The ACA4 gene of Arabidopsis encodes a vacuolar membrane calcium pump that improves salt tolerance in yeast

Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice

Ca²⁺ homeostasis is required to maintain a delicate balance of cytosolic Ca²⁺ during normal and adverse growth conditions. Various Ca²⁺ transporters actively participate to maintain this delicate balance especially during abiotic stresses and developmental events in plants. In this study, we present a genome-wide account, detailing expression profiles, subcellular localization and functional analysis of rice Ca²⁺ transport elements. Exhaustive in silico data mining and analysis resulted in the identification of 81 Ca²⁺ transport element genes, which belong to various groups such as Ca²⁺-ATPases (pumps), exchangers, channels, glutamate receptor homologs and annexins. Phylogenetic analysis revealed that different Ca²⁺ transporters are evolutionarily conserved across different plant species. Comprehensive expression analysis by gene chip microarray and quantitative RT-PCR revealed that a substantial proportion of Ca²⁺ transporter genes were expressed differentially under abiotic stresses (salt, cold and drought) and reproductive developmental stages (panicle and seed) in rice. These findings suggest a possible role of rice Ca²⁺ transporters in abiotic stress and development triggered signaling pathways. Subcellular localization of Ca²⁺ transporters from different groups in Nicotiana benthamiana revealed their variable localization to different compartments, which could be their possible sites of action. Complementation of Ca²⁺ transport activity of K616 yeast mutant by Ca²⁺-ATPase OsACA7 and involvement in salt tolerance verified its functional behavior. This study will encourage detailed characterization of potential candidate Ca²⁺ transporters for their functional role in planta.

Receptor-mediated transport of vacuolar proteins: a critical analysis and a new model

In this article we challenge the widely accepted view that receptors for soluble vacuolar proteins (VSRs) bind to their ligands at the trans-Golgi network (TGN) and transport this cargo via clathrin-coated vesicles (CCV) to a multivesicular prevacuolar compartment. This notion, which we term the "classical model" for vacuolar protein sorting, further assumes that low pH in the prevacuolar compartment causes VSR-ligand dissociation, resulting in a retromer-mediated retrieval of the VSRs to the TGN. We have carefully evaluated the literature with respect to morphology and function of the compartments involved, localization of key components of the sorting machinery, and conclude that there is little direct evidence in its favour. Firstly, unlike mammalian cells where the sorting receptor for lysosomal hydrolases recognizes its ligand in the TGN, the available data suggests that in plants VSRs interact with vacuolar cargo ligands already in the endoplasmic reticulum. Secondly, the evidence supporting the packaging of VSR-ligand complexes into CCV at the TGN is not conclusive. Thirdly, the prevacuolar compartment appears to have a pH unsuitable for VSR-ligand dissociation and lacks the retromer core and the sorting nexins needed for VSR recycling. We present an alternative model for protein sorting in the TGN that draws attention to the much overlooked role of Ca(2+) in VSR-ligand interactions and which may possibly also be a factor in the sequestration of secretory proteins.

Calcium Signals from the Vacuole

The vacuole is by far the largest intracellular Ca(2+) store in most plant cells. Here, the current knowledge about the molecular mechanisms of vacuolar Ca(2+) release and Ca(2+) uptake is summarized, and how different vacuolar Ca(2+) channels and Ca(2+) pumps may contribute to Ca(2+) signaling in plant cells is discussed. To provide a phylogenetic perspective, the distribution of potential vacuolar Ca(2+) transporters is compared for different clades of photosynthetic eukaryotes. There are several candidates for vacuolar Ca(2+) channels that could elicit cytosolic [Ca(2+)] transients. Typical second messengers, such as InsP₃ and cADPR, seem to trigger vacuolar Ca(2+) release, but the molecular mechanism of this Ca(2+) release still awaits elucidation. Some vacuolar Ca(2+) channels have been identified on a molecular level, the voltage-dependent SV/TPC1 channel, and recently two cyclic-nucleotide-gated cation channels. However, their function in Ca(2+) signaling still has to be demonstrated. Ca(2+) pumps in addition to establishing long-term Ca(2+) homeostasis can shape cytosolic [Ca(2+)] transients by limiting their amplitude and duration, and may thus affect Ca(2+) signaling.

ATP protects against FITC labeling of Solanum lycopersicon and Arabidopsis thaliana Ca2+-ATPase ATP binding domains

Ca(2+)-ATPases are integral membrane proteins that actively transport Ca(2+) against substantial concentration gradients in eukaryotic cells. This active transport is energized by coupling ion translocation with ATP hydrolysis. In order to better understand this coupling mechanism, we studied the nucleotide specificities of isolated ATP binding domains (ABDs) of Solanum lycopersicon Ca(2+)-ATPase (LCA), a type IIA non-calmodulin regulated P-type pump found in tomato plants that is very similar to mammalian sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA), and Arabidopsis Ca(2+)-ATPase, isoform 2 (ACA2), a type IIB calmodulin regulated P-type ATPase found in the endoplasmic reticulum of Arabidopsis cells. We used nucleotide protection against FITC labeling as a measure of binding since both LCA and ACA contained the KGAP(S,V,F)E motif, which has been shown to be modified by fluorescein isothiocyanate (FITC) in P-type pumps from animal cells. We demonstrated that the heterologously expressed GST-tagged ABDs from both LCA and ACA2 were modified by FITC and that ATP protects against this modification. Moreover, GTP was able to reduce, but not eliminate, the level of FITC labeling in both ABD constructs, suggesting that these plant pumps may also bind GTP with low affinity, which is in contrast to mammalian SERCA and PMCA type pumps which do not bind GTP.

Global calcium transducer P-type Ca²⁺-ATPases open new avenues for agriculture by regulating stress signalling

Food security is in danger under the continuous growing threat of various stresses including climate change and global warming, which ultimately leads to a reduction in crop yields. Calcium plays a very important role in many signal transduction pathways including stress signalling. Different extracellular stimuli trigger increases in cytosolic calcium, which is detrimental to plants. To cope with such stresses, plants need to develop efficient efflux mechanisms to maintain ionic homeostasis. The Ca(2+)-ATPases are members of the P-type ATPase superfamily, which perform many fundamental processes in organisms by actively transporting ions across cellular membranes. In recent years, many studies have revealed that, as well as efflux mechanisms, Ca(2+)-ATPases also play critical roles in sensing calcium fluctuations and relaying downstream signals by activating definitive targets, thus modulating corresponding metabolic pathways. As calcium-activated calmodulin (CaM) is reported to play vital roles in stress tolerance, the presence of a unique CaM-binding site in type IIB Ca(2+)-ATPases indicates their potential role in biotic as well as abiotic stress tolerance. The key roles of Ca(2+)-ATPases in transport systems and stress signalling in cellular homeostasis are addressed in this review. A complete understanding of plant defence mechanisms under stress will allow bioengineering of improved crop plants, which will be crucial for food security currently observed worldwide in the context of global climate changes. Overall, this article covers classification, evolution, structural aspects of Ca(2+)-ATPases, and their emerging roles in plant stress signalling.

Genome-wide analysis of plant-type II Ca(2+)ATPases gene family from rice and Arabidopsis: potential role in abiotic stresses

The Plant Ca(2+)ATPases are members of the P-type ATPase superfamily and play essential roles in pollen tube growth, vegetative development, inflorescence architecture, stomatal opening or closing as well as transport of Ca(2+), Mn(2+) and Zn(2+). Their role in abiotic stress adaptation by activation of different signaling pathways is emerging. In Arabidopsis, the P-type Ca(2+)ATPases can be classified in two distinct groups: type IIA (ECA) and type IIB (ACA). The availability of rice genome sequence allowed performing a genome-wide search for P-type Ca(2+)ATPases proteins, and the comparison of the identified proteins with their homologs in Arabidopsis model plant. In the present study, we identified the P-type II Ca(2+)ATPases from rice by analyzing their phylogenetic relationship, multiple alignment, cis-regulatory elements, protein domains, motifs and homology percentage. The phylogenetic analysis revealed that rice type IIA Ca(2+)ATPases clustered with Arabidopsis type IIA Ca(2+)ATPases and showed high sequence similarity within the group, whereas rice type IIB Ca(2+)ATPases presented variable sequence similarities with Arabidopsis type IIB members. The protein homology modeling, identification of putative transmembrane domains and conserved motifs of rice P-type II Ca(2+)ATPases provided information on their functions and structural architecture. The analysis of P-type II Ca(2+)ATPases promoter regions in rice showed multiple stress-induced cis-acting elements. The expression profile analysis indicated vital roles of P-type II Ca(2+)ATPases in stress signaling, plant development and abiotic stress responses. The comprehensive analysis and expression profiling provided a critical platform for functional characterization of P-type II Ca(2+)ATPase genes that could be applied in engineering crop plants with modified calcium signaling and homeostatic pathways.

Reproductive organ and vascular specific promoter of the rice plasma membrane Ca2+ATPase mediates environmental stress responses in plants

BACKGROUND

Plasma membrane Ca(2+)ATPase is a transport protein in the plasma membrane of cells and helps in removal of calcium (Ca(2+)) from the cell, hence regulating Ca(2+) level within cells. Though plant Ca(2+)ATPases have been shown to be involved in plant stress responses but their promoter regions have not been well studied.

RESULTS

The 1478 bp promoter sequence of rice plasma membrane Ca(2+)ATPase contains cis-acting elements responsive to stresses and plant hormones. To identify the functional region, serial deletions of the promoter were fused with the GUS sequence and four constructs were obtained. These were differentially activated under NaCl, PEG cold, methyl viologen, abscisic acid and methyl jasmonate treatments. We demonstrated that the rice plasma membrane Ca(2+)ATPase promoter is responsible for vascular-specific and multiple stress-inducible gene expression. Only full-length promoter showed specific GUS expression under stress conditions in floral parts. High GUS activity was observed in roots with all the promoter constructs. The -1478 to -886 bp flanking region responded well upon treatment with salt and drought. Only the full-length promoter presented cold-induced GUS expression in leaves, while in shoots slight expression was observed for -1210 and -886 bp flanking region. The -1210 bp deletion significantly responded to exogenous methyl viologen and abscisic acid induction. The -1210 and -886 bp flanking region resulted in increased GUS activity in leaves under methyl jasmonate treatments, whereas in shoots the -886 bp and -519 bp deletion gave higher expression. Salicylic acid failed to induce GUS activities in leaves for all the constructs.

CONCLUSIONS

The rice plasma membrane Ca(2+)ATPase promoter is a reproductive organ-specific as well as vascular-specific. This promoter contains drought, salt, cold, methyl viologen, abscisic acid and methyl jasmonate related cis-elements, which regulated gene expression. Overall, the tissue-specificity and inducible nature of this promoter could grant wide applicability in plant biotechnology.

Energization of vacuolar transport in plant cells and its significance under stress

The plant vacuole is of prime importance in buffering environmental perturbations and in coping with abiotic stress caused by, for example, drought, salinity, cold, or UV. The large volume, the efficient integration in anterograde and retrograde vesicular trafficking, and the dynamic equipment with tonoplast transporters enable the vacuole to fulfill indispensible functions in cell biology, for example, transient and permanent storage, detoxification, recycling, pH and redox homeostasis, cell expansion, biotic defence, and cell death. This review first focuses on endomembrane dynamics and then summarizes the functions, assembly, and regulation of secretory and vacuolar proton pumps: (i) the vacuolar H(+)-ATPase (V-ATPase) which represents a multimeric complex of approximately 800 kDa, (ii) the vacuolar H(+)-pyrophosphatase, and (iii) the plasma membrane H(+)-ATPase. These primary proton pumps regulate the cytosolic pH and provide the driving force for secondary active transport. Carriers and ion channels modulate the proton motif force and catalyze uptake and vacuolar compartmentation of solutes and deposition of xenobiotics or secondary compounds such as flavonoids. ABC-type transporters directly energized by MgATP complement the transport portfolio that realizes the multiple functions in stress tolerance of plants.

New insights into the transport mechanisms in plant vacuoles

The vacuole is the largest compartment in plant cells, often occupying more than 80% of the total cell volume. This organelle accumulates a large variety of endogenous ions, metabolites, and xenobiotics. The compartmentation of divergent substances is relevant for a wide range of biological processes, such as the regulation of stomata movement, defense mechanisms against herbivores, flower coloration, etc. Progress in molecular and cellular biology has revealed that a large number of transporters and channels exist at the tonoplast. In recent years, various biochemical and physiological functions of these proteins have been characterized in detail. Some are involved in maintaining the homeostasis of ions and metabolites, whereas others are related to defense mechanisms against biotic and abiotic stresses. In this review, we provide an updated inventory of vacuolar transport mechanisms and a comprehensive summary of their physiological functions.

Sweet potato calmodulin SPCAM is involved in salt stress-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression

The sweet potato calmodulin gene, SPCAM, was previously cloned and shown to participate in ethephon-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression. In this report, an association of SPCAM with NaCl stress is reported. Expression of SPCAM was significantly enhanced by NaCl on days 1 and 2 after salt treatment in a dose-dependent manner and drastically decreased again on the third day. Starting on day 6, salt stress also remarkably promoted leaf senescence, H₂O₂ elevation and senescence-associated gene expression in a dose-dependent manner. These salt stress-mediated effects were strongly inhibited by chlorpromazine, a calmodulin inhibitor, and the chlorpromazine-induced repression could be reversed by exogenous application of purified calmodulin fusion protein. These data suggest an involvement of calmodulin in salt stress-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression in sweet potato. Exogenous application of SPCAM fusion protein alone, however, did not significantly accelerate leaf senescence and senescence-associated gene expression, but only showed a slight effect 12 days after treatment. These data suggest that additional components are involved in salt stress-mediated leaf senescence in sweet potato, possibly induced by and coordinated with SPCAM. In conclusion, the sweet potato calmodulin gene is NaCl-inducible and participates in salt stress-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression.

Regulation of the major vacuolar Ca²⁺ transporter genes, by intercellular Ca²⁺ concentration and abiotic stresses, in tip-burn resistant Brassica oleracea

Calcium is an essential plant macronutrient that has unique structural and signaling roles related to tip-burn disorder in Brassica spp. crops. For two types of cabbage inbred lines, tip-burn susceptible and resistant, we measured and compared major macronutrient cations, including Ca(2+), in leaves. In both lines, Ca(2+), Mg(2+), Na(+), and K(+), accumulated more in leaf base than in leaf apex. Ca(2+) and K(+) were >2 times more abundant in the tip-burn resistant line, while Na(+) was higher in the susceptible line. Ca(2+) differences between the two lines resulted from differential accumulation of calcium into cell vacuoles. We profiled major vacuolar Ca(2+) transporters, in both cabbage lines, by growth time and intercellular Ca(2+) concentration. Expression pattern of several Ca(2+) transporter genes differed between tip-burn susceptible and resistant lines by growth time points. We also identified promoter regions of the major Ca(2+) vacuole transporter genes, CAX1, ACA4, and ACA11, which displayed hormonal, light and defense-related cis-acting regulatory elements. Finally, transporter genes in the two cabbage lines responded differently to abiotic stresses, demonstrating diversity in gene regulation among orthologous genes.

In and out of the plant storage vacuole

The plant storage vacuole is involved in a wide variety of metabolic functions a great many of which necessitate the transport of substances across the tonoplast. Some solutes, depending on the origin, have to cross the plasma membrane as well. The cell is equipped with a complex web of transport systems, cellular routes, and unique intracellular environments that support their transport and accumulation against a concentration gradient. These are capable of processing a diverse nature of substances of distinct sizes, chemical properties, and origins. In this review we describe the various mechanism involved in solute transport into the vacuole of storage cells with special emphasis placed on solutes arriving through the apoplast. Transport of solutes from the cytosol to the vacuole is carried out by tonoplast-bound ABC transporters, solute/H(+) antiporters, and ion channels whereas transport from the apoplast requires additional plasma membrane-bound solute/H(+) symporters and fluid-phase endocytosis. In addition, and based on new evidence accumulated within the last decade, we re-evaluate the current notion of extracellular solute uptake as partially based on facilitated diffusion, and offer an alternative interpretation that involves membrane bound transporters and fluid-phase endocytosis. Finally, we make several assertions in regards to solute export from the vacuole as predicted by the limited available data suggesting that both membrane-bound carriers and vesicle mediated exocytosis are involved during solute mobilization.

Vacuolar transporters in their physiological context

Vacuoles in vegetative tissues allow the plant surface to expand by accumulating energetically cheap inorganic osmolytes, and thereby optimize the plant for absorption of sunlight and production of energy by photosynthesis. Some specialized cells, such as guard cells and pulvini motor cells, exhibit rapid volume changes. These changes require the rapid release and uptake of ions and water by the vacuole and are a prerequisite for plant survival. Furthermore, seed vacuoles are important storage units for the nutrients required for early plant development. All of these fundamental processes rely on numerous vacuolar transporters. During the past 15 years, the transporters implicated in most aspects of vacuolar function have been identified and characterized. Vacuolar transporters appear to be integrated into a regulatory network that controls plant metabolism. However, little is known about the mode of action of these fundamental processes, and deciphering the underlying mechanisms remains a challenge for the future.

Calcium efflux systems in stress signaling and adaptation in plants

Transient cytosolic calcium ([Ca(2+)](cyt)) elevation is an ubiquitous denominator of the signaling network when plants are exposed to literally every known abiotic and biotic stress. These stress-induced [Ca(2+)](cyt) elevations vary in magnitude, frequency, and shape, depending on the severity of the stress as well the type of stress experienced. This creates a unique stress-specific calcium "signature" that is then decoded by signal transduction networks. While most published papers have been focused predominantly on the role of Ca(2+) influx mechanisms to shaping [Ca(2+)](cyt) signatures, restoration of the basal [Ca(2+)](cyt) levels is impossible without both cytosolic Ca(2+) buffering and efficient Ca(2+) efflux mechanisms removing excess Ca(2+) from cytosol, to reload Ca(2+) stores and to terminate Ca(2+) signaling. This is the topic of the current review. The molecular identity of two major types of Ca(2+) efflux systems, Ca(2+)-ATPase pumps and Ca(2+)/H(+) exchangers, is described, and their regulatory modes are analyzed in detail. The spatial and temporal organization of calcium signaling networks is described, and the importance of existence of intracellular calcium microdomains is discussed. Experimental evidence for the role of Ca(2+) efflux systems in plant responses to a range of abiotic and biotic factors is summarized. Contribution of Ca(2+)-ATPase pumps and Ca(2+)/H(+) exchangers in shaping [Ca(2+)](cyt) signatures is then modeled by using a four-component model (plasma- and endo-membrane-based Ca(2+)-permeable channels and efflux systems) taking into account the cytosolic Ca(2+) buffering. It is concluded that physiologically relevant variations in the activity of Ca(2+)-ATPase pumps and Ca(2+)/H(+) exchangers are sufficient to fully describe all the reported experimental evidence and determine the shape of [Ca(2+)](cyt) signatures in response to environmental stimuli, emphasizing the crucial role these active efflux systems play in plant adaptive responses to environment.

Membrane transport, sensing and signaling in plant adaptation to environmental stress

Plants are generally well adapted to a wide range of environmental conditions. Even though they have notably prospered in our planet, stressful conditions such as salinity, drought and cold or heat, which are increasingly being observed worldwide in the context of the ongoing climate changes, limit their growth and productivity. Behind the remarkable ability of plants to cope with these stresses and still thrive, sophisticated and efficient mechanisms to re-establish and maintain ion and cellular homeostasis are involved. Among the plant arsenal to maintain homeostasis are efficient stress sensing and signaling mechanisms, plant cell detoxification systems, compatible solute and osmoprotectant accumulation and a vital rearrangement of solute transport and compartmentation. The key role of solute transport systems and signaling proteins in cellular homeostasis is addressed in the present work. The full understanding of the plant cell complex defense mechanisms under stress may allow for the engineering of more tolerant plants or the optimization of cultivation practices to improve yield and productivity, which is crucial at the present time as food resources are progressively scarce.

Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation

Gas exchange in plants is controlled by guard cells, specialized cells acting as turgor pressure-driven valves. Malate is one of the major anions accumulated inside the vacuole during stomatal opening counteracting the positive charge of potassium. AtALMT6, a member of the aluminum-activated malate transporter family, is expressed in guard cells of leaves and stems as well as in flower organs of Arabidopsis thaliana. An AtALMT6-GFP fusion protein was targeted to the vacuolar membrane both in transient and stable expression systems. Patch-clamp experiments on vacuoles isolated from AtALMT6-GFP over-expressing Arabidopsis plants revealed large inward-rectifying malate currents only in the presence of micromolar cytosolic calcium concentrations. Further analyses showed that vacuolar pH and cytosolic malate regulate the threshold of activation of AtALMT6-mediated currents. The interplay of these two factors determines the AtALMT6 function as a malate influx or efflux channel depending on the tonoplast potential. Guard cell vacuoles isolated from Atalmt6 knock-out plants displayed reduced malate currents compared with wild-type vacuoles. This reduction, however, was not accompanied by phenotypic differences in the stomatal movements in knock-out plants, probably because of functional redundancy of malate transporters in guard cell vacuoles.

Experimental and computational approaches for the study of calmodulin interactions

Ca(2+), a universal messenger in eukaryotes, plays a major role in signaling pathways that control many growth and developmental processes in plants as well as their responses to various biotic and abiotic stresses. Cellular changes in Ca(2+) in response to diverse signals are recognized by protein sensors that either have their activity modulated or that interact with other proteins and modulate their activity. Calmodulins (CaMs) and CaM-like proteins (CMLs) are Ca(2+) sensors that have no enzymatic activity of their own but upon binding Ca(2+) interact and modulate the activity of other proteins involved in a large number of plant processes. Protein-protein interactions play a key role in Ca(2+)/CaM-mediated in signaling pathways. In this review, using CaM as an example, we discuss various experimental approaches and computational tools to identify protein-protein interactions. During the last two decades hundreds of CaM-binding proteins in plants have been identified using a variety of approaches ranging from simple screening of expression libraries with labeled CaM to high-throughput screens using protein chips. However, the high-throughput methods have not been applied to the entire proteome of any plant system. Nevertheless, the data provided by these screens allows the development of computational tools to predict CaM-interacting proteins. Using all known binding sites of CaM, we developed a computational method that predicted over 700 high confidence CaM interactors in the Arabidopsis proteome. Most (>600) of these are not known to bind calmodulin, suggesting that there are likely many more CaM targets than previously known. Functional analyses of some of the experimentally identified Ca(2+) sensor target proteins have uncovered their precise role in Ca(2+)-mediated processes. Further studies on identifying novel targets of CaM and CMLs and generating their interaction network - "calcium sensor interactome" - will help us in understanding how Ca(2+) regulates a myriad of cellular and physiological processes.

Regulating cytoplasmic calcium homeostasis can reduce aluminum toxicity in yeast

Our previous study suggested that increased cytoplasmic calcium (Ca) signals may mediate aluminum (Al) toxicity in yeast (Saccharomyces cerevisiae). In this report, we found that a yeast mutant, pmc1, lacking the vacuolar calcium ion (Ca²⁺) pump Ca²⁺-ATPase (Pmc1p), was more sensitive to Al treatment than the wild-type strain. Overexpression of either PMC1 or an anti-apoptotic factor, such as Bcl-2, Ced-9 or PpBI-1, decreased cytoplasmic Ca²⁺ levels and rescued yeast from Al sensitivity in both the wild-type and pmc1 mutant. Moreover, pretreatment with the Ca²⁺ chelator BAPTA-AM sustained cytoplasmic Ca²⁺ at low levels in the presence of Al, effectively making the cells more tolerant to Al exposure. Quantitative RT-PCR revealed that the expression of calmodulin (CaM) and phospholipase C (PLC), which are in the Ca²⁺ signaling pathway, was down-regulated under Al stress. This effect was largely counteracted when cells overexpressed anti-apoptotic Ced-9 or were pretreated with BAPTA-AM. Taken together, our results suggest that the negative regulation of Al-induced cytoplasmic Ca signaling is a novel mechanism underlying internal resistance to Al toxicity.

Differential salt tolerance in seedlings derived from dimorphic seeds of Atriplex centralasiatica: from physiology to molecular analysis

Seed dimorphism provides plants with alternative strategies for survival in unfavorable environments. Here, we investigated the physiological responses and differential gene expression caused by salinity exposure in Atriplex centralasiatica plants grown from the two different seed morphs. Seedlings derived from yellow seeds (YS) showed a greater salt tolerance than those derived from brown seeds (BS). Salt treatment induced nitric oxide (NO) synthesis in roots, and seedlings derived from YS produced greater amounts of NO than did those from BS. Analyses of NO scavenging during salt stress revealed that NO contributed to the differential salt tolerance in seedlings derived from the two seed morphs by modulating antioxidative enzyme activity, hydrogen peroxide accumulation and the ion equilibrium. We also applied transcriptomics and subsequent microarray analysis to evaluate the differential gene expression during salt treatment. These genes encoded proteins related to osmotic and ionic homeostasis, redox equilibrium and signal transduction. A select group of genes including GH3.3, CAT1/2, TIP1, SIHP1 and EXP1 were further confirmed with RT-PCR analysis. These results revealed that the enhanced salt tolerance of seedlings from YS appeared to be governed by a superior ability to achieve ionic homeostasis and redox equilibrium, a rapid response to salt stress, and ultimately better growth potential. NO serves as a vital regulator in these processes.

The plant Ca2+ -ATPase repertoire: biochemical features and physiological functions

Ca(2+)-ATPases are P-type ATPases that use the energy of ATP hydrolysis to pump Ca(2+) from the cytoplasm into intracellular compartments or into the apoplast. Plant cells possess two types of Ca(2+) -pumping ATPase, named ECAs (for ER-type Ca(2+)-ATPase) and ACAs (for auto-inhibited Ca(2+)-ATPase). Each type comprises different isoforms, localised on different membranes. Here, we summarise available knowledge of the biochemical characteristics and the physiological role of plant Ca(2+)-ATPases, greatly improved after gene identification, which allows both biochemical analysis of single isoforms through heterologous expression in yeast and expression profiling and phenotypic analysis of single isoform knock-out mutants.

The plant vacuole: emitter and receiver of calcium signals

This review portrays the plant vacuole as both a source and a target of Ca(2+) signals. In plants, the vacuole represents a Ca(2+) store of enormous size and capacity. Total and free Ca(2+) concentrations in the vacuole vary with plant species, cell type, and environment, which is likely to have an impact on vacuolar function and the release of vacuolar Ca(2+). It is known that cytosolic Ca(2+) signals are often generated by release of the ion from internal stores, but in very few cases has a role of the vacuole been directly demonstrated. Biochemical and electrophysical studies have provided evidence for the operation of ligand- and voltage-gated Ca(2+)-permeable channels in the vacuolar membrane. The underlying molecular mechanisms are largely unknown with one exception: the slow vacuolar channel, encoded by TPC1, is the only vacuolar Ca(2+)-permeable channel cloned to date. However, due to its complex regulation and its low selectivity amongst cations, the role of this channel in Ca(2+) signalling is still debated. Many transport proteins at the vacuolar membrane are also targets of Ca(2+) signals, both by direct binding of Ca(2+) and by Ca(2+)-dependent phosphorylation. This enables the operation of feedback mechanisms and integrates vacuolar transport systems in the wider signalling network of the plant cell.

Vacuolar Ca(2+) uptake

Calcium transporters that mediate the removal of Ca(2+) from the cytosol and into internal stores provide a critical role in regulating Ca(2+) signals following stimulus induction and in preventing calcium toxicity. The vacuole is a major calcium store in many organisms, particularly plants and fungi. Two main pathways facilitate the accumulation of Ca(2+) into vacuoles, Ca(2+)-ATPases and Ca(2+)/H(+) exchangers. Here I review the biochemical and regulatory features of these transporters that have been characterised in yeast and plants. These Ca(2+) transport mechanisms are compared with those being identified from other vacuolated organisms including algae and protozoa. Studies suggest that Ca(2+) uptake into vacuoles and other related acidic Ca(2+) stores occurs by conserved mechanisms which developed early in evolution.

Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis

The physiological role and mechanism of nutrient storage within vacuoles of specific cell types is poorly understood. Transcript profiles from Arabidopsis thaliana leaf cells differing in calcium concentration ([Ca], epidermis <10 mM versus mesophyll >60 mM) were compared using a microarray screen and single-cell quantitative PCR. Three tonoplast-localized Ca(2+) transporters, CAX1 (Ca(2+)/H(+)-antiporter), ACA4, and ACA11 (Ca(2+)-ATPases), were identified as preferentially expressed in Ca-rich mesophyll. Analysis of respective loss-of-function mutants demonstrated that only a mutant that lacked expression of both CAX1 and CAX3, a gene ectopically expressed in leaves upon knockout of CAX1, had reduced mesophyll [Ca]. Reduced capacity for mesophyll Ca accumulation resulted in reduced cell wall extensibility, stomatal aperture, transpiration, CO(2) assimilation, and leaf growth rate; increased transcript abundance of other Ca(2+) transporter genes; altered expression of cell wall-modifying proteins, including members of the pectinmethylesterase, expansin, cellulose synthase, and polygalacturonase families; and higher pectin concentrations and thicker cell walls. We demonstrate that these phenotypes result from altered apoplastic free [Ca(2+)], which is threefold greater in cax1/cax3 than in wild-type plants. We establish CAX1 as a key regulator of apoplastic [Ca(2+)] through compartmentation into mesophyll vacuoles, a mechanism essential for optimal plant function and productivity.

Roles of enzymatic and nonenzymatic antioxidants in plants during abiotic stress

Reactive oxygen species (ROS) are produced in plants as byproducts during many metabolic reactions, such as photosynthesis and respiration. Oxidative stress occurs when there is a serious imbalance between the production of ROS and antioxidant defense. Generation of ROS causes rapid cell damage by triggering a chain reaction. Cells have evolved an elaborate system of enzymatic and nonenzymatic antioxidants which help to scavenge these indigenously generated ROS. Various enzymes involved in ROS-scavenging have been manipulated, over expressed or downregulated to add to the present knowledge and understanding the role of the antioxidant systems. The present article reviews the manipulation of enzymatic and nonenzymatic antioxidants in plants to enhance the environmental stress tolerance and also throws light on ROS and redox signaling, calcium signaling, and ABA signaling.

Disruption of the vacuolar calcium-ATPases in Arabidopsis results in the activation of a salicylic acid-dependent programmed cell death pathway

Calcium (Ca(2+)) signals regulate many aspects of plant development, including a programmed cell death pathway that protects plants from pathogens (hypersensitive response). Cytosolic Ca(2+) signals result from a combined action of Ca(2+) influx through channels and Ca(2+) efflux through pumps and cotransporters. Plants utilize calmodulin-activated Ca(2+) pumps (autoinhibited Ca(2+)-ATPase [ACA]) at the plasma membrane, endoplasmic reticulum, and vacuole. Here, we show that a double knockout mutation of the vacuolar Ca(2+) pumps ACA4 and ACA11 in Arabidopsis (Arabidopsis thaliana) results in a high frequency of hypersensitive response-like lesions. The appearance of macrolesions could be suppressed by growing plants with increased levels (greater than 15 mm) of various anions, providing a method for conditional suppression. By removing plants from a conditional suppression, lesion initials were found to originate primarily in leaf mesophyll cells, as detected by aniline blue staining. Initiation and spread of lesions could also be suppressed by disrupting the production or accumulation of salicylic acid (SA), as shown by combining aca4/11 mutations with a sid 2 (for salicylic acid induction-deficient2) mutation or expression of the SA degradation enzyme NahG. This indicates that the loss of the vacuolar Ca(2+) pumps by itself does not cause a catastrophic defect in ion homeostasis but rather potentiates the activation of a SA-dependent programmed cell death pathway. Together, these results provide evidence linking the activity of the vacuolar Ca(2+) pumps to the control of a SA-dependent programmed cell death pathway in plants.

Arabidopsis PCR2 is a zinc exporter involved in both zinc extrusion and long-distance zinc transport

Plants strictly regulate the uptake and distribution of Zn, which is essential for plant growth and development. Here, we show that Arabidopsis thaliana PCR2 is essential for Zn redistribution and Zn detoxification. The pcr2 loss-of-function mutant was compromised in growth, both in Zn-excessive and -deficient conditions. The roots of pcr2 accumulated more Zn than did control plants, whereas the roots of plants overexpressing PCR2 contained less Zn, indicating that PCR2 removes Zn from the roots. Consistent with a role for PCR2 as a Zn-efflux transporter, PCR2 reduced the intracellular concentration of Zn when expressed in yeast cells. PCR2 is located mainly in epidermal cells and in the xylem of young roots, while it is expressed in epidermal cells in fully developed roots. Zn accumulated in the epidermis of the roots of pcr2 grown under Zn-limiting conditions, whereas it was found in the stele of wild-type roots. The transport pathway mediated by PCR2 does not seem to overlap with that mediated by the described Zn translocators (HMA2 and HMA4) since the growth of pcr2 hma4 double and pcr2 hma2 hma4 triple loss-of-function mutants was more severely inhibited than the individual single knockout mutants, both under conditions of excess or deficient Zn. We propose that PCR2 functions as a Zn transporter essential for maintaining an optimal Zn level in Arabidopsis.

A functional calcium-transporting ATPase encoded by chlorella viruses

Calcium-transporting ATPases (Ca²⁺ pumps) are major players in maintaining calcium homeostasis in the cell and have been detected in all cellular organisms. Here, we report the identification of two putative Ca²⁺ pumps, M535L and C785L, encoded by chlorella viruses MT325 and AR158, respectively, and the functional characterization of M535L. Phylogenetic and sequence analyses place the viral proteins in group IIB of P-type ATPases even though they lack a typical feature of this class, a calmodulin-binding domain. A Ca²⁺ pump gene is present in 45 of 47 viruses tested and is transcribed during virus infection. Complementation analysis of the triple yeast mutant K616 confirmed that M535L transports calcium ions and, unusually for group IIB pumps, also manganese ions. In vitro assays show basal ATPase activity. This activity is inhibited by vanadate, but, unlike that of other Ca²⁺ pumps, is not significantly stimulated by either calcium or manganese. The enzyme forms a ³²P-phosphorylated intermediate, which is inhibited by vanadate and not stimulated by the transported substrate Ca²⁺, thus confirming the peculiar properties of this viral pump. To our knowledge this is the first report of a functional P-type Ca²⁺-transporting ATPase encoded by a virus.

Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system

Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress.

[Plant calcium sensors in osmotic signaling]

Calcium is an essential second messenger that mediates plant responses to developmental and environmental clues. Specific calcium signatures are sensed and decoded by diverse Ca(2+) sensors to induce appropriate downstream responses. Calmodulin is the most important and conserved Ca(2+) transducer in all eukaryotes. Additional plant-specific sensors are encoded by multigene families, i.e. calcineurin B-like and Ca(2+)-dependent protein kinases. Calcium binding induces structural conformational changes in Ca(2+) sensors, resulting in the modification of protein interaction or enzymatic activity. Activated Ca(2+) sensors subsequently regulate downstream targets which can be involved in signal transduction, like protein kinases and transcription factors, or in direct cell protection from stress damages, like ion transporters or detoxification enzymes. Ca(2+) plays an important role in osmotic signaling triggered by cold, drought and salinity. The multiplicity of plant calcium sensors associated with diverse cellular targets constitute a tightly regulated signaling network that induces specific stress responses to improve plant survival under unfavourable conditions.

Ca(2+)-dependent activation of guard cell anion channels, triggered by hyperpolarization, is promoted by prolonged depolarization

Rapid stomatal closure is driven by the activation of S-type anion channels in the plasma membrane of guard cells. This response has been linked to Ca(2+) signalling, but the impact of transient Ca(2+) signals on S-type anion channel activity remains unknown. In this study, transient elevation of the cytosolic Ca(2+) level was provoked by voltage steps in guard cells of intact Nicotiana tabacum plants. Changes in the activity of S-type anion channels were monitored using intracellular triple-barrelled micro-electrodes. In cells kept at a holding potential of -100 mV, voltage steps to -180 mV triggered elevation of the cytosolic free Ca(2+) concentration. The increase in the cytosolic Ca(2+) level was accompanied by activation of S-type anion channels. Guard cell anion channels were activated by Ca(2+) with a half maximum concentration of 515 nm (SE = 235) and a mean saturation value of -349 pA (SE = 107) at -100 mV. Ca(2+) signals could also be evoked by prolonged (100 sec) depolarization of the plasma membrane to 0 mV. Upon returning to -100 mV, a transient increase in the cytosolic Ca(2+) level was observed, activating S-type channels without measurable delay. These data show that cytosolic Ca(2+) elevation can activate S-type anion channels in intact guard cells through a fast signalling pathway. Furthermore, prolonged depolarization to 0 mV alters the activity of Ca(2+) transport proteins, resulting in an overshoot of the cytosolic Ca(2+) level after returning the membrane potential to -100 mV.

Acidic calcium stores open for business: expanding the potential for intracellular Ca2+ signaling

Changes in cytosolic calcium concentration are crucial for a variety of cellular processes in all cells. It has long been appreciated that calcium is stored and released from intracellular calcium stores such as the endoplasmic reticulum. However, emerging evidence indicates that calcium is also dynamically regulated by a seemingly disparate collection of acidic organelles. In this paper, we review the defining features of these 'acidic calcium stores' and highlight recent progress in understanding the mechanisms of uptake and release of calcium from these stores. We also examine the nature of calcium buffering within the stores, and summarize the physiological and pathophysiological significance of these ubiquitous organelles in calcium signaling.

Making sense out of Ca(2+) signals: their role in regulating stomatal movements

Plant cells maintain high Ca(2+) concentration gradients between the cytosol and the extracellular matrix, as well as intracellular compartments. During evolution, the regulatory mechanisms, maintaining low cytosolic free Ca(2+) concentrations, most likely provided the backbone for the development of Ca(2+)-dependent signalling pathways. In this review, the current understanding of molecular mechanisms involved in Ca(2+) homeostasis of plants cells is evaluated. The question is addressed to which extent the mechanisms, controlling the cytosolic Ca(2+) concentration, are linked to Ca(2+)-based signalling. A large number of environmental stimuli can evoke Ca(2+) signals, but the Ca(2+)-induced responses are likely to differ depending on the stimulus applied. Two mechanisms are put forward to explain signal specificity of Ca(2+)-dependent responses. A signal may evoke a specific Ca(2+) signature that is recognized by downstream signalling components. Alternatively, Ca(2+) signals are accompanied by Ca(2+)-independent signalling events that determine the specificity of the response. The existence of such parallel-acting pathways explains why guard cell responses to abscisic acid (ABA) can occur in the absence, as well as in the presence, of Ca(2+) signals. Future research may shed new light on the relation between parallel acting Ca(2+)-dependent and -independent events, and may provide insights in their evolutionary origin.

Calcium signals: the lead currency of plant information processing

Ca(2+) signals are core transducers and regulators in many adaptation and developmental processes of plants. Ca(2+) signals are represented by stimulus-specific signatures that result from the concerted action of channels, pumps, and carriers that shape temporally and spatially defined Ca(2+) elevations. Cellular Ca(2+) signals are decoded and transmitted by a toolkit of Ca(2+) binding proteins that relay this information into downstream responses. Major transduction routes of Ca(2+) signaling involve Ca(2+)-regulated kinases mediating phosphorylation events that orchestrate downstream responses or comprise regulation of gene expression via Ca(2+)-regulated transcription factors and Ca(2+)-responsive promoter elements. Here, we review some of the remarkable progress that has been made in recent years, especially in identifying critical components functioning in Ca(2+) signal transduction, both at the single-cell and multicellular level. Despite impressive progress in our understanding of the processing of Ca(2+) signals during the past years, the elucidation of the exact mechanistic principles that underlie the specific recognition and conversion of the cellular Ca(2+) currency into defined changes in protein-protein interaction, protein phosphorylation, and gene expression and thereby establish the specificity in stimulus response coupling remain to be explored.

Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply

The ability to adjust growth and development to the availability of mineral nutrients in the soil is an essential life skill of plants but the underlying signaling pathways are poorly understood. In Arabidopsis thaliana, shortage of potassium (K) induces a number of genes related to the phytohormone jasmonic acid (JA). Using comparative microarray analysis of wild-type and coi1-16 mutant plants, we classified transcriptional responses to K with respect to their dependence on COI1, a central component of oxylipin signaling. Expression profiles obtained in a short-term experiment clearly distinguished between COI1-dependent and COI1-independent K-responsive genes, and identified both known and novel targets of JA-COI1-signaling. During long-term K-deficiency, coi-16 mutants displayed de novo responses covering similar functions as COI1-targets except for defense. A putative role of JA for enhancing the defense potential of K-deficient plants was further supported by the observation that plants grown on low K were less damaged by thrips than plants grown with sufficient K.

The language of calcium signaling

Ca(2+) signals are a core regulator of plant cell physiology and cellular responses to the environment. The channels, pumps, and carriers that underlie Ca(2+) homeostasis provide the mechanistic basis for generation of Ca(2+) signals by regulating movement of Ca(2+) ions between subcellular compartments and between the cell and its extracellular environment. The information encoded within the Ca(2+) transients is decoded and transmitted by a toolkit of Ca(2+)-binding proteins that regulate transcription via Ca(2+)-responsive promoter elements and that regulate protein phosphorylation. Ca(2+)-signaling networks have architectural structures comparable to scale-free networks and bow tie networks in computing, and these similarities help explain such properties of Ca(2+)-signaling networks as robustness, evolvability, and the ability to process multiple signals simultaneously.

Differential expression of candidate salt-tolerance genes in the halophyte Helianthus paradoxus and its glycophyte progenitors H. annuus and H. petiolaris (Asteraceae)

Adaptation to different habitats is considered to be a major force in the generation of organismal diversity. Understanding the genetic mechanisms that produce such adaptations will provide insights into long-standing questions in evolutionary biology and, at the same time, improve predictions of plant responses to changing environmental conditions. Here we used semiquantitative RT-PCR to study the expression of eight candidate salt-tolerance genes in leaves of the highly salt-tolerant diploid hybrid species Helianthus paradoxus and its salt-sensitive progenitor species H. annuus and H. petiolaris. Samples were collected after germination and growth under four different treatments: nonsaline (control), near-natural saline, saline with increased K(+), and saline with decreased Mg(2+) and Ca(2+). Three individuals from three populations per species were used. The hybrid species H. paradoxus constitutively under- or overexpressed genes related to potassium and calcium transport (homologues of KT1, KT2, ECA1), suggesting that these genes may contribute to the adaptation of H. paradoxus to salinity. In two other genes, variation between populations within species exceeded species level variation. Furthermore, homologues of the potassium transporter HAK8 and of a transcriptional regulator were generally overexpressed in saline treatments, suggesting that these genes are involved in sustained growth under saline conditions in Helianthus.

Ca2+ signatures: the role of Ca2+-ATPases

Calcium ions (Ca²⁺) are well known signaling molecules in plant signal transduction pathways including the response to abiotic stress. Particular stimuli cause specific transient elevations in cytosolic Ca²⁺ ([Ca²⁺]_cyt) with a stimulus-dependent amplitude and temporal pattern. These Ca²⁺ transients, known as Ca²⁺ signatures, rely on the counteractive activities of Ca²⁺-permeable channels and Ca²⁺-transporting proteins. Whereas the channels causing an increase in [Ca²⁺]_cyt were partly identified, direct evidence for the role of Ca²⁺-transporting proteins in the determination of Ca²⁺ signatures was missing. We recently reported on the functional characterization of a stress-responsive P_IIB-type Ca²⁺-ATPase (PCA1) from the moss Physcomitrella patens. This study revealed an essential role of this Ca²⁺ pump in the adjustment of salt stress tolerance. Most strikingly, the generation of a specific Ca²⁺ signature in response to salt was abolished in Physcomitrella mutant lines lacking PCA1 activity. Thus, we can provide a direct link for the function of a Ca²⁺-ATPase in the generation of a specific Ca²⁺ signature in plants.

Regulation of macronutrient transport

In addition to light, water and CO(2), plants require a number of mineral nutrients, in particular the macronutrients nitrogen, sulphur, phosphorus, magnesium, calcium and potassium. After uptake from the soil by the root system they are either immediately assimilated into organic compounds or distributed within the plant for usage in different tissues. A good understanding of how the transport of macronutrients into and between plant cells is adjusted to different environmental conditions is essential to achieve an increase of nutrient usage efficiency and nutritional value in crops. Here, we review the current state of knowledge regarding the regulation of macronutrient transport, taking both a physiological and a mechanistic approach. We first describe how nutrient transport is linked to environmental and internal cues such as nutrient, carbon and water availability via hormonal, metabolic and physical signals. We then present information on the molecular mechanisms for regulation of transport proteins, including voltage gating, auto-inhibition, interaction with other proteins, oligomerization and trafficking. Combining of evidence for different nutrients, signals and regulatory levels creates an opportunity for making new connections within a large body of data, and thus contributes to an integrative understanding of nutrient transport.

Shaping the calcium signature

In numerous plant signal transduction pathways, Ca2+ is a versatile second messenger which controls the activation of many downstream actions in response to various stimuli. There is strong evidence to indicate that information encoded within these stimulus-induced Ca2+ oscillations can provide signalling specificity. Such Ca2+ signals, or 'Ca2+ signatures', are generated in the cytosol, and in noncytosolic locations including the nucleus and chloroplast, through the coordinated action of Ca2+ influx and efflux pathways. An increased understanding of the functions and regulation of these various Ca2+ transporters has improved our appreciation of the role these transporters play in specifically shaping the Ca2+ signatures. Here we review the evidence which indicates that Ca2+ channel, Ca2+-ATPase and Ca2+ exchanger isoforms can indeed modulate specific Ca2+ signatures in response to an individual signal.

A PIIB-type Ca2+-ATPase is essential for stress adaptation in Physcomitrella patens

Transient cytosolic Ca(2+) ([Ca(2+)](cyt)) elevations are early events in plant signaling pathways including those related to abiotic stress. The restoration of [Ca(2+)](cyt) to prestimulus levels involves ATP-driven Ca(2+) pumps, but direct evidence for an essential role of a plant Ca(2+)-ATPase in abiotic stress adaptation is missing. Here, we report on a stress-responsive Ca(2+)-ATPase gene (PCA1) from the moss Physcomitrella patens. Functional analysis of PCA1 in a Ca(2+) transport-deficient yeast mutant suggests that PCA1 encodes a P(IIB)-type Ca(2+)-ATPase harboring an N-terminal autoinhibitory domain. In vivo localizations identified membranes of small vacuoles as the integration site for a PCA1:GFP fusion protein. PCA1 mRNA levels are up-regulated by dehydration, NaCl, and abscisic acid, and PCA1 loss-of-function mutants (DeltaPCA1) exhibit an enhanced susceptibility to salt stress. The DeltaPCA1 lines show sustained elevated [Ca(2+)](cyt) in response to salt treatment in contrast to WT that shows transient Ca(2+) elevations, indicating a direct role for PCA1 in the restoration of prestimulus [Ca(2+)](cyt). The altered Ca(2+) response of the DeltaPCA1 mutant lines correlates with altered expression levels of stress-induced genes, suggesting disturbance of a stress-associated signaling pathway. We propose that PCA1 is an essential component for abiotic stress adaptation in Physcomitrella involved in the generation of a specific salt-induced Ca(2+) signature.

AtCCX3 is an Arabidopsis endomembrane H+ -dependent K+ transporter

The Arabidopsis (Arabidopsis thaliana) cation calcium exchangers (CCXs) were recently identified as a subfamily of cation transporters; however, no plant CCXs have been functionally characterized. Here, we show that Arabidopsis AtCCX3 (At3g14070) and AtCCX4 (At1g54115) can suppress yeast mutants defective in Na(+), K(+), and Mn(2+) transport. We also report high-capacity uptake of (86)Rb(+) in tonoplast-enriched vesicles from yeast expressing AtCCX3. Cation competition studies showed inhibition of (86)Rb(+) uptake in AtCCX3 cells by excess Na(+), K(+), and Mn(2+). Functional epitope-tagged AtCCX3 fusion proteins were localized to endomembranes in plants and yeast. In Arabidopsis, AtCCX3 is primarily expressed in flowers, while AtCCX4 is expressed throughout the plant. Quantitative polymerase chain reaction showed that expression of AtCCX3 increased in plants treated with NaCl, KCl, and MnCl(2). Insertional mutant lines of AtCCX3 and AtCCX4 displayed no apparent growth defects; however, overexpression of AtCCX3 caused increased Na(+) accumulation and increased (86)Rb(+) transport. Uptake of (86)Rb(+) increased in tonoplast-enriched membranes isolated from Arabidopsis lines expressing CCX3 driven by the cauliflower mosaic virus 35S promoter. Overexpression of AtCCX3 in tobacco (Nicotiana tabacum) produced lesions in the leaves, stunted growth, and resulted in the accumulation of higher levels of numerous cations. In summary, these findings suggest that AtCCX3 is an endomembrane-localized H(+)-dependent K(+) transporter with apparent Na(+) and Mn(2+) transport properties distinct from those of previously characterized plant transporters.

The secretory system of Arabidopsis

Over the past few years, a vast amount of research has illuminated the workings of the secretory system of eukaryotic cells. The bulk of this work has been focused on the yeast Saccharomyces cerevisiae, or on mammalian cells. At a superficial level, plants are typical eukaryotes with respect to the operation of the secretory system; however, important differences emerge in the function and appearance of endomembrane organelles. In particular, the plant secretory system has specialized in several ways to support the synthesis of many components of the complex cell wall, and specialized kinds of vacuole have taken on a protein storage role-a role that is intended to support the growing seedling, but has been co-opted to support human life in the seeds of many crop plants. In the past, most research on the plant secretory system has been guided by results in mammalian or fungal systems but recently plants have begun to stand on their own as models for understanding complex trafficking events within the eukaryotic endomembrane system.

A distinct endosomal Ca2+/Mn2+ pump affects root growth through the secretory process

Ca(2+) is required for protein processing, sorting, and secretion in eukaryotic cells, although the particular roles of the transporters involved in the secretory system of plants are obscure. One endomembrane-type Ca-ATPase from Arabidopsis (Arabidopsis thaliana), AtECA3, diverges from AtECA1, AtECA2, and AtECA4 in protein sequence; yet, AtECA3 appears similar in transport activity to the endoplasmic reticulum (ER)-bound AtECA1. Expression of AtECA3 in a yeast (Saccharomyces cerevisiae) mutant defective in its endogenous Ca(2+) pumps conferred the ability to grow on Ca(2+)-depleted medium and tolerance to toxic levels of Mn(2+). A green fluorescent protein-tagged AtECA3 was functionally competent and localized to intracellular membranes of yeast, suggesting that Ca(2+) and Mn(2+) loading into internal compartment(s) enhanced yeast proliferation. In mesophyll protoplasts, AtECA3-green fluorescent protein associated with a subpopulation of endosome/prevacuolar compartments based on partial colocalization with the Ara7 marker. Interestingly, three independent eca3 T-DNA disruption mutants showed severe reduction in root growth normally stimulated by 3 mm Ca(2+), indicating that AtECA3 function cannot be replaced by an ER-associated AtECA1. Furthermore, root growth of mutants is sensitive to 50 microm Mn(2+), indicating that AtECA3 is also important for the detoxification of excess Mn(2+). Curiously, Ateca3 mutant roots produced 65% more apoplastic protein than wild-type roots, as monitored by peroxidase activity, suggesting that the secretory process was altered. Together, these results demonstrate that the role of AtECA3 is distinct from that of the more abundant ER AtECA1. AtECA3 supports Ca(2+)-stimulated root growth and the detoxification of high Mn(2+), possibly through activities mediated by post-Golgi compartments that coordinate membrane traffic and sorting of materials to the vacuole and the cell wall.

The origin and function of calmodulin regulated Ca2+ pumps in plants

While Ca2+ signaling plays an important role in both plants and animals, the machinery that codes and decodes these signals have evolved to show interesting differences and similarities. For example, typical plant and animal cells both utilize calmodulin (CaM)-regulated Ca2+ pumps at the plasma membrane to help control cytoplasmic Ca2+ levels. However, in flowering plants this family of pumps has evolved with a unique structural arrangement in which the regulatory domain is located at the N-terminal instead of C-terminal end. In addition, some of the plant isoforms have evolved to function at endomembrane locations. For the 14 Ca2+ pumps present in the model plant Arabidopsis, molecular genetic analyses are providing exciting insights into their function in diverse aspects of plant growth and development.

The ACA10 Ca2+-ATPase regulates adult vegetative development and inflorescence architecture in Arabidopsis

The Arabidopsis (Arabidopsis thaliana) compact inflorescence (cif) genotype causes altered adult vegetative development and a reduction in elongation of inflorescence internodes resulting in formation of floral clusters. The cif trait requires both a recessive mutation, cif1, and the activity of a naturally occurring dominant allele of an unlinked gene, CIF2(D). We show here that the pseudoverticillata mutation is allelic with cif1 and that the product of the CIF1 gene is ACA10, a member of the large family of P-type Ca(2+)-ATPases found in higher plants. T-DNA insertion mutations in ACA10, but not in the two other Arabidopsis plasma membrane Ca(2+)-ATPase-encoding genes, ACA8 and ACA9, cause a cif phenotype when combined with the dominant CIF2(D) modifier allele. Therefore, ACA10 has a unique function in regulating adult phase growth and inflorescence development. The wild-type ACA8 and ACA10 mRNAs are present at similar levels, and the two promoter-beta-glucuronidase fusion transgenes show very similar expression patterns. Moreover, transformation of the cif mutant with an extra copy of the ACA8 gene, which causes overexpression of the ACA8 transcript, can complement the cif phenotype. This suggests that these two Ca(2+) pump genes have distinct but related activities and that their differential functions can be altered by relatively small changes in their patterns or levels of expression. The correspondence between cif1 and mutations in ACA10 establishes a genetic link between calcium transport, vegetative phase change, and inflorescence architecture.

Novel tonoplast transporters identified using a proteomic approach with vacuoles isolated from cauliflower buds

Young meristematic plant cells contain a large number of small vacuoles, while the largest part of the vacuome in mature cells is composed by a large central vacuole, occupying 80% to 90% of the cell volume. Thus far, only a limited number of vacuolar membrane proteins have been identified and characterized. The proteomic approach is a powerful tool to identify new vacuolar membrane proteins. To analyze vacuoles from growing tissues we isolated vacuoles from cauliflower (Brassica oleracea) buds, which are constituted by a large amount of small cells but also contain cells in expansion as well as fully expanded cells. Here we show that using purified cauliflower vacuoles and different extraction procedures such as saline, NaOH, acetone, and chloroform/methanol and analyzing the data against the Arabidopsis (Arabidopsis thaliana) database 102 cauliflower integral proteins and 214 peripheral proteins could be identified. The vacuolar pyrophosphatase was the most prominent protein. From the 102 identified proteins 45 proteins were already described. Nine of these, corresponding to 46% of peptides detected, are known vacuolar proteins. We identified 57 proteins (55.9%) containing at least one membrane spanning domain with unknown subcellular localization. A comparison of the newly identified proteins with expression profiles from in silico data revealed that most of them are highly expressed in young, developing tissues. To verify whether the newly identified proteins were indeed localized in the vacuole we constructed and expressed green fluorescence protein fusion proteins for five putative vacuolar membrane proteins exhibiting three to 11 transmembrane domains. Four of them, a putative organic cation transporter, a nodulin N21 family protein, a membrane protein of unknown function, and a senescence related membrane protein were localized in the vacuolar membrane, while a white-brown ATP-binding cassette transporter homolog was shown to reside in the plasma membrane. These results demonstrate that proteomic analysis of highly purified vacuoles from specific tissues allows the identification of new vacuolar proteins and provides an additional view of tonoplastic proteins.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists

Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools.