Cellular ion homeostasis: emerging roles of intracellular NHX Na+/H+ antiporters in plant growth and development

The potential of Burkholderia gladioli KRS027 in plant growth promotion and biocontrol against Verticillium dahliae revealed by dual transcriptome of pathogen and host

Verticillium dahliae is a destructive, soil-borne pathogen that causes significant losses on numerous important dicots. Recently, beneficial microbes inhabiting the rhizosphere have been exploited and used to control plant diseases. In the present study, Burkholderia gladioli KRS027 demonstrated excellent inhibitory effects against Verticillium wilt in cotton seedlings. Plant growth and development was promoted by affecting the biosynthesis and signaling pathways of brassinosteroids (BRs), gibberellins (GAs), and auxins, consequently promoting stem elongation, shoot apical meristem, and root apical tissue division in cotton. Furthermore, based on the host transcriptional response to V. dahliae infection, it was found that KRS027 modulates the plants to maintain cell homeostasis and respond to other pathogen stress. Moreover, KRS027 induced disruption of V. dahliae cellular structures, as evidenced by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses. Based on the comparative transcriptomic analysis between KRS027 treated and control group of V. dahliae, KRS027 induced substantial alterations in the transcriptome, particularly affecting genes encoding secreted proteins, small cysteine-rich proteins (SCRPs), and protein kinases. In addition, KRS027 suppressed the growth of different clonal lineages of V. dahliae strains through metabolites, and volatile organic compounds (VOCs) released by KRS027 inhibited melanin biosynthesis and microsclerotia development. These findings provide valuable insights into an alternative biocontrol strategy for Verticillium wilt, demonstrating that the antagonistic bacterium KRS027 holds promise as a biocontrol agent for promoting plant growth and managing disease occurrence.

Genome-wide identification and drought stress-induced expression analysis of the NHX gene family in potato

NHX proteins are transmembrane antiporters belonging to the cation/proton antiporter gene family, with a conserved Na+ (K+)/H+ exchange (PF00999) protein domain. NHXs play a prominent role in plant growth, development, and defense. However, the role of NHX gene family in potato (Solanum tuberosum L.) is yet to be known. In this study, we conducted a genome-wide analysis of the potato NHX gene family. A total of 25 StNHX family members were identified to be unevenly distributed on 10 chromosomes. The proteins ranged in length from 252 to 1,153 amino acids, with molecular masses ranging from 27516.32 to 127860.87 kD, and isoelectric points (pI) ranging from 4.96 to 9.3. Analyses of gene structures and conserved motifs indicated that StNHX genes in the same phylogenetic cluster are conserved. Phylogenetic analysis divided the StNHX genes into three subfamilies (Classes I, II, and III). Synteny analysis indicated that StNHX gene family Class III of NHX and all Arabidopsis thaliana NHXs shared a close evolutionary relationship. Analysis of cis-acting elements in the upstream 1,500 bp promoter region of potato NHX genes showed that these genes could be regulated by light, stress, and hormones such as abscisic acid and gibberellic acid. Protein-protein interaction network analysis indicated that StNHX proteins may participate in the regulation of potato growth and stress response. Besides, To determine a potential role of these genes in tissue development and drought response, we analyzed the RNA-seq data of different DM potato tissues. The results showed that NHX genes exhibited distinct tissue-specific expression patterns. We further examined the expression patterns of StNHX in different tissues (leaves, roots, shoots, tubers, stolons, and flowers) during the flowering stage in 'Jizhangshu NO.8.' potato. The qRT-PCR results further confirmed the importance of StNHX genes in potato plant growth and development. We further analyzed the RNA-seq data (DM potato) under different abiotic stresses (salt, drought, and heat), and found that the expression of StNHX genes was induced under abiotic stress. qRT-PCR analysis of shoots and roots of 'Jizhangshu NO.8.' potato treated for 0, 6, 12, and 24 h with 15% PEG6000 confirmed that the 25 StNHX genes are involved in the response to drought stress in potato. The results of this study may be useful for selecting appropriate candidate genes for the breeding of new drought-tolerant potato varieties. Furthermore, this study lays a foundation for prospective analysis of StNHX gene functions.

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.

HgS2, a novel salt-responsive gene from the Halophyte Halogeton glomeratus, confers salt tolerance in transgenic Arabidopsis

Halophyte Halogeton glomeratus mostly grows in saline desert areas in arid and semi-arid regions and is able to adapt to adverse conditions such as salinity and drought. Earlier transcriptomic studies revealed activation of the HgS2 gene in the leaf of H. glomeratus seedlings when exposed to saline conditions. To identify the properties of HgS2 in H. glomeratus, we used yeast transformation and overexpression in Arabidopsis. Yeast cells genetically transformed with HgS2 exhibited K+ uptake and Na+ efflux compared with control (empty vector). Stable overexpression of HgS2 in Arabidopsis improved its resistance to salt stress and led to a notable rise in seed germination in salinity conditions compared to the wild type (WT). Transgenic Arabidopsis regulated ion homeostasis in plant cells by increasing Na+ absorption and decreasing K+ efflux in leaves, while reducing Na+ absorption and K+ efflux in roots. In addition, overexpression of HgS2 altered transcription levels of stress response genes and regulated different metabolic pathways in roots and leaves of Arabidopsis. These results offer new insights into the role of HgS2 in plants' salt tolerance.

A B-box transcription factor OsBBX17 regulates saline-alkaline tolerance through the MAPK cascade pathway in rice

Rice OsBBX17 encodes a B-box zinc finger transcription factor in which the N-terminal B-box structural domain interacts with OsMPK1. In addition, it directly binds to the G-box of OsHAK2 and OsHAK7 promoters and represses their transcription. Under saline-alkaline conditions, the expression of OsBBX17 was inhibited. Meanwhile, activation of the OsMPK1-mediated mitogen-activated protein kinase cascade pathway caused OsMPK1 to interact with OsBBX17 and phosphorylate OsBBX17 at the Thr-95 site. It reduced OsBBX17 DNA-binding activity and enhanced saline-alkaline tolerance by deregulating transcriptional repression of OsHAK2 and OsHAK7. Genetic assays showed that the osbbx17-KO had an excellent saline-alkaline tolerance, whereas the opposite was in OsBBX17-OE. In addition, overexpression of OsMPK1 significantly improved saline-alkaline tolerance, but knockout of OsMPK1 caused an increased sensitivity. Further overexpression of OsBBX17 in the osmpk1-KO caused extreme saline-alkaline sensitivity, even a quick death. OsBBX17 was validated in saline-alkaline tolerance from two independent aspects, transcriptional level and post-translational protein modification, unveiling a mechanistic framework by which OsMPK1-mediated phosphorylation of OsBBX17 regulates the transcription of OsHAK2 and OsHAK7 to enhance the Na+ /K+ homeostasis, which partially explains light on the molecular mechanisms of rice responds to saline-alkaline stress via B-box transcription factors for the genetic engineering of saline-alkaline tolerant crops.

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.

Differential gene expression patterns and physiological responses improve adaptation to high salinity concentration in pepper accessions

High salinity decreases the productivity of crops worldwide. Pepper is particularly sensitive to high salt concentrations. Herein, we subjected three tolerant pepper accessions (C12, B14 and A25) to high sodium chloride concentration (70 mM NaCl). The aerial and root biomass, leaf and root osmotic potential (Ψπ ), Na+ , Cl- , K+ and proline concentrations and the relative expression of the putative genes CaSOS1, CaHKT1, three CaNHXs and CaP5CS were measured. Different salinity tolerance strategies depending on the pepper accession were identified. In C12, tolerance was attributed to the accumulation of Na+ in vacuoles and endosomes by the activation of vacuolar CaNHXs genes and the reduction in Ψπ ; additionally, the activation of CaHKT1 and CaSOS1 in leaves and roots moved and accumulated Na+ ions in the xylem and xylem parenchyma cells (XPC) as well as expulsed it out of the root cells. A25 accession, on the contrary, was specialized in compartmentalizing Na+ ions in root and leaf vacuoles and root XPC by the up-regulation of CaNHXs and CaHKT1, respectively, avoiding a toxic accumulation in leaves. Finally, B14 accession moved and accumulated Na+ in xylem and XPC, reducing its concentration in roots by the activation of CaSOS1 and CaHKT1. This study shade light on different tolerance mechanisms of pepper plants to overcome salt stress.

The Morphological Parameters and Cytosolic pH of Cells of Root Zones in Tobacco Plants (Nicotiana tabacum L.): Nonlinear Effects of NaCl Concentrations

Salinity impacts important processes in plants, reducing their yield. The effect of salinity on the cytosolic pH (pHcyt) has been little studied. In this research, we employed transgenic tobacco plants expressing the pH sensor Pt-GFP to investigate the alterations in pHcyt in cells across various root zones. Furthermore, we examined a wide spectrum of NaCl concentrations (ranging from 0 to 150 mM) and assessed morphological parameters and plant development. Our findings revealed a pattern of cytosolic acidification in cells across all root zones at lower NaCl concentrations (50, 100 mM). Interestingly, at 150 mM NaCl, pHcyt levels either increased or returned to normal, indicating a nonlinear effect of salinity on pHcyt. Most studied parameters related to development and morphology exhibited an inhibitory influence in response to NaCl. Notably, a nonlinear relationship was observed in the cell length within the elongation and differentiation zones. While cell elongation occurred at 50 and 100 mM NaCl, it was not evident at 150 mM NaCl. This suggests a complex interplay between stimulating and inhibitory effects of salinity, contributing to the nonlinear relationship observed between pHcyt, cell length, and NaCl concentration.

How do plants maintain pH and ion homeostasis under saline-alkali stress?

Salt and alkaline stresses often occur together, severely threatening plant growth and crop yields. Salt stress induces osmotic stress, ionic stress, and secondary stresses, such as oxidative stress. Plants under saline-alkali stress must develop suitable mechanisms for adapting to the combined stress. Sustained plant growth requires maintenance of ion and pH homeostasis. In this review, we focus on the mechanisms of ion and pH homeostasis in plant cells under saline-alkali stress, including regulation of ion sensing, ion uptake, ion exclusion, ion sequestration, and ion redistribution among organs by long-distance transport. We also discuss outstanding questions in this field.

LcERF10 functions as a positive regulator of litchi fruitlet abscission

Phytohormone ethylene is well-known in positive modulation of plant organ abscission. However, the molecular mechanism underlying ethylene-induced abscission remains largely unknown. Here, we identified an ethylene-responsive factor, LcERF10, as a key regulatory gene in litchi fruitlet abscission. LcERF10 was strongly induced in the fruitlet abscission zone (FAZ) during the ethylene-activated abscission. Silencing of LcERF10 in litchi weakened the cytosolic alkalization of the FAZ and reduced fruitlet abscission. Moreover, LcERF10 directly bound the promoter and repressed the expression of LcNHX7, a Na+/H+ exchanger that was down-regulated in FAZ following the ethylene-activated abscission and up-regulated after LcERF10 silencing. Additionally, ectopic expression of LcERF10 in Arabidopsis promoted the cytosolic alkalization of the floral organ AZ and accelerated the floral organ abscission. Collectively, our results suggest that the transcription factor LcERF10 plays a positive role in litchi fruitlet abscission.

Vesicle trafficking in rice: too little is known

The vesicle trafficking apparatus is a fundamental machinery to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. Thus, it is broadly conserved in eukaryotes including plants. Intensive studies in the model organisms have produced a comprehensive picture of vesicle trafficking in yeast and human. However, with respect to the vesicle trafficking of plants including rice, our understanding of the components and their coordinated regulation is very limited. At present, several vesicle trafficking apparatus components and cargo proteins have been identified and characterized in rice, but there still remain large unknowns concerning the organization and function of the rice vesicle trafficking system. In this review, we outline the main vesicle trafficking pathways of rice based on knowledge obtained in model organisms, and summarize current advances of rice vesicle trafficking. We also propose to develop methodologies applicable to rice and even other crops for further exploring the mysteries of vesicle trafficking in plants.

LeGRXS14 Reduces Salt Stress Tolerance in Arabidopsis thaliana

Salt stress represents a significant abiotic stressor for plants and poses a severe threat to agricultural productivity. Glutaredoxins (GRXs) are small disulfide reductases that can scavenge cellular reactive oxygen species and are crucial for plant growth and development, particularly under stressful circumstances. Although CGFS-type GRXs were found to be involved in various abiotic stresses, the intrinsic mechanism mediated by LeGRXS14, a tomato (Lycopersicon esculentum Mill.) CGFS-type GRX, is not yet fully understood. We discovered that LeGRXS14 is relatively conserved at the N-terminus and exhibits an increase in expression level under salt and osmotic stress conditions in tomatoes. The expression levels of LeGRXS14 in response to osmotic stress peaked relatively rapidly at 30 min, while the response to salt stress only peaked at 6 h. We constructed LeGRXS14 overexpression Arabidopsis thaliana (OE) lines and confirmed that LeGRXS14 is located on the plasma membrane, nucleus, and chloroplasts. In comparison to the wild-type Col-0 (WT), the OE lines displayed greater sensitivity to salt stress, resulting in a profound inhibition of root growth under the same conditions. Analysis of the mRNA levels of the WT and OE lines revealed that salt stress-related factors, such as ZAT12, SOS3, and NHX6, were downregulated. Based on our research, it can be concluded that LeGRXS14 plays a significant role in plant tolerance to salt. However, our findings also suggest that LeGRXS14 may act as a negative regulator in this process by exacerbating Na+ toxicity and the resulting oxidative stress.

Plants' Response Mechanisms to Salinity Stress

Soil salinization is a severe abiotic stress that negatively affects plant growth and development, leading to physiological abnormalities and ultimately threatening global food security. The condition arises from excessive salt accumulation in the soil, primarily due to anthropogenic activities such as irrigation, improper land uses, and overfertilization. The presence of Na⁺, Cl^-, and other related ions in the soil above normal levels can disrupt plant cellular functions and lead to alterations in essential metabolic processes such as seed germination and photosynthesis, causing severe damage to plant tissues and even plant death in the worst circumstances. To counteract the effects of salt stress, plants have developed various mechanisms, including modulating ion homeostasis, ion compartmentalization and export, and the biosynthesis of osmoprotectants. Recent advances in genomic and proteomic technologies have enabled the identification of genes and proteins involved in plant salt-tolerance mechanisms. This review provides a short overview of the impact of salinity stress on plants and the underlying mechanisms of salt-stress tolerance, particularly the functions of salt-stress-responsive genes associated with these mechanisms. This review aims at summarizing recent advances in our understanding of salt-stress tolerance mechanisms, providing the key background knowledge for improving crops' salt tolerance, which could contribute to the yield and quality enhancement in major crops grown under saline conditions or in arid and semiarid regions of the world.

Improvement of Salinity Tolerance in Water-Saving and Drought-Resistance Rice (WDR)

Rice is one of the most economically important staple food crops in the world. Soil salinization and drought seriously restrict sustainable rice production. Drought aggravates the degree of soil salinization, and, at the same time, increased soil salinity also inhibits water absorption, resulting in physiological drought stress. Salt tolerance in rice is a complex quantitative trait controlled by multiple genes. This review presents and discusses the recent research developments on salt stress impact on rice growth, rice salt tolerance mechanisms, the identification and selection of salt-tolerant rice resources, and strategies to improve rice salt tolerance. In recent years, the increased cultivation of water-saving and drought-resistance rice (WDR) has shown great application potential in alleviating the water resource crisis and ensuring food and ecological security. Here, we present an innovative germplasm selection strategy of salt-tolerant WDR, using a population that is developed by recurrent selection based on dominant genic male sterility. We aim to provide a reference for efficient genetic improvement and germplasm innovation of complex traits (drought and salt tolerance) that can be translated into breeding all economically important cereal crops.

RAP2.6 enhanced salt stress tolerance by reducing Na+ accumulation and stabilizing the electron transport in Arabidopsis thaliana

The transcription factors of the AP2/ERF family are involved in plant growth and development and responses to biotic and abiotic stresses. Here, we found RAP2.6, a transcription factor which belongs to the ERF subfamily, was responsive to salt stress in Arabidopsis. Under salt stress conditions, rap2.6 mutant seedlings were the sensitivity deficiency to salt stress which was reflected in higher germination rate and longer root length compared to the wild type. Also, the expressions of salt-related gene including SOS1, SOS2, SOS3, NHX1, NHX3, NHX5 and HKT1 in rap2.6 mutant seedlings were lower than the wild type under salt stress. rap2.6 mutant adult lacked salt stress tolerance based on the results of the phenotype, survival rates and ion leakage. Compared to wild type, rap2.6 mutant adult accumulated more Na⁺ in leaves and roots while the salt-related gene expressions were lower. In addition, the photosynthetic electron transport and PSII energy distribution in rap2.6 mutant plant leaves had been more seriously affected under salt stress conditions compared to the wild type. In summary, this study identified essential roles of RAP2.6 in regulating salt stress tolerance in Arabidopsis.

Mechanisms of plant saline-alkaline tolerance

Saline-alkaline soil affects crop growth and development, thereby suppressing the yields. Human activities and climate changes are putting arable land under the threat of saline-alkalization. To feed a growing global population in limited arable land, it is of great urgence to breed saline-alkaline tolerant crops to cope with food security. Plant salt-tolerance mechanisms have already been explored for decades. However, to date, the molecular mechanisms underlying plants responses to saline-alkaline stress have remained largely elusive. Here, we summarize recent advances in plant response to saline-alkaline stress and propose some points deserving of further exploration.

Transcription Factor SiDi19-3 Enhances Salt Tolerance of Foxtail Millet and Arabidopsis

Salt stress is an important limiting factor of crop production. Foxtail millet (Setaria italica L.) is an important model crop for studying tolerance to various abiotic stressors. Therefore, examining the response of foxtail millet to salt stress at the molecular level is critical. Herein, we discovered that SiDi19-3 interacts with SiPLATZ12 to control salt tolerance in transgenic Arabidopsis and foxtail millet seedlings. SiDi19-3 overexpression increased the transcript levels of most Na⁺/H⁺ antiporter (NHX), salt overly sensitive (SOS), and calcineurin B-like protein (CBL) genes and improved the salt tolerance of foxtail millet and Arabidopsis. Six SiDi19 genes were isolated from foxtail millet. Compared with roots, stems, and leaves, panicles and seeds had higher transcript levels of SiDi19 genes. All of them responded to salt, alkaline, polyethylene glycol, and/or abscisic acid treatments with enhanced expression levels. These findings indicate that SiDi19-3 and other SiDi19 members regulate salt tolerance and other abiotic stress response in foxtail millet.

Transcriptome-Wide Identification and Functional Characterization of CIPK Gene Family Members in Actinidia valvata under Salt Stress

Fruit plants are severely constrained by salt stress in the soil due to their sessile nature. Ca²⁺ sensors, which are known as CBL-interacting protein kinases (CIPKs), transmit abiotic stress signals to plants. Therefore, it is imperative to investigate the molecular regulatory role of CIPKs underlying salt stress tolerance in kiwifruit. In the current study, we have identified 42 CIPK genes from Actinidia. valvata (A.valvata). All the AvCIPKs were divided into four different phylogenetic groups. Moreover, these genes showed different conserved motifs. The expression pattern analysis showed that AvCIPK11 was specifically highly expressed under salt stress. The overexpression of AvCIPK11 in 'Hongyang' (a salt sensitive commercial cultivar from Actinidia chinensis) enhanced salt tolerance by maintaining K⁺/Na⁺ homeostasis in the leaf and positively improving the activity of POD. In addition, the salt-related genes AcCBL1 and AcNHX1 had higher expression in overexpression lines. Collectively, our study suggested that AvCIPK11 is involved in the positive regulation of salt tolerance in kiwifruit.

Identification of a Saltol-Independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung

The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from - 0.68 to - 0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na⁺ in roots, stems, and leaves and Ca²⁺ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance-related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3' untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salinity-tolerant varieties in the Mekong Delta population and a promising new genetic resource.

Loss-of-function mutations of OsbHLH044 transcription factor lead to salinity sensitivity and a greater chalkiness in rice (Oryza sativa L.)

The most hazardous abiotic stress, salinity, restricted the world crop production, and grain chalkiness affected the grain quality to limit consumers' acceptance. The basic helix-loop-helix (bHLH) proteins modulate massive biological processes in plants. Here the CRISPR/Cas9 gene editing mutants were obtained to detect the function of OsbHLH044. The loss-of-function of OsbHLH044 mutants showed numerous altered plant phenotypes. Notably, the osbhlh044 mutants resulted in prominently reduced morphological and physiological parameters under salt stress. Lower antioxidant activities and higher lipid peroxidation and hydrogen peroxide (H₂O₂) accumulation in the osbhlh044 mutants caused salinity sensitivity due to elevated reactive oxygen species (ROS). Under salt stress, both shoots and roots of the osbhlh044 mutants acquired higher Na⁺. Moreover, the expression of ion homeostasis-related genes (OsHKTs, OsHAK, OsSOSs, and OsNHX) and ABA-responsive gene (OsLEA3) was significantly altered in the osbhlh044 mutants after salt stress. The expression levels of genes coding for starch (OsAGPL1, OsSSIIa, OsWx, and OsFLO2) and seed storage proteins (GluA1 and Globulin 1) were significantly decreased, indicating that they synthesize less store starch and proteins, resulting in grain chalkiness in the osbhlh044 mutants. Yeast one Hybrid (Y1H) showed that OsbHLH044 could activate salt- (OsHKT1;3, OsHAK7, OsSOS1, OsSOS2, OsNHX2, and OsLEA3 but not OsHKT2;1), and starch-related genes (OsSSIIa, OsWx, and OsFLO2) by binding to the G-boxes of their promoters. Therefore, the OsbHLH044 gene editing mutants revealed multiple functions, specifically a positive regulator of salt stress and grain quality, which might bring new insights into the breeding of rice varieties.

New insights into the influence of NHX-type Cation/H+ antiporter on flower color in Phalaenopsis orchids

Vacuolar sodium/proton Na⁺(K⁺)/H⁺ exchanger (NHX) influence color formation because of their effects on cellular pH and Na⁺/K⁺ homeostasis. Research regarding NHXs has mainly focused on the vacuolar NHX family members. However, the NHX functions related to Phalaenopsis flower coloration remain relatively uncharacterized. In this study, we cloned and characterized PeNHX1, a vacuolar cation/H⁺ antiporter-encoding gene that is highly expressed in the Phalaenopsis equestris (orchid) flower lip. Phylogenetic and sequence analyses showed that PeNHX1 is a vacuolar NHX protein family member that is similar to other known vacuolar antiporters. The PeNHX1-GFP fusion protein was clearly localized to the vacuolar membrane in a transient transfection assay. A quantitative real-time PCR analysis revealed the increased expression of PeNHX1 in different flower developmental stages. Moreover, it was more highly expressed in the lip than in the other flower organs. On the basis of virus-induced gene silencing, we determined that decreased PeNHX1 expression significantly reduces P. equestris petal coloration. Furthermore, the overexpression of PeNHX1 in Phalaenopsis Big Chili caused the pH to increase and the petal color to change from red to blue. The results indicate that NHX1 may mediates the Na ⁺ or K⁺/H⁺ exchange, thereby regulating the vacuolar pH to promote blue coloration. This research provides a theoretical basis for the development of orchid varieties with blue flowers.

The high pH value of alkaline salt destroys the root membrane permeability of Reaumuria trigyna and leads to its serious physiological decline

Variable climatic conditions frequently have harmful effects on plants. Reaumuria trigyna, a salt-secreting xerophytic shrub, occurs in Inner Mongolia, which has a poor environment for plant growth. To explore the physiological and molecular mechanisms of R. trigyna in response to environmental stress, this study investigated the abiotic resistance of R. trigyna in terms of growth regulation, antioxidant defense, osmotic regulation, ion transport, and ion homeostasis-related genes. R. trigyna seedlings were treated with 400 mM NaCl, 400 mM neutral salts (NaCl:Na₂SO₄ = 9:1), 50 mM alkaline salts (NaHCO₃:Na₂CO₃ = 9:1), 10% polyethylene glycol (PEG), and UV-B. Seedlings under 400 mM NaCl and 400 mM neutral salt stress showed less damage. While alkaline salt, PEG, and UV stress caused more damage, specifically in oxidative damage, proline levels, electrolyte leakage, and activation of antioxidant defenses. Furthermore, under the abiotic stress treatments, the accumulation of Na⁺ increased while the accumulation of K⁺ decreased. Further analysis showed that the flow rate of Na⁺ and K⁺ under alkaline salt stress was higher than under neutral salt stress. Neutral salt induced high expression of RtNHX1 and RtSOS1, while alkaline salt induced high expression of RtHKT1, and alkaline salt stress significantly reduced the activity of root cells. These results indicated that R. trigyna seedlings were more tolerant to neutral than alkaline salts; this might be because root activity decreased at high pH levels, which impaired membrane permeability and the ion transfer system, leading to an imbalance between Na⁺ and K⁺, and in turn to excessive accumulation of reactive oxygen species (ROS) and decreased plant stress resistance.

A soybean sodium/hydrogen exchanger GmNHX6 confers plant alkaline salt tolerance by regulating Na+/K+ homeostasis

Alkaline soil has a high pH due to carbonate salts and usually causes more detrimental effects on crop growth than saline soil. Sodium hydrogen exchangers (NHXs) are pivotal regulators of cellular Na⁺/K⁺ and pH homeostasis, which is essential for salt tolerance; however, their role in alkaline salt tolerance is largely unknown. Therefore, in this study, we investigated the function of a soybean NHX gene, GmNHX6, in plant response to alkaline salt stress. GmNHX6 encodes a Golgi-localized sodium/hydrogen exchanger, and its transcript abundance is more upregulated in alkaline salt tolerant soybean variety in response to NaHCO₃ stress. Ectopic expression of GmNHX6 in Arabidopsis enhanced alkaline salt tolerance by maintaining high K⁺ content and low Na⁺/K⁺ ratio. Overexpression of GmNHX6 also improved soybean tolerance to alkaline salt stress. A single nucleotide polymorphism in the promoter region of NHX6 is associated with the alkaline salt tolerance in soybean germplasm. A superior promoter of GmNHX6 was isolated from an alkaline salt tolerant soybean variety, which showed stronger activity than the promoter from an alkaline salt sensitive soybean variety in response to alkali stress, by luciferase transient expression assays. Our results suggested soybean NHX6 gene plays an important role in plant tolerance to alkaline salt stress.

Molecular Pathways of WRKY Genes in Regulating Plant Salinity Tolerance

Salinity is a natural and anthropogenic process that plants overcome using various responses. Salinity imposes a two-phase effect, simplified into the initial osmotic challenges and subsequent salinity-specific ion toxicities from continual exposure to sodium and chloride ions. Plant responses to salinity encompass a complex gene network involving osmotic balance, ion transport, antioxidant response, and hormone signaling pathways typically mediated by transcription factors. One particular transcription factor mega family, WRKY, is a principal regulator of salinity responses. Here, we categorize a collection of known salinity-responding WRKYs and summarize their molecular pathways. WRKYs collectively play a part in regulating osmotic balance, ion transport response, antioxidant response, and hormone signaling pathways in plants. Particular attention is given to the hormone signaling pathway to illuminate the relationship between WRKYs and abscisic acid signaling. Observed trends among WRKYs are highlighted, including group II WRKYs as major regulators of the salinity response. We recommend renaming existing WRKYs and adopting a naming system to a standardized format based on protein structure.

Transcriptome and Metabonomic Analysis of Tamarix ramosissima Potassium (K+) Channels and Transporters in Response to NaCl Stress

Potassium ion (K+) channels and transporters are key components of plant K+ absorption and transportation and play an important role in plant growth and development. This study revealed that K+ channels and transporters are involved in the salt tolerance molecular mechanism and metabolites of the halophyte representative plant Tamarix ramosissima (T. ramosissima) in response to NaCl stress, providing a theoretical basis for the mitigation of salt stress using halophytes. Through transcriptome sequencing and metabolite detection analysis of 0 h, 48 h and 168 h by applying exogenous K+ to the roots of T. ramosissima under NaCl stress, 15 high-quality Clean Data bases were obtained, Q20 reached more than 97%, Q30 reached more than 92%, and GC content reached 44.5%, which is in line with further bioinformatics analysis. Based on the Liquid chromatography−mass spectrometry (LC-MS) analysis, the roots of T. ramosissima were exposed to exogenous potassium for 48 h and 168 h under NaCl stress, and 1510 and 1124 metabolites were identified in positive and negative ion mode, respectively. Through orthogonal projections to latent structures discriminant analysis (OPLS-DA) model analysis, its metabolomic data have excellent predictability and stability. The results of this study showed that there were 37 differentially expressed genes (DEGs) annotated as Class 2 K+ channels (Shaker-like K+ channel and TPK channel) and Class 3 K+ transporters (HAK/KUP/KT, HKT and CPAs transporter families). Among them, 29 DEGs were annotated to the gene ontology (GO) database, and the most genes were involved in the GO Biological Process. In addition, the expression levels of Unigene0014342 in the HAK/KUP/KT transporter and Unigene0088276 and Unigene0103067 in the CPAs transporter both first decreased and then increased when treated with 200 mM NaCl for 48 h and 168 h. However, when treated with 200 mM NaCl + 10 mM KCl for 48 h and 168 h, a continuous upward trend was shown. Notably, the expression level of Unigene0016813 in CPAS transporter continued to increase when treated with 200 mM NaCl and 200 mM NaCl + 10 mM KCl for 48 h and 168 h. 3 DEGs, Unigene0088276, Unigene0016813 and Unigene0103067, were dominated by the positive regulation of their related metabolites, and this correlation was significant. The results showed that these DEGs increased the absorption of K+ and the ratio of K+/Na+ under NaCl stress at 48 h and 168 h after adding exogenous potassium and enhanced the salt tolerance of T. ramosissima. Notably, the expression level of Unigene0103067 in the CPAs transporter was consistently upregulated when 200 mM NaCl + 10 mM KCl was treated for 48 h and 168 h. The positive regulatory metabolites were always dominant, which better helped T. ramosissima resist salt stress. Unigene0103067 plays an important role in enhancing the salt tolerance of T. ramosissima and reducing the toxicity of NaCl in roots. Additionally, phylogenetic tree analysis showed that Unigene0103067 and Reaumuria trigyna had the closest genetic distance in the evolutionary relationship. Finally, 9 DEGs were randomly selected for quantitative real-time PCR (qRT-PCR) verification. Their expression trends were completely consistent with the transcriptome sequencing analysis results, proving that this study’s data are accurate and reliable. This study provides resources for revealing the molecular mechanism of NaCl stress tolerance in T. ramosissima and lays a theoretical foundation for cultivating new salt-tolerant varieties.

Function of Rice High-Affinity Potassium Transporters in Pollen Development and Fertility

Plant High-affinity K+ transporters/K+ uptake permeases/K+ transporters (HAK/KUP/KT) transporters have been predicted as membrane H+-K+ symporters in facilitating K+ uptake and distribution, while their role in seed production remains to be elucidated. In this study, we report that OsHAK26 is preferentially expressed in anthers and seed husks and located in the Golgi apparatus. Knockout of either OsHAK26 or plasma membrane located H+-K+ symporter gene OsHAK1 or OsHAK5 in both Nipponbare and Dongjin cultivars caused distorted anthers, reduced number and germination rate of pollen grains. Seed-setting rate assay by reciprocal cross-pollination between the mutants of oshak26, oshak1, oshak5 and their wild types confirmed that each HAK transporter is foremost for pollen viability, seed-setting and grain yield. Intriguingly, the pollens of oshak26 showed much thinner wall and were more vulnerable to desiccation than those of oshak1 or oshak5. In vitro assay revealed that the pollen germination rate of oshak5 was dramatically affected by external K+ concentration. The results suggest that the role of OsHAK26 in maintaining pollen development and fertility may relate to its proper cargo sorting for construction of pollen walls, while the role of OsHAK1 and OsHAK5 in maintaining seed production likely relates to their transcellular K+ transport activity.

The Role of Serendipita indica (Piriformospora indica) in Improving Plant Resistance to Drought and Salinity Stresses

Simple Summary

Environmental stresses are one of the biggest threats to modern agriculture, and climate change has heightened the risks of these stresses in different parts of the world. Among all the environmental stresses, salinity and drought are a severe threat to arid and semi-arid regions of the world, and for a long time, scientists have been searching for ways to reduce the risk of these stresses. In recent decades, solutions have been developed to reduce the risk of environmental stress on plants by identifying beneficial soil microorganisms. This study was conducted to identify morphophysiological and molecular changes of plants in coexistence with Serendipita indica and their impact on drought and salinity stress reduction. The study also has investigated the stressors’ impact on plants and the plants’ mechanisms to cope with them; Furthermore, sharing results with researchers provides a clear path for future research.

Abstract

Plant stress is one of the biggest threats to crops, causing irreparable damage to farmers’ incomes; Therefore, finding suitable, affordable, and practical solutions will help the agricultural economy and prevent the loss of millions of tons of agricultural products. Scientists have taken significant steps toward improving farm productivity in the last few decades by discovering how beneficial soil microorganisms enhance plant resistance to environmental stresses. Among these microorganisms is Serendipita indica, which the benefits of coexisting this fungus with plant roots have been extensively explored in recent years. By investigating fungus specification and its effects on plants’ morphological, physiological, and molecular traits, the present study seeks to understand how Serendipita indica affects plant resistance to salinity and drought conditions. Furthermore, this study attempts to identify the unknown mechanisms of action of the coexistence of Serendipita indica with plants in the face of stress using information from previous studies. Thus, it provides a way for future research to assess the impact of this fungus on tackling environmental stresses and enhancing agricultural productivity.

Salt tolerance in relation to elemental concentrations in leaf cell vacuoles and chloroplasts of a C4 monocotyledonous halophyte

Halophytes accumulate and sequester high concentrations of salt in vacuoles while maintaining lower levels of salt in the cytoplasm. The current data on cellular and subcellular partitioning of salt in halophytes are, however, limited to only a few dicotyledonous C₃ species. Using cryo-scanning electron microscopy X-ray microanalysis, we assessed the concentrations of Na, Cl, K, Ca, Mg, P and S in various cell types within the leaf-blades of a monocotyledonous C₄ halophyte, Rhodes grass (Chloris gayana). We also linked, for the first time, elemental concentrations in chloroplasts of mesophyll and bundle sheath cells to their ultrastructure and photosynthetic performance of plants grown in nonsaline and saline (200 mM NaCl) conditions. Na and Cl accumulated to the highest levels in xylem parenchyma and epidermal cells, but were maintained at lower concentrations in photosynthetically active mesophyll and bundle sheath cells. Concentrations of Na and Cl in chloroplasts of mesophyll and bundle sheath cells were lower than in their respective vacuoles. No ultrastructural changes were observed in either mesophyll or bundle sheath chloroplasts, and photosynthetic activity was maintained in saline conditions. Salinity tolerance in Rhodes grass is related to specific cellular Na and Cl distributions in leaf tissues, and the ability to regulate Na and Cl concentrations in chloroplasts.

The red seaweed Kappaphycus alvarezii antiporter gene (KaNa+/H+) confers abiotic stress tolerance in transgenic tobacco

BACKGROUND

Plant establishment, growth, development and productivity are adversely affected by abiotic stresses that are dominant characteristics of environmentally challenged/degraded habitats created in the Anthropocene. Crop breeding for climate resilience properties is need of the hour to sustain the crop productivity. We report on the characterization of Kappaphycus alvarezii (a red seaweed) Na+/H+ antiporter gene (KaNa+/H+) for enhanced salt and osmotic stress tolerance.

METHODS

The KaNa+/H+ antiporter gene was cloned and over-expressed in tobacco under the control of CaMV35S promoter. Transgenic analysis was carried out to assess the stress tolerance ability of tobacco over-expressing KaNa+/H+ antiporter gene.

RESULTS

Over-expression of KaNa+/H+ gene improved the seed germination and seed vigor index under stress. Transgenic plants grew better and exhibited delayed leaf senescence. Improved K+/Na+, carotenoid/total chlorophyll and relative water content; lower accumulation of reactive oxygen species (ROS), MDA and Na+; lower electrolyte leakage; better membrane stability index and accumulation of K+, photosynthetic pigment, starch, sugar, free amino acid, proline and polyphenol contents indicated better physiological health of the transgenic tobacco under stress. Transgenic tobacco exhibited higher photosynthesis, photosystem II efficiency, electron transfer rate, photochemical quenching and activity of water splitting complex. Compared with control tobacco, transgenic tobacco exhibited higher expression of stress-defence genes under stress and better recovery after long-term osmotic stress.

CONCLUSIONS

Lower Na+ cytotoxicity, lower accumulation of ROS and maintenance of the membrane integrity helped transgenic tobacco to maintain the physiological functioning under stress. Present results established K. alvarezii as a potential gene resource and the KaNa+/H+ antiporter gene as a potential candidate gene in molecular breeding of crops for development of the degraded land.

Metabolites Reprogramming and Na+/K+ Transportation Associated With Putrescine-Regulated White Clover Seed Germination and Seedling Tolerance to Salt Toxicity

Soil salinization is a serious challenge to many countries worldwide. Putrescine (Put) is related to the improvement of seed germination under salt stress, but molecular and metabolic mechanisms are still not fully understood. The objectives of this study were to determine the effect of seed soaking with Put on germination characteristics under salt stress induced by 100 mm sodium chloride (NaCl) and to further analyze subsequent stress tolerance associated with amylolysis, oxidative damage, sodium (Na+)/ potassium (K+) accumulation and transportation, and metabolic homeostasis in white clover (Trifolium repens cv. Haifa) seedlings. The results showed that seed soaking with Put significantly alleviated salt-induced decreases in the endogenous Put content, germination rate, germination vigor, germination index, Rl/SL, and fresh/dry weight of seedlings. Put application also significantly promoted starch metabolism through activating α-amylase and β-amylase activities under salt stress. The metabolomic analysis showed that seed soaking with Put significantly increased the accumulation of polyamines (Put and spermidine), amino acids (γ-aminobutyric acid, glutamate, alanine, proline, citrulline, etc.), organic acids (ketopentanic acid, malonic acid, malic acid, ketopentanic acid, cis-sinapinic acid, etc.), lipids and fatty acids (glycerol, stearic acid, linoleic acid, palmitic acid, etc.), sugars (levoglucosan, fucose, and anhydro-D-galactose), alcohols (myo-inositol, allo-inositol, hexadecanol, and threitol), and other metabolites (thymine, xanthine, adenine, guanine, and glycerol 1-phosphate, etc.) associated with enhanced tricarboxylic acid (TCA) cycle and γ-aminobutyric acid (GABA) shunt contributing to better osmotic adjustment, cell membrane stability, energy supply, and metabolic homeostasis when seeds germinated under salt stress. In addition, Put significantly up-regulated the AsSOS1, NHX6, SKOR, HKT1, and HKT8 expression levels which played critical roles in Na+ rejection and K+ retention resulting in higher K+/Na+ ratio during seed germination under salt stress. The Put-induced up-regulation of HAL2 transcription level could reduce the toxicity of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) in cells. Current findings will provide an integrative understanding of Put-induced salt tolerance associated with amylolysis, metabolic regulation, and ionic homeostasis during seed germination.

NHX-Type Na+/H+ Antiporter Gene Expression Under Different Salt Levels and Allelic Diversity of HvNHX in Wild and Cultivated Barleys

Salinity tolerance is a multifaceted trait attributed to various mechanisms. Wild barley is highly specialized to grow under severe environmental conditions of Tibet and is well-known for its diverse germplasm with high tolerance to abiotic stresses. The present study focused on determining the profile of the expression of isoforms of the HvNHX gene in 36 wild and two cultivated barley under salt stress. Our findings revealed that in leaves and roots, expression of HvNHX1 and HvNHX3 in XZ16 and CM72 was upregulated at all times as compared with sensitive ones. The HvNHX2 and HvNHX4 isoforms were also induced by salt stress, although not to the same extent as HvNHX1 and HvNHX3. Gene expression analysis revealed that HvNHX1 and HvNHX3 are the candidate genes that could have the function of regulators of ions by sequestration of Na⁺ in the vacuole. HvNHX1 and HvNHX3 showed a wide range of sequence variations in an amplicon, identified via single-nucleotide polymorphisms (SNPs). Evaluation of the sequencing data of 38 barley genotypes, including Tibetan wild and cultivated varieties, showed polymorphisms, including SNPs, and small insertion and deletion (INDEL) sites in the targeted genes HvNHX1 and HvNHX3. Comprehensive analysis of the results revealed that Tibetan wild barley has distinctive alleles of HvNHX1 and HvNHX3 which confer tolerance to salinity. Furthermore, less sodium accumulation was observed in the root of XZ16 than the other genotypes as visualized by CoroNa-Green, a sodium-specific fluorophore. XZ16 is the tolerant genotype, showing least reduction of root and leaf dry weight under moderate (150 mM) and severe (300 mM) NaCl stress. Evaluation of genetic variation and identification of salt tolerance mechanism in wild barley could be promoting approaches to unravel the novel alleles involved in salinity tolerance.

The Tiny Companion Matters: The Important Role of Protons in Active Transports in Plants

In plants, the translocation of molecules, such as ions, metabolites, and hormones, between different subcellular compartments or different cells is achieved by transmembrane transporters, which play important roles in growth, development, and adaptation to the environment. To facilitate transport in a specific direction, active transporters that can translocate their substrates against the concentration gradient are needed. Examples of major active transporters in plants include ATP-binding cassette (ABC) transporters, multidrug and toxic compound extrusion (MATE) transporters, monosaccharide transporters (MSTs), sucrose transporters (SUTs), and amino acid transporters. Transport via ABC transporters is driven by ATP. The electrochemical gradient across the membrane energizes these secondary transporters. The pH in each cell and subcellular compartment is tightly regulated and yet highly dynamic, especially when under stress. Here, the effects of cellular and subcellular pH on the activities of ABC transporters, MATE transporters, MSTs, SUTs, and amino acid transporters will be discussed to enhance our understanding of their mechanics. The relation of the altered transporter activities to various biological processes of plants will also be addressed. Although most molecular transport research has focused on the substrate, the role of protons, the tiny counterparts of the substrate, should also not be ignored.

Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza

Rice (Oryza sativa), a staple crop for a substantial part of the world’s population, is highly sensitive to soil salinity; however, some wild Oryza relatives can survive in highly saline environments. Sodium/hydrogen antiporter (NHX) family members contribute to Na⁺ homeostasis in plants and play a major role in conferring salinity tolerance. In this study, we analyzed the evolution of NHX family members using phylogeny, conserved domains, tertiary structures, expression patterns, and physiology of cultivated and wild Oryza species to decipher the role of NHXs in salt tolerance in Oryza. Phylogenetic analysis showed that the NHX family can be classified into three subfamilies directly related to their subcellular localization: endomembrane, plasma membrane, and tonoplast (vacuolar subfamily, vNHX1). Phylogenetic and structural analysis showed that vNHX1s have evolved from streptophyte algae (e.g., Klebsormidium nitens) and are abundant and highly conserved in all major land plant lineages, including Oryza. Moreover, we showed that tissue tolerance is a crucial trait conferring tolerance to salinity in wild rice species. Higher Na⁺ accumulation and reduced Na⁺ effluxes in leaf mesophyll were observed in the salt-tolerant wild rice species O. alta, O. latifolia, and O. coarctata. Among the key genes affecting tissue tolerance, expression of NHX1 and SOS1/NHX7 exhibited significant correlation with salt tolerance among the rice species and cultivars. This study provides insights into the evolutionary origin of plant NHXs and their role in tissue tolerance of Oryza species and facilitates the inclusion of this trait during the development of salinity-tolerant rice cultivars.

Ammonium and nitrate affect sexually different responses to salt stress in Populus cathayana

Nitrogen (N) fertilization is a promising approach to improve salt tolerance. However, it is poorly known how plant sex and inorganic N alter salt stress-induced Na⁺ uptake, distribution and tolerance. This study employed Populus cathayana Rehder females and males to examine sex-related mechanisms of salt tolerance under nitrate (NO₃ ^- ) and ammonium (NH₄ ⁺ ) nutrition. Males had a higher root Na⁺ efflux, lower root-to-shoot translocation of Na⁺ , and higher K⁺ /Na⁺ , which enhanced salt tolerance under both N forms compared to females. On the other hand, decreased root Na⁺ efflux and K⁺ retention, and an increased ratio of Na⁺ in leaves relative to shoots in females caused greater salt sensitivity. Females receiving NH₄ ⁺ rather than NO₃ ^- had greater net root Na⁺ uptake, K⁺ efflux, and translocation to the shoots, especially in leaves. In contrast, males receiving NO₃ ^- rather than NH₄ ⁺ had increased Na⁺ translocation to the shoots, especially in the bark, which may narrow the difference in leaf damage by salt stress between N forms despite a higher shoot Na⁺ accumulation and lower root Na⁺ efflux. Genes related to cell wall synthesis, K⁺ and Na⁺ transporters, and denaturized protein scavenging in the barks showed differential expression between females and males in response to salt stress under both N forms. These results suggested that the regulation of N forms in salt stress tolerance was sex-dependent, which was related to the maintenance of the K⁺ /Na⁺ ratio in tissues, the ability of Na⁺ translocation to the shoots, and the transcriptional regulation of bark cell wall and proteolysis profiles.

Salt stress proteins in plants: An overview

Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.

NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis

Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants, such as Arabidopsis thaliana and cotton; however, not much is known about NHXs in tea plant. In the present study, NHX genes of tea were obtained through a genome-wide search using A. thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER; CsNHX8) and plasma membrane (PM; CsNHX9), respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location, and protein-conserved motifs and domains were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes is subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in Camellia sinensis based on the orthologous genes in A. thaliana. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.

Transcriptome revealed the molecular mechanism of Glycyrrhiza inflata root to maintain growth and development, absorb and distribute ions under salt stress

BACKGROUND

Soil salinization extensively hampers the growth, yield, and quality of crops worldwide. The most effective strategies to counter this problem are a) development of crop cultivars with high salt tolerance and b) the plantation of salt-tolerant crops. Glycyrrhiza inflata, a traditional Chinese medicinal and primitive plant with salt tolerance and economic value, is among the most promising crops for improving saline-alkali wasteland. However, the underlying molecular mechanisms for the adaptive response of G. inflata to salinity stress remain largely unknown.

RESULT

G. inflata retained a high concentration of Na+ in roots and maintained the absorption of K+, Ca2+, and Mg2+ under 150 mM NaCl induced salt stress. Transcriptomic analysis of G. inflata roots at different time points of salt stress (0 min, 30 min, and 24 h) was performed, which resulted in 70.77 Gb of clean data. Compared with the control, we detected 2645 and 574 differentially expressed genes (DEGs) at 30 min and 24 h post-salt-stress induction, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that G. inflata response to salt stress post 30 min and 24 h was remarkably distinct. Genes that were differentially expressed at 30 min post-salt stress induction were enriched in signal transduction, secondary metabolite synthesis, and ion transport. However, genes that were differentially expressed at 24 h post-salt-stress induction were enriched in phenylpropane biosynthesis and metabolism, fatty acid metabolism, glycerol metabolism, hormone signal transduction, wax, cutin, and cork biosynthesis. Besides, a total of 334 transcription factors (TFs) were altered in response to 30 min and 24 h of salt stress. Most of these TFs belonged to the MYB, WRKY, AP2-EREBP, C2H2, bHLH, bZIP, and NAC families.

CONCLUSION

For the first time, this study elucidated the salt tolerance in G. inflata at the molecular level, including the activation of signaling pathways and genes that regulate the absorption and distribution of ions and root growth in G. inflata under salt stress conditions. These findings enhanced our understanding of the G. inflata salt tolerance and provided a theoretical basis for cultivating salt-tolerant crop varieties.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Molecular insights into the role of plant transporters in salt stress response

Salt stress disturbs the cellular osmotic and ionic balance, which then creates a negative impact on plant growth and development. The Na⁺ and Cl^- ions can enter into plant cells through various membrane transporters, including specific and non-specific Na⁺ , K⁺ , and Ca²⁺ transporters. Therefore, it is important to understand Na⁺ and K⁺ transport mechanisms in plants along with the isolation of genes, their characterization, the structural features, and their post-translation regulation under salt stress. This review summarizes the molecular insights of plant ion transporters, including non-selective cation transporters, cyclic nucleotide-gated cation transporters, glutamate-like receptors, membrane intrinsic proteins, cation proton antiporters, and sodium proton antiporter families. Further, we discussed the K⁺ transporter families such as high-affinity K⁺ transporters, HAK/KUP/KT transporters, shaker type K⁺ transporters, and K⁺ efflux antiporters. Besides the ion transport process, we have shed light on available literature on epigenetic regulation of transport processes under salt stress. Recent advancements of salt stress sensing mechanisms and various salt sensors within signaling transduction pathways are discussed. Further, we have compiled salt-stress signaling pathways, and their crosstalk with phytohormones.

Understanding the potential of root microbiome influencing salt-tolerance in plants and mechanisms involved at the transcriptional and translational level

Soil salinity severely affects plant growth and development and imparts inevitable losses to crop productivity. Increasing the concentration of salts in the vicinity of plant roots has severe consequences at the morphological, biochemical, and molecular levels. These include loss of chlorophyll, decrease in photosynthetic rate, reduction in cell division, ROS generation, inactivation of antioxidative enzymes, alterations in phytohormone biosynthesis and signaling, and so forth. The association of microorganisms, viz. plant growth-promoting rhizobacteria, endophytes, and mycorrhiza, with plant roots constituting the root microbiome can confer a greater degree of salinity tolerance in addition to their inherent ability to promote growth and induce defense mechanisms. The mechanisms involved in induced stress tolerance bestowed by these microorganisms involve the modulation of phytohormone biosynthesis and signaling pathways (including indole acetic acid, gibberellic acid, brassinosteroids, abscisic acid, and jasmonic acid), accumulation of osmoprotectants (proline, glycine betaine, and sugar alcohols), and regulation of ion transporters (SOS1, NHX, HKT1). Apart from this, salt-tolerant microorganisms are known to induce the expression of salt-responsive genes via the action of several transcription factors, as well as by posttranscriptional and posttranslational modifications. Moreover, the potential of these salt-tolerant microflora can be employed for sustainably improving crop performance in saline environments. Therefore, this review will briefly focus on the key responses of plants under salinity stress and elucidate the mechanisms employed by the salt-tolerant microorganisms in improving plant tolerance under saline environments.

Regulation of Cytosolic pH: The Contributions of Plant Plasma Membrane H+-ATPases and Multiple Transporters

Cytosolic pH homeostasis is a precondition for the normal growth and stress responses in plants, and H+ flux across the plasma membrane is essential for cytoplasmic pH control. Hence, this review focuses on seven types of proteins that possess direct H+ transport activity, namely, H+-ATPase, NHX, CHX, AMT, NRT, PHT, and KT/HAK/KUP, to summarize their plasma-membrane-located family members, the effect of corresponding gene knockout and/or overexpression on cytosolic pH, the H+ transport pathway, and their functional regulation by the extracellular/cytosolic pH. In general, H+-ATPases mediate H+ extrusion, whereas most members of other six proteins mediate H+ influx, thus contributing to cytosolic pH homeostasis by directly modulating H+ flux across the plasma membrane. The fact that some AMTs/NRTs mediate H+-coupled substrate influx, whereas other intra-family members facilitate H+-uncoupled substrate transport, demonstrates that not all plasma membrane transporters possess H+-coupled substrate transport mechanisms, and using the transport mechanism of a protein to represent the case of the entire family is not suitable. The transport activity of these proteins is regulated by extracellular and/or cytosolic pH, with different structural bases for H+ transfer among these seven types of proteins. Notably, intra-family members possess distinct pH regulatory characterization and underlying residues for H+ transfer. This review is anticipated to facilitate the understanding of the molecular basis for cytosolic pH homeostasis. Despite this progress, the strategy of their cooperation for cytosolic pH homeostasis needs further investigation.

Heterologous Expression of the Melatonin-Related Gene HIOMT Improves Salt Tolerance in Malus domestica

Melatonin, a widely known indoleamine molecule that mediates various animal and plant physiological processes, is formed from N-acetyl serotonin via N-acetylserotonin methyltransferase (ASMT). ASMT is an enzyme that catalyzes melatonin synthesis in plants in the rate-determining step and is homologous to hydroxyindole-O-methyltransferase (HIOMT) melatonin synthase in animals. To date, little is known about the effect of HIOMT on salinity in apple plants. Here, we explored the melatonin physiological function in the salinity condition response by heterologous expressing the homologous human HIOMT gene in apple plants. We discovered that the expression of melatonin-related gene (MdASMT) in apple plants was induced by salinity. Most notably, compared with the wild type, three transgenic lines indicated higher melatonin levels, and the heterologous expression of HIOMT enhanced the expression of melatonin synthesis genes. The transgenic lines showed reduced salt damage symptoms, lower relative electrolyte leakage, and less total chlorophyll loss from leaves under salt stress. Meanwhile, through enhanced activity of antioxidant enzymes, transgenic lines decreased the reactive oxygen species accumulation, downregulated the expression of the abscisic acid synthesis gene (MdNCED3), accordingly reducing the accumulation of abscisic acid under salt stress. Both mechanisms regulated morphological changes in the stomata synergistically, thereby mitigating damage to the plants' photosynthetic ability. In addition, transgenic plants also effectively stabilized their ion balance, raised the expression of salt stress-related genes, as well as alleviated osmotic stress through changes in amino acid metabolism. In summary, heterologous expression of HIOMT improved the adaptation of apple leaves to salt stress, primarily by increasing melatonin concentration, maintaining a high photosynthetic capacity, reducing reactive oxygen species accumulation, and maintaining normal ion homeostasis.

RsSOS1 Responding to Salt Stress Might Be Involved in Regulating Salt Tolerance by Maintaining Na+ Homeostasis in Radish (Raphanus sativus L.)

Radish is a kind of moderately salt-sensitive vegetable. Salt stress seriously decreases the yield and quality of radish. The plasma membrane Na+/H+ antiporter protein Salt Overly Sensitive 1 (SOS1) plays a crucial role in protecting plant cells against salt stress, but the biological function of the RsSOS1 gene in radish remains to be elucidated. In this study, the RsSOS1 gene was isolated from radish genotype ‘NAU-TR17’, and contains an open reading frame of 3414 bp encoding 1137 amino acids. Phylogenetic analysis showed that RsSOS1 had a high homology with BnSOS1, and clustered together with Arabidopsis plasma membrane Na+/H+ antiporter (AtNHX7). The result of subcellular localization indicated that the RsSOS1 was localized in the plasma membrane. Furthermore, RsSOS1 was strongly induced in roots of radish under 150 mmol/L NaCl treatment, and its expression level in salt-tolerant genotypes was significantly higher than that in salt-sensitive ones. In addition, overexpression of RsSOS1 in Arabidopsis could significantly improve the salt tolerance of transgenic plants. Meanwhile, the transformation of RsSOS1△999 could rescue Na+ efflux function of AXT3 yeast. In summary, the plasma membrane Na+/H+ antiporter RsSOS1 plays a vital role in regulating salt-tolerance of radish by controlling Na+ homeostasis. These results provided useful information for further functional characterization of RsSOS1 and facilitate clarifying the molecular mechanism underlying salt stress response in radish.

Post-translational regulation of the membrane transporters contributing to salt tolerance in plants

This review article summarises the role of membrane transporters and their regulatory kinases in minimising the toxicity of Na+ in the plant under salt stress. The salt-tolerant plants keep their cytosolic level of Na+ up to 10-50mM. The first line of action in this context is the generation of proton motive force by the plasma membrane H+-ATPase. The generated proton motive force repolarises the membrane that gets depolarised due to passive uptake of Na+ under salt stress. The proton motive force generated also drives the plasma membrane Na+/H+ antiporter, SOS1 that effluxes the cytosolic Na+ back into the environment. At the intracellular level, Na+ is sequestered by the vacuole. Vacuolar Na+ uptake is mediated by Na+/H+ antiporter, NHX, driven by the electrochemical gradient for H+, generated by tonoplast H+ pumps, both H+ATPase and PPase. However, it is the expression of the regulatory kinases that make these transporters active through post-translational modification enabling them to effectively manage the cytosolic level of Na+, which is essential for tolerance to salinity in plants. Yet our knowledge of the expression and functioning of the regulatory kinases in plant species differing in tolerance to salinity is scant. Bioinformatics-based identification of the kinases like OsCIPK24 in crop plants, which are mostly salt-sensitive, may enable biotechnological intervention in making the crop cultivar more salt-tolerant, and effectively increasing its annual yield.

Genetic Diversity and Synergistic Modulation of Salinity Tolerance Genes in Aegilops tauschii Coss

Aegilops tauschii Coss. (2n = 2x = 14, DD) is a problematic weed and a rich source of genetic material for wheat crop improvement programs. We used physiological traits (plant height, dry weight biomass, Na⁺ and K⁺ concentration) and 14 microsatellite markers to evaluate the genetic diversity and salinity tolerance in 40 Ae. tauschii populations. The molecular marker allied with salinity stress showed polymorphisms, and a cluster analysis divided the populations into different groups, which indicated diversity among populations. Results showed that the expression level of AeHKT1;4 and AeNHX1 were significantly induced during salinity stress treatments (50 and 200 mM), while AeHKT1;4 showed relative expression in roots, and AeNHX1 was expressed in leaves under the control conditions. Compared with the control conditions, the expression level of AeHKT1;4 significantly increased 1.7-fold under 50 mM salinity stress and 4.7-fold under 200 mM salinity stress in the roots of Ae. tauschii. AeNHX1 showed a relative expression level of 1.6-fold under 50 mM salinity stress and 4.6-fold under 200 mM salinity stress compared with the control conditions. The results provide strong evidence that, under salinity stress conditions, AeHKT1;4 and AeNHX1 synergistically regulate the Na⁺ homeostasis through regulating Na⁺ transport in Ae. tauschii. AeNHX1 sequestrated the Na⁺ into vacuoles, which control the regulation of Na⁺ transport from roots to leaves under salinity stress conditions in Ae. tauschii.

Tissue tolerance mechanisms conferring salinity tolerance in a halophytic perennial species Nitraria sibirica Pall

Plant salt tolerance relies on a coordinated functioning of different tissues and organs. Salinity tissue tolerance is one of the key traits that confer plant adaptation to saline environment. This trait implies maintenance low cytosolic Na+/K+ ratio in metabolically active cellular compartments. In this study, we used Nitraria sibirica Pall., a perennial woody halophyte species, to understand the mechanistic basis of its salinity tissue tolerance. The results showed that the growth of seedlings was stimulated by 100-200 mM NaCl treatment. The ions distribution analysis showed that the leaves act as an Na+ sink, while the plant roots possess superior K+ retention. The excessive Na+ absorbed from the soil was mainly transported to the shoot and was eventuallysequestrated into mesophyll vacuoles in the leaves. As a result, N. sibirica could keep the optimal balance of K+/Na+ at a tissue- and cell-specific level under saline condition. To enable this, N. sibirica increased both vacuolar H+-ATPase and H+-PPase enzymes activities and up-regulated the expressions of NsVHA, NsVP1 and NsNHX1 genes. Vacuolar Na+ sequestration in the leaf mesophyll, mediated by NsVHA, NsVP1 and NsNHX1, reduced the Na+ concentration in cytosol and inhibited further K+ loss. Meanwhile, N. sibirica enhanced the Two Pore K+ expression at the transcriptional level to promote K+ efflux from vacuole into cytoplasm, assisting in maintaining cytosolic K+ homeostasis. It is concluded that the tissue tolerance traits such as vacuolar Na+ sequestration and intracellular K+ homeostasis are critical to confer adaptation of N. sibirica to soil salinity.

Somatic variations led to the selection of acidic and acidless orange cultivars

Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour.

Identification and characterisation of monovalent cation/proton antiporters (CPAs) in Phyllostachys edulis and the functional analysis of PheNHX2 in Arabidopsis thaliana

Plant monovalent cation/proton antiporters (CPAs), types of transmembrane transporters, play important roles in resistance to salt stress. In this study, 37 CPA genes from moso bamboo (Phyllostachys edulis) were identified and characterised. The expression profiles of 10 CPA1 genes (PheNHXs) of moso bamboo were detected by qRT-PCR, which showed that they were specifically expressed in six tissues. In addition, the expression of 10 PheNHXs in leaves and roots changed significantly under 150/200 mM NaCl and 100 μM ABA treatments. In particular, the expression of PheNHX2 in leaves and roots was significantly upregulated under NaCl treatment, thus, we cloned PheNHX2 and analysed its function. Subcellular localisation analysis showed that PheNHX2 was located on the vacuolar membrane. Overexpression of PheNHX2 reduced seed germination and root growth of Arabidopsis thaliana under salt stress, as well as severely affecting cellular Na⁺ and K⁺ content, which in turn reduced the salt tolerance of transgenic Arabidopsis. Measurements of physiological indicators, including chlorophyll content, malondialdehyde content, peroxidase and catalase enzyme activities and relative electrical conductivity, all supported this conclusion. Under salt stress, PheNHX2 also inhibited the expression of some stress-related and ion transport-related genes in transgenic Arabidopsis. Overall, these results indicate that overexpression of PheNHX2 reduces the salt tolerance of transgenic Arabidopsis. This investigation establishes a foundation for subsequent functional studies of moso bamboo CPA genes, and it provides a deeper understanding of PheNHX2 regulation in relation to the salt tolerance of moso bamboo.

Potential Networks of Nitrogen-Phosphorus-Potassium Channels and Transporters in Arabidopsis Roots at a Single Cell Resolution

Nitrogen (N), phosphorus (P), and potassium (K) are three major macronutrients essential for plant life. These nutrients are acquired and transported by several large families of transporters expressed in plant roots. However, it remains largely unknown how these transporters are distributed in different cell-types that work together to transfer the nutrients from the soil to different layers of root cells and eventually reach vasculature for massive flow. Using the single cell transcriptomics data from Arabidopsis roots, we profiled the transcriptional patterns of putative nutrient transporters in different root cell-types. Such analyses identified a number of uncharacterized NPK transporters expressed in the root epidermis to mediate NPK uptake and distribution to the adjacent cells. Some transport genes showed cortex- and endodermis-specific expression to direct the nutrient flow toward the vasculature. For long-distance transport, a variety of transporters were shown to express and potentially function in the xylem and phloem. In the context of subcellular distribution of mineral nutrients, the NPK transporters at subcellular compartments were often found to show ubiquitous expression patterns, which suggests function in house-keeping processes. Overall, these single cell transcriptomic analyses provide working models of nutrient transport from the epidermis across the cortex to the vasculature, which can be further tested experimentally in the future.