Calcium Sensors as Key Hubs in Plant Responses to Biotic and Abiotic Stresses

Positive roles of the Ca2+ sensors GbCML45 and GbCML50 in improving cotton Verticillium wilt resistance

As a universal second messenger, cytosolic calcium (Ca2+) functions in multifaceted intracellular processes, including growth, development and responses to biotic/abiotic stresses in plant. The plant-specific Ca2+ sensors, calmodulin and calmodulin-like (CML) proteins, function as members of the second-messenger system to transfer Ca2+ signal into downstream responses. However, the functions of CMLs in the responses of cotton (Gossypium spp.) after Verticillium dahliae infection, which causes the serious vascular disease Verticillium wilt, remain elusive. Here, we discovered that the expression level of GbCML45 was promoted after V. dahliae infection in roots of cotton, suggesting its potential role in Verticillium wilt resistance. We found that knockdown of GbCML45 in cotton plants decreased resistance while overexpression of GbCML45 in Arabidopsis thaliana plants enhanced resistance to V. dahliae infection. Furthermore, there was physiological interaction between GbCML45 and its close homologue GbCML50 by using yeast two-hybrid and bimolecular fluorescence assays, and both proteins enhanced cotton resistance to V. dahliae infection in a Ca2+-dependent way in a knockdown study. Detailed investigations indicated that several defence-related pathways, including salicylic acid, ethylene, reactive oxygen species and nitric oxide signalling pathways, as well as accumulations of lignin and callose, are responsible for GbCML45- and GbCML50-modulated V. dahliae resistance in cotton. These results collectively indicated that GbCML45 and GbCML50 act as positive regulators to improve cotton Verticillium wilt resistance, providing potential targets for exploitation of improved Verticillium wilt-tolerant cotton cultivars by genetic engineering and molecular breeding.

CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling

Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.

Transcriptome sequencing and metabolome analysis reveal the molecular mechanism of Salvia miltiorrhiza in response to drought stress

Salvia miltiorrhiza is commonly used as a Chinese herbal medicine to treat different cardiovascular and cerebrovascular illnesses due to its active ingredients. Environmental conditions, especially drought stress, can affect the yield and quality of S. miltiorrhiza. However, moderate drought stress could improve the quality of S. miltiorrhiza without significantly reducing the yield, and the mechanism of this initial drought resistance is still unclear. In our study, transcriptome and metabolome analyses of S. miltiorrhiza under different drought treatment groups (CK, A, B, and C groups) were conducted to reveal the basis for its drought tolerance. We discovered that the leaves of S. miltiorrhiza under different drought treatment groups had no obvious shrinkage, and the malondialdehyde (MDA) contents as well as superoxide dismutase (SOD) and peroxidase (POD) activities dramatically increased, indicating that our drought treatment methods were moderate, and the leaves of S. miltiorrhiza began to initiate drought resistance. The morphology of root tissue had no significant change under different drought treatment groups, and the contents of four tanshinones significantly enhanced. In all, 5213, 6611, and 5241 differentially expressed genes (DEGs) were shared in the A, B, and C groups compared with the CK group, respectively. The results of KEGG and co-expression analysis showed that the DEGs involved in plant-pathogen interactions, the MAPK signaling pathway, phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction responded to drought stress and were strongly correlated with tanshinone biosynthesis. Furthermore, the results of metabolism analysis indicated that 67, 72, and 92 differentially accumulated metabolites (DAMs), including fumarate, ferulic acid, xanthohumol, and phytocassanes, which were primarily involved in phenylpropanoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis pathways, were detected in these groups. These discoveries provide valuable information on the molecular mechanisms by which S. miltiorrhiza responds to drought stress and will facilitate the development of drought-resistant and high-quality S. miltiorrhiza production.

Symbiont effector-guided mapping of proteins in plant networks to improve crop climate stress resilience: Symbiont effectors inform highly interconnected plant protein networks and provide an untapped resource for crop climate resilience strategies

There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe-derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno-suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution-driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments.

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.

Factors influencing fruit cracking: an environmental and agronomic perspective

Fruit cracking, a widespread physiological disorder affecting various fruit crops and vegetables, has profound implications for fruit quality and marketability. This mini review delves into the multifaceted factors contributing to fruit cracking and emphasizes the pivotal roles of environmental and agronomic factors in its occurrence. Environmental variables such as temperature, relative humidity, and light exposure are explored as determinants factors influencing fruit cracking susceptibility. Furthermore, the significance of mineral nutrition and plant growth regulators in mitigating fruit cracking risk is elucidated, being calcium deficiency identified as a prominent variable in various fruit species. In recent years, precision farming and monitoring systems have emerged as valuable tools for managing environmental factors and optimizing fruit production. By meticulously tracking parameters such as temperature, humidity, soil moisture, and fruit skin temperature, growers can make informed decisions to prevent or alleviate fruit cracking. In conclusion, effective prevention of fruit cracking necessitates a comprehensive approach that encompasses both environmental and agronomic factors.

Positive regulation of ABA signaling by MdCPK4 interacting with and phosphorylating MdPYL2/12 in Arabidopsis

The phytohormone abscisic acid (ABA) regulates plant growth and development and stress resistance through the ABA receptor PYLs. To date, no interaction between CPK and PYL has been reported, even in Arabidopsis and rice. In this study, we found that MdCPK4 from Malus domestica (Md for short) interacts with two MdPYLs, MdPYL2/12, in the nucleus and the cytoplasm in vivo and phosphorylates the latter in vitro as well. Compared with the wild type (WT), the MdCPK4- or MdPYL2/12-overexpressing Arabidopsis lines showed more sensitivity to ABA, and therefore stronger drought resistance. The ABA-related genes (ABF1, ABF2, ABF4, RD29A and SnRK2.2) were significantly upregulated in the overexpressing (OE) lines after ABA treatment. These results indicate that MdCPK4 and MdPYL2/12 act as positive regulators in response to ABA-mediated drought resistance in apple. Our results reveal the relationship between MdCPK4 and MdPYL2/12 in ABA signaling, which will further enrich the molecular mechanism of drought resistance in plants.

Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Introduction

The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods

To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and Discussion

The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

A Mitochondrial Localized Chaperone Regulator OsBAG6 Functions in Saline-Alkaline Stress Tolerance in Rice

B-cell lymphoma 2 (Bcl-2)-associated athanogene (BAG) family genes play prominent roles in regulating plant growth, development, and stress response. Although the molecular mechanism underlying BAG's response to abiotic stress has been studied in Arabidopsis, the function of OsBAG underlying saline-alkaline stress tolerance in rice remains unclear. In this study, OsBAG6, a chaperone regulator localized to mitochondria, was identified as a novel negative regulator of saline-alkaline stress tolerance in rice. The expression level of OsBAG6 was induced by high concentration of salt, high pH, heat and abscisic acid treatments. Overexpression of OsBAG6 in rice resulted in significantly reduced plant heights, grain size, grain weight, as well as higher sensitivity to saline-alkaline stress. By contrast, the osbag6 loss-of-function mutants exhibited decreased sensitivity to saline-alkaline stress. The transcriptomic analysis uncovered differentially expressed genes related to the function of "response to oxidative stress", "defense response", and "secondary metabolite biosynthetic process" in the shoots and roots of OsBAG6-overexpressing transgenic lines. Furthermore, cytoplasmic levels of Ca2+ increase rapidly in plants exposed to saline-alkaline stress. OsBAG6 bound to calcium sensor OsCaM1-1 under normal conditions, which was identified by comparative interactomics, but not in the presence of elevated Ca2+. Released OsCaM1-1 saturated with Ca2+ is then able to regulate downstream stress-responsive genes as part of the response to saline-alkaline stress. OsBAG6 also interacted with energy biosynthesis and metabolic pathway proteins that are involved in plant growth and saline-alkaline stress response mechanisms. This study reveals a novel function for mitochondrial localized OsBAG6 proteins in the saline-alkaline stress response alongside OsCaM1-1.

Can nutrients act as signals under abiotic stress?

Plant cells are in constant communication to coordinate development processes and environmental reactions. Under stressful conditions, such communication allows the plant cells to adjust their activities and development. This is due to intercellular signaling events which involve several components. In plant development, cell-to-cell signaling is ensured by mobile signals hormones, hydrogen peroxide (H2O2), nitric oxide (NO), or hydrogen sulfide (H2S), as well as several transcription factors and small RNAs. Mineral nutrients, including macro and microelements, are determinant factors for plant growth and development and are, currently, recognized as potential signal molecules. This review aims to highlight the role of nutrients, particularly calcium, potassium, magnesium, nitrogen, phosphorus, and iron as signaling components with special attention to the mechanism of response against stress conditions.

Straining the root on and off triggers local calcium signalling

A fundamental function of an organ is the ability to perceive mechanical cues. Yet, how this is accomplished is not fully understood, particularly in plant roots. In plants, the majority of studies dealing with the effects of mechanical stress have investigated the aerial parts. However, in natural conditions roots are also subjected to mechanical cues, for example when the root encounters a hard obstacle during its growth or when the soil settles. To investigate root cellular responses to root compression, we developed a microfluidic system associated with a microvalve allowing the delivery of controlled and reproducible mechanical stimulations to the root. In this study, examining plants expressing the R-GECO1-mTurquoise calcium reporter, we addressed the root cell deformation and calcium increase induced by the mechanical stimulation. Lateral pressure applied on the root induced a moderate elastic deformation of root cortical cells and elicited a multicomponent calcium signal at the onset of the pressure pulse, followed by a second one at the release of the pressure. This indicates that straining rather than stressing of tissues is relevant to trigger the calcium signal. Although the intensity of the calcium response increases with the pressure applied, successive pressure stimuli led to a remarkable attenuation of the calcium signal. The calcium elevation was restricted to the tissue under pressure and did not propagate. Strain sensing, spatial restriction and habituation to repetitive stimulation represent the fundamental properties of root signalling in response to local mechanical stimulation. These data linking mechanical properties of root cells to calcium elevation contribute to elucidating the pathway allowing the root to adapt to the mechanical cues generated by the soil.

Lipid profiling reveals Leymus Chinensis root insensitivity to Ca limitation

BACKGROUND

Leymus chinensis (L. chinensis) is a perennial native forage grass widely distributed in the steppe of Inner Mongolia as the dominant species. Calcium (Ca) is an essential mineral element important for plant adaptation to the growth environment. Ca limitation was previously shown to strongly inhibit Arabidopsis (Arabidopsis thaliana) seedling growth and disrupt plasma membrane stability and selectivity, increasing fluid-phase-based endocytosis and contents of all major membrane lipids.

RESULTS

In this study, we investigated the significance of Ca for L. chinensis growth and membrane stability relative to Arabidopsis. Our results showed that Ca limitation did not affect L. chinensis seedling growth and endocytosis in roots. Moreover, the plasma membrane maintained high selectivity. The lipid phosphatidylcholine (PC): phosphatidylethanolamine (PE) ratio, an indicator of the membrane stability, was five times higher in L. chinensis than in Arabidopsis. Furthermore, in L. chinensis, Ca limitation did not affect the content of any major lipid types, decreased malondialdehyde (MDA) content, and increased superoxide dismutase (SOD) activity, showing an opposite pattern to that in Arabidopsis. L. chinensis roots accumulated higher contents of PC, phosphatidylinositol (PI), monogalactosyldiacylglycerol (MGDG), phosphatidylglycerol (PG), cardiolipin (CL), digalactosyldiacylglycerol (DGDG), and lysophosphatidylcholine (LPC) but less phosphatidylethanolamine (PE), diacylglycerol (DAG), triacylglycerolv (TAG), phosphatidylserine (PS), lysobisphosphatidic acids (LPAs), lysophosphatidylethanolamine (LPE), and lysophosphatidylserine (LPS) than Arabidopsis roots. Moreover, we detected 31 and 66 unique lipids in L. chinensis and Arabidopsis, respectively.

CONCLUSIONS

This study revealed that L. chinensis roots have unique membrane lipid composition that was not sensitive to Ca limitation, which might contribute to the wider natural distribution of this species.

The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

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.

Light signaling as cellular integrator of multiple environmental cues in plants

Plants being sessile need to rapidly adapt to the constantly changing environment through modifications in their internal clock, metabolism, and gene expression. They have evolved an intricate system to perceive and transfer the signals from the primary environmental factors namely light, temperature and water to regulate their growth development and survival. Over past few decades rigorous research using molecular genetics approaches, especially in model plant Arabidopsis, has resulted in substantial progress in discovering various photoreceptor systems and light signaling components. In parallel several molecular pathways operating in response to other environmental cues have also been elucidated. Interestingly, the studies have shown that expression profiles of genes involved in photomorphogenesis can undergo modulation in response to other cues from the environment. Recently, the photoreceptor, PHYB, has been shown to function as a thermosensor. Downstream components of light signaling pathway like COP1 and PIF have also emerged as integrating hubs for various kinds of signals. All these findings indicate that light signaling components may act as central integrator of various environmental cues to regulate plant growth and development processes. In this review, we present a perspective on cross talk of signaling mechanisms induced in response to myriad array of signals and their integration with the light signaling components. By putting light signals on the central stage, we propose the possibilities of enhancing plant resilience to the changing environment by fine-tuning the genetic manipulation of its signaling components in the future.

Exogenous methyl jasmonate combined with Ca2+ promote resveratrol biosynthesis and stabilize sprout growth for the production of resveratrol-rich peanut sprouts

Promoting resveratrol accumulation in plants and utilizing resveratrol-rich plants as raw materials for the development of functional foods is a promising development direction. The effects of methyl jasmonate (MeJA), in combination with CaCl2 and Ca2+ inhibitors, on physiological metabolism and resveratrol enrichment of peanut sprouts were investigated. MeJA combined with CaCl2 increased Ca2+ content, calmodulin content, and Ca2+- adenosine triphosphatase activity, as well as upregulated calcium-binding proteinase expression levels. Treatment with MeJA plus CaCl2 significantly increased peroxidase and superoxide dismutase activities and antioxidant capacities, significantly decreased the content of malondialdehyde and hydrogen peroxide, which resulted in a significantly increased in sprout length and fresh weight, and alleviated the inhibition of sprout growth. MeJA plus CaCl2 significantly increased the activities of phenylalanine ammonia-lyase and 4-coumarate coenzyme A ligase and upregulated the expression levels of phenylalanine ammonia-lyase, cinnamic acid 4-hydroxylase, and resveratrol synthase, thus significantly increasing resveratrol content. However, MeJA combined with Ca2+ antagonists reversed these effects. These results indicate that MeJA interacts with Ca2+ to promote resveratrol synthesis in peanut sprouts and to improve sprout stress tolerances.

Identification of Dioscorea opposite Thunb. CDPK gene family reveals that DoCDPK20 is related to heat resistance

Temperature affects the growth and yield of yam (Dioscorea opposite Thunb.), and calcium-dependent protein kinases (CDPKs) play an important role in the plant stress response. However, there has been a lack of system analyses of yam's CDPK gene family. In this study, 29 CDPK transcriptome sequences with complete open reading frames (ORFs) were identified from yam RNA sequencing data. The sequences were classified into four groups (I-VI) using phylogenetic analysis. Two DoCDPK genes were randomly selected from each group and the gene patterns of yam leaves were determined using quantitative real-time PCR (qRT-PCR) under high and low temperature stress in order to show their unique functions in mediating specific responses. Among them, DoCDPK20 was significantly induced in high temperatures. The pPZP221-DoCDPK20 was transformed into tobacco leaves using an agrobacterium-mediated method. Under high temperature stress, DoCDPK20 overexpression reduced photosynthesis and improved heat tolerance in transgenic tobacco. Our research offers meaningful perspectives into CDPK genes and new avenues for the genetic engineering and molecular breeding of yam.

Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes

AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.

Evolution and diversification of CaM/CML gene family in green plants

Calmodulin (CaM) and calmodulin-like (CML) proteins are crucial Ca2+ sensors, which are widely involved in different biological processes of plants, including their growth and development, and stress responses. However, the origin and evolution of the CaM/CML gene family in plants remain elusive. In this study, 2133 CaM and 23094 CML genes were identified from the 1000 plants project (1 KP) species and the sequenced plants, covering algae, mosses, monilophytes, lycophytes, flowering plants, and all other green plant branches. Analysis showed that the size of the CML subfamily was correlated with the genome size of corresponding plant species, as well as the total gene number in the genome. Moreover, with the evolution from algae to angiosperms, the number of CML genes in plants increased gradually which could have been driven mainly by genome-wide segmental duplication events, while the number of CaMs remained basically stable at 2-3. Phylogenetic analysis demonstrated that CaM first appeared in green algae, while CML appeared earlier and has already been presented in dinoflagellates. Further analysis showed that the number and sequence of EF-hand domain in CaMs are highly conserved, while those of CMLs are diverse among different plant taxa. Expression analysis revealed that the expression level of CaMs was generally higher than that of CMLs, indicating that the high-expression genes have essential functions, while the low-expression genes are the main reasons for the functional diversity of the CaM/CML gene family in plants. The results might contribute to understanding the evolution of CaM/CML genes as well as their molecular functions.

Genome-Wide Characterization of Calmodulin and Calmodulin-like Protein Gene Families in Paulownia fortunei and Identification of Their Potential Involvement in Paulownia Witches' Broom

As significant Ca2+ sensors, calmodulin (CaM) and calmodulin-like proteins (CML), have been associated with a variety of environmental conditions in plants. However, whether CaMs/CMLs are related to the stress of phytoplasma infection has not been reported in Paulownia fortunei. In the current study, 5 PfCaMs and 58 PfCMLs were detected through a genome-wide investigation. The number of EF-hand motifs in all PfCaMs/CMLs varied. Bioinformatics analyses, including protein characteristics, conserved domain, gene structure, cis-elements, evolutionary relationship, collinearity, chromosomal location, post-translation modification site, subcellular localization and expression pattern analyses, represented the conservation and divergence of PfCaMs/CMLs. Furthermore, some PfCaMs/CMLs might be involved in plants' reaction to phytoplasma infection and exogenous calcium therapy, indicating these genes may play a role in abiotic as well as biotic stress responses. In addition, subcellular localization analysis showed that PfCML10 was located in the cell membrane and nucleus. In summary, these findings establish a stronger platform for their subsequent functional investigation in trees and further characterize their roles in Paulownia witches' broom (PaWB) occurrence.

Calcium-dependent protein kinase GhCDPK4 plays a role in drought and abscisic acid stress responses

Drought is an important factor limiting the yield and quality of cotton. In the present study, the gene encoding the cotton calcium-dependent protein kinase GhCDPK4 was identified and characterized in the transcriptome of cotton under PEG-induced drought stress. In RT-qPCR experiments, GhCDPK4 expression was found to be up-regulated under drought and abscisic acid (ABA) stress. Under drought conditions, heterologous overexpression of GhCDPK4 in tobacco showed a better phenotypic status, higher antioxidant enzyme activity, and lower relative electrolyte leakage (REL) and malondialdehyde (MDA) content. Meanwhile, ghcdpk4-silenced cotton plants, which were extremely sensitive to drought, exhibited higher levels of O^2-，H₂O₂, and MDA contents compared to the control. Meanwhile, silenced lines showed impaired stomatal closure under drought stress, resulting in increased water loss from transpiration in silenced lines. GhCDPK4 expression was induced by ABA, and there are five ABA-responsive elements in its promoter. and C2-DOMAIN ABA-RELATED 4(CAR4, Gh_D09G1653) were found to interact and be co-expressed in the GhCDPK4 interaction network. Therefore, GhCDPK4 may reduce the extent of water loss and oxidative damage in cotton under drought by positively regulating ABA-controlled stomatal closure and reactive oxygen species (ROS) scavenging systems. This study demonstrates the great potential of GhCDPK4 in improving drought resistance in crops.

Supplementation of the Plant Conditioner ELICE Vakcina® Product with β-Aminobutyric Acid and Salicylic Acid May Lead to Trans-Priming Signaling in Barley (Hordeum vulgare)

Plant immunological memory, priming, is a defense mechanism that can be triggered by external stimuli, leading to the activation of biochemical pathways and preparing plants for disease resistance. Plant conditioners improve yield and crop quality through nutrient efficiency and abiotic stress tolerance, which is enhanced by the addition of resistance- and priming-induced compounds. Based on this hypothesis, this study aimed to investigate plant responses to priming actives of different natures, including salicylic acid and beta-aminobutyric acid, in combination with the plant conditioning agent ELICE Vakcina^®. Phytotron experiments and RNA-Seq analyses of differentially expressed genes using the combinations of these three investigated compounds were performed in a barley culture to investigate possible synergistic relationships in the genetic regulatory network. The results indicated a strong regulation of defense responses, which was enhanced by supplemental treatments; however, both synergistic and antagonistic effects were enhanced with one or two components, depending on the supplementation. The overexpressed transcripts were functionally annotated to assess their involvement in jasmonic acid and salicylic acid signaling; however, their determinant genes were highly dependent on the supplemental treatments. Although the effects overlapped, the potential effects of trans-priming the two supplements tested could be largely separated.

Role of Polyamines in the Response to Salt Stress of Tomato

Plants irrigated with saline solutions undergo osmotic and oxidative stresses, which affect their growth, photosynthetic activity and yield. Therefore, the use of saline water for irrigation, in addition to the increasing soil salinity, is one of the major threats to crop productivity worldwide. Plant tolerance to stressful conditions can be improved using different strategies, i.e., seed priming and acclimation, which elicit morphological and biochemical responses to overcome stress. In this work, we evaluated the combined effect of priming and acclimation on salt stress response of a tomato cultivar (Solanum lycopersicum L.), very sensitive to salinity. Chemical priming of seeds was performed by treating seeds with polyamines (PAs): 2.5 mM putrescine (PUT), 2.5 mM spermine (SPM) and 2.5 mM spermidine (SPD). Germinated seeds of primed and non-primed (controls) were sown in non-saline soil. The acclimation consisted of irrigating the seedlings for 2 weeks with tap water, followed by irrigation with saline and non-saline water for 4 weeks. At the end of the growth period, morphological, physiological and biochemical parameters were determined. The positive effects of combined treatments were evident, when primed plants were compared to non-primed, grown under the same conditions. Priming with PAs improved tolerance to salt stress, reduced the negative effects of salinity on growth, improved membrane integrity, and increased photosynthetic pigments, proline and enzymatic and non-enzymatic antioxidant responses in all salt-exposed plants. These results may open new perspectives and strategies to increase tolerance to salt stress in sensitive species, such as tomato.

Transcriptomic analysis reveals that Bacillomycin D-C16 induces multiple pathways of disease resistance in cherry tomato

BACKGROUND

Bacillomycin D-C16 can induce resistance in cherry tomato against pathogens; however, the underlying molecular mechanism is poorly understood. Here, the effect of Bacillomycin D-C16 on induction of disease resistance in cherry tomato was investigated using a transcriptomic analysis.

RESULTS

Transcriptomic analysis revealed a series of obvious enrichment pathways. Bacillomycin D-C16 induced phenylpropanoid biosynthesis pathways and activated the synthesis of defense-related metabolites including phenolic acids and lignin. Moreover, Bacillomycin D-C16 triggered a defense response through both hormone signal transduction and plant-pathogen interactions pathways, and increased the transcription of several transcription factors (e.g., AP2/ERF, WRKY and MYB). These transcription factors might contribute to the further activated the expression of defense-related genes (PR1, PR10 and CHI) and stimulated the accumulation of H2O2.

CONCLUSION

Bacillomycin D-C16 can induce resistance in cherry tomato by activating the phenylpropanoid biosynthesis pathway, hormone signal transduction pathway and plant-pathogen interactions pathway, thus activating comprehensive defense reaction against pathogen invasion. These results provided a new insight into the bio-preservation of cherry tomato by the Bacillomycin D-C16.

Comprehensive Analysis of Calcium Sensor Families, CBL and CIPK, in Aeluropus littoralis and Their Expression Profile in Response to Salinity

Plants have acquired sets of highly regulated and complex signaling pathways to respond to unfavorable environmental conditions during evolution. Calcium signaling, as a vital mechanism, enables plants to respond to external stimuli, including abiotic and biotic stresses, and coordinate the basic processes of growth and development. In the present study, two calcium sensor families, CBL and CIPK, were investigated in a halophyte plant, Aeluropus littoralis, with a comprehensive analysis. Here, six AlCBL genes, and twenty AlCIPK genes were studied. The analysis of the gene structure and conserved motifs, as well as physicochemical properties, showed that these genes are highly conserved during evolution. The expression levels of AlCBL genes and AlCIPK genes were evaluated under salt stress in leaf and root tissue. Based on the real-time RT-PCR results, the AlCIPK gene family had a higher variation in mRNA abundance than the AlCBL gene family. AlCIPK genes were found to have a higher abundance in leaves than in roots. The results suggest that the correlation between AlCBL genes and AlCIPK is tissue-specific, and different correlations can be expected in leaves and roots. Based on these correlations, AlCIPK3.1-AlCBL4.1 and AlCIPK1.2-AlCBL4.4 can be co-expressed in the root tissue, while AlCBL10 has the potential to be co-expressed with AlCIPK5, AlCIPK26, and AlCIPK12.3 in the leaf tissue. Our findings reveal valuable information on the structure and function of calcium sensor families in A. littoralis, a halophyte plant, that can be used in future research on the biological function of CBLs and CIPKs on salt stress resistance.

Characterization of Dendrobium catenatum CBL-CIPK signaling networks and their response to abiotic stress

Dendrobium catenatum is a traditional Chinese medicine listing as rare and endangered due to environmental impacts. But little is known about its stress resistance mechanism. The CBL-CIPK signaling pathway played vital roles in various stress responses. In this study, we identified 9 calcineurin B-like (CBL) genes and 28 CBL-interacting protein kinase (CIPK) genes from D. catenatum. Phylogenetic analysis showed that DcCBL and DcCIPK families could be divided into four and six subgroups, respectively. Members in each subgroup had similar gene structures. Cis-acting element analyses showed that these genes were involved in stress responses and hormone signaling. Spatial expression profiles showed that they were tissue-specific, and expressed lower in vegetative organs than reproductive organs. Gene expression analyses revealed that these genes were involved in drought, heat, cold, and salt responses and depended on abscisic acid (ABA) and salicylic acid (SA) signaling pathways. Furthermore, we cloned 19 DcCIPK genes and 9 DcCBL genes and detected ten interacting CBL-CIPK combinations using yeast two-hybrid system. Finally, we constructed 20 CBL-CIPK signaling pathways based on their expression patterns and interaction relationships. These results established CBL-CIPK signaling pathway responding to abiotic stress and provided a molecular basis for improving D. catenatum stress resistance in the future.

Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation

Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.

Field plus lab experiments help identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees: A case study of Camellia oleifera

The molecular mechanisms of freezing tolerance are unresolved in the perennial trees that can survive under much lower freezing temperatures than annual herbs. Since natural conditions involve many factors and temperature usually cannot be controlled, field experiments alone cannot directly identify the effects of freezing stress. Lab experiments are insufficient for trees to complete cold acclimation and cannot reflect natural freezing-stress responses. In this study, a new method was proposed using field plus lab experiments to identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees using Camellia oleifera as a case. Cultivated C. oleifera is the dominant woody oil crop in China. Wild C. oleifera at the high-elevation site in Lu Mountain could survive below -30°C, providing a valuable genetic resource for the breeding of freezing tolerance. In the field experiment, air temperature was monitored from autumn to winter on wild C. oleifera at the high-elevation site in Lu Mountain. Leave samples were taken from wild C. oleifera before cold acclimation, during cold acclimation and under freezing temperature. Leaf transcriptome analyses indicated that the gene functions and expression patterns were very different during cold acclimation and under freezing temperature. In the lab experiments, leaves samples from wild C. oleifera after cold acclimation were placed under -10°C in climate chambers. A cultivated C. oleifera variety "Ganwu 1" was used as a control. According to relative conductivity changes of leaves, wild C. oleifera showed more freezing-tolerant than cultivated C. oleifera. Leaf transcriptome analyses showed that the gene expression patterns were very different between wild and cultivated C. oleifera in the lab experiment. Combing transcriptome results in both of the field and lab experiments, the common genes associated with freezing-stress responses were identified. Key genes of the flg22, Ca²⁺ and gibberellin signal transduction pathways and the lignin biosynthesis pathway may be involved in the freezing-stress responses. Most of the genes had the highest expression levels under freezing temperature in the field experiment and showed higher expression in wild C. oleifera with stronger freezing tolerance in the lab experiment. Our study may help identify freezing tolerance and underlying molecular mechanisms in trees.

Characterization of three tandem-duplicated calcium binding protein (CaBP) genes and promoters reveals their roles in the phytohormone and wounding responses in citrus

Accumulated evidences have revealed the critical roles of calcium binding protein (CaBP) in growth and stress responses of plants. However, its function in woody plants is poorly understood. In this study, we cloned the CDS, gDNA and promoter sequences of three tandem-duplicated CaBPs (CsCaBP1, CsCaBP2 and CsCaBP3) from Citrus sinensis, analyzed their sequence characteristics, and investigated their gene expression patterns and promoter activities under treatments of CaCl₂, several phytohormones and wounding. Results showed that the three CsCaBPs have high sequence similarity. Their expression was strongly induced by CaCl₂, ethylene, jasmonic acid, salicylic acid and wounding, and the promoting effect of wounding on their expression was found to be partially ethylene-dependent. Consistently, we identified many phytohormone-related cis-acting elements in their promoters, and their promoter activity could be induced significantly by ethylene, jasmonic acid, salicylic acid and wounding. All the three CsCaBPs can interact with WRKY40, whose encoding gene showed a similar expression pattern to CsCaBPs under phytohormone and wounding treatments. In addition, CsERF14, CsERF21, CsERF3 and CsERF2 could bind to their promoters. The results obtained in this study indicated that the three duplicated CsCaBPs were functionally redundant and played similar roles in the phytohormone and wounding responses of C. sinensis.

Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber

Background

The calmodulin-like (CML) protein is a crucial Ca²⁺-binding protein that can sense and conduct the Ca²⁺ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable.

Methods

In this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR).

Results

Forty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs.

Genome-wide identification and analysis of the IQM gene family in soybean

IQM, a plant-specific calmodulin-binding protein, plays multiple roles in plant growth and development. Although a comprehensive analysis has been carried out on the IQM family genes in Arabidopsis and rice, the number and functions of IQM genes in other species have not been explored. In this study, we identified 15 members of the soybean (Glycine max) IQM gene family using BLASTP tools. These members were distributed on 12 soybean chromosomes and constitute six pairs caused by fragment duplication events. According to phylogeny, the 15 genes were divided into three subfamilies (I, II, and III), and members of the same subfamily had similar gene and protein structures. Yeast two-hybrid experiments revealed that the IQ motif is critical for the binding of GmIQM proteins to GmCaM, and its function is conserved in soybean, Arabidopsis, and rice. Based on real-time PCR, the soybean IQM genes were strongly induced by PEG and NaCl, suggesting their important biological functions in abiotic stress responses. Overall, this genome-wide analysis of the soybean IQM gene family lays a solid theoretical foundation for further research on the functions of GmIQM genes and could serve as a reference for the improvement and breeding of soybean stress resistance traits.

Identification of Saccharum CaM gene family and function characterization of ScCaM1 during cold and oxidant exposure in Pichia pastoris

BACKGROUND

Calmodulin (CaM) plays an essential role in binding calcium ions and mediating the interpretation of Ca²⁺ signals in plants under various stresses. However, the evolutionary relationship of CaM family proteins in Saccharum has not been elucidated.

OBJECTIVE

To deduce and explore the evolution and function of Saccharum CaM family.

METHODS

A total of 104 typical CaMs were obtained from Saccharum spontaneum and other 18 plant species. The molecular characteristics and evolution of those CaM proteins were analyzed. A typical CaM gene, ScCaM1, was subsequently cloned from sugarcane (Saccharum spp. hybrid). Its expression patterns in different tissues and under various abiotic stresses were assessed by quantitative real-time PCR. Then the green fluorescent protein was used to determine the subcellular localization of ScCaM1. Finally, the function of ScCaM1 was evaluated via heterologous yeast expression systems.

RESULTS

Three typical CaM members (SsCaM1, SsCaM2, and SsCaM3) were identified from the S. spontaneum genome database. CaMs were originated from the two last common ancestors before the origin of angiosperms. The number of CaM family members did not correlate to the genome size but correlated with allopolyploidization events. The ScCaM1 was more highly expressed in buds and roots than in other tissues. The expression patterns of ScCaM1 suggested that it was involved in responses to various abiotic stresses in sugarcane via different hormonal signaling pathways. Noteworthily, its expression levels appeared relatively stable during the cold exposure in the cold-tolerant variety but significantly suppressed in the cold-susceptible variety. Moreover, the recombinant yeast (Pichia pastoris) overexpressing ScCaM1 grew better than the wild-type yeast strain under cold and oxidative stresses. It was revealed that the ScCaM1 played a positive role in reactive oxygen species scavenging and conferred enhanced cold and oxidative stress tolerance to cells.

CONCLUSION

This study provided comprehensive information on the CaM gene family in Saccharum and would facilitate further investigation of their functional characterization.

Perspectives in Plant Abiotic Stress Signaling

State-of-the-art collections of strategies, approaches, and methods are immediately useful for ongoing characterizations or for novel discoveries in the scientific field of plant abiotic stress signaling. It must however be kept in mind that, in the future, these strategies, approaches, and methods will be facing a number of increasingly complex issues. The development of the necessary confrontation of laboratory-based knowledge on abiotic stress signaling mechanisms with real-life in natura situations of plant-stress interactions involves at least five levels of complexity: (i) plant biodiversity, (ii) the spatio-temporal heterogeneity of stress-related parameters, (iii) the unknowns of future stress-related constraints, (iv) the influence of biotic interactions, (v) the crosstalk between various signaling pathways and their final integration into physiological responses. These complexities are major bottlenecks for assessing the evolutionary, ecological, and agronomical relevance of abiotic stress signaling studies. All of the presently-described strategies, approaches, and methods will have to be gradually complemented with the development of real-time and in natura tools, with systematic application of mathematical modeling to complex interactions and with further research on the impact of stress memory mechanisms on long-term responses.

Interplay of Methodology and Conceptualization in Plant Abiotic Stress Signaling

Characterizing the mechanisms of plant sensitivity and reactivity to physicochemical cues related to abiotic stresses is of utmost importance for understanding plant-environment interactions, adaptations of the sessile lifestyle, and the evolutionary dynamics of plant species and populations. Moreover, plant communities are confronted with an environmental context of global change, involving climate changes, planetary pollutions of soils, waters and atmosphere, and additional anthropogenic changes. The mechanisms through which plants perceive abiotic stress stimuli and transduce stress perception into physiological responses constitute the primary line of interaction between the plant and the environment, and therefore between the plant and global changes. Understanding how plants perceive complex combinations of abiotic stress signals and transduce the resulting information into coordinated responses of abiotic stress tolerance is therefore essential for devising genetic, agricultural, and agroecological strategies that can ensure climate change resilience, global food security, and environmental protection. Discovery and characterization of sensing and signaling mechanisms of plant cells are usually carried out within the general framework of eukaryotic sensing and signal transduction. However, further progress depends on a close relationship between the conceptualization of sensing and signaling processes with adequate methodologies and techniques that encompass biochemical and biophysical approaches, cell biology, molecular biology, and genetics. The integration of subcellular and cellular analyses as well as the integration of in vitro and in vivo analyses are particularly important to evaluate the efficiency of sensing and signaling mechanisms in planta. Major progress has been made in the last 10-20 years with the caveat that cell-specific processes and in vivo processes still remain difficult to analyze and with the additional caveat that the range of plant models under study remains rather limited relatively to plant biodiversity and to the diversity of stress situations.

Effects of calcium on cell wall metabolism enzymes and expression of related genes associated with peel creasing in Citrus fruits

Fruit peel creasing is a serious pre-harvest physiological disorder in citrus, influencing fruit quality, storage, and yield. Four- and eight-year-old 'Hongjiang' oranges grafted onto Canton lemon rootstocks were treated with calcium and calcium inhibitors, respectively, to study the effects of different treatments on fruit creasing rate, mechanical properties of the peel, cell wall metabolism enzyme activities, and the expression of related genes. Foliar application of 0.5% calcium nitrate significantly reduced the fruit creasing rate, while treatment with EGTA and LaCl₃, inhibitors of calcium uptake, increased the fruit creasing rate; But the effect of calcium nitrate treatment on changing the mechanical properties of pericarp and inhibiting the activity of hydrolase (PG, Cx and PE) was not very significant. Furthermore, it was observed that the expression levels of genes (PG, Cx, and PE) encoding cell wall-degrading enzymes were significantly lower in the normal fruit peel than in the creased fruit peel. Meanwhile, the expression levels of PG, Cx, and PE were higher in the peel of shaded fruit than in the peel of exposed fruit. During the high incidence period of fruit creasing, calcium nitrate treatment down-regulated the expression of PG, Cx, and PE, while EGTA treatment up-regulated the expression of these genes. In conclusion, foliar spraying of calcium nitrate at the fruit rapid enlargement stage can increase the Ca content in the peel of 'Hongjiang' orange and significantly suppress the expression of cell wall degrading enzymes genes (PG, PE and Cx) in 'Hongjiang' orange peel during the high occurrence period of fruit creasing, resulting in reducing the occurrence of fruit creasing and cracking.

Plant Disease Resistance-Related Signaling Pathways: Recent Progress and Future Prospects

Plant-pathogen interactions induce a signal transmission series that stimulates the plant's host defense system against pathogens and this, in turn, leads to disease resistance responses. Plant innate immunity mainly includes two lines of the defense system, called pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). There is extensive signal exchange and recognition in the process of triggering the plant immune signaling network. Plant messenger signaling molecules, such as calcium ions, reactive oxygen species, and nitric oxide, and plant hormone signaling molecules, such as salicylic acid, jasmonic acid, and ethylene, play key roles in inducing plant defense responses. In addition, heterotrimeric G proteins, the mitogen-activated protein kinase cascade, and non-coding RNAs (ncRNAs) play important roles in regulating disease resistance and the defense signal transduction network. This paper summarizes the status and progress in plant disease resistance and disease resistance signal transduction pathway research in recent years; discusses the complexities of, and interactions among, defense signal pathways; and forecasts future research prospects to provide new ideas for the prevention and control of plant diseases.

Apoptotic-like PCD inducing HRC gene when silenced enhances multiple disease resistance in plants

Programmed cell death (PCD) plays an important role in plant environmental stress and has the potential to be manipulated to enhance disease resistance. Plants have innate immunity and, following pathogen perception, the host induces a Hypersensitive Response PCD (HR-PCD), leading to pattern (PTI) or effector triggered immunity (ETI). Here we report a non-HR type or Apoptotic-Like PCD (AL-PCD) in pathogen infected wheat and potato based on apoptotic-like DNA fragmentation. A deletion mutation in the gene encoding histidine rich calcium binding protein (TaHRC) in FHB-resistant wheat (R-NIL) failed to induce AL-PCD. Similarly, the CRISPR-Cas9 based silencing of StHRC gene in Russet Burbank potato failed to induce apoptotic-like DNA fragmentation, proved based on DNA laddering and TUNEL assays. The absence of AL-PCD in wheat R-NIL reduced pathogen biomass and mycotoxins, increasing the accumulation of resistance metabolites and FHB-resistance, and in potato it enhanced resistance to multiple pathogens. In addition, the reduced expressions of metacaspase (StMC7) and Ca²⁺ dependent endonuclease 2 (StCaN2) genes in potato with Sthrc indicated an involvement of a hierarchy of genes in the induction of AL-PCD. The HRC in commercial varieties of different crops, if functional, can be silenced by genome editing possibly to enhance resistance to multiple pathogens.

Genome-wide survey of Calcium-Dependent Protein Kinases (CPKs) in five Brassica species and identification of CPKs induced by Plasmodiophora brassicae in B. rapa, B. oleracea, and B. napus

Calcium-dependent protein kinase (CPK) is a class of Ser/Thr protein kinase that exists in plants and some protozoa, possessing Ca²⁺ sensing functions and kinase activity. To better reveal the roles that Brassica CPKs played during plant response to stresses, five Brassica species, namely Brassica rapa (B. rapa), Brassica nigra (B. nigra), Brassica oleracea (B. oleracea), Brassica juncea (B. juncea), and Brassica napus (B. napus) were selected and analyzed. In total, 51 BraCPK, 56 BniCPK, 56 BolCPK, 88 BjuCPK, and 107 BnaCPK genes were identified genome wide and phylogenetics, chromosomal mapping, collinearity, promoter analysis, and biological stress analysis were conducted. The results showed that a typical CPK gene was constituted by a long exon and tandem short exons. They were unevenly distributed on most chromosomes except chromosome A08 in B. napus and B. rapa, and almost all CPK genes were located on regions of high gene density as non-tandem form. The promoter regions of BraCPKs, BolCPKs, and BnaCPKs possessed at least three types of cis-elements, among which the abscisic acid responsive-related accounted for the largest proportion. In the phylogenetic tree, CPKs were clustered into four primary groups, among which group I contained the most CPK genes while group IV contained the fewest. Some clades, like AT5G23580.1(CPK12) and AT2G31500.1 (CPK24) contained much more gene members than others, indicating a possibility that gene expansion occurred during evolution. Furthermore, 4 BraCPKs, 14 BolCPKs, and 31 BnaCPKs involved in the Plasmodiophora brassicae (P. brassicae) defense response in resistant (R) or susceptible (S) materials were derived from online databases, leading to the discovery that some R-specific induced CPKs, such as BnaC02g08720D, BnaA03g03800D, and BolC04g018270.2J.m1 might be ideal candidate genes for P. brassicae resistant research. Overall, these results provide valuable information for research on the function and evolution of CDK genes.

Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress

Calcium (Ca²⁺) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca²⁺ deficiency in orphan crops such as Tef [(Eragrostis tef) (Zucc.) Trotter], which accumulate high levels of Ca in the grains, remained unknown. Tef is a staple crop for nearly 70 million people in East Africa, particularly in Ethiopia and Eritrea. It is one of the most nutrient-dense grains, and is also more resistant to marginal soils and climatic conditions than main cereals like corn, wheat, and rice. In this study, tef plants were grown in a hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca²⁺, and plant growth parameters and whole-genome transcriptome were analyzed. Ca⁺²-deficient plants exhibited leaf necrosis, leaf curling, and growth stunting symptoms. Ca²⁺ deficiency significantly decreased root and shoot Ca, potassium (K), and copper content in both root and shoots. At the same time, it greatly increased root iron (Fe) content, suggesting the role of Ca²⁺ in the uptake and/or translocation of these minerals. Transcriptomic analysis using RNA-seq revealed that members of Ca²⁺ channels, including the cyclic nucleotide-gated channels and glutamate receptor-like channels, Ca²⁺-transporters, Ca²⁺-binding proteins and Ca²⁺-dependent protein kinases were differentially regulated by Ca⁺² treatment. Moreover, several Fe/metal transporters, including members of vacuolar Fe transporters, yellow stripe-like, natural resistance-associated macrophage protein, and oligo-peptide transporters, were differentially regulated between shoot and root in response to Ca²⁺ treatment. Taken together, our findings suggest that Ca²⁺ deficiency affects plant growth and mineral accumulation by regulating the transcriptomes of several transporters and signaling genes.

Genome-wide identification of the CDPK gene family reveals the CDPK-RBOH pathway potential involved in improving chilling tolerance in peach fruit

Calcium-dependent protein kinase (CDPK), as an essential calcium receptor, plays a major role in the perception and decoding of intracellular calcium signaling in plant development and stress responses. Here, the CDPK gene family was analyzed at the genome-wide level in peach. This study identified 17 PpCDPK gene members from the peach genome, and systematically investigated phylogenetic relationships, conserved motifs, exon-intron structures, chromosome distribution, and cis-acting elements of each PpCDPK gene using bioinformatics. Furthermore, the expression levels of most PpCDPK genes were significantly changed under the CaCl₂, EBR, GB, cold shock, hot water treatments, and various temperatures in the cold storage of peach fruits. RNA-seq data showed that PpCDPK2, PpCDPK7, PpCDPK10, and PpCDPK13 were related to postharvest chilling stress in peach. The interaction network of PpCDPK7 protein showed that the interaction between PpCDPK7 and PpRBOH may be the intersectional point of Ca²⁺ and ROS signal transmission during cold storage of peach fruits. These systematic analyses are helpful to further characterize the regulation of PpCDPKs and CDPK-RBOH mediated signal cascades in postharvest chilling injury in peach fruit.

Cold Tolerance of ScCBL6 Is Associated with Tonoplast Transporters and Photosynthesis in Arabidopsis

Plants that are adapted to harsh environments offer enormous opportunity to understand stress responses in ecological systems. Stipa capillacea is widely distributed in the frigid and arid region of the Tibetan Plateau, but its signal transduction system under cold stress has not been characterized. In this study, we isolated a cDNA encoding the signal transduction protein, ScCBL6, from S. capillacea, and evaluated its role in cold tolerance by ectopically expressing it in Arabidopsis. Full-length ScCBL6 encode 227 amino acids, and are clustered with CBL6 in Stipa purpurea and Oryza sativa in a phylogenetic analysis. Compared with tolerance in wild-type (WT) plants, ScCBL6-overexpressing plants (ScCBL6-OXP) were more tolerant to cold stress but not to drought stress, as confirmed by their high photosynthetic capacity (Fv/Fm) and survival rate under cold stress. We further compared their cold-responsive transcriptome profiles by RNA sequencing. In total, 3931 genes were differentially expressed by the introduction of ScCBL6. These gene products were involved in multiple processes such as the immune system, lipid catabolism, and secondary metabolism. A KEGG pathway analysis revealed that they were mainly enriched in plant hormone signal transduction and biomacromolecule metabolism. Proteins encoded by differentially expressed genes were predicted to be localized in chloroplasts, mitochondria, and vacuoles, suggesting that ScCBL6 exerts a wide range of functions. Based on its tonoplast subcellular location combined with integrated transcriptome and physiological analyses of ScCBL6-OXP, we inferred that ScCBL6 improves plant cold stress tolerance in Arabidopsis via the regulation of photosynthesis, redox status, and tonoplast metabolite transporters.

Stomata at the crossroad of molecular interaction between biotic and abiotic stress responses in plants

Increasing global food production is threatened by harsh environmental conditions along with biotic stresses, requiring massive new research into integrated stress resistance in plants. Stomata play a pivotal role in response to many biotic and abiotic stresses, but their orchestrated interactions at the molecular, physiological, and biochemical levels were less investigated. Here, we reviewed the influence of drought, pathogen, and insect herbivory on stomata to provide a comprehensive overview in the context of stomatal regulation. We also summarized the molecular mechanisms of stomatal response triggered by these stresses. To further investigate the effect of stomata-herbivore interaction at a transcriptional level, integrated transcriptome studies from different plant species attacked by different pests revealed evidence of the crosstalk between abiotic and biotic stress. Comprehensive understanding of the involvement of stomata in some plant-herbivore interactions may be an essential step towards herbivores' manipulation of plants, which provides insights for the development of integrated pest management strategies. Moreover, we proposed that stomata can function as important modulators of plant response to stress combination, representing an exciting frontier of plant science with a broad and precise view of plant biotic interactions.

Pangenome-wide analysis of cyclic nucleotide-gated channel (CNGC) gene family in citrus Spp. Revealed their intraspecies diversity and potential roles in abiotic stress tolerance

Cyclic nucleotide-gated channels (CNGC) gene family has been found to be involved in physiological processes including signaling pathways, environmental stresses, plant growth, and development. This gene family of non-selective cation channels is known to regulate the uptake of calcium and is reported in several plant species. The pangenome-wide studies enable researchers to understand the genetic diversity comprehensively; as a comparative analysis of multiple plant species or member of a species at once helps to better understand the evolutionary relationships and diversity present among them. In the current study, pangenome-wide analysis of the CNGC gene family has been performed on five Citrus species. As a result, a total of 32 genes in Citrus sinensis, 27 genes in Citrus recticulata, 30 genes in Citrus grandis, 31 genes in Atalantia buxfolia, and 30 genes in Poncirus trifoliata were identified. In addition, two unique genes CNGC13 and CNGC14 were identified, which may have potential roles. All the identified CNGC genes were unevenly distributed on 9 chromosomes except P. trifoliata had genes distributed on 7 chromosomes and were classified into four major groups and two sub-groups namely I, II, III, IV-A, and IV-B. Cyclic nucleotide binding (CNB) motif, calmodulin-binding motif (CaMB), and motif for IQ-domain were conserved in Citrus Spp. Intron exon structures of citrus species were not exactly as same as the gene structures of Arabidopsis. The majority of cis-regulatory elements (CREs) were light responsive and others include growth, development, and stress-related indicating potential roles of the CNGC gene family in these functions. Both segmental and tandem duplication were involved in the expansion of the CNGC gene family in Citrus Spp. The miRNAs are involved in the response of CsCNGC genes towards drought stress along with having regulatory association in the expression of these genes. Protein- Protein interaction (PPI) analysis also showed the interaction of CNGC proteins with other CNGCs which suggested their potential role in pathways regulating different biological processes. GO enrichment revealed that CNGC genes were involved in the transport of ions across membranes. Furthermore, tissue-specific expression patterns of leaves sample of C. sinensis were studied under drought stress. Out of 32 genes of C. sinensis 3 genes i.e., CsCNGC1.4, CsCNGC2.1, and CsCNGC4.2 were highly up-regulated, and only CsCNGC4.6 was highly down-regulated. The qRT-PCR analysis also showed that CNGC genes were highly expressed after treatment with drought stress, while gene expression was lower under controlled conditions. This work includes findings based on multiple genomes instead of one, therefore, this will provide more genomic information rather than single genome-based studies. These findings will serve as a basis for further functional insights into the CNGC gene family.

ABA-Dependent Regulation of Calcium-Dependent Protein Kinase Gene GmCDPK5 in Cultivated and Wild Soybeans

Calcium-dependent protein kinases (CDPKs) regulate plant development and stress responses. However, the interaction of these protein kinases with the abscisic acid (ABA) stress hormone signalling system has not been studied in detail. In Arabidopsis, AtCPK1 plays an important role in the acclimation of plants to environmental stresses. Phylogenetic and molecular analyses showed that, among 50 isoforms of Glycine max (L.) Merrill CDPKs, the GmCDPK27/GmCDPK48, GmCDPK5/GmCDPK24, and GmCDPK10/GmCDPK46 paralogous pairs were the isoforms most related to AtCDPK1. We investigated the expression of the corresponding six GmCDPKs genes during treatment with cold, heat, and salt stress. Wild soybean was the most resistant to stresses, and among the three cultivars studied (Sfera, Hodgson, and Hefeng25), Sfera was close to the wild type in terms of resistance. GmCDPK5 and GmCDPK10 were the most responsive to stress treatments, especially in wild soybean, compared with cultivars. Among the studied GmCDPK isoforms, only GmCDPK5 expression increased after treatment with abscisic acid (ABA) in a dose- and time-dependent manner. Targeted LC-MS/MS analysis of endogenous ABA levels showed that wild soybean and Sfera had nearly twice the ABA content of Hodgson and Hefeng25. An analysis of the expression of marker genes involved in ABA biosynthesis showed that GmNCED1-gene-encoding 9-cis-epoxycarotenoid dioxygenase 1 is induced to the greatest extent in wild soybean and Sfera under salt, cold, and heat exposure. Our data established a correlation between the induction of GmCDPK5 and ABA biosynthesis genes. GmCDPK5 is an interesting target for genetic and bioengineering purposes and can be used for genetic editing, overexpression, or as a marker gene in soybean varieties growing under unfavourable conditions.

Involvement of Calcium and Calmodulin in NO-Alleviated Salt Stress in Tomato Seedlings

Salt stress is an adverse impact on the growth and development of plants, leading to yield losses in crops. It has been suggested that nitric oxide (NO) and calcium ion (Ca2+) act as critical signals in regulating plant growth. However, their crosstalk remains unclear under stress condition. In this study, we demonstrate that NO and Ca2+ play positive roles in the growth of tomato (Lycopersicum esculentum) seedlings under salt stress. Our data show that Ca2+ channel inhibitor lanthanum chloride (LaCl3), Ca2+ chelator ethylene glycol-bis (2-aminoethylether)-N,N,N,N-tetraacetic acid (EGTA), or calmodulin (CaM) antagonist N-(6-aminohexyl)-5-chloro-1-naphthalenesulfona-mide hydrochloride (W-7) significantly reversed the effect of NO-promoted the growth of tomato seedlings under salt stress. We further show that NO and Ca2+ significantly decreased reactive oxygen accumulation, increased proline content, and increased the activity of antioxidant enzymes, as well as increased expression of antioxidant enzymes related genes. However, LaCl3, EGTA, and W-7 prevented the positive roles of NO. In addition, the activity of downstream target enzymes related to Ca2+/CaM was increased by NO under salt stress, while LaCl3, EGTA, and W-7 reversed this enhancement. Taken together, these results demonstrate that Ca2+/CaM might be involved in NO-alleviate salt stress.

Evolution, gene expression, and protein‒protein interaction analyses identify candidate CBL-CIPK signalling networks implicated in stress responses to cold and bacterial infection in citrus

BACKGROUND

Cold is a major abiotic stress and Huanglongbing and citrus canker disease are two devastating bacterial diseases for citrus. The Ca²⁺-CBL-CIPK network is known to regulate different types of stress signalling in plants. How do CBL-CIPK signalling networks function in response to cold and infection by CLas or Xcc in citrus?

RESULTS

Eight calcineurin B-like proteins (CBLs) and seventeen CBL-interacting protein kinases (CIPKs) were identified from the cold-tolerant satsuma mandarin 'Guijing2501' (Citrus. unshiu) and CLas/Xcc-sensitive sweet orange (C. sinensis). Phylogenetic analysis revealed that both CBL and CIPK family members in citrus were classified into an ancient and a recent clade according to their conserved domain characteristics and/or intron/exon structures. Genome duplication analysis suggested that both tandem and segmental duplications contributed to the amplification of the CBL and CIPK gene families in citrus under intense purifying selection, and the duplication events only existed in the recent clades. Expression comparison of the duplicated gene pairs indicated that the duplicated CBL and CIPK genes underwent functional differentiation. Further expression analysis identified that CBL1, 5, 6, and 8 and CIPK2, 8, 12, 15, 16, and 17 were significantly regulated by multiple stresses, including cold, Xcc infection and/or CLas infection, in citrus, whereas CBL2/7 and CIPK1/4/5/11/13/14 were independently highly regulated by cold and CIPK3 was uniquely responsive to Xcc infection. The combination analyses of targeted Y2H assay and expression analysis revealed that CBL6-CIPK8 was the common signalling network in response to cold and Xcc infection, while CBL6/CBL8-CIPK14 was uniquely responsive to cold in citrus. Further stable transformation and cold tolerance assay indicated that overexpression of CuCIPK16 enhanced the cold tolerance of transgenic Arabidopsis with higher POD activity and lower MDA content.

CONCLUSIONS

In this study, evolution, gene expression and protein‒protein interaction analyses of citrus CBLs and CIPKs were comprehensively conducted over a genome-wide range. The results will facilitate future functional characterization of individual citrus CBLs and CIPKs under specific stresses and provide clues for the clarification of cold tolerance and disease susceptibility mechanisms in corresponding citrus cultivars.

Calcium-Dependent Protein Kinase 28 Maintains Potato Photosynthesis and Its Tolerance under Water Deficiency and Osmotic Stress

Calcium-dependent protein kinases (CDPK) are implicated in signaling transduction in eukaryotic organisms. It is largely unknown whether StCDPK28 plays a role in the response to water deficiency and osmotic stress in potato plants (Solanum tuberosum L.). Potato cv. Zihuabai was cultivated under natural, moderate, and severe water deficiency conditions; to induce osmotic stress, potato plants were treated with 10% or 20% PEG. StCDPK28-overexpression and StCDPK28-knockdown plants were constructed. StCDPKs were evaluated by qRT-PCR. The subcellular location of the StCDPK28 protein was observed with confocal scanning laser microscopy. Phenotypic changes were indicated by photosynthetic activity, the contents of H₂O₂, MDA and proline, and the activities of CAT, SOD and POD. Results showed water deficiency and osmotic stress altered StCDPK expression patterns. StCDPK28 exhibited a membrane, cytosolic and nuclear localization. Water deficiency and osmotic stress induced StCDPK28 upregulation. Photosynthetic activity was enhanced by StCDPK28 overexpression, while decreased by StCDPK2 knockdown under water deficiency and osmotic stress. StCDPK28 overexpression decreased H₂O₂ and MDA, and increased proline, while StCDPK28 knockdown showed reverse results, compared with the wild type, in response to water deficiency and osmotic stress. StCDPK28 overexpression increased the activities of CAT, SOD and POD, while StCDPK28-knockdown plants indicated the reverse trend under water deficiency and osmotic stress conditions. Regulation of StCDPK28 expression could be a promising approach to improve the tolerance ability of potato plants in response to drought or high salt media.