Salt-dependent regulation of a CNG channel subfamily in Arabidopsis

A cyclic nucleotide-gated channel gene HcCNGC21 positively regulates salt and drought stress responses in kenaf (Hibiscus cannabinus L.)

Cyclic Nucleotide-Gated Channels (CNGCs) serve as Ca2+ permeable cation transport pathways, which are involved in the regulation of various biological functions such as plant cell ion selective permeability, growth and development, responses to biotic and abiotic stresses. At the present study, a total of 31 CNGC genes were identified and bioinformatically analyzed in kenaf. Among these genes, HcCNGC21 characterized to localize at the plasma membrane, with the highest expression levels in leaves, followed by roots. In addition, HcCNGC21 could be significantly induced under salt or drought stress. Virus-induced gene silencing (VIGS) of HcCNGC21 in kenaf caused notable growth inhibition under salt or drought stress, characterized by reductions in plant height, stem diameter, leaf area, root length, root surface area, and root tip number. Meanwhile, the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were significantly decreased, accompanied by reduced levels of osmoregulatory substances and total chlorophyll content. However, ROS accumulation and Na+ content increased. The expression of stress-responsive genes, such as HcSOD, HcPOD, HcCAT, HcERF3, HcNAC29, HcP5CS, HcLTP, and HcNCED, was significantly downregulated in these silenced lines. However, under salt or drought stress, the physiological performance and expression of stress-related genes in transgenic Arabidopsis thaliana plants overexpressing HcCNGC21 were diametrically opposite to those of TRV2-HcCNGC21 kenaf line. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that HcCNGC21 interacts with HcAnnexin D1. These findings collectively underscore the positive role of HcCNGC21 in plant resistance to salt and drought stress.

Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance

Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.

Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study in Spartina alterniflora

Salt stress poses a significant threat to global cereal crop production, emphasizing the need for a comprehensive understanding of salt tolerance mechanisms. Accurate functional annotations of differentially expressed genes are crucial for gaining insights into the salt tolerance mechanism. The challenge of predicting gene functions in under-studied species, especially when excluding infrequent GO terms, persists. Therefore, we proposed the use of NetGO 3.0, a machine learning-based annotation method that does not rely on homology information between species, to predict the functions of differentially expressed genes under salt stress. Spartina alterniflora, a halophyte with salt glands, exhibits remarkable salt tolerance, making it an excellent candidate for in-depth transcriptomic analysis. However, current research on the S. alterniflora transcriptome under salt stress is limited. In this study we used S. alterniflora as an example to investigate its transcriptional responses to various salt concentrations, with a focus on understanding its salt tolerance mechanisms. Transcriptomic analysis revealed substantial changes impacting key pathways, such as gene transcription, ion transport, and ROS metabolism. Notably, we identified a member of the SWEET gene family in S. alterniflora, SA_12G129900.m1, showing convergent selection with the rice ortholog SWEET15. Additionally, our genome-wide analyses explored alternative splicing responses to salt stress, providing insights into the parallel functions of alternative splicing and transcriptional regulation in enhancing salt tolerance in S. alterniflora. Surprisingly, there was minimal overlap between differentially expressed and differentially spliced genes following salt exposure. This innovative approach, combining transcriptomic analysis with machine learning-based annotation, avoids the reliance on homology information and facilitates the discovery of unknown gene functions, and is applicable across all sequenced species.

Insights into plant salt stress signaling and tolerance

Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity. It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction. Multiple determinants of salt tolerance have been identified in plants, and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized. Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism. This review summarizes the advances in salt stress perception, signaling, and response in plants. A better understanding of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.

Molecular switches in plant stress adaptation

Climate change poses a significant threat to the global ecosystem, prompting plants to use various adaptive mechanisms via molecular switches to combat biotic and abiotic stress factors. These switches activate stress-induced pathways by altering their configuration between stable states. In this review, we investigated the regulation of molecular switches in different plant species in response to stress, including the stress-regulated response of multiple switches in Arabidopsis thaliana. We also discussed techniques for developing stress-resilient crops using molecular switches through advanced biotechnological tools. The literature search, conducted using databases such as PubMed, Google Scholar, Web of Science, and SCOPUS, utilized keywords such as molecular switch, plant adaptation, biotic and abiotic stresses, transcription factors, Arabidopsis thaliana, and crop improvement. Recent studies have shown that a single molecular switch can regulate multiple stress networks, and multiple switches can regulate a single stress condition. This multifactorial understanding provides clarity to the switch regulatory network and highlights the interrelationships of different molecular switches. Advanced breeding techniques, along with genomic and biotechnological tools, have paved the way for further research on molecular switches in crop improvement. The use of synthetic biology in molecular switches will lead to a better understanding of plant stress biology and potentially bring forth a new era of stress-resilient, climate-smart crops worldwide.

A histochemical reporter system to study extracellular ATP response in plants

When cells experience acute mechanical distress, they release ATP from their cellular compartment into the surrounding microenvironment. This extracellular ATP (eATP) can then act as a danger signal-signaling cellular damage. In plants, cells adjacent to damage detect rising eATP concentrations through the cell-surface receptor kinase, P2K1. Following eATP perception, P2K1 initiates a signaling cascade mobilizing plant defense. Recent transcriptome analysis revealed a profile of eATP-induced genes sharing pathogen- and wound-response hallmarks-consistent with a working model for eATP as a defense-mobilizing danger signal. To build on the transcriptional footprint and broaden our understanding of dynamic eATP signaling responses in plants, we aimed to i) generate a visual toolkit for eATP-inducible marker genes using a β-glucuronidase (GUS) reporter system and ii) evaluate the spatiotemporal response of these genes to eATP in plant tissues. Here, we demonstrate that the promoter activities of five genes, ATPR1, ATPR2, TAT3, WRKY46, and CNGC19, were highly sensitive to eATP in the primary root meristem and elongation zones with maximal responses at 2 h after treatment. These results suggest the primary root tip as a hub to study eATP-signaling activity and provide a proof-of-concept toward using these reporters to further dissect eATP and damage signaling in plants.

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

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

Transcriptome analysis reveals the regulation of cyclic nucleotide-gated ion channels in response to exogenous abscisic acid and calcium treatment under drought stress in tomato

Background: Drought stress can limit the growth and development of tomato seedlings and cause considerable loss of tomato yield. Exogenous abscisic acid (ABA) and calcium (Ca²⁺) can effectively alleviate the damage of drought stress to plants in part because Ca²⁺ acts as a second messenger in the drought resistance pathway. Although cyclic nucleotide-gated ion channels (CNGCs) are common non-specific Ca²⁺ osmotic channels in cell membranes, a thorough understanding of the transcriptome characteristics of tomato treated with exogenous ABA and Ca²⁺ under drought stress is necessary to characterize the molecular mechanism of CNGC involved in tomato drought resistance. Results: There were 12,896 differentially expressed genes in tomato under drought stress, as well as 11,406 and 12,502 differentially expressed genes after exogenous ABA and Ca²⁺ application, respectively. According to functional annotations and reports, the 19 SlCNGC genes related to Ca²⁺ transport were initially screened, with 11 SlCNGC genes that were upregulated under drought stress and downregulated after exogenous ABA application. After exogenous Ca²⁺ application, the data showed that two of these genes were upregulated, while nine genes were downregulated. Based on these expression patterns, we predicted the role of SlCNGC genes in the drought resistance pathway and their regulation by exogenous ABA and Ca²⁺ in tomato. Conclusion: The results of this study provide foundational data for further study of the function of SlCNGC genes and a more comprehensive understanding of drought resistance mechanisms in tomato.

Genome-Wide Identification and Expression Analysis of BraGLRs Reveal Their Potential Roles in Abiotic Stress Tolerance and Sexual Reproduction

Glutamate receptors (GLRs) are involved in multiple functions during the plant life cycle through affecting the Ca²⁺ concentration. However, GLRs in Brassica species have not yet been reported. In this study, 16 glutamate receptor-like channels (GLR) belonged to two groups were identified in the Brassica rapa (B. rapa) genome by bioinformatic analysis. Most members contain domains of ANF_receptor, Peripla_BP_6, Lig_chan, SBP_bac_3, and Lig_chan_Glu_bd that are closely related to glutamate receptor channels. This gene family contains many elements associated with drought stress, low temperature stress, methyl jasmonate (MeJA), salicylic acid (SA), and other stress resistance. Gene expression profiles showed that BraGLR genes were expressed in roots, stems, leaves, flowers, and siliques. BraGLR5 expression was elevated after drought stress in drought-sensitive plants. BraGLR1, BraGLR8, and BraGLR11 expression were significantly upregulated after salt stress. BraGLR3 expression is higher in the female sterile-line mutants than in the wild type. The expression levels of BraGLR6, BraGLR9, BraGLR12, and BraGLR13 were significantly higher in the male sterile-line mutants than in the wild type. The expression of most BraGLRs increased after self-pollination, with BraGLR9 exhibiting the greatest increase. These results suggest that BraGLRs play an important role in abiotic stress tolerance and sexual reproduction.

Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance

BACKGROUND

Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that participate in a variety of biological functions, such as signaling pathways, plant development, and environmental stress and stimulus responses. Nevertheless, there have been few studies on CNGC gene family in cotton.

RESULTS

In this study, a total of 114 CNGC genes were identified from the genomes of 4 cotton species. These genes clustered into 5 main groups: I, II, III, IVa, and IVb. Gene structure and protein motif analysis showed that CNGCs on the same branch were highly conserved. In addition, collinearity analysis showed that the CNGC gene family had expanded mainly by whole-genome duplication (WGD). Promoter analysis of the GhCNGCs showed that there were a large number of cis-acting elements related to abscisic acid (ABA). Combination of transcriptome data and the results of quantitative RT-PCR (qRT-PCR) analysis revealed that some GhCNGC genes were induced in response to salt and drought stress and to exogenous ABA. Virus-induced gene silencing (VIGS) experiments showed that the silencing of the GhCNGC32 and GhCNGC35 genes decreased the salt tolerance of cotton plants (TRV:00). Specifically, physiological indexes showed that the malondialdehyde (MDA) content in gene-silenced plants (TRV:GhCNGC32 and TRV:GhCNGC35) increased significantly under salt stress but that the peroxidase (POD) activity decreased. After salt stress, the expression level of ABA-related genes increased significantly, indicating that salt stress can trigger the ABA signal regulatory mechanism.

CONCLUSIONS

we comprehensively analyzed CNGC genes in four cotton species, and found that GhCNGC32 and GhCNGC35 genes play an important role in cotton salt tolerance. These results laid a foundation for the subsequent study of the involvement of cotton CNGC genes in salt tolerance.

Comparative Physiological and Transcriptome Profiles Uncover Salt Tolerance Mechanisms in Alfalfa

Salinity is a major limiting factor that affects crop production. Understanding of the mechanisms of plant salt tolerance is critical for improving crop yield on saline land. Alfalfa (Medicago sativa L.) is the most important forage crop, while its salt tolerance mechanisms are largely unknown. The physiological and transcriptomic responses in two contrasting salt tolerant cultivars to salinity stress were investigated in the present study. "Magnum Salt" showed higher salt tolerance than "Adrenalin," with higher relative germination rate, survival rate, biomass and K⁺/Na⁺ ratio after salt treatment. Activities of antioxidant enzymes SOD, CAT and GR, and proline concentrations were upregulated to higher levels in roots and shoots in Magnum Salt than in Adrenalin after salinity stress, except for no difference in GR activity in shoots, and lower levels of O₂ ^⋅- and H₂O₂ were accumulated in leaves. It was interesting to find that salinity caused a decrease in total unsaturated fatty acid in Adrenalin other than Magnum Salt, C18:2 was increased significantly after salinity in Magnum Salt, while it was unaltered in Adrenalin. High quality RNA sequencing (RNA-seq) data was obtained from samples of Magnum Salt and Adrenalin at different time points (0, 2, and 26 h). Generally, "phagosome," "TCA cycle" and "oxidative phosphorylation" pathways were inhibited by salinity stress. Upregulated DEGs in Magnum Salt were specifically enriched in "fatty acid metabolism," "MAPK signaling" and "hormone signal transduction" pathways. The DEGs involved in ionic homeostasis, reactive oxygen species (ROS) scavenging and fatty acid metabolism could partially explain the difference in salt tolerance between two cultivars. It is suggested that salt tolerance in alfalfa is associated with regulation of ionic homeostasis, antioxidative enzymes and fatty acid metabolism at both transcriptional and physiological level.

Full-Length Transcriptomics Reveals Complex Molecular Mechanism of Salt Tolerance in Bromus inermis L

Bromus inermis L. (commonly known as smooth bromegrass) is a grass species with high nutritional value, great palatability, cold tolerance, and grazing resistance, which has been widely cultivated for pasture and sand fixation in northern and northwestern China. Salt stress is a main environmental factor limiting growth and production of smooth bromegrass. In this study, we performed PacBio Iso-Seq to construct the first full-length transcriptome database for smooth bromegrass under 300 mM NaCl treatment at different time points. Third-generation full-length transcriptome sequencing yielded 19.67 G polymerase read bases, which were assembled into 355,836 full-length transcripts with an average length of 2,542 bp. A total of 116,578 differentially expressed genes were obtained by comparing the results of third-generation sequencing and second-generation sequencing. GO and KEGG enrichment analyses revealed that multiple pathways were differently activated in leaves and roots. In particular, a number of genes participating in the molecular network of plant signal perception, signal transduction, transcription regulation, antioxidant defense, and ion regulation were affected by NaCl treatment. In particular, the CBL-CIPK, MAPK, ABA signaling network, and SOS core regulatory pathways of Ca²⁺ signal transduction were activated to regulate salt stress response. In addition, the expression patterns of 10 salt-responsive genes were validated by quantitative real-time PCR, which were consistent with those detected by RNA-Seq. Our results reveal the molecular regulation of smooth bromegrass in response to salt stress, which are important for further investigation of critical salt responsive genes and molecular breeding of salt-tolerant smooth bromegrass.

Dynamic Expression, Differential Regulation and Functional Diversity of the CNGC Family Genes in Cotton

Cyclic nucleotide-gated channels (CNGCs) constitute a family of non-selective cation channels that are primarily permeable to Ca2+ and activated by the direct binding of cyclic nucleotides (i.e., cAMP and cGMP) to mediate cellular signaling, both in animals and plants. Until now, our understanding of CNGCs in cotton (Gossypium spp.) remains poorly addressed. In the present study, we have identified 40, 41, 20, 20, and 20 CNGC genes in G. hirsutum, G. barbadense, G. herbaceum, G. arboreum, and G. raimondii, respectively, and demonstrated characteristics of the phylogenetic relationships, gene structures, chromosomal localization, gene duplication, and synteny. Further investigation of CNGC genes in G. hirsutum, named GhCNGC1-40, indicated that they are not only extensively expressed in various tissues and at different developmental stages, but also display diverse expression patterns in response to hormones (abscisic acid, salicylic acid, methyl jasmonate, ethylene), abiotic (salt stress) and biotic (Verticillium dahlia infection) stimuli, which conform with a variety of cis-acting regulatory elements residing in the promoter regions; moreover, a set of GhCNGCs are responsive to cAMP signaling during cotton fiber development. Protein–protein interactions supported the functional aspects of GhCNGCs in plant growth, development, and stress responses. Accordingly, the silencing of the homoeologous gene pair GhCNGC1&18 and GhCNGC12&31 impaired plant growth and development; however, GhCNGC1&18-silenced plants enhanced Verticillium wilt resistance and salt tolerance, whereas GhCNGC12&31-silenced plants had opposite effects. Together, these results unveiled the dynamic expression, differential regulation, and functional diversity of the CNGC family genes in cotton. The present work has laid the foundation for further studies and the utilization of CNGCs in cotton genetic improvement.

Fighting salt or enemies: shared perception and signaling strategies

Plants react to a myriad of biotic and abiotic environmental signals through specific cellular mechanisms required for survival under stress. Although pathogen perception has been widely studied and characterized, salt stress perception and signaling remain largely elusive. Recent observations, obtained in the model plant Arabidopsis thaliana, show that perception of specific features of pathogens also allows plants to mount salt stress resilience pathways, highlighting the possibility that salt sensing and pathogen perception mechanisms partially overlap. We discuss these overlapping strategies and examine the emerging role of A. thaliana cell wall and plasma membrane components in activating both salt- and pathogen-induced responses, as part of exquisite mechanisms underlying perception of damage and danger. This knowledge helps understanding the complexity of plant responses to pathogens and salinity, leading to new hypotheses that could explain why plants evolved similar strategies to respond to these, at first sight, very different types of stimuli.

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.

Molecular characterization and expression of cyclic nucleotide gated ion channels 19 and 20 in Arabidopsis thaliana for their potential role in salt stress

Cyclic nucleotide gated ion channels (CNGCs) in plants have very important role in signaling and development. The study reports role of CNGC19 and CNGC20 in salt stress in A. thaliana. In-silico, genome wide analysis showed that CNGC19 and CNGC20 are related to salt stress with maximum expression after 6 h in A. thaliana. The position of inserted T-DNA was determined (in-vivo) through TAIL-PCR for activation tagged mutants of CNGC19 and CNGC20 under salt stress. The expression of AtCNGC19 and AtCNGC20 after cloning under 35S promoter of expression vectors pBCH1 and pEarleyGate100 was determined in A. thaliana by real-time PCR analysis. Genome wide analysis showed that AtCNGC11 had lowest and AtCNGC20 highest molecular weight as well as number of amino acid residues. In-vivo expression of AtCNGC19 and AtCNGC20 was enhanced through T-DNA insertion and 35S promoter in over-expressed plants under high salt concentration. AtCNGC19 was activated twice in control and about five times under 150 mM NaCl stress level, and expression value was also higher than AtCNGC20. Phenotypically, over-expressed plants and calli were healthier while knock-out plants and calli showed retarded growth under salinity stress. The study provides new insight for the role of AtCNGC19 and AtCNGC20 under salt stress regulation in A. thaliana and will be helpful for improvement of crop plants for salt stress to combat food shortage and security.

Deciphering the Role of Ion Channels in Early Defense Signaling against Herbivorous Insects

Plants and insect herbivores are in a relentless battle to outwit each other. Plants have evolved various strategies to detect herbivores and mount an effective defense system against them. These defenses include physical and structural barriers such as spines, trichomes, cuticle, or chemical compounds, including secondary metabolites such as phenolics and terpenes. Plants perceive herbivory by both mechanical and chemical means. Mechanical sensing can occur through the perception of insect biting, piercing, or chewing, while chemical signaling occurs through the perception of various herbivore-derived compounds such as oral secretions (OS) or regurgitant, insect excreta (frass), or oviposition fluids. Interestingly, ion channels or transporters are the first responders for the perception of these mechanical and chemical cues. These transmembrane pore proteins can play an important role in plant defense through the induction of early signaling components such as plasma transmembrane potential (V_m) fluctuation, intracellular calcium (Ca²⁺), and reactive oxygen species (ROS) generation, followed by defense gene expression, and, ultimately, plant defense responses. In recent years, studies on early plant defense signaling in response to herbivory have been gaining momentum with the application of genetically encoded GFP-based sensors for real-time monitoring of early signaling events and genetic tools to manipulate ion channels involved in plant-herbivore interactions. In this review, we provide an update on recent developments and advances on early signaling events in plant-herbivore interactions, with an emphasis on the role of ion channels in early plant defense signaling.

Recent Advances in the Physiology of Ion Channels in Plants

Our knowledge of plant ion channels was significantly enhanced by the first application of the patch-clamp technique to isolated guard cell protoplasts over 35 years ago. Since then, research has demonstrated the importance of ion channels in the control of gas exchange in guard cells, their role in nutrient uptake in roots, and the participation of calcium-permeable cation channels in the regulation of cell signaling affected by the intracellular concentrations of this second messenger. In recent years, through the employment of reverse genetics, mutant proteins, and heterologous expression systems, research on ion channels has identified mechanisms that modify their activity through protein-protein interactions or that result in activation and/or deactivation of ion channels through posttranslational modifications. Additional and confirmatory information on ion channel functioning has been derived from the crystallization and molecular modeling of plant proteins that, together with functional analyses, have helped to increase our knowledge of the functioning of these important membrane proteins that may eventually help to improve crop yield. Here, an update on the advances obtained in plant ion channel function during the last few years is presented.

A mis-regulated cyclic nucleotide-gated channel mediates cytosolic calcium elevation and activates immunity in Arabidopsis

Calcium (Ca²⁺ ) is a second messenger for plant cell surface and intracellular receptors mediating pattern-triggered and effector-triggered immunity (respectively, PTI and ETI). Several CYCLIC NUCLEOTIDE-GATED CHANNELS (CNGCs) were shown to control transient cytosolic Ca²⁺ influx upon PTI activation. The contributions of specific CNGC members to PTI and ETI remain unclear. ENHANCED DISEASE SUSCEPTIBLITY1 (EDS1) regulates ETI signaling. In an Arabidopsis genetic screen for suppressors of eds1, we identify a recessive gain-of-function mutation in CNGC20, denoted cngc20-4, which partially restores disease resistance in eds1. cngc20-4 enhances PTI responses and ETI hypersensitive cell death. A cngc20-4 single mutant exhibits autoimmunity, which is dependent on genetically parallel EDS1 and salicylic acid (SA) pathways. CNGC20 self-associates, forms heteromeric complexes with CNGC19, and is phosphorylated and stabilized by BOTRYTIS INDUCED KINASE1 (BIK1). The cngc20-4 L371F exchange on a predicted transmembrane channel inward surface does not disrupt these interactions but leads to increased cytosolic Ca²⁺ accumulation, consistent with mis-regulation of CNGC20 Ca²⁺ -permeable channel activity. Our data show that ectopic Ca²⁺ influx caused by a mutant form of CNGC20 in cngc20-4 affects both PTI and ETI responses. We conclude that tight control of the CNGC20 Ca²⁺ ion channel is important for regulated immunity.

Plant mineral transport systems and the potential for crop improvement

Nutrient transporter genes could be a potential candidate for improving crop plants, with enhanced nutrient uptake leading to increased crop yield by providing tolerance against different biotic and abiotic stresses. The world's food supply is nearing a crisis in meeting the demands of an ever-growing global population, and an increase in both yield and nutrient value of major crops is vitally necessary to meet the increased population demand. Nutrients play an important role in plant metabolism as well as growth and development, and nutrient deficiency results in retarded plant growth and leads to reduced crop yield. A variety of cellular processes govern crop plant nutrient absorption from the soil. Among these, nutrient membrane transporters play an important role in the acquisition of nutrients from soil and transport of these nutrients to their target sites. In addition, as excess nutrient delivery has toxic effects on plant growth, these membrane transporters also play a significant role in the removal of excess nutrients in the crop plant. The key function provided by membrane transporters is the ability to supply the crop plant with an adequate level of tolerance against environmental stresses, such as soil acidity, alkalinity, salinity, drought, and pathogen attack. Membrane transporter genes have been utilized for the improvement of crop plants, with enhanced nutrient uptake leading to increased crop yield by providing tolerance against different biotic and abiotic stresses. Further understanding of the basic mechanisms of nutrient transport in crop plants could facilitate the advanced design of engineered plant crops to achieve increased yield and improve nutrient quality through the use of genetic technologies as well as molecular breeding. This review is focused on nutrient toxicity and tolerance mechanisms in crop plants to aid in understanding and addressing the anticipated global food demand.

The Complex Story of Plant Cyclic Nucleotide-Gated Channels

Plant cyclic nucleotide-gated channels (CNGCs) are tetrameric cation channels which may be activated by the cyclic nucleotides (cNMPs) adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP). The genome of Arabidopsis thaliana encodes 20 CNGC subunits associated with aspects of development, stress response and immunity. Recently, it has been demonstrated that CNGC subunits form heterotetrameric complexes which behave differently from the homotetramers produced by their constituent subunits. These findings have widespread implications for future signalling research and may help explain how specificity can be achieved by CNGCs that are known to act in disparate pathways. Regulation of complex formation may involve cyclic nucleotide-gated channel-like proteins.

In vitro effects of CaO nanoparticles on Triticale callus exposed to short and long-term salt stress

Ca²⁺ NPs enhanced tolerance of Triticale callus under salt stress by improving biochemical activity and confocal laser scanning analysis, conferring salt tolerance on callus cells. CaO NPs (Ca²⁺) are significant components that act as transducers in many adaptive and developmental processes in plants. In this study, effect of Ca²⁺ NPs on the response and regulation of the protective system in Triticale callus under short and long-salt treatments was investigated. The activation of Ca²⁺ NPs was induced by salt stress in callus of Triticale cultivars. MDA, H₂O₂, POD, and protein activities were determined in callus tissues. Concerning MDA, H₂O₂, protein activities, it was found that the Ca²⁺ NPs treatment was significant, and it demonstrated a high correlation with the tolerance levels of cultivars. Tatlıcak cultivar was detected for better MDA activities in the short time with 1.5 ppm Ca²⁺ NPs concentration of 50 g and 100 g NaCl. Similarly, the same cultivar responded with better H₂O₂ activity at 1.5 ppm Ca²⁺ NPs 100 g NaCl in the short time. POD activities exhibited a decreasing trend in response to the increasing concentrations of Ca²⁺ NPs. The best result was observed at 1.5 ppm Ca²⁺ NPs 100 g NaCl in the short term. Based on the protein content, treatment of short-term cultured callus cells with 1.5 ppm Ca²⁺ NPs inhibited stress response and it significantly promoted Ca²⁺ NPs signals as compared to control callus. Confocal laser scanning analysis proved that the application of Ca²⁺ NPs could alleviate the adverse effects of salt stress by the inhibition of stress severity in callus cells. This study demonstrated, under in vitro conditions, that the application of Ca²⁺ NPs can significantly suppress the adverse effects of salt stress on Triticale callus; it was also verified that the concentration of Ca²⁺ NPs could be important parameter to be considered in adjusting the micronutrient content in the media for this plant.

Adaptation Strategies of Halophytic Barley Hordeum marinum ssp. marinum to High Salinity and Osmotic Stress

The adaptation strategies of halophytic seaside barley Hordeum marinum to high salinity and osmotic stress were investigated by nuclear magnetic resonance imaging, as well as ionomic, metabolomic, and transcriptomic approaches. When compared with cultivated barley, seaside barley exhibited a better plant growth rate, higher relative plant water content, lower osmotic pressure, and sustained photosynthetic activity under high salinity, but not under osmotic stress. As seaside barley is capable of controlling Na⁺ and Cl⁻ concentrations in leaves at high salinity, the roots appear to play the central role in salinity adaptation, ensured by the development of thinner and likely lignified roots, as well as fine-tuning of membrane transport for effective management of restriction of ion entry and sequestration, accumulation of osmolytes, and minimization of energy costs. By contrast, more resources and energy are required to overcome the consequences of osmotic stress, particularly the severity of reactive oxygen species production and nutritional disbalance which affect plant growth. Our results have identified specific mechanisms for adaptation to salinity in seaside barley which differ from those activated in response to osmotic stress. Increased knowledge around salt tolerance in halophytic wild relatives will provide a basis for improved breeding of salt-tolerant crops.

CYCLIC NUCLEOTIDE-GATED ION CHANNELs 14 and 16 Promote Tolerance to Heat and Chilling in Rice

Calcium signaling has been postulated to be critical for both heat and chilling tolerance in plants, but its molecular mechanisms are not fully understood. Here, we investigated the function of two closely related cyclic nucleotide-gated ion channel (CNGC) proteins, OsCNGC14 and OsCNGC16, in temperature-stress tolerance in rice (Oryza sativa) by examining their loss-of-function mutants generated by genome editing. Under both heat and chilling stress, both the cngc14 and cngc16 mutants displayed reduced survival rates, higher accumulation levels of hydrogen peroxide, and increased cell death. In the cngc16 mutant, the extent to which some genes were induced and repressed in response to heat stress was altered and some Heat Shock factor (HSF) and Heat Shock Protein (HSP) genes were slightly more induced compared to the wild type. Furthermore, the loss of either OsCNGC14 or OsCNGC16 reduced or abolished cytosolic calcium signals induced by either heat or chilling stress. Therefore, OsCNGC14 and OsCNGC16 are required for heat and chilling tolerance and are modulators of calcium signals in response to temperature stress. In addition, loss of their homologs AtCNGC2 and AtCNGC4 in Arabidopsis (Arabidopsis thaliana) also led to compromised tolerance of low temperature. Thus, this study indicates a critical role of CNGC genes in both chilling and heat tolerance in plants, suggesting a potential overlap in calcium signaling in response to high- and low-temperature stress.

Cyclic AMP: A Polyhedral Signalling Molecule in Plants

The cyclic nucleotide cAMP (3',5'-cyclic adenosine monophosphate) is nowadays recognised as an important signalling molecule in plants, involved in many molecular processes, including sensing and response to biotic and abiotic environmental stresses. The validation of a functional cAMP-dependent signalling system in higher plants has spurred a great scientific interest on the polyhedral role of cAMP, as it actively participates in plant adaptation to external stimuli, in addition to the regulation of physiological processes. The complex architecture of cAMP-dependent pathways is far from being fully understood, because the actors of these pathways and their downstream target proteins remain largely unidentified. Recently, a genetic strategy was effectively used to lower cAMP cytosolic levels and hence shed light on the consequences of cAMP deficiency in plant cells. This review aims to provide an integrated overview of the current state of knowledge on cAMP's role in plant growth and response to environmental stress. Current knowledge of the molecular components and the mechanisms of cAMP signalling events is summarised.

Calcium channel CNGC19 mediates basal defense signaling to regulate colonization by Piriformospora indica in Arabidopsis roots

The activation of calcium signaling is a crucial event for perceiving environmental stress. Colonization by Piriformospora indica, a growth-promoting root endosymbiont, activates cytosolic Ca2+ in Arabidopsis roots. In this study, we examined the role and functional relevance of calcium channels responsible for Ca2+ fluxes. Expression profiling revealed that CYCLIC NUCLEOTIDE GATED CHANNEL 19 (CNGC19) is an early-activated gene, induced by unidentified components in P. indica cell-wall extract. Functional analysis showed that loss-of-function of CNGC19 resulted in growth inhibition by P.indica, due to increased colonization and loss of controlled fungal growth. The cngc19 mutant showed reduced elevation of cytosolic Ca2+ in response to P. indica cell-wall extract in comparison to the wild-type. Microbe-associated molecular pattern-triggered immunity was compromised in the cngc19 lines, as evidenced by unaltered callose deposition, reduced cis-(+)-12-oxo-phytodienoic acid, jasmonate, and jasmonoyl isoleucine levels, and down-regulation of jasmonate and other defense-related genes, which contributed to a shift towards a pathogenic response. Loss-of-function of CNGC19 resulted in an inability to modulate indole glucosinolate content during P. indica colonization. CNGC19-mediated basal immunity was dependent on the AtPep receptor, PEPR. CNGC19 was also crucial for P. indica-mediated suppression of AtPep-induced immunity. Our results thus demonstrate that Arabidopsis CNGC19 is an important Ca2+ channel that maintains a robust innate immunity and is crucial for growth-promotion signaling upon colonization by P. indica.

Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (Medicago sativa L.)

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (Medicago sativa L.)

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

Arabidopsis cyclic nucleotide-gated channel 6 is negatively modulated by multiple calmodulin isoforms during heat shock

An increased concentration of cytosolic Ca2+ is an early response of plant cells to heat shock. Arabidopsis cyclic nucleotide-gated ion channel 6 (CNGC6) mediates heat-induced Ca2+ influx and is activated by cAMP. However, it remains unclear how the Ca2+ conductivity of CNGC6 is negatively regulated under the elevated cytosolic Ca2+ concentration. In this study, Arabidopsis calmodulin isoforms CaM1/4, CaM2/3/5, CaM6, and CaM7 were found to bind to CNGC6 to varying degrees, and this binding was dependent on the presence of Ca2+ and IQ6, an atypical isoleucine-glutamine motif in CNGC6. Knockout of CaM2, CaM3, CaM5, and CaM7 genes led to a marked increase in plasma membrane inward Ca2+ current under heat shock conditions; however, knockout of CaM1, CaM4, and CaM6 genes had no significant effect on plasma membrane Ca2+ current. Moreover, the deletion of IQ6 from CNGC6 led to a marked increase in plasma membrane Ca2+ current under heat shock conditions. Taken together, the data suggest that CNGC6-mediated Ca2+ influx is likely to be negatively regulated by CaM2/3/5 and CaM7 isoforms under heat shock conditions, and that IQ6 plays an important role in CaM binding and the feedback regulation of the channel.

Cyclic nucleotide gated channels (CNGCs) in plant signalling-Current knowledge and perspectives

Cell signaling is an evolutionarily conserved mechanism that responds and adapts to various internal and external factors. Generally, a signal is mediated by various signaling molecules and is transferred to a cascade of effector proteins. To date, there is significant evidence that cyclic nucleotides (cNMPs), e.g., adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP), may represent important elements of many signaling pathways in plants. However, in contrast to the impressive progress made in understanding cyclic nucleotide signaling in mammalian hosts, only few studies have investigated this topic in plants. Existing evidence indicates that cNMPs participate in growth and developmental processes, as well as the response to various stresses. Once synthesized by adenylyl or guanylyl cyclases, these signals are transduced by acting through a number of cellular effectors. The regulatory effects of cNMPs in eukaryotes can be mediated via various downstream effector proteins, such as protein kinases, Exchange Protein directly Activated by cAMP (EPAC), and Cyclic Nucleotide-Gated ion Channels (CNGC). These proteins sense changes in intracellular cNMP levels and regulate numerous cellular responses. Moreover, the amplitude of cNMP levels and the duration of its signal in the cell is also governed by phosphodiesterases (PDEs), enzymes that are responsible for the breakdown of cNMPs. Data collected in recent years strongly suggest that cyclic nucleotide gated channels are the main cNMP effectors in plant cells. These channels are important cellular switches that transduce changes in intracellular concentrations of cyclic nucleotides into changes in membrane potential and ion concentrations. Structurally, these channels belong to the superfamily of pore-loop cation channels. In this review, we provide an overview of the molecular properties of CNGC structure, regulation and ion selectivity, and subcellular localization, as well as describing the signal transduction pathways in which these channels are involved. We will also summarize recent insights into the role of CNGC proteins in plant growth, development and response to stressors.

Piriformospora indica confers salinity tolerance on tomato (Lycopersicon esculentum Mill.) through amelioration of nutrient accumulation, K+/Na+ homeostasis and water status

Piriformospora indica confers salt tolerance in tomato seedlings by increasing the uptake of nutrients such as N, P and Ca, improving K⁺/Na⁺ homoeostasis by regulating the expression of NHXs, SOS1 and CNGC15 genes, maintaining water status by regulating the expression of aquaporins. Piriformospora indica, an endophytic basidiomycete, has been shown to increase the growth and improve the plants tolerance to stressful conditions, especially salinity, by establishing the arbuscular mycorrhiza-like symbiotic relationship in various plant hosts. In the present research, the effect of NaCl treatment (150 mM) and P. indica inoculation on growth, accumulation of nutrients, the transcription level of genes involved in ionic homeostasis (NHXs, SOS1 and CNGC15) and regulating water status (PIP1;2, PIP2;4, TIP1;1 and TIP2;2) in roots and leaves of tomato seedlings were investigated. The P. indica improved the uptake of N, P, Ca and K, and reduced Na accumulation, and had no significant effect on Cl accumulation in roots and leaves. The endophytic fungus also increased in K⁺/Na⁺ ratio in roots and leaves of tomato by regulating the expression of NHX isoforms and upregulating SOS1 and CNGC15 expression. Salinity stress increased the transcription of PIP2;4 gene and reduced the transcription of PIP1;2, TIP1;1 and TIP2;2 genes compared to the control treatment. However, P. indica inoculation upregulated the expression of PIP1;2 and PIP2;4 genes versus non-inoculated plants but did not have a significant effect on TIP1;1 and TIP2;2 expression. These results conclude that the positive effects of P. indica on nutrients accumulation, ionic homeostasis and water status lead to the increased salinity tolerance and the improved plant growth under NaCl treatment.

The Ca2+ Channel CNGC19 Regulates Arabidopsis Defense Against Spodoptera Herbivory

Cellular calcium elevation is an important signal used by plants for recognition and signaling of environmental stress. Perception of the generalist insect, Spodoptera litura, by Arabidopsis (Arabidopsis thaliana) activates cytosolic Ca2+ elevation, which triggers downstream defense. However, not all the Ca2+ channels generating the signal have been identified, nor are their modes of action known. We report on a rapidly activated, leaf vasculature- and plasma membrane-localized, CYCLIC NUCLEOTIDE GATED CHANNEL19 (CNGC19), which activates herbivory-induced Ca2+ flux and plant defense. Loss of CNGC19 function results in decreased herbivory defense. The cngc19 mutant shows aberrant and attenuated intravascular Ca2+ fluxes. CNGC19 is a Ca2+-permeable channel, as hyperpolarization of CNGC19-expressing Xenopus oocytes in the presence of both cyclic adenosine monophosphate and Ca2+ results in Ca2+ influx. Breakdown of Ca2+-based defense in cngc19 mutants leads to a decrease in herbivory-induced jasmonoyl-l-isoleucine biosynthesis and expression of JA responsive genes. The cngc19 mutants are deficient in aliphatic glucosinolate accumulation and hyperaccumulate its precursor, methionine. CNGC19 modulates aliphatic glucosinolate biosynthesis in tandem with BRANCHED-CHAIN AMINO ACID TRANSAMINASE4, which is involved in the chain elongation pathway of Met-derived glucosinolates. Furthermore, CNGC19 interacts with herbivory-induced CALMODULIN2 in planta. Together, our work reveals a key mechanistic role for the Ca2+ channel CNGC19 in the recognition of herbivory and the activation of defense signaling.

Distinct leaf transcriptomic response of water deficient Eucalyptus grandis submitted to potassium and sodium fertilization

While potassium fertilization increases growth yield in Brazilian eucalyptus plantations, it could also increase water requirements, making trees more vulnerable to drought. Sodium fertilization, which has been shown to promote eucalyptus growth compared to K-deficient trees, could partially mitigate this adverse effect of potassium. However, little is known about the influence of K and Na fertilization on the tree metabolic response to water deficit. The aim of the present study was thus to analyze the transcriptome of leaves sampled from Eucalyptus grandis trees subjected to 37% rainfall reduction, and fertilized with potassium (K), sodium (Na), compared to control trees (C). The multifactorial experiment was set up in a field with a throughfall exclusion system. Transcriptomic analysis was performed on leaves from two-year-old trees, and data analyzed using multifactorial statistical analysis and weighted gene co-expression network analysis (WGCNA). Significant sets of genes were seen to respond to rainfall reduction, in interaction with K or Na fertilization, or to fertilization only (regardless of the water supply regime). The genes were involved in stress signaling, primary and secondary metabolism, secondary cell wall formation and photosynthetic activity. Our focus on key genes related to cation transporters and aquaporins highlighted specific regulation of ion homeostasis, and plant adjustment to water deficit. While water availability significantly affects the transcriptomic response of eucalyptus species, this study points out that the transcriptomic response is highly dependent on the fertilization regime. Our study is based on the first large-scale field trial in a tropical region, specifically designed to study the interaction between water availability and nutrition in eucalyptus. To our knowledge, this is the first global transcriptomic analysis to compare the influence of K and Na fertilization on tree adaptive traits in water deficit conditions.

Genome-wide identification and functional analysis of the cyclic nucleotide-gated channel gene family in Chinese cabbage

Cyclic nucleotide-gated channels (CNGCs) are a class of nonselective cationic channels that are widely found in animals and plants. Plant CNGCs participate in numerous biological functions that vary from development to stress tolerance. Most CNGC genes have been identified in plant genomes, but no such comprehensive study has yet been conducted on Chinese cabbage. In this study, thirty BrCNGC genes were identified, divided into five groups, and used for evolutionary analysis. We assigned names of all individual CNGC members on the basis of phylogenetic relationship with A. thaliana CNGCs. All BrCNGC genes were randomly distributed on chromosomes, and the A08 chromosome did not carry any CNGC gene. The CNGC genes of Chinese cabbage and A. thaliana from the same group displayed similar conserved motifs and gene structures. Especially the closer the homology, the higher the similarity. Quantitative expression analysis showed that most of the CNGC genes were expressed under four stresses, indicating that they play a key role in the stress response of Chinese cabbage. Expression patterns of 12 BrCNGC in the roots, stems, leaves, flowers, and siliques showed that BrCNGC8 and BrCNGC16 were specifically expressed only in flowers but not in other parts. This study lays a theoretical foundation for future research on the function of the CNGC gene family in Chinese cabbage.

Genome-wide identification, evolution and expression analysis of cyclic nucleotide-gated channels in tobacco (Nicotiana tabacum L.)

Tobacco (Nicotiana tabacum) serve as the top leading commercial, non-food, and model crop worldwide. Cyclic nucleotide-gated channels (CNGCs) are ligand-gated, calcium-permeable, divalent, cation-selective channels, involved in important biological functions. Here, we systematically characterized thirty-five CNGC genes in the genome of Nicotiana tabacum, and classified into four phylogenetic groups. Evolutionary analysis showed that NtabCNGC family of N. tabacum originated from the parental genome of N. sylvestris and N. tomentosiformis, and further expanded via tandem and segmental duplication events. Tissue-specific expression analysis showed that twenty-three NtabCNGC genes are involved in the development of various tobacco tissues. Subsequent RT-qPCR analyses indicated that these genes are sensitive towards external abiotic and biotic stresses. Notable performances were exhibited by group-I and IV CNGC genes against black shank, Cucumber mosaic virus, Potato virus Y, cold, drought, and cadmium stresses. Our analyses also suggested that NtabCNGCs can be regulated by phosphorylation and miRNAs, and multiple light, temperature, and pathogen-responsive cis-acting regulatory elements present in promotors. These results will be useful for elaborating the biological roles of NtabCNGCs in tobacco growth and development.

Arabidopsis CNGC Family Members Contribute to Heavy Metal Ion Uptake in Plants

Heavy metal ions, including toxic concentrations of essential ions, negatively affect diverse metabolic and cellular processes. Heavy metal ions are known to enter cells in a non-selective manner; however, few studies have examined the regulation of heavy metal ion transport. Plant cyclic nucleotide-gated channels (CNGCs), a type of Ca2+-permeable-channel, have been suggested to be involved in the uptake of both essential and toxic cations. To determine the candidates responsible for heavy metal ion transport, a series of Arabidopsis CNGC mutants were examined for their response to Pb2+ and Cd2+ ions. The primary focus was on root growth and the analysis of the concentration of heavy metals in plants. Results, based on the analysis of primary root length, indicated that AtCNGC1, AtCNGC10, AtCNGC13 and AtCNGC19 play roles in Pb2+ toxicity, while AtCNGC11, AtCNGC13, AtCNGC16 and AtCNGC20 function in Cd2+ toxicity in Arabidopsis. Ion content analysis verified that the mutations of AtCNGC1 and AtCNGC13 resulted in reduced Pb2+ accumulation, while the mutations of AtCNGC11, AtCNGC15 and AtCNGC19 resulted in less Pb2+ and Cd2+ accumulation in plants. These findings provide functional evidence which support the roles of these AtCNGCs in the uptake and transport of Pb2+ or Cd2+ ion in plants.

Genome-wide identification and analysis of the CNGC gene family in maize

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

An apple cyclic nucleotide-gated ion channel gene highly responsive to Botryosphaeria dothidea infection enhances the susceptibility of Nicotiana benthamiana to bacterial and fungal pathogens

Apple ring rot caused by the fungus Botryosphaeria dothidea is one of the devastating diseases. Up to date, the responsive mechanism of apple plant to this disease remains unclear. In the present study, an apple CNGC gene (designated as MdCNGC1) was found among highly expressed genes responding to B. dothidea infection. The expression of MdCNGC1 was different among apple cultivars with different resistance to B. dothidea. Intriguingly, MdCNGC1 expression was not induced by other two apple pathogens, Marssonina coronaria and Valsa ceratosperma. Ectopic overexpression of MdCNGC1 in Nicotiana benthamiana conferred elevated susceptibility to bacterial and fungal pathogens. Notably, overexpression of MdCNGC1 reduced salicylic acid (SA) accumulation induced by Alternaria alternata or Pseudomonas syringae. Decreased induction of pathogenesis-related (PR) genes and ROS accumulation were also observed in MdCNGC1-overexpressing plants. Up-regulated scavenging systems as indicated by enhanced expressions of CAT, APX, SOD genes and activities of antioxidative enzymes may in part contribute to reduced ROS accumulation. MdCNGC1 expression in N. benthamiana also decreased flg22 and chitosan-induced callose deposition and lowered the expression of NbPMR4, an ortholog of Arabidopsis callose synthase gene PMR4. These combined results suggested that MdCNGC1 might be a negative factor to plant resistance to bacterial and fungal pathogens.

Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut

HIGHLIGHTS Metabolites and transcripts related to plant physiology in salt stress conditions, especially to the recovery process were disclosed in peanut. Peanut (Arachis hypogaea L.) is considered as a moderately salt-sensitive species and thus soil salinity can be a limiting factor for peanut cultivation. To gain insights into peanut plant physiology in response to salt stress and alleviation, we comprehensively characterized leaf relative electrolyte leakage (REC), photosynthesis, leaf transpiration, and metabolism of plants under salt stress and plants that were subjected to salt stress followed by salt alleviation period. As expected, we found that REC levels were higher when plants were subjected to salt stress compared with the untreated plants. However, in contrast to expectations, REC was even higher compared with salt treated plants when plants were transferred from salt stress to standard conditions. To decipher REC variation in response to salt stress, especial during the recovery, metabolite, and transcript variations were analyzed by GC/MS and RNA-seq method, respectively. Ninety two metabolites, among total 391 metabolites identified, varied in response to salt and 42 metabolites responded to recovery specially. Transcriptomics data showed 1,742 in shoots and 3,281 in roots transcript varied in response to salt stress and 372 in shoots and 1,386 transcripts in roots responded specifically to recovery, but not salt stress. Finally, 95 transcripts and 1 metabolite are indicated as candidates involved in REC, photosynthesis, transpiration, and Na⁺ accumulation variation were revealed by using the principal component analysis (PCA) and correlation analysis. This study provides valuable information on peanut response to salt stress and recovery and may inspire further study to improve salt tolerance in peanut germplasm innovation.

The role of ion disequilibrium in induction of root cell death and autophagy by environmental stresses

Environmental stresses such as salinity, drought, oxidants, heavy metals, hypoxia, extreme temperatures and others can induce autophagy and necrosis-type programmed cell death (PCD) in plant roots. These reactions are accompanied by the generation of reactive oxygen species (ROS) and ion disequilibrium, which is induced by electrolyte/K+ leakage through ROS-activated ion channels, such as the outwardly-rectifying K+ channel GORK and non-selective cation channels. Here, we discuss mechanisms of the stress-induced ion disequilibrium and relate it with ROS generation and onset of morphological, biochemical and genetic symptoms of autophagy and PCD in roots. Based on our own data and that in the literature, we propose a hypothesis on the induction of autophagy and PCD in roots by loss of cytosolic K+. To support this, we present data showing that in conditions of salt stress-induced autophagy, gork1-1 plants lacking root K+ efflux channel have fewer autophagosomes compared with the wild type. Overall, literature analyses and presented data strongly suggest that stress-induced root autophagy and PCD are controlled by the level of cytosolic potassium and ROS.

Cyclic Nucleotide Monophosphates and Their Cyclases in Plant Signaling

The cyclic nucleotide monophosphates (cNMPs), and notably 3',5'-cyclic guanosine monophosphate (cGMP) and 3',5'-cyclic adenosine monophosphate (cAMP) are now accepted as key signaling molecules in many processes in plants including growth and differentiation, photosynthesis, and biotic and abiotic defense. At the single molecule level, we are now beginning to understand how cNMPs modify specific target molecules such as cyclic nucleotide-gated channels, while at the systems level, a recent study of the Arabidopsis cNMP interactome has identified novel target molecules with specific cNMP-binding domains. A major advance came with the discovery and characterization of a steadily increasing number of guanylate cyclases (GCs) and adenylate cyclases (ACs). Several of the GCs are receptor kinases and include the brassinosteroid receptor, the phytosulfokine receptor, the Pep receptor, the plant natriuretic peptide receptor as well as a nitric oxide sensor. We foresee that in the near future many more molecular mechanisms and biological roles of GCs and ACs and their catalytic products will be discovered and further establish cNMPs as a key component of plant responses to the environment.

Calcium-Mediated Abiotic Stress Signaling in Roots

Roots are subjected to a range of abiotic stresses as they forage for water and nutrients. Cytosolic free calcium is a common second messenger in the signaling of abiotic stress. In addition, roots take up calcium both as a nutrient and to stimulate exocytosis in growth. For calcium to fulfill its multiple roles must require strict spatio-temporal regulation of its uptake and efflux across the plasma membrane, its buffering in the cytosol and its sequestration or release from internal stores. This prompts the question of how specificity of signaling output can be achieved against the background of calcium's other uses. Threats to agriculture such as salinity, water availability and hypoxia are signaled through calcium. Nutrient deficiency is also emerging as a stress that is signaled through cytosolic free calcium, with progress in potassium, nitrate and boron deficiency signaling now being made. Heavy metals have the capacity to trigger or modulate root calcium signaling depending on their dose and their capacity to catalyze production of hydroxyl radicals. Mechanical stress and cold stress can both trigger an increase in root cytosolic free calcium, with the possibility of membrane deformation playing a part in initiating the calcium signal. This review addresses progress in identifying the calcium transporting proteins (particularly channels such as annexins and cyclic nucleotide-gated channels) that effect stress-induced calcium increases in roots and explores links to reactive oxygen species, lipid signaling, and the unfolded protein response.

Role of Cyclic Nucleotide Gated Channels in Stress Management in Plants

Tolerance of plants to a number of biotic and abiotic stresses such as pathogen and herbivore attack, drought, salinity, cold and nutritional limitations is ensued by complex multimodule signaling pathways. The outcome of this complex signaling pathways results in adaptive responses by restoring the cellular homeostasis and thus promoting survival. Functions of many plant cation transporter and channel protein families such as glutamate receptor homologs (GLRs), cyclic nucleotide-gated ion channel (CNGC) have been implicated in providing biotic and abiotic stress tolerance. Ion homeostasis regulated by several transporters and channels is one of the crucial parameters for the optimal growth, development and survival of all living organisms. The CNGC family members are known to be involved in the uptake of cations such as Na(+), K(+) and Ca(2+) and regulate plant growth and development. Detail functional genomics approaches have given an emerging picture of CNGCs wherein these protein are believed to play crucial role in pathways related to cellular ion homeostasis, development and as a 'guard' in defense against biotic and abiotic challenges. Here, we discuss the current knowledge of role of CNGCs in mediating stress management and how they aid plants in survival under adverse conditions.

Changes in the Arabidopsis thaliana Proteome Implicate cAMP in Biotic and Abiotic Stress Responses and Changes in Energy Metabolism

The second messenger 3',5'-cyclic adenosine monophosphate (cAMP) is increasingly recognized as having many different roles in plant responses to environmental stimuli. To gain further insights into these roles, Arabidopsis thaliana cell suspension culture was treated with 100 nM of cell permeant 8-bromo-cAMP for 5 or 10 min. Here, applying mass spectrometry and comparative proteomics, 20 proteins were identified as differentially expressed and we noted a specific bias in proteins with a role in abiotic stress, particularly cold and salinity, biotic stress as well as proteins with a role in glycolysis. These findings suggest that cAMP is sufficient to elicit specific stress responses that may in turn induce complex changes to cellular energy homeostasis.

Ion Channels in Plant Bioenergetic Organelles, Chloroplasts and Mitochondria: From Molecular Identification to Function

Recent technical advances in electrophysiological measurements, organelle-targeted fluorescence imaging, and organelle proteomics have pushed the research of ion transport a step forward in the case of the plant bioenergetic organelles, chloroplasts and mitochondria, leading to the molecular identification and functional characterization of several ion transport systems in recent years. Here we focus on channels that mediate relatively high-rate ion and water flux and summarize the current knowledge in this field, focusing on targeting mechanisms, proteomics, electrophysiology, and physiological function. In addition, since chloroplasts evolved from a cyanobacterial ancestor, we give an overview of the information available about cyanobacterial ion channels and discuss the evolutionary origin of chloroplast channels. The recent molecular identification of some of these ion channels allowed their physiological functions to be studied using genetically modified Arabidopsis plants and cyanobacteria. The view is emerging that alteration of chloroplast and mitochondrial ion homeostasis leads to organelle dysfunction, which in turn significantly affects the energy metabolism of the whole organism. Clear-cut identification of genes encoding for channels in these organelles, however, remains a major challenge in this rapidly developing field. Multiple strategies including bioinformatics, cell biology, electrophysiology, use of organelle-targeted ion-sensitive probes, genetics, and identification of signals eliciting specific ion fluxes across organelle membranes should provide a better understanding of the physiological role of organellar channels and their contribution to signaling pathways in plants in the future.

AtCNGC2 is involved in jasmonic acid-induced calcium mobilization

Calcium (Ca(2+)) mobilization is a central theme in various plant signal transduction pathways. We demonstrate that Arabidopsis thaliana cyclic nucleotide-gated channel 2 (AtCNGC2) is involved in jasmonic acid (JA)-induced apoplastic Ca(2+) influx in Arabidopsis epidermal cells. Ca(2+) imaging results showed that JA can induce an elevation in the cytosolic cAMP concentration ([cAMP]cyt), reaching a maximum within 3 min. Dibutyryl cAMP (db-cAMP), a cell membrane-permeable analogue of cAMP, induced an increase in the cytosolic Ca(2+) concentration ([Ca(2+)]cyt), with a peak at 4 min. This [Ca(2+)]cyt increase was triggered by the JA-induced increase in [cAMP]cyt. W-7[N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide], an antagonist of calmodulin, positively modulated the JA-induced increase in [Ca(2+)]cyt, while W-5[N-(6-aminohexyl)-1-naphthalenesulfonamide], an inactive antagonist of calmodulin, had no apparent effect. db-cAMP and JA positively induced the expression of primary (i.e. JAZ1 and MYC2) and secondary (i.e. VSP1) response genes in the JA signalling pathway in wild-type Arabidopsis thaliana, whereas they had no significant effect in the AtCNGC2 mutant 'defense, no death (dnd1) plants. These data provide evidence that JA first induces the elevation of cAMP, and cAMP, as an activating ligand, activates the AtCNGC2 channel, resulting in apoplastic Ca(2+) influx through AtCNGC2.

Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis

Plant genomes contain large numbers of duplicated genes that contribute to the evolution of new functions. Following duplication, genes can exhibit divergence in their coding sequence and their expression patterns. Changes in the cis-regulatory element landscape can result in changes in gene expression patterns. High-throughput methods developed recently can identify potential cis-regulatory elements on a genome-wide scale. Here, we use a recent comprehensive data set of DNase I sequencing-identified cis-regulatory binding sites (footprints) at single-base-pair resolution to compare binding sites and network connectivity in duplicated gene pairs in Arabidopsis (Arabidopsis thaliana). We found that duplicated gene pairs vary greatly in their cis-regulatory element architecture, resulting in changes in regulatory network connectivity. Whole-genome duplicates (WGDs) have approximately twice as many footprints in their promoters left by potential regulatory proteins than do tandem duplicates (TDs). The WGDs have a greater average number of footprint differences between paralogs than TDs. The footprints, in turn, result in more regulatory network connections between WGDs and other genes, forming denser, more complex regulatory networks than shown by TDs. When comparing regulatory connections between duplicates, WGDs had more pairs in which the two genes are either partially or fully diverged in their network connections, but fewer genes with no network connections than the TDs. There is evidence of younger TDs and WGDs having fewer unique connections compared with older duplicates. This study provides insights into cis-regulatory element evolution and network divergence in duplicated genes.

Phylogeny and evolution of plant cyclic nucleotide-gated ion channel (CNGC) gene family and functional analyses of tomato CNGCs

Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that are involved in various biological functions. Nevertheless, phylogeny and function of plant CNGCs are not well understood. In this study, 333 CNGC genes from 15 plant species were identified using comprehensive bioinformatics approaches. Extensive bioinformatics analyses demonstrated that CNGCs of Group IVa were distinct to those of other groups in gene structure and amino acid sequence of cyclic nucleotide-binding domain. A CNGC-specific motif that recognizes all identified plant CNGCs was generated. Phylogenetic analysis indicated that CNGC proteins of flowering plant species formed five groups. However, CNGCs of the non-vascular plant Physcomitrella patens clustered only in two groups (IVa and IVb), while those of the vascular non-flowering plant Selaginella moellendorffii gathered in four (IVa, IVb, I and II). These data suggest that Group IV CNGCs are most ancient and Group III CNGCs are most recently evolved in flowering plants. Furthermore, silencing analyses revealed that a set of CNGC genes might be involved in disease resistance and abiotic stress responses in tomato and function of SlCNGCs does not correlate with the group that they are belonging to. Our results indicate that Group IVa CNGCs are structurally but not functionally unique among plant CNGCs.