Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast

Genome-Wide Identification and Expression Analysis of ACA/ECAs in Capsicum annuum L

Pepper (Capsicum annuum L.) is a popular vegetable in people's daily lives. During pepper growth, calcium (Ca) is an essential macronutrient, and calcium-transporting ATPase (ACA/ECA) is a vital protein for calcium transport. However, reports on the ACA/ECA gene family in the pepper genome are lacking. Hence, we used various bioinformatics methods to identify the ACA/ECA gene family in pepper. We identified eleven CaACA/ECA-family genes in pepper. The chromosomal distribution, phylogenetic evolution, characteristics, gene collinearity, gene and protein structures, cis-acting elements, and specific expression patterns of CaACA/ECAs were analyzed, revealing evolutionary relationships and correlations between CaACA/ECAs and other species (Arabidopsis, rice, and tomato). The experimental results indicate that CaACA/ECAs are stable and hydrophobic proteins, with each of the eleven CaACA/ECA proteins containing all ten motifs. Eleven CaACA/ECA genes are unevenly distributed on the eight chromosomes, and they substantially differ in the number of exons. We found a close correlation between the ACA/ECAs of pepper, Arabidopsis, and tomato. The CaACA/ECA genes contain various plant-hormone-, growth-, and stress-related cis-acting elements. The qRT-PCR results indicate that the expression levels of the eleven CaACA/ECAs exhibit differential temporal expression patterns under various exogenous Ca2+ concentrations. These results provide a theoretical basis for further studying the function of the pepper ACA/ECA gene family and valuable information for identifying and screening genes for pepper stress tolerance breeding.

Regulating programmed cell death in plant cells: Intracellular acidification plays a pivotal role together with calcium signaling

Programmed cell death (PCD) occurs in different tissues in response to a number of different signals in plant cells. Drawing from work in several different contexts, including root-cap cell differentiation, plant response to biotic and abiotic stress, and some self-incompatibility (SI) systems, the data suggest that, despite differences, there are underlying commonalities in the early decision-making stages of PCD. Here, we focus on how 2 cellular events, increased [Ca2+]cyt levels and cytosolic acidification, appear to act as early signals involved in regulating both developmental and stimulus-induced PCD in plant cells.

The Role of Female and Male Genes in Regulating Pollen Tube Guidance in Flowering Plants

In flowering plants, fertilization is a complex process governed by precise communication between the male and female gametophytes. This review focuses on the roles of various female gametophyte cells-synergid, central, and egg cells-in facilitating pollen tube guidance and ensuring successful fertilization. Synergid cells play a crucial role in attracting the pollen tube, while the central cell influences the direction of pollen tube growth, and the egg cell is responsible for preventing polyspermy, ensuring correct fertilization. The review also examines the role of the pollen tube in this communication, highlighting the mechanisms involved in its growth regulation, including the importance of pollen tube receptors, signal transduction pathways, cell wall dynamics, and ion homeostasis. The Ca2+ concentration gradient is identified as a key factor in guiding pollen tube growth toward the ovule. Moreover, the review briefly compares these communication processes in angiosperms with those in non-flowering plants, such as mosses, ferns, and early gymnosperms, providing evolutionary insights into gametophytic signaling. Overall, this review synthesizes the current understanding of male-female gametophyte interactions and outlines future directions for research in plant reproductive biology.

Pollen-expressed RLCKs control pollen tube burst

In angiosperms, the pollen tube enters the receptive synergid cell, where it ruptures to release its cytoplasm along with two sperm cells. This interaction is complex, and the exact signal transducers that trigger the bursting of pollen tubes are not well understood. In this study, we identify three homologous receptor-like cytoplasmic kinases (RLCKs) expressed in pollen tubes of Arabidopsis, Delayed Burst 1/2/3 (DEB1/2/3), which play a crucial role in this process. These genes produce proteins localized on the plasma membrane, and their knockout causes delayed pollen tube burst and entrance of additional pollen tubes into the embryo sac due to fertilization recovery. We show that DEBs interact with the Ca2+ pump ACA9, influencing the dynamics of cytoplasmic Ca2+ in pollen tubes through phosphorylation. These results highlight the importance of DEBs as key signal transducers and the critical function of the DEB-ACA9 axis in timely pollen tube burst in synergids.

Ammonium nutrition modifies cellular calcium distribution influencing ammonium-induced growth inhibition

Proper plant growth requires balanced nutrient levels. In this study, we analyzed the relationship between ammonium (NH4+) nutrition and calcium (Ca2+) homeostasis in the leaf tissues of wild-type and mutant Arabidopsis specimens provided with different nitrogen sources (NH4+ and nitrate, NO3-). Providing plants with NH4+ as the sole nitrogen source disrupts Ca2+ homeostasis, which is essential for activating signaling pathways and maintaining the cell wall structure. The results revealed that the lower Ca2+ content in Arabidopsis leaves under NH4+ stress might result from reduced transpiration pull, which could impair root-to-shoot Ca2+ transport. Moreover, NH4+ nutrition increased the expression of genes encoding proteins responsible for exporting Ca2+ from the cytosol of leaf cells. Furthermore, overexpression of the Ca2+/H+ antiporter 1 (CAX1) gene alleviates the effects of NH4+ syndrome, including stunted growth. The oeCAX1 plants, characterized by a lower apoplastic Ca2+ level, grew better under NH4+ stress than wild-type plants. Evaluation of the mechanical properties of the leaf blades, including stiffness, strength, toughness, and extensibility, showed that the wild-type and oeCAX1 plants responded differently to the nitrogen source, highlighting the role of cell wall metabolism in inhibiting the growth of NH4+-stressed plants.

P-type calcium ATPases play important roles in biotic and abiotic stress signaling

MAIN CONCLUSION

Knowledge of Ca2+-ATPases is imperative for improving crop quality/ food security, highly threatened due to global warming. Ca2+-ATPases modulates calcium, essential for stress signaling and modulating growth, development, and immune activities. Calcium is considered a versatile secondary messenger and essential for short- and long-term responses to biotic and abiotic stresses in plants. Coordinated transport activities from both calcium influx and efflux channels are required to generate cellular calcium signals. Various extracellular stimuli cause an induction in cytosolic calcium levels. To cope with such stresses, it is important to maintain intracellular Ca2+ levels. Plants need to evolve efficient efflux mechanisms to maintain Ca2+ ion homeostasis. Plant Ca2+-ATPases are members of the P-type ATPase superfamily and localized in the plasma membrane and endoplasmic reticulum (ER). They are required for various cellular processes, including plant growth, development, calcium signaling, and even retorts to environmental stress. These ATPases play an essential role in Ca2+ homeostasis and are actively involved in Ca2+ transport. Plant Ca2+-ATPases are categorized into two major classes: type IIA and type IIB. Although these two classes of ATPases share similarities in protein sequence, they differ in their structure, cellular localization, and sensitivity to inhibitors. Due to the emerging role of Ca2+-ATPase in abiotic and biotic plant stress, members of this family may help promote agricultural improvement under stress conditions. This review provides a comprehensive overview of P-type Ca2+-ATPase, and their role in Ca2+ transport, stress signaling, and cellular homeostasis focusing on their classification, evolution, ion specificities, and catalytic mechanisms. It also describes the main aspects of the role of Ca2+-ATPase in transducing signals during plant biotic and abiotic stress responses and its role in plant development and physiology.

Sequential removal of cation/H+ exchangers reveals their additive role in elemental distribution, calcium depletion and anoxia tolerance

Multiple Arabidopsis H+ /Cation exchangers (CAXs) participate in high-capacity transport into the vacuole. Previous studies have analysed single and double mutants that marginally reduced transport; however, assessing phenotypes caused by transport loss has proven enigmatic. Here, we generated quadruple mutants (cax1-4: qKO) that exhibited growth inhibition, an 85% reduction in tonoplast-localised H+ /Ca transport, and enhanced tolerance to anoxic conditions compared to CAX1 mutants. Leveraging inductively coupled plasma mass spectrometry (ICP-MS) and synchrotron X-ray fluorescence (SXRF), we demonstrate CAX transporters work together to regulate leaf elemental content: ICP-MS analysis showed that the elemental concentrations in leaves strongly correlated with the number of CAX mutations; SXRF imaging showed changes in element partitioning not present in single CAX mutants and qKO had a 40% reduction in calcium (Ca) abundance. Reduced endogenous Ca may promote anoxia tolerance; wild-type plants grown in Ca-limited conditions were anoxia tolerant. Sequential reduction of CAXs increased mRNA expression and protein abundance changes associated with reactive oxygen species and stress signalling pathways. Multiple CAXs participate in postanoxia recovery as their concerted removal heightened changes in postanoxia Ca signalling. This work showcases the integrated and diverse function of H+ /Cation transporters and demonstrates the ability to improve anoxia tolerance through diminishing endogenous Ca levels.

Calcium signal regulated carbohydrate metabolism in wheat seedlings under salinity stress

This study aimed to explore the mechanism by which calcium (Ca) signal regulated carbohydrate metabolism and exogenous Ca alleviated salinity toxicity. Wheat seedlings were treated with sodium chloride (NaCl, 150 mM) alone or combined with 500 μM calcium chloride (CaCl2), lanthanum chloride (LaCl3) and/or ethylene glycol tetraacetic acid (EGTA) to primarily analyse carbohydrate starch and sucrose metabolism, as well as Ca signaling components. Treatment with NaCl, EGTA, or LaCl3 alone retarded wheat-seedling growth and decreased starch content accompanied by weakened ribulose-1,5-bisphosphate carboxylation/oxygenase (Rubisco) and Rubisco activase activities, as well as enhanced glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, alpha-amylase, and beta-amylase activities. However, it increased the sucrose level, up-regulated the sucrose phosphate synthase (SPS) and sucrose synthase (SuSy) activities and TaSPS and TaSuSy expression together, but down-regulated the acid invertase (SA-Inv) and alkaline/neutral invertase (A/N-Inv) activities and TaSA-Inv and TaA/N-Inv expression. Except for unchanged A/N-Inv activities and TaA/N-Inv expression, adding CaCl2 effectively blocked the sodium salt-induced changes of these parameters, which was partially eliminated by EGTA or LaCl3 presence. Furthermore, NaCl treatment also significantly inhibited Ca-dependent protein kinases and Ca2+-ATPase activities and their gene expression in wheat leaves, which was effectively relieved by adding CaCl2. Taken together, CaCl2 application effectively alleviated the sodium salt-induced retardation of wheat-seedling growth by enhancing starch anabolism and sucrose catabolism, and intracellular Ca signal regulated the enzyme activities and gene expression of starch and sucrose metabolism in the leaves of sodium salt-stressed wheat seedlings.

Calcium Ion Channels in Saccharomyces cerevisiae

Regulating calcium ion (Ca²⁺) channels to improve the cell cycle and metabolism is a promising technology, ensuring increased cell growth, differentiation, and/or productivity. In this regard, the composition and structure of Ca²⁺ channels play a vital role in controlling the gating states. In this review, Saccharomyces cerevisiae, as a model eukaryotic organism and an essential industrial microorganism, was used to discuss the effect of its type, composition, structure, and gating mechanism on the activity of Ca²⁺ channels. Furthermore, the advances in the application of Ca²⁺ channels in pharmacology, tissue engineering, and biochemical engineering are summarized, with a special focus on exploring the receptor site of Ca²⁺ channels for new drug design strategies and different therapeutic uses, targeting Ca²⁺ channels to produce functional replacement tissues, creating favorable conditions for tissue regeneration, and regulating Ca²⁺ channels to enhance biotransformation efficiency.

Resting cytosol Ca2+ level maintained by Ca2+ pumps affects environmental responses in Arabidopsis

Calcium ion transporting systems control cytosol Ca2+ levels ([Ca2+]cyt) and generate transient calcium (Ca2+) signatures that are key to environmental responses. Here, we report an impact of resting [Ca2+]cyt on plants from the functional study of calmodulin-regulated Ca2+ pumps or Ca2+-ATPases in Arabidopsis (Arabidopsis thaliana). The plasma membrane-localized pumps ACA8 (autoinhibited Ca2+-ATPase) and ACA10, as well as the vacuole-localized pumps ACA4 and ACA11, were critical in maintaining low resting [Ca2+]cyt and essential for plant survival under chilling and heat-stress conditions. Their loss-of-function mutants aca8 aca10 and aca4 aca11 had autoimmunity at normal temperatures, and this deregulated immune activation was enhanced by low temperature, leading to chilling lethality. Furthermore, these mutants showed an elevated resting [Ca2+]cyt, and a reduction of external Ca2+ lowered [Ca2+]cyt and repressed their autoimmunity and cold susceptibility. The aca8 aca10 and the aca4 aca11 mutants were also susceptible to heat, likely resulting from more closed stomata and higher leaf surface temperature than the wild type. These observations support a model in which the regulation of resting [Ca2+]cyt is critical to how plants regulate biotic and abiotic responses.

Calcium channels and transporters: Roles in response to biotic and abiotic stresses

Calcium (Ca2+) serves as a ubiquitous second messenger by mediating various signaling pathways and responding to numerous environmental conditions in eukaryotes. Therefore, plant cells have developed complex mechanisms of Ca2+ communication across the membrane, receiving the message from their surroundings and transducing the information into cells and organelles. A wide range of biotic and abiotic stresses cause the increase in [Ca2+]cyt as a result of the Ca2+ influx permitted by membrane-localized Ca2+ permeable cation channels such as CYCLIC NUCLEOTIDE-GATE CHANNELs (CNGCs), and voltage-dependent HYPERPOLARIZATION-ACTIVATED CALCIUM2+ PERMEABLE CHANNELs (HACCs), as well as GLUTAMATE RECEPTOR-LIKE RECEPTORs (GLRs) and TWO-PORE CHANNELs (TPCs). Recently, resistosomes formed by some NUCLEOTIDE-BINDING LEUCINE-RICH REPEAT RECEPTORs (NLRs) are also proposed as a new type of Ca2+ permeable cation channels. On the contrary, some Ca2+ transporting membrane proteins, mainly Ca2+-ATPase and Ca2+/H+ exchangers, are involved in Ca2+ efflux for removal of the excessive [Ca2+]cyt in order to maintain the Ca2+ homeostasis in cells. The Ca2+ efflux mechanisms mediate the wide ranges of cellular activities responding to external and internal stimuli. In this review, we will summarize and discuss the recent discoveries of various membrane proteins involved in Ca2+ influx and efflux which play an essential role in fine-tuning the processing of information for plant responses to abiotic and biotic stresses.

Evolutionary and Regulatory Pattern Analysis of Soybean Ca2+ ATPases for Abiotic Stress Tolerance

P₂-type Ca²⁺ ATPases are responsible for cellular Ca²⁺ transport, which plays an important role in plant development and tolerance to biotic and abiotic stresses. However, the role of P₂-type Ca²⁺ ATPases in stress response and stomatal regulation is still elusive in soybean. In this study, a total of 12 P₂-type Ca²⁺ ATPases genes (GmACAs and GmECAs) were identified from the genome of Glycine max. We analyzed the evolutionary relationship, conserved motif, functional domain, gene structure and location, and promoter elements of the family. Chlorophyll fluorescence imaging analysis showed that vegetable soybean leaves are damaged to different extents under salt, drought, cold, and shade stresses. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that most of the GmACAs and GmECAs are up-regulated after drought, cold, and NaCl treatment, but are down-regulated after shading stress. Microscopic observation showed that different stresses caused significant stomatal closure. Spatial location and temporal expression analysis suggested that GmACA8, GmACA9, GmACA10, GmACA12, GmACA13, and GmACA11 might promote stomatal closure under drought, cold, and salt stress. GmECA1 might regulate stomatal closure in shading stress. GmACA1 and GmECA3 might have a negative function on cold stress. The results laid an important foundation for further study on the function of P₂-type Ca²⁺ ATPase genes GmACAs and GmECAs for breeding abiotic stress-tolerant vegetable soybean.

Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.)

BACKGROUND

Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood.

RESULTS

Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61-26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain.

CONCLUSION

To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.

Proton and calcium pumping P-type ATPases and their regulation of plant responses to the environment

Plant plasma membrane H+-ATPases and Ca2+-ATPases maintain low cytoplasmic concentrations of H+ and Ca2+, respectively, and are essential for plant growth and development. These low concentrations allow plasma membrane H+-ATPases to function as electrogenic voltage stats, and Ca2+-ATPases as "off" mechanisms in Ca2+-based signal transduction. Although these pumps are autoregulated by cytoplasmic concentrations of H+ and Ca2+, respectively, they are also subject to exquisite regulation in response to biotic and abiotic events in the environment. A common paradigm for both types of pumps is the presence of terminal regulatory (R) domains that function as autoinhibitors that can be neutralized by multiple means, including phosphorylation. A picture is emerging in which some of the phosphosites in these R domains appear to be highly, nearly constantly phosphorylated, whereas others seem to be subject to dynamic phosphorylation. Thus, some sites might function as major switches, whereas others might simply reduce activity. Here, we provide an overview of the relevant transport systems and discuss recent advances that address their relation to external stimuli and physiological adaptations.

Calcium Signaling Mechanisms Across Kingdoms

Calcium (Ca²⁺) is a unique mineral that serves as both a nutrient and a signal in all eukaryotes. To maintain Ca²⁺ homeostasis for both nutrition and signaling purposes, the toolkit for Ca²⁺ transport has expanded across kingdoms of eukaryotes to encode specific Ca²⁺ signals referred to as Ca²⁺ signatures. In parallel, a large array of Ca²⁺-binding proteins has evolved as specific sensors to decode Ca²⁺ signatures. By comparing these coding and decoding mechanisms in fungi, animals, and plants, both unified and divergent themes have emerged, and the underlying complexity will challenge researchers for years to come. Considering the scale and breadth of the subject, instead of a literature survey, in this review we focus on a conceptual framework that aims to introduce to readers to the principles and mechanisms of Ca²⁺ signaling. We finish with several examples of Ca²⁺-signaling pathways, including polarized cell growth, immunity and symbiosis, and systemic signaling, to piece together specific coding and decoding mechanisms in plants versus animals. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Finger Millet [Eleusine coracana (L.) Gaertn]: An Orphan Crop With a Potential to Alleviate the Calcium Deficiency in the Semi-arid Tropics of Asia and Africa

Finger millet plays a vital role in the food and nutritional security of many people in developing countries particularly in Asia and Africa. It is a staple food for poor people in many regions of Asian (India, China, Nepal, and Sri Lanka etc.) and African (South Africa, Ethiopia, Kenya, Uganda, and Nigeria etc.) countries. Finger millet contains nutrient rich components such as dietary fibers, minerals, vitamins, and phytochemicals that include phenolic compounds with several potential health benefits. Calcium (Ca) is an important macronutrient for healthy life of plants, humans and animals. It plays an indispensable role in structure and signaling and its deficiency causes low bone density, osteoporosis, colon cancer etc. Finger millet grains contain exceptionally higher amount of Ca (>300 mg/100 g) when compared to other major cereals. Ca transporter and sensor family genes are involved in the uptake, transport and accumulation of Ca. Understanding the molecular mechanisms of Ca transporter and sensor family genes is important for growth, development and seed fortification in finger millet. Expression analysis of Ca transporter and sensor family genes has been carried out in various tissues of finger millet. Only a very little research work has been done to understand the Ca accumulation in the grains of finger millet. In this review, we discuss the nutritional importance and health benefits of finger millet. We discuss the studies on Ca sensor, accumulation and transport genes that help to improve the grains of finger millet with special reference to Ca. Improved Ca content in finger millet may help to alleviate the Ca deficiency throughout the world particularly in the semi-arid tropics of Asia and Africa.

Identification and Expression Profiling Analysis of the Cation/Ca2+ Exchanger (CCX) Gene Family: Overexpression of SlCCX1-LIKE Regulates the Leaf Senescence in Tomato Flowering Phase

Cation gradients in plant cellular compartments are maintained by the synergistic actions of various ion exchangers, pumps, and channels. Cation/Ca2+ exchanger (CCX) is one of the clades of the Ca2+/cation antiporter super family. Here, five SlCCX genes were identified in tomato. Sequence analysis indicated that SlCCXs have the conserved motifs as the CCX domain. Analysis of the expression level of each member of tomato CCX gene family under cation (Mg2+, Mn2+, Na+, and Ca2+) treatment was determined by qRT-PCR. Tomato CCX demonstrated different degrees of responding to cation treatment. Changes in SlCCX1-LIKE expression was induced by Mg2+ and Mn2+ treatment. Analysis of the expression of SlCCX genes in different tissues demonstrated that constitutive high expression of a few genes, including SlCCX1-LIKE and SlCCX5, indicated their role in tomato organ growth and development. Overexpression of SlCCX1-LIKE dramatically induced leaf senescence. Transcriptome analysis showed that genes related to ROS and several IAA signaling pathways were significantly downregulated, whereas ETH and ABA signaling pathway-related genes were upregulated in overexpression of SlCCX1-LIKE (OE-SlCCX1-LIKE) plants, compared with the wild type (WT). Moreover, overexpression of SlCCX1-LIKE plants accumulated more ROS content but less Mg2+ content. Collectively, the findings of this study provide insights into the base mechanism through which CCXs regulate leaf senescence in tomato.

Cottonseed Protein, Oil, and Minerals in Cotton (Gossypium hirsutum L.) Lines Differing in Curly Leaf Morphology

Cottonseed is an important source of protein, oil, and minerals for human health and livestock feed. Therefore, understanding the physiological and genetic traits influencing the nutrient content is critical. To our knowledge, there is no information available on the effects of leaf shape—curly leaf (CRL)—on cottonseed protein, oil, and minerals. Therefore, the objective of the current research was to investigate the effect of the curly leaf trait on cottonseed protein, oil, and minerals in cotton lines differing in leaf shape. Our hypothesis was that since leaf shape is known to be associated with nutrient uptake, assimilation, and photosynthesis process, leaf shape can influence seed protein, oil, and minerals. A two-year field experiment using two curly leaf lines (Uzbek CRL and DP 5690 CRL) and one normal leaf (DP 5690 wild type) line was conducted in 2014 and 2015 in Stoneville, MS, USA. The experiment was a randomized complete block design with three replicates. The results showed that both Uzbek CRL and DP 5690 wild type lines had higher seed oil, and nutrients N, P, K, and Mg than DP 5690 CRL. Calcium was higher in DP 5690 CRL for two years and protein was only higher than the parents in 2015. Consistent significant positive and negative correlations between some nutrients were observed, which may be due to environmental conditions, especially heat. This indicates that curly leaf trait may partially regulate the accumulation of these nutrients in seeds. The results demonstrated that leaf shape trait—curly leaf—can affect cottonseed nutritional qualities. This research is important to breeders for cotton selection for high seed oil or protein, and to other researchers to further understand the genetic impact of leaf shapes on seed nutritional quality. It is also important for scientists to use leaf shape as a tool for physiological, biochemical, and morphological research related to leaf development.

Calcium signaling is involved in diverse cellular processes in fungi

Calcium (Ca²⁺) is a universal signalling molecule of life. The Ca²⁺ signalling is an evolutionarily conserved process from prokaryotes to eukaryotes. Ca²⁺ at high concentration is deleterious to the cell; therefore, cell maintains a low resting level of intracellular free Ca²⁺ concentration ([Ca²⁺]_c). The resting [Ca²⁺]_c is tightly regulated, and a transient increase of the [Ca²⁺]_c initiates a signalling cascade in the cell. Ca²⁺ signalling plays an essential role in various processes, including growth, development, reproduction, tolerance to stress conditions, and virulence in fungi. In this review, we describe the evolutionary aspects of Ca²⁺ signalling and cell functions of major Ca²⁺ signalling proteins in different fungi.

The role of P-type IIA and P-type IIB Ca2+-ATPases in plant development and growth

As sessile organisms, plants have evolved mechanisms to adapt to variable and rapidly fluctuating environmental conditions. Calcium (Ca2+) in plant cells is a versatile intracellular second messenger that is essential for stimulating short- and long-term responses to environmental stresses through changes in its concentration in the cytosol ([Ca2+]cyt). Increases in [Ca2+]cyt direct the strength and length of these stimuli. In order to terminate them, the cells must then remove the cytosolic Ca2+ against a concentration gradient, either taking it away from the cell or storing it in organelles such as the endoplasmic reticulum (ER) and/or vacuoles. Here, we review current knowledge about the biological roles of plant P-type Ca2+-ATPases as potential actors in the regulation of this cytosolic Ca2+ efflux, with a focus the IIA ER-type Ca2+-ATPases (ECAs) and the IIB autoinhibited Ca2+-ATPases (ACAs). While ECAs are analogous proteins to animal sarcoplasmic-endoplasmic reticulum Ca2+-ATPases (SERCAs), ACAs are equivalent to animal plasma membrane-type ATPases (PMCAs). We examine their expression patterns in cells exhibiting polar growth and consider their appearance during the evolution of the plant lineage. Full details of the functions and coordination of ECAs and ACAs during plant growth and development have not yet been elucidated. Our current understanding of the regulation of fluctuations in Ca2+ gradients in the cytoplasm and organelles during growth is in its infancy, but recent technological advances in Ca2+ imaging are expected to shed light on this subject.

Calcium signaling and salt tolerance are diversely entwined in plants

In plants dehydration imposed by salinity can invoke physical changes at the interface of the plasma membrane and cell wall. Changes in hydrostatic pressure activate ion channels and cause depolarization of the plasma membrane due to disturbance in ion transport. During the initial phases of salinity stress, the relatively high osmotic potential of the rhizosphere enforces the plant to use a diverse spectrum of strategies to optimize water and nutrient uptake. Signals of salt stress are recognized by specific root receptors that activate an osmosensing network. Plant response to hyperosmotic tension is closely linked to the calcium (Ca2+) channels and interacting proteins such as calmodulin. A rapid rise in cytosolic Ca2+ levels occurs within seconds of exposure to salt stress. Plants employ multiple sensors and signaling components to sense and respond to salinity stress, of which most are closely related to Ca2+ sensing and signaling. Several tolerance strategies such as osmoprotectant accumulation, antioxidant boosting, polyaminses and nitric oxide (NO) machineries are also coordinated by Ca2+ signaling. Substantial research has been done to discover the salt stress pathway and tolerance mechanism in plants, resulting in new insights into the perception of salt stress and the downstream signaling that happens in response. Nevertheless, the role of multifunctional components such as Ca2+ has not been sufficiently addressed in the context of salt stress. In this review, we elaborate that the salt tolerance signaling pathway converges with Ca2+ signaling in diverse pathways. We summarize knowledge related to different dimensions of salt stress signaling pathways in the cell by emphasizing the administrative role of Ca2+ signaling on salt perception, signaling, gene expression, ion homeostasis and adaptive responses.

Are calcium oxalate crystals a dynamic calcium store in plants?

Calcium oxalate (CaOx) crystals occur as intravacuolar deposits in most angiosperm species. Different functions have been attributed to these crystals, some of which are very speculative, until now. Calcium regulation and homeostasis seem to be the most widespread function of CaOx crystals. Being rich in calcium, these crystals constitute a reserve of calcium for plants. However, despite being bioavailable, this reserve is functional in just a few situations due to the low mobility of calcium for phloem translocation. Therefore, CaOx crystals as a calcium reserve is a paradox because in most cases the reserve cannot be used. However, in most plants, these crystals occur in organs or tissues that will be discarded, which allows the elimination of excess calcium. This suggests that CaOx crystals have a functional role in excess calcium excretion. There is some evidence that, for calcium, this excretory function is relevant for plants since they lack an excretory system dedicated to discarding solid wastes, such as calcium salts.

Sieve element biology provides leads for research on phytoplasma lifestyle in plant hosts

Phytoplasmas reside exclusively in sieve tubes, tubular arrays of sieve element-companion cell complexes. Hence, the cell biology of sieve elements may reveal (ultra)structural and functional conditions that are of significance for survival, propagation, colonization, and effector spread of phytoplasmas. Electron microscopic images suggest that sieve elements offer facilities for mobile and stationary stages in phytoplasma movement. Stationary stages may enable phytoplasmas to interact closely with diverse sieve element compartments. The unique, reduced sieve element outfit requires permanent support by companion cells. This notion implies a future focus on the molecular biology of companion cells to understand the sieve element-phytoplasma inter-relationship. Supply of macromolecules by companion cells is channelled via specialized symplasmic connections. Ca2+-mediated gating of symplasmic corridors is decisive for the communication within and beyond the sieve element-companion cell complex and for the dissemination of phytoplasma effectors. Thus, Ca2+ homeostasis, which affects sieve element Ca2+ signatures and induces a range of modifications, is a key issue during phytoplasma infection. The exceptional physical and chemical environment in sieve elements seems an essential, though not the only factor for phytoplasma survival.

Boron Deficiency Increases Cytosolic Ca2+ Levels Mainly via Ca2+ Influx from the Apoplast in Arabidopsis thaliana Roots

Boron (B) is a micronutrient for plant development, and its deficiency alters many physiological processes. However, the current knowledge on how plants are able to sense the B-starvation signal is still very limited. Recently, it has been reported that B deprivation induces an increase in cytosolic calcium concentration ([Ca²⁺]_cyt) in Arabidopsis thaliana roots. The aim of this work was to research in Arabidopsis whether [Ca²⁺]_cyt is restored to initial levels when B is resupplied and elucidate whether apoplastic Ca²⁺ is the major source for B-deficiency-induced rise in [Ca²⁺]_cyt. The use of chemical compounds affecting Ca²⁺ homeostasis showed that the rise in root [Ca²⁺]_cyt induced by B deficiency was predominantly owed to Ca²⁺ influx from the apoplast through plasma membrane Ca²⁺ channels in an IP₃-independent manner. Furthermore, B resupply restored the root [Ca²⁺]_cyt. Interestingly, expression levels of genes encoding Ca²⁺ transporters (ACA10, plasma membrane P_IIB-type Ca²⁺-ATPase; and CAX3, vacuolar cation/proton exchanger) were upregulated by ethylene glycol tetraacetic acid (EGTA) and abscisic acid (ABA). The results pointed out that ACA10, and especially CAX3, would play a major role in the restoration of Ca²⁺ homeostasis after 24 h of B deficiency.

Calcium transport across plant membranes: mechanisms and functions

Contents Summary 49 I. Introduction 49 II. Physiological and structural characteristics of plant Ca²⁺ -permeable ion channels 50 III. Ca²⁺ extrusion systems 61 IV. Concluding remarks 64 Acknowledgements 64 References 64 SUMMARY: Calcium is an essential structural, metabolic and signalling element. The physiological functions of Ca²⁺ are enabled by its orchestrated transport across cell membranes, mediated by Ca²⁺ -permeable ion channels, Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers. Bioinformatics analysis has not determined any Ca²⁺ -selective filters in plant ion channels, but electrophysiological tests do reveal Ca²⁺ conductances in plant membranes. The biophysical characteristics of plant Ca²⁺ conductances have been studied in detail and were recently complemented by molecular genetic approaches. Plant Ca²⁺ conductances are mediated by several families of ion channels, including cyclic nucleotide-gated channels (CNGCs), ionotropic glutamate receptors, two-pore channel 1 (TPC1), annexins and several types of mechanosensitive channels. Key Ca²⁺ -mediated reactions (e.g. sensing of temperature, gravity, touch and hormones, and cell elongation and guard cell closure) have now been associated with the activities of specific subunits from these families. Structural studies have demonstrated a unique selectivity filter in TPC1, which is passable for hydrated divalent cations. The hypothesis of a ROS-Ca²⁺ hub is discussed, linking Ca²⁺ transport to ROS generation. CNGC inactivation by cytosolic Ca²⁺ , leading to the termination of Ca²⁺ signals, is now mechanistically explained. The structure-function relationships of Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers, and their regulation and physiological roles are analysed.

Unraveling Field Crops Sensitivity to Heat Stress：Mechanisms, Approaches, and Future Prospects

The astonishing increase in temperature presents an alarming threat to crop production worldwide. As evident by huge yield decline in various crops, the escalating drastic impacts of heat stress (HS) are putting global food production as well as nutritional security at high risk. HS is a major abiotic stress that influences plant morphology, physiology, reproduction, and productivity worldwide. The physiological and molecular responses to HS are dynamic research areas, and molecular techniques are being adopted for producing heat tolerant crop plants. In this article, we reviewed recent findings, impacts, adoption, and tolerance at the cellular, organellar, and whole plant level and reported several approaches that are used to improve HS tolerance in crop plants. Omics approaches unravel various mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward HS. Our review about physiological and molecular mechanisms may enlighten ways to develop thermo-tolerant cultivars and to produce crop plants that are agriculturally important in adverse climatic conditions.

Plasma Membrane-Localized Calcium Pumps and Copines Coordinately Regulate Pollen Germination and Fertility in Arabidopsis

Calcium plays an important role in plant growth, development, and response to environmental stimuli. Copines are conserved plasma membrane-localized calcium-binding proteins which regulate plant immune responses and development. In this study, we found that copine proteins BON2 and BON3, the paralogs of BON1, physically interact with calcium pumps ACA8 and ACA10 in Arabidopsis. Notably, ACA9, the closest homologue of ACA8 and ACA10 functioning in pollen tube growth, interacts with all three copines. This is consistent with the protein–protein interactions between the two protein families, the aca8, aca10, aca8/aca10, bon1/2/3 mutants as well as aca9 mutant exhibited defects on pollen germination and seed production. Taken together, plasma membrane-localized interacting calcium pumps and copines coordinately control pollen tube growth, likely through manipulating calcium efflux.

Calcium dynamics in tomato pollen tubes using the Yellow Cameleon 3.6 sensor

In vitro tomato pollen tubes show a cytoplasmic calcium gradient that oscillates with the same period as growth. Pollen tube growth requires coordination between the tip-focused cytoplasmic calcium concentration ([Ca²⁺]_cyt) gradient and the actin cytoskeleton. This [Ca²⁺]_cyt gradient is necessary for exocytosis of small vesicles, which contributes to the delivery of new membrane and cell wall at the pollen tube tip. The mechanisms that generate and maintain this [Ca²⁺]_cyt gradient are not completely understood. Here, we studied calcium dynamics in tomato (Solanum lycopersicum) pollen tubes using transgenic tomato plants expressing the Yellow Cameleon 3.6 gene under the pollen-specific promoter LAT52. We use tomato as an experimental model because tomato is a Solanaceous plant that is easy to transform, and has an excellent genomic database and genetic stock center, and unlike Arabidopsis, tomato pollen is a good system to do biochemistry. We found that tomato pollen tubes showed an oscillating tip-focused [Ca²⁺]_cyt gradient with the same period as growth. Then, we used a pharmacological approach to disturb the intracellular Ca²⁺ homeostasis, evaluating how the [Ca²⁺]_cyt gradient, pollen germination and in vitro pollen tube growth were affected. We found that cyclopiazonic acid (CPA), a drug that inhibits plant P_IIA-type Ca²⁺-ATPases, increased [Ca²⁺]_cyt in the subapical zone, leading to the disappearance of the Ca²⁺ oscillations and inhibition of pollen tube growth. In contrast, 2-aminoethoxydiphenyl borate (2-APB), an inhibitor of Ca²⁺ released from the endoplasmic reticulum to the cytoplasm in animals cells, completely reduced [Ca²⁺]_cyt at the tip of the tube, blocked the gradient and arrested pollen tube growth. Although both drugs have antagonistic effects on [Ca²⁺]_cyt, both inhibited pollen tube growth triggering the disappearance of the [Ca²⁺]_cyt gradient. When CPA and 2-APB were combined, their individual inhibitory effects on pollen tube growth were partially compensated. Finally, we found that GsMTx-4, a peptide from spider venom that blocks stretch-activated Ca²⁺ channels, inhibited tomato pollen germination and had a heterogeneous effect on pollen tube growth, suggesting that these channels are also involved in the maintenance of the [Ca²⁺]_cyt gradient. All these results indicate that tomato pollen tube is an excellent model to study calcium dynamics.

Molecular characterization and differential expression suggested diverse functions of P-type II Ca2+ATPases in Triticum aestivum L

Background

Plant P-type II Ca²⁺ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca²⁺ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca²⁺ATPase gene family in an important crop plant Triticum aestivum.

Results

Herein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum. Phylogenetic analysis revealed clustering of the homoeologous TaACA and TaECA proteins into 11 and 3 distinct groups that exhibited high sequence homology and comparable structural organization as well. Both TaACA and TaECA group proteins consisted of eight to ten transmembrane regions, and their respective domains and motifs. Prediction of sub-cellular localization was found variable for most of the proteins; moreover, it was consistent with the evolutionarily related proteins from rice and Arabidopsis in certain cases. The occurrence of assorted sets of cis-regulatory elements indicated their diverse functions. The differential expression of various TaACA and TaECA genes during developmental stages suggested their roles in growth and development. The modulated expression during heat, drought, salt and biotic stresses along with the occurrence of various stress specific cis-regulatory elements suggested their association with stress response. Interaction of these genes with numerous development and stress related genes indicated their decisive role in various biological processes and signaling.

Conclusion

T. aestivum genome consisted of a maximum of 42 P-type II Ca²⁺ATPase genes, derived from each A, B and D sub-genome. These genes may play diverse functions during plant growth and development. They may also be involved in signalling during abiotic and biotic stresses. The present study provides a comprehensive insight into the role of P-type II Ca²⁺ATPase genes in T. aestivum. However, the specific function of each gene needs to be established, which could be utilized in future crop improvement programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4792-9) contains supplementary material, which is available to authorized users.

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.

Overlapping and differential roles of plasma membrane calcium ATPases in Arabidopsis growth and environmental responses

Plant cells have multiple plasma membrane (PM)-localized calcium ATPases (ACAs) pumping calcium ions out of the cytosol. Although the involvement of some of these ACAs in plant growth and immunity has been reported, their individual and combined functions have not been fully examined. Here, we analysed the effects of single and combined mutations of four ACA genes, ACA8, ACA10, ACA12, and ACA13, in a number of processes. We found that these four genes had both overlapping and differential involvements in vegetative growth, inflorescence growth, seeds setting, disease resistance and stomatal movement. Disruption of any of these four genes reduces seed setting, indicating their contribution to the overall fitness of the plants. While ACA10 and ACA8 play major roles in vegetative growth and immunity, ACA13 and ACA12 are also involved in these processes especially when the function of ACA10 and/or ACA8 is compromised. The loss of ACA13 and ACA10 function in combination with a reduction in function of ACA8 leads to seedling death at bolting, revealing the essential role of their collective function in plant growth. Taken together, this study indicates a highly tuned calcium system involving these PM-localized calcium pumps in plant growth and environmental responses.

Differential gene expression profiling through transcriptome approach of Saccharum spontaneum L. under low temperature stress reveals genes potentially involved in cold acclimation

Sugarcane (Saccharum sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8-9 months mainly due to winter's low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant S. spontaneum IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and transcriptome was validated using qRT-PCR. The differential gene expression (DGE) analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated upon low temperature stress. A total of 170 cold responsive transcriptional factors belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a DNA binding transcriptional activation protein associated with cold acclimation and freezing tolerance was differentially upregulated. Many low temperature responsive genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity, calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially upregulated. Potential cold responsive genes and transcriptional factors involved in cold tolerance mechanism in cold tolerant S. spontaneum IND 00-1037 were identified. Together, this study provides insights into the cold tolerance to low temperature stress in S. spontaneum, thus opening applications in the genetic improvement of cold stress tolerance in sugarcane.

Mechanisms of cytosolic calcium elevation in plants: the role of ion channels, calcium extrusion systems and NADPH oxidase-mediated 'ROS-Ca2+ Hub'

Elevation in the cytosolic free calcium is crucial for plant growth, development and adaptation. Calcium influx into plant cells is mediated by Ca2+ depolarisation-activated, hyperpolarisation-activated and voltage-independent Ca2+-permeable channels (DACCs, HACCs and VICCs respectively). These channels are encoded by the following gene families: (1) cyclic nucleotide-gated channels (CNGCs), (2) ionotropic glutamate receptors (GLRs), (3) annexins, (4) 'mechanosensitive channels of small (MscS) conductance'-like channels (MSLs), (5) 'mid1-complementing activity' channels (MCAs), Piezo channels, and hyperosmolality-induced [Ca2+]cyt. channel 1 (OSCA1). Also, a 'tandem-pore channel1' (TPC1) catalyses Ca2+ efflux from the vacuole in response to the plasma membrane-mediated Ca2+ elevation. Recent experimental data demonstrated that Arabidopsis thaliana (L.) Heynh. CNGCs 2, 5-10, 14, 16 and 18, GLRs 1.2, 3.3, 3.4, 3.6 and 3.7, TPC1, ANNEXIN1, MSL9 and MSL10,MCA1 and MCA2, OSCA1, and some their homologues counterparts in other species, are responsible for Ca2+ currents and/or cytosolic Ca2+ elevation. Extrusion of Ca2+ from the cytosol is mediated by Ca2+-ATPases and Ca2+/H+ exchangers which were recently examined at the level of high resolution crystal structure. Calcium-activated NADPH oxidases and reactive oxygen species (ROS)-activated Ca2+ conductances form a self-amplifying 'ROS-Ca2+hub', enhancing and transducing Ca2+ and redox signals. The ROS-Ca2+ hub contributes to physiological reactions controlled by ROS and Ca2+, demonstrating synergism and unity of Ca2+ and ROS signalling mechanisms.

Genome-wide analysis of wheat calcium ATPases and potential role of selected ACAs and ECAs in calcium stress

BACKGROUND

P₂- type calcium ATPases (ACAs-auto inhibited calcium ATPases and ECAs-endoplasmic reticulum calcium ATPases) belong to the P- type ATPase family of active membrane transporters and are significantly involved in maintaining accurate levels of Ca²⁺, Mn²⁺ and Zn²⁺ in the cytosol as well as playing a very important role in stress signaling, stomatal opening and closing and pollen tube growth. Here we report the identification and possible role of some of these ATPases from wheat.

RESULTS

In this study, ACA and ECA sequences of six species (belonging to Poaceae) were retrieved from different databases and a phylogenetic tree was constructed. A high degree of evolutionary relatedness was observed among P₂ sequences characterized in this study. Members of the respective groups from different plant species were observed to fall under the same clade. This pattern highlights the common ancestry of P_2- type calcium ATPases. Furthermore, qRT-PCR was used to analyse the expression of selected ACAs and ECAs from Triticum aestivum (wheat) under calcium toxicity and calcium deficiency. The data indicated that expression of ECAs is enhanced under calcium stress, suggesting possible roles of these ATPases in calcium homeostasis in wheat. Similarly, the expression of ACAs was significantly different in plants grown under calcium stress as compared to plants grown under control conditions. This gives clues to the role of ACAs in signal transduction during calcium stress in wheat.

CONCLUSION

Here we concluded that wheat genome consists of nine P_2B and three P_2A -type calcium ATPases. Moreover, gene loss events in wheat ancestors lead to the loss of a particular homoeolog of a gene in wheat. To elaborate the role of these wheat ATPases, qRT-PCR was performed. The results indicated that when plants are exposed to calcium stress, both P_2A and P_2B gene expression get enhanced. This further gives clues about the possible role of these ATPases in wheat in calcium management. These findings can be useful in future for genetic manipulations as well as in wheat genome annotation process.

Regulation of calcium and magnesium homeostasis in plants: from transporters to signaling network

Calcium (Ca²⁺) and magnesium (Mg²⁺) are the most abundant divalent cations in plants. As a nutrient and a signaling ion, Ca²⁺ levels in the cell are tightly controlled by an array of channels and carriers that provide mechanistic basis for Ca²⁺ homeostasis and the generation of Ca²⁺ signals. Although a family of CorA-type Mg²⁺ transporters plays a key role in controlling Mg²⁺ homeostasis in plants, more components are yet to be identified. Ca²⁺ and Mg²⁺ appear to have antagonistic interactions in plant cells, and therefore plants depend on a homeostatic balance between Ca²⁺ and Mg²⁺ for optimal growth and development. Maintenance of such a balance in response to changing nutrient status in the soil emerges as a critical feature of plant mineral nutrition. Studies have uncovered signaling mechanisms that perceive nutrient status as a signal and regulate transport activities as adaptive responses. This 'nutrient sensing' network is exemplified by the Ca²⁺-dependent CBL (calcineurin B-like)-CIPK (CBL-interacting protein kinase) pathway that serves as a major link between environmental nutrient status and transport activities. In this review, we analyze the recent literature on Ca²⁺ and Mg²⁺ transport systems and their regulation and provide our perspectives on future research.

Proteomics analysis reveals the molecular mechanism underlying the transition from primary to secondary growth of poplar

Wood is the most important natural source of energy and also provides fuel and fiber. Considering the significant role of wood, it is critical to understand how wood is formed. Integration of knowledge about wood development at the cellular and molecular levels will allow more comprehensive understanding of this complex process. In the present study, we used a comparative proteomic approach to investigate the differences in protein profiles between primary and secondary growth in young poplar stems using tandem mass tag (TMT)-labeling. More than 10,816 proteins were identified, and, among these, 3106 proteins were differentially expressed during primary to secondary growth. Proteomic data were validated using a combination of histochemical staining, enzyme activity assays, and quantitative real-time PCR. Bioinformatics analysis revealed that these differentially expressed proteins are related to various metabolic pathways, mainly including signaling, phytohormones, cell cycle, cell wall, secondary metabolism, carbohydrate and energy metabolism, and protein metabolism as well as redox and stress pathways. This large proteomics dataset will be valuable for uncovering the molecular changes occurring during the transition from primary to secondary growth. Further, it provides new and accurate information for tree breeding to modify wood properties.

Differential Roles for Six P-Type Calcium ATPases in Sustaining Intracellular Ca2+ Homeostasis, Asexual Cycle and Environmental Fitness of Beauveria bassiana

A global insight into the roles of multiple P-type calcium ATPase (CA) pumps in sustaining the life of a filamentous fungal pathogen is lacking. Here we elucidated the functions of five CA pumps (Eca1, Spf1 and PmcA/B/C) following previous characterization of Pmr1 in Beauveria bassiana, a fungal insect pathogen. The fungal CA pumps interacted at transcriptional level, at which singular deletions of five CA genes depressed eca1 expression by 76–98% and deletion of spf1 resulted in drastic upregulation of four CA genes by 36–50-fold. Intracellular Ca²⁺ concentration increased differentially in most deletion mutants exposed to the stresses of Ca²⁺, EDTA chelator, and/or endoplasmic reticulum and calcineurin inhibitors, accompanied with their changed sensitivities to not only the mentioned agents but also Fe²⁺, Cu²⁺ and Zn²⁺. Liquid culture acidification was delayed in the Δspf1, Δpmr1 and ΔpmcA mutants, coinciding well with altered levels of their extracellular lactic and oxalic acids. Moreover, all deletion mutants showed differential defects in conidial germination, vegetative growth, conidiation capacity, antioxidant activity, cell wall integrity, conidial UV-B resistance and/or virulence. Our results provide the first global insight into differential roles for six CA pumps in sustaining intracellular Ca²⁺ level, asexual cycle and environmental fitness of B. bassiana.

Transcript, protein and metabolite temporal dynamics in the CAM plant Agave

Already a proven mechanism for drought resilience, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency by means of an inverse (compared to C₃ and C₄ photosynthesis) day/night pattern of stomatal closure/opening to shift CO₂ uptake to the night, when evapotranspiration rates are low. A systems-level understanding of temporal molecular and metabolic controls is needed to define the cellular behaviour underpinning CAM. Here, we report high-resolution temporal behaviours of transcript, protein and metabolite abundances across a CAM diel cycle and, where applicable, compare the observations to the well-established C₃ model plant Arabidopsis. A mechanistic finding that emerged is that CAM operates with a diel redox poise that is shifted relative to that in Arabidopsis. Moreover, we identify widespread rescheduled expression of genes associated with signal transduction mechanisms that regulate stomatal opening/closing. Controlled production and degradation of transcripts and proteins represents a timing mechanism by which to regulate cellular function, yet knowledge of how this molecular timekeeping regulates CAM is unknown. Here, we provide new insights into complex post-transcriptional and -translational hierarchies that govern CAM in Agave. These data sets provide a resource to inform efforts to engineer more efficient CAM traits into economically valuable C₃ crops.

The ataxia related G1107D mutation of the plasma membrane Ca2+ ATPase isoform 3 affects its interplay with calmodulin and the autoinhibition process

The plasma membrane Ca²⁺ ATPases (PMCA pumps) have a long, cytosolic C-terminal regulatory region where a calmodulin-binding domain (CaM-BD) is located. Under basal conditions (low Ca²⁺), the C-terminal tail of the pump interacts with autoinhibitory sites proximal to the active center of the enzyme. In activating conditions (i.e., high Ca²⁺), Ca²⁺-bound CaM displaces the C-terminal tail from the autoinhibitory sites, restoring activity. We have recently identified a G1107D replacement within the CaM-BD of isoform 3 of the PMCA pump in a family affected by X-linked congenital cerebellar ataxia. Here, we investigate the effects of the G1107D replacement on the interplay of the mutated CaM-BD with both CaM and the pump core, by combining computational, biochemical and functional approaches. We provide evidence that the affinity of the isolated mutated CaM-BD for CaM is significantly reduced with respect to the wild type (wt) counterpart, and that the ability of CaM to activate the pump in vitro is thus decreased. Multiscale simulations support the conclusions on the detrimental effect of the mutation, indicating reduced stability of the CaM binding. We further show that the G1107D replacement impairs the autoinhibition mechanism of the PMCA3 pump as well, as the introduction of a negative charge perturbs the contacts between the CaM-BD and the pump core. Thus, the mutation affects both the ability of the pump to optimally transport Ca²⁺ in the activated state, and the autoinhibition mechanism in its resting state.

Tissue-specific root ion profiling reveals essential roles of the CAX and ACA calcium transport systems in response to hypoxia in Arabidopsis

Waterlogging is a major abiotic stress that limits the growth of plants. The crucial role of Ca(2+) as a second messenger in response to abiotic and biotic stimuli has been widely recognized in plants. However, the physiological and molecular mechanisms of Ca(2+) distribution within specific cell types in different root zones under hypoxia is poorly understood. In this work, whole-plant physiological and tissue-specific Ca(2+) changes were studied using several ACA (Ca(2+)-ATPase) and CAX (Ca(2+)/proton exchanger) knock-out Arabidopsis mutants subjected to waterlogging treatment. In the wild-type (WT) plants, several days of hypoxia decreased the expression of ACA8, CAX4, and CAX11 by 33% and 50% compared with the control. The hypoxic treatment also resulted in an up to 11-fold tissue-dependent increase in Ca(2+) accumulation in root tissues as revealed by confocal microscopy. The increase was much higher in stelar cells in the mature zone of Arabidopsis mutants with loss of function for ACA8, ACA11, CAX4, and CAX11 In addition, a significantly increased Ca(2+) concentration was found in the cytosol of stelar cells in the mature zone after hypoxic treatment. Three weeks of waterlogging resulted in dramatic loss of shoot biomass in cax11 plants (67% loss in shoot dry weight), while in the WT and other transport mutants this decline was only 14-22%. These results were also consistent with a decline in leaf chlorophyll fluorescence (F v/F m). It is suggested that CAX11 plays a key role in maintaining cytosolic Ca(2+) homeostasis and/or signalling in root cells under hypoxic conditions.

On a quest for stress tolerance genes: membrane transporters in sensing and adapting to hostile soils

Abiotic stresses such as salinity, drought, and flooding severely limit food and fibre production and result in penalties of in excess of US$100 billion per annum to the agricultural sector. Improved abiotic stress tolerance to these environmental constraints via traditional or molecular breeding practices requires a good understanding of the physiological and molecular mechanisms behind roots sensing of hostile soils, as well as downstream signalling cascades to effectors mediating plant adaptive responses to the environment. In this review, we discuss some common mechanisms conferring plant tolerance to these three major abiotic stresses. Central to our discussion are: (i) the essentiality of membrane potential maintenance and ATP production/availability and its use for metabolic versus adaptive responses; (ii) reactive oxygen species and Ca(2+) 'signatures' mediating stress signalling; and (iii) cytosolic K(+) as the common denominator of plant adaptive responses. We discuss in detail how key plasma membrane and tonoplast transporters are regulated by various signalling molecules and processes observed in plants under stress conditions (e.g. changes in membrane potential; cytosolic pH and Ca(2+); reactive oxygen species; polyamines; abscisic acid) and how these stress-induced changes are related to expression and activity of specific ion transporters. The reported results are then discussed in the context of strategies for breeding crops with improved abiotic stress tolerance. We also discuss a classical trade-off between tolerance and yield, and possible avenues for resolving this dilemma.

Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis

Calcium (Ca(2+) ) is vital for plant growth, development, hormone response and adaptation to environmental stresses, yet the mechanisms regulating plant cytosolic Ca(2+) homeostasis are not fully understood. Here, we characterize an Arabidopsis Ca(2+) -regulated Na(+) /Ca(2+) exchanger AtNCL that regulates Ca(2+) and multiple physiological processes. AtNCL was localized to the tonoplast in yeast and plant cells. AtNCL appeared to mediate sodium (Na(+) ) vacuolar sequestration and meanwhile Ca(2+) release. The EF-hand domains within AtNCL regulated Ca(2+) binding and transport of Ca(2+) and Na(+) . Plants with diminished AtNCL expression were more tolerant to high CaCl2 but more sensitive to both NaCl and auxin; heightened expression of AtNCL rendered plants more sensitive to CaCl2 but tolerant to NaCl. AtNCL expression appeared to be regulated by the diurnal rhythm and suppressed by auxin. DR5::GUS expression and root responses to auxin were altered in AtNCL mutants. The auxin-induced suppression of AtNCL was attenuated in SLR/IAA14 and ARF6/8 mutants. The mutants with altered AtNCL expression also altered flowering time and FT and CO expression; FT may mediate AtNCL-regulated flowering time change. Therefore, AtNCL is a vacuolar Ca(2+) -regulated Na(+) /Ca(2+) exchanger that regulates auxin responses and flowering time.

Mining candidate genes associated with powdery mildew resistance in cucumber via super-BSA by specific length amplified fragment (SLAF) sequencing

BACKGROUND

Powdery mildew (PM) is the most common fungal disease of cucumber and other cucurbit crops, while breeding the PM-resistant materials is the effective way to defense this disease, and the recent development of modern genetics and genomics make us aware of that studying the resistance genes is the essential way to breed the PM high-resistance plant. With the ever increasing throughput of next-generation sequencing (NGS), the development of specific length amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for large-scale de novo SNP discovery is gradually applied for functional gene mining. Here we combined the bulked segregant analysis (BSA) with SLAF-seq to identify candidate genes associated with PM resistance in cucumber.

METHODS

A segregating population comprising 251 F2 individuals was developed using H136 (female parent) as susceptible parent and BK2 (male parent) as resistance donor. After PMR test, total genomic DNA was prepared from each plant. Systemic genomic analysis of the GC content, repeat sequence, etc. was carried out by prediction software SLAF_Predict to establish condition to ensure the uniformity and density of the molecular markers. After samples were gel purified, SLAFs were generated at Biomarker Technologies Corporation in Beijing. Based on SLAF tags and the PMR test result, the hot region were annotated.

RESULTS

A total of 73,100 high-quality SLAF tags with an average depth of 99.11× were sequenced. Among these, 5,355 polymorphic tags were identified with a polymorphism rate of 7.34 %, including 7.09 % SNPs and other polymorphism types. Finally, 140 associated SLAFs were identified, and two main Hot Regions were detected on chromosome 1 and 6, which contained five genes invovled in defense response, toxin metabolism, cell stress response, and injury response in cucumber.

CONCLUSIONS

Associated markers identified by super-BSA in this study, could not only speed up the study of the PMR genes, but also provide a feasible solution for breeding the marker-assisted PMR cucumber. Moreover, this study could also be extended to any other species with reference genome.

A rice tonoplastic calcium exchanger, OsCCX2 mediates Ca2+/cation transport in yeast

In plant cell, cations gradient in cellular compartments is maintained by synergistic action of various exchangers, pumps and channels. The Arabidopsis exchanger family members (AtCCX3 and AtCCX5) were previously studied and belong to CaCA (calcium cation exchangers) superfamily while none of the rice CCXs has been functionally characterized for their cation transport activities till date. Rice genome encode four CCXs and only OsCCX2 transcript showed differential expression under abiotic stresses and Ca(2+) starvation conditions. The OsCCX2 localized to tonoplast and suppresses the Ca(2+) sensitivity of K667 (low affinity Ca(2+) uptake deficient) yeast mutant under excess CaCl2 conditions. In contrast to AtCCXs, OsCCX2 expressing K667 yeast cells show tolerance towards excess Na(+), Li(+), Fe(2+), Zn(2+) and Co(2+) and suggest its ability to transport both mono as well as divalent cations in yeast. Additionally, in contrast to previously characterized AtCCXs, OsCCX2 is unable to complement yeast trk1trk2 double mutant suggesting inability to transport K(+) in yeast system. These finding suggest that OsCCX2 having distinct metal transport properties than previously characterized plant CCXs. OsCCX2 can be used as potential candidate for enhancing the abiotic stress tolerance in plants as well as for phytoremediation of heavy metal polluted soil.

Dissecting blue light signal transduction pathway in leaf epidermis using a pharmacological approach

Blue light signalling pathway in broad bean leaf epidermal cells includes key membrane transporters: plasma- and endomembrane channels and pumps of H (+) , Ca (2+) and K (+) ions, and plasma membrane redox system. Blue light signalling pathway in epidermal tissue isolated from the abaxial side of fully developed Vicia faba leaves was dissected by measuring the effect of inhibitors of second messengers on net K(+), Ca(2+) and H(+) fluxes using non-invasive ion-selective microelectrodes (the MIFE system). Switching the blue light on-off caused transient changes of the ion fluxes. The effects of seven groups of inhibitors were tested in this study: CaM antagonists, ATPase inhibitors, Ca(2+) anatagonists or chelators, agents affecting IP3 formation, redox system inhibitors, inhibitors of endomembrane Ca(2+) transport systems and an inhibitor of plasma membrane Ca(2+)-permeable channels. Most of the inhibitors had a significant effect on steady-state (basal) net fluxes, as well as on the magnitude of the transient ion flux responses to blue light fluctuations. The data presented in this study suggest that redox signalling and, specifically, plasma membrane NADPH oxidase and coupled Ca(2+) and K(+) fluxes play an essential role in blue light signal transduction.

Low temperature tolerance in plants: Changes at the protein level

Low temperature (LT) is one of several important environmental stresses influencing plant performance and distribution. Adaptation to LT is a highly dynamic stress-response phenomenon and involves complex cross-talk between different regulatory levels. Although plants differ in their sensitivity to LT, in temperate species low nonfreezing temperatures cause noticeable alterations in various biochemical and physiological processes that can potentially improve freezing tolerance. This adaptation is associated with changes in the expression pattern of genes and their protein products. Proteins are the major players in most cellular events and are directly involved in plant LT responses, thereby proteome analysis could help uncover additional novel proteins associated with LT tolerance. Proteomics is recommended as an appropriate strategy for complementing transcriptome level changes and characterizing translational and post-translational regulations. In this review, we considered alterations in the expression and accumulation of proteins in response to LT stress in the three major cereal crops produced worldwide (wheat, barley, and rice). LT stress down-regulates many photosynthesis-related proteins. On the contrary, pathways/protein sets that are up-regulated by LT include carbohydrate metabolism (ATP formation), ROS scavenging, redox adjustment, cell wall remodelling, cytoskeletal rearrangements, cryoprotection, defence/detoxification. These modifications are common adaptation reactions also observed in the plant model Arabidopsis, thus representing key potential biomarkers and critical intervention points for improving LT tolerance of crop plants in cold regions with short summers. We believe that an assessment of the proteome within a broad time frame and during the different phenological stages may disclose the molecular mechanisms related to the developmental regulation of LT tolerance and facilitate the progress of genetically engineered stress-resistant plant varieties.

Sodium efflux in plant roots: what do we really know?

The efflux of sodium (Na(+)) ions across the plasma membrane of plant root cells into the external medium is surprisingly poorly understood. Nevertheless, Na(+) efflux is widely regarded as a major mechanism by which plants restrain the rise of Na(+) concentrations in the cytosolic compartments of root cells and, thus, achieve a degree of tolerance to saline environments. In this review, several key ideas and bodies of evidence concerning root Na(+) efflux are summarized with a critical eye. Findings from decades past are brought to bear on current thinking, and pivotal studies are discussed, both "purely physiological", and also with regard to the SOS1 protein, the only major Na(+) efflux transporter that has, to date, been genetically characterized. We find that the current model of rapid transmembrane sodium cycling (RTSC), across the plasma membrane of root cells, is not adequately supported by evidence from the majority of efflux studies. An alternative hypothesis cannot be ruled out, that most Na(+) tracer efflux from the root in the salinity range does not proceed across the plasma membrane, but through the apoplast. Support for this idea comes from studies showing that Na(+) efflux, when measured with tracers, is rarely affected by the presence of inhibitors or the ionic composition in saline rooting media. We conclude that the actual efflux of Na(+) across the plasma membrane of root cells may be much more modest than what is often reported in studies using tracers, and may predominantly occur in the root tips, where SOS1 expression has been localized.