Calcium signalling components underlying NPK homeostasis: potential avenues for exploration.

Plants require the major macronutrients, nitrogen (N), phosphorus (P) and potassium (K) for normal growth and development. Their deficiency in soil directly affects vital cellular processes, particularly root growth and architecture. Their perception, uptake and assimilation are regulated by complex signalling pathways. To overcome nutrient deficiencies, plants have developed certain response mechanisms that determine developmental and physiological adaptations. The signal transduction pathways underlying these responses involve a complex interplay of components such as nutrient transporters, transcription factors and others. In addition to their involvement in cross-talk with intracellular calcium signalling pathways, these components are also engaged in NPK sensing and homeostasis. The NPK sensing and homeostatic mechanisms hold the key to identify and understand the crucial players in nutrient regulatory networks in plants under both abiotic and biotic stresses. In this review, we discuss calcium signalling components/pathways underlying plant responses to NPK sensing, with a focus on the sensors, transporters and transcription factors involved in their respective signalling and homeostasis.

Overexpression of ARM repeat/U-box containing E3 ligase, PUB2 positively regulates growth and oxidative stress response in Arabidopsis.

Plant growth and development are governed by selective protein synthesis and degradation. Ubiquitination mediated protein degradation is governed by activating enzyme E1 followed by conjugating enzyme E2 and E3 ligase. Plant Armadillo (ARM) repeat/U-box (PUB) protein family is one of the important classes of E3 ligase. We studied the function of AtPUB2 by loss-of-function (knockout and knock down mutants) and gain-of-function (CaMV 35S promoter driven overexpression lines) approach in Arabidopsis. Under normal growth condition, we observed that loss-of-function mutant plants did not show any significant difference in growth when compared with wild-type possibly due to functional redundancy between PUB2 and PUB4. However, AtPUB2-OE lines exhibit early flowering and improved vegetative growth. Also, AtPUB2-OE seedlings showed sensitive phenotype in the presence of exogenous cytokinin. We found that AtPUB2 expression is induced under oxidative stress. Subcellular localization analysis shows that AtPUB2 is predominantly localized in the nucleus. We performed the phenotypic analysis under oxidative stress condition induced by methyl viologen (MV) and observed that overexpression lines display tolerance to oxidative stress in light and dark conditions. Furthermore, we found less amount of ROS accumulation, enhanced proline accumulation and decreased levels of MDA after MV treatment in AtPUB2-OE lines. PUB2-OE lines showed enhanced oxidative stress marker genes expression. By in vitro auto-ubiquitination assay, we also show that it possesses the E3 ligase activity. Overall, our findings suggest the possible role of AtPUB2 in plants ability to tolerate oxidative stress by enhancing the activity of antioxidant enzymes, which in turn improves ROS scavenging activity and homeostasis.

CIPK9 targets VDAC3 and modulates oxidative stress responses in Arabidopsis.

Calcium (Ca2+ ) is widely recognized as a key second messenger in mediating various plant adaptive responses. Here we show that calcineurin B-like interacting protein kinase CIPK9 along with its interacting partner VDAC3 identified in the present study are involved in mediating plant responses to methyl viologen (MV). CIPK9 physically interacts with and phosphorylates VDAC3. Co-localization, co-immunoprecipitation, and fluorescence resonance energy transfer experiments proved their physical interaction in planta. Both cipk9 and vdac3 mutants exhibited a tolerant phenotype against MV-induced oxidative stress, which coincided with the lower-level accumulation of reactive oxygen species in their roots. In addition, the analysis of cipk9vdac3 double mutant and VDAC3 overexpressing plants revealed that CIPK9 and VDAC3 were involved in the same pathway for inducing MV-dependent oxidative stress. The response to MV was suppressed by the addition of lanthanum chloride, a non-specific Ca2+ channel blocker indicating the role of Ca2+ in this pathway. Our study suggest that CIPK9-VDAC3 module may act as a key component in mediating oxidative stress responses in Arabidopsis.

The integration of reactive oxygen species (ROS) and calcium signalling in abiotic stress responses.

Reactive oxygen species (ROS) and calcium (Ca2+ ) signalling are interconnected in the perception and transmission of environmental signals that control plant growth, development and defence. The concept that systemically propagating Ca2+ and ROS waves function together with electric signals in directional cell-to-cell systemic signalling and even plant-to-plant communication, is now firmly imbedded in the literature. However, relatively few mechanistic details are available regarding the management of ROS and Ca2+ signals at the molecular level, or how synchronous and independent signalling might be achieved in different cellular compartments. This review discusses the proteins that may serve as nodes or connecting bridges between the different pathways during abiotic stress responses, highlighting the crosstalk between ROS and Ca2+ pathways in cell signalling. We consider putative molecular switches that connect these signalling pathways and the molecular machinery that achieves the synergistic operation of ROS and Ca2+ signals.

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.

Delineating Calcium Signaling Machinery in Plants: Tapping the Potential through Functional Genomics.

Plants have developed calcium (Ca2+) signaling as an important mechanism of  regulation of  stress perception,  developmental cues, and  responsive gene  expression. The  post-genomic era has witnessed the successful unravelling of the functional characterization of genes and the creation of large datasets of molecular information. The major elements of Ca2+ signaling machinery include Ca2+ sensors and responders such as Calmodulins (CaMs), Calmodulin-like proteins (CMLs), Ca2+/CaM-dependent protein kinases (CCaMKs), Ca2+-dependent protein kinases (CDPKs), Calcineurin B-like proteins (CBLs) as well as transporters, such as Cyclic nucleotide-gated channels (CNGCs), Glutamate-like receptors (GLRs), Ca2+-ATPases, Ca2+/H+ exchangers (CAXs) and mechanosensitive channels. These elements play an important role in the regulation of physiological processes and plant responses to various stresses. Detailed genomic analysis can help us in the identification of potential molecular targets that can be exploited towards the development of stress-tolerant crops. The information sourced from model systems through omics approaches helps in the prediction and simulation of regulatory networks involved in responses to different stimuli at the molecular and cellular levels. The molecular delineation of Ca2+ signaling pathways could be a stepping stone for engineering climate-resilient crop plants. Here, we review the recent developments in Ca2+ signaling in the context of transport, responses, and adaptations significant for crop improvement through functional genomics approaches.

Ca2+-CBL-CIPK: a modulator system for efficient nutrient acquisition.

Calcium (Ca2+) is a universal second messenger essential for the growth and development of plants in normal and stress situations. In plants, the proteins, CBL (calcineurin B-like) and CIPK (CBL-interacting protein kinase), form one of the important Ca2+ decoding complexes to decipher Ca2+ signals elicited by environmental challenges. Multiple interactors distinguish CBL and CIPK protein family members to form a signaling network for regulated perception and transduction of environmental signals, e.g., signals generated under nutrient stress conditions. Conservation of equilibrium in response to varying soil nutrient status is an important aspect for plant vigor and yield. Signaling processes have been reported to observe nutrient fluctuations as a signal responsible for regulated nutrient transport adaptation. Recent studies have identified downstream targets of CBL-CIPK modules as ion channels or transporters and their association in signaling nutrient disposal including potassium, nitrate, ammonium, magnesium, zinc, boron, and iron. Ca2+-CBL-CIPK pathway modulates ion transporters/channels and hence maintains a homeostasis of several important plant nutrients in the cytosol and sub-cellular compartments. In this article, we summarize recent literature to discuss the role of the Ca2+-CBL-CIPK pathway in cellular osmoregulation and homeostasis on exposure to nutrient excess or deprived soils. This further establishes a link between taking up the nutrient in the roots and its distribution and homeostasis during the generation of signal for the development and survival of plants.

Ectopic expression of finger millet calmodulin confers drought and salinity tolerance in Arabidopsis thaliana.

KEY MESSAGE: Overexpression of finger millet calmodulin imparts drought and salt tolerance in plants. Drought and salinity are major environmental stresses which affect crop productivity and therefore are major hindrance in feeding growing population world-wide. Calcium (Ca2+) signaling plays a crucial role during the plant's response to these stress stimuli. Calmodulin (CaM), a crucial Ca2+sensor, is involved in transducing the signal downstream in various physiological, developmental and stress responses by modulating a plethora of target proteins. The role of CaM has been well established in the model plant Arabidopsis thaliana for regulating various developmental processes, stress signaling and ion transport. In the current study, we investigate the CaM of Eleusine coracana (common name finger millet, known especially for its drought tolerance and superior Ca2+ content). In-silico analysis showed that Eleusine CaM (EcCaM) has greater similarity to rice CaM as compared to Arabidopsis CaM due to the presence of highly conserved four EF-hand domains. To decipher the in-planta function of EcCaM, we have adopted the gain-of-function approach by generating the 35S::EcCaM over-expression transgenic in Arabidopsis. Overexpression of EcCaM in Arabidopsis makes the plant tolerant to polyethylene glycol (PEG) induced drought and salt stress (NaCl) as demonstrated by post-germination based phenotypic assay, ion leakage, MDA and proline estimation, ROS detection under stressed and normal conditions. Moreover, EcCaM overexpression leads to hypersensitivity toward exogenously applied ABA at the seed germination stage. These findings reveal that EcCaM mediates tolerance to drought and salinity stress. Also, our results indicate that EcCaM is involved in modulating ABA signaling. Summarizing our results, we report for the first time that EcCaM is involved in modulating plants response to stress and this information can be used for the generation of future-ready crops that can tolerate a wide range of abiotic stresses.

CBL-CIPK module-mediated phosphoregulation: facts and hypothesis.

Calcium (Ca2+) signaling is a versatile signaling network in plant and employs very efficient signal decoders to transduce the encoded message. The CBL-CIPK module is one of the sensor-relay decoders that have probably evolved with the acclimatization of land plant. The CBLs are unique proteins with non-canonical Ca2+ sensing EF-hands, N-terminal localization motif and a C-terminal phosphorylation motif. The partner CIPKs are Ser/Thr kinases with kinase and regulatory domains. Phosphorylation plays a major role in the functioning of the module. As the module has a functional kinase to transduce signal, it employs phosphorylation as a preferred mode for modulation of targets as well as its interaction with CBL. We analyze the data on the substrate regulation by the module from the perspective of substrate phosphorylation. We have also predicted some of the probable sites in the identified substrates that may be the target of the CIPK mediated phosphorylation. In addition, phosphatases have been implicated in reversing the CIPK mediated phosphorylation of substrates. Therefore, we have also presented the role of phosphatases in the modulation of the CBL-CIPK and its targets. We present here an overview of the phosphoregulation mechanism of the CBL-CIPK module.

Genome-wide identification and biochemical characterization of calcineurin B-like calcium sensor proteins in Chlamydomonas reinhardtii.

Calcium (Ca2+) signaling is involved in the regulation of diverse biological functions through association with several proteins that enable them to respond to abiotic and biotic stresses. Though Ca2+-dependent signaling has been implicated in the regulation of several physiological processes in Chlamydomonas reinhardtii, Ca2+ sensor proteins are not characterized completely. C. reinhardtii has diverged from land plants lineage, but shares many common genes with animals, particularly those encoding proteins of the eukaryotic flagellum (or cilium) along with the basal body. Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is an important effector of Ca2+ signaling in animals, while calcineurin B-like proteins (CBLs) play an important role in Ca2+ sensing and signaling in plants. The present study led to the identification of 13 novel CBL-like Ca2+ sensors in C. reinhardtii genome. One of the archetypical genes of the newly identified candidate, CrCBL-like1 was characterized. The ability of CrCBL-like1 protein to sense as well as bind Ca2+ were validated using two-step Ca2+-binding kinetics. The CrCBL-like1 protein localized around the plasma membrane, basal bodies and in flagella, and interacted with voltage-gated Ca2+ channel protein present abundantly in the flagella, indicating its involvement in the regulation of the Ca2+ concentration for flagellar movement. The CrCBL-like1 transcript and protein expression were also found to respond to abiotic stresses, suggesting its involvement in diverse physiological processes. Thus, the present study identifies novel Ca2+ sensors and sheds light on key players involved in Ca2+signaling in C. reinhardtii, which could further be extrapolated to understand the evolution of Ca2+ mediated signaling in other eukaryotes.

Emerging concepts of potassium homeostasis in plants.

Potassium (K+) is an essential cation in all organisms that influences crop production and ecosystem stability. Although most soils are rich in K minerals, relatively little K+ is present in forms that are available to plants. Moreover, leaching and run-off from the upper soil layers contribute to K+ deficiencies in agricultural soils. Hence, the demand for K fertilizer is increasing worldwide. K+ regulates multiple processes in cells and organs, with K+ deficiency resulting in decreased plant growth and productivity. Here, we discuss the complexity of the reactive oxygen species-calcium-hormone signalling network that is responsible for the sensing of K+ deficiency in plants, together with genetic approaches using K+ transporters that have been used to increase K+ use efficiency (KUE) in plants, particularly under environmental stress conditions such as salinity and heavy metal contamination. Publicly available rice transcriptome data are used to demonstrate the two-way relationship between K+ and nitrogen nutrition, highlighting how each nutrient can regulate the uptake and root to shoot translocation of the other. Future research directions are discussed in terms of this relationship, as well as prospects for molecular approaches for the generation of improved varieties and the implementation of new agronomic practices. An increased knowledge of the systems that sense and take up K+, and their regulation, will not only improve current understanding of plant K+ homeostasis but also facilitate new research and the implementation of measures to improve plant KUE for sustainable food production.

VDAC and its interacting partners in plant and animal systems: an overview.

Molecular trafficking between different subcellular compartments is the key for normal cellular functioning. Voltage-dependent anion channels (VDACs) are small-sized proteins present in the outer mitochondrial membrane, which mediate molecular trafficking between mitochondria and cytoplasm. The conductivity of VDAC is dependent on the transmembrane voltage, its oligomeric state and membrane lipids. VDAC acts as a convergence point to a diverse variety of mitochondrial functions as well as cell survival. This functional diversity is attained due to their interaction with a plethora of proteins inside the cell. Although, there are hints toward functional conservation/divergence between animals and plants; knowledge about the functional role of the VDACs in plants is still limited. We present here a comparative overview to provide an integrative picture of the interactions of VDAC with different proteins in both animals and plants. Also discussed are their physiological functions from the perspective of cellular movements, signal transduction, cellular fate, disease and development. This in-depth knowledge of the biological importance of VDAC and its interacting partner(s) will assist us to explore their function in the applied context in both plant and animal.

PP2A Phosphatases Take a Giant Leap in the Post-Genomics Era.

BACKGROUND: Protein phosphorylation is an important reversible post-translational modifica-tion, which regulates a number of critical cellular processes. Phosphatases and kinases work in a con-certed manner to act as a "molecular switch" that turns-on or - off the regulatory processes driving the growth and development under normal circumstances, as well as responses to multiple stresses in plant system. The era of functional genomics has ushered huge amounts of information to the framework of plant systems. The comprehension of who's who in the signaling pathways is becoming clearer and the investigations challenging the conventional functions of signaling components are on a rise. Protein phosphatases have emerged as key regulators in the signaling cascades. PP2A phosphatases due to their diverse holoenzyme compositions are difficult to comprehend. CONCLUSION: In this review, we highlight the functional versatility of PP2A members, deciphered through the advances in the post-genomic era.

Arabidopsis calcineurin B-like proteins differentially regulate phosphorylation activity of CBL-interacting protein kinase 9.

Calcium (Ca2+) is a versatile and ubiquitous second messenger in all eukaryotes including plants. In response to various stimuli, cytosolic calcium concentration ([Ca2+]cyt) is increased, leading to activation of Ca2+ sensors including Arabidopsis calcineurin B-like proteins (CBLs). CBLs interact with CBL-interacting protein kinases (CIPKs) to form CBL-CIPK complexes and transduce the signal downstream in the signalling pathway. Although there are many reports on the regulation of downstream targets by CBL-CIPK module, knowledge about the regulation of upstream components by individual CIPKs is inadequate. In the present study, we have carried out a detailed biochemical characterization of CIPK9, a known regulator of K+ deficiency in Arabidopsis, with its interacting CBLs. The present study suggests that CIPK9 specifically interacts with four CBLs, i.e. CBL1, CBL2, CBL3 and CBL9, in yeast two-hybrid assays. Out of these four CBLs, CBL2 and CBL3, specifically enhance the kinase activity of CIPK9, while the CBL1 and CBL9 decrease it as examined by in vitro kinase assays. In contrast, truncated CIPK9 (CIPK9ΔR), without the CBL-interacting regulatory C-terminal region, is not differentially activated by interacting CBLs. The protein phosphorylation assay revealed that CBL2 and CBL3 serve as preferred substrates of CIPK9. CBL2- and CBL3-CIPK9 complexes show altered requirement for metal cofactors when compared with CIPK9 alone. Moreover, the autophosphorylation of constitutively active CIPK9 (CIPK9T178D) and less active CIPK9 (CIPK9T178A) in the presence of CBL2 and CBL3 was further enhanced. Our study suggests that CIPK9 differentially phosphorylates interacting CBLs, and furthermore, the kinase activity of CIPK9 is also differentially regulated by specific interacting CBLs.

Rice phytoglobins regulate responses under low mineral nutrients and abiotic stresses in Arabidopsis thaliana.

Just like animals, plants also contain haemoglobins (known as phytoglobins in plants). Plant phytoglobins (Pgbs) have been categorized into 6 different classes, namely, Phytogb0 (Pgb0), Phytogb1 (Pgb1), Phytogb2 (Pgb2), SymPhytogb (sPgb), Leghaemoglobin (Lb), and Phytogb3 (Pgb3). Among the 6 Phytogbs, sPgb and Lb have been functionally characterized, whereas understanding of the roles of other Pgbs is still evolving. In our present study, we have explored the function of 2 rice Pgbs (OsPgb1.1 and OsPgb1.2). OsPgb1.1, OsPgb1.2, OsPgb1.3, and OsPgb1.4 displayed increased level of transcript upon salt, drought, cold, and ABA treatment. The overexpression (OX) lines of OsPgb1.2 in Arabidopsis showed a tolerant phenotype in terms of better root growth in low potassium (K+ ) conditions. The expression of the known K+ gene markers such as LOX2, HAK5, and CAX3 was much higher in the OsPgb1.2 OX as compared to wild type. Furthermore, the OsPgb1.2 OX lines showed a decrease in reactive oxygen species (ROS) production and conversely an increase in the K+ content, both in root and shoot, as compared to wild type in K+ limiting condition. Our results indicated the potential involvement of OsPgb1.2 in signalling networks triggered by the nutrient deficiency stresses.

A protein phosphatase 2C, AP2C1, interacts with and negatively regulates the function of CIPK9 under potassium-deficient conditions in Arabidopsis.

Potassium (K+) is a major macronutrient required for plant growth. An adaptive mechanism to low-K+ conditions involves activation of the Ca2+ signaling network that consists of calcineurin B-like proteins (CBLs) and CBL-interacting kinases (CIPKs). The CBL-interacting protein kinase 9 (CIPK9) has previously been implicated in low-K+ responses in Arabidopsis thaliana. Here, we report a protein phosphatase 2C (PP2C), AP2C1, that interacts with CIPK9. Fluorescence resonance energy transfer (FRET), bimolecular fluorescence complementation (BiFC), and co-localization analyses revealed that CIPK9 and AP2C1 interact in the cytoplasm. AP2C1 dephosphorylates the auto-phosphorylated form of CIPK9 in vitro, presenting a regulatory mechanism for CIPK9 function. Furthermore, genetic and molecular analyses revealed that ap2c1 null mutants (ap2c1-1 and ap2c1-2) are tolerant to low-K+ conditions, retain higher K+ content, and show higher expression of K+-deficiency related genes contrary to cipk9 mutants (cipk9-1 and cipk9-2). In contrast, transgenic plants overexpressing AP2C1 were sensitive to low-K+ conditions. Thus, this study shows that AP2C1 and CIPK9 interact to regulate K+-deficiency responses in Arabidopsis. CIPK9 functions as positive regulator whereas AP2C1 acts as a negative regulator of Arabidopsis root growth and seedling development under low-K+ conditions.

Recent Advances in Substrate Identification of Protein Kinases in Plants and Their Role in Stress Management.

Protein phosphorylation-dephosphorylation is a well-known regulatory mechanism in biological systems and has become one of the significant means of protein function regulation, modulating most of the biological processes. Protein kinases play vital role in numerous cellular processes. Kinases transduce external signal into responses such as growth, immunity and stress tolerance through phosphorylation of their target proteins. In order to understand these cellular processes at the molecular level, one needs to be aware of the different substrates targeted by protein kinases. Advancement in tools and techniques has bestowed practice of multiple approaches that enable target identification of kinases. However, so far none of the methodologies has been proved to be as good as a panacea for the substrate identification. In this review, the recent advances that have been made in the identifications of putative substrates and the implications of these kinases and their substrates in stress management are discussed.

Calcineurin B-Like Protein-Interacting Protein Kinase CIPK21 Regulates Osmotic and Salt Stress Responses in Arabidopsis.

The role of calcium-mediated signaling has been extensively studied in plant responses to abiotic stress signals. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) constitute a complex signaling network acting in diverse plant stress responses. Osmotic stress imposed by soil salinity and drought is a major abiotic stress that impedes plant growth and development and involves calcium-signaling processes. In this study, we report the functional analysis of CIPK21, an Arabidopsis (Arabidopsis thaliana) CBL-interacting protein kinase, ubiquitously expressed in plant tissues and up-regulated under multiple abiotic stress conditions. The growth of a loss-of-function mutant of CIPK21, cipk21, was hypersensitive to high salt and osmotic stress conditions. The calcium sensors CBL2 and CBL3 were found to physically interact with CIPK21 and target this kinase to the tonoplast. Moreover, preferential localization of CIPK21 to the tonoplast was detected under salt stress condition when coexpressed with CBL2 or CBL3. These findings suggest that CIPK21 mediates responses to salt stress condition in Arabidopsis, at least in part, by regulating ion and water homeostasis across the vacuolar membranes.

Plant protein phosphatases 2C: from genomic diversity to functional multiplicity and importance in stress management.

Protein phosphatases (PPs) counteract kinases in reversible phosphorylation events during numerous signal transduction pathways in eukaryotes. Type 2C PPs (PP2Cs) represent the major group of PPs in plants, and recent discovery of novel abscisic acid (ABA) receptors (ABARs) has placed the PP2Cs at the center stage of the major signaling pathway regulating plant responses to stresses and plant development. Several studies have provided deep insight into vital roles of the PP2Cs in various plant processes. Global analyses of the PP2C gene family in model plants have contributed to our understanding of their genomic diversity and conservation, across plant species. In this review, we discuss the genomic and structural accounts of PP2Cs in plants. Recent advancements in their interaction paradigm with ABARs and sucrose nonfermenting related kinases 2 (SnRK2s) in ABA signaling are also highlighted. In addition, expression analyses and important roles of PP2Cs in the regulation of biotic and abiotic stress responses, potassium (K+) deficiency signaling, plant immunity and development are elaborated. Knowledge of functional roles of specific PP2Cs could be exploited for the genetic manipulation of crop plants. Genetic engineering using PP2C genes could provide great impetus in the agricultural biotechnology sector in terms of imparting desired traits, including a higher degree of stress tolerance and productivity without a yield penalty.