Calcium signals: the lead currency of plant information processing

Hydrogen sulfide mechanism of action in plants; from interaction with regulatory molecules to persulfidation of proteins

Hydrogen sulfide (H2S), previously known as a toxic gas, is currently considered one of the most important gaseous transmitters in plants. This novel signaling molecule has been determined to play notable roles in plant growth, development, and maturation. In addition, pharmacological and genetic evidence indicated that this regulatory molecule effectively ameliorates various plant stress conditions. H2S is involved in these processes by changing gene expression, enzyme activities, and metabolite concentrations. During its regulatory function, H2S interacts with other signaling pathways such as hydrogen peroxide (H2O2), nitric oxide (NO), Ca2+, carbon monoxide (CO), phosphatidic acid (PA), phytohormones, etc. The H2S mechanism of action may depend on the persulfidation post-translational modification (PTM), which attacks the cysteine (Cys) residues on the target proteins and changes their structure and activities. This review summarized H2S biosynthesis pathways, its role in sulfide state, and its donors in plant biology. We also discuss recent progress in the research on the interactions of H2S with other signaling molecules, as well as the role of persulfidation in modulating various plant reactions.

CsCIPK20 Improves Tea Plant Cold Tolerance by Modulating Ascorbic Acid Synthesis Through Attenuation of CsCSN5-CsVTC1 Interaction

Low temperature is a limiting environmental factor for tea plant growth and development. CBL-interacting protein kinases (CIPKs) are important components of the calcium pathway and involved in plant development and stress responses. Herein, we report the function and regulatory mechanisms of a low-temperature-inducible gene, CsCIPK20, in tea plants. The overexpression of CsCIPK20 in Arabidopsis and its transient knockdown in tea plants confirmed its positive role in cold resistance. Notably, the ascorbic acid (AsA) levels increased in the overexpression lines and decreased in the CsCIPK20 knockdown tea plants under freezing stress. Transcriptomic analysis revealed that genes involved in flavonoid metabolism, glutathione metabolism, and AsA biosynthesis were significantly regulated by CsCIPK20. Furthermore, we found that CsCSN5, a key component of the COP9 signalosome, interacted with CsCIPK20 to mediate CsCIPK20 degradation. CsCSN5 interacted with CsVTC1, a key enzyme in AsA biosynthesis, and mediated CsVTC1 degradation. Knockdown of CsVTC1 in tea plants enhanced sensitivity to low temperature. Moreover, we demonstrated that CsCIPK20 competed with CsVTC1 to bind to CsCSN5, which protected CsVTC1 from degradation mediated by CsCSN5 and contributed to AsA accumulation. Overall, our findings uncovered a mechanistic framework through which the CsCIPK20-CsCSN5-CsVTC1 module mediated AsA accumulation and low-temperature resistance in tea plants.

Sparingly-soluble CaCO3 promotes plant growth and arsenic accumulation in As-hyperaccumulator Pteris vittata: Oxidative stress and gene expression in As metabolisms

Being a lithophytic plant and arsenic-hyperaccumulator, Pteris vittata can efficiently utilize sparingly-soluble CaCO3, which enhances its arsenic (As) uptake and plant growth with the underlying mechanisms being unclear. Here, after growing P. vittata for 14 days under hydroponics containing 50 μM As and 8.0 mM CaCO3 or 0.8 mM CaCl2, the plant biomass, Ca, As and malondialdehyde (MDA) contents and As-metabolizing gene expressions in P. vittata were determined. Compared to CaCl2 control, CaCO3 increased plant biomass by 44-57 % to 2.4-3.9 g plant-1. Consistent with its better growth, P. vittata effectively solubilized CaCO3, with Ca being increased from 42-57 to 356-369 μM in the growth media, resulting in 38-76 % greater Ca uptake in the roots. Due to its continued Ca supply, CaCO3+As treatment enhanced the As content in P. vittata fronds by 39 % to 1460 mg kg-1 compared to the CaCl2+As control, with MDA being decreased by 16 %. The increased As accumulation was probably attributed to 1.3-1.6 fold upregulation of phosphate transporters PvPht1;3/1;4 for As uptake in P. vittata roots, and 1.4-fold upregulation of arsenite antiporters PvACR3;2/3;3 for As translocation to and sequestration in P. vittata fronds. Overall, the efficient CaCO3 utilization and its enhanced As accumulation in P. vittata shed light on its potential application in phytoremediation of As-contaminated soils.

Revealing non-trivial information structures in aneural biological tissues via functional connectivity

A central challenge in the progression of a variety of open questions in biology, such as morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Information-theoretic approaches provide a quantitative framework for extracting patterns from data, but so far have been predominantly applied to neuronal systems at the tissue-level. Here, we demonstrate how time series of Ca2+ dynamics can be used to identify the structure and information dynamics of other biological tissues. To this end, we expressed the calcium reporter GCaMP6s in an organoid system of explanted amphibian epidermis derived from the African clawed frog Xenopus laevis, and imaged calcium activity pre- and post- a puncture injury, for six replicate organoids. We constructed functional connectivity networks by computing mutual information between cells from time series derived using medical imaging techniques to track intracellular Ca2+. We analyzed network properties including degree distribution, spatial embedding, and modular structure. We find organoid networks exhibit potential evidence for more connectivity than null models, with our models displaying high degree hubs and mesoscale community structure with spatial clustering. Utilizing functional connectivity networks, our model suggests the tissue retains non-random features after injury, displays long range correlations and structure, and non-trivial clustering that is not necessarily spatially dependent. In the context of this reconstruction method our results suggest increased integration after injury, possible cellular coordination in response to injury, and some type of generative structure of the anatomy. While we study Ca2+ in Xenopus epidermal cells, our computational approach and analyses highlight how methods developed to analyze functional connectivity in neuronal tissues can be generalized to any tissue and fluorescent signal type. We discuss expanded methods of analyses to improve models of non-neuronal information processing highlighting the potential of our framework to provide a bridge between neuroscience and more basal modes of information processing.

Genome-Wide Characterization of CaM/CML Gene Family in Cabbage (Brassica oleracea var. capitata): Expression Profiling and Functional Implications During Hyaloperonospora parasitica Infection

Calmodulin (CaM) and calmodulin-like proteins (CMLs) are crucial for calcium signal transduction in plants. Although CaM/CML genes have been extensively studied in various plant species, research on these genes in Brassica oleracea is still limited. In this study, 14 BoCaM and 75 BoCML genes were identified in the B. oleracea genome through a genome-wide search. Phylogenetic analysis categorized these genes, along with their homologs in Arabidopsis and rice, into six distinct groups. All BoCaM/BoCML genes were unevenly distributed across the nine chromosomes of B. oleracea, with 52 of them lacking introns. Collinearity analysis revealed that CaM/CML genes in Arabidopsis are present in multiple copies in the B. oleracea genome. Moreover, the majority of BoCaM/BoCML genes exhibited distinct expression patterns across the different tissues, indicating their role in the growth and development of B. oleracea. A clustering heatmap of BoCaM/BoCML gene expression showed distinct patterns before and four days after Hyaloperonospora parasitica infection, dividing the genes into five groups based on their expression patterns. Notably, BoCML46-2 is significantly downregulated in both susceptible and resistant materials, suggesting that it plays an important role in responding to H. parasitica infection. This study conducted a comprehensive survey of the BoCaM/BoCML gene family in B. oleracea. It could serve as a theoretical foundation for further functional identification and utilization of family members and their role in the interaction between B. oleracea and H. parasitica.

Transcriptome Analysis of the CML Gene Family in Bletilla striata and Regulation of Militarine Synthesis Under Sodium Acetate and Salicylic Acid Treatments

Calmodulin-like proteins (CMLs) are essential for calcium signal transduction in plants, influencing growth, development, stress responses, and the regulation of medicinal secondary metabolites. Despite their importance, the roles of CML genes in B. striata have not been characterized. This study aimed to elucidate the composition and function of the BsCML gene family in B. striata, identifying 38 genes across eight subfamilies. Evolutionary analysis showed that BsCML genes are stable and conserved, while functional predictions indicated involvement in environmental stress response, hormone regulation, and circadian rhythms. Expression profiling revealed that BsCML27 and BsCML16 were highly expressed during callus culture, suggesting their involvement in growth and development. Notably, BsCML32 and BsCML37 exhibited bidirectional regulation of militarine synthesis under sodium acetate (NaAc) and salicylic acid (SA) treatments, with tissue-specific expression strongly correlated (p < 0.01) with metabolite accumulation. These findings highlight the significant roles of BsCML genes in stress response and secondary metabolite synthesis, providing a foundation for enhancing the medicinal quality of B. striata.

Differential Modulation of Brassinosteroid and Ethylene Signalling Systems by Native and Constitutively Active Forms of the AtCPK1 Gene in Transgenic Tobacco Plants Under Heat Stress

Among other calcium decoders, Ca2+-dependent protein kinases (CDPK) stands out for its ability, depending on calcium levels, to activate key components of the defence system. However, calcium dependence prevents the effective use of CDPKs in comprehensive investigations of their functions. Previously, we showed that a modified constitutively active form of AtCPK1 improved heat tolerance in tobacco plants. At present, the role of calcium ions and their decoders in the regulation of heat tolerance is not fully understood. The response of plant cells to excessive temperature increases is regulated by complex interactions of hormonal signalling systems, among which the least studied is BR signalling. In the present work, we investigated the role of CDPK in the interactions of BR and ET signalling during heat stress. The use of a modified calcium-independent form of AtCPK1 in this work allowed us to answer a number of questions. We showed that dependence on heat-induced calcium ion currents determines the priority of the activation of ABA signalling. Thus, CPK-dependent activation of ABA signalling may not lead to an insufficient response from BR and ET signalling. Modified CPK1 activates BR signalling, which has a positive effect on the tolerance of transgenic plants to increased temperature. The obtained data shed light on heat-associated molecular processes and can draw attention to the possibility of using intradomain modifications of CDPK both for a comprehensive study of its functional features and as a bioengineering tool.

Comprehensive Genomic Analysis of the CDPK Gene Family in Pecan (Carya illinoinensis) and Their Potential Roles in Salt Stress Response

Calcium-dependent protein kinases (CDPKs) are crucial for plant development and stress responses. In this study, we performed a comprehensive genomic analysis of the CDPK gene family in pecan (Carya illinoinensis) and evaluated their potential roles in salt stress responses. A total of 31 CiCDPK genes were identified and classified into four subgroups through phylogenetic analysis. Structural and promoter analyses revealed conserved motifs and regulatory elements linked to stress responses. Gene duplication analysis showed that WGD and DSD events were primary drivers of CiCDPK expansion, shaped by purifying selection. GO and KEGG annotations highlighted roles in kinase activity, calcium binding, and signal transduction, while interaction networks suggested involvement in ROS regulation and ATP-dependent phosphorylation. Tissue-specific expression patterns indicated distinct roles of CiCDPKs, with CiCDPK20 and CiCDPK31 predominantly expressed in male flowers and seeds, respectively. Transcriptome data showed that CiCDPKs exhibited distinct responses to abiotic and biotic stress, highlighting their functional specialization under various conditions. qRT-PCR analysis further confirmed the involvement of 16 CiCDPKs in salt stress adaptation, supporting their critical roles in signal transduction pathways during salinity stress. This study provides insights into CiCDPK functions, offering potential applications in breeding pecan varieties with enhanced salt tolerance.

Agave macroacantha Transcriptome Reveals Candidate CNGC Genes Responsive to Cold Stress in Agave

Agave, with its unique appearance and ability to produce hard fibers, holds high economic value. However, low temperatures during winter can restrict its growth and even damage the leaves, causing a loss of ornamental appeal or affecting the fiber quality. Conversely, the plant cyclic nucleotide-gated channel (CNGC) family plays an important role in the growth and development of plants and the response to stress. Studying the CNGC family genes is of great importance for analyzing the mechanism by which agave responds to cold stress. This research conducted a transcriptomic analysis of the ornamental plant Agave macroacantha. Through assembly via Illumina sequencing, 119,911 transcripts were obtained, including 78,083 unigenes. In total, 6, 10, 11, and 13 CNGC genes were successfully identified from A. macroacantha, Agave. H11648, Agave. deserti, and Agave. tequilana, respectively. These CNGC genes could be divided into four groups (I, II, III, and IV), and group IV could be divided into two subgroups (IV-A and IV-B). The relative expression levels were quantified by qRT-PCR assays, which revealed that AhCNGC4.1 was significantly upregulated after cold treatment and Ca(NO3)2 treatment, suggesting its importance in cold stress and calcium signaling. Additionally, the Y2H assay has preliminarily identified interacting proteins of AhCNGC4.1, including AhCML19 and AhCBSX3. This study has established a completely new transcriptome dataset of A. macroacantha for the first time, enriching the bioinformatics of agave's transcriptome. The identified CNGC genes are of great significance for understanding the evolution of agave species. The cloned CNGC genes, expression pattern analysis, and protein interaction results laid a foundation for future research related to the molecular functions of agave CNGC genes in cold tolerance.

Enhancing Tolerance to Combined Heat and Drought Stress in Cool-Season Grain Legumes: Mechanisms, Genetic Insights, and Future Directions

The increasing frequency of concurrent heat and drought stress poses a significant challenge to agricultural productivity, particularly for cool-season grain legumes, including broad bean (Vicia Faba L.), lupin (Lupinus spp.), lentil (Lens culinaris Medik), chickpea (Cicer arietinum L.), grasspea (Lathyrus sativus L.), pea (Pisum sativum L.), and common vetch (Vicia sativa L.). These legumes play a vital role in sustainable agricultural systems due to their nitrogen-fixing ability and high nutritional value. This review synthesizes current knowledge of the impacts and tolerance mechanisms associated with combined heat and drought stresses in these crops. We evaluate physiological and biochemical responses to combined heat and drought stress, focusing on their detrimental effects on growth, development, and yield. Key genetic and molecular mechanisms, such as the roles of osmolytes, antioxidants, and stress-responsive genes, are explored. We also discuss the intricate interplay between heat and drought stress signaling pathways, including the involvement of Ca2+ ions, reactive oxygen species, transcription factor DREB2A, and the endoplasmic reticulum in mediating stress responses. This comprehensive analysis offers new insights into developing resilient legume varieties to enhance agricultural sustainability under climate change. Future research should prioritize integrating omics technologies to unravel plant responses to combined abiotic stresses.

Conservative mechanism through various rapeseed (Brassica napus L.) varieties respond to heavy metal (Cadmium, Lead, Arsenic) stress

Introduction

Heavy metal soil pollution is a global issue that can be efficiently tackled through the process of phytoremediation. The use of rapeseed in the phytoremediation of heavy metal-contaminated agricultural land shows great potential. Nevertheless, its ability to tolerate heavy metal stress at the molecular level remains unclear.

Methods

Here, with 7-day seedlings as raw materials, we investigated physiological and biochemical indexes, analyzed the transcriptome sequencing for different treated materials (control, 50×, and 100×), combined with the results of transcriptome and proteome sequencing of the near-isogenic lines (F338 and F335) to reveal the response mechanism to heavy metal stress. Due to oxidative stress response caused by heavy metal stress, there are heavy effects on the emergence of rapeseeds and the growth of seedlings. Although rapeseed can alleviate oxidative stress by enhancing the enzyme activity, especially peroxidase in the oxidation system, this process has its limits. Rapeseed plants activate antioxidase, transport enzymes, and biological regulation to cope with heavy metal stress. Among these responses, peroxidase, ABC transporters, and abscisic acid are particularly significant in this process.

Results and discussion

Based on this study, we identified a breeding material with high adsorption capacity for heavy metals, which contributed to the research on resistance breeding in rapeseed. The results of this study may be useful to alleviate heavy metal soil pollution and tackle edible oil shortages in China.

Overexpression of the Vitis amurensis Ca2+-binding protein gene VamCP1 in Arabidopsis thaliana and grapevine improves cold tolerance

Calcium ions (Ca2+) are important second messengers and are known to participate in cold signal transduction. In the current study, we characterized a Ca2+-binding protein gene, VamCP1, from the extremely cold-tolerant grape species Vitis amurensis. VamCP1 expression varied among organs but was highest in leaves following cold treatment, peaking 24 h after treatment onset. VamCP1 was found to localize to the plasma membrane and nucleus and the gene showed transcriptional autoactivation activity. Overexpression of VamCP1 in Arabidopsis thaliana and grapevine (V. vinifera) resulted in transgenic plants that were more tolerant to cold stress than the wild type. This correlated with reduced accumulation of reactive oxygen species (ROS), elevated activity of antioxidant enzymes and proline content, as well as lower levels of malondialdehyde and electrolyte leakage. Additionally, the expression of genes related to cold tolerance, including C-repeat binding factors (CBF) and cold-regulated (COR) genes, was higher in the transgenic lines. Taken together, our results indicate that overexpression of VamCP1 enhanced cold tolerance in plants by promoting the upregulation of genes related to cold tolerance and scavenging of excessive ROS. These findings provide a foundation for the molecular breeding of cold-tolerant grapevine.

Overexpression of the constitutively-active AtCPK1 mutant in tobacco plants confers cold and heat tolerance, possibly through modulating abscisic acid and salicylic acid signalling

Calcium-dependent protein kinases (CDPKs) are very effective calcium signal decoders due to their unique structure, which mediates substrate-specific [Ca2+]cyt signalling through phosphorylation. However, Ca2+-dependence makes it challenging to study CDPKs. This work focused on the effects of the overexpression of native and modified forms of the AtCPK1 gene on the tolerance of tobacco plants to heat and cold. We studied the interaction between the calcium and signalling systems of abscisic acid (ABA) at various temperatures. The hormonal state, stress-induced senescence, and expression of important corresponding genes were investigated. We showed that inactivation of the autoinhibitory domain of the modified constitutively active form of AtCPK1 has a positive effect on resistance not only to long-term cold but also to heat. We showed that the constitutively active form of AtCPK1 under nonstressed conditions activated biosynthesis of ABA, but a decrease in ABA content was detected upon heat exposure. On the basis of our results, we can assume that this effect is achieved through the CPK-dependent activation of salicylic acid (SA) signalling. The obtained data shed light on heat-associated molecular processes and support the possibility of using intradomain modifications of CDPK both for comprehensive study of its functional features and as a bioengineering tool.

Functional and Structural Analysis Reveals Distinct Biological Roles of Plant Synaptotagmins in Response to Environmental Stress

Endoplasmic reticulum-plasma membrane contact sites (ER-PM CSs) are evolutionarily conserved membrane domains found in all eukaryotes, where the ER closely interfaces with the PM. This short distance is achieved in plants through the action of tether proteins such as synaptotagmins (SYTs). Arabidopsis comprises five SYT members (SYT1-SYT5), but whether they possess overlapping or distinct biological functions remains elusive. SYT1, the best-characterized member, plays an essential role in the resistance to abiotic stress. This study reveals that the functionally redundant SYT1 and SYT3 genes, but not SYT5, are involved in salt and cold stress resistance. We also show that, unlike SYT5, SYT1 and SYT3 are not required for Pseudomonas syringae resistance. Since SYT1 and SYT5 interact in vivo via their SMP domains, the distinct functions of these proteins cannot be caused by differences in their localization. Interestingly, structural phylogenetic analysis indicates that the SYT1 and SYT5 clades emerged early in the evolution of land plants. We also show that the SYT1 and SYT5 clades exhibit different structural features in their SMP and Ca2+ binding of their C2 domains, rationalizing their distinct biological roles.

Identification and characterization of CmPP2C31 playing a positive role in the abiotic stress resistance of Chinese chestnut via an integrated strategy

Chinese chestnut (Castanea mollissima Blume) is an important economic forest tree species and mainly cultivated in mountainous areas and wastelands, subjecting it to various abiotic stresses. The protein phosphatase 2C (PP2C) genes contributes largely to stress responses in plants. However, the characteristics and functions of PP2C genes in C. mollissima remain unknown. This study provides comprehensive analyses (including phylogenetic, synteny, RNA-seq, transgenic and yeast one-hybrid methods) revealing the characteristics of CmPP2C gene, which plays an important role in response to abiotic stress. Here, we identified 68 CmPP2Cs in the Chinese chestnut genome, and analyzed their characteristics and phylogenetic relationships. Furthermore, synteny analysis revealed that segmental and tandem duplication drove the expansion of the CmPP2C family to adapt to natural environmental pressures. RNA sequencing and co-expression analyses indicated that four hub CmPP2Cs in two key modules probably play important roles in the resistance to abiotic stress in chestnut. Among them, CmPP2C31 was significantly down-regulated under drought stress. Transgenic experiments via pollen magnetofection revealed that CmPP2C31 could positively and significantly regulate the drought resistance of Chinese chestnut seedlings. Subcellular localization showed that CmPP2C31 was a nuclear protein. Yeast one-hybrid assays suggested that EVM0007407 could regulate CmPP2C31 expression by binding to its promoter, thereby participating in abiotic stress resistance. These findings in our study provided detailed information on the CmPP2C family genes and laid a foundation for further elucidating the molecular mechanism of resistance to abiotic stress chestnut.

Exogenous Calcium Enhances Castor Tolerance to Saline-Alkaline Stress by Regulating Antioxidant Enzyme Activity and Activating Ca2+ and ROS Signaling Crosstalk

Saline-alkaline stress is a major factor limiting agricultural development, with calcium (Ca2+) playing a role in regulating plant tolerance through multiple signaling pathways. However, the specific mechanisms by which Ca2+ mediates saline-alkaline stress tolerance at the molecular level remain incompletely understood. This study investigates the effects of exogenous Ca2+ application on enhancing plant tolerance to saline-alkaline stress, focusing on its impact on the antioxidant system and Ca2+ and reactive oxygen species (ROS) signaling pathways. Through physiological assays and transcriptomic analyses, we evaluated oxidative damage markers, antioxidant enzyme activities, and the expression of key Ca2+ and ROS signaling genes. The results showed that saline-alkaline stress significantly elevated ROS levels, which led to increased membrane lipid peroxidation and induced upregulation of antioxidant response elements in castor roots. Exogenous calcium treatment reduced ROS accumulation by increasing superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and decreasing malondialdehyde (MDA) levels, demonstrating a marked improvement in the antioxidant system. Transcriptomic analysis identified CAT2 (LOC107261240) as the primary target gene associated with increased CAT activity in response to exogenous calcium. Additionally, the upregulation of specific Ca2+ channels, Ca2+ sensors, ROS receptors, and antioxidant-related genes with calcium treatment highlights the critical role of Ca2+-ROS signaling crosstalk in enhancing stress tolerance. Protein-protein interaction analysis identified APX3 and other hub genes involved in Ca2+-ROS signaling transduction and the regulation of antioxidant activity. These findings enhance our understanding of calcium's complex regulatory roles in plant abiotic stress responses, offering new theoretical insights for improving crop resilience in agriculture.

Analysis of abiotic and biotic stress-induced Ca2+ transients in the crop species Solanum tuberosum

Secondary messengers, such as calcium ions (Ca2+), are integral parts of a system that transduces environmental stimuli into appropriate cellular responses. Different abiotic and biotic stresses as well as developmental processes trigger temporal increases in cytosolic free Ca2+ levels by an influx from external and internal stores. Stimulus-specificity is obtained by a certain amplitude, duration, oscillation and localisation of the response. Most knowledge on stress-specific Ca2+ transient, called calcium signatures, has been gained in the model plant Arabidopsis thaliana, while reports about stress-related Ca2+ signalling in crop plants are comparatively scarce. In this study, we introduced the Ca2+ biosensor apoaequorin into potato (Solanum tuberosum, Lcv. Désirée). We observed dose-dependent calcium signatures in response to a series of stress stimuli, including H2O2, NaCl, mannitol and pathogen-associated molecular patterns (PAMPs) with stimuli-specific kinetics. Direct comparison with Arabidopsis revealed differences in the kinetics and amplitude of Ca2+ transients between both species, implying species-specific sensitivity for different stress conditions. The potato line generated in this work provides a useful tool for further investigations on stress-induced signalling pathways, which could contribute to the generation of novel, stress-tolerant potato varieties.

Acidic Stress Induces Cytosolic Free Calcium Oscillation, and an Appropriate Low pH Helps Maintain the Circadian Clock in Arabidopsis

Acidic stress is a formidable environmental factor that exerts adverse effects on plant growth and development, ultimately leading to a potential reduction in agricultural productivity. A low pH triggers Ca2+ influx across the plasma membrane (PM), eliciting distinct responses under various acidic pH levels. However, the underlying mechanisms by which Arabidopsis plant cells generate stimulus-specific Ca2+ signals in response to acidic stress remain largely unexplored. The experimentally induced stimulus may elicit spikes in cytosolic free Ca2+ concentration ([Ca2+]i) spikes or complex [Ca2+]i oscillations that persist for 20 min over a long-term of 24 h or even several days within the plant cytosol and chloroplast. This study investigated the increase in [Ca2+]i under a gradient of low pH stress ranging from pH 3.0 to 6.0. Notably, the peak of [Ca2+]i elevation was lower at pH 4.0 than at pH 3.0 during the initial 8 h, while other pH levels did not significantly increase [Ca2+]i compared to low acidic stress conditions. Lanthanum chloride (LaCl3) can effectively suppress the influx of [Ca2+]i from the apoplastic to the cytoplasm in plants under acid stress, with no discernible difference in intracellular calcium levels observed in Arabidopsis. Following 8 h of acid treatment in the darkness, the intracellular baseline Ca2+ levels in Arabidopsis were significantly elevated when exposed to low pH stress. A moderately low pH, specifically 4.0, may function as a spatial-temporal input into the circadian clock system. These findings suggest that acid stimulation can exert a continuous influence on intracellular calcium levels, as well as plant growth and development.

Effects of exogenous calcium on flavonoid biosynthesis and accumulation in peanut roots under salt stress through multi-omics

Flavonoids possess antioxidant properties and are crucial in enhancing plant resistance to abiotic stress. Exogenous calcium has been found to regulate the biosynthesis and accumulation of secondary metabolites, including flavonoids. However, the mechanism by which exogenous calcium influences flavonoid regulation in peanut roots under salt stress remains unclear. In this study, four treatment conditions were established: no salt stress, salt stress, exogenous calcium, and a combination of salt stress and exogenous calcium. The peanut root flavonoid profile was comprehensively analyzed using both a broadly targeted metabolomic approach and an absolute quantitative flavonoid metabolome. A total of 168 flavonoids were identified in the broad-target metabolome, while 68 were quantified in the absolute quantification analysis. The findings revealed that salt stress generally increased flavonoid content in peanut roots, while co-treatment with exogenous calcium significantly reduced this accumulation. Additionally, the activities of key enzymes and the expression of genes involved in the flavonoid biosynthesis pathway were upregulated under salt stress, but downregulated following the combined treatment. This study offers valuable insights into the physiological and ecological roles of flavonoids in response to environmental stressors in economically important crops.

Two calcium sensor-activated kinases function in root hair growth

Plant pollen tubes and root hairs typically polarized tip growth. It is well established that calcium ions (Ca2+) play essential roles in maintaining cell polarity and guiding cell growth orientation. Ca2+ signals are encoded by Ca2+ channels and transporters and are decoded by a variety of Ca2+-binding proteins often called Ca2+ sensors, in which calcineurin B-like protein (CBL) proteins function by interacting with and activating a group of kinases and activate CBL-interacting protein kinases (CIPKs). Some CBL-CIPK complexes, such as CBL2/3-CIPK12/19, act as crucial regulators of pollen tube growth. Whether these calcium decoding components regulate the growth of root hairs, another type of plant cell featuring Ca2+-regulated polarized growth, remains unknown. In this study, we identified CIPK13 and CIPK18 as genes specifically expressed in Arabidopsis (Arabidopsis thaliana) root hairs. The cipk13 cipk18 double mutants showed reduced root hair length and lower growth rates. The calcium oscillations at the root hair tip were attenuated in the cipk13 cipk18 mutants as compared to the wild-type plants. Through yeast 2-hybrid screens, CBL2 and CBL3 were identified as interacting with CIPK13 and CIPK18. cbl2 cbl3 displayed a shortened root hair phenotype similar to cipk13 cipk18. This genetic analysis, together with biochemical assays showing activation of CIPK13/18 by CBL2/3, supported the conclusion that CBL2/3 and CIPK13/18 may work as Ca2+-decoding modules in controlling root hair growth. Thus, the findings that CIPK12/19 and CIPK13/18 function in pollen tube and root hair growth, respectively, illustrate a molecular mechanism in which the same CBLs recruit distinct CIPKs in regulating polarized tip growth in different types of plant cells.

Integrated transcriptomic, metabolomic, and functional analyses unravel the mechanism of bagging delaying fruit cracking of pomegranate (Punica granatum L.)

The economic impact of fruit cracking in pomegranate products is substantial. In this study, we present the inaugural comprehensive analysis of transcriptome and metabolome in the outermost pericarp of pomegranate fruit in bagging conditions. Our investigation revealed a notable upregulation of differentially expressed genes (DEGs) associated with the calcium signaling pathway (76.92%) and xyloglucan endotransglucosylase/hydrolase (XTH) genes (87.50%) in the fruit peel of non-cracking fruit under bagging. Metabolomic analysis revealed that multiple phenolics, flavonoids, and tannins were identified in pomegranate. Among these, calmodulin-like 23 (PgCML23) exhibited a significant correlation with triterpenoids and demonstrated a marked upregulation under bagging treatment. The transgenic tomatoes overexpressing PgCML23 exhibited significantly higher cellulose content and xyloglucan endotransglucosylase (XET) enzyme activity in the pericarp at the red ripening stage compared to the wild type. Conversely, water-soluble pectin content, polygalacturonase (PG), and β-galactosidase (β-GAL) enzyme activities were significantly lower in the transgenic tomatoes. Importantly, the heterologous expression of PgCML23 led to a substantial reduction in the fruit cracking rate in tomatoes. Our findings highlight the reduction of fruit cracking in bagging conditions through the manipulation of PgCML23 expression.

Quantitative Trait Loci Mapping of Heading Date in Wheat under Phosphorus Stress Conditions

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments.

A novel role of the cotton calcium sensor CBL3 was involved in Verticillium wilt resistance in cotton

BACKGROUND

Verticillium wilt, causes mainly by the soilborne pathogen Verticillium dahliae, is a devastated vascular disease resulting in huge financial losses in cotton, so research on improving V. dahliae stress tolerance in cotton is the utmost importance. Calcium as the second messenger acts as a crucial role in plant innate immunity. Cytosolic Ca2+during the pathogen infection is a significant increase in plant immune responses. Calcineurin B-like (CBL) proteins are widely known calcium sensors that regulate abiotic stress responses. However, the role of cotton CBLs in response to V. dahliae stress remains unclear.

OBJECTIVE

To discover and utilize the gene to Verticillium wilt resistance and defense response mechanism of cotton.

METHODS

Through screening the gene to Verticillium wilt resistance in cotton, four GhCBL3 copies were obtained from the current common cotton genome sequences. The protein domain and phylogenetic analyses of GhCBL3 were performed using NCBI Blast, DNAMAN, and MotifScan programs. Real-time RT-PCR was used to detect the expression of GhCBL3 gene in cotton seedlings under various stress treatments. The expression construct including GhCBL3 cDNA was transduced into Agrobacterium tumefaciens (GV3101) by heat shock method and transformed into cotton plants by Virus-Induced Gene Silencing (VIGS) method. The results of silencing of GhCBl3 on ROS accumulation and plant disease resistance in cotton plants were assessed.

RESULTS

A member of calcineurin B-like proteins (defined as GhCBL3) in cotton was obtained. The expression of GhCBL3 was significantly induced and raised by various stressors, including dahliae, jasmonic acid (JA) and H2O2 stresses. Knockdown GhCBL3 in cotton by Virus-Induced Gene Silencing analysis enhanced Verticillium wilt tolerance and changed the occurrence of reactive oxygen species. Some disease-resistant genes were increased in GhCBL3-silencing cotton lines.

CONCLUSION

GhCBL3 may function on regulating the Verticillium dahliae stress response of plants.

Calcium-Dependent Protein Kinase GhCDPK16 Exerts a Positive Regulatory Role in Enhancing Drought Tolerance in Cotton

Cotton is essential for the textile industry as a primary source of natural fibers. However, environmental factors like drought present significant challenges to its cultivation, adversely affecting both production levels and fiber quality. Enhancing cotton's drought resilience has the potential to reduce yield losses and support the growth of cotton farming. In this study, the cotton calcium-dependent protein kinase GhCDPK16 was characterized, and the transcription level of GhCDPK16 was significantly upregulated under drought and various stress-related hormone treatments. Physiological analyses revealed that the overexpression of GhCDPK16 improved drought stress resistance in Arabidopsis by enhancing osmotic adjustment capacity and boosting antioxidant enzyme activities. In contrast, silencing GhCDPK16 in cotton resulted in increased dehydration compared with the control. Furthermore, reduced antioxidant enzyme activities and downregulation of ABA-related genes were observed in GhCDPK16-silenced plants. These findings not only enhanced our understanding of the biological functions of GhCDPK16 and the mechanisms underlying drought stress resistance but also underscored the considerable potential of GhCDPK16 in improving drought resilience in cotton.

Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in passion fruit (Passiflora edulis) and their involvement in flower and fruit development

BACKGROUND

The calmodulin (CaM) and calmodulin-like (CML) proteins play regulatory roles in plant growth and development, responses to biotic and abiotic stresses, and other biological processes. As a popular fruit and ornamental crop, it is important to explore the regulatory mechanism of flower and fruit development of passion fruit.

RESULTS

In this study, 32 PeCaM/PeCML genes were identified from passion fruit genome and were divided into 9 groups based on phylogenetic analysis. The structural analysis, including conserved motifs, gene structure and homologous modeling, illustrates that the PeCaM/PeCML in the same subgroup have relative conserved structural features. Collinearity analysis suggested that the expansion of the CaM/CML gene family likely took place mainly by segmental duplication, and the whole genome replication events were closely related with the rapid expansion of the gene group. PeCaM/PeCMLs were potentially required for different floral tissues development. Significantly, PeCML26 had extremely high expression levels during ovule and fruit development compared with other PeCML genes, suggesting that PeCML26 had potential functions involved in the development of passion fruit flowers and fruits. The co-presence of various cis-elements associated with growth and development, hormone responsiveness, and stress responsiveness in the promoter regions of these PeCaM/PeCMLs might contribute to their diverse regulatory roles. Furthermore, PeCaM/PeCMLs were also induced by various abiotic stresses. This work provides a comprehensive understanding of the CaM/CML gene family and valuable clues for future studies on the function and evolution of CaM/CML genes in passion fruit.

CONCLUSION

A total of 32 PeCaM/PeCML genes were divided into 9 groups. The PeCaM/PeCML genes showed differential expression patterns in floral tissues at different development stages. It is worth noting that PeCML26, which is highly homologous to AtCaM2, not only interacts with multiple BBR-BPC TFs, but also has high expression levels during ovule and fruit development, suggesting that PeCML26 had potential functions involved in the development of passion fruit flowers and fruits. This research lays the foundation for future investigations and validation of the potential function of PeCaM/PeCML genes in the growth and development of passion fruit.

Promising New Methods Based on the SOD Enzyme and SAUR36 Gene to Screen for Canola Materials with Heavy Metal Resistance

Canola is the largest self-produced vegetable oil source in China, although excessive levels of cadmium, lead, and arsenic seriously affect its yield. Therefore, developing methods to identify canola materials with good heavy metal tolerance is a hot topic for canola breeding. In this study, canola near-isogenic lines with different oil contents (F338 (40.62%) and F335 (46.68%) as the control) and heavy metal tolerances were used as raw materials. In an experiment with 100 times the safe standard values, the superoxide dismutase (SOD) and peroxidase (POD) activities of F335 were 32.02 mmol/mg and 71.84 mmol/mg, while the activities of F338 were 24.85 mmol/mg and 63.86 mmol/mg, exhibiting significant differences. The DEGs and DAPs in the MAPK signaling pathway of the plant hormone signal transduction pathway and other related pathways were analyzed and verified using RT-qPCR. SAUR36 and SAUR32 were identified as the key differential genes. The expression of the SAUR36 gene in canola materials planted in the experimental field was significantly higher than in the control, and FY958 exhibited the largest difference (27.82 times). In this study, SOD and SAUR36 were found to be closely related to heavy metal stress tolerance. Therefore, they may be used to screen for new canola materials with good heavy metal stress tolerance for canola breeding.

Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.

Genome-wide identification of the CNGC gene family and negative regulation of drought tolerance by HvCNGC3 and HvCNGC16 in transgenic Arabidopsis thaliana

Cyclic nucleotide-gated ion channels (CNGCs), as non-selective cation channels, play essential roles in plant growth and stress responses. However, they have not been identified in Qingke (Hordeum vulgare L.). Here, we performed a comprehensive genome-wide identification and function analysis of the HvCNGC gene family to determine its role in drought tolerance. Phylogenetic analysis showed that 27 HvCNGC genes were divided into four groups and unevenly located on seven chromosomes. Transcription analysis revealed that two closely related members of HvCNGC3 and HvCNGC16 were highly induced and the expression of both genes were distinctly different in two extremely drought-tolerant materials. Transient expression revealed that the HvCNGC3 and HvCNGC16 proteins both localized to the plasma membrane and karyotheca. Overexpression of HvCNGC3 and HvCNGC16 in Arabidopsis thaliana led to impaired seed germination and seedling drought tolerance, which was accompanied by higher hydrogen peroxide (H2O2), malondialdehyde (MDA), proline accumulation and increased cell damage. In addition, HvCNGC3 and HvCNGC16-overexpression lines reduced ABA sensitivity, as well as lower expression levels of some ABA biosynthesis and stress-related gene in transgenic lines. Furthermore, Yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that HvCNGC3 and HvCNGC16 interacted with calmodulin/calmodulin-like proteins (CaM/CML), which, as calcium sensors, participate in the perception and decoding of intracellular calcium signaling. Thus, this study provides information on the CNGC gene family and provides insight into the function and potential regulatory mechanism of HvCNGC3 and HvCNGC16 in drought tolerance in Qingke.

CAMTA3 repressor destabilization triggers TIR domain protein TN2-mediated autoimmunity in the Arabidopsis exo70B1 mutant

Calcium-dependent protein kinases (CPKs) can decode and translate intracellular calcium signals to induce plant immunity. Mutation of the exocyst subunit gene EXO70B1 causes autoimmunity that depends on CPK5 and the Toll/interleukin-1 receptor (TIR) domain resistance protein TIR-NBS2 (TN2), where direct interaction with TN2 stabilizes CPK5 kinase activity. However, how the CPK5-TN2 interaction initiates downstream immune responses remains unclear. Here, we show that, besides CPK5 activity, the physical interaction between CPK5 and functional TN2 triggers immune activation in exo70B1 and may represent reciprocal regulation between CPK5 and the TIR domain functions of TN2 in Arabidopsis (Arabidopsis thaliana). Moreover, we detected differential phosphorylation of the calmodulin-binding transcription activator 3 (CAMTA3) in the cpk5 background. CPK5 directly phosphorylates CAMTA3 at S964, contributing to its destabilization. The gain-of-function CAMTA3A855V variant that resists CPK5-induced degradation rescues immunity activated through CPK5 overexpression or exo70B1 mutation. Thus, CPK5-mediated immunity is executed through CAMTA3 repressor degradation via phosphorylation-induced and/or calmodulin-regulated processes. Conversely, autoimmunity in camta3 also partially requires functional CPK5. While the TIR domain activity of TN2 remains to be tested, our study uncovers a TN2-CPK5-CAMTA3 signaling module for exo70B1-mediated autoimmunity, highlighting the direct embedding of a calcium-sensing decoder element within resistance signalosomes.

External jasmonic acid isoleucine mediates amplification of plant elicitor peptide receptor (PEPR) and jasmonate-based immune signalling

Jasmonic acid-isoleucine (JA-Ile) is a plant defence hormone whose cellular levels are elevated upon herbivory and regulate defence signalling. Despite their pivotal role, our understanding of the rapid cellular perception of bioactive JA-Ile is limited. This study identifies cell type-specific JA-Ile-induced Ca2+ signal and its role in self-amplification and plant elicitor peptide receptor (PEPR)-mediated signalling. Using the Ca2+ reporter, R-GECO1 in Arabidopsis, we have characterized a monophasic and sustained JA-Ile-dependent Ca2+ signature in leaf epidermal cells. The rapid Ca2+ signal is independent of positive feedback by the JA-Ile receptor, COI1 and the transporter, JAT1. Microarray analysis identified up-regulation of receptors, PEPR1 and PEPR2 upon JA-Ile treatment. The pepr1 pepr2 double mutant in R-GECO1 background exhibits impaired external JA-Ile induced Ca2+ cyt elevation and impacts the canonical JA-Ile responsive genes. JA responsive transcription factor, MYC2 binds to the G-Box motif of PEPR1 and PEPR2 promoter and activates their expression upon JA-Ile treatment and in myc2 mutant, this is reduced. External JA-Ile amplifies AtPep-PEPR pathway by increasing the AtPep precursor, PROPEP expression. Our work shows a previously unknown non-canonical PEPR-JA-Ile-Ca2+ -MYC2 signalling module through which plants sense JA-Ile rapidly to amplify both AtPep-PEPR and jasmonate signalling in undamaged cells.

Understanding the salt overly sensitive pathway in Prunus: Identification and characterization of NHX, CIPK, and CBL genes

Salinity is a major abiotic stress factor that can significantly impact crop growth, and productivity. In response to salt stress, the plant Salt Overly Sensitive (SOS) signaling pathway regulates the homeostasis of intracellular sodium ion concentration. The SOS1, SOS2, and SOS3 genes play critical roles in the SOS pathway, which belongs to the members of Na+/H+ exchanger (NHX), CBL-interacting protein kinase (CIPK), and calcineurin B-like (CBL) gene families, respectively. In this study, we performed genome-wide identifications and phylogenetic analyses of NHX, CIPK, and CBL genes in six Rosaceae species: Prunus persica, Prunus dulcis, Prunus mume, Prunus armeniaca, Pyrus ussuriensis × Pyrus communis, and Rosa chinensis. NHX, CIPK, and CBL genes of Arabidopsis thaliana were used as controls for phylogenetic analyses. Our analysis revealed the lineage-specific and adaptive evolutions of Rosaceae genes. Our observations indicated the existence of two primary classes of CIPK genes: those that are intron-rich and those that are intron-less. Intron-rich CIPKs in Rosaceae and Arabidopsis can be traced back to algae CIPKs and CIPKs found in early plants, suggesting that intron-less CIPKs evolved from their intron-rich counterparts. This study identified one gene for each member of the SOS signaling pathway in P. persica: PpSOS1, PpSOS2, and PpSOS3. Gene expression analyses indicated that all three genes of P. persica were expressed in roots and leaves. Yeast two-hybrid-based protein-protein interaction analyses revealed a direct interaction between PpSOS3 and PpSOS2; and between PpSOS2 and PpSOS1C-terminus region. Our findings indicate that the SOS signaling pathway is highly conserved in P. persica.

Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress

Calcium is known to improve seed-germination rates under salt stress. We investigated the involvement of calcium ions (Ca2+) in regulating HIGH-AFFINITY K+ TRANSPORTER 1 (HKT1; 1), which encodes a Na+/K+ transporter, and its post-translational regulator TYPE 2C PROTEIN PHOSPHATASE 49 (PP2C49), in germinating Arabidopsis (Arabidopsis thaliana) seedlings. Germination rates of hkt1 mutant seeds under salt stress remained unchanged by CaCl2 treatment in wild-type Arabidopsis, whereas pp2c49 mutant seeds displayed improved salt-stress tolerance in the absence of CaCl2 supplementation. Analysis of HKT1;1 and PP2C49 promoter activity revealed that CaCl2 treatment results in radicle-focused expression of HKT1;1 and reduction of the native radicle-exclusive expression of PP2C49. Ion-content analysis indicated that CaCl2 treatment improves K+ retention in germinating wild-type seedlings under salt stress, but not in hkt1 seedlings. Transgenic seedlings designed to exclusively express HKT1;1 in the radicle during germination displayed higher germination rates under salt stress than the wild type in the absence of CaCl2 treatment. Transcriptome analysis of germinating seedlings treated with CaCl2, NaCl, or both revealed 118 upregulated and 94 downregulated genes as responsive to the combined treatment. Bioinformatics analysis of the upstream sequences of CaCl2-NaCl-treatment-responsive upregulated genes revealed the abscisic acid response element CACGTGTC, a potential CaM-binding transcription activator-binding motif, as most prominent. Our findings suggest a key role for Ca2+ in mediating salt-stress responses during germination by regulating genes that function to maintain Na+ and K+ homeostasis, which is vital for seed germination under salt stress.

Genome-wide analysis of the peanut CaM/CML gene family reveals that the AhCML69 gene is associated with resistance to Ralstonia solanacearum

BACKGROUND

Calmodulins (CaMs)/CaM-like proteins (CMLs) are crucial Ca2+-binding sensors that can decode and transduce Ca2+ signals during plant development and in response to various stimuli. The CaM/CML gene family has been characterized in many plant species, but this family has not yet been characterized and analyzed in peanut, especially for its functions in response to Ralstonia solanacearum. In this study, we performed a genome-wide analysis to analyze the CaM/CML genes and their functions in resistance to R. solanacearum.

RESULTS

Here, 67, 72, and 214 CaM/CML genes were identified from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. The genes were divided into nine subgroups (Groups I-IX) with relatively conserved exon‒intron structures and motif compositions. Gene duplication, which included whole-genome duplication, tandem repeats, scattered repeats, and unconnected repeats, produced approximately 81 pairs of homologous genes in the AhCaM/CML gene family. Allopolyploidization was the main reason for the greater number of AhCaM/CML members. The nonsynonymous (Ka) versus synonymous (Ks) substitution rates (less than 1.0) suggested that all homologous pairs underwent intensive purifying selection pressure during evolution. AhCML69 was constitutively expressed in different tissues of peanut plants and was involved in the response to R. solanacearum infection. The AhCML69 protein was localized in the cytoplasm and nucleus. Transient overexpression of AhCML69 in tobacco leaves increased resistance to R. solanacearum infection and induced the expression of defense-related genes, suggesting that AhCML69 is a positive regulator of disease resistance.

CONCLUSIONS

This study provides the first comprehensive analysis of the AhCaM/CML gene family and potential genetic resources for the molecular design and breeding of peanut bacterial wilt resistance.

The 14-3-3 Protein BdGF14a Increases the Transcriptional Regulation Activity of BdbZIP62 to Confer Drought and Salt Resistance in Tobacco

BdGF14a, a 14-3-3 gene from Brachypodium distachyon, induced by salt, H2O2, and abscisic acid (ABA), improved tolerance to drought and salt in tobacco, with a higher survival rate and longer roots under these stresses. Additionally, physiological index analyses showed that the heterologous expression of BdGF14a induced higher expression levels of antioxidant enzymes and their activities, leading to lighter DAB and NBT staining, denoting decreased H2O2 content. Additionally, the lower MDA content and ion leakage indicated enhanced cell membrane stability. Moreover, exogenous ABA resulted in shorter roots and a lower stomatal aperture in BdGF14a transgenic plants. BdGF14a interacted with NtABF2 and regulated the expression of stress-related genes. However, adding an ABA biosynthesis inhibitor suppressed most of these changes. Furthermore, similar salt and drought resistance phenotypes and physiological indicators were characterized in tobacco plants expressing BdbZIP62, an ABRE/ABF that interacts with BdGF14a. And Y1H and LUC assays showed that BdGF14a could enhance the transcription regulation activity of NtABF2 and BdbZIP62, targeting NtNECD1 by binding to the ABRE cis-element. Thus, BdGF14a confers resistance to drought and salinity through interaction with BdbZIP62 and enhances its transcriptional regulation activity via an ABA-mediated signaling pathway. Therefore, this work offers novel target genes for breeding salt- and drought-tolerant plants.

SCAB1 coordinates sequential Ca2+ and ABA signals during osmotic stress induced stomatal closure in Arabidopsis

Hyperosmotic stress caused by drought is a detrimental threat to plant growth and agricultural productivity due to limited water availability. Stomata are gateways of transpiration and gas exchange, the swift adjustment of stomatal aperture has a strong influence on plant drought resistance. Despite intensive investigations of stomatal closure during drought stress in past decades, little is known about how sequential signals are integrated during complete processes. Here, we discovered that the rapid Ca2+ signaling and subsequent abscisic acid (ABA) signaling contribute to the kinetics of both F-actin reorganizations and stomatal closure in Arabidopsis thaliana, while STOMATAL CLOSURE-RELATED ACTIN BINDING PROTEIN1 (SCAB1) is the molecular switch for this entire process. During the early stage of osmotic shock responses, swift elevated calcium signaling promotes SCAB1 phosphorylation through calcium sensors CALCIUM DEPENDENT PROTEIN KINASE3 (CPK3) and CPK6. The phosphorylation restrained the microfilament binding affinity of SCAB1, which bring about the F-actin disassembly and stomatal closure initiation. As the osmotic stress signal continued, both the kinase activity of CPK3 and the phosphorylation level of SCAB1 attenuated significantly. We further found that ABA signaling is indispensable for these attenuations, which presumably contributed to the actin filament reassembly process as well as completion of stomatal closure. Notably, the dynamic changes of SCAB1 phosphorylation status are crucial for the kinetics of stomatal closure. Taken together, our results support a model in which SCAB1 works as a molecular switch, and directs the microfilament rearrangement through integrating the sequentially generated Ca2+ and ABA signals during osmotic stress induced stomatal closure.

Genome-wide analyses of calmodulin and calmodulin-like proteins in the halophyte Nitraria sibirica reveal their involvement in response to salinity, drought and cold stress

The calmodulin (CaM) and calmodulin-like (CML) proteins are major calcium sensors that play a critical role in environmental stimulus response in plants. Nevertheless, the CaM/CML proteins from the specific plants with extreme tolerance to abiotic stresses remained so far uncharacterized. In this study, 66 candidate proteins (three NsCaMs and sixty-three NsCMLs) were identified from the halophyte Nitraria sibirica, which can withstand an extreme salinity. Bioinformatic analysis of upstream cis-acting elements predicted the potential involvement of NsCaM/CMLs in abiotic stress responses and various hormone responses. Additionally, the Nitraria sibirica transcriptome revealed that 17 and 7 NsCMLs were significantly upregulated under 100 mM or 400 mM NaCl treatment. Transcription of most salt-responsive genes was similarly upregulated under cold stress, yet downregulated under drought treatment. Moreover, predictive subcellular localization analysis suggested that the stress-responsive NsCML proteins mainly localize at the cellular membrane and within the nucleus. Furthermore, transgenic overexpression of two NsCMLs (NISI03G1136 and NISI01G1645) was found to mitigate H2O2 accumulation caused by salt stress. These results provide insights into the potential function of Nitraria sibirica CaM/CML proteins, which could aid the investigation of molecular mechanisms of extreme tolerance to abiotic stresses in halophytes.

An Arabidopsis mutant line lacking the mitochondrial calcium transport regulator MICU shows an altered metabolite profile

Plant metabolism is constantly changing and requires input signals for efficient regulation. The mitochondrial calcium uniporter (MCU) couples organellar and cytoplasmic calcium oscillations leading to oxidative metabolism regulation in a vast array of species. In Arabidopsis thaliana, genetic deletion of AtMICU leads to altered mitochondrial calcium handling and ultrastructure. Here we aimed to further assess the consequences upon genetic deletion of AtMICU. Our results confirm that AtMICU safeguards intracellular calcium transport associated with carbohydrate, amino acid, and phytol metabolism modifications. The implications of such alterations are discussed.

Survival of Nutrient-Starved Diatoms Under Ocean Acidification: Perspective from Nutrient Sensing, Cadmium Detection, and Nitrogen Assimilation

Increased anthropogenic emissions of carbon dioxide (CO2) have resulted in ocean acidification (OA) that is intertwined with enhanced ocean stratification. Diatoms are assumed to suffer from a more nutrient-limited condition in the future ocean. This study aimed to explore how OA affects the diatom dynamics under nutrient-poor conditions and the ability of diatoms to perceive nutrients (nitrogen, phosphorus, silicon, and trace metals) and cadmium (Cd) stimuli and assimilate nitrogen when receiving nutrients or Cd supplementation. Our study observed that diatom population grown under OA condition declined faster than those grown under ambient condition. Ocean acidification greatly lower intracellular Ca2+ concentration in diatom cells. Intracellular Ca2+ burst was involved in phosphorus accumulation but not in nitrogen, silicon, essential metals, and cadmium uptake. Our data demonstrate slower NO3- assimilation rates of diatoms grown in acidified seawater. Our study also indicates that diatoms have a poor perception of phosphorus availability under OA condition.

Calcium Signaling and the Response to Heat Shock in Crop Plants

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

Ion Changes and Signaling under Salt Stress in Wheat and Other Important Crops

High concentrations of sodium (Na+), chloride (Cl-), calcium (Ca2+), and sulphate (SO42-) are frequently found in saline soils. Crop plants cannot successfully develop and produce because salt stress impairs the uptake of Ca2+, potassium (K+), and water into plant cells. Different intracellular and extracellular ionic concentrations change with salinity, including those of Ca2+, K+, and protons. These cations serve as stress signaling molecules in addition to being essential for ionic homeostasis and nutrition. Maintaining an appropriate K+:Na+ ratio is one crucial plant mechanism for salt tolerance, which is a complicated trait. Another important mechanism is the ability for fast extrusion of Na+ from the cytosol. Ca2+ is established as a ubiquitous secondary messenger, which transmits various stress signals into metabolic alterations that cause adaptive responses. When plants are under stress, the cytosolic-free Ca2+ concentration can rise to 10 times or more from its resting level of 50-100 nanomolar. Reactive oxygen species (ROS) are linked to the Ca2+ alterations and are produced by stress. Depending on the type, frequency, and intensity of the stress, the cytosolic Ca2+ signals oscillate, are transient, or persist for a longer period and exhibit specific "signatures". Both the influx and efflux of Ca2+ affect the length and amplitude of the signal. According to several reports, under stress Ca2+ alterations can occur not only in the cytoplasm of the cell but also in the cell walls, nucleus, and other cell organelles and the Ca2+ waves propagate through the whole plant. Here, we will focus on how wheat and other important crops absorb Na+, K+, and Cl- when plants are under salt stress, as well as how Ca2+, K+, and pH cause intracellular signaling and homeostasis. Similar mechanisms in the model plant Arabidopsis will also be considered. Knowledge of these processes is important for understanding how plants react to salinity stress and for the development of tolerant crops.

Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae

Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.

Calmodulin and calmodulin-like protein-mediated plant responses to biotic stresses

Plants have evolved a set of finely regulated mechanisms to respond to various biotic stresses. Transient changes in intracellular calcium (Ca2+ ) concentration have been well documented to act as cellular signals in coupling environmental stimuli to appropriate physiological responses with astonishing accuracy and specificity in plants. Calmodulins (CaMs) and calmodulin-like proteins (CMLs) are extensively characterized as important classes of Ca2+ sensors. The spatial-temporal coordination between Ca2+ transients, CaMs/CMLs and their target proteins is critical for plant responses to environmental stresses. Ca2+ -loaded CaMs/CMLs interact with and regulate a broad spectrum of target proteins, such as ion transporters (including channels, pumps, and antiporters), transcription factors, protein kinases, protein phosphatases, metabolic enzymes and proteins with unknown biological functions. This review focuses on mechanisms underlying how CaMs/CMLs are involved in the regulation of plant responses to diverse biotic stresses including pathogen infections and herbivore attacks. Recent discoveries of crucial functions of CaMs/CMLs and their target proteins in biotic stress resistance revealed through physiological, molecular, biochemical, and genetic analyses have been described, and intriguing insights into the CaM/CML-mediated regulatory network are proposed. Perspectives for future directions in understanding CaM/CML-mediated signalling pathways in plant responses to biotic stresses are discussed. The application of accumulated knowledge of CaM/CML-mediated signalling in biotic stress responses into crop cultivation would improve crop resistance to various biotic stresses and safeguard our food production in the future.

Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut (Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency

This study identified 45 calcium-dependent protein kinase (CDPK) genes in cultivated peanut (Arachis hypogaea L.), which are integral in plant growth, development, and stress responses. These genes, classified into four subgroups based on phylogenetic relationships, are unevenly distributed across all twenty peanut chromosomes. The analysis of the genetic structure of AhCDPKs revealed significant similarity within subgroups, with their expansion primarily driven by whole-genome duplications. The upstream promoter sequences of AhCDPK genes contained 46 cis-acting regulatory elements, associated with various plant responses. Additionally, 13 microRNAs were identified that target 21 AhCDPK genes, suggesting potential post-transcriptional regulation. AhCDPK proteins interacted with respiratory burst oxidase homologs, suggesting their involvement in redox signaling. Gene ontology and KEGG enrichment analyses affirmed AhCDPK genes' roles in calcium ion binding, protein kinase activity, and environmental adaptation. RNA-seq data revealed diverse expression patterns under different stress conditions. Importantly, 26 AhCDPK genes were significantly induced when exposed to Ca deficiency during the pod stage. During the seedling stage, four AhCDPKs (AhCDPK2/-25/-28/-45) in roots peaked after three hours, suggesting early signaling roles in pod Ca nutrition. These findings provide insights into the roles of CDPK genes in plant development and stress responses, offering potential candidates for predicting calcium levels in peanut seeds.

Caffeine Produced in Rice Plants Provides Tolerance to Water-Deficit Stress

Exogenous or endogenous caffeine application confers resistance to diverse biotic stresses in plants. In this study, we demonstrate that endogenous caffeine in caffeine-producing rice (CPR) increases tolerance even to abiotic stresses such as water deficit. Caffeine produced by CPR plants influences the cytosolic Ca2+ ion concentration gradient. We focused on examining the expression of Ca2+-dependent protein kinase genes, a subset of the numerous proteins engaged in abiotic stress signaling. Under normal conditions, CPR plants exhibited increased expressions of seven OsCPKs (OsCPK10, OsCPK12, OsCPK21, OsCPK25, OsCPK26, OsCPK30, and OsCPK31) and biochemical modifications, including antioxidant enzyme (superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase) activity and non-enzymatic antioxidant (ascorbic acid) content. CPR plants exhibited more pronounced gene expression changes and biochemical alterations in response to water-deficit stress. CPR plants revealed increased expressions of 16 OsCPKs (OsCPK1, OsCPK2, OsCPK3, OsCPK4, OsCPK5, OsCPK6, OsCPK9, OsCPK10, OsCPK11, OsCPK12, OsCPK14, OsCPK16, OsCPK18, OsCPK22, OsCPK24, and OsCPK25) and 8 genes (OsbZIP72, OsLEA25, OsNHX1, OsRab16d, OsDREB2B, OsNAC45, OsP5CS, and OsRSUS1) encoding factors related to abiotic stress tolerance. The activity of antioxidant enzymes increased, and non-enzymatic antioxidants accumulated. In addition, a decrease in reactive oxygen species, an accumulation of malondialdehyde, and physiological alterations such as the inhibition of chlorophyll degradation and the protection of photosynthetic machinery were observed. Our results suggest that caffeine is a natural chemical that increases the potential ability of rice to cope with water-deficit stress and provides robust resistance by activating a rapid and comprehensive resistance mechanism in the case of water-deficit stress. The discovery, furthermore, presents a new approach for enhancing crop tolerance to abiotic stress, including water deficit, via the utilization of a specific natural agent.

Enhanced Ca2+ binding to EF-hands through phosphorylation of conserved serine residues activates MpRBOHB and chitin-triggered ROS production

NADPH oxidases/RBOHs catalyze apoplastic ROS production and act as key signaling nodes, integrating multiple signal transduction pathways regulating plant development and stress responses. Although RBOHs have been suggested to be activated by Ca2+ binding and phosphorylation by various protein kinases, a mechanism linking Ca2+ binding and phosphorylation in the activity regulation remained elusive. Chitin-triggered ROS production required cytosolic Ca2+ elevation and Ca2+ binding to MpRBOHB in a liverwort Marchantia polymorpha. Heterologous expression analysis of truncated variants revealed that a segment of the N-terminal cytosolic region highly conserved among land plant RBOHs encompassing the two EF-hand motifs is essential for the activation of MpRBOHB. Within the conserved regulatory domain, we have identified two Ser residues whose phosphorylation is critical for the activation in planta. Isothermal titration calorimetry analyses revealed that phosphorylation of the two Ser residues increased the Ca2+ binding affinity of MpRBOHB, while Ca2+ binding is indispensable for the activation, even if the two Ser residues are phosphorylated. Our findings shed light on a mechanism through which phosphorylation potentiates the Ca2+ -dependent activation of MpRBOHB, emphasizing the pivotal role of Ca2+ binding in mediating the Ca2+ and phosphorylation-driven activation of MpRBOHB, which is likely to represent a fundamental mechanism conserved among land plant RBOHs.

Genome-Wide Investigation and Expression Analysis of the Catalase Gene Family in Oat Plants (Avena sativa L.)

Through the degradation of reactive oxygen species (ROS), different antioxidant enzymes, such as catalase (CAT), defend organisms against oxidative stress. These enzymes are crucial to numerous biological functions, like plant development and defense against several biotic and abiotic stresses. However, despite the major economic importance of Avena sativa around the globe, little is known about the CAT gene's structure and organization in this crop. Thus, a genome-wide investigation of the CAT gene family in oat plants has been carried out to characterize the potential roles of those genes under different stressors. Bioinformatic approaches were used in this study to predict the AvCAT gene's structure, secondary and tertiary protein structures, physicochemical properties, phylogenetic tree, and expression profiling under diverse developmental and biological conditions. A local Saudi oat variety (AlShinen) was used in this work. Here, ten AvCAT genes that belong to three groups (Groups I-III) were identified. All identified CATs harbor the two conserved domains (pfam00199 and pfam06628), a heme-binding domain, and a catalase activity motif. Moreover, identified AvCAT proteins were located in different compartments in the cell, such as the peroxisome, mitochondrion, and cytoplasm. By analyzing their promoters, different cis-elements were identified as being related to plant development, maturation, and response to different environmental stresses. Gene expression analysis revealed that three different AvCAT genes belonging to three different subgroups showed noticeable modifications in response to various stresses, such as mannitol, salt, and ABA. As far as we know, this is the first report describing the genome-wide analysis of the oat catalase gene family, and these data will help further study the roles of catalase genes during stress responses, leading to crop improvement.

Genome-Wide Identification of the CDPK Gene Family and Their Involvement in Taproot Cracking in Radish

Taproot cracking, a severe and common physiological disorder, markedly reduces radish yield and commercial value. Calcium-dependent protein kinase (CDPK) plays a pivotal role in various plant developmental processes; however, its function in radish taproot cracking remains largely unknown. Here, 37 RsCDPK gene members were identified from the long-read radish genome "QZ-16". Phylogenetic analysis revealed that the CDPK members in radish, tomato, and Arabidopsis were clustered into four groups. Additionally, synteny analysis identified 13 segmental duplication events in the RsCDPK genes. Analysis of paraffin-embedded sections showed that the density and arrangement of fleshy taproot cortex cells are important factors that affect radish cracking. Transcriptome sequencing of the fleshy taproot cortex revealed 5755 differentially expressed genes (DEGs) (3252 upregulated and 2503 downregulated) between non-cracking radish "HongYun" and cracking radish "505". These DEGs were significantly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction KEGG pathways. Furthermore, when comparing the 37 RsCDPK gene family members and RNA-seq DEGs, we identified six RsCDPK genes related to taproot cracking in radish. Soybean hairy root transformation experiments showed that RsCDPK21 significantly and positively regulates root length development. These findings provide valuable insights into the relationship between radish taproot cracking and RsCDPK gene function.

The calcium connection: exploring the intricacies of calcium signaling in plant-microbe interactions

The process of plant immune response is orchestrated by intracellular signaling molecules. Since plants are devoid of a humoral system, they develop extensive mechanism of pathogen recognition, signal perception, and intricate cell signaling for their protection from biotic and abiotic stresses. The pathogenic attack induces calcium ion accumulation in the plant cells, resulting in calcium signatures that regulate the synthesis of proteins of defense system. These calcium signatures induct different calcium dependent proteins such as calmodulins (CaMs), calcineurin B-like proteins (CBLs), calcium-dependent protein kinases (CDPKs) and other signaling molecules to orchestrate the complex defense signaling. Using advanced biotechnological tools, the role of Ca2+ signaling during plant-microbe interactions and the role of CaM/CMLs and CDPKs in plant defense mechanism has been revealed to some extent. The Emerging perspectives on calcium signaling in plant-microbe interactions suggest that this complex interplay could be harnessed to improve plant resistance against pathogenic microbes. We present here an overview of current understanding in calcium signatures during plant-microbe interaction so as to imbibe a future direction of research.

The CBL-CIPK network is involved in the physiological crosstalk between plant growth and stress adaptation

Plants have evolved to deal with different stresses during plant growth, relying on complex interactions or crosstalk between multiple signalling pathways in plant cells. In this sophisticated regulatory network, Ca2+ transients in the cytosol ([Ca2+ ]cyt ) act as major physiological signals to initiate appropriate responses. The CALCINEURIN B-LIKE PROTEIN (CBL)-CBL-INTERACTING PROTEIN KINASE (CIPK) network relays physiological signals characterised by [Ca2+ ]cyt transients during plant development and in response to environmental changes. Many studies are aimed at elucidating the role of the CBL-CIPK network in plant growth and stress responses. This review discusses the involvement of the CBL-CIPK pathways in two levels of crosstalk between plant development and stress adaptation: direct crosstalk through interaction with regulatory proteins, and indirect crosstalk through adaptation of correlated physiological processes that affect both plant development and stress responses. This review thus provides novel insights into the physiological roles of the CBL-CIPK network in plant growth and stress adaptation.

Role of myristoylation in modulating PCaP1 interaction with calmodulin

Plasma membrane-associated Cation-binding Protein 1 (PCaP1) belongs to the plant-unique DREPP protein family with largely unknown biological functions but ascertained roles in plant development and calcium (Ca2+) signaling. PCaP1 is anchored to the plasma membrane via N-myristoylation and a polybasic cluster, and its N-terminal region can bind Ca2+/calmodulin (CaM). However, the molecular determinants of PCaP1-Ca2+-CaM interaction and the functional impact of myristoylation in the complex formation and Ca2+ sensitivity of CaM remained to be elucidated. Herein, we investigated the direct interaction between Arabidopsis PCaP1 (AtPCaP1) and CaM1 (AtCaM1) using both myristoylated and non-myristoylated peptides corresponding to the N-terminal region of AtPCaP1. ITC analysis showed that AtCaM1 forms a high affinity 1:1 complex with AtPCaP1 peptides and the interaction is strictly Ca2+-dependent. Spectroscopic and kinetic Ca2+ binding studies showed that the myristoylated peptide dramatically increased the Ca2+-binding affinity of AtCaM1 and slowed the Ca2+ dissociation rates from both the C- and N-lobes, thus suggesting that the myristoylation modulates the mechanism of AtPCaP1 recognition by AtCaM1. Furthermore, NMR and CD spectroscopy revealed that the structure of both the N- and C-lobes of Ca2+-AtCaM1 changes markedly in the presence of the myristoylated AtPCaP1 peptide, which assumes a helical structure in the final complex. Overall, our results indicate that AtPCaP1 biological function is strictly related to the presence of multiple ligands, i.e., the myristoyl moiety, Ca2+ ions and AtCaM1 and only a full characterization of their equilibria will allow for a complete molecular understanding of the putative role of PCaP1 as signal protein.