Combining genetics and cell biology to crack the code of plant cell calcium signaling

Mechanism of calcium signal response to cadmium stress in duckweed

Cadmium (Cd) causes serious damage to plants. Although calcium (Ca) signal has been found to respond to certain stress, the localization of Ca and molecular mechanisms underlying Ca signal in plants during Cd stress are largely unknown. In this study, Ca²⁺-sensing fluorescent reporter (GCaMP3) transgenic duckweed showed the Ca²⁺ signal response in Lemna turionifera 5511 (duckweed) during Cd stress. Subsequently, the subcellular localization of Ca²⁺ has been studied during Cd stress by transmission electron microscopy, showing the accumulation of Ca²⁺ in vacuoles. Also, Ca²⁺ flow during Cd stress has been measured. At the same time, the effects of exogenous glutamic acid (Glu) and γ-aminobutyric (GABA) on duckweed can better clarify the signal operation mechanism of plants to Cd stress. The molecular mechanism of Ca²⁺ signal responsed during Cd stress showed that Cd treatment promotes the positive response of Ca signaling channels in plant cells, and thus affects the intracellular Ca content. These novel signal studies provided an important Ca²⁺ signal molecular mechanism during Cd stress.

Comprehensive structural, interaction and expression analysis of CBL and CIPK complement during abiotic stresses and development in rice

Calcium ion is involved in diverse physiological and developmental pathways. One of the important roles of calcium is a signaling messenger, which regulates signal transduction in plants. CBL (calcineurin B-like protein) is one of the calcium sensors that specifically interact with a family of serine-threonine protein kinases designated as CBL-interacting protein kinases (CIPKs). The coordination of these two gene families defines complexity of the signaling networks in several stimulus-response-coupling during various environmental stresses. In Arabidopsis, both of these gene families have been extensively studied. To understand in-depth mechanistic interplay of CBL-CIPK mediated signaling pathways, expression analysis of entire set of CBL and CIPK genes in rice genome under three abiotic stresses (salt, cold and drought) and different developmental stages (3-vegetative stages and 11-reproductive stages) were done using microarray expression data. Interestingly, expression analysis showed that rice CBLs and CIPKs are not only involved in the abiotic stress but their significant role is also speculated in the developmental processes. Chromosomal localization of rice CBL and CIPK genes reveals that only OsCBL7 and OsCBL8 shows tandem duplication among CBLs whereas CIPKs were evolved by many tandem as well as segmental duplications. Duplicated OsCIPK genes showed variable expression pattern indicating the role of gene duplication in the extension and functional diversification of CIPK gene family in rice. Arabidopsis SOS3/CBL4 related genes in rice (OsCBL4, OsCBL5, OsCBL7 and OsCBL8) were employed for interaction studies with rice and Arabidopsis CIPKs. OsCBLs and OsCIPKs are not only found structurally similar but likely to be functionally equivalent to Arabidopsis CBLs and CIPKs genes since SOS3/CBL4 related OsCBLs interact with more or less similarly to rice and Arabidopsis CIPKs and exhibited an interaction pattern comparable with Arabidopsis SOS3/CBL4.

Preliminary crystallographic analysis of the ankyrin-repeat domain of Arabidopsis thaliana AKT1: identification of the domain boundaries for protein crystallization

The Arabidopsis thaliana K(+) transporter 1 (AKT1) participates in the maintenance of an adequate cell potassium (K(+)) concentration. The CBL-interacting protein kinase 23 (CIPK23) activates AKT1 for K(+) uptake under low-K(+) conditions. This process is mediated by the interaction between the cytosolic ankyrin-repeat (AR) domain of AKT1 and the kinase domain of CIPK23. However, the precise boundaries of the AR domain and the residues responsible for the interaction are still unknown. Here, the optimization procedure to obtain an AR domain construct suitable for crystallization and the preliminary crystallographic analysis of the obtained crystals are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 34.83, b = 65.89, c = 85.44 Å, and diffracted to 1.98 Å resolution.

Inositol trisphosphate-induced Ca2+ signaling modulates auxin transport and PIN polarity

The phytohormone auxin is an important determinant of plant development. Directional auxin flow within tissues depends on polar localization of PIN auxin transporters. To explore regulation of PIN-mediated auxin transport, we screened for suppressors of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase mutant (supo1), with elevated inositol trisphosphate (InsP(3)) and cytosolic Ca(2+) levels. Pharmacological and genetic increases in InsP(3) or Ca(2+) levels also suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN localization, auxin transport and auxin-mediated development. In contrast, the reductions in InsP(3) levels and Ca(2+) signaling antagonized the effects of the supo1 mutation and disrupted preferentially apical PIN localization. InsP(3) and Ca(2+) are evolutionarily conserved second messengers involved in various cellular functions, particularly stress responses. Our findings implicate them as modifiers of cell polarity and polar auxin transport, and highlight a potential integration point through which Ca(2+) signaling-related stimuli could influence auxin-mediated development.

Cryptogein, a fungal elicitor, remodels the phenylpropanoid metabolism of tobacco cell suspension cultures in a calcium-dependent manner

Plant cells use calcium-based signalling pathways to transduce biotic and/or abiotic stimuli into adaptive responses. However, little is known about the coupling between calcium signalling, transcriptional regulation and the downstream biochemical processes. To understand these relationships better, we challenged tobacco BY-2 cells with cryptogein and evaluated how calcium transients (monitored through the calcium sensor aequorin) impact (1) transcript levels of phenylpropanoid genes (assessed by RT-qPCR); and (2) derived-phenolic compounds (analysed by mass spectrometry). Most genes of the phenylpropanoid pathway were up-regulated by cryptogein and cell wall-bound phenolic compounds accumulated (mainly 5-hydroxyferulic acid). The accumulation of both transcripts and phenolics was calcium-dependent. The transcriptional regulation of phenylpropanoid genes was correlated in a non-linear manner with stimulus intensity and with components of the cryptogein-induced calcium signature. In addition, calmodulin inhibitors increased the sensitivity of cells to low concentrations of cryptogein. These results led us to propose a model of coupling between the cryptogein signal, calcium signalling and the transcriptional response, exerting control of transcription through the coordinated action of two decoding modules exerting opposite effects.

De-regulated expression of the plant glutamate receptor homolog AtGLR3.1 impairs long-term Ca2+-programmed stomatal closure

Cytosolic Ca(2+) ([Ca(2+)](cyt)) mediates diverse cellular responses in both animal and plant cells in response to various stimuli. Calcium oscillation amplitude and frequency control gene expression. In stomatal guard cells, [Ca(2+)](cyt) has been shown to regulate stomatal movements, and a defined window of Ca(2+) oscillation kinetic parameters encodes necessary information for long-term stomatal movements. However, it remains unknown how the encrypted information in the cytosolic Ca(2+) signature is decoded to maintain stomatal closure. Here we report that the Arabidopsis glutamate receptor homolog AtGLR3.1 is preferentially expressed in guard cells compared to mesophyll cells. Furthermore, over-expression of AtGLR3.1 using a viral promoter resulted in impaired external Ca(2+)-induced stomatal closure. Cytosolic Ca(2+) activation of S-type anion channels, which play a central role in Ca(2+)-reactive stomatal closure, was normal in the AtGLR3.1 over-expressing plants. Interestingly, AtGLR3.1 over-expression did not affect Ca(2+)-induced Ca(2+) oscillation kinetics, but resulted in a failure to maintain long-term 'Ca(2+)-programmed' stomatal closure when Ca(2+) oscillations containing information for maintaining stomatal closure were imposed. By contrast, prompt short-term Ca(2+)-reactive closure was not affected in AtGLR3.1 over-expressing plants. In wild-type plants, the translational inhibitor cyclohexamide partially inhibited Ca(2+)-programmed stomatal closure induced by experimentally imposed Ca(2+) oscillations without affecting short-term Ca(2+)-reactive closure, mimicking the guard cell behavior of the AtGLR3.1 over-expressing plants. Our results suggest that over-expression of AtGLR3.1 impairs Ca(2+) oscillation-regulated stomatal movements, and that de novo protein synthesis contributes to the maintenance of long-term Ca(2+)-programmed stomatal closure.

In SYNC: the ins and outs of circadian oscillations in calcium

Many stimuli induce short-term increases in the cytosolic concentration of free calcium ions ([Ca(2+)](i)) that encode signaling information about diverse physiological and developmental events. Slow cytosolic Ca(2+) oscillations that span an entire day have also been discovered in both plants and animals; it is thought that these daily Ca(2+) oscillations may encode circadian clock signaling information. A recent study focusing on the characterization of the extracellular Ca(2+)-sensing receptor (CAS) has provided insight into the molecular mechanisms by which the daily Ca(2+) oscillation in plants is generated. We summarize the major findings regarding daily oscillations of cytosolic Ca(2+) concentrations in plants and animals, and discuss hypothetical biological roles for the circadian clock-regulated physiology in plants.

Plant calmodulins and calmodulin-related proteins: multifaceted relays to decode calcium signals

The calmodulin (CaM) family is a major class of calcium sensor proteins which collectively play a crucial role in cellular signaling cascades through the regulation of numerous target proteins. Although CaM is one of the most conserved proteins in all eukaryotes, several features of CaM and its downstream effector proteins are unique to plants. The continuously growing repertoire of CaM-binding proteins includes several plant-specific proteins. Plants also possess a particular set of CaM isoforms and CaM-like proteins (CMLs) whose functions have just begun to be elucidated. This review summarizes recent insights that help to understand the role of this multigene family in plant development and adaptation to environmental stimuli.

Calcium: just another regulator in the machinery of life?

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BACKGROUND

Current hypotheses imply that stimulus-response systems in plants are networks of signal transduction pathways. It is usually assumed that these pathways connect receptors with effectors via chains of molecular events. Diverse intermediate signalling components (transducers) participate in these processes. However, many cellular transducers respond to several stimuli. Hence, there are no discrete chains but rather pathways that interconnect network-modules of different command structure. In particular, the cytosolic free Ca2+ concentration ([Ca2+](cyt)) is thought to perform many different tasks in a wide range of cellular events. However, this range of putative functions is so wide that it is often questioned how Ca2+ can comply with the definition of a second messenger. *THE Ca2+ SIGNATURE HYPOTHESIS: Some authors have suggested the concept of a specific signature of the ([Ca2+](cyt)) response. This implies that characteristics of the time course of changes in ([Ca2+](cyt)) and their localized sites of appearance in cells are used by the plant to identify the type and intensity of the stimulus. This hypothesis has triggered many investigations, which have yielded contradictory results. * THE CURRENT PICTURE: Much evidence suggests that the functions of calcium can be grouped into three classes: Ca2+ as a protective agent, Ca2+ as a chemical switch and Ca2+ as a 'digital' information carrier. Examples of the first two classes are presented here. The third is more controversial; while some investigations seem to support this idea, others call the Ca2+ signature hypothesis into question. Further investigations are needed to shed more light on Ca(2+)-driven signalling cascades.

Proteomics of calcium-signaling components in plants

Calcium functions as a versatile messenger in mediating responses to hormones, biotic/abiotic stress signals and a variety of developmental cues in plants. The Ca(2+)-signaling circuit consists of three major "nodes"--generation of a Ca(2+)-signature in response to a signal, recognition of the signature by Ca2+ sensors and transduction of the signature message to targets that participate in producing signal-specific responses. Molecular genetic and protein-protein interaction approaches together with bioinformatic analysis of the Arabidopsis genome have resulted in identification of a large number of proteins at each "node"--approximately 80 at Ca2+ signature, approximately 400 sensors and approximately 200 targets--that form a myriad of Ca2+ signaling networks in a "mix and match" fashion. In parallel, biochemical, cell biological, genetic and transgenic approaches have unraveled functions and regulatory mechanisms of a few of these components. The emerging paradigm from these studies is that plants have many unique Ca2+ signaling proteins. The presence of a large number of proteins, including several families, at each "node" and potential interaction of several targets by a sensor or vice versa are likely to generate highly complex networks that regulate Ca(2+)-mediated processes. Therefore, there is a great demand for high-throughput technologies for identification of signaling networks in the "Ca(2+)-signaling-grid" and their roles in cellular processes. Here we discuss the current status of Ca2+ signaling components, their known functions and potential of emerging high-throughput genomic and proteomic technologies in unraveling complex Ca2+ circuitry.

Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks

Calcium signals mediate a multitude of plant responses to external stimuli and regulate a wide range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, represent important relays in plant calcium signaling. These proteins form a complex network with their target kinases being the CBL-interacting protein kinases (CIPKs). Here, we present a comparative genomics analysis of the full complement of CBLs and CIPKs in Arabidopsis and rice (Oryza sativa). We confirm the expression and transcript composition of the 10 CBLs and 25 CIPKs encoded in the Arabidopsis genome. Our identification of 10 CBLs and 30 CIPKs from rice indicates a similar complexity of this signaling network in both species. An analysis of the genomic evolution suggests that the extant number of gene family members largely results from segmental duplications. A phylogenetic comparison of protein sequences and intron positions indicates an early diversification of separate branches within both gene families. These branches may represent proteins with different functions. Protein interaction analyses and expression studies of closely related family members suggest that even recently duplicated representatives may fulfill different functions. This work provides a basis for a defined further functional dissection of this important plant-specific signaling system.

The calcium sensor CBL1 integrates plant responses to abiotic stresses

Calcium ions represent both an integrative signal and an important convergence point of many disparate signaling pathways. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, have been implicated as important relays in calcium signaling. Here, we report the in vivo study of CBL1 function in Arabidopsis. Analyses of loss-of-function as well as CBL1-overexpressing lines indicate a crucial function of this calcium sensor protein in abiotic stress responses. Mutation of CBL1 impairs plant responses to drought and salt stresses and affects gene expression of cold-regulated genes, but does not affect abscisic acid (ABA) responsiveness. Conversely, overexpression of CBL1 reduces transpirational water loss and induces the expression of early stress-responsive transcription factors and stress adaptation genes in non-stressed plants. Together, our data indicate that the calcium sensor protein CBL1 may constitute an integrative node in plant responses to abiotic stimuli and contributes to the regulation of early stress-related transcription factors of the C-Repeat-Binding Factor/dehydration-responsive element (CBF/DREB) type.

Calcium: just a chemical switch?

The calcium-signature hypothesis has evolved as a concept to explain specificity in signaling pathways that utilise calcium as a second messenger. In plant biology, this hypothesis was purely conceptual and based only upon correlative observations until recently. In the past few years, however, empirical data have emerged from experiments that were specifically designed to tackle the question of how specificity is encoded by calcium. In light of the attractive calcium-signature hypothesis, other potential explanations for signalling specificity have been overshadowed and ignored: it has been assumed that the calcium-signature dogma will explain all plant calcium signaling. However, there is a good deal of evidence supporting a counter-hypothesis in which calcium does not itself encode specificity but is merely an essential 'switch' in signaling. At the very least, both hypotheses are likely to be true in different situations, and it may well be that the calcium-signature hypothesis describes the exception rather than the rule.