Plant cation/H+ exchangers (CAXs): biological functions and genetic manipulations

The cation/H+ exchanger OsCAX2 is involved in cadmium uptake and contributes to differential grain cadmium accumulation between Indica and Japonica rice

Rice is a major source of dietary cadmium (Cd), a toxic heavy metal that poses serious threat to human health. How rice takes up and accumulates Cd is not fully understood. Here, we characterize the function of a cation/H+ exchanger, OsCAX2, in Cd uptake in roots and Cd accumulation in shoots and grains. OsCAX2 exhibited Cd and calcium (Ca) transport activities when was heterologously expressed in yeast. OsCAX2 was mainly expressed in roots, particularly in lateral roots, and in the exodermis and endodermis of primary roots. OsCAX2 is localized at the plasma membrane. Knockout of OsCAX2 significantly decreased Cd uptake in roots and Cd accumulation in shoots and grains. Knockout of OsCAX2 also decreased the Ca concentration in roots, but not in shoots or grains. Surprisingly, overexpression of OsCAX2 also resulted in a significant decrease in the Cd concentrations in roots and shoots. We further reveal that the variation in the coding sequence of OsCAX2 contributes to differential grain Cd accumulation between two major rice subspecies, Indica and Japonica. Our results demonstrate that OsCAX2 functions in Cd/Ca uptake in roots and could be a useful target for breeding or genetic engineering low Cd rice varieties.

Cellular calcium homeostasis and regulation of its dynamic perturbation

Calcium ions (Ca2+) play pivotal roles in a host of cellular signalling processes. The requirement to maintain resting cytosolic Ca2+ levels in the 100-200 nM range provides a baseline for dynamic excursions from resting levels that determine the nature of many physiological responses to external stimuli and developmental processes. This review provides an overview of the key components of the Ca2+ homeostatic machinery, including known channel-mediated Ca2+ entry pathways along with transporters that act to shape the cytosolic Ca2+ signature. The relative roles of the vacuole and endoplasmic reticulum as sources or sinks for cytosolic Ca2+ are considered, highlighting significant gaps in our understanding. The components contributing to mitochondrial, chloroplast and nuclear Ca2+ homeostasis and organellar Ca2+ signals are also considered. Taken together, a complex picture of the cellular Ca2+ homeostatic machinery emerges with some clear differences from mechanisms operating in many animal cells.

Optimizing 'Red Fuji' apple quality: Auxin-mediated calcium distribution via fruit-stalk in bagging practices

In apples, a bottleneck effect in calcium (Ca) transport within fruit stalk has been observed. To elucidate that how auxin affects Ca forms and distribution in the apple fruit stalk, we investigated the effects of different concentrations of auxin treatment (0, 10, 20, and 30 mg·L-1) on Ca content, forms, distribution, and fruit quality during later stages of fruit expansion. The results showed that auxin treatment led to a dramatic reduction in total Ca content in stalk, while an approximately 30 % increase in fruit. Furthermore, auxin treatment effectively enhanced the functionality of xylem vessels in vascular bundles of the stalk in bagged apples. Finally, TOPSIS method was used to assess fruit quality, with treatments ranked as follows: IAA20 > NAA20 > IAA30 > IAA10 > CK > NPA. The findings lay a foundation for further studies on the bottleneck in Ca transport within stalk, uneven distribution of Ca in fruit, and provide insights into Ca utilization efficiency in bagged apples.

The Rice Online Expression Profiles Array Database Version 2 (ROADv2): An Interactive Atlas for Rice Functional Genomics

The Rice Online expression profiles Array Database version 2 (ROADv2; https://roadv2.khu.ac.kr ), an enhanced database for rice gene expression analysis, transitions from the previous microarray platforms to RNA-Seq data for improved accuracy. It encompasses 328 datasets from diverse experimental series, including anatomy, abiotic and biotic stress, hormone response, and nutrient starvation. Key updates include gene annotation (upgraded to RGAP version 7) and functional enrichment data (utilizing recent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) versions). ROADv2 debuts protein-protein interaction (PPI) network analysis and broadens interactive visualization across all features. Gene expression data are segmented into anatomy, biotic, abiotic, nutrient, and hormone categories, with user-interactive heatmaps displaying normalized log2 expression and log2 fold change data. Coexpression correlation analysis identifies genes with similar patterns, visualized through interactive network graphs. Functional enrichment tools display GO and KEGG analyses with significant terms emphasized in various formats. PPI network analysis integrates coexpression data to enhance prediction accuracy. Validation studies affirm the database's reliability, demonstrating reproducible tissue/organ-specific expression patterns. ROADv2 provides a comprehensive resource for rice functional genomics studies.

CAX control: multiple roles of vacuolar cation/H+ exchangers in metal tolerance, mineral nutrition and environmental signalling

Plant vacuolar transporters, particularly CAX (Cation/H+ Exchangers) responsible for Ca2+/H+ exchange on the vacuole tonoplast, play a central role in governing cellular pH, ion balance, nutrient storage, metal accumulation, and stress responses. Furthermore, CAX variants have been employed to enhance the calcium content of crops, contributing to biofortification efforts. Recent research has uncovered the broader significance of these transporters in plant signal transduction and element partitioning. The use of genetically encoded Ca2+ sensors has begun to highlight the crucial role of CAX isoforms in generating cytosolic Ca2+ signals, underscoring their function as pivotal hubs in diverse environmental and developmental signalling networks. Interestingly, it has been observed that the loss of CAX function can be advantageous in specific stress conditions, both for biotic and abiotic stressors. Determining the optimal timing and approach for modulating the expression of CAX is a critical concern. In the future, strategically manipulating the temporal loss of CAX function in agriculturally important crops holds promise to bolster plant immunity, enhance cold tolerance, and fortify resilience against one of agriculture's most significant challenges, namely flooding.

Sugarcane ScCAX4 is a Negative Regulator of Resistance to Pathogen Infection

Calcium (Ca2+) is a second messenger in various physiological processes within plants. The significance of the Ca2+/H+ exchanger (CAX) has been established in facilitating Ca2+ transport in plants; however, disease resistance functions of the CAX gene remain elusive. In this study, we conducted sequence characterization and expression analysis for a sugarcane CAX gene, ScCAX4 (GenBank Accession Number: MW206380). In order to further investigate the disease resistance functions, this gene was then transiently overexpressed in Nicotiana benthamiana leaves, which were subsequently inoculated with Fusarium solani var. coeruleum. Results showed that ScCAX4 overexpression increased the susceptibility of N. benthamiana to pathogen infection by regulating the expression of genes related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways, suggesting its negative role in disease resistance. Furthermore, we genetically transformed the ScCAX4 gene into N. benthamiana and obtained three positive T2 generation lines. Interestingly, the symptomatology of transgenic plants was consistent with that of transient overexpression after pathogen inoculation. Notably, the JA content in transgenic overexpression lines was significantly higher than that in the wild-type. RNA-seq revealed that ScCAX4 could mediate multiple signaling pathways, and the JA signaling pathway played a key role in modulating disease resistance. Finally, a regulatory model was depicted for the increased susceptibility to pathogen infection conferred by the ScCAX4 gene. This study provides genetic resources for sugarcane molecular breeding and the research direction for plant CAX genes.

Transcriptional Regulation of SugarCane Response to Sporisorium scitamineum: Insights from Time-Course Gene Coexpression and Ca2+ Signaling

Sugarcane response to Sporisorium scitamineum is determined by multiple major genes and numerous microeffector genes. Here, time-ordered gene coexpression networks were applied to explore the interaction between sugarcane and S. scitamineum. Totally, 2459 differentially expressed genes were identified and divided into 10 levels, and several stress-related subnetworks were established. Interestingly, the Ca2+ signaling pathway was activated to establish the response to sugarcane smut disease. Accordingly, two CAX genes (ScCAX2 and ScCAX3) were cloned and characterized from sugarcane. They were significantly upregulated under ABA stress but inhibited by MeJA treatment. Furthermore, overexpression of ScCAX2 and ScCAX3 enhanced the susceptibility of transgenic plants to the pathogen infection, suggesting its negative role in disease resistance. A regulatory model for ScCAX genes in disease response was thus depicted. This work helps to clarify the transcriptional regulation of sugarcane response to S. scitamineum stress and the function of the CAX gene in disease response.

Functional differentiation and genetic diversity of rice cation exchanger (CAX) genes and their potential use in rice improvement

Cation exchanger (CAX) genes play an important role in plant growth/development and response to biotic and abiotic stresses. Here, we tried to obtain important information on the functionalities and phenotypic effects of CAX gene family by systematic analyses of their expression patterns, genetic diversity (gene CDS haplotypes, structural variations, gene presence/absence variations) in 3010 rice genomes and nine parents of 496 Huanghuazhan introgression lines, the frequency shifts of the predominant gcHaps at these loci to artificial selection during modern breeding, and their association with tolerances to several abiotic stresses. Significant amounts of variation also exist in the cis-regulatory elements (CREs) of the OsCAX gene promoters in 50 high-quality rice genomes. The functional differentiation of OsCAX gene family were reflected primarily by their tissue and development specific expression patterns and in varied responses to different treatments, by unique sets of CREs in their promoters and their associations with specific agronomic traits/abiotic stress tolerances. Our results indicated that OsCAX1a and OsCAX2 as general signal transporters were in many processes of rice growth/development and responses to diverse environments, but they might be of less value in rice improvement. OsCAX1b, OsCAX1c, OsCAX3 and OsCAX4 was expected to be of potential value in rice improvement because of their associations with specific traits, responsiveness to specific abiotic stresses or phytohormones, and relatively high gcHap and CRE diversity. Our strategy was demonstrated to be highly efficient to obtain important genetic information on genes/alleles of specific gene family and can be used to systematically characterize the other rice gene families.

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.

Sequential removal of cation/H+ exchangers reveals their additive role in elemental distribution, calcium depletion and anoxia tolerance

Multiple Arabidopsis H+ /Cation exchangers (CAXs) participate in high-capacity transport into the vacuole. Previous studies have analysed single and double mutants that marginally reduced transport; however, assessing phenotypes caused by transport loss has proven enigmatic. Here, we generated quadruple mutants (cax1-4: qKO) that exhibited growth inhibition, an 85% reduction in tonoplast-localised H+ /Ca transport, and enhanced tolerance to anoxic conditions compared to CAX1 mutants. Leveraging inductively coupled plasma mass spectrometry (ICP-MS) and synchrotron X-ray fluorescence (SXRF), we demonstrate CAX transporters work together to regulate leaf elemental content: ICP-MS analysis showed that the elemental concentrations in leaves strongly correlated with the number of CAX mutations; SXRF imaging showed changes in element partitioning not present in single CAX mutants and qKO had a 40% reduction in calcium (Ca) abundance. Reduced endogenous Ca may promote anoxia tolerance; wild-type plants grown in Ca-limited conditions were anoxia tolerant. Sequential reduction of CAXs increased mRNA expression and protein abundance changes associated with reactive oxygen species and stress signalling pathways. Multiple CAXs participate in postanoxia recovery as their concerted removal heightened changes in postanoxia Ca signalling. This work showcases the integrated and diverse function of H+ /Cation transporters and demonstrates the ability to improve anoxia tolerance through diminishing endogenous Ca levels.

The apple Ca2+/H+ exchanger MdCAX2L-2 functions positively in modulation of Ba2+ tolerance

Calcium is an essential element for plant growth and development, and it plays an important role in the responses of plants to abiotic stress. High concentrations of heavy metal ions in soil significantly affect the yield and quality of crops and pose human health threats when these ions accumulate in edible organs. The Ca2+/H+ exchanger (CAX) family is a class of transporters that mediate the transmembrane transport of both Ca2+ and metal ions, and they are widely involved in regulating plant growth and development and stress responses. Here, we cloned an AtCAX2 ortholog, MdCAX2L-2, from apple. It is constitutively expressed in various apple tissues and significantly induced by Ca2+ and Ba2+ treatments. The MdCAX2L-2 protein is located in the vacuolar membrane in both plant and yeast cells. Overexpression of MdCAX2L-2 enhanced the tolerance of the yeast mutant K667 to high concentrations of Ca2+ and Ba2+. In addition, the role of MdCAX2L-2 in modulating Ba2+ tolerance was identified using MdCAX2L-2-overexpressing transgenic Arabidopsis plants and apple calli. Comparison of growth phenotypes and stress-related physiological indexes under BaCl2 treatment indicated that MdCAX2L-2 could enhance the Ba2+ tolerance of plants by promoting Ba2+ compartmentalization into the vacuoles and eliminating excess ROS. Our results provide insights that will aid future studies examining the function of CAX proteins in regulating stress tolerance in fruit crops, as well as their underlying mechanisms.

Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca2+ Transport and Ca2+ Deficiency-Induced Tip-Burn in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables.

Transcriptomic, epigenomic and physiological comparisons reveal key factors for different manganese tolerances in three Chenopodium ambrosioides L. populations

Chenopodium ambrosioides is a manganese (Mn) hyperaccumulator that can be used for Mn-polluted soil phytoremediation. However, the mechanism of Mn tolerance of C. ambrosioides remains largely unknown. In this study, the key factors for Mn tolerance of C. ambrosioides was investigated from the aspects of DNA methylation pattern, gene expression regulation and physiological function. We found that the two genotypes of C. ambrosioides populations have differentiated tolerance to Mn stress (Mn-tolerant: CS and XC, Mn-sensitive: WH). Although there was no difference in Mn accumulation between two types under excess Mn, the biomass and photosynthetic systems were more severely inhibited in Mn-sensitive type, as well as suffering more serious oxidative damage. More differentially expressed genes (DEGs) were downregulated in the Mn-tolerant type, indicating that the Mn-tolerant type tends to inhibit gene expression to cope with Mn stress. DEGs related to metal transport, antioxidant system, phytohormone and transcription factors contribute to the tolerance of C. ambrosioides to Mn, and account for difference in Mn stress sensitivities between the Mn-sensitive and tolerant types. We also found that DNA methylation variation may help to cope with Mn stress. The global DNA methylation level in C. ambrosioides increased under Mn stress, especially in the Mn-sensitive type. Dozens of methylated loci were significantly associated with the Mn accumulation trait of C. ambrosioides, and some critical DEGs were regulated by DNA methylation. Our study comprehensively demonstrated the Mn tolerance mechanism of C. ambrosioides for the first time, and highlighted the roles of epigenetic modification in C. ambrosioides response to Mn stress. Our findings may contribute to elucidating the adaptation mechanism of hyperaccumulator to the heavy metal toxicity.

Evaluation of the alkalinity stress tolerance of three Brassica rapa CAX1 TILLING mutants

Alkalinity is an important environmental factor that affects crop production and will be exacerbated in the current climate change scenario. Thus, the presence of carbonates and high pH in soils negatively impacts nutrient assimilation and photosynthesis and causes oxidative stress. A potential strategy to improve tolerance to alkalinity could be the modification of cation exchanger (CAX) activity, given that these transporters are involved in calcium (Ca²⁺) signaling under stresses. In this study, we used three Brassica rapa mutants (BraA.cax1a-4, BraA.cax1a-7, and BraA.cax1a-12) from the parental line 'R-o-18' that were generated by Targeting Induced Local Lesions in Genomes (TILLING) and grown under control and alkaline conditions. The objective was to assess the tolerance of these mutants to alkalinity stress. Biomass, nutrient accumulation, oxidative stress, and photosynthesis parameters were analyzed. ^{The results showed} that BraA.cax1a-7 mutation was negative for alkalinity tolerance because it reduced plant biomass, increased oxidative stress, partially inhibited antioxidant response, and lowered photosynthesis performance. Conversely, the BraA.cax1a-12 mutation increased plant biomass and Ca²⁺ accumulation, reduced oxidative stress, and improved antioxidant response and photosynthesis performance. Hence, this study identifies BraA.cax1a-12 as a useful CAX1 mutation to enhance the tolerance of plants grown under alkaline conditions.

Transcriptomic analysis reveals key genes and pathways corresponding to Cd and Pb in the hyperaccumulator Arabis paniculata

Soil and water are increasingly at risk of contamination from the toxic heavy metals lead (Pb) and cadmium (Cd). Arabis paniculata (Brassicaceae) is a hyperaccumulator of heavy metals (HMs) found widely distributed in areas impacts by mining activities. However, the mechanism by which A. paniculata tolerates HMs is still uncharacterized. For this experiment, we employed RNA sequencing (RNA-seq) in order to find Cd (0.25 mM)- and Pb (2.50 mM)-coresponsive genes A. paniculata. In total, 4490 and 1804 differentially expressed genes (DEGs) were identified in root tissue, and 955 and 2209 DEGs were identified in shoot tissue, after Cd and Pb exposure, respectively. Interestingly in root tissue, gene expression corresponded similarly to both Cd and Pd exposure, of which 27.48% were co-upregulated and 41.00% were co-downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the co-regulated genes were predominantly involved in transcription factors (TFs), cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. Many critical Pb/Cd-induced DEGs involved in phytohormone biosynthesis and signal transduction, HM transport, and transcription factors were also identified. Especially the gene ABCC9 was co-downregulated in root tissues but co-upregulated in shoot tissues. The co-downregulation of ABCC9 in the roots prevented Cd and Pb from entering the vacuole rather than the cytoplasm for transporting HMs to shoots. While in shoots, the ABCC9 co-upregulated results in vacuolar Cd and Pb accumulation, which may explain why A. paniculata is a hyperaccumulator. These results will help to reveal the molecular and physiological processes underlying tolerance to HM exposure in the hyperaccumulator A. paniculata, and aid in future efforts to utilize this plant in phytoremediation.

Genetic Analyses of Seed Longevity in Capsicum annuum L. in Cold Storage Conditions

Seed longevity is the most important trait in the genebank management system. No seed can remain infinitely viable. There are 1241 accessions of Capsicum annuum L. available at the German Federal ex situ genebank at IPK Gatersleben. C. annuum (Capsicum) is the most economically important species of the genus Capsicum. So far, there is no report that has addressed the genetic basis of seed longevity in Capsicum. Here, we convened a total of 1152 Capsicum accessions that were deposited in Gatersleben over forty years (from 1976 to 2017) and assessed their longevity by analyzing the standard germination percentage after 5-40 years of storage at -15/-18 °C. These data were used to determine the genetic causes of seed longevity, along with 23,462 single nucleotide polymorphism (SNP) markers covering all of the 12 Capsicum chromosomes. Using the association-mapping approach, we identified a total of 224 marker trait associations (MTAs) (34, 25, 31, 35, 39, 7, 21 and 32 MTAs after 5-, 10-, 15-, 20-, 25-, 30-, 35- and 40-year storage intervals) on all the Capsicum chromosomes. Several candidate genes were identified using the blast analysis of SNPs, and these candidate genes are discussed.

MdbHLH4 negatively regulates apple cold tolerance by inhibiting MdCBF1/3 expression and promoting MdCAX3L-2 expression

Low temperature affects the yield and quality of crops. Inducer of CBF expression 1 (ICE1) plays a positive role in plant cold tolerance by promoting the expression of CRT binding factor (CBF) and cold-responsive (COR) genes. Several ICE1-interacting transcription factors (TFs) that regulate plant cold tolerance have been identified. However, how these TFs affect the function of ICE1 and CBF expression under cold conditions remains unclear. Here, we identified the MYC-type TF MdbHLH4, a negative regulator of cold tolerance in Arabidopsis (Arabidopsis thaliana) and apple (Malus domestica) plants. Under cold conditions, MdbHLH4 inhibits the expression of MdCBF1 and MdCBF3 by directly binding to their promoters. It also interacts with MdICE1L, a homolog of AtICE1 in apple, and inhibits the binding of MdICE1L to the promoters of MdCBF1/3 and thus their expression. We showed that MdCAX3L-2, a Ca2+/H+ exchanger (CAX) family gene that negatively regulates plant cold tolerance, is also a direct target of MdbHLH4. MdbHLH4 reduced apple cold tolerance by promoting MdCAX3L-2 expression. Moreover, overexpression of either MdCAX3L-2 or MdbHLH4 promoted the cold-induced ubiquitination and degradation of MdICE1L. Overall, our results reveal that MdbHLH4 negatively regulates plant cold tolerance by inhibiting MdCBF1/3 expression and MdICE1L promoter-binding activity, as well as by promoting MdCAX3L-2 expression and cold-induced MdICE1L degradation. These findings provide insights into the mechanisms by which ICE1-interacting TFs regulate CBF expression and ICE1 function and thus plant cold tolerance.

The vacuolar H+/Ca transporter CAX1 participates in submergence and anoxia stress responses

A plant's oxygen supply can vary from normal (normoxia) to total depletion (anoxia). Tolerance to anoxia is relevant to wetland species, rice (Oryza sativa) cultivation, and submergence tolerance of crops. Decoding and transmitting calcium (Ca) signals may be an important component to anoxia tolerance; however, the contribution of intracellular Ca transporters to this process is poorly understood. Four functional cation/proton exchangers (CAX1-4) in Arabidopsis (Arabidopsis thaliana) help regulate Ca homeostasis around the vacuole. Our results demonstrate that cax1 mutants are more tolerant to both anoxic conditions and submergence. Using phenotypic measurements, RNA-sequencing, and proteomic approaches, we identified cax1-mediated anoxia changes that phenocopy changes present in anoxia-tolerant crops: altered metabolic processes, diminished reactive oxygen species production post anoxia, and altered hormone signaling. Comparing wild-type and cax1 expressing genetically encoded Ca indicators demonstrated altered cytosolic Ca signals in cax1 during reoxygenation. Anoxia-induced Ca signals around the plant vacuole are involved in the control of numerous signaling events related to adaptation to low oxygen stress. This work suggests that cax1 anoxia response pathway could be engineered to circumvent the adverse effects of flooding that impair production agriculture.

Calcium channels and transporters: Roles in response to biotic and abiotic stresses

Calcium (Ca2+) serves as a ubiquitous second messenger by mediating various signaling pathways and responding to numerous environmental conditions in eukaryotes. Therefore, plant cells have developed complex mechanisms of Ca2+ communication across the membrane, receiving the message from their surroundings and transducing the information into cells and organelles. A wide range of biotic and abiotic stresses cause the increase in [Ca2+]cyt as a result of the Ca2+ influx permitted by membrane-localized Ca2+ permeable cation channels such as CYCLIC NUCLEOTIDE-GATE CHANNELs (CNGCs), and voltage-dependent HYPERPOLARIZATION-ACTIVATED CALCIUM2+ PERMEABLE CHANNELs (HACCs), as well as GLUTAMATE RECEPTOR-LIKE RECEPTORs (GLRs) and TWO-PORE CHANNELs (TPCs). Recently, resistosomes formed by some NUCLEOTIDE-BINDING LEUCINE-RICH REPEAT RECEPTORs (NLRs) are also proposed as a new type of Ca2+ permeable cation channels. On the contrary, some Ca2+ transporting membrane proteins, mainly Ca2+-ATPase and Ca2+/H+ exchangers, are involved in Ca2+ efflux for removal of the excessive [Ca2+]cyt in order to maintain the Ca2+ homeostasis in cells. The Ca2+ efflux mechanisms mediate the wide ranges of cellular activities responding to external and internal stimuli. In this review, we will summarize and discuss the recent discoveries of various membrane proteins involved in Ca2+ influx and efflux which play an essential role in fine-tuning the processing of information for plant responses to abiotic and biotic stresses.

Natural Molecular Mechanisms of Plant Hyperaccumulation and Hypertolerance towards Heavy Metals

The main mechanism of plant tolerance is the avoidance of metal uptake, whereas the main mechanism of hyperaccumulation is the uptake and neutralization of metals through specific plant processes. These include the formation of symbioses with rhizosphere microorganisms, the secretion of substances into the soil and metal immobilization, cell wall modification, changes in the expression of genes encoding heavy metal transporters, heavy metal ion chelation, and sequestration, and regenerative heat-shock protein production. The aim of this work was to review the natural plant mechanisms that contribute towards increased heavy metal accumulation and tolerance, as well as a review of the hyperaccumulator phytoremediation capacity. Phytoremediation is a strategy for purifying heavy-metal-contaminated soils using higher plants species as hyperaccumulators.

Calcium affects uranium responses in Arabidopsis thaliana: From distribution to toxicity

Uranium, a heavy metal and primordial radionuclide, is present in surface waters and soils both naturally and due to industrial activities. Uranium is known to be toxic to plants and its uptake and toxicity can be influenced by multiple factors such as pH and the presence of different ions. However, the precise role of the different ions in uranium uptake is not yet known. Here we investigated whether calcium influences uranium uptake and toxicity in the terrestrial plant Arabidopsis thaliana. To this end, A. thaliana plants were exposed to different calcium and uranium concentrations and furthermore, calcium channels were blocked using the calcium channel blocker lanthanum chloride (LaCl₃). Fresh weight, relative growth rate, concentration of nutrients and uranium and gene expression of oxidative stress-related genes and calcium transporters were determined in roots and shoots. Calcium affected plant growth and oxidative stress in both control (no uranium) and uranium-exposed plants. In shoots, this was influenced by the total calcium concentration, but not by the different tested uranium concentrations. Uranium in turn did influence calcium uptake and distribution. Uranium-exposed plants grown in a medium with a higher calcium concentration showed an increase in gene expression of NADPH oxidases RBOHC and RBOHE and calcium transporter CAX7 after uranium exposure. In roots, these calcium-dependent responses in gene expression were not observed. This indicates that calcium indeed affects uranium toxicity, but only in shoots. In addition, a clear influence of uranium and LaCl₃ (separately and combined) on the expression of calcium transporters was observed.

Infection by phloem-limited phytoplasma affects mineral nutrient homeostasis in tomato leaf tissues

Phytoplasmas are sieve-elements restricted wall-less, pleomorphic pathogenic microorganisms causing devastating damage to over 700 plant species worldwide. The invasion of sieve elements by phytoplasmas has several consequences on nutrient transport and metabolism, anyway studies about changes of the mineral-nutrient profile following phytoplasma infections are scarce and offer contrasting results. Here, we examined changes in macro- and micronutrient concentration in tomato plant upon 'Candidatus Phytoplasma solani' infection. To investigate possible effects of 'Ca. P. solani' infection on mineral element allocation, the mineral elements were separately analysed in leaf midrib, leaf lamina and root. Moreover, we focused our analysis on the transcriptional regulation of genes encoding trans-membrane transporters of mineral nutrients. To this aim, a manually curated inventory of differentially expressed genes encoding transporters in tomato leaf midribs was mined from the transcriptional profile of healthy and infected tomato leaf midribs. Results highlighted changes in ion homeostasis in the host plant, and significant modulations at transcriptional level of genes encoding ion transporters and channels.

Genome-wide analysis and expression profiling of Cation/H+ exchanger (CAX) family genes reveal likely functions in cadmium stress responses in poplar

Cadmium, a toxic heavy metal, seriously affects human health and ecological security. The cation/H⁺ exchanger (CAX) family is a unique metal transporter that plays a crucial role in Cd acquisition, transfer, and remission in plants. Although there are many studies related to the genome-wide analysis of Populus trichocarpa, little research has been done on the CAX family genes, especially concerning Cd stress. In this study, genome-wide analysis of the Populus CAX family identified seven stress-related CAX genes. The evolutionary tree indicated that the CaCA family genes were grouped into four clusters. Moreover, seven pairs of genes were derived by segmental duplication in poplars. Cis-acting element analysis identified numerous stress-related elements in the promoters of diverse PtrCAXs. Furthermore, some PtrCAXs were up-regulated by drought, beetle, and mechanical damage, indicating their possible function in regulating stress response. Under cadmium stress, all CAX genes in the roots were up-regulated. Our findings suggest that plants may regulate their response to Cd stress through the TF-CAXs module. Comprehensively investigating the CAX family provides a scientific basis for the phytoremediation of heavy metal pollution by Populus.

Network response of two cherry tomato (Lycopersicon esculentum) cultivars to Cadmium stress as revealed by transcriptome analysis

Soil cadmium (Cd) contamination severely threatens human health. Therefore, screening and breeding low-Cd absorption cultivars of cherry tomato (Solanum lycopersicum L.) is essential to restrict human Cd intake. In this study, a hydroponic experiment was conducted to perform a comparative transcriptome analysis of the leaves of two cherry tomato cultivars with different Cd contents under different Cd stress (0, 10, and 50 μM), for the purpose of exploring the differences in the transcriptional responses to Cd stress between the two cultivars. Our results revealed that the Cd content in the leaves of HLZ (Hanluzhe; a low-Cd accumulation cultivar) was significantly lower than that in the leaves of LFC (Lvfeicui; a high-Cd accumulation cultivar). Transcriptome analysis showed that the different expression genes (DEGs) were mainly involved in plant hormone signal transduction, antioxidant enzymes, cell wall biosynthesis, and metal transportation. In the LFC leaves, DEGs in the IAA signal transduction and antioxidant enzymes exhibited higher transcription levels. However, the DEGs in the ETH signal transduction demonstrated a lower transcription level compared to that of HLZ. Over-expressed genes in the pectin biosynthesis and pectin methylesterase (PME) of the LFC leaves might result in the trapping of Cd by increased levels of low-methylated pectin around the cell wall. Furthermore, Cd transporter genes, such as HMA5, NRAMP6, CAX3, ABCC3, and PDR1, were up-regulated in the HLZ leaves, indicating that the HLZ cultivar comprised an active Cd transport capacity from apoplast to vacuolar. This may contribute to the low Cd concentration observed in the HLZ leaves. Overall, our study provides a molecular basis for tomato screening and breeding.

The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress

BACKGROUND

In plants, Calcium (Ca2+) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes. The Ca2+/cation antiporter (CaCA) superfamily proteins play vital roles in the transport of Ca2+ and/or other cations. However, the characteristics of these superfamily members in Saccharum and their evolutionary and functional implications have remained unclear.

RESULTS

A total of 34 CaCA genes in Saccharum spontaneum, 5 CaCA genes in Saccharum spp. R570, and 14 CaCA genes in Sorghum bicolor were identified and characterized. These genes consisted of the H+/cation exchanger (CAX), cation/Ca2+ exchanger (CCX), EF-hand / CAX (EFCAX), and Mg2+/H+ exchanger (MHX) families, among which the CCX and EFCAX could be classified into three groups while the CAX could be divided into two groups. The exon/intron structures and motif compositions suggested that the members in the same group were highly conserved. Synteny analysis of CaCAs established their orthologous and paralogous relationships among the superfamily in S. spontaneum, R570, and S. bicolor. The results of protein-protein interactions indicated that these CaCA proteins had direct or indirect interactions. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis demonstrated that most members of Saccharum CaCA genes exhibited a similar expression pattern in response to hormonal (abscisic acid, ABA) treatment but played various roles in response to biotic (Sporisorium scitamineum) and abiotic (cold) stresses. Furthermore, ScCAX4, a gene encoding a cytoplasm, plasma membrane and nucleus positioning protein, was isolated from sugarcane. This gene was constitutively expressed in different sugarcane tissues and its expression was only induced at 3 and 6 h time points after ABA treatment, however was inhibited and indued in the whole process under cold and S. scitamineum stresses, respectively.

CONCLUSIONS

This study systematically conducted comparative analyses of CaCA superfamily genes among S. spontaneum, R570, and S. bicolor, delineating their sequence and structure characteristics, classification, evolutionary history, and putative functions. These results not only provided rich gene resources for exploring the molecular mechanism of the CaCA superfamily genes but also offered guidance and reference for research on other gene families in Saccharum.

Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

BACKGROUND

Calcium (Ca²⁺) plays an important role in plant growth and development, and the maintenance of calcium homeostasis is necessary for the survival of all plant species. Ca²⁺/H⁺ exchangers (CAXs) are a subgroup of the CaCA (Ca²⁺/cation antiporter) superfamily. In general, CAX proteins mediate cytosolic Ca²⁺ entry into vacuoles to prevent excessive accumulation of Ca²⁺ in the cytosol. The CaCA superfamily has been identified and characterised in many plant species; however, characterisation of the CaCA superfamily and functional study of apple CAX proteins have yet to be conducted in apple (Malus × domestica Borkh.).

RESULTS

Here, we identified 21 CaCA family proteins in apple for the first time. Phylogenetic and gene structure analysis, as well as prediction of conserved motifs, suggested that these proteins could be classified into four groups: CAX, CCX, NCL, and MHX. Expression analysis showed that the 10 MdCAX genes we cloned strongly responded to calcium and abiotic stress treatments. Collinearity analysis and characterisation of calcium transport capacity resulted in the identification of a pair of segmental duplication genes: MdCAX3L-1 and MdCAX3L-2; MdCAX3L-2 showed strong calcium transport capacity, whereas MdCAX3L-1 showed no calcium transport capacity. Yeast two-hybrid (Y2H) assays showed that these two proteins could interact with each other. The high sequence similarity (94.6%) makes them a good model for studying the crucial residues and structural basis of the calcium transport of CAX proteins. Prediction of the protein interaction network revealed several proteins that may interact with CAX proteins and play important roles in plant stress responses, such as SOS2, CXIP1, MHX, NRAMP3, and MTP8.

CONCLUSIONS

Our analysis indicated that MdCAX proteins have strong calcium transport capacity and are involved in the abiotic stress response in apple. These findings provide new insight and rich resources for future studies of MdCAX proteins in apple.

Phylogenetic and ion-response analyses reveal a relationship between gene expansion and functional divergence in the Ca2+/cation antiporter family in Angiosperms

Plant CaCA superfamily genes with higher tendency to retain after WGD are more gene expression and function differentiated in ion-response. Plants and animals face different environmental stresses but share conserved Ca²⁺ signaling pathways, such as Ca²⁺/Cation transport. The Ca²⁺/cation antiporters superfamily (CaCAs) is an ancient and widespread family of ion-coupled cation transporters found in all kingdoms of life. We analyzed the molecular evolution progress of the family through comparative genomics and phylogenetics of CaCAs genes from plants and animals, grouping these genes into several families and clades, and identified multiple gene duplication retention events, particularly in the CAX (H⁺/cation exchanger), CCX (cation/Ca²⁺ exchanger), and NCL (Na⁺/Ca²⁺ exchanger-like) families. The tendency of duplication retention differs between families and gene clades. The gene duplication events were probably the result of whole-genome duplication (WGD) in plants and might have led to functional divergence. Tissue and ion-response expression analyses revealed that CaCAs genes with more highly differentiated expression patterns are more likely to be retained as duplicates than those with more conserved expression profiles. Phenotype of Arabidopsis thaliana mutants showed that loss of genes with a greater tendency to be retained after duplication resulted in more severe growth deficiency. CaCAs genes in salt-tolerant species tended to inherit the expression characteristics of their most recent common ancestral genes, with conservative ion-response expression. This study indicates a possible evolutionary scheme for cation transport and illustrates distinct fates and a mechanism for the evolution of gene duplicates. The increased copy numbers of genes and divergences in expression might have contributed to the divergent functions of CaCAs protein, allowing plants to cope with environmental stresses and adapt to a larger number of ecological niches.

Description of AtCAX4 in Response to Abiotic Stress in Arabidopsis

High-capacity tonoplast cation/H⁺ antiport in plants is partially mediated by a family of CAX transporters. Previous studies have reported that CAX activity is affected by an N-terminal autoinhibitory region. CAXs may be present as heterodimers in plant cells, and this phenomenon necessitates further study. In this study, we demonstrate that there is an interaction between CAX4 and CAX1 as determined by the use of a yeast two-hybrid system and a bimolecular fluorescence complementation assay. More specifically, the N-terminal of CAX4 interacts with CAX1. We further observed the over-expression and either a single or double mutant of CAX1 and CAX4 in response to abiotic stress in Arabidopsis. These results suggest that CAX1 and CAX4 can interact to form a heterodimer, and the N-terminal regions of CAX4 play important roles in vivo; this may provide a foundation for a deep study of CAX4 function in the future.

Organellar calcium signaling in plants: An update

Calcium ion (Ca²⁺) is a versatile signaling transducer in all eukaryotic organisms. In plants, intracellular changes in free Ca²⁺ levels act as regulators in many growth and developmental processes. Ca²⁺ also mediates the cellular responses to environmental stimuli and thus plays an important role in providing stress tolerance to plants. Ca²⁺ signals are decoded by a tool kit of various families of Ca²⁺-binding proteins and their downstream targets, which mediate the transformation of the Ca²⁺ signal into appropriate cellular response. Early interest and research on Ca²⁺ signaling focused on its function in the cytosol, however it has become evident that this important regulatory pathway also exists in organelles such as nucleus, chloroplast, mitochondria, peroxisomes and the endomembrane system. In this review, we give an overview on the knowledge about organellar Ca²⁺ signaling with a focus on recent advances and developments.

CAX3 (cation/proton exchanger) mediates a Cd tolerance by decreasing ROS through Ca elevation in Arabidopsis

KEY MESSAGE

Over-expression of CAX3 encoding a cation/proton exchanger enhances Cd tolerance by decreasing ROS (Reactive Oxygen Species) through activating anti-oxidative enzymes via elevation of Ca level in Arabidopsis CAXs (cation/proton exchangers) are involved in the sequestration of cations such as Mn, Li, and Cd, as well as Ca, from cytosol into the vacuole using proton gradients. In addition, it has been reported that CAX1, 2 and 4 are involved in Cd tolerance. Interestingly, it has been reported that CAX3 expressions were enhanced by Cd in Cd-tolerant transgenic plants expressing Hb1 (hemoglobin 1) or UBC1 (Ub-conjugating enzyme 1). Therefore, to investigate whether CAX3 plays a role in increasing Cd tolerance, CAX3 of Arabidopsis and tobacco were over-expressed in Arabidopsis thaliana. Compared to control plants, both transgenic plants displayed an increase in Cd tolerance, no change in Cd accumulation, and enhanced Ca levels. In support of these, AtCAX3-Arabidopsis showed no change in expressions of Cd transporters, but reduced expressions of Ca exporters and lower rate of Ca efflux. By contrast, atcax3 knockout Arabidopsis exhibited a reduced Cd tolerance, while the Cd level was not altered. The expression of Δ90-AtCAX3 (deletion of autoinhibitory domain) increased Cd and Ca tolerance in yeast, while AtCAX3 expression did not. Interestingly, less accumulation of ROS (H2O2 and O2-) was observed in CAX3-expressing transgenic plants and was accompanied with higher antioxidant enzyme activities (SOD, CAT, GR). Taken together, CAX3 over-expression may enhance Cd tolerance by decreasing Cd-induced ROS production by activating antioxidant enzymes and by intervening the positive feedback circuit between ROS generation and Cd-induced spikes of cytoplasmic Ca.

The grapevine CAX-interacting protein VvCXIP4 is exported from the nucleus to activate the tonoplast Ca2+/H+ exchanger VvCAX3

The nuclear-localized CAX-interacting protein VvCXIP4 is exported to the cytosol after a Ca²⁺ pulse, to activate the tonoplast-localized Ca²⁺/H⁺ exchanger VvCAX3. Vacuolar cation/H⁺ exchangers (CAXs) have long been recognized as 'housekeeping' components in cellular Ca²⁺ and trace metal homeostasis, being involved in a range of key cellular and physiological processes. However, the mechanisms that drive functional activation of the transporters are largely unknown. In the present study, we investigated the function of a putative grapevine CAX-interacting protein, VvCXIP4, by testing its ability to activate VvCAX3, previously characterized as a tonoplast-localized Ca²⁺/H⁺ exchanger. VvCAX3 contains an autoinhibitory domain that drives inactivation of the transporter and thus, is incapable of suppressing the Ca²⁺-hypersensitive phenotype of the S. cerevisiae mutant K667. In this study, the co-expression of VvCXIP4 and VvCAX3 in this strain efficiently rescued its growth defect at high Ca²⁺ levels. Flow cytometry experiments showed that yeast harboring both proteins effectively accumulated higher Ca²⁺ levels than cells expressing each of the proteins separately. Bimolecular fluorescence complementation (BiFC) assays allowed visualization of the direct interaction between the proteins in tobacco plants and in yeast, and also showed the self-interaction of VvCAX3 but not of VvCXIP4. Subcellular localization studies showed that, despite being primarily localized to the nucleus, VvCXIP4 is able to move to other cell compartments upon a Ca²⁺ stimulus, becoming prone to interaction with the tonoplast-localized VvCAX3. qPCR analysis showed that both genes are more expressed in grapevine stems and leaves, followed by the roots, and that the steady-state transcript levels were higher in the pulp than in the skin of grape berries. Also, both VvCXIP4 and VvCAX3 were upregulated by Ca²⁺ and Na⁺, indicating they share common regulatory mechanisms. However, VvCXIP4 was also upregulated by Li⁺, Cu²⁺ and Mn²⁺, and its expression increased steadily throughout grape berry development, contrary to VvCAX3, suggesting additional physiological roles for VvCXIP4, including the regulation of VvCAXs not yet functionally characterized. The main novelty of the present study was the demonstration of physical interaction between CXIP and CAX proteins from a woody plant model by BiFC assays, demonstrating the intracellular mobilization of CXIPs in response to Ca²⁺.

Expression of Genes Involved in Heavy Metal Trafficking in Plants Exposed to Salinity Stress and Elevated Cd Concentrations

Many areas intended for crop production suffer from the concomitant occurrence of heavy metal pollution and elevated salinity; therefore, halophytes seem to represent a promising perspective for the bioremediation of contaminated soils. In this study, the influence of Cd treatment (0.01-10.0 mM) and salinity stress (0.4 M NaCl) on the expression of genes involved in heavy metal uptake (irt2-iron-regulated protein 2, zip4-zinc-induced protein 4), vacuolar sequestration (abcc2-ATP-binding cassette 2, cax4-cation exchanger 2 pcs1-phytochelatin synthase 1) and translocation into aerial organs (hma4-heavy metal ATPase 4) were analyzed in a soil-grown semi-halophyte Mesembryanthemum crystallinum. The upregulation of irt2 expression induced by salinity was additionally enhanced by Cd treatment. Such changes were not observed for zip4. Stressor-induced alterations in abcc2, cax4, hma4 and pcs1 expression were most pronounced in the root tissue, and the expression of cax4, hma4 and pcs1 was upregulated in response to salinity and Cd. However, the cumulative effect of both stressors, similar to the one described for irt2, was observed only in the case of pcs1. The importance of salt stress in the irt2 expression regulation mechanism is proposed. To the best of our knowledge, this study is the first to report the combined effect of salinity and heavy metal stress on genes involved in heavy metal trafficking.

Characterization and Expression Analysis of the Ca2+/Cation Antiporter Gene Family in Tomatoes

The Ca²⁺/cation antiporter (CaCA) superfamily plays an important role in the regulation of the essential element Ca²⁺ and cation concentrations. Characterization and expression analyses of CaCA superfamily genes were performed in the tomato (Solanum lycopersicum) as a representative of dicotyledonous plants and fruit crops. Sixteen CaCA candidate genes were found and identified as tomato CaCA, SlCaCA, by a domain search. In a phylogenetic analysis of the SlCaCA superfamily, the 16 genes were classified into SlCAX, SlNCL, SlCCX, and SlMHX families. Among them, Solyc12g011070, belonging to the SlCAX family, had four splice variants, three of which were predicted to be nonfunctional because of a lack of important motifs. EF-hand domains were only found in SlNCL, in addition to consensus Na_Ca_ex domains, and the region containing EF-hand domains was characteristically long in some members of SlNCL. Furthermore, four genes of the SlCCX family were found to be intronless. As for intracellular localization, one SlCCX member was predicted to be localized to the plasma membrane, while other SlCCXs, SlCAXs, and SlMHXs were predicted to be localized to the vacuolar membrane. The expression patterns of SlCaCAs in various organs, including during several developmental stages of fruit, were classified into four groups. Genes involved in each of the SlCAX, SlNCL, and SlCCX gene families were categorized into three or four groups according to expression patterns, suggesting role sharing within each family. The main member in each subfamily and the members with characteristic fruit expression patterns included genes whose expression was regulated by sugar or auxin and that were highly expressed in a line having metabolite-rich fruit.

Calcium-mediation of jasmonate biosynthesis and signaling in plants

Jasmonates (JAs) play vital roles in regulating a range of plant growth and development processes including seed germination, seedling development, reproduction, formation and development of storage organs, and senescence. JAs are also involved in the regulation of plant responses to environmental stimuli. The biosynthesis of JAs takes place in three different subcellular compartments, namely, the chloroplast, peroxisome, and cytoplasm. JAs activate the expression of JA-responsive genes by degrading jasmonate zinc-finger-inflorescence meristem (Zim) domain (JAZ) repressors via the E3 ubiquitin-ligase Skp/Cullin/F-box protein CORONATINE INSENSITIVE1 (COI1) complex (SCF^COI1) by using 26S proteasome. Calcium, reactive oxygen species (ROS), mitogen-activated protein kinase (MAPK), and nitric oxide (NO) are involved in the regulation of the biosynthesis and signaling of JAs in plants. Among these signaling molecules, calcium is one of the most important within plant cells. In plants, intracellular calcium levels change in response to JAs, resulting in calcium signatures with temporal and spatial features. Calcium channels are involved in the generation of calcium signatures. Calcium sensors, including calmodulins (CaMs), CaM-like proteins (CMLs), calcineurin B-like proteins (CBLs), and calcium-dependent protein kinases (CDPKs), can act to regulate the biosynthesis and signaling of JAs.

Calcium transport across plant membranes: mechanisms and functions

Contents Summary 49 I. Introduction 49 II. Physiological and structural characteristics of plant Ca²⁺ -permeable ion channels 50 III. Ca²⁺ extrusion systems 61 IV. Concluding remarks 64 Acknowledgements 64 References 64 SUMMARY: Calcium is an essential structural, metabolic and signalling element. The physiological functions of Ca²⁺ are enabled by its orchestrated transport across cell membranes, mediated by Ca²⁺ -permeable ion channels, Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers. Bioinformatics analysis has not determined any Ca²⁺ -selective filters in plant ion channels, but electrophysiological tests do reveal Ca²⁺ conductances in plant membranes. The biophysical characteristics of plant Ca²⁺ conductances have been studied in detail and were recently complemented by molecular genetic approaches. Plant Ca²⁺ conductances are mediated by several families of ion channels, including cyclic nucleotide-gated channels (CNGCs), ionotropic glutamate receptors, two-pore channel 1 (TPC1), annexins and several types of mechanosensitive channels. Key Ca²⁺ -mediated reactions (e.g. sensing of temperature, gravity, touch and hormones, and cell elongation and guard cell closure) have now been associated with the activities of specific subunits from these families. Structural studies have demonstrated a unique selectivity filter in TPC1, which is passable for hydrated divalent cations. The hypothesis of a ROS-Ca²⁺ hub is discussed, linking Ca²⁺ transport to ROS generation. CNGC inactivation by cytosolic Ca²⁺ , leading to the termination of Ca²⁺ signals, is now mechanistically explained. The structure-function relationships of Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers, and their regulation and physiological roles are analysed.

The Evolution of Calcium-Based Signalling in Plants

The calcium-based intracellular signalling system is used ubiquitously to couple extracellular stimuli to their characteristic intracellular responses. It is becoming clear from genomic and physiological investigations that while the basic elements in the toolkit are common between plants and animals, evolution has acted in such a way that, in plants, some components have diversified with respect to their animal counterparts, while others have either been lost or have never evolved in the plant lineages. In comparison with animals, in plants there appears to have been a loss of diversity in calcium-influx mechanisms at the plasma membrane. However, the evolution of the calcium-storing vacuole may provide plants with additional possibilities for regulating calcium influx into the cytosol. Among the proteins that are involved in sensing and responding to increases in calcium, plants possess specific decoder proteins that are absent from the animal lineage. In seeking to understand the selection pressures that shaped the plant calcium-signalling toolkit, we consider the evolution of fast electrical signalling. We also note that, in contrast to animals, plants apparently do not make extensive use of cyclic-nucleotide-based signalling. It is possible that reliance on a single intracellular second-messenger-based system, coupled with the requirement to adapt to changing environmental conditions, has helped to define the diversity of components found in the extant plant calcium-signalling toolkit.

Changes of cationic transport in AtCAX5 transformant yeast by electromagnetic field environments

The electromagnetic field (EMF) is newly considered as an exogenous environmental stimulus that is closely related to ion transportation on the cellular membrane, maintaining the internal ionic homeostasis. Cation transports of Ca²⁺ and other metal ions, Cd²⁺, Zn²⁺, and Mn²⁺were studied in terms of the external Ca²⁺ stress, [Ca²⁺]_ext, and exposure to the physical EMF. A specific yeast strain K667 was used for controlling CAX5 (cation/H⁺ exchanger) expression. Culture samples were exposed to 60 Hz, 0.1 mT sinusoidal or square magnetics waves, and intracellular cations of each sample were measured and analyzed. AtCAX5 transformant yeast grew normally under the metallic stress. However, the growth of the control group was significantly inhibited under the same cation concentration; 60 Hz and 0.1 mT magnetic field enhanced intracellular cation concentrations significantly as exposure time increased both in the AtCAX5 transformed yeast and in the control group. However, the AtCAX5-transformed yeast showed higher concentration of the intracellular cations than the control group under the same exposure EMF. AtCAX5-transformed yeasts displayed an increment in [Ca²⁺]_int, [K⁺]_int, [Na⁺]_int, and [Zn²⁺]_int concentration under the presence of both sinusoidal and square-waved EMF stresses compared to the control group, which shows that AtCAX5 expressed in the vacuole play an important role in maintaining the homeostasis of intracellular cations. These findings could be utilized in the cultivation of the crops which were resistant to excessive exogenous ions or in the production of biomass containing a large proportion of ions for nutritional food or in the bioremediation process in metal-polluted environments.

The contribution of organelles to plant intracellular Calcium signalling

Calcium (Ca2+) is among the most important intracellular messengers in living organisms. Understanding of the players and dynamics of Ca2+ signalling pathways in plants may help to unravel the molecular basis of their exceptional flexibility to respond and to adapt to different stimuli. In the present review we focus on new tools that have recently revolutionized our view of organellar Ca2+ signalling as well as on the current knowledge regarding the pathways mediating Ca2+ fluxes across intracellular membranes. The contribution of organelles and cellular subcompartments to the orchestrated response via Ca2+ signalling within a cell is also discussed, underlining the fact that one of the greatest challenges in the field is the elucidation of how influx and efflux Ca2+ transporters/channels are regulated in a concerted manner to translate specific information into a Ca2+ signature.

Advances and current challenges in calcium signaling

Content Summary 414 I. Introduction 415 II. Ca²⁺ importer and exporter in plants 415 III. The Ca²⁺ decoding toolkit in plants 415 IV. Mechanisms of Ca²⁺ signal decoding 417 V. Immediate Ca²⁺ signaling in the regulation of ion transport 418 VI. Ca²⁺ signal integration into long-term ABA responses 419 VII Integration of Ca²⁺ and hormone signaling through dynamic complex modulation of the CCaMK/CYCLOPS complex 420 VIII Ca²⁺ signaling in mitochondria and chloroplasts 422 IX A view beyond recent advances in Ca²⁺ imaging 423 X Modeling approaches in Ca²⁺ signaling 424 XI Conclusions: Ca²⁺ signaling a still young blooming field of plant research 424 Acknowledgements 425 ORCID 425 References 425 SUMMARY: Temporally and spatially defined changes in Ca²⁺ concentration in distinct compartments of cells represent a universal information code in plants. Recently, it has become evident that Ca²⁺ signals not only govern intracellular regulation but also appear to contribute to long distance or even organismic signal propagation and physiological response regulation. Ca²⁺ signals are shaped by an intimate interplay of channels and transporters, and during past years important contributing individual components have been identified and characterized. Ca²⁺ signals are translated by an elaborate toolkit of Ca²⁺ -binding proteins, many of which function as Ca²⁺ sensors, into defined downstream responses. Intriguing progress has been achieved in identifying specific modules that interconnect Ca²⁺ decoding proteins and protein kinases with downstream target effectors, and in characterizing molecular details of these processes. In this review, we reflect on recent major advances in our understanding of Ca²⁺ signaling and cover emerging concepts and existing open questions that should be informative also for scientists that are currently entering this field of ever-increasing breath and impact.

Mechanisms of cytosolic calcium elevation in plants: the role of ion channels, calcium extrusion systems and NADPH oxidase-mediated 'ROS-Ca2+ Hub'

Elevation in the cytosolic free calcium is crucial for plant growth, development and adaptation. Calcium influx into plant cells is mediated by Ca2+ depolarisation-activated, hyperpolarisation-activated and voltage-independent Ca2+-permeable channels (DACCs, HACCs and VICCs respectively). These channels are encoded by the following gene families: (1) cyclic nucleotide-gated channels (CNGCs), (2) ionotropic glutamate receptors (GLRs), (3) annexins, (4) 'mechanosensitive channels of small (MscS) conductance'-like channels (MSLs), (5) 'mid1-complementing activity' channels (MCAs), Piezo channels, and hyperosmolality-induced [Ca2+]cyt. channel 1 (OSCA1). Also, a 'tandem-pore channel1' (TPC1) catalyses Ca2+ efflux from the vacuole in response to the plasma membrane-mediated Ca2+ elevation. Recent experimental data demonstrated that Arabidopsis thaliana (L.) Heynh. CNGCs 2, 5-10, 14, 16 and 18, GLRs 1.2, 3.3, 3.4, 3.6 and 3.7, TPC1, ANNEXIN1, MSL9 and MSL10,MCA1 and MCA2, OSCA1, and some their homologues counterparts in other species, are responsible for Ca2+ currents and/or cytosolic Ca2+ elevation. Extrusion of Ca2+ from the cytosol is mediated by Ca2+-ATPases and Ca2+/H+ exchangers which were recently examined at the level of high resolution crystal structure. Calcium-activated NADPH oxidases and reactive oxygen species (ROS)-activated Ca2+ conductances form a self-amplifying 'ROS-Ca2+hub', enhancing and transducing Ca2+ and redox signals. The ROS-Ca2+ hub contributes to physiological reactions controlled by ROS and Ca2+, demonstrating synergism and unity of Ca2+ and ROS signalling mechanisms.

Transcriptomic Profiling and Physiological Analysis of Haloxylon ammodendron in Response to Osmotic Stress

Haloxylon ammodendron, a perennial xero-halophyte, is an essential species for investigating the effects of drought on desert tree. To gain a comprehensive knowledge on the responses of H. ammodendron to drought stress, we specially performed the molecular and physiological analysis of H. ammodendron in response to -0.75 MPa osmotic stress for six and 24 h in lab condition via RNA-seq and digital gene expression (DGE). In total, 87,109 unigenes with a mean length of 680 bp and 13,486 potential simple sequence repeats (SSRs) were generated, and 3353 differentially expressed genes (DEGs) in shoots and 4564 in roots were identified under stress. These DEGs were mainly related to ion transporters, signal transduction, ROS-scavenging, photosynthesis, cell wall organization, membrane stabilization and hormones. Moreover, the physiological changes of inorganic ions and organic solute content, peroxidase (POD) activity and osmotic potential were in accordance with dynamic transcript profiles of the relevant genes. In this study, a detailed investigation of the pathways and candidate genes identified promote the research on the molecular mechanisms of abiotic stress tolerance in the xero-halophytic species. Our data provides valuable genetic resources for future improvement of forage and crop species for better adaptation to abiotic stresses.

The grapevine VvCAX3 is a cation/H+ exchanger involved in vacuolar Ca2+ homeostasis

The grapevine VvCAX3 mediates calcium transport in the vacuole and is mostly expressed in green grape berries and upregulated by Ca ²⁺ , Na ⁺ and methyl jasmonate. Calcium is an essential plant nutrient with important regulatory and structural roles in the berries of grapevine (Vitis vinifera L.). On the other hand, the proton-cation exchanger CAX proteins have been shown to impact Ca²⁺ homeostasis with important consequences for fruit integrity and resistance to biotic/abiotic stress. Here, the CAX gene found in transcriptomic databases as having one of the highest expressions in grapevine tissues, VvCAX3, was cloned and functionally characterized. Heterologous expression in yeast showed that a truncated version of VvCAX3 lacking its NNR autoinhibitory domain (sCAX3) restored the ability of the yeast strain to grow in 100-200 mM Ca²⁺, demonstrating a role in Ca²⁺ transport. The truncated VvCAX3 was further shown to be involved in the transport of Na⁺, Li⁺, Mn²⁺ and Cu²⁺ in yeast cells. Subcellular localization studies using fluorescently tagged proteins confirmed VvCAX3 as a tonoplast transporter. VvCAX3 is expressed in grapevine stems, leaves, roots, and berries, especially at pea size, decreasing gradually throughout development, in parallel with the pattern of calcium accumulation in the fruit. The transcript abundance of VvCAX3 was shown to be regulated by methyl jasmonate (MeJA), Ca²⁺, and Na⁺ in grape cell suspensions, and the VvCAX3 promotor contains several predicted cis-acting elements related to developmental and stress response processes. As a whole, the results obtained add new insights on the mechanisms involved in calcium homeostasis and intracellular compartmentation in grapevine, and indicate that VvCAX3 may be an interesting target towards the development of strategies for enhancement of grape berry properties.

Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency

Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation (SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea (Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-(MmSWRI9)-chickpea and M. ciceri CP-31-(McCP-31)-chickpea associations under Pi-sufficient and Pi-deficient conditions, of which the McCP-31-chickpea association has a better SNF capacity than the MmSWRI9-chickpea association during Pi starvation. Our investigation revealed that more genes showed altered expression patterns in MmSWRI9-induced nodules than in McCP-31-induced nodules (540 vs. 225) under Pi deficiency, suggesting that the Pi-starvation-more-sensitive MmSWRI9-induced nodules required expression change in a larger number of genes to cope with low-Pi stress than the Pi-starvation-less-sensitive McCP-31-induced nodules. The functional classification of differentially expressed genes (DEGs) was examined to gain an understanding of how chickpea nodules respond to Pi starvation, caused by soil Pi deficiency. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Pi remobilization and signalling were found in Pi-starved MmSWRI9-induced nodules than in Pi-starved McCP-31-induced nodules. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of nodules to Pi deficiency, ultimately leading to the development of Pi-efficient chickpea symbiotic associations suitable for Pi-deficient soils.

Heterodimerization of Arabidopsis calcium/proton exchangers contributes to regulation of guard cell dynamics and plant defense responses

Arabidopsis thaliana cation exchangers (CAX1 and CAX3) are closely related tonoplast-localized calcium/proton (Ca2+/H+) antiporters that contribute to cellular Ca2+ homeostasis. CAX1 and CAX3 were previously shown to interact in yeast; however, the function of this complex in plants has remained elusive. Here, we demonstrate that expression of CAX1 and CAX3 occurs in guard cells. Additionally, CAX1 and CAX3 are co-expressed in mesophyll tissue in response to wounding or flg22 treatment, due to the induction of CAX3 expression. Having shown that the transporters can be co-expressed in the same cells, we demonstrate that CAX1 and CAX3 can form homomeric and heteromeric complexes in plants. Consistent with the formation of a functional CAX1-CAX3 complex, CAX1 and CAX3 integrated into the yeast genome suppressed a Ca2+-hypersensitive phenotype of mutants defective in vacuolar Ca2+ transport, and demonstrated enzyme kinetics different from those of either CAX protein expressed by itself. We demonstrate that the interactions between CAX proteins contribute to the functioning of stomata, because stomata were more closed in cax1-1, cax3-1, and cax1-1/cax3-1 loss-of-function mutants due to an inability to buffer Ca2+ effectively. We hypothesize that the formation of CAX1-CAX3 complexes may occur in the mesophyll to affect intracellular Ca2+ signaling during defense responses.

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. Molecular characterization of these proteins has been performed in certain plants, but they are still not characterized in Triticum aestivum (bread wheat). Herein, we identified 34 TaCaCA superfamily proteins, which were classified into TaCAX, TaCCX, TaNCL, and TaMHX protein families based on their structural organization and evolutionary relation with earlier reported proteins. Since the T. aestivum comprises an allohexaploid genome, TaCaCA genes were derived from each A, B, and D subgenome and homeologous chromosome (HC), except chromosome-group 1. Majority of genes were derived from more than one HCs in each family that were considered as homeologous genes (HGs) due to their high similarity with each other. These HGs showed comparable gene and protein structures in terms of exon/intron organization and domain architecture. Majority of TaCaCA proteins comprised two Na_Ca_ex domains. However, TaNCLs consisted of an additional EF-hand domain with calcium binding motifs. Each TaCaCA protein family consisted of about 10 transmembrane and two α-repeat regions with specifically conserved signature motifs except TaNCL, which had single α-repeat. Variable expression of most of the TaCaCA genes during various developmental stages suggested their specified role in development. However, constitutively high expression of a few genes like TaCAX1-A and TaNCL1-B indicated their role throughout the plant growth and development. The modulated expression of certain genes during biotic (fungal infections) and abiotic stresses (heat, drought, salt) suggested their role in stress response. Majority of TaCCX and TaNCL family genes were found highly affected during various abiotic stresses. However, the role of individual gene needs to be established. The present study unfolded the opportunity for detail functional characterization of TaCaCA proteins and their utilization in future crop improvement programs.

CAX-ing a wide net: Cation/H(+) transporters in metal remediation and abiotic stress signalling

Cation/proton exchangers (CAXs) are a class of secondary energised ion transporter that are being implicated in an increasing range of cellular and physiological functions. CAXs are primarily Ca(2+) efflux transporters that mediate the sequestration of Ca(2+) from the cytosol, usually into the vacuole. Some CAX isoforms have broad substrate specificity, providing the ability to transport trace metal ions such as Mn(2+) and Cd(2+) , as well as Ca(2+) . In recent years, genomic analyses have begun to uncover the expansion of CAXs within the green lineage and their presence within non-plant species. Although there appears to be significant conservation in tertiary structure of CAX proteins, there is diversity in function of CAXs between species and individual isoforms. For example, in halophytic plants, CAXs have been recruited to play a role in salt tolerance, while in metal hyperaccumulator plants CAXs are implicated in cadmium transport and tolerance. CAX proteins are involved in various abiotic stress response pathways, in some cases as a modulator of cytosolic Ca(2+) signalling, but in some situations there is evidence of CAXs acting as a pH regulator. The metal transport and abiotic stress tolerance functions of CAXs make them attractive targets for biotechnology, whether to provide mineral nutrient biofortification or toxic metal bioremediation. The study of non-plant CAXs may also provide insight into both conserved and novel transport mechanisms and functions.

Tissue-specific root ion profiling reveals essential roles of the CAX and ACA calcium transport systems in response to hypoxia in Arabidopsis

Waterlogging is a major abiotic stress that limits the growth of plants. The crucial role of Ca(2+) as a second messenger in response to abiotic and biotic stimuli has been widely recognized in plants. However, the physiological and molecular mechanisms of Ca(2+) distribution within specific cell types in different root zones under hypoxia is poorly understood. In this work, whole-plant physiological and tissue-specific Ca(2+) changes were studied using several ACA (Ca(2+)-ATPase) and CAX (Ca(2+)/proton exchanger) knock-out Arabidopsis mutants subjected to waterlogging treatment. In the wild-type (WT) plants, several days of hypoxia decreased the expression of ACA8, CAX4, and CAX11 by 33% and 50% compared with the control. The hypoxic treatment also resulted in an up to 11-fold tissue-dependent increase in Ca(2+) accumulation in root tissues as revealed by confocal microscopy. The increase was much higher in stelar cells in the mature zone of Arabidopsis mutants with loss of function for ACA8, ACA11, CAX4, and CAX11 In addition, a significantly increased Ca(2+) concentration was found in the cytosol of stelar cells in the mature zone after hypoxic treatment. Three weeks of waterlogging resulted in dramatic loss of shoot biomass in cax11 plants (67% loss in shoot dry weight), while in the WT and other transport mutants this decline was only 14-22%. These results were also consistent with a decline in leaf chlorophyll fluorescence (F v/F m). It is suggested that CAX11 plays a key role in maintaining cytosolic Ca(2+) homeostasis and/or signalling in root cells under hypoxic conditions.

Vacuolar compartmentalization as indispensable component of heavy metal detoxification in plants

Plant cells orchestrate an array of molecular mechanisms for maintaining plasmatic concentrations of essential heavy metal (HM) ions, for example, iron, zinc and copper, within the optimal functional range. In parallel, concentrations of non-essential HMs and metalloids, for example, cadmium, mercury and arsenic, should be kept below their toxicity threshold levels. Vacuolar compartmentalization is central to HM homeostasis. It depends on two vacuolar pumps (V-ATPase and V-PPase) and a set of tonoplast transporters, which are directly driven by proton motive force, and primary ATP-dependent pumps. While HM non-hyperaccumulator plants largely sequester toxic HMs in root vacuoles, HM hyperaccumulators usually sequester them in leaf cell vacuoles following efficient long-distance translocation. The distinct strategies evolved as a consequence of organ-specific differences particularly in vacuolar transporters and in addition to distinct features in long-distance transport. Recent molecular and functional characterization of tonoplast HM transporters has advanced our understanding of their contribution to HM homeostasis, tolerance and hyperaccumulation. Another important part of the dynamic vacuolar sequestration syndrome involves enhanced vacuolation. It involves vesicular trafficking in HM detoxification. The present review provides an updated account of molecular aspects that contribute to the vacuolar compartmentalization of HMs.