Calmodulin-related proteins step out from the shadow of their namesake

Genome-wide identification of Rosa roxburghii CML family genes identifies an RrCML13-RrGGP2 interaction involved in calcium-mediated regulation of ascorbate biosynthesis

Calmodulin-like proteins (CMLs) are an essential family of calcium sensors involved in multiple Ca2+-mediated cellular processes in plants. Rosa roxburghii Tratt, known for the abundance of L-ascorbic acid (AsA) in its fruits, is widely distributed in calcium-rich soil of the karst region in southwestern China. The aim of this study was to identify key CMLs that respond to exogenous Ca2+ levels and regulate AsA biosynthesis in R. roxburghii. A genome-wide scan revealed the presence of 41 RrCML genes with 1-4 EF-hand motif (s) unevenly distributed across the 7 chromosomes of R. roxburghii. qRT-PCR analysis revealed that RrCML13, RrCML10, and RrCML36 responded significantly to exogenous Ca2+ treatment, and RrCML13 was positively correlated with GDP-L-galactose phosphorylase encoding gene (RrGGP2) expression and AsA content in the developing fruit. Overexpression of RrCML13 in fruits and roots significantly promoted the transcription of RrGGP2 and the accumulation of AsA, while virus-induced silencing of RrCML13 reduced the transcription of RrGGP2 and the content of AsA. Furthermore, Moreover, the yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analysis confirmed the interaction between RrCML13 and RrGGP2 proteins, indicating that RrCML13 plays a regulatory role in calcium-mediated AsA biosynthesis. This study enhances our understanding of R. roxburghii CMLs and sheds light on the calcium-mediated regulation of AsA biosynthesis.

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.

Natural variation in CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 reveals a novel role of calcium signaling in vegetative phase change in Arabidopsis

The timing of vegetative phase change (VPC) in plants is regulated by a temporal decline in the expression of miR156. Both exogenous cues and endogenous factors, such as temperature, light, sugar, nutrients, and epigenetic regulators, have been shown to affect VPC by altering miR156 expression. However, the genetic basis of natural variation in VPC remains largely unexplored. Here, we conducted a genome-wide association study on the variation of the timing of VPC in Arabidopsis. We identified CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 (CNGC4) as a significant locus associated with the diversity of VPC. Mutations in CNGC4 delayed VPC, accompanied by an increased expression level of miR156 and a corresponding decrease in SQUAMOSA PROMOTER BINDING-LIKE (SPL) gene expression. Furthermore, mutations in CNGC2 and CATION EXCHANGER 1/3 (CAX1/3) also led to a delay in VPC. Polymorphisms in the CNGC4 promoter contribute to the natural variation in CNGC4 expression and the diversity of VPC. Specifically, the early CNGC4 variant promotes VPC and enhances plant adaptation to local environments. In summary, our findings offer genetic insights into the natural variation in VPC in Arabidopsis, and reveal a previously unidentified role of calcium signaling in the regulation of VPC.

A calmodulin-like protein PvCML9 negatively regulates salt tolerance

Calmodulin-like proteins (CMLs) are unique Ca2+ sensors and play crucial roles in response to abiotic stress in plants. A salt-repressed PvCML9 from halophyte seashore paspalum (Paspalum vaginatum O. Swartz) was identified. PvCML9 was localized in the cytoplasm and nucleus and highly expressed in roots and stems. Overexpression of PvCML9 led to reduced salt tolerance in rice and seashore paspalum, whereas downregulating expression of PvCML9 showed increased salt tolerance in seashore paspalum as compared with the wild type (WT), indicating that PvCML9 regulated salt tolerance negatively. Na+ and K+ homeostasis was altered by PvCML9 expression. Lower level of Na+/K+ ratio in roots and shoots was maintained in PvCML9-RNAi lines compared with WT under salt stress, but higher level in overexpression lines. Moreover, higher levels of SOD and CAT activities and proline accumulation were observed in PvCML9-RNAi lines compared with WT under salt stress, but lower levels in overexpression lines, which altered ROS homeostasis. Based on the above data, mutation of its homolog gene OsCML9 in rice by CRISPR/Cas9 was performed. The mutant had enhanced salt tolerance without affecting rice growth and development, suggesting that OsCML9 gene is an ideal target gene to generate salt tolerant cultivars by genome editing in the future.

Arabidopsis CML13 and CML14 Have Essential and Overlapping Roles in Plant Development

Calmodulin (CaM)-like proteins (CMLs) are the largest family of calcium-binding proteins in plants, yet the functions of most CMLs are unknown. Arabidopsis CML13 and CML14 are closely related paralogs that interact with the isoleucine-glutamine (IQ) domains of myosins, IQ-domain proteins and CaM-binding transcription activators (CAMTAs). Here, we explored the physiological roles of CML13 and CML14 during development by using dexamethasone (Dex)-inducible RNA silencing to suppress either CML13 or CML14 transcript levels. In the absence of inducible suppression, CML13- and CML14-RNA-interference lines were indistinguishable from wild-type (WT) plants throughout development. In contrast, induction of silencing treatment led to rapid increases in RNA-hairpin production that correlated with a targeted reduction in CML13 or CML14 transcript levels and a range of developmental and morphological effects. RNA-suppression treatment did not impair the germination of CML13- or 14-RNA-interference lines, but these seedlings were chlorotic, displayed high mortality and failed to achieve seedling establishment. Under Dex treatment, seeds of CML13- and CML14-RNA-interference lines exhibited differential sensitivity to exogenous ABA compared to WT seeds. Induced RNA suppression of mature plants led to reduced silique length, shorter roots and rapid leaf senescence in CML13- and 14-RNA-interference plants, which correlated with increased gene expression of the senescence marker Senescence-Associated Gene13 (SAG13). Plants induced for RNA suppression at 2 weeks post-germination exhibited a much stronger phenotype than treatment of 3-, 4- or 5-week-old plants. Collectively, our data indicate that both CML13 and CML14 are essential for normal development and function across a broad range of tissues and developmental stages.

Arabidopsis Calmodulin-like Proteins CML13 and CML14 Interact with Calmodulin-Binding Transcriptional Activators and Function in Salinity Stress Response

Eukaryotic cells use calcium ions (Ca2+) as second messengers, particularly in response to abiotic and biotic stresses. These signals are detected by Ca2+ sensor proteins, such as calmodulin (CaM), which regulate the downstream target proteins. Plants also possess many CaM-like proteins (CMLs), most of which remain unstudied. We recently demonstrated that Arabidopsis CML13 and CML14 interact with proteins containing isoleucine/glutamine (IQ) domains, including CaM-binding transcriptional activators (CAMTAs). Here, we show that CaM, CML13 and CML14 bind all six members of the Arabidopsis CAMTA family. Using a combination of in planta and in vitro protein-interaction assays, we tested 11 members of the CaM/CML family and demonstrated that only CaM, CML13 and CML14 bind to CAMTA IQ domains. CaM, CML13 and CML14 showed Ca2+-independent binding to the IQ region of CAMTA6 and CAMTA3, and CAMTA6 in vitro exhibited some specificity toward individual IQ domains within CAMTA6 in split-luciferase in planta assays. We show that cml13 mutants exhibited enhanced salinity tolerance during germination compared to wild-type plants, a phenotype similar to camta6 mutants. In contrast, plants overexpressing CML13-GFP or CML14-GFP in the wild-type background showed increased NaCl sensitivity. Under mannitol stress, cml13 mutants were more susceptible than camta6 mutants or wild-type plants. The phenotype of cml13 mutants could be rescued with the wild-type CML13 gene. Several salinity-marker genes under CAMTA6 control were similarly misregulated in both camta6 and cml13 mutants, further supporting a role for CML13 in CAMTA6 function. Collectively, our data suggest that CML13 and CML14 participate in abiotic stress signaling as CAMTA effectors.

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.

Calcium imaging: a technique to monitor calcium dynamics in biological systems

Calcium ion (Ca2+) is a multifaceted signaling molecule that acts as an important second messenger. During the course of evolution, plants and animals have developed Ca2+ signaling in order to respond against diverse stimuli, to regulate a large number of physiological and developmental pathways. Our understanding of Ca2+ signaling and its components in physiological phenomena ranging from lower to higher organisms, and from single cell to multiple tissues has grown exponentially. The generation of Ca2+ transients or signatures for various stress factor is a well-known mechanism adopted in plant and animal systems. However, the decoding of such remarkable signatures is an uphill task and is always an interesting goal for the scientific community. In the past few decades, studies on the concentration and dynamics of intracellular Ca2+ are significantly increasing and have become a trend in modern biology. The advancement in approaches from Ca2+ binding dyes to in vivo Ca2+ imaging through the use of Ca2+ biosensors to achieve spatio-temporal resolution in micro and milliseconds range, provide us phenomenal opportunities to study live cell Ca2+ imaging or dynamics. Here, we describe the usage, improvement and advancement of Ca2+ based dyes, genetically encoded probes and sensors to achieve extraordinary Ca2+ imaging in plants and animals.

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A chitosan-coated lentinan-loaded calcium alginate hydrogel induces broad-spectrum resistance to plant viruses by activating Nicotiana benthamiana calmodulin-like (CML) protein 3

Control of plant virus diseases largely depends on the induced plant defence achieved by the external application of synthetic chemical inducers with the ability to modify defence-signalling pathways. However, most of the molecular mechanisms underlying these chemical inducers remain unknown. Here, we developed a chitosan-coated lentinan-loaded hydrogel and discovered how it protects plants from different virus infections. The hydrogel was synthesized by coating chitosan on the surface of the calcium alginate-lentinan (LNT) hydrogel (SL-gel) to form a CSL-gel. CSL-gels exhibit the capacity to prolong the stable release of lentinan and promote Ca2+ release. Application of CSL-gels on the root of plants induces broad-spectrum resistance against plant viruses (TMV, TRV, PVX and TuMV). RNA-seq analysis identified that Nicotiana benthamiana calmodulin-like protein gene 3 (NbCML3) is upregulated by the sustained release of Ca2+ from the CSL-gel, and silencing and overexpression of NbCML alter the susceptibility and resistance of tobacco to TMV. Our findings provide evidence that this novel and synthetic CSL-gel strongly inhibits the infection of plant viruses by the sustainable release of LNT and Ca2+ . This study uncovers a novel mode of action by which CSL-gels trigger NbCML3 expression through the stable and sustained release of Ca2+ .

Growth or survival: What is the role of calmodulin-like proteins in plant?

Calcium signalling, including pulse, amplitude, and duration, is essential for plant development and response to various stimuli. However, the calcium signalling should be decoded and translated by calcium sensors. In plants, three classes of calcium-binding proteins have been identified as calcium sensors, including calcium-dependent protein kinase (CDPK), calcineurin B-like protein (CBL), and calmodulin (CaM). Calmodulin-like proteins (CMLs), which have several EF-hands, also serve as specific calcium sensors and can sense, bind, and interpret the calcium signal during the plant's growth and defense decision-making processes. In recent decades, the function of CMLs in plant development and response to various stimuli has been systematically reviewed, shedding light on the molecular mechanism of plant CML-mediated networks in calcium signal transduction. Here, by providing an overview of CML expression and biological function in plants, we demonstrate that growth-defense trade-offs occur during calcium sensing, an aspect that has not been well studied in recent years.

Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress

The calmodulin-like (CML) family is an important calcium (Ca²⁺) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT-PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum.

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.

The Ca2+ sensor proteins CML37 and CML42 antagonistically regulate plant stress responses by altering phytohormone signals

Calmodulin-like-proteins (CML) belong to a family of calcium-sensing proteins that are unique for plants and involved in many different developmental and stress-related reactions. In defense against herbivory, some pathogens and drought, CML37 acts as a positive and CML42 as a negative regulator, respectively. We provide evidence that both CMLs act antagonistically in the regulation of induced defense responses. A double knock-out line, cml37 x cml42, thus shows wild-type phenotypes upon all kind of stresses we used. A transient increase in the cytosolic calcium concentration is one of the first reactions that can be measured in plant cells upon abiotic as well as biotic stress treatments. These calcium signals are sensed by calcium binding proteins such as calmodulin-like proteins (CMLs), which transduce the sensed information into appropriate stress responses by interacting with downstream target proteins. In previous studies, CML37 has been shown to positively regulate the plants' defense against both the insect herbivore Spodoptera littoralis and the response to drought stress. In contrast, CML42 is known to negatively regulate those two stress responses. Here, we provide evidence that these two CMLs act antagonistically in the regulation of induced responses directed against drought and herbivory stress as well as in the defense against the necrotrophic pathogen Alternaria brassicicola. Both CMLs shape the plant reactions by altering the phytohormone signaling. Consequently, the phytohormone-regulated production of defensive compounds like glucosinolates is also antagonistically mediated by both CMLs. The finding that CML37 and CML42 have antagonistic roles in diverse stress-related responses suggests that these calcium sensor proteins represent important tools for the plant to balance and fine-tune the signaling and downstream reactions upon environmental stress.

Overview of the roles of calcium sensors in plants’ response to osmotic stress signalling

Calcium signals serve an important function as secondary messengers between cells in various biological processes due to their robust homeostatic mechanism, maintaining an intracellular free Ca2+ concentration. Plant growth, development, and biotic and abiotic stress are all regulated by Ca2+ signals. Ca2+ binding proteins decode and convey the messages encoded by Ca2+ ions. In the presence of high quantities of Mg2+ and monovalent cations, such sensors bind to Ca2+ ions and modify their conformation in a Ca2+ -dependent manner. Calcium-dependent protein kinases (CPKs), calmodulins (CaMs), and calcineurin B-like proteins are all calcium sensors (CBLs). To transmit Ca2+ signals, CPKs, CBLs, and CaMs interact with target proteins and regulate the expression of their genes. These target proteins may be protein kinases, metabolic enzymes, or cytoskeletal-associated proteins. Beyond its role in plant nutrition as a macroelement and its involvement in the plant cell wall structure, calcium modulates many aspects of development, growth and adaptation to environmental constraints such as drought, salinity and osmotic stresses. This review summarises current knowledge on calcium sensors in plant responses to osmotic stress signalling.

A novel calmodulin-interacting Domain of Unknown Function 506 protein represses root hair elongation in Arabidopsis

Domain of Unknown Function 506 proteins are ubiquitous in plants. The phosphorus (P) stress-inducible REPRESSOR OF EXCESSIVE ROOT HAIR GROWTH1 (AtRXR1) gene encodes the first characterized DUF506. AtRXR1 inhibits root hair elongation by interacting with RabD2c GTPase. However, functions of other P-responsive DUF506 genes are still missing. Here, we selected two additional P-inducible DUF506 genes for further investigation. The expression of both genes was induced by auxin. Under P-stress, At3g07350 gene expressed ubiquitously in seedlings, whereas At1g62420 (AtRXR3) expression was strongest in roots. AtRXR3 overexpressors and knockouts had shorter and longer root hairs, respectively. A functional AtRXR3-green fluorescent protein fusion localized to root epidermal cells. Chromatin immunoprecipitation and quantitative reverse-transcriptase-polymerase chain reaction revealed that AtRXR3 was transcriptionally activated by RSL4. Bimolecular fluorescence complementation and calmodulin (CaM)-binding assays showed that AtRXR3 interacted with CaM in the presence of Ca²⁺ . Moreover, cytosolic Ca²⁺ ([Ca²⁺ ]_cyt ) oscillations in root hairs of rxr3 mutants exhibited elevated frequencies and dampened amplitudes compared to those of wild type. Thus, AtRXR3 is another DUF506 protein that attenuates P-limitation-induced root hair growth through mechanisms that involve RSL4 and interaction with CaM to modulate tip-focused [Ca²⁺ ]_cyt oscillations.

Genome-Wide Identification and Characterization of CDPK Family Reveal Their Involvements in Growth and Development and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives

Calcium-dependent protein kinase (CDPKs) is one of the calcium-sensing proteins in plants. They are likely to play important roles in growth and development and abiotic stress responses. However, these functions have not been explored in sweet potato. In this study, we identified 39 CDPKs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 35 CDPKs in diploid relative Ipomoea trifida (2n = 2x = 30), and 35 CDPKs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological property, chromosome localization, phylogenetic relationship, gene structure, promoter cis-acting regulatory elements, and protein interaction network were systematically investigated to explore the possible roles of homologous CDPKs in the growth and development and abiotic stress responses of sweet potato. The expression profiles of the identified CDPKs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting the difference in the evolutionary trajectories of hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato CDPK genes and provide more candidate genes for improving yield and abiotic stress tolerance in cultivated sweet potato.

With a Little Help from My Cell Wall: Structural Modifications in Pectin May Play a Role to Overcome Both Dehydration Stress and Fungal Pathogens

Cell wall structural modifications through pectin cross-linkages between calcium ions and/or boric acid may be key to mitigating dehydration stress and fungal pathogens. Water loss was profiled in a pure pectin system and in vivo. While calcium and boron reduced water loss in pure pectin standards, the impact on Allium species was insignificant (p > 0.05). Nevertheless, synchrotron X-ray microscopy showed the localization of exogenously applied calcium to the apoplast in the epidermal cells of Allium fistulosum. Exogenous calcium application increased viscosity and resistance to shear force in Allium fistulosum, suggesting the formation of calcium cross-linkages ("egg-box" structures). Moreover, Allium fistulosum (freezing tolerant) was also more tolerant to dehydration stress compared to Allium cepa (freezing sensitive). Furthermore, the addition of boric acid (H₃BO₃) to pure pectin reduced water loss and increased viscosity, which indicates the formation of RG-II dimers. The Arabidopsis boron transport mutant, bor1, expressed greater water loss and, based on the lesion area of leaf tissue, a greater susceptibility to Colletotrichum higginsianum and Botrytis cinerea. While pectin modifications in the cell wall are likely not the sole solution to dehydration and biotic stress resistance, they appear to play an important role against multiple stresses.

Rapid kinetics of calcium dissociation from plant calmodulin and calmodulin-like proteins and effect of target peptides

Calcium (Ca²⁺) signaling represents a universal information code in plants, playing crucial roles spanning developmental processes to stress responses. Ca²⁺ signals are decoded into defined plant adaptive responses by different Ca²⁺ sensing proteins, including calmodulin (CaM) and calmodulin-like (CML) proteins. Although major advances have been achieved in describing how these Ca²⁺ decoding proteins interact and regulate downstream target effectors, the molecular details of these processes remain largely unknown. Herein, the kinetics of Ca²⁺ dissociation from a conserved CaM and two CML isoforms from A. thaliana has been studied by fluorescence stopped-flow spectroscopy. Kinetic data were obtained for the isolated Ca²⁺-bound proteins as well as for the proteins complexed with different target peptides. Moreover, the lobe specific interactions between the Ca²⁺ sensing proteins and their targets were characterized by using a panel of protein mutants deficient in Ca²⁺ binding at the N-lobe or C-lobe. Results were analyzed and discussed in the context of the Ca²⁺-decoding and Ca²⁺-controlled target binding mechanisms in plants.

A Comprehensive Analysis of Calmodulin-Like Proteins of Glycine max Indicates Their Role in Calcium Signaling and Plant Defense Against Insect Attack

The calcium (Ca²⁺) signaling is a crucial event during plant-herbivore interaction, which involves a transient change in cytosolic Ca²⁺ concentration, which is sensed by Ca²⁺-sensors, and the received message is transduced to downstream target proteins leading to appropriate defense response. Calmodulin-like proteins (CMLs) are calcium-sensing plant-specific proteins. Although CMLs have been identified in a few plants, they remained uncharacterized in leguminous crop plants. Therefore, a wide-range analysis of CMLs of soybean was performed, which identified 41 true CMLs with greater than 50% similarity with Arabidopsis CMLs. The phylogenetic study revealed their evolutionary relatedness with known CMLs. Further, the identification of conserved motifs, gene structure analysis, and identification of cis-acting elements strongly supported their identity as members of this family and their involvement in stress responses. Only a few Glycine max CMLs (GmCMLs) exhibited differential expression in different tissue types, and rest of them had minimal expression. Additionally, differential expression patterns of GmCMLs were observed during Spodoptera litura-feeding, wounding, and signaling compound treatments, indicating their role in plant defense. The three-dimensional structure prediction, identification of interactive domains, and docking with Ca²⁺ ions of S. litura-inducible GmCMLs, indicated their identity as calcium sensors. This study on the characterization of GmCMLs provided insights into their roles in calcium signaling and plant defense during herbivory.

Inducible Enrichment of Osa-miR1432 Confers Rice Bacterial Blight Resistance through Suppressing OsCaML2

MicroRNAs (miRNAs) handle immune response to pathogens by adjusting the function of target genes in plants. However, the experimentally documented miRNA/target modules implicated in the interplay between rice and Xanthomonas oryzae pv. oryzae (Xoo) are still in the early stages. Herein, the expression of osa-miR1432 was induced in resistant genotype IRBB5, but not susceptible genotype IR24, under Xoo strain PXO86 attack. Overexpressed osa-miR1432 heightened rice disease resistance to Xoo, indicated by enhancive enrichment of defense marker genes, raised reactive oxygen species (ROS) levels, repressed bacterial growth and shortened leaf lesion length, whilst the disruptive accumulation of osa-miR1432 accelerated rice susceptibility to Xoo infection. Noticeably, OsCaML2 (LOC_Os03g59770) was experimentally confirmed as a target gene of osa-miR1432, and the overexpressing OsCaML2 transgenic plants exhibited compromised resistance to Xoo infestation. Our results indicate that osa-miR1432 and OsCaML2 were differently responsive to Xoo invasion at the transcriptional level and fine-tune rice resistance to Xoo infection, which may be referable in resistance gene discovery and valuable in the pursuit of improving Xoo resistance in rice breeding.

StCaM2, a calcium binding protein, alleviates negative effects of salinity and drought stress in tobacco

KEY MESSAGE

Overexpression of StCaM2 in tobacco promotes plant growth and confers increased salinity and drought tolerance by enhancing the photosynthetic efficiency, ROS scavenging, and recovery from membrane injury. Calmodulins (CaMs) are important Ca2+ sensors that interact with effector proteins and drive a network of signal transduction pathways involved in regulating the growth and developmental pattern of plants under stress. Herein, using in silico analysis, we identified 17 CaM isoforms (StCaM) in potato. Expression profiling revealed different temporal and spatial expression patterns of these genes, which were modulated under abiotic stress. Among the identified StCaM genes, StCaM2 was found to have the largest number of abiotic stress responsive promoter elements. In addition, StCaM2 was upregulated in response to some of the selected abiotic stress in potato tissues. Overexpression of StCaM2 in transgenic tobacco plants enhanced their tolerance to salinity and drought stress. Accumulation of reactive oxygen species was remarkably decreased in transgenic lines compared to that in wild type plants. Chlorophyll a fluorescence analysis suggested better performance of photosystem II in transgenic plants under stress compared to that in wild type plants. The increase in salinity stress tolerance in StCaM2-overexpressing plants was also associated with a favorable K+/Na+ ratio. The enhanced tolerance to abiotic stresses correlated with the increase in the activities of anti-oxidative enzymes in transgenic tobacco plants. Overall, our results suggest that StCaM2 can be a novel candidate for conferring salt and drought tolerance in plants.

Isolation and Functional Characterization of a Salt-Responsive Calmodulin-Like Gene MpCML40 from Semi-Mangrove Millettia pinnata

Salt stress is a major increasing threat to global agriculture. Pongamia (Millettia pinnata), a semi-mangrove, is a good model to study the molecular mechanism of plant adaptation to the saline environment. Calcium signaling pathways play critical roles in the model plants such as Arabidopsis in responding to salt stress, but little is known about their function in Pongamia. Here, we have isolated and characterized a salt-responsive MpCML40, a calmodulin-like (CML) gene from Pongamia. MpCML40 protein has 140 amino acids and is homologous with Arabidopsis AtCML40. MpCML40 contains four EF-hand motifs and a bipartite NLS (Nuclear Localization Signal) and localizes both at the plasma membrane and in the nucleus. MpCML40 was highly induced after salt treatment, especially in Pongamia roots. Heterologous expression of MpCML40 in yeast cells improved their salt tolerance. The 35S::MpCML40 transgenic Arabidopsis highly enhanced seed germination rate and root length under salt and osmotic stresses. The transgenic plants had a higher level of proline and a lower level of MDA (malondialdehyde) under normal and stress conditions, which suggested that heterologous expression of MpCML40 contributed to proline accumulation to improve salt tolerance and protect plants from the ROS (reactive oxygen species) destructive effects. Furthermore, we did not observe any measurable discrepancies in the development and growth between the transgenic plants and wild-type plants under normal growth conditions. Our results suggest that MpCML40 is an important positive regulator in response to salt stress and of potential application in producing salt-tolerant crops.

Plant Defense Responses to Biotic Stress and Its Interplay With Fluctuating Dark/Light Conditions

Plants are subjected to a plethora of environmental cues that cause extreme losses to crop productivity. Due to fluctuating environmental conditions, plants encounter difficulties in attaining full genetic potential for growth and reproduction. One such environmental condition is the recurrent attack on plants by herbivores and microbial pathogens. To surmount such attacks, plants have developed a complex array of defense mechanisms. The defense mechanism can be either preformed, where toxic secondary metabolites are stored; or can be inducible, where defense is activated upon detection of an attack. Plants sense biotic stress conditions, activate the regulatory or transcriptional machinery, and eventually generate an appropriate response. Plant defense against pathogen attack is well understood, but the interplay and impact of different signals to generate defense responses against biotic stress still remain elusive. The impact of light and dark signals on biotic stress response is one such area to comprehend. Light and dark alterations not only regulate defense mechanisms impacting plant development and biochemistry but also bestow resistance against invading pathogens. The interaction between plant defense and dark/light environment activates a signaling cascade. This signaling cascade acts as a connecting link between perception of biotic stress, dark/light environment, and generation of an appropriate physiological or biochemical response. The present review highlights molecular responses arising from dark/light fluctuations vis-à-vis elicitation of defense mechanisms in plants.

Tomato calmodulin-like protein SlCML37 is a calcium (Ca2+) sensor that interacts with proteasome maturation factor SlUMP1 and plays a role in tomato fruit chilling stress tolerance

Calmodulin-like proteins (CMLs), as well as their targets, play significant roles in various key developmental and stress responses in the plant. In tomato (Solanum lycopersicum), there are at least 52 CML genes in its genome. However, most of their functions are not well known, especially in response to cold stress. Here, we investigated SlCML37 biochemical and structural characteristics, including a typical α-helical secondary structure and exposing its hydrophobic regions after binding to Ca²⁺. Then we certificated that SlCML37 protein could physically interact with SlUMP1 by using yeast two-hybrid, bimolecular florescence complementation (BiFC) and GST pull-down assays. Further analysis showed that SlCML37-transgenic tomato fruit conferred significantly improved tolerance to chilling stress. This study indicates a possible role of calmodulin-like protein-mediated proteasome assemble in the regulation of plant cold response.

Organellar calcium signaling in plants: An update

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

Nucleoredoxin Gene TaNRX1 Positively Regulates Drought Tolerance in Transgenic Wheat (Triticum aestivum L.)

Drought is the main abiotic stress factor limiting the growth and yield of wheat (Triticum aestivum L.). Therefore, improving wheat tolerance to drought stress is essential for maintaining yield. Previous studies have reported on the important role of TaNRX1 in conferring drought stress tolerance. Therefore, to elucidate the regulation mechanism by which TaNRX1 confers drought resistance in wheat, we generated TaNRX1 overexpression (OE) and RNA interference (RNAi) wheat lines. The results showed that the tolerance of the OE lines to drought stress were significantly enhanced. The survival rate, leaf chlorophyll, proline, soluble sugar content, and activities of the antioxidant enzymes (catalase, superoxide dismutase, and peroxidase) of the OE lines were higher than those of the wild type (WT); however, the relative electrical conductivity and malondialdehyde, hydrogen peroxide, and superoxide anion levels of the OE lines were lower than those of the WT; the RNAi lines showed the opposite results. RNA-seq results showed that the common differentially expressed genes of TaNRX1 OE and RNAi lines, before and after drought stress, were mainly distributed in the plant-pathogen interaction, plant hormone signal transduction, phenylpropane biosynthesis, starch and sucrose metabolism, and carbon metabolism pathways and were related to the transcription factors, including WRKY, MYB, and bHLH families. This study suggests that TaNRX1 positively regulates drought stress tolerance in wheat.

Interactions between calcium and ABA signaling pathways in the regulation of fruit ripening

Fruit ripening and senescence are finely controlled by plant hormones such as ethylene and abscisic acid (ABA) but also by calcium ions and by calcium-dependent signaling pathways. Although there are extensive data supporting an interaction between ethylene and calcium in fruit ripening, the regulatory mechanisms resulting from the interaction between ABA and calcium have not yet been fully clarified. In this article, we have reviewed the full roles of calcium and its sensors (CaM, CMLs, CDPKs, CBLs) as well as ABA and the interactions between the two signaling pathways in the regulation of stress responses and in fruit ripening. To illustrate the possible interaction between calcium sensors and ABA signaling components in the control of fruit ripening, we propose an interaction model between the calcium and ABA signaling pathways.

Ca2+/Calmodulin Complex Triggers CAMTA Transcriptional Machinery Under Stress in Plants: Signaling Cascade and Molecular Regulation

Calcium (Ca2+) ion is a critical ubiquitous intracellular second messenger, acting as a lead currency for several distinct signal transduction pathways. Transient perturbations in free cytosolic Ca2+ ([Ca2+]cyt) concentrations are indispensable for the translation of signals into adaptive biological responses. The transient increase in [Ca2+]cyt levels is sensed by an array of Ca2+ sensor relay proteins such as calmodulin (CaM), eventually leading to conformational changes and activation of CaM. CaM, in a Ca2+-dependent manner, regulates several transcription factors (TFs) that are implicated in various molecular, physiological, and biochemical functions in cells. CAMTA (calmodulin-binding transcription activator) is one such member of the Ca2+-loaded CaM-dependent family of TFs. The present review focuses on Ca2+ as a second messenger, its interaction with CaM, and Ca2+/CaM-mediated CAMTA transcriptional regulation in plants. The review recapitulates the molecular and physiological functions of CAMTA in model plants and various crops, confirming its probable involvement in stress signaling pathways and overall plant development. Studying Ca2+/CaM-mediated CAMTA TF will help in answering key questions concerning signaling cascades and molecular regulation under stress conditions and plant growth, thus improving our knowledge for crop improvement.

Identification of salinity responsive genes in lavender through cDNA-AFLP

Currently, a global demand exists forlavender as a significant medicinal plant and source of essential oils. Freshwater and arable lands are two major factors that inhibit extensive farming of medicinal plants in Iran. Saline water from seas and salty soil may be new resources for agricultural use, especially for medicinal plants. We sought to extend our knowledge of the Lavandula angustifolia genome and molecular basis of its salinity tolerance by using cDNA amplified fragment length polymorphism (cDNA-AFLP) to investigate the changes in plant transcriptomes in response to NaCl. All identified transcript derived fragments (TDF) were assigned as novel L. angustifolia genes related to signal transduction, regulation of gene expression, alternative splicing, autophagy, and secondary metabolite biosynthesis. qRT-PCR analysis of the TDFs in response to different concentrations of NaCl revealed various levels of mRNA of the identified genes in this plant. Our findings provided primary insights into the molecular response of L. angustifolia to salinity.

Exogenous Calcium Improved Resistance to Botryosphaeria dothidea by Increasing Autophagy Activity and Salicylic Acid Level in Pear

Pear ring rot, caused by Botryosphaeria dothidea, is one of the most serious diseases in pear. Calcium (Ca²⁺) was reported to play a key role in the plant defense response. Here, we found that exogenous calcium could enhance resistance to B. dothidea in pear leaves. Less H₂O₂ and O₂^- but more activated reactive oxygen species scavenge enzymes accumulated in calcium-treated leaves than in H₂O-treated leaves. Moreover, the increased level of more ascorbic acid-glutathione was maintained by Ca²⁺ treatment under pathogen infection. The expression of core autophagy-related genes and autophagosome formations were enhanced in Ca²⁺-treated leaves. Silencing of PbrATG5 in Pyrus betulaefolia conferred sensitivity to inoculation, which was only slightly recovered by Ca²⁺ treatment. Moreover, the salicylic acid (SA) level and SA-related gene expression were induced more strongly by B. dothidea in Ca²⁺-treated leaves than in H₂O-treated leaves. Taken together, these results demonstrated that exogenous Ca²⁺ enhanced resistance to B. dothidea by increasing autophagic activity and SA accumulation. Our findings reveal a new mechanism of Ca²⁺ in increasing the tolerance of pear to B. dothidea infection.

Protein partners of plant ubiquitin-specific proteases (UBPs)

As one type of deubiquitinases (DUBs), ubiquitin-specific proteases (UBPs) play an extensive and significant role in plant life involving the regulation of plant development and stress responses. However, comprehensive studies are still needed to determine the functional mechanisms, which are largely unclear. Here, we summarized recent progress of plant UBPs' functional partners, particularly the molecular mechanisms by which UBPs work with their partners. We believe that functional analyses of UBPs and their partners will provide new insights into protein deubiquitination and lead to a better understanding of the physiological roles of UBPs in plants.

Cation and peptide binding properties of CML7, a calmodulin-like protein from Arabidopsis thaliana

Plants contain a large family of so-called calmodulin-like proteins (CMLs) which differ from canonical calmodulin in that they show greater variability in sequence, length, and number of EF-hand domains. The presence of this extended CML family has raised questions regarding the role of these proteins: are they functionally redundant or do they play specific functions in physiological plant processes? To answer these questions, comprehensive biochemical and structural information on CML proteins is fundamental. Among the 50 CMLs from Arabidopsis thaliana, herein we described the ability of CML7 to bind metal ions focusing on the Ca²⁺ and Mg²⁺ sensing properties, as well as on metal-induced conformational changes. Circular dichroism and nuclear magnetic resonance (NMR) studies indicated that both Ca²⁺ and Mg²⁺ stabilize CML7, as reflected in conformational rearrangements in secondary and tertiary structure and in increases in thermal stability of the protein. However, the conformational changes that binding induces differ between the two metal ions, and only Ca²⁺ binding controls a structural transition that leads to hydrophobic exposure, as suggested by 8-anilino-1-naphthalenesulfonic acid fluorescence. Isothermal titration calorimetry data coupled with NMR experiments revealed the presence of two high affinity Ca²⁺-binding sites in the C-lobe of CML7 and two weaker sites in the N-lobe. The paired nature of these CML7 EF-hands enables them to bind Ca²⁺ with positive cooperativity within each globular domain. Our results clearly place CML7 in the category of Ca²⁺ sensors. Along with this, the protein can bind to a model target peptide (melittin) in a Ca²⁺-dependent manner.

GhCPK33 Negatively Regulates Defense against Verticillium dahliae by Phosphorylating GhOPR3

Verticillium wilt, caused by the soil-borne fungus Verticillium dahliae, is a destructive vascular disease in plants. Approximately 200 dicotyledonous plant species in temperate and subtropical regions are susceptible to this notorious pathogen. Previous studies showed that jasmonic acid (JA) plays a crucial role in plant-V. dahliae interactions. V. dahliae infection generally induces significant JA accumulation in local and distal tissues of the plant. Although JA biosynthesis and the associated enzymes have been studied intensively, the precise mechanism regulating JA biosynthesis upon V. dahliae infection remains unknown. Here, we identified the calcium-dependent protein kinase GhCPK33 from upland cotton (Gossypium hirsutum) as a negative regulator of resistance to V. dahliae that directly manipulates JA biosynthesis. Knockdown of GhCPK33 by Agrobacterium tumefaciens-mediated virus-induced gene silencing constitutively activated JA biosynthesis and JA-mediated defense responses and enhanced resistance to V dahliae Further analysis revealed that GhCPK33 interacts with 12-oxophytodienoate reductase3 (GhOPR3) in peroxisomes. GhCPK33 phosphorylates GhOPR3 at threonine-246, leading to decreased stability of GhOPR3, which consequently limits JA biosynthesis. We propose that GhCPK33 is a potential molecular target for improving resistance to Verticillium wilt disease in cotton.

Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis

Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.

Identification, characterization, and expression analysis of calmodulin and calmodulin-like genes in grapevine (Vitis vinifera) reveal likely roles in stress responses

Calcium (Ca²⁺) is an ubiquitous key second messenger in plants, where it modulates many developmental and adaptive processes in response to various stimuli. Several proteins containing Ca²⁺ binding domain have been identified in plants, including calmodulin (CaM) and calmodulin-like (CML) proteins, which play critical roles in translating Ca²⁺ signals into proper cellular responses. In this work, a genome-wide analysis conducted in Vitis vinifera identified three CaM- and 62 CML-encoding genes. We assigned gene family nomenclature, analyzed gene structure, chromosomal location and gene duplication, as well as protein motif organization. The phylogenetic clustering revealed a total of eight subgroups, including one unique clade of VviCaMs distinct from VviCMLs. VviCaMs were found to contain four EF-hand motifs whereas VviCML proteins have one to five. Most of grapevine CML genes were intronless, while VviCaMs were intron rich. All the genes were well spread among the 19 grapevine chromosomes and displayed a high level of duplication. The expression profiling of VviCaM/VviCML genes revealed a broad expression pattern across all grape organs and tissues at various developmental stages, and a significant modulation in biotic stress-related responses. Our results highlight the complexity of CaM/CML protein family also in grapevine, supporting the versatile role of its different members in modulating cellular responses to various stimuli, in particular to biotic stresses. This work lays the foundation for further functional and structural studies on specific grapevine CaMs/CMLs in order to better understand the role of Ca²⁺-binding proteins in grapevine and to explore their potential for further biotechnological applications.

Arabidopsis IQM4, a Novel Calmodulin-Binding Protein, Is Involved With Seed Dormancy and Germination in Arabidopsis

Seed dormancy and germination are regulated by complex mechanisms controlled by diverse hormones and environmental cues. Abscisic acid (ABA) promotes seed dormancy and inhibits seed germination and post-germination growth. Calmodulin (CaM) signals are involved with the inhibition of ABA during seed germination and seedling growth. In this study, we showed that Arabidopsis thaliana IQM4 could bind with calmodulin 5 (CaM5) both in vitro and in vivo, and that the interaction was the Ca2+-independent type. The IQM4 protein was localized in the chloroplast and the IQM4 gene was expressed in most tissues, especially the embryo and germinated seedlings. The T-DNA insertion mutants of IQM4 exhibited the reduced primary seed dormancy and lower ABA levels compared with wild type seeds. Moreover, IQM4 plays key roles in modulating the responses to ABA, salt, and osmotic stress during seed germination and post-germination growth. T-DNA insertion mutants exhibited ABA-insensitive and salt-hypersensitive phenotypes during seed germination and post-germination growth, whereas IQM4-overexpressing lines had ABA- and osmotic-hypersensitive, and salt-insensitive phenotypes. Gene expression analyses showed that mutation of IQM4 inhibited the expression of ABA biosynthetic genes NCED6 and NCED9, and seed maturation regulators LEC1, LEC2, ABI3, and ABI5 during the silique development, as well as promoted the expression of WRKY40 and inhibited that of ABI5 in ABA-regulated seed germination. These observations suggest that IQM4 is a novel Ca2+-independent CaM-binding protein, which is positively involved with seed dormancy and germination in Arabidopsis.

Towards Understanding Plant Calcium Signaling through Calmodulin-Like Proteins: A Biochemical and Structural Perspective

Ca2+ ions play a key role in a wide variety of environmental responses and developmental processes in plants, and several protein families with Ca2+-binding domains have evolved to meet these needs, including calmodulin (CaM) and calmodulin-like proteins (CMLs). These proteins have no catalytic activity, but rather act as sensor relays that regulate downstream targets. While CaM is well-studied, CMLs remain poorly characterized at both the structural and functional levels, even if they are the largest class of Ca2+ sensors in plants. The major structural theme in CMLs consists of EF-hands, and variations in these domains are predicted to significantly contribute to the functional versatility of CMLs. Herein, we focus on recent advances in understanding the features of CMLs from biochemical and structural points of view. The analysis of the metal binding and structural properties of CMLs can provide valuable insight into how such a vast array of CML proteins can coexist, with no apparent functional redundancy, and how these proteins contribute to cellular signaling while maintaining properties that are distinct from CaM and other Ca2+ sensors. An overview of the principal techniques used to study the biochemical properties of these interesting Ca2+ sensors is also presented.

The calmodulin-like protein, CML39, is involved in regulating seed development, germination, and fruit development in Arabidopsis

We show that the calcium sensor, CML39, is important in various developmental processes from seeds to mature plants. This study bridges previous work on CML39 as a stress-induced gene and highlights the importance of calcium signalling in plant development. In addition to the evolutionarily-conserved Ca²⁺ sensor, calmodulin (CaM), plants possess a large family of CaM-related proteins (CMLs). Using a cml39 loss-of-function mutant, we investigated the roles of CML39 in Arabidopsis and discovered a range of phenotypes across developmental stages and in different tissues. In mature plants, loss of CML39 results in shorter siliques, reduced seed number per silique, and reduced number of ovules per pistil. We also observed changes in seed development, germination, and seed coat properties in cml39 mutants in comparison to wild-type plants. Using radicle emergence as a measure of germination, cml39 mutants showed more rapid germination than wild-type plants. In marked contrast to wild-type seeds, the germination of developing, immature cml39 seeds was not sensitive to cold-stratification. In addition, germination of cml39 seeds was less sensitive than wild-type to inhibition by ABA or by treatments that impaired gibberellic acid biosynthesis. Tetrazolium red staining indicated that the seed-coat permeability of cml39 seeds is greater than that of wild-type seeds. RNA sequencing analysis of cml39 seedlings suggests that changes in chromatin modification may underlie some of the phenotypes associated with cml39 mutants, consistent with previous reports that orthologs of CML39 participate in gene silencing. Aberrant ectopic expression of transcripts for seed storage proteins in 7-day old cml39 seedlings was observed, suggesting mis-regulation of early developmental programs. Collectively, our data support a model where CML39 serves as an important Ca²⁺ sensor during ovule and seed development, as well as during germination and seedling establishment.

Calcium Signalling in Plant Biotic Interactions

Calcium (Ca2+) is a universal second messenger involved in various cellular processes, leading to plant development and to biotic and abiotic stress responses. Intracellular variation in free Ca2+ concentration is among the earliest events following the plant perception of environmental change. These Ca2+ variations differ in their spatio-temporal properties according to the nature, strength and duration of the stimulus. However, their conversion into biological responses requires Ca2+ sensors for decoding and relaying. The occurrence in plants of calmodulin (CaM) but also of other sets of plant-specific Ca2+ sensors such as calmodulin-like proteins (CMLs), Ca2+-dependent protein kinases (CDPKs) and calcineurin B-like proteins (CBLs) indicate that plants possess specific tools and machineries to convert Ca2+ signals into appropriate responses. Here, we focus on recent progress made in monitoring the generation of Ca2+ signals at the whole plant or cell level and their long distance propagation during biotic interactions. The contribution of CaM/CMLs and CDPKs in plant immune responses mounted against bacteria, fungi, viruses and insects are also presented.

Arabidopsis thaliana rapid alkalinization factor 1-mediated root growth inhibition is dependent on calmodulin-like protein 38

Arabidopsis thaliana rapid alkalinization factor 1 (AtRALF1) is a small secreted peptide hormone that inhibits root growth by repressing cell expansion. Although it is known that AtRALF1 binds the plasma membrane receptor FERONIA and conveys its signals via phosphorylation, the AtRALF1 signaling pathway is largely unknown. Here, using a yeast two-hybrid system to search for AtRALF1-interacting proteins in Arabidopsis, we identified calmodulin-like protein 38 (CML38) as an AtRALF1-interacting partner. We also found that CML38 and AtRALF1 are both secreted proteins that physically interact in a Ca2+- and pH-dependent manner. CML38-knockout mutants generated via T-DNA insertion were insensitive to AtRALF1, and simultaneous treatment with both AtRALF1 and CML38 proteins restored sensitivity in these mutants. Hybrid plants lacking CML38 and having high accumulation of the AtRALF1 peptide did not exhibit the characteristic short-root phenotype caused by AtRALF1 overexpression. Although CML38 was essential for AtRALF1-mediated root inhibition, it appeared not to have an effect on the AtRALF1-induced alkalinization response. Moreover, acridinium-labeling of AtRALF1 indicated that the binding of AtRALF1 to intact roots is CML38-dependent. In summary, we describe a new component of the AtRALF1 response pathway. The new component is a calmodulin-like protein that binds AtRALF1, is essential for root growth inhibition, and has no role in AtRALF1 alkalinization.

Arabidopsis Calmodulin-Like Proteins, CML15 and CML16 Possess Biochemical Properties Distinct from Calmodulin and Show Non-overlapping Tissue Expression Patterns

Calcium ions are used as ubiquitous, key second messengers in cells across eukaryotic taxa. In plants, calcium signal transduction is involved in a wide range of cellular processes from abiotic and biotic stress responses to development and growth. Calcium signals are detected by calcium sensor proteins, of which calmodulin (CaM), is the most evolutionarily conserved and well-studied. These sensors regulate downstream targets to propagate the information in signaling pathways. Plants possess a large family of calcium sensors related to CaM, termed CaM-like (CMLs), that are not found in animals and remain largely unstudied at the structural and functional level. Here, we investigated the biochemical properties and gene promoter activity of two closely related members of the Arabidopsis CML family, CML15 and CML16. Biochemical characterization of recombinant CML15 and CML16 indicated that they possess properties consistent with their predicted roles as calcium sensors. In the absence of calcium, CML15 and CML16 display greater intrinsic hydrophobicity than CaM. Both CMLs displayed calcium-dependent and magnesium-independent conformational changes that expose hydrophobic residues, but the degree of hydrophobic exposure was markedly less than that observed for CaM. Isothermal titration calorimetry indicated two and three calcium-binding sites for CML15 and CML16, respectively, with affinities expected to be within a physiological range. Both CML15 and CML16 bound calcium with high affinity in the presence of excess magnesium. Promoter-reporter analysis demonstrated that the CML16 promoter is active across a range of Arabidopsis tissues and developmental stages, whereas the CML15 promoter activity is very restricted and was observed only in floral tissues, specifically anthers and pollen. Collectively, our data indicate that these CMLs behave biochemically like calcium sensors but with properties distinct from CaM and likely have non-overlapping roles in floral development. We discuss our findings in the broader context of calcium sensors and signaling in Arabidopsis.

An Overview of Signaling Regulons During Cold Stress Tolerance in Plants

Plants, being sessile organisms, constantly withstand environmental fluctuations, including low-temperature, also referred as cold stress. Whereas cold poses serious challenges at both physiological and developmental levels to plants growing in tropical or sub-tropical regions, plants from temperate climatic regions can withstand chilling or freezing temperatures. Several cold inducible genes have already been isolated and used in transgenic approach to generate cold tolerant plants. The conventional breeding methods and marker assisted selection have helped in developing plant with improved cold tolerance, however, the development of freezing tolerant plants through cold acclimation remains an unaccomplished task. Therefore, it is essential to have a clear understanding of how low temperature sensing strategies and corresponding signal transduction act during cold acclimation process. Herein, we synthesize the available information on the molecular mechanisms underlying cold sensing and signaling with an aim that the summarized literature will help develop efficient strategies to obtain cold tolerant plants.

Binding of calcium and target peptide to calmodulin-like protein CML19, the centrin 2 of Arabidopsis thaliana

Calmodulin-like protein 19 (CML19) is an Arabidopsis centrin that modulates nucleotide excision repair (NER) by binding to RAD4 protein, the Arabidopsis homolog of human Xeroderma pigmentosum complementation group C protein. Although the necessity of CML19 as a part of the RAD4 plant recognition complex for functional NER is known at a cellular level, little is known at a molecular level. Herein, we used a combination of biophysical and biochemical approaches to investigate the structural and ion and target-peptide binding properties of CML19. We found that CML19 possesses four Ca²⁺-specific binding sites, two of high affinity in the N-terminal domain and two of low affinity in the C-terminal domain. Binding of Ca²⁺ to CML19 increases its alpha-helix content, stabilizes the tertiary structure, and triggers a conformational change, resulting in the exposure of a hydrophobic patch instrumental for target protein recognition. Using bioinformatics tools we identified a CML19-binding site at the C-terminus of RAD4, and through in vitro binding experiments we analyzed the interaction between a 17-mer peptide representing this site and CML19. We found that the peptide shows a high affinity for CML19 in the presence of Ca²⁺ (stoichiometry 1:1) and the interaction primarily involves the C-terminal half of CML19.

rgs-CaM Detects and Counteracts Viral RNA Silencing Suppressors in Plant Immune Priming

Primary infection of a plant with a pathogen that causes high accumulation of salicylic acid in the plant typically via a hypersensitive response confers enhanced resistance against secondary infection with a broad spectrum of pathogens, including viruses. This phenomenon is called systemic acquired resistance (SAR), which is a plant priming for adaption to repeated biotic stress. However, the molecular mechanisms of SAR-mediated enhanced inhibition, especially of virus infection, remain unclear. Here, we show that SAR against cucumber mosaic virus (CMV) in tobacco plants (Nicotiana tabacum) involves a calmodulin-like protein, rgs-CaM. We previously reported the antiviral function of rgs-CaM, which binds to and directs degradation of viral RNA silencing suppressors (RSSs), including CMV 2b, via autophagy. We found that rgs-CaM-mediated immunity is ineffective against CMV infection in normally growing tobacco plants but is activated as a result of SAR induction via salicylic acid signaling. We then analyzed the effect of overexpression of rgs-CaM on salicylic acid signaling. Overexpressed and ectopically expressed rgs-CaM induced defense reactions, including cell death, generation of reactive oxygen species, and salicylic acid signaling. Further analysis using a combination of the salicylic acid analogue benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) and the Ca2+ ionophore A23187 revealed that rgs-CaM functions as an immune receptor that induces salicylic acid signaling by simultaneously perceiving both viral RSS and Ca2+ influx as infection cues, implying its autoactivation. Thus, secondary infection of SAR-induced tobacco plants with CMV seems to be effectively inhibited through 2b recognition and degradation by rgs-CaM, leading to reinforcement of antiviral RNA silencing and other salicylic acid-mediated antiviral responses.IMPORTANCE Even without an acquired immune system like that in vertebrates, plants show enhanced whole-plant resistance against secondary infection with pathogens; this so-called systemic acquired resistance (SAR) has been known for more than half a century and continues to be extensively studied. SAR-induced plants strongly and rapidly express a number of antibiotics and pathogenesis-related proteins targeted against secondary infection, which can account for enhanced resistance against bacterial and fungal pathogens but are not thought to control viral infection. This study showed that enhanced resistance against cucumber mosaic virus is caused by a tobacco calmodulin-like protein, rgs-CaM, which detects and counteracts the major viral virulence factor (RNA silencing suppressor) after SAR induction. rgs-CaM-mediated SAR illustrates the growth versus defense trade-off in plants, as it targets the major virulence factor only under specific biotic stress conditions, thus avoiding the cost of constitutive activation while reducing the damage from virus infection.

Arabidopsis calmodulin-like protein CML36 is a calcium (Ca2+) sensor that interacts with the plasma membrane Ca2+-ATPase isoform ACA8 and stimulates its activity

Calmodulin-like (CML) proteins are major EF-hand-containing, calcium (Ca2+)-binding proteins with crucial roles in plant development and in coordinating plant stress tolerance. Given their abundance in plants, the properties of Ca2+ sensors and identification of novel target proteins of CMLs deserve special attention. To this end, we recombinantly produced and biochemically characterized CML36 from Arabidopsis thaliana We analyzed Ca2+ and Mg2+ binding to the individual EF-hands, observed metal-induced conformational changes, and identified a physiologically relevant target. CML36 possesses two high-affinity Ca2+/Mg2+ mixed binding sites and two low-affinity Ca2+-specific sites. Binding of Ca2+ induced an increase in the α-helical content and a conformational change that lead to the exposure of hydrophobic regions responsible for target protein recognition. Cation binding, either Ca2+ or Mg2+, stabilized the secondary and tertiary structures of CML36, guiding a large structural transition from a molten globule apo-state to a compact holoconformation. Importantly, through in vitro binding and activity assays, we showed that CML36 interacts directly with the regulative N terminus of the Arabidopsis plasma membrane Ca2+-ATPase isoform 8 (ACA8) and that this interaction stimulates ACA8 activity. Gene expression analysis revealed that CML36 and ACA8 are co-expressed mainly in inflorescences. Collectively, our results support a role for CML36 as a Ca2+ sensor that binds to and modulates ACA8, uncovering a possible involvement of the CML protein family in the modulation of plant-autoinhibited Ca2+ pumps.