanobacteria are ubiquitously distributed in nature and are the most abundant photoautotrophs on Earth. Their long evolutionary history reveals that cyanobacteria have a remarkable capacity and strong adaptive tendencies to thrive in a variety of conditions. Thus, they can survive successfully, especially in harsh environmental conditions such as salty environments, high radiation, or extreme temperatures. Among others, salt stress because of excessive salt accumulation in salty environments, is the most common abiotic stress in nature and hampers agricultural growth and productivity worldwide. These detrimental effects point to the importance of understanding the molecular mechanisms underlying the salt stress response. While it is generally accepted that the stress response mechanism is a complex network, fewer efforts have been made to represent it as a network. Substantial evidence revealed that salt-tolerant cyanobacteria have evolved genomic specific mechanisms and high adaptability in response to environmental changes. For example, extended gene families and/or clusters of genes encoding proteins involved in the adaptation to high salinity have been collectively reported. This chapter focuses on recent advances and provides an overview of the molecular basis of halotolerance mechanisms in salt‑tolerant cyanobacteria as well as multiple regulatory pathways. We elaborate on the major protective mechanisms, molecular mechanisms associated with halotolerance, and the global transcriptional landscape to provide a gateway to uncover gene regulation principles. Both knowledge and omics approaches are utilized in this chapter to decipher the mechanistic insights into halotolerance. Collectively, this chapter would have a profound impact on providing a comprehensive understanding of halotolerance in salt‑tolerant cyanobacteria.

Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed (Brassica napus L.)

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs-BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS-have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.

Silencing of PpNRAMP5 improves manganese toxicity tolerance in peach (Prunus persica) seedlings

The natural resistance-associated macrophage protein (NRAMP) gene family assists in the transport of metal ions in plants. However, the role and underlying physiological mechanism of NRAMP genes under heavy metal toxicity in perennial trees remain to be elucidated. In Prunus persica, five NRAMP family genes were identified and named according to their predicted phylogenetic relationships. The expression profiling analysis indicated that PpNRAMPs were significantly induced by excess manganese (Mn), iron, zinc, and cadmium treatments, suggesting their potential role in heavy metal uptake and transportation. Notably, the expression of PpNRAMP5 was tremendously increased under Mn toxicity stress. Heterologous expression of PpNRAMP5 in yeast cells also confirmed Mn transport. Suppression of PpNRAMP5 through virus-induced gene silencing enhanced Mn tolerance, which was compromised when PpNRAMP5 was overexpressed in peach. The silencing of PpNRAMP5 mitigated Mn toxicity by dramatically reducing Mn contents in roots, and effectively reduced the chlorophyll degradation and improved the photosynthetic apparatus under Mn toxicity stress. Therefore, PpNRAMP5-silenced plants were less damaged by oxidative stress, as signified by lowered H₂O₂ contents and O₂^•- staining intensity, also altered the reactive oxygen species (ROS) homeostasis by activating enzymatic antioxidants. Consistently, these physiological changes showed an opposite trend in the PpNRAMP5-overexpressed peach plants. Altogether, our findings suggest that downregulation of PpNRAMP5 markedly reduces the uptake and transportation of Mn, thus activating enzymatic antioxidants to strengthen ROS scavenging capacity and photosynthesis activity, thereby mitigating Mn toxicity in peach plants.

Yeast Heterologous Expression Systems for the Study of Plant Membrane Proteins

Researchers are often interested in proteins that are present in cells in small ratios compared to the total amount of proteins. These proteins include transcription factors, hormones and specific membrane proteins. However, sufficient amounts of well-purified protein preparations are required for functional and structural studies of these proteins, including the creation of artificial proteoliposomes and the growth of protein 2D and 3D crystals. This aim can be achieved by the expression of the target protein in a heterologous system. This review describes the applications of yeast heterologous expression systems in studies of plant membrane proteins. An initial brief description introduces the widely used heterologous expression systems of the baker's yeast Saccharomyces cerevisiae and the methylotrophic yeast Pichia pastoris. S. cerevisiae is further considered a convenient model system for functional studies of heterologously expressed proteins, while P. pastoris has the advantage of using these yeast cells as factories for producing large quantities of proteins of interest. The application of both expression systems is described for functional and structural studies of membrane proteins from plants, namely, K⁺- and Na⁺-transporters, various ATPases and anion transporters, and other transport proteins.

The Sweet Potato K+ Transporter IbHAK11 Regulates K+ Deficiency and High Salinity Stress Tolerance by Maintaining Positive Ion Homeostasis

The K⁺ transporter KT/HAK/KUP (K⁺ transporter/high-affinity K⁺/K⁺ uptake) family has a critical effect on K⁺ uptake and translocation in plants under different environmental conditions. However, the functional analysis of KT/HAK/KUP members in sweet potatoes is still limited. The present work reported the physiological activity of a new gene, IbHAK11, in the KT/HAK/KUP family in sweet potatoes. IbHAK11 expression increased significantly in the low K⁺-tolerant line compared with the low K⁺-sensitive line following treatment with low K⁺ concentrations. IbHAK11 upregulation promoted root growth in Arabidopsis under low K⁺ conditions. Under high saline stress, transgenic lines had superior growth and photosynthetic characteristics compared with the wild-type (WT). As for IbHAK11-overexpressing plants, activation of both the non-enzymatic and enzymatic reactive oxygen species (ROS) scavenging systems was observed. Therefore, IbHAK11-overexpressing plants had lower malondialdehyde (MDA) and ROS levels (including H₂O₂ and O^2-) compared with WT under salt-induced stress. We also found that under both low K⁺ and high salinity conditions, overexpression of IbHAK11 enhanced K⁺ translocation from the root to the shoot and decreased Na⁺ absorption in Arabidopsis. Consequently, IbHAK11 positively regulated K⁺ deficiency and high salinity stresses by regulating K⁺ translocation and Na⁺ uptake, thus maintaining K⁺/Na⁺ homeostasis in plants.

Identification and Characterization of Dmct: A Cation Transporter in Yarrowia lipolytica Involved in Metal Tolerance

Yarrowia lipolytica is a dimorphic fungus used as a model organism to investigate diverse biotechnological and biological processes, such as cell differentiation, heterologous protein production, and bioremediation strategies. However, little is known about the biological processes responsible for cation concentration homeostasis. Metals play pivotal roles in critical biochemical processes, and some are toxic at unbalanced intracellular concentrations. Membrane transport proteins control intracellular cation concentrations. Analysis of the Y. lipolytica genome revealed a characteristic functional domain of the cation efflux protein family, i.e., YALI0F19734g, which encodes YALI0F19734p (a putative Yl-Dmct protein), which is related to divalent metal cation tolerance. We report the in silico analysis of the putative Yl-Dmct protein's characteristics and the phenotypic response to divalent cations (Ca²⁺, Cu²⁺, Fe²⁺, and Zn²⁺) in the presence of mutant strains, Δdmct and Rdmct, constructed by deletion and reinsertion of the DMCT gene, respectively. The absence of the Yl-Dmct protein induces cellular and growth rate changes, as well as dimorphism differences, when calcium, copper, iron, and zinc are added to the cultured medium. Interestingly, the parental and mutant strains were able to internalize the ions. Our results suggest that the protein encoded by the DMCT gene is involved in cell development and cation homeostasis in Y. lipolytica.

Physiological and molecular mechanisms of medicinal plants in response to cadmium stress: Current status and future perspective

Medicinal plants have a wide range of uses worldwide. However, the quality of medicinal plants is affected by severe cadmium pollution. Cadmium can reduce photosynthetic capacity, lead to plant growth retardation and oxidative stress, and affect secondary metabolism. Medicinal plants have complex mechanisms to cope with cadmium stress. On the one hand, an antioxidant system can effectively scavenge excess reactive oxygen species produced by cadmium stress. On the other hand, cadmium chelates are formed by chelating peptides and then sequestered through vacuolar compartmentalization. Cadmium has no specific transporter in plants and is generally transferred to plant tissues through competition for the transporters of divalent metal ions, such as zinc, iron, and manganese. In recent years, progress has been achieved in exploring the physiological mechanisms by which medicinal plants responding to cadmium stress. The exogenous regulation of cadmium accumulation in medicinal plants has been studied, and the aim is reducing the toxicity of cadmium. However, research into molecular mechanisms is still lagging. In this paper, we review the physiological and molecular mechanisms and regulatory networks of medicinal plants exposed to cadmium, providing a reference for the study on the responses of medicinal plants to cadmium stress.

Considerations in production of the prokaryotic ZIP family transporters for structural and functional studies

Zinc ions play essential roles as components of enzymes and many other important biomolecules, and are associated with numerous diseases. The uptake of Zn2+ and other metal ions require a widely distributed transporter protein family called Zrt/Irt-like Proteins (ZIP family), the majority members of which tend to have eight transmembrane helices with both N- and C- termini located on the extracellular or periplasmic side. Their small sizes and dynamic conformations bring many difficulties in their production for structural studies either by crystallography or Cryo-EM. Here, we summarize the problems that may encounter at the various steps of processing the ZIP proteins from gene to structural and functional studies, and provide some solutions and examples from our and other labs for the cloning, expression, purification, stability screening, metal ion transport assays and structural studies of prokaryotic ZIP family transporters using Escherichia coli as a heterologous host.

A novel mutant allele of AtCNGC15 reveals a dual function of nuclear calcium release in the root meristem

Calcium release to the nucleoplasm of root meristem cells was demonstrated to modulate root development. The calcium channel encoded by cyclic nucleotide-gated channel (CNGC) 15 localizes at the nuclear envelope in young Arabidopsis seedlings. In contrast, at later stages of root growth, overexpression analysis showed that AtCNGC15 can relocalize to the plasma membrane to mediate primary nitrate-induced gene expression. This raises the question as to whether nuclear localized AtCNGC15 is required for root apical meristem development in young Arabidopsis seedlings, and whether nitrate signalling occurs independently of nuclear localized AtCNGC15 at this developmental stage. In this study, we characterize a novel mutant allele of AtCNGC15 and demonstrate that the mutation of a highly conserved aspartic acid in the C-linker domain is sufficient to impair the gating of AtCNCG15. We demonstrate that AtCNGC15 mediates the nuclear calcium release that modulates root apical meristem development and nitrate-induced LBD39 expression. We also show that, in the presence of nitrate, the relocalization of AtCNGC15 at the plasma membrane occurs specifically in the columella cells. Our results further suggest that the induction of LBD37, LBD38, and LBD39 in the presence of nitrate is modulated by different inputs of cytoplasmic or nuclear calcium release.

Systematic Analysis of NRAMP Family Genes in Areca catechu and Its Response to Zn/Fe Deficiency Stress

Areca catechu is a commercially important medicinal plant widely cultivated in tropical regions. The natural resistance-associated macrophage protein (NRAMP) is widespread in plants and plays critical roles in transporting metal ions, plant growth, and development. However, the information on NRAMPs in A. catechu is quite limited. In this study, we identified 12 NRAMPs genes in the areca genome, which were classified into five groups by phylogenetic analysis. Subcellular localization analysis reveals that, except for NRAMP2, NRAMP3, and NRAMP11, which are localized in chloroplasts, all other NRAMPs are localized on the plasma membrane. Genomic distribution analysis shows that 12 NRAMPs genes are unevenly spread on seven chromosomes. Sequence analysis shows that motif 1 and motif 6 are highly conserved motifs in 12 NRAMPs. Synteny analysis provided deep insight into the evolutionary characteristics of AcNRAMP genes. Among the A. catechu and the other three representative species, we identified a total of 19 syntenic gene pairs. Analysis of Ka/Ks values indicates that AcNRAMP genes are subjected to purifying selection in the evolutionary process. Analysis of cis-acting elements reveals that AcNRAMP genes promoter sequences contain light-responsive elements, defense- and stress-responsive elements, and plant growth/development-responsive elements. Expression profiling confirms distinct expression patterns of AcNRAMP genes in different organs and responses to Zn/Fe deficiency stress in leaves and roots. Taken together, our results lay a foundation for further exploration of the AcNRAMPs regulatory function in areca response to Fe and Zn deficiency.

The captivating role of calcium in plant-microbe interaction

Plant immune response is fascinating due to the complete absence of a humoral system. The adaptive immune response in plants relies on the intracellular orchestration of signalling molecules or intermediates associated with transcriptional reprogramming. Plant disease response phenomena largely depend on pathogen recognition, signal perception, and intracellular signal transduction. The pathogens possess specific pathogen-associated molecular patterns (PAMP) or microbe-associated molecular patterns (MAMP), which are first identified by pattern recognition receptors (PRRs) of host plants for successful infection. After successful pathogen recognition, the defence response is initiated within plants. The first line of non-specific defence response is called PAMP-triggered immunity (PTI), followed by the specific robust signalling is called effector-triggered immunity (ETI). Calcium plays a crucial role in both PTI and ETI. The biphasic induction of reactive oxygen species (ROS) is inevitable in any plant-microbe interaction. Calcium ions play crucial roles in the initial oxidative burst and ROS induction. Different pathogens can induce calcium accumulation in the cytosol ([Ca²⁺]_Cyt), called calcium signatures. These calcium signatures further control the diverse defence-responsive proteins in the intracellular milieu. These calcium signatures then activate calcium-dependent protein kinases (CDPKs), calcium calmodulins (CaMs), calcineurin B-like proteins (CBLs), etc., to impart intricate defence signalling within the cell. Decoding this calcium ionic map is imperative to unveil any plant microbe interplay and modulate defence-responsive pathways. Hence, the present review is unique in developing concepts of calcium signature in plants and their subsequent decoding mechanism. This review also intends to articulate early sensing of calcium oscillation, signalling events, and comprehensive mechanistic roles of calcium within plants during pathogenic ingression. This will accumulate and summarize the exciting roles of calcium ions in plant immunity and provide the foundation for future research.

Novel biofortification candidate: MTP1 increases microelement contents and decreases toxic heavy metal accumulation in grains

Decreases in microelement contents and increases in toxic element levels seriously affect crop growth and human health. Thus, improving the elemental content of food crops is an important environmental issue for enhancing crop production and quality. Previous research showed that metal tolerance protein 1 (MTP1) is localized at the vacuole membrane, wherein it mediates the translocation of heavy metal ions. Therefore, LmMTP1 was isolated from annual ryegrass (Lolium multiflorum). Real-time quantitative PCR analyses revealed LmMTP1 expression increased significantly in the roots after Zn, Co, and Cd treatments. Confocal microscopy images indicated LmMTP1 was localized at the vacuole membrane. The expression of LmMTP1 in transgenic yeast and rice resulted in increased Zn, Co, and Cd tolerance. The examination of heavy metal contents detected increases in the Zn and Co contents, but decreases in the Cd contents, of yeast and rice. Moreover, the grains of LmMTP1-expressing transgenic rice had higher Zn/Co contents and lower Cd contents than wild-type rice grains. These results imply that LmMTP1 influences Zn, Co, and Cd tolerance and accumulation. Furthermore, LmMTP1 might be a novel biofortification-related candidate gene useful for improving the storage of essential elements and eliminating toxic heavy metals from crops.

A non-K+-solubilizing PGPB (Bacillus megaterium) increased K+ deprivation tolerance in Oryza sativa seedlings by up-regulating root K+ transporters

Potassium is one of the principal macronutrients required by all plants, but its mobility is restricted between soil compartments. Numerous studies have shown that Plant Growth Promoting Bacteria (PGPB) can facilitate nutrient uptake. The present work examined the effects of the PGPB (Bacillus megaterium) on rice plants subjected to potassium deprivation. To study only direct effects of B. megaterium, we first checked its lack of capacity to solubilize soil K. Rice plants were provided with 1.5 mM K (100%) or 0.015 mM K (1%) and growth related parameters, nutrient concentrations and gene expression of K⁺ transporters were determined. After two weeks, the 1% K treatment reduced growth of non-inoculated plants by about 50% compared with the 100% K treatment. However, there was no effect of reduced K nutrition on growth of inoculated plants. The reduction in growth in non-inoculated plants was accompanied by a similar reduction in K⁺ concentration in both roots and leaves and an overall 80% reduction of the plant potassium concentrations. In inoculated plants a 50% reduction occurred only in leaves. The expression of the K⁺ transporters HKT1;1, 1;2, 1;5, 2;2, 2;3 and 2;4 was up-regulated by the inoculation of B. megaterium under K deprivation conditions, explaining their higher K tissue concentrations and growth. Thus, the bacterial strain improved plant potassium nutrition without affecting K⁺ availability in the soil. The results demonstrate the potential of this bacteria for using as a biofertilizer to reduce the amount of potassium fertilizers to be applied in the field.

Phenotypes of cyclic nucleotide-gated cation channel mutants: probing the nature of native channels

Plant cyclic nucleotide gated channels (CNGCs) facilitate cytosolic Ca²⁺ influx as an early step in numerous signaling cascades. CNGC-mediated Ca²⁺ elevations are essential for plant immune defense and high temperature thermosensing. In the present study, we evaluated phenotypes of CNGC2, CNGC4, CNGC6, and CNGC12 null mutants in these two pathways. It is shown CNGC2, CNGC4, and CNGC6 physically interact in vivo, whereas CNGC12 does not. CNGC involvement in immune signaling was evaluated by monitoring mutant response to elicitor peptide Pep3. Pep3 response cascades involving CNGCs included mitogen-activated kinase activation mediated by Ca²⁺ -dependent protein kinase phosphorylation. Pep3-induced reactive oxygen species generation was impaired in cngc2, cngc4, and cngc6, but not in cngc12, suggesting that CNGC2, CNGC4, and CNGC6 (which physically interact) may be components of a multimeric CNGC channel complex for immune signaling. However, unlike cngc2 and cngc4, cngc6 is not sensitive to high Ca²⁺ and displays no pleiotropic dwarfism. All four cngc mutants showed thermotolerance compared to wild-type, although CNGC12 does not interact with the other three CNGCs. These results imply that physically interacting CNGCs may, in some cases, function in a signaling cascade as components of a heteromeric channel complex, although this may not be the case in other signaling pathways.

Zinc/iron-regulated transporter-like protein gene family in Theobroma cacao L: Characteristics, evolution, function and 3D structure analysis

The zinc/iron-regulated transporter-like protein (ZIP) gene family first identified in plants is highly distributed in the plant kingdom. This family has previously been reported to transport several essential and non-essential cationic elements, including those toxic to many economically important crops such as cacao (Theobroma cacao L.). In this article, we present a detailed study on physicochemical properties, evolution, duplication, gene structure, promoter region and TcZIP family three-dimensional protein structure. A total of 11 TcZIP genes have been identified to encode proteins from 309 to 435 aa, with localization in the plasma membrane and chloroplast, containing 6-9 putative domains (TM). Interspecies phylogenetic analysis subdivided the ZIP proteins into four groups. Segmental duplication events significantly contributed to the expansion of TcZIP genes. These genes underwent high pressure of purifying selection. The three-dimensional structure of the proteins showed that α helix conformations are predominant with several pocket sites, containing the metal binding site, with the residues leucine (LEU), alanine (ALA), glycine (GLY), serine (SER), lysine (LYS) and histidine (HIS) the most predicted. Regarding the analysis of the protein-protein interaction and enrichment of the gene ontology, four biological processes were assigned, the most important being the cation transport. These new discoveries expand the knowledge about the function, evolution, protein structures and interaction of ZIP family proteins in cacao and contribute to develop cacao genotypes enriched with important mineral nutrients as well as genotypes that bioaccumulate or exclude toxic metals.

Genome-Wide Identification, Characterization and Experimental Expression Analysis of CNGC Gene Family in Gossypium

Cyclic nucleotide-gated ion channels (CNGCs) are channel proteins for calcium ions, and have been reported to play important roles in regulating survival and environmental response of various plants. However, little is known about how the CNGC family works in Gossypium. In this study, 173 CNGC genes, which were identified from two diploid and five tetraploid Gossypium species, were classified into four groups by phylogenetic analysis. The collinearity results demonstrated that CNGC genes are integrally conservative among Gossypium species, but four gene losses and three simple translocations were detected, which is beneficial to analyzing the evolution of CNGCs in Gossypium. The various cis-acting regulatory elements in the CNGCs' upstream sequences revealed their possible functions in responding to multiple stimuli such as hormonal changes and abiotic stresses. In addition, expression levels of 14 CNGC genes changed significantly after being treated with various hormones. The findings in this study will contribute to understanding the function of the CNGC family in cotton, and lay a foundation for unraveling the molecular mechanism of cotton plants' response to hormonal changes.

Comparative Transcriptome Profiling Reveals Key MicroRNAs and Regulatory Mechanisms for Aluminum Tolerance in Olive

Aluminum toxicity (Al) is one of the major constraints to crop production in acidic soils. MicroRNAs (miRNAs) have emerged as key regulatory molecules at post-transcriptional levels, playing crucial roles in modulating various stress responses in plants. However, miRNAs and their target genes conferring Al tolerance are poorly studied in olive (Olea europaea L.). Here, genome-wide expression changes in miRNAs of the roots from two contrasting olive genotypes Zhonglan (ZL, Al-tolerant) and Frantoio selezione (FS, Al-sensitive) were investigated by high-throughput sequencing approaches. A total of 352 miRNAs were discovered in our dataset, consisting of 196 conserved miRNAs and 156 novel miRNAs. Comparative analyses showed 11 miRNAs have significantly different expression patterns in response to Al stress between ZL and FS. In silico prediction identified 10 putative target gene of these miRNAs, including MYB transcription factors, homeobox-leucine zipper (HD-Zip) proteins, auxin response factors (ARF), ATP-binding cassette (ABC) transporters and potassium efflux antiporter. Further functional classification and enrichment analysis revealed these Al-tolerance associated miRNA-mRNA pairs are mainly involved in transcriptional regulation, hormone signaling, transportation and metabolism. These findings provide new information and perspectives into the regulatory roles of miRNAs and their target for enhancing Al tolerance in olives.

Exogenous brassinosteroid alleviates calcium deficiency induced tip-burn by regulating calcium transport in Brassica rapa L. ssp. pekinensis

Mini Chinese cabbage (Brassica rapa L. ssp. Pekinensis) plays an important role in the supply of summer vegetables on the plateau in western China. In recent years, tip-burn has seriously affected the yield, quality and commodity value of mini Chinese cabbage. Calcium (Ca²⁺) deficiency is a key inducer of tip-burn. As a new type plant hormone, brassinolide (BR) is involved in regulating a variety of biotic and abiotic stresses. To explore the alleviation role of BR in tip-burn caused by Ca²⁺ deficiency, a hydroponic experiment was conducted to study the relationship between BR and Ca²⁺ absorption and transport. The results showed that foliar spraying with 0.5 µM BR significantly reduced tip-burn incidence rate and disease index of mini Chinese cabbage caused by Ca²⁺ deficiency. Moreover, the dynamic monitoring results of tip-burn incidence rate showed that the value reached the highest on the ninth day after treatment. BR promoted the Ca²⁺ transport from roots to shoots and from outer leaves to inner leaves by increasing the activities of Ca²⁺-ATPase and H⁺-ATPase as well as the total ATP content, which provided power for Ca²⁺ transport. In addition, exogenous BR upregulated the relative expression levels of BrACA4, BrACA11, BrECA1, BrECA3, BrECA4, BrCAX1, BrCAS and BrCRT2, whereas Ca²⁺ deficiency induced down-regulation. In conclusion, exogenous BR can alleviate the Ca²⁺-deficiency induced tip-burn of mini Chinese cabbage by promoting the transport and distribution of Ca²⁺.

Potassium nutrient status drives posttranslational regulation of a low-K response network in Arabidopsis

Under low-potassium (K+) stress, a Ca2+ signaling network consisting of calcineurin B-like proteins (CBLs) and CBL-interacting kinases (CIPKs) play essential roles. Specifically, the plasma membrane CBL1/9-CIPK pathway and the tonoplast CBL2/3-CIPK pathway promotes K+ uptake and remobilization, respectively, by activating a series of K+ channels. While the dual CBL-CIPK pathways enable plants to cope with low-K+ stress, little is known about the early events that link external K+ levels to the CBL-CIPK proteins. Here we show that K+ status regulates the protein abundance and phosphorylation of the CBL-CIPK-channel modules. Further analysis revealed low K+-induced activation of VM-CBL2/3 happened earlier and was required for full activation of PM-CBL1/9 pathway. Moreover, we identified CIPK9/23 kinases to be responsible for phosphorylation of CBL1/9/2/3 in plant response to low-K+ stress and the HAB1/ABI1/ABI2/PP2CA phosphatases to be responsible for CBL2/3-CIPK9 dephosphorylation upon K+-repletion. Further genetic analysis showed that HAB1/ABI1/ABI2/PP2CA phosphatases are negative regulators for plant growth under low-K+, countering the CBL-CIPK network in plant response and adaptation to low-K+ stress.

Advanced biotechnological strategies towards the development of crops with enhanced micronutrient content

Micronutrients are essential mineral elements required for both plant and human development.An integrated system involving soil, climatic conditions, and types of crop plants determines the level of micronutrient acquisition and utilization. Most of the staple food crops consumed globally predominantly include the cereal grains, tubers and roots, respectively and in many cases, particularly in the resource-poor countries they are grown in nutrient-deficient soils. These situations frequently lead to micronutrient deficiency in crops. Moreover, crop plants with micronutrient deficiency also show high level of susceptibility to various abiotic and biotic stress factors. Apart from this, climate change and soil pollution severely affect the accumulation of micronutrients, such as zinc (Zn), iron (Fe), selenium (Se), manganese (Mn), and copper (Cu) in food crops. Therefore, overcoming the issue of micronutrient deficiency in staple crops and to achieve the adequate level of food production with enriched nutrient value is one of the major global challenges at present. Conventional breeding approaches are not adequate to feed the increasing global population with nutrient-rich staple food crops. To address these issues, alongside traditional approaches, genetic modification strategies have been adopted during the past couple of years in order to enhance the transport, production, enrichment and bioavailability of micronutrients in staple crops. Recent advances in agricultural biotechnology and genome editing approaches have shown promising response in the development of micronutrient enriched biofortified crops. This review highlights the current advancement of our knowledge on the possible implications of various biotechnological tools for the enrichment and enhancement of bioavailability of micronutrients in crops.

Genome-Wide Identification and Expression Analysis Reveals Roles of the NRAMP Gene Family in Iron/Cadmium Interactions in Peanut

The natural resistance-associated macrophage protein (NRAMP) family plays crucial roles in metal uptake and transport in plants. However, little is known about their functions in peanut. To understand the roles of AhNRAMP genes in iron/cadmium interactions in peanut, genome-wide identification and bioinformatics analysis was performed. A total of 15 AhNRAMP genes were identified from the peanut genome, including seven gene pairs derived from whole-genome duplication and a segmental duplicated gene. AhNRAMP proteins were divided into two distinct subfamilies. Subfamily I contains eight acid proteins with a specific conserved motif 7, which were predicted to localize in the vacuole membrane, while subfamily II includes seven basic proteins sharing specific conserved motif 10, which were localized to the plasma membrane. Subfamily I genes contained four exons, while subfamily II had 13 exons. AhNRAMP proteins are perfectly modeled on the 5m94.1.A template, suggesting a role in metal transport. Most AhNRAMP genes are preferentially expressed in roots, stamens, or developing seeds. In roots, the expression of most AhNRAMPs is induced by iron deficiency and positively correlated with cadmium accumulation, indicating crucial roles in iron/cadmium interactions. The findings provide essential information to understand the functions of AhNRAMPs in the iron/cadmium interactions in peanuts.

Two Trk/Ktr/HKT-type potassium transporters, TrkG and TrkH, perform distinct functions in Escherichia coli K-12

Escherichia coli K-12 possesses two versions of Trk/Ktr/HKT-type potassium ion (K⁺) transporters, TrkG and TrkH. The current paradigm is that TrkG and TrkH have largely identical characteristics, and little information is available regarding their functional differences. Here, we show using cation uptake experiments with K⁺ transporter knockout mutants that TrkG and TrkH have distinct ion transport activities and physiological roles. K⁺-transport by TrkG required Na⁺, whereas TrkH-mediated K⁺ uptake was not affected by Na⁺. An aspartic acid located five residues away from a critical glycine in the third pore-forming region might be involved in regulation of Na⁺-dependent activation of TrkG. In addition, we found that TrkG but not TrkH had Na⁺ uptake activity. Our analysis of K⁺ transport mutants revealed that TrkH supported cell growth more than TrkG; however, TrkG was able to complement loss of TrkH-mediated K⁺ uptake in E. coli. Furthermore, we determined that transcription of trkG in E. coli was downregulated but not completely silenced by the xenogeneic silencing factor H-NS (histone-like nucleoid structuring protein or heat-stable nucleoid-structuring protein). Taken together, the transport function of TrkG is clearly distinct from that of TrkH, and TrkG seems to have been accepted by E. coli during evolution as a K⁺ uptake system that coexists with TrkH.