Phylogenetic relationships within cation transporter families of Arabidopsis

HLM1, an essential signaling component in the hypersensitive response, is a member of the cyclic nucleotide-gated channel ion channel family

The hypersensitive response (HR) in plants is a programmed cell death that is commonly associated with disease resistance. A novel mutation in Arabidopsis, hlm1, which causes aberrant regulation of cell death, manifested by a lesion-mimic phenotype and an altered HR, segregated as a single recessive allele. Broad-spectrum defense mechanisms remained functional or were constitutive in the mutant plants, which also exhibited increased resistance to a virulent strain of Pseudomonas syringae pv tomato. In response to avirulent strains of the same pathogen, the hlm1 mutant showed differential abilities to restrict bacterial growth, depending on the avirulence gene expressed by the pathogen. The HLM1 gene encodes a cyclic nucleotide-gated channel, CNGC4. Preliminary study of the HLM1/CNGC4 gene pro-duct in Xenopus oocytes (inside-out patch-clamp technique) showed that CNGC4 is permeable to both K(+) and Na(+) and is activated by both cGMP and cAMP. HLM1 gene expression is induced in response to pathogen infection and some pathogen-related signals. Thus, HLM1 might constitute a common downstream component of the signaling pathways leading to HR/resistance.

The Arabidopsis cax1 mutant exhibits impaired ion homeostasis, development, and hormonal responses and reveals interplay among vacuolar transporters

The Arabidopsis Ca(2+)/H(+) transporter CAX1 (Cation Exchanger1) may be an important regulator of intracellular Ca(2+) levels. Here, we describe the preliminary localization of CAX1 to the tonoplast and the molecular and biochemical characterization of cax1 mutants. We show that these mutants exhibit a 50% reduction in tonoplast Ca(2+)/H(+) antiport activity, a 40% reduction in tonoplast V-type H(+)-translocating ATPase activity, a 36% increase in tonoplast Ca(2+)-ATPase activity, and increased expression of the putative vacuolar Ca(2+)/H(+) antiporters CAX3 and CAX4. Enhanced growth was displayed by the cax1 lines under Mn(2+) and Mg(2+) stress conditions. The mutants exhibited altered plant development, perturbed hormone sensitivities, and altered expression of an auxin-regulated promoter-reporter gene fusion. We propose that CAX1 regulates myriad plant processes and discuss the observed phenotypes with regard to the compensatory alterations in other transporters.

ARAMEMNON, a novel database for Arabidopsis integral membrane proteins

A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

Mechanisms and Control of Nutrient Uptake in Plants

This review is a distillation of the vast amount of physiological and molecular data on plant membrane transport, to provide a concise overview of the main processes involved in the uptake of mineral nutrients in plants. Emphasis has been placed on transport across the plasma membrane, and on the primary uptake from soil into roots, or in the case of aquatic plants, from their aqueous environment. Control of uptake has been mainly considered in terms of local effects on the rate of transport and not in terms of long-distance signaling. The general picture emerging is of a large array of membrane transporters, few of which display any strong selectivity for individual nutrients. Instead, many transporters allow low-affinity uptake of several different nutrients. These features, plus the huge number of potential transporter genes that has been revealed by sequencing of plant genomes, raise some interesting questions about their evolution and likely function.

ARAMEMNON, a novel database for Arabidopsis integral membrane proteins

A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

Molecular mechanisms and regulation of K+ transport in higher plants

Potassium (K+) plays a number of important roles in plant growth and development. Over the past few years, molecular approaches associated with electrophysiological analyses have greatly advanced our understanding of K+ transport in plants. A large number of genes encoding K+ transport systems have been identified, revealing a high level of complexity. Characterization of some transport systems is providing exciting information at the molecular level on functions such as root K+ uptake and secretion into the xylem sap, K+ transport in guard cells, or K+ influx into growing pollen tubes. In this review, we take stock of this recent molecular information. The main families of plant K+ transport systems (Shaker and KCO channels, KUP/HAK/KT and HKT transporters) are described, along with molecular data on how these systems are regulated. Finally, we discuss a few physiological questions on which molecular studies have shed new light.

Arabidopsis thaliana root non-selective cation channels mediate calcium uptake and are involved in growth

Calcium is a critical structural and regulatory nutrient in plants. However, mechanisms of its uptake by root cells are poorly understood. We have found that Ca2+ influx in Arabidopsis root epidermal protoplasts is mediated by voltage-independent rapidly activating Ca2+-permeable non-selective cation channels (NSCCs). NSCCs showed the following permeability (P) sequence: PCa (1.00) = PBa (0.93) > PZn (0.51), PCa/PNa = 0.19, PCa/PK = 0.14. They were inhibited by quinine, Gd3+, La3+ and the His modifier diethylpyrocarbonate, but not by the Ca2+ or K+ channel antagonists, verapamil and tetraethylammonium (TEA+). Single channel conductance measured in 20 mm external Ca2+ was 5.9 pS. Calcium-permeable NSCCs co-existed with hyperpolarisation-activated Ca2+ channels (HACCs), which activated 40-60 min after forming the whole-cell configuration. HACCs activated at voltages <-130 to -150 mV, showed slow activation kinetics and were regulated by cytosolic Ca2+ ([Ca2+]cyt). Using aequorin-expressing plants, a linear relationship between membrane potential (Vm) and resting [Ca2+]cyt was observed, indicating the involvement of NSCCs. Intact root 45Ca2+ influx was reduced by Gd3+ (NSCC blocker) but was verapamil and TEA+ insensitive. In the root elongation zone, both root net Ca2+ influx (measured by Ca2+-selective vibrating microelectrode) and NSCC activity were increased compared to the mature epidermis, suggesting the involvement of NSCC in growth. A Ca2+ acquisition system based on NSCC and HACC co-existence is proposed. In mature epidermal cells, NSCC-mediated Ca2+ influx dominates whereas in specialised root cells (root hairs and elongation zone cells) where elevated [Ca2+]cyt activates HACCs, HACC-mediated Ca2+ influx predominates.

Knock-out of Arabidopsis metal transporter gene IRT1 results in iron deficiency accompanied by cell differentiation defects

IRT1 and IRT2 are members of the Arabidopsis ZIP metal transporter family that are specifically induced by iron deprivation in roots and act as heterologous suppressors of yeast mutations inhibiting iron and zinc uptake. Although IRT1 and IRT2 are thought to perform redundant functions as root-specific metal transporters, insertional inactivation of the IRT1 gene alone results in typical symptoms of iron deficiency causing severe leaf chlorosis and lethality in soil. The irt1 mutation is characterized by specific developmental defects, including a drastic reduction of chloroplast thylakoid stacking into grana and lack of palisade parenchyma differentiation in leaves, reduced number of vascular bundles in stems, and irregular patterns of enlarged endodermal and cortex cells in roots. Pulse labeling with 59Fe through the root system shows that the irt1 mutation reduces iron accumulation in the shoots. Short-term labeling with 65Zn reveals no alteration in spatial distribution of zinc, but indicates a lower level of zinc accumulation. In comparison to wild-type, the irt1 mutant responds to iron and zinc deprivation by altered expression of certain zinc and iron transporter genes, which results in the activation of ZIP1 in shoots, reduction of ZIP2 transcript levels in roots, and enhanced expression of IRT2 in roots. These data support the conclusion that IRT1 is an essential metal transporter required for proper development and regulation of iron and zinc homeostasis in Arabidopsis.

Molecular cloning and functional expression in bacteria of the potassium transporters CnHAK1 and CnHAK2 of the seagrass Cymodocea nodosa

The cDNAs CnHAK1 and CnHAK2, encoding K+ transporters, were amplified from the leaves of the seagrass Cymodocea nodosa. None of these transporters suppressed the K+ deficiency of a Saccharomyces cerevisiae mutant, but both suppressed the equivalent defect of an Escherichia coli mutant. Overexpression of the transporter CnHAKI, but not CnHAK2, mediated very rapid K+ or Rb+ influxes in the E. coli mutant. The concentration dependence of these influxes demonstrated that CnHAK1 is a low-affinity K+ transporter, which does not discriminate between K+ and Rb+. CnHAK1 expressed in E. coli worked in reverse when the external K+ concentrations were low, and we established the condition of a simple functional test of K+ loss for transporters of the Kup-HAK family. In comparison with its homologue barley transporter HvHAK2, CnHAKI was insensitive to Na+.

Distinct N-terminal regulatory domains of Ca(2+)/H(+) antiporters

The regulation of intracellular Ca(2+) levels is achieved in part by high-capacity vacuolar Ca(2+)/H(+) antiporters. An N-terminal regulatory region (NRR) on the Arabidopsis Ca(2+)/H(+) antiporter CAX1 (cation exchanger 1) has been shown previously to regulate Ca(2+) transport by a mechanism of N-terminal auto-inhibition. Here, we examine the regulation of other CAX transporters, both within Arabidopsis and from another plant, mung bean (Vigna radiata), to ascertain if this mechanism is commonly used among Ca(2+)/H(+) antiporters. Biochemical analysis of mung bean VCAX1 expressed in yeast (Saccharomyces cerevisiae) showed that N-terminal truncated VCAX1 had approximately 70% greater antiport activity compared with full-length VCAX1. A synthetic peptide corresponding to the NRR of CAX1, which can strongly inhibit Ca(2+) transport by CAX1, could not dramatically inhibit Ca(2+) transport by truncated VCAX1. The N terminus of Arabidopsis CAX3 was also shown to contain an NRR. Additions of either the CAX3 or VCAX1 regulatory regions to the N terminus of an N-terminal truncated CAX1 failed to inhibit CAX1 activity. When fused to N-terminal truncated CAX1, both the CAX3 and VCAX1 regulatory regions could only auto-inhibit CAX1 after mutagenesis of specific amino acids within this NRR region. These findings demonstrate that N-terminal regulation is present in other plant CAX transporters, and suggest distinct regulatory features among these transporters.

Identification and characterization of a NaCl-inducible vacuolar Na+/H+ antiporter in Beta vulgaris

We have cloned, by RT-PCR and the use of degenerate oligonucleotide primers, a Na+/H+ antiporter from Beta vulgaris that is homologous to NHX1 of Arabidopsis thaliana and is a member of the family of recently cloned plant NHX-genes. This antiporter, BvNHX1, partially complements the salt-sensitive phenotype of a Deltaena1-4Deltanhx1 yeast strain. Antibodies were raised against a central portion of the BvNHX1 open reading frame that was predicted from the cloned cDNA. This antiporter was found to be highly enriched in tonoplast membranes isolated from plant tissues. BvNHX1 transcript abundance increased after salt treatments, in both suspension-cell cultures and whole plants. BvNHX1 protein abundance in the tonoplast-enriched membranes was also elevated after salt treatments. The vacuolar Na+/H+ antiporter activity increased up to 3-fold when the cell were exposed to 100 mM NaCl. The increase in protein abundance in response to the salt treatment, together with the salt-induced vacuolar Na+/H+ antiporter activity in B. vulgaris suggests that BvNHX1 plays an important role in salinity tolerance.

A role for HKT1 in sodium uptake by wheat roots

The high affinity potassium transporter, HKT1 from wheat was introduced into Florida wheat in sense and antisense orientation under control of a ubiquitin promoter. Ten transgenic lines expressing the transgene were identified and two of these showed strong down-regulation of the native HKT1 transcript. One line (271) was expressing the antisense construct and the other (223) was expressing a truncated sense construct. The two lines were examined further for phenotype relating to cation transport. Membrane depolarisations were measured in low (0.1 mm) K+ and high (100 mm) NaCl. Under these conditions there was no difference between line 271 and the control at low K+, but at high Na+ there was a rapid depolarisation that was significantly larger in control plants. 22Na uptake was measured in this line and there was a significant decrease in uptake at 100 mm NaCl in the transgenic line when compared with the control. The two transgenic lines were grown at high NaCl (200 mm) and analysed for growth and root sodium content. Lines 271 and 223 showed enhanced growth under salinity when compared with the control and had lower sodium in the root. Secondary ion mass spectrometry (SIMS) analysis of transverse sections of the root showed that Na+ and K+ were strongly localised to stelar regions when compared with other ions, and that the Na+ : K+ ratios were reduced in salt-stressed transgenic tissue when compared with the control.

Inventory and functional characterization of the HAK potassium transporters of rice

Plants take up large amounts of K(+) from the soil solution and distribute it to the cells of all organs, where it fulfills important physiological functions. Transport of K(+) from the soil solution to its final destination is mediated by channels and transporters. To better understand K(+) movements in plants, we intended to characterize the function of the large KT-HAK-KUP family of transporters in rice (Oryza sativa cv Nipponbare). By searching in databases and cDNA cloning, we have identified 17 genes (OsHAK1-17) encoding transporters of this family and obtained evidence of the existence of other two genes. Phylogenetic analysis of the encoded transporters reveals a great diversity among them, and three distant transporters, OsHAK1, OsHAK7, and OsHAK10, were expressed in yeast (Saccharomyces cerevisiae) and bacterial mutants to determine their functions. The three transporters mediate K(+) influxes or effluxes, depending on the conditions of the experiment. A comparative kinetic analysis of HAK-mediated K(+) influx in yeast and in roots of K(+)-starved rice seedlings demonstrated the involvement of HAK transporters in root K(+) uptake. We discuss that all HAK transporters may mediate K(+) transport, but probably not only in the plasma membrane. Transient expression of the OsHAK10-green fluorescent protein fusion protein in living onion epidermal cells targeted this protein to the tonoplast.

The metal ion transporter IRT1 is necessary for iron homeostasis and efficient photosynthesis in Arabidopsis thaliana

The mutants irt1-1 and irt1-2 of Arabidopsis thaliana were identified among a collection of T-DNA-tagged lines on the basis of a decrease in the effective quantum yield of photosystem II. The mutations responsible interfere with expression of IRT1, a nuclear gene that encodes the metal ion transporter IRT1. In irt1 mutants, photosensitivity and chlorophyll fluorescence parameters, as well as abundance and composition of the photosynthetic apparatus, are significantly altered. Additional effects of the mutation under greenhouse conditions, including chlorosis and a drastic reduction in growth rate and fertility, are compatible with a deficiency in iron transport. Propagation of irt1 plants on media supplemented with additional quantities of iron salts restores almost all aspects of wild-type behaviour. The irt2-1 mutant, which carries an En insertion in the highly homologous IRT2 gene of Arabidopsis thaliana, was identified by reverse genetics and shows no symptoms of iron deficiency. This, together with the finding that irt1-1 can be complemented by 35S::IRT1 but not by 35S::IRT2, demonstrates that, although the products of the two genes are closely related, only AtIRT1 is required for iron homeostasis under physiological conditions.

Genes for calcium-permeable channels in the plasma membrane of plant root cells

In plant cells, Ca(2+) is required for both structural and biophysical roles. In addition, changes in cytosolic Ca(2+) concentration ([Ca(2+)](cyt)) orchestrate responses to developmental and environmental signals. In many instances, [Ca(2+)](cyt) is increased by Ca(2+) influx across the plasma membrane through ion channels. Although the electrophysiological and biochemical characteristics of Ca(2+)-permeable channels in the plasma membrane of plant cells are well known, genes encoding putative Ca(2+)-permeable channels have only recently been identified. By comparing the tissue expression patterns and electrophysiology of Ca(2+)-permeable channels in the plasma membrane of root cells with those of genes encoding candidate plasma membrane Ca(2+) channels, the genetic counterparts of specific Ca(2+)-permeable channels can be deduced. Sequence homologies and the physiology of transgenic antisense plants suggest that the Arabidopsis AtTPC1 gene encodes a depolarisation-activated Ca(2+) channel. Members of the annexin gene family are likely to encode hyperpolarisation-activated Ca(2+) channels, based on their corresponding occurrence in secretory or elongating root cells, their inhibition by La(3+) and nifedipine, and their increased activity as [Ca(2+)](cyt) is raised. Based on their electrophysiology and tissue expression patterns, AtSKOR encodes a depolarisation-activated outward-rectifying (Ca(2+)-permeable) K(+) channel (KORC) in stelar cells and AtGORK is likely to encode a KORC in the plasma membrane of other Arabidopsis root cells. Two candidate gene families, of cyclic-nucleotide gated channels (CNGC) and ionotropic glutamate receptor (GLR) homologues, are proposed as the genetic correlates of voltage-independent cation (VIC) channels.

The expression of HAK-type K(+) transporters is regulated in response to salinity stress in common ice plant

Four transcripts homologous to K(+) transporters of the HAK/KT/KUP family have been characterized from the common ice plant (Mesembryanthemum crystallinum). We report tissue-specific expression of McHAK1 and McHAK4 transcripts abundant in roots, leaves, and stems. McHAK2 was predominantly present in stems and McHAK3 in root tissues. By in situ hybridizations, the McHAKs showed signals in the leaf vascular bundles, mesophyll, and epidermal cells as well as in epidermal bladder cells. In mature roots, transcripts were mainly localized to the vasculature, and in differentiated root tips, the strongest signals were obtained from the epidermis. Expression of McHAK1, McHAK2, and McHAK4 complemented a yeast mutant defective in low- and high-affinity K(+) uptake. Growth of the yeast mutant was restored at low-millimolar K(+) concentrations and was inhibited by Rb(+) and Cs(+) but was not affected by Na(+). Transcript levels of McHAK1 and McHAK4 increased by K(+) starvation and by salt stress of 400 mM NaCl in leaves and roots. Expression of McHAK2 and McHAK3 was stimulated in leaves and was transiently induced in roots in response to high salinity with prestress transcript levels restored in salt-adapted plants. We discuss possible roles for such transporters in ion homeostasis at high salinity.

Characterization of a HKT-type transporter in rice as a general alkali cation transporter

We report the characterization of rice OsHKT1 (Oryza sativa ssp. indica) homologous to the wheat K+/Na+-symporter HKT1. Expression of OsHKT1 in the yeast strain CY162 defective in K+-uptake restored growth at mM and micro M concentrations of K+ and mediated hypersensitivity to Na+. When expressed in Xenopus oocytes, rice OsHKT1 showed uptake characteristics of a Na+-transporter but mediated transport of other alkali cations as well. OsHKT1 expression was analysed in salt-tolerant rice Pokkali and salt-sensitive IR29 in response to external cation concentrations. OsHKT1 is expressed in roots and leaves. Exposure to Na+, Rb+, Li+, and Cs+ reduced OsHKT1 transcript amounts in both varieties and, in some cases, incompletely spliced transcripts were observed. By in situ hybridizations the expression of OsHKT1 was localized to the root epidermis and the vascular tissue inside the endodermis. In leaves, OsHKT1 showed strongest signals in cells surrounding the vasculature. The repression of OsHKT1 in the two rice varieties during salt stress was different in various cell types with main differences in the root vascular tissue. The data suggest control over HKT expression as a factor that may distinguish salt stress-sensitive and stress-tolerant lines. Differences in transcript expression in space and time in different lines of the same species appear to be a component of ion homeostasis correlated with salt sensitivity and tolerance.

Outer pore residues control the H(+) and K(+) sensitivity of the Arabidopsis potassium channel AKT3

The Arabidopsis phloem channel AKT3 is the founder of a subfamily of shaker-like plant potassium channels characterized by weak rectification, Ca(2+) block, proton inhibition, and, as shown in this study, K(+) sensitivity. In contrast to inward-rectifying, acid-activated K(+) channels of the KAT1 family, extracellular acidification decreases AKT3 currents at the macroscopic and single-channel levels. Here, we show that two distinct sites within the outer mouth of the K(+)-conducting pore provide the molecular basis for the pH sensitivity of this phloem channel. After generation of mutant channels and functional expression in Xenopus oocytes, we identified the His residue His-228, which is proximal to the K(+) selectivity filter (GYGD) and the distal Ser residue Ser-271, to be involved in proton susceptibility. Mutations of these sites, H228D and S271E, drastically reduced the H(+) and K(+) sensitivity of AKT3. Although in K(+)-free bath solutions outward K(+) currents were abolished completely in wild-type AKT3, S271E as well as the AKT3-HDSE double mutant still mediated K(+) efflux. We conclude that the pH- and K(+)-dependent properties of the AKT3 channel involve residues in the outer mouth of the pore. Both properties, H(+) and K(+) sensitivity, allow the fine-tuning of the phloem channel and thus seem to represent important elements in the control of membrane potential and sugar loading.

Mechanism of N-terminal autoinhibition in the Arabidopsis Ca(2+)/H(+) antiporter CAX1

Regulation of Ca(2+)/H(+) antiporters may be an important function in determining the duration and amplitude of cytosolic Ca(2+) oscillations. Previously the Arabidopsis Ca(2+)/H(+) transporter, CAX1 (cation exchanger 1), was identified by its ability to suppress yeast mutants defective in vacuolar Ca(2+) transport. Recently, a 36-amino acid N-terminal regulatory region on CAX1 has been identified that inhibits CAX1-mediated Ca(2+)/H(+) antiport. Here we show that a synthetic peptide designed against the CAX1 36 amino acids inhibited Ca(2+)/H(+) transport mediated by an N-terminal-truncated CAX1 but did not inhibit Ca(2+) transport by other Ca(2+)/H(+) antiporters. Ca(2+)/H(+) antiport activity measured from vacuolar-enriched membranes of Arabidopsis root was also inhibited by the CAX1 peptide. Through analyzing CAX chimeric constructs the region of interaction of the N-terminal regulatory region was mapped to include 7 amino acids (residues 56-62) within CAX1. The CAX1 N-terminal regulatory region was shown to physically interact with this 7-amino acid region by yeast two-hybrid analysis. Mutagenesis of amino acids within the N-terminal regulatory region implicated several residues as being essential for regulation. These findings describe a unique mode of antiporter autoinhibition and demonstrate the first detailed mechanisms for the regulation of a Ca(2+)/H(+) antiporter from any organism.

Plant K+ transport: not just an uphill struggle

Most plant cells can accumulate K+ to concentrations much higher than those in the external medium. Recent studies are providing new insights into the relative roles of channels and transporters in K+ accumulation. These studies are also pointing to specific roles for K+ channels and transporters in polarized development.

Arabidopsis and the Genetic Potential for the Phytoremediation of Toxic Elemental and Organic Pollutants

In a process called phytoremediation, plants can be used to extract, detoxify, and/or sequester toxic pollutants from soil, water, and air. Phytoremediation may become an essential tool in cleaning the environment and reducing human and animal exposure to potential carcinogens and other toxins. Arabidopsis has provided useful information about the genetic, physiological, and biochemical mechanisms behind phytoremediation, and it is an excellent model genetic organism to test foreign gene expression. This review focuses on Arabidopsis studies concerning: 1) the remediation of elemental pollutants; 2) the remediation of organic pollutants; and 3) the phytoremediation genome. Elemental pollutants include heavy metals and metalloids (e.g., mercury, lead, cadmium, arsenic) that are immutable. The general goal of phytoremediation is to extract, detoxify, and hyperaccumulate elemental pollutants in above-ground plant tissues for later harvest. A few dozen Arabidopsis genes and proteins that play direct roles in the remediation of elemental pollutants are discussed. Organic pollutants include toxic chemicals such as benzene, benzo(a)pyrene, polychlorinated biphenyls, trichloroethylene, trinitrotoluene, and dichlorodiphenyltrichloroethane. Phytoremediation of organic pollutants is focused on their complete mineralization to harmless products, however, less is known about the potential of plants to act on complex organic chemicals. A preliminary survey of the Arabidopsis genome suggests that as many as 700 genes encode proteins that have the capacity to act directly on environmental pollutants or could be modified to do so. The potential of the phytoremediation proteome to be used to reduce human exposure to toxic pollutants appears to be enormous and untapped.

Characterization of CAX4, an Arabidopsis H(+)/cation antiporter

Ion compartmentalization is essential for plant growth and development. The Arabidopsis open reading frames for CAX1, CAX2, and CAX3 (cation exchangers 1, 2, and 3) were previously identified as transporters that may modulate ion fluxes across the vacuolar membrane. To understand the diversity and role of H(+)/cation transporters in controlling plant ion levels, another homolog of the CAX genes, CAX4, was cloned from an Arabidopsis cDNA library. CAX4 is 53% identical to CAX1 at the amino acid level, 42% identical to CAX2, and 54% identical to CAX3. CAX4 transcripts appeared to be expressed at low levels in all tissues and levels of CAX4 RNA increased after Mn(2+), Na(+), and Ni(2+) treatment. An N-terminal CAX4-hemagglutinin fusion appeared to localize to both yeast and plant vacuolar membranes. When expressed in yeast, CAX4, like CAX3, failed to suppress the Ca(2+) sensitivity of yeast strains deficient in vacuolar Ca(2+) transport. Several modifications to CAX4 allowed the protein to transport Ca(2+). Addition of amino acids to the N terminus of CAX4 and CAX3 caused both transporters to suppress the sensitivity of yeast strains deficient in vacuolar Ca(2+) transport. These findings suggest that CAX transporters may modulate their ion transport properties through alterations at the N terminus.

Limiting nutrients: an old problem with new solutions?

Iron and phosphorus are essential minerals for both humans and plants. Advances in our understanding of the molecular mechanisms involved in the mobilization, transport and storage of these minerals now allow us to engineer plants to improve the yield and mineral nutrition of crops. Strategies range from increasing the expression of endogenous genes, such as that encoding the iron storage protein ferritin, to expressing a phytase gene from the fungus Aspergillus in Arabidopsis, thereby allowing the plants to obtain a previously unusable pool of phosphorus.

Genes encoding calmodulin-binding proteins in the Arabidopsis genome

Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

Vacuolar membrane localization of the Arabidopsis 'two-pore' K+ channel KCO1

Potassium (K+) channels play multiple roles in higher plants, and have been characterized electrophysiologically in various subcellular membranes. The K+ channel AtKCO1 from Arabidopsis thaliana is the prototype of a new family of plant K+ channels. In a previous study the protein has been functionally characterized after heterologous expression in Baculovirus-infected insect cells. In order to obtain further information on the physiological function of AtKCO1, the gene expression pattern and subcellular localization of the protein in plants were investigated. The regulatory function of the 5' region of the AtKCO1 gene was examined in transgenic A. thaliana plants carrying beta-glucuronidase (GUS) fusion constructs. Our analysis demonstrates that the AtKCO1 promoter is active in various tissues and cell types, and the highest GUS activity could be detected in mitotically active tissues of the plant. Promoter activity was strongly dependent on the presence of a 5' leader intron. The same overall structure was identified in two genes encoding AtKCO1-like K+ channels from Solanum tuberosum (StKCO1alpha and StKCO1beta). To investigate the subcellular localization of AtKCO1, the channel protein, as well as a fusion protein of AtKCO1 with green fluorescence protein (GFP), were expressed in transgenic tobacco BY2 cells. In sucrose density gradients, both proteins co-fractionate with tonoplast markers (Nt-TIPa, vATPase). In fluorescence images from transgenic AtKCO1-GFP BY2 cells fluorescence was exclusively detected in the tonoplast. Thus AtKCO1 is the first cloned K+ channel demonstrated to be a vacuolar K+ channel.

Electrophysiological analysis of cloned cyclic nucleotide-gated ion channels

Electrophysiological studies were conducted on the cloned plant cyclic nucleotide-gated ion channels AtCNGC2 and AtCNGC1 from Arabidopsis, and NtCBP4 from tobacco (Nicotiana tobacum). The nucleotide coding sequences for these proteins were expressed in Xenopus laevis oocytes or HEK 293 cells. Channel characteristics were evaluated using voltage clamp analysis of currents in the presence of cAMP. AtCNGC2 was demonstrated to conduct K(+) and other monovalent cations, but exclude Na(+); this conductivity profile is unique for any ion channel not possessing the amino acid sequence found in the selectivity filter of K(+)-selective ion channels. Application of cAMP evoked currents in membrane patches of oocytes injected with AtCNGC2 cRNA. Direct activation of the channel by cyclic nucleotide, demonstrated by application of cyclic nucleotide to patches of membranes expressing such channels, is a hallmark characteristic of this ion channel family. Voltage clamp studies (two-electrode configuration) demonstrated that AtCNGC1 and NtCBP4 are also cyclic nucleotide-gated channels. Addition of a lipophilic analog of cAMP to the perfusion bath of oocytes injected with NtCBP4 and AtCNGC1 cRNAs induced inward rectified, noninactivating K(+) currents.

Pollen tube development and competitive ability are impaired by disruption of a Shaker K(+) channel in Arabidopsis

Sexual reproduction in plants requires elongation of the pollen tube through the transmitting tissues toward the ovary. Tube growth rate is a major determinant of pollen competitive ability. We report that a K(+) channel of the Shaker family in Arabidopsis, SPIK, plays an important role in pollen tube development. SPIK was found to be specifically expressed in pollen. When SPIK was heterologously expressed in COS cells, its product formed hyperpolarization-activated K(+) channels. Disruption (T-DNA insertion) of the SPIK coding sequence strongly affected inwardly rectifying K(+)-channel activity in the pollen-grain plasma membrane. Measurements of membrane potential in growing pollen tubes yielded data compatible with a contribution of SPIK to K(+) influx. In vitro pollen germination assays were performed, revealing that the disruption results in impaired pollen tube growth. Analysis of the transmission rate of the disrupted allele in the progeny of heterozygous plants revealed a decrease in pollen competitive ability, the probability of fertilization by mutant pollen being approximately 1.6 times lower than that by wild-type pollen. The whole set of data supports the hypothesis that functional expression of SPIK plays a role in K(+) uptake in the growing pollen tube, and thereby in tube development and pollen competitive ability.

KCO1 is a component of the slow-vacuolar (SV) ion channel

The Arabidopsis double pore K+ channel KCO1 was fused to green fluorescent protein and expressed in tobacco protoplasts. Microscopic analysis revealed a bright green fluorescence at the vacuolar membrane. RT-PCR experiments showed that KCO1 is expressed in the mesophyll. Vacuoles from Arabidopsis wild-type and kco1 knockout plants were isolated for patch-clamp analyses. Currents mediated by slow-activating vacuolar (SV) channels of mesophyll cell vacuoles were significantly smaller in kco1 plants compared to the wild-type. This shows that KCO1 is involved in the formation of SV channels.

Plants and sodium ions: keeping company with the enemy

Plants face a dilemma about sodium metabolism. Uptake of ubiquitous sodium ions is desirable as a way to build osmotic potential, absorb water and sustain turgor, but excess sodium ions may be toxic. Information from a number of plant species about the proteins involved in sodium-ion uptake helps to explain how plants manage to take in just the right amount.

Nonselective cation channels in plants

Nonselective cation channels are a diverse group of ion channels characterized by their low discrimination between many essential and toxic cations. They are ubiquitous in plant tissues and are active in the plasma membrane, tonoplast, and other endomembranes. Members of this group are likely to function in low-affinity nutrient uptake, in distribution of cations within and between cells, and as plant Ca2+ channels. They are gated by diverse mechanisms, which can include voltage, cyclic nucleotides, glutamate, reactive oxygen species, and stretch. These channels dominate tonoplast cation transport, and the selectivity and gating mechanisms of tonoplast nonselective cation channels are comprehensively reviewed here. This review presents the first classification of plant nonselective cation channels and the first full description of nonselective cation channel candidate sequences in the Arabidopsis genome.

A mutation in the Arabidopsis KT2/KUP2 potassium transporter gene affects shoot cell expansion

Potassium ions (K(+)) are the most abundant cations in plants and are necessary for cell growth. Arabidopsis shy3-1 mutant plants have a short hypocotyl, small leaves, and a short flowering stem, and these defects result from decreased cell expansion. The semidominant shy3-1 mutation changes an amino acid in KT2/KUP2, a K(+) transporter related to the Escherichia coli Kup protein. Second mutations in the KT2/KUP2/SHY3 gene, including presumed null mutations, suppress the shy3-1 phenotypes. Plants with these intragenic suppressor mutations appear similar to wild-type plants, suggesting that KT2/KUP2/SHY3 acts redundantly with other genes. Expression of the shy3-1 mutant version of KT2/KUP2/SHY3 in wild-type plants confers shy3-1-like phenotypes, indicating that shy3-1 probably either causes a gain of function or creates an interfering protein. The shy3-1 mutation does not eliminate the ability of the KT2/KUP2 cDNA to rescue the growth of a potassium transport-deficient E. coli mutant. A P(SHY3)::GUS fusion is expressed in growing portions of the plant. These results suggest that KT2/KUP2/SHY3 mediates K(+)-dependent cell expansion in growing tissues.

Sodium uptake in Arabidopsis roots is regulated by cyclic nucleotides

Sodium uptake from the soil is a major cause of salinity toxicity in plants, yet little is known about the mechanisms that underlie Na(+) influx. We have characterized voltage independent channels (VICs) in Arabidopsis roots that are thought to contribute to Na(+) entry. VICs showed no selectivity among monovalent cations, and their gating was found to be voltage independent. However, VIC open probability showed sensitivity to cyclic nucleotides. The presence of micromolar concentrations of cAMP or cGMP at the cytoplasmic side of the plasma membrane evoked a rapid decrease in channel open probability. In accord with predictions from electrophysiological data, our results show that short-term unidirectional Na(+) influx is also reduced in the presence of cyclic nucleotides. Moreover, addition of membrane permeable cyclic nucleotides during growth assays improved plant salinity tolerance, which corresponded with lower levels of Na(+) accumulation in plants. In summary, these data imply that Arabidopsis plants may contain a cyclic nucleotide-based signaling pathway that directly affects Na(+) transport via VICs.

Sodium uptake in Arabidopsis roots is regulated by cyclic nucleotides

Sodium uptake from the soil is a major cause of salinity toxicity in plants, yet little is known about the mechanisms that underlie Na(+) influx. We have characterized voltage independent channels (VICs) in Arabidopsis roots that are thought to contribute to Na(+) entry. VICs showed no selectivity among monovalent cations, and their gating was found to be voltage independent. However, VIC open probability showed sensitivity to cyclic nucleotides. The presence of micromolar concentrations of cAMP or cGMP at the cytoplasmic side of the plasma membrane evoked a rapid decrease in channel open probability. In accord with predictions from electrophysiological data, our results show that short-term unidirectional Na(+) influx is also reduced in the presence of cyclic nucleotides. Moreover, addition of membrane permeable cyclic nucleotides during growth assays improved plant salinity tolerance, which corresponded with lower levels of Na(+) accumulation in plants. In summary, these data imply that Arabidopsis plants may contain a cyclic nucleotide-based signaling pathway that directly affects Na(+) transport via VICs.

Sodium uptake in Arabidopsis roots is regulated by cyclic nucleotides

Sodium uptake from the soil is a major cause of salinity toxicity in plants, yet little is known about the mechanisms that underlie Na(+) influx. We have characterized voltage independent channels (VICs) in Arabidopsis roots that are thought to contribute to Na(+) entry. VICs showed no selectivity among monovalent cations, and their gating was found to be voltage independent. However, VIC open probability showed sensitivity to cyclic nucleotides. The presence of micromolar concentrations of cAMP or cGMP at the cytoplasmic side of the plasma membrane evoked a rapid decrease in channel open probability. In accord with predictions from electrophysiological data, our results show that short-term unidirectional Na(+) influx is also reduced in the presence of cyclic nucleotides. Moreover, addition of membrane permeable cyclic nucleotides during growth assays improved plant salinity tolerance, which corresponded with lower levels of Na(+) accumulation in plants. In summary, these data imply that Arabidopsis plants may contain a cyclic nucleotide-based signaling pathway that directly affects Na(+) transport via VICs.

Strategies to identify transport systems in plants

Since the first molecular structures of plant transporters were discovered over a decade ago, considerable advances have been made in the study of plant membrane transport, but we still do not understand transport regulation. The genes encoding the transport systems in the various cell membranes are still to be identified, as are the physiological roles of most transport systems. A wide variety of complementary strategies are now available to study transport systems in plants, including forward and reverse genetics, proteomics, and in silico exploitation of the huge amount of information contained in the completely known genomic sequence of Arabidopsis.

Structural determinants of Ca2+ transport in the Arabidopsis H+/Ca2+ antiporter CAX1

Ca(2+) levels in plants, fungi, and bacteria are controlled in part by H(+)/Ca(2+) exchangers; however, the relationship between primary sequence and biological activity of these transporters has not been reported. The Arabidopsis H(+)/cation exchangers, CAX1 and CAX2, were identified by their ability to suppress yeast mutants defective in vacuolar Ca(2+) transport. CAX1 has a much higher capacity for Ca(2+) transport than CAX2. An Arabidopsis thaliana homolog of CAX1, CAX3, is 77% identical (93% similar) and, when expressed in yeast, localized to the vacuole but did not suppress yeast mutants defective in vacuolar Ca(2+) transport. Chimeric constructs and site-directed mutagenesis showed that CAX3 could suppress yeast vacuolar Ca(2+) transport mutants if a nine-amino acid region of CAX1 was inserted into CAX3 (CAX3-9). Biochemical analysis in yeast showed CAX3-9 had 36% of the H(+)/Ca(2+) exchange activity as compared with CAX1; however, CAX3-9 and CAX1 appear to differ in their transport of other ions. Exchanging the nine-amino acid region of CAX1 into CAX2 doubled yeast vacuolar Ca(2+) transport but did not appear to alter the transport of other ions. This nine-amino acid region is highly variable among the plant CAX-like transporters. These findings suggest that this region is involved in CAX-mediated Ca(2+) specificity.

Regulation of CAX1, an Arabidopsis Ca(2+)/H+ antiporter. Identification of an N-terminal autoinhibitory domain

Regulation of Ca(2+) transport determines the duration of a Ca(2+) signal, and hence, the nature of the biological response. Ca(2+)/H+ antiporters such as CAX1 (cation exchanger 1), play a key role in determining cytosolic Ca(2+) levels. Analysis of a full-length CAX1 clone suggested that the CAX1 open reading frame contains an additional 36 amino acids at the N terminus that were not found in the original clone identified by suppression of yeast (Saccharomyces cerevisiae) vacuolar Ca(2+) transport mutants. The long CAX1 (lCAX1) could not suppress the yeast Ca(2+) transport defects despite localization to the yeast vacuole. Calmodulin could not stimulate lCAX1 Ca(2+)/H+ transport in yeast; however, minor alterations in the 36-amino acid region restored Ca(2+)/H+ transport. Sequence analysis suggests that a 36-amino acid N-terminal regulatory domain may be present in all Arabidopsis CAX-like genes. Together, these results suggest a structural feature involved in regulation of Ca(2+)/H+ antiport.

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

Plant hormones, light receptors, pathogens, and abiotic signals trigger elevations in the cytosolic calcium concentration, which mediate physiological and developmental responses. Recent studies are reviewed here that reveal how specific genetic mutations impair or modify stimulus-induced calcium elevations in plant cells. These studies provide genetic evidence for the importance of calcium as a second messenger in plant signal transduction. A fundamental question arises: How can different stimuli use the same second messenger, calcium, to mediate different responses? Recent research and models are reviewed that suggest that several important mechanisms contribute to specificity in calcium signaling in plant cells. These mechanisms include (i) activation of different calcium channels in the plasma membrane and organellar membranes, (ii) stimulus-specific calcium oscillation parameters, (iii) cell type-specific responses, and (iv) intracellular localization of calcium gradients and calcium elevations in plant cells.

Dominant negative guard cell K+ channel mutants reduce inward-rectifying K+ currents and light-induced stomatal opening in arabidopsis

Inward-rectifying potassium (K+(in)) channels in guard cells have been suggested to provide a pathway for K+ uptake into guard cells during stomatal opening. To test the proposed role of guard cell K+(in) channels in light-induced stomatal opening, transgenic Arabidopsis plants were generated that expressed dominant negative point mutations in the K+(in) channel subunit KAT1. Patch-clamp analyses with transgenic guard cells from independent lines showed that K+(in) current magnitudes were reduced by approximately 75% compared with vector-transformed controls at -180 mV, which resulted in reduction in light-induced stomatal opening by 38% to 45% compared with vector-transformed controls. Analyses of intracellular K+ content using both sodium hexanitrocobaltate (III) and elemental x-ray microanalyses showed that light-induced K+ uptake was also significantly reduced in guard cells of K+(in) channel depressor lines. These findings support the model that K+(in) channels contribute to K+ uptake during light-induced stomatal opening. Furthermore, transpirational water loss from leaves was reduced in the K+(in) channel depressor lines. Comparisons of guard cell K+(in) current magnitudes among four different transgenic lines with different K+(in) current magnitudes show the range of activities of K+(in) channels required for guard cell K+ uptake during light-induced stomatal opening.

Dominant negative guard cell K+ channel mutants reduce inward-rectifying K+ currents and light-induced stomatal opening in arabidopsis

Inward-rectifying potassium (K+(in)) channels in guard cells have been suggested to provide a pathway for K+ uptake into guard cells during stomatal opening. To test the proposed role of guard cell K+(in) channels in light-induced stomatal opening, transgenic Arabidopsis plants were generated that expressed dominant negative point mutations in the K+(in) channel subunit KAT1. Patch-clamp analyses with transgenic guard cells from independent lines showed that K+(in) current magnitudes were reduced by approximately 75% compared with vector-transformed controls at -180 mV, which resulted in reduction in light-induced stomatal opening by 38% to 45% compared with vector-transformed controls. Analyses of intracellular K+ content using both sodium hexanitrocobaltate (III) and elemental x-ray microanalyses showed that light-induced K+ uptake was also significantly reduced in guard cells of K+(in) channel depressor lines. These findings support the model that K+(in) channels contribute to K+ uptake during light-induced stomatal opening. Furthermore, transpirational water loss from leaves was reduced in the K+(in) channel depressor lines. Comparisons of guard cell K+(in) current magnitudes among four different transgenic lines with different K+(in) current magnitudes show the range of activities of K+(in) channels required for guard cell K+ uptake during light-induced stomatal opening.

Dominant negative guard cell K+ channel mutants reduce inward-rectifying K+ currents and light-induced stomatal opening in arabidopsis

Inward-rectifying potassium (K+(in)) channels in guard cells have been suggested to provide a pathway for K+ uptake into guard cells during stomatal opening. To test the proposed role of guard cell K+(in) channels in light-induced stomatal opening, transgenic Arabidopsis plants were generated that expressed dominant negative point mutations in the K+(in) channel subunit KAT1. Patch-clamp analyses with transgenic guard cells from independent lines showed that K+(in) current magnitudes were reduced by approximately 75% compared with vector-transformed controls at -180 mV, which resulted in reduction in light-induced stomatal opening by 38% to 45% compared with vector-transformed controls. Analyses of intracellular K+ content using both sodium hexanitrocobaltate (III) and elemental x-ray microanalyses showed that light-induced K+ uptake was also significantly reduced in guard cells of K+(in) channel depressor lines. These findings support the model that K+(in) channels contribute to K+ uptake during light-induced stomatal opening. Furthermore, transpirational water loss from leaves was reduced in the K+(in) channel depressor lines. Comparisons of guard cell K+(in) current magnitudes among four different transgenic lines with different K+(in) current magnitudes show the range of activities of K+(in) channels required for guard cell K+ uptake during light-induced stomatal opening.

Inventory of the superfamily of P-type ion pumps in Arabidopsis

A total of 45 genes encoding for P-type ATPases have been identified in the complete genome sequence of Arabidopsis. Thus, this plant harbors a primary transport capability not seen in any other eukaryotic organism sequenced so far. The sequences group in all five subfamilies of P-type ATPases. The most prominent subfamilies are P(1B) ATPases (heavy metal pumps; seven members), P(2A) and P(2B) ATPases (Ca(2+) pumps; 14 in total), P(3A) ATPases (plasma membrane H(+) pumps; 12 members including a truncated pump, which might represent a pseudogene or an ATPase-like protein with an alternative function), and P(4) ATPases (12 members). P(4) ATPases have been implicated in aminophosholipid flipping but it is not known whether this is a direct or an indirect effect of pump activity. Despite this apparent plethora of pumps, Arabidopsis appears to be lacking Na(+) pumps and secretory pathway (PMR1-like) Ca(2+)-ATPases. A cluster of Arabidopsis heavy metal pumps resembles bacterial Zn(2+)/Co(2+)/Cd(2+)/Pb(2+) transporters. Two members of the cluster have extended C termini containing putative heavy metal binding motifs. The complete inventory of P-type ATPases in Arabidopsis is an important starting point for reverse genetic and physiological approaches aiming at elucidating the biological significance of these pumps.