The calmodulin-like proteins AtCML4 and AtCML5 are single-pass membrane proteins targeted to the endomembrane system by an N-terminal signal anchor sequence

Calcium (Ca2+ ) sensors and MYC2 are crucial players during jasmonates-mediated abiotic stress tolerance in plants

Plants evolve stress-specific responses that sense changes in their external environmental conditions and develop various mechanisms for acclimatization and survival. Calcium (Ca2+ ) is an essential stress-sensing secondary messenger in plants. Ca2+ sensors, including calcium-dependent protein kinases (CDPKs), calmodulins (CaMs), CaM-like proteins (CMLs), and calcineurin B-like proteins (CBLs), are involved in jasmonates (JAs) signalling and biosynthesis. Moreover, JAs are phospholipid-derived phytohormones that control plant response to abiotic stresses. The JAs signalling pathway affects hormone-receptor gene transcription by binding to the basic helix-loop-helix (bHLH) transcription factor. MYC2 acts as a master regulator of JAs signalling module assimilated through various genes. The Ca2+ sensor CML regulates MYC2 and is involved in a distinct mechanism mediating JAs signalling during abiotic stresses. This review highlights the pivotal role of the Ca2+ sensors in JAs biosynthesis and MYC2-mediated JAs signalling during abiotic stresses in plants.

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.

A CCaMK/Cyclops response element in the promoter of Lotus japonicus calcium-binding protein 1 (CBP1) mediates transcriptional activation in root symbioses

Early gene expression in arbuscular mycorrhiza (AM) and the nitrogen-fixing root nodule symbiosis (RNS) is governed by a shared regulatory complex. Yet many symbiosis-induced genes are specifically activated in only one of the two symbioses. The Lotus japonicus T-DNA insertion line T90, carrying a promoterless uidA (GUS) gene in the promoter of Calcium Binding Protein 1 (CBP1) is exceptional as it exhibits GUS activity in both root endosymbioses. To identify the responsible cis- and trans-acting factors, we subjected deletion/modification series of CBP1 promoter : reporter fusions to transactivation and spatio-temporal expression analysis and screened ethyl methanesulphonate (EMS)-mutagenized T90 populations for aberrant GUS expression. We identified one cis-regulatory element required for GUS expression in the epidermis and a second element, necessary and sufficient for transactivation by the calcium and calmodulin-dependent protein kinase (CCaMK) in combination with the transcription factor Cyclops and conferring gene expression during both AM and RNS. Lack of GUS expression in T90 white mutants could be traced to DNA hypermethylation detected in and around this element. We concluded that the CCaMK/Cyclops complex can contribute to at least three distinct gene expression patterns on its direct target promoters NIN (RNS), RAM1 (AM), and CBP1 (AM and RNS), calling for yet-to-be identified specificity-conferring factors.

Characterization of the Calmodulin/Calmodulin-like Protein (CAM/CML) Family in Ginkgo biloba, and the Influence of an Ectopically Expressed GbCML Gene (Gb_30819) on Seedling and Fruit Development of Transgenic Arabidopsis

Calmodulins (CAMs) and calmodulin-like proteins (CMLs) can participate in the regulation of various physiological processes via sensing and decoding Ca²⁺ signals. To reveal the characteristics of the CAM/CML family in Ginkgo biloba, a comprehensive analysis was performed at the genome-wide level. A total of 26 CAMs/CMLs, consisting of 5 GbCAMs and 21 GbCMLs, was identified on 11 out of 12 chromosomes in G. biloba. They displayed a certain degree of multiplicity in their sequences, albeit with conserved EF hands. Collinearity analysis suggested that tandem rather than segmental or whole-genome duplications were likely to play roles in the evolution of the Ginkgo CAM/CML family. Furthermore, GbCAMs/GbCMLs were grouped into higher, lower, and moderate expression in magnitude. The cis-acting regulatory elements involved in phytohormone-responsiveness within GbCAM/GbCML promotors may explain their varied expression profiles. The ectopic expression of a GbCML gene (Gb_30819) in transgenic Arabidopsis led to phenotypes with significantly shortened root length and seedling height, and decreased yields of both pods and seeds. Moreover, an electrophoresis mobility shift assay demonstrated the Ca²⁺-binding activity of Gb_30819 in vitro. Altogether, these results contribute to insights into the characteristics of the evolution and expression of GbCAMs/GbCMLs, as well as evidence for Ca²⁺-CAM/CML pathways functioning within the ancient gymnosperm G. biloba.

Transport, functions, and interaction of calcium and manganese in plant organellar compartments

Calcium (Ca2+) and manganese (Mn2+) are essential elements for plants and have similar ionic radii and binding coordination. They are assigned specific functions within organelles, but share many transport mechanisms to cross organellar membranes. Despite their points of interaction, those elements are usually investigated and reviewed separately. This review takes them out of this isolation. It highlights our current mechanistic understanding and points to open questions of their functions, their transport, and their interplay in the endoplasmic reticulum (ER), vesicular compartments (Golgi apparatus, trans-Golgi network, pre-vacuolar compartment), vacuoles, chloroplasts, mitochondria, and peroxisomes. Complex processes demanding these cations, such as Mn2+-dependent glycosylation or systemic Ca2+ signaling, are covered in some detail if they have not been reviewed recently or if recent findings add to current models. The function of Ca2+ as signaling agent released from organelles into the cytosol and within the organelles themselves is a recurrent theme of this review, again keeping the interference by Mn2+ in mind. The involvement of organellar channels [e.g. glutamate receptor-likes (GLR), cyclic nucleotide-gated channels (CNGC), mitochondrial conductivity units (MCU), and two-pore channel1 (TPC1)], transporters (e.g. natural resistance-associated macrophage proteins (NRAMP), Ca2+ exchangers (CAX), metal tolerance proteins (MTP), and bivalent cation transporters (BICAT)], and pumps [autoinhibited Ca2+-ATPases (ACA) and ER Ca2+-ATPases (ECA)] in the import and export of organellar Ca2+ and Mn2+ is scrutinized, whereby current controversial issues are pointed out. Mechanisms in animals and yeast are taken into account where they may provide a blueprint for processes in plants, in particular, with respect to tunable molecular mechanisms of Ca2+ versus Mn2+ selectivity.

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.

Homologous Proteins of the Manganese Transporter PAM71 Are Localized in the Golgi Apparatus and Endoplasmic Reticulum

Chloroplast manganese transporter 1 (CMT1) and photosynthesis-affected mutant 71 (PAM71) are two membrane proteins that function sequentially to mediate the passage of manganese across the chloroplast envelope and the thylakoid membrane. CMT1 and PAM71 belong to a small five-member protein family in Arabidopsis thaliana. The other three, photosynthesis-affected mutant 71 like 3 (PML3), PML4 and PML5 are not predicted to reside in chloroplast membranes. In this study, the subcellular localization of PML3:GFP, PML4:GFP and PML5:GFP was determined using transient and stable expression assays. PML3:GFP localizes to the Golgi apparatus, whereas PML4:GFP and PML5:GFP are found in the endoplasmic reticulum. We also examined patterns of PML3, PML4 and PML5 promoter activity. Although the precise expression pattern of each promoter was unique, all three genes were expressed in the leaf vasculature and in roots. Greenhouse grown single mutants pml3, pml4, pml5 and the pml4/pml5 double mutant did not exhibit growth defects, however an inspection of the root growth revealed a difference between pml3 and the other genotypes, including wild-type, in 500 µM manganese growth conditions. Strikingly, overexpression of PML3 resulted in a stunted growth phenotype. Putative functions of PML3, PML4 and PML5 are discussed in light of what is known about PAM71 and CMT1.

Chloroplast Calcium Signaling in the Spotlight

Calcium has long been known to regulate the metabolism of chloroplasts, concerning both light and carbon reactions of photosynthesis, as well as additional non photosynthesis-related processes. In addition to undergo Ca²⁺ regulation, chloroplasts can also influence the overall Ca²⁺ signaling pathways of the plant cell. Compelling evidence indicate that chloroplasts can generate specific stromal Ca²⁺ signals and contribute to the fine tuning of cytoplasmic Ca²⁺ signaling in response to different environmental stimuli. The recent set up of a toolkit of genetically encoded Ca²⁺ indicators, targeted to different chloroplast subcompartments (envelope, stroma, thylakoids) has helped to unravel the participation of chloroplasts in intracellular Ca²⁺ handling in resting conditions and during signal transduction. Intra-chloroplast Ca²⁺ signals have been demonstrated to occur in response to specific environmental stimuli, suggesting a role for these plant-unique organelles in transducing Ca²⁺-mediated stress signals. In this mini-review we present current knowledge of stimulus-specific intra-chloroplast Ca²⁺ transients, as well as recent advances in the identification and characterization of Ca²⁺-permeable channels/transporters localized at chloroplast membranes. In particular, the potential role played by cMCU, a chloroplast-localized member of the mitochondrial calcium uniporter (MCU) family, as component of plant environmental sensing is discussed in detail, taking into account some specific structural features of cMCU. In summary, the recent molecular identification of some players of chloroplast Ca²⁺ signaling has opened new avenues in this rapidly developing field and will hopefully allow a deeper understanding of the role of chloroplasts in shaping physiological responses in plants.

Calcium-mediation of jasmonate biosynthesis and signaling in plants

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

The High Light Response in Arabidopsis Requires the Calcium Sensor Protein CAS, a Target of STN7- and STN8-Mediated Phosphorylation

Reversible phosphorylation of thylakoid proteins contributes to photoacclimation responses in photosynthetic organisms, enabling the fine-tuning of light harvesting under changing light conditions and promoting the onset of photoprotective processes. However, the precise functional role of many of the described phosphorylation events on thylakoid proteins remains elusive. The calcium sensor receptor protein (CAS) has previously been indicated as one of the targets of the state transition kinase 8 (STN8). Here we show that in Arabidopsis thaliana, CAS is also phosphorylated by the state transition kinase 7 (STN7), as well as by another, so-far unknown, Ca2+-dependent kinase. Phosphoproteomics analysis and in vitro phosphorylation assays on CAS variants identified the phylogenetically conserved residues Thr-376, Ser-378, and Thr-380 as the major phosphorylation sites of the STN kinases. Spectroscopic analyses of chlorophyll fluorescence emission at 77K further showed that, while the cas mutant is not affected in state transition, it displays a persistent strong excitation of PSI under high light exposure, similar to the phenotype previously observed in other mutants defective in photoacclimation mechanisms. Together with the observation of a strong concomitant phosphorylation of light harvesting complex II (LHCII) and photosynthetic core proteins under high irradiance in the cas mutant this suggests a role for CAS in the STN7/STN8/TAP38 network of phosphorylation-mediated photoacclimation processes in Arabidopsis.

A mongolian pine specific endoplasmic reticulum localized CALMODULIN-LIKE calcium binding protein enhances arabidopsis growth

Stress-adapted wild plants are natural sources of novel genes for molecular breeding. Here, we conducted a transcriptional analysis of Pinus sylvestris var. mongolica Litv, an evergreen pine in northeastern China, to identify a novel CALMODULIN-LIKE protein-encoding gene, PsCML1, no significant homologs found in other plant species. PsCML1 encodes a protein predicted to have a single trans-membrane domain at its N-terminal. Four EF-hand motifs (calcium [Ca]-binding structures) are located at its C-terminal and showed Ca²⁺-specific affinity in isothermal titration calorimetric analysis. Transient expression of PsCML1 in Nicotiana benthamiana showed that the PsCML1 localizes to the endoplasmic reticulum (ER). Heterologous expression of PsCML1 in Arabidopsis significantly promoted seedling growth, and increased resistance to stress from NaCl and Ca²⁺ deficiency. The roots of the transgenic seedlings had higher contents of cellulose and pectin, but less hemicellulose than those of the wild type (WT). The biosynthesis of cell wall components is linked with protein glycosylation in the ER and reactive oxygen species (ROS) homeostasis. No significant difference was found in the extent of protein glycosylation between the transgenic and WT plants. However, the transgenic roots had higher steady-state levels of ROS, NADPH oxidase activity, and endo-membrane dynamics than those of the WT. A working model was proposed to delineate the interaction among Ca²⁺, ROS homeostasis, and cell wall loosening-dependent cell division.

Pharmacological Strategies for Manipulating Plant Ca2+ Signalling

Calcium is one of the most pleiotropic second messengers in all living organisms. However, signalling specificity is encoded via spatio-temporally regulated signatures that act with surgical precision to elicit highly specific cellular responses. How this is brought about remains a big challenge in the plant field, in part due to a lack of specific tools to manipulate/interrogate the plant Ca2+ toolkit. In many cases, researchers resort to tools that were optimized in animal cells. However, the obviously large evolutionary distance between plants and animals implies that there is a good chance observed effects may not be specific to the intended plant target. Here, we provide an overview of pharmacological strategies that are commonly used to activate or inhibit plant Ca2+ signalling. We focus on highlighting modes of action where possible, and warn for potential pitfalls. Together, this review aims at guiding plant researchers through the Ca2+ pharmacology swamp.

The contribution of organelles to plant intracellular Calcium signalling

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

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.

Spatio-temporal Aspects of Ca2+ Signalling: Lessons from Guard Cells and Pollen Tubes

Changes in cytosolic Ca2+ concentration ([Ca2+]cyt) serve to transmit information in eukaryotic cells. The involvement of this second messenger in plant cell growth as well as osmotic- and water relations is well established. After almost 40 years of intense research on the coding and decoding of plant Ca2+ signals, numerous proteins involved in Ca2+ action have been identified. However, we are still far from understanding the complexity of Ca2+ networks. New in vivo Ca2+ imaging techniques combined with molecular genetics allow visualisation of spatio-temporal aspects of Ca2+ signalling. In parallel, cell biology together with protein biochemistry and electrophysiology are able to dissect information processing by this second messenger in space and time. Here we focus on the time-resolved changes in cellular events upon Ca2+ signals, concentrating on the two best-studied cell types, pollen tubes and guard cells. We put their signalling networks side by side, compare them with those of other cell types and discuss rapid signalling in the context of Ca2+ transients and oscillations to regulate ion homeostasis.

The ins and outs of Ca2+ in plant endomembrane trafficking

Trafficking of proteins and lipids within the plant endomembrane system is essential to support cellular functions and is subject to rigorous regulation. Despite this seemingly strict regulation, endomembrane trafficking needs to be dynamically adjusted to ever-changing internal and environmental stimuli, while maintaining cellular integrity. Although often overlooked, the versatile second messenger Ca²⁺ is intimately connected to several endomembrane-associated processes. Here, we discuss the impact of electrostatic interactions between Ca²⁺ and anionic phospholipids on endomembrane trafficking, and illustrate the direct role of Ca²⁺ sensing proteins in regulating endomembrane trafficking and membrane integrity preservation. Moreover, we discuss how Ca²⁺ can control protein sorting within the plant endomembrane system. We thus highlight Ca²⁺ signaling as a versatile mechanism by which numerous signals are integrated into plant endomembrane trafficking dynamics.

Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

L. japonicus, a model plant of legumes plants, is widely used in symbiotic nitrogen fixation. A large number of studies on it have been published based on the genetic, biochemical, structural studies. These results are secondhand reports that CaM is a key regulator during Rhizobial infection. In plants, there are multiple CaM genes encoding several CaM isoforms with only minor amino acid differences. Moreover, the regulation mechanism of this family of proteins during rhizobia infection is still unclear. In the current study, a family of genes encoding CaMs and CMLs that possess only the Ca2+-binding EF-hand motifs were analyzed. Using ML and BI tree based on amino acid sequence similarity, seven loci defined as CaMs and 19 CMLs, with at least 23% identity to CaM, were identified. The phylogenetics, gene structures, EF hand motif organization, and expression characteristics were evaluated. Seven CaM genes, encoding only 4 isoforms, were found in L. japonicus. According to qRT-PCR, four LjCaM isoforms are involved in different rhizobia infection stages. LjCaM1 might be involved in the early rhizobia infection epidermal cells stage. Furthermore, additional structural differences and expression behaviors indicated that LjCMLs may have different potential functions from LjCaMs.