CLC chloride channels and transporters: from genes to protein structure, pathology and physiology

Stochastic Sensing of Chloride Anions Using an α-Hemolysin Pore with a semiaza-Bambusuril Adapter

Pores containing molecular adapters provide internal selective binding sites, thereby allowing the stochastic sensing of analytes. Herein, we demonstrate that semiaza-bambusuril (BU) acts as a non-covalent molecular adapter when lodged within the lumen of the wild-type α-hemolysin (WT-αHL) protein pore. Because the bambusurils are recognized as anion receptors, the anion binding site within the adapter-nanopore complex allows the detection of chloride anions, thus converting a non-selective pore into an anion sensor.

In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo

Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating the electrolytes' balance in kidneys and other organs. In order to define the chloride voltage-gated channel (CLCN) gene family in buffalo, this study used in silico analyses to examine physicochemical properties, evolutionary patterns, and genome-wide identification. We identified eight CLCN genes in buffalo. The ProtParam tool analysis identified a number of important physicochemical properties of these proteins, including hydrophilicity, thermostability, in vitro instability, and basic nature. Based on their evolutionary relationships, a phylogenetic analysis divided the eight discovered genes into three subfamilies. Furthermore, a gene structure analysis, motif patterns, and conserved domains using TBtool demonstrated the significant conservation of this gene family among selected species over the course of evolution. A comparative amino acid analysis using ClustalW revealed similarities and differences between buffalo and cattle CLCN proteins. Three duplicated gene pairs were identified, all of which were segmental duplications except for CLCN4-CLCN5, which was a tandem duplication in buffalo. For each gene pair, the Ka/Ks test ratio findings showed that none of the ratios was more than one, indicating that these proteins were likely subject to positive selection. A synteny analysis confirmed a conserved pattern of genomic blocks between buffalo and cattle. Transcriptional control in cells relies on the binding of transcription factors to specific sites in the genome. The number of transcription factor binding sites (TFBSs) was higher in cattle compared to buffalo. Five main recombination breakpoints were identified at various places in the recombination analysis. The outcomes of our study provide new knowledge about the CLCN gene family in buffalo and open the door for further research on candidate genes in vertebrates through genome-wide studies.

Advances in Circular RNA in the Pathogenesis of Epilepsy

Recent studies evidenced the involvement of circular RNA (circRNA) in neuroinflammation, apoptosis, and synaptic remodeling suggesting an important role for circRNA in the occurrence and development of epilepsy. This review provides an overview of circRNAs considered to be playing regulatory roles in the process of epilepsy and to be involved in multiple biological epilepsy-related processes, such as hippocampal sclerosis, inflammatory response, cell apoptosis, synaptic remodeling, and cell proliferation and differentiation. This review covers the current research status of differential expression of circRNA-mediated seizures, m6A methylation, demethylation-mediated seizures in post transcriptional circRNA modification, as well as the mechanisms of m5C- and m7G-modified circRNA. In summary, this article reviews the research progress on the relationship between circRNA in non-coding RNA and epilepsy.

The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress

A key mechanism employed by plants to adapt to salinity stress involves maintaining ion homeostasis via the actions of ion transporters. While the function of cation transporters in maintaining ion homeostasis in plants has been extensively studied, little is known about the roles of their anion counterparts in this process. Here, we describe a mechanism of salt adaptation in plants. We characterized the chloride channel (CLC) gene AtCLCf, whose expression is regulated by WRKY transcription factor under salt stress in Arabidopsis thaliana. Loss-of-function atclcf seedlings show increased sensitivity to salt, whereas AtCLCf overexpression confers enhanced resistance to salt stress. Salt stress induces the translocation of GFP-AtCLCf fusion protein to the plasma membrane (PM). Blocking AtCLCf translocation using the exocytosis inhibitor brefeldin-A or mutating the small GTPase gene AtRABA1b/BEX5 (RAS GENES FROM RAT BRAINA1b homolog) increases salt sensitivity in plants. Electrophysiology and liposome-based assays confirm the Cl-/H+ antiport function of AtCLCf. Therefore, we have uncovered a mechanism of plant adaptation to salt stress involving the NaCl-induced translocation of AtCLCf to the PM, thus facilitating Cl- removal at the roots, and increasing the plant's salinity tolerance.

Genotype-phenotype correlation in CLCN4-related developmental and epileptic encephalopathy

CLCN4-related disorder is a rare X-linked neurodevelopmental condition with a pathogenic mechanism yet to be elucidated. CLCN4 encodes the vesicular 2Cl-/H+ exchanger ClC-4, and CLCN4 pathogenic variants frequently result in altered ClC-4 transport activity. The precise cellular and molecular function of ClC-4 remains unknown; however, together with ClC-3, ClC-4 is thought to have a role in the ion homeostasis of endosomes and intracellular trafficking. We reviewed our research database for patients with CLCN4 variants and epilepsy, and performed thorough phenotyping. We examined the functional properties of the variants in mammalian cells using patch-clamp electrophysiology, protein biochemistry, and confocal fluorescence microscopy. Three male patients with developmental and epileptic encephalopathy were identified, with differing phenotypes. Patients #1 and #2 had normal growth parameters and normal-appearing brains on MRI, while patient #3 had microcephaly, microsomia, complete agenesis of the corpus callosum and cerebellar and brainstem hypoplasia. The p.(Gly342Arg) variant of patient #1 significantly impaired ClC-4's heterodimerization capability with ClC-3 and suppressed anion currents. The p.(Ile549Leu) variant of patient #2 and p.(Asp89Asn) variant of patient #3 both shift the voltage dependency of transport activation by 20 mV to more hyperpolarizing potentials, relative to the wild-type, with p.(Asp89Asn) favouring higher transport activity. We concluded that p.(Gly342Arg) carried by patient #1 and the p.(Ile549Leu) expressed by patient #2 impair ClC-4 transport function, while the p.(Asp89Asn) variant results in a gain-of-transport function; all three variants result in epilepsy and global developmental impairment, but with differences in epilepsy presentation, growth parameters, and presence or absence of brain malformations.

Bio-Inspired Subnanofluidics: Advanced Fabrication and Functionalization

Biological ion channels can realize high-speed and high-selective ion transport through the protein filter with the sub-1-nanometer channel. Inspired by biological ion channels, various kinds of artificial subnanopores, subnanochannels, and subnanoslits with improved ion selectivity and permeability are recently developed for efficient separation, energy conversion, and biosensing. This review article discusses the advanced fabrication and functionalization methods for constructing subnanofluidic pores, channels, tubes, and slits, which have shown great potential for various applications. Novel fabrication methods for producing subnanofluidics, including top-down techniques such as electron beam etching, ion irradiation, and electrochemical etching, as well as bottom-up approaches starting from advanced microporous frameworks, microporous polymers, lipid bilayer embedded subnanochannels, and stacked 2D materials are well summarized. Meanwhile, the functionalization methods of subnanochannels are discussed based on the introduction of functional groups, which are classified into direct synthesis, covalent bond modifications, and functional molecule fillings. These methods have enabled the construction of subnanochannels with precise control of structure, size, and functionality. The current progress, challenges, and future directions in the field of subnanofluidic are also discussed.

The hybrid RAVE complex plays V-ATPase-dependent and -independent pathobiological roles in Cryptococcus neoformans

V-ATPase, which comprises 13-14 subunits, is essential for pH homeostasis in all eukaryotes, but its proper function requires a regulator to assemble its subunits. While RAVE (regulator of H+-ATPase of vacuolar and endosomal membranes) and Raboconnectin-3 complexes assemble V-ATPase subunits in Saccharomyces cerevisiae and humans, respectively, the function of the RAVE complex in fungal pathogens remains largely unknown. In this study, we identified two RAVE complex components, Rav1 and Wdr1, in the fungal meningitis pathogen Cryptococcus neoformans, and analyzed their roles. Rav1 and Wdr1 are orthologous to yeast RAVE and human Rabconnectin-3 counterparts, respectively, forming the hybrid RAVE (hRAVE) complex. Deletion of RAV1 caused severe defects in growth, cell cycle control, morphogenesis, sexual development, stress responses, and virulence factor production, while the deletion of WDR1 resulted in similar but modest changes, suggesting that Rav1 and Wdr1 play central and accessary roles, respectively. Proteomics analysis confirmed that Wdr1 was one of the Rav1-interacting proteins. Although the hRAVE complex generally has V-ATPase-dependent functions, it also has some V-ATPase-independent roles, suggesting a unique role beyond conventional intracellular pH regulation in C. neoformans. The hRAVE complex played a critical role in the pathogenicity of C. neoformans, and RAV1 deletion attenuated virulence and impaired blood-brain barrier crossing ability. This study provides comprehensive insights into the pathobiological roles of the fungal RAVE complex and suggests a novel therapeutic strategy for controlling cryptococcosis.

Nitrogen transport and assimilation in tea plant (Camellia sinensis): a review

Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.

Comprehensive analysis and experimental validation reveal elevated CLCN4 is a promising biomarker in endometrial cancer

Several studies have reported the role of CLCN4 in tumor progression. However, its mechanism remains to be thoroughly studied. The objective of this study was to explore the potential pathogenic role of CLCN4 in endometrial carcinoma (UCEC) with a better understanding of the pathological mechanisms involved. The potential roles of CLCN4 in different tumors were explored based on The Cancer Genome Atlas (TCGA), the expression difference, mutation, survival, pathological stage, Immunity subtypes, Immune infiltration, tumor microenvironment (TME), tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR) related to CLCN4 were analyzed. Then, the expression, prognosis, mutation, and functional enrichment of CLCN4 in UCEC were analyzed. Immunohistochemical experiment was used to verify the expression of CLCN4 in endometrial cancer tissues and normal tissues. In vitro, we knocked down of CLCN4 in HEC-1-A cells and performed CCK8, WB, RT-PCR, wound-healing, transwell assays to further validation of the molecular function. Results revealed that high expression of CLCN4 was observed in 20 cancer types of TCGA. CLCN4 expression correlates with poor survival in MESO, BLCA, THCA, especially UCEC tumors. CLCN4 expression was significantly associated with CD4+ T-cell infiltration, especially CD4+ Th1-cell. Immunohistochemical experiment reveals that CLCN4 is high expressed in endometrial tumors, in vitro experiment reveals that knockdown of CLCN4 inhibits the cells proliferation, migration and invasion. Our study is the first to offer a comprehensive understanding of the oncogenic roles of CLCN4 on different tumors. CLCN4 may become a potential biomarker in UCEC.

Small Molecules Targeting Kidney ClC-K Chloride Channels: Applications in Rare Tubulopathies and Common Cardiovascular Diseases

Given the key role played by ClC-K chloride channels in kidney and inner ear physiology and pathology, they can be considered important targets for drug discovery. Indeed, ClC-Ka and ClC-Kb inhibition would interfere with the urine countercurrent concentration mechanism in Henle's loop, which is responsible for the reabsorption of water and electrolytes from the collecting duct, producing a diuretic and antihypertensive effect. On the other hand, ClC-K/barttin channel dysfunctions in Bartter Syndrome with or without deafness will require the pharmacological recovery of channel expression and/or activity. In these cases, a channel activator or chaperone would be appealing. Starting from a brief description of the physio-pathological role of ClC-K channels in renal function, this review aims to provide an overview of the recent progress in the discovery of ClC-K channel modulators.

Modus operandi of ClC-K2 Cl- Channel in the Collecting Duct Intercalated Cells

The renal collecting duct is known to play a critical role in many physiological processes, including systemic water-electrolyte homeostasis, acid-base balance, and the salt sensitivity of blood pressure. ClC-K2 (ClC-Kb in humans) is a Cl^--permeable channel expressed on the basolateral membrane of several segments of the renal tubule, including the collecting duct intercalated cells. ClC-Kb mutations are causative for Bartters' syndrome type 3 manifested as hypotension, urinary salt wasting, and metabolic alkalosis. However, little is known about the significance of the channel in the collecting duct with respect to the normal physiology and pathology of Bartters' syndrome. In this review, we summarize the available experimental evidence about the signaling determinants of ClC-K2 function and the regulation by systemic and local factors as well as critically discuss the recent advances in understanding the collecting-duct-specific roles of ClC-K2 in adaptations to changes in dietary Cl^- intake and maintaining systemic acid-base homeostasis.

Genetic diagnosis of Bartter syndrome in Iranian patients and detection of a novel homozygous CLCNKB mutation

An Iranian girl with clinical symptoms of Bartter syndrome like hypokalemia, polyuria, polydipsia, hyponatremia, and hypochloremic alkalosis was referred to us in whom the CLCNKB gene was genetically evaluated using Sanger sequencing. A homozygous pathogenic variant of c.1332_1335delCTCT was detected in this patient.

Angstrom-scale ion channels towards single-ion selectivity

Artificial ion channels with ion permeability and selectivity comparable to their biological counterparts are highly desired for efficient separation, biosensing, and energy conversion technologies. In the past two decades, both nanoscale and sub-nanoscale ion channels have been successfully fabricated to mimic biological ion channels. Although nanoscale ion channels have achieved intelligent gating and rectification properties, they cannot realize high ion selectivity, especially single-ion selectivity. Artificial angstrom-sized ion channels with narrow pore sizes <1 nm and well-defined pore structures mimicking biological channels have accomplished high ion conductivity and single-ion selectivity. This review comprehensively summarizes the research progress in the rational design and synthesis of artificial subnanometer-sized ion channels with zero-dimensional to three-dimensional pore structures. Then we discuss cation/anion, mono-/di-valent cation, mono-/di-valent anion, and single-ion selectivities of the synthetic ion channels and highlight their potential applications in high-efficiency ion separation, energy conversion, and biological therapeutics. The gaps of single-ion selectivity between artificial and natural channels and the connections between ion selectivity and permeability of synthetic ion channels are covered. Finally, the challenges that need to be addressed in this research field and the perspective of angstrom-scale ion channels are discussed.

The EcCLC antiporter embedded in lipidic liquid crystalline films - molecular dynamics simulations and electrochemical methods

Lipidic-liquid crystalline nanostructures (lipidic cubic phases), which are biomimetic and stable in an excess of water, were used as a convenient environment to investigate the transport properties of the membrane antiporter E. coli CLC-1 (EcCLC). The chloride ion transfer by EcCLC was studied by all-atom molecular dynamics simulations combined with electrochemical methods at pH 7 and pH 5. The cubic phase film was used as the membrane between the chloride donor and receiving compartments and it was placed on the glassy carbon electrode and immersed in the chloride solution. Structural characterization of lipidic mesoscopic systems with and without the incorporation of EcCLC was performed using small-angle X-ray scattering. The EcCLC transported chloride ions more efficiently at more acidic pH, and the resistance of the film decreased at lower pH. 4,4-Diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS) employed as an inhibitor of the protein was shown to decrease the transport efficiency upon hydrolysis to DADS at both pH 7 and pH 5. The molecular dynamics simulations, performed for the first time in lipidic cubic phases for EcCLC, allowed studying the collective movements of chloride ions which can help in elucidating the mechanism of transporting the ions by the EcCLC antiporter. The protein modified lipidic cubic phase film is a convenient and simple system for screening potential inhibitors of integral membrane proteins, as demonstrated by the example of the EcCLC antiporter. The use of lipidic cubic phases may also be important for the further development of new electrochemical sensors for membrane proteins and enzyme electrodes.

Molecular Cloning and Characterization of SaCLCd, SaCLCf, and SaCLCg, Novel Proteins of the Chloride Channel Family (CLC) from the Halophyte Suaeda altissima (L.) Pall

Coding sequences of the CLC family genes SaCLCd, SaCLCf, and SaCLCg, the putative orthologs of Arabidopsis thaliana AtCLCd, AtCLCf, and AtCLCg genes, were cloned from the euhalophyte Suaeda altissima (L.) Pall. The key conserved motifs and glutamates inherent in proteins of the CLC family were identified in SaCLCd, SaCLCf, and SaCLCg amino acid sequences. SaCLCd and SaCLCg were characterized by higher homology to eukaryotic (human) CLCs, while SaCLCf was closer to prokaryotic CLCs. Ion specificities of the SaCLC proteins were studied in complementation assays by heterologous expression of the SaCLC genes in the Saccharomyces cerevisiae GEF1 disrupted strain Δgef1. GEF1 encoded the only CLC family protein, the Cl^- transporter Gef1p, in undisrupted strains of this organism. Expression of SaCLCd in Δgef1 cells restored their ability to grow on selective media. The complementation test and the presence of both the "gating" and "proton" conservative glutamates in SaCLCd amino acid sequence and serine specific for Cl^- in its selectivity filter suggest that this protein operates as a Cl^-/H⁺ antiporter. By contrast, expression of SaCLCf and SaCLCg did not complement the growth defect phenotype of Δgef1 cells. The selectivity filters of SaCLCf and SaCLCg also contained serine. However, SaCLCf included only the "gating" glutamate, while SaCLCg contained the "proton" glutamate, suggesting that SaCLCf and SaCLCg proteins act as Cl^- channels. The SaCLCd, SaCLCf, and SaCLCg genes were shown to be expressed in the roots and leaves of S. altissima. In response to addition of NaCl to the growth medium, the relative transcript abundances of all three genes of S. altissima increased in the leaves but did not change significantly in the roots. The increase in expression of SaCLCd, SaCLCf, and SaCLCg in the leaves in response to increasing salinity was in line with Cl^- accumulation in the leaf cells, indicating the possible participation of SaCLCd, SaCLCf, and SaCLCg proteins in Cl^- sequestration in cell organelles. Generally, these results suggest the involvement of SaCLC proteins in the response of S. altissima plants to increasing salinity and possible participation in mechanisms underlying salt tolerance.

Phagosomal chloride dynamics in the alveolar macrophage

Acidification in intracellular organelles is tightly linked to the influx of Cl- counteracting proton translocation by the electrogenic V-ATPase. We quantified the dynamics of Cl- transfer accompanying cargo incorporation into single phagosomes in alveolar macrophages (AMs). Phagosomal Cl- concentration and acidification magnitude were followed in real time with maximal acidification achieved at levels of approximately 200 mM. Live cell confocal microscopy verified that phagosomal Cl- influx utilized predominantly the Cl- channel CFTR. Relative levels of elemental chlorine (Cl) in hard X-ray fluorescence microprobe (XFM) analysis within single phagosomes validated the increase in Cl- content. XFM revealed the complex interplay between elemental K content inside the phagosome and changes in Cl- during phagosomal particle uptake. Cl- -dependent changes in phagosomal membrane potential were obtained using second harmonic generation (SHG) microscopy. These studies provide a mechanistic insight for screening studies in drug development targeting pulmonary inflammatory disease.

Identification and validation of a signature involving voltage-gated chloride ion channel genes for prediction of prostate cancer recurrence

Voltage-gated chloride ion channels (CLCs) are transmembrane proteins that maintain chloride ion homeostasis in various cells. Accumulating studies indicated CLCs were related to cell growth, proliferation, and cell cycle. Nevertheless, the role of CLCs in prostate cancer (PCa) has not been systematically profiled. The purpose of this study was to investigate the expression profiles and biofunctions of CLCs genes, and construct a novel risk signature to predict biochemical recurrence (BCR) of PCa patients. We identified five differentially expressed CLCs genes in our cohort and then constructed a signature composed of CLCN2 and CLCN6 through Lasso-Cox regression analysis in the training cohort from the Cancer Genome Atlas (TCGA). The testing and entire cohorts from TCGA and the GSE21034 from the Gene Expression Omnibus (GEO) were used as internal and independent external validation datasets. This signature could divide PCa patients into the high and low risk groups with different prognoses, was apparently correlated with clinical features, and was an independent excellent prognostic indicator. Enrichment analysis indicated our signature was primarily concentrated in cellular process and metabolic process. The expression patterns of CLCN2 and CLCN6 were detected in our own cohort based immunohistochemistry staining, and we found CLCN2 and CLCN6 were highly expressed in PCa tissues compared with benign tissues and positively associated with higher Gleason score and shorter BCR-free time. Functional experiments revealed that CLCN2 and CLCN6 downregulation inhibited cell proliferation, colony formation, invasion, and migration, but prolonged cell cycle and promoted apoptosis. Furthermore, Seahorse assay showed that silencing CLCN2 or CLCN6 exerted potential inhibitory effects on energy metabolism in PCa. Collectively, our signature could provide a novel and robust strategy for the prognostic evaluation and improve treatment decision making for PCa patients.

A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces

Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge-and thus to define a quantitative paradigm for facile proton transport in confined spaces-a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl^-/H⁺ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and-by the simple measure of the mere existence of a water structure-the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.

Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl-/H+ Antiporter

Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl⁻ anion and a proton (H⁺), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu_in and Glu_ex.

Protective role of taurine against oxidative stress (Review)

Taurine is a fundamental mediator of homeostasis that exerts multiple roles to confer protection against oxidant stress. The development of hypertension, muscle/neuro‑​associated disorders, hepatic cirrhosis, cardiac dysfunction and ischemia/reperfusion are examples of some injuries that are linked with oxidative stress. The present review gives a comprehensive description of all the underlying mechanisms of taurine, with the aim to explain its anti‑oxidant actions. Taurine is regarded as a cytoprotective molecule due to its ability to sustain normal electron transport chain, maintain glutathione stores, upregulate anti‑oxidant responses, increase membrane stability, eliminate inflammation and prevent calcium accumulation. In parallel, the synergistic effect of taurine with other potential therapeutic modalities in multiple disorders are highlighted. Apart from the results derived from research findings, the current review bridges the gap between bench and bedside, providing mechanistic insights into the biological activity of taurine that supports its potential therapeutic efficacy in clinic. In the future, further clinical studies are required to support the ameliorative effect of taurine against oxidative stress.

Apical CLC-2 in retinal pigment epithelium is crucial for survival of the outer retina

Knockout of the chloride channel protein 2 (CLC‐2; CLCN2) results in fast progressing blindness in mice. Retinal Pigment Epithelium (RPE) and photoreceptors undergo, in parallel, rapid, and profound morphological changes and degeneration. Immunohistochemistry and electron microscopy of the outer retina and electroretinography of the CLC‐2 KO mouse demonstrated normal morphology at postnatal day 2, followed by drastic changes in RPE and photoreceptor morphology and loss of vision during the first postnatal month. To investigate whether the RPE or the photoreceptors are the primary cause of the degeneration, we injected lentiviruses carrying HA‐tagged CLC‐2 with an RPE‐specific promotor in the subretinal space of CLC‐2‐KO mice at the time of eye opening. As expected, CLC‐2‐HA was expressed exclusively in RPE; strikingly, this procedure rescued the degeneration of both RPE and photoreceptors. Light response in transduced eyes was also recovered. Only a fraction of RPE was transduced with the lentivirus; however, the entire RPE monolayer appears healthy, even the RPE cells not expressing the CLC‐2‐HA. Surprisingly, in contrast with previous physiological observations that postulate that CLC‐2 has a basolateral localization in RPE, our immunofluorescence experiments demonstrated CLC‐2 has an apical distribution, facing the subretinal space and the photoreceptor outer segments. Our findings suggest that CLC‐2 does not play the postulated role in fluid transport at the basolateral membrane. Rather, they suggest that CLC‐2 performs a critical homeostatic role in the subretinal compartment involving a chloride regulatory mechanism that is critical for the survival of both RPE and photoreceptors.

Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops

Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology.

Specific PIP2 binding promotes calcium activation of TMEM16A chloride channels

TMEM16A is a widely expressed Ca²⁺-activated Cl⁻ channel that regulates crucial physiological functions including fluid secretion, neuronal excitability, and smooth muscle contraction. There is a critical need to understand the molecular mechanisms of TMEM16A gating and regulation. However, high-resolution TMEM16A structures have failed to reveal an activated state with an unobstructed permeation pathway even with saturating Ca²⁺. This has been attributed to the requirement of PIP₂ for preventing TMEM16A desensitization. Here, atomistic simulations show that specific binding of PIP₂ to TMEM16A can lead to spontaneous opening of the permeation pathway in the Ca²⁺-bound state. The predicted activated state is highly consistent with a wide range of mutagenesis and functional data. It yields a maximal Cl⁻ conductance of ~1 pS, similar to experimental estimates, and recapitulates the selectivity of larger SCN⁻ over Cl⁻. The resulting molecular mechanism of activation provides a basis for understanding the interplay of multiple signals in controlling TMEM16A channel function.

Chen and Jia investigate the synergistic regulating role of Ca²⁺ binding and the signaling lipid PIP₂ in TMEM16A channel gating. Their study is significant as it provides new insights into the activated state of TMEM16A and highlights an example of functional importance of lipids in regulating membrane-associated proteins.

Roles of the ClC chloride channel CLH-1 in food-associated salt chemotaxis behavior of C. elegans

The ability of animals to process dynamic sensory information facilitates foraging in an ever-changing environment. However, molecular and neural mechanisms underlying such ability remain elusive. The ClC anion channels/transporters play a pivotal role in cellular ion homeostasis across all phyla. Here, we find a ClC chloride channel is involved in salt concentration chemotaxis of Caenorhabditis elegans. Genetic screening identified two altered-function mutations of clh-1 that disrupt experience-dependent salt chemotaxis. Using genetically encoded fluorescent sensors, we demonstrate that CLH-1 contributes to regulation of intracellular anion and calcium dynamics of salt-sensing neuron, ASER. The mutant CLH-1 reduced responsiveness of ASER to salt stimuli in terms of both temporal resolution and intensity, which disrupted navigation strategies for approaching preferred salt concentrations. Furthermore, other ClC genes appeared to act redundantly in salt chemotaxis. These findings provide insights into the regulatory mechanism of neuronal responsivity by ClCs that contribute to modulation of navigation behavior.

Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

BACKGROUNDS

Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl^- and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl^-, NO₃^-, HCO₃^- and I^-, but its characteristics have not been reported on pomegranate.

RESULTS

In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO₃^-/H⁺ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl^-. We determined the content of Cl^-, NO₃^-, H₂PO₄^-, and SO₄^2- in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl^- content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO₃^- and SO₄^2-, but accelerated H₂PO₄^- uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl^- into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl^- from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO₃^- was transported into leaves to mitigate the nitrogen deficiency.

CONCLUSIONS

Our findings suggested that the PgCLC genes played important roles in balancing of Cl^- and NO₃^- in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate.

CLIC2α Chloride Channel Orchestrates Immunomodulation of Hemocyte Phagocytosis and Bactericidal Activity in Crassostrea gigas

Chloride ion plays critical roles in modulating immunological interactions. Herein, we demonstrated that the anion channel CLIC2α mediates Cl⁻ flux to regulate hemocytes functions in the Pacific oyster (Crassostrea gigas). Specifically, during infection by Vibrio parahemolyticus, chloride influx was activated following onset of phagocytosis. Phosphorylation of Akt was stimulated by Cl⁻ ions entering host cells, further contributing to signal transduction regulating internalization of bacteria through the PI3K/Akt signaling pathway. Concomitantly, Cl⁻ entered phagosomes, promoted the acidification and maturation of phagosomes, and contributed to production of HOCl to eradicate engulfed bacteria. Finally, genomic screening reveals CLIC2α as a major Cl⁻ channel gene responsible for regulating Cl⁻ influx in oysters. Knockdown of CLIC2α predictably impeded phagosome acidification and restricted bacterial killing in oysters. In conclusion, our work has established CLIC2α as a prominent regulator of Cl⁻ influx and thus Cl⁻ function in C. gigas in bacterial infection contexts.

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Influx of chloride ions is switched on during phagocytosis in oyster hemocytes

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PI3K/Akt signaling pathway mediates chloride-dependent activation of phagocytosis

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Cl⁻ promotes phagosomal acidification and HOCl production

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CLIC2α is the principal chloride channel encoding gene within oyster genome

Divergent Cl- and H+ pathways underlie transport coupling and gating in CLC exchangers and channels

The CLC family comprises H+-coupled exchangers and Cl- channels, and mutations causing their dysfunction lead to genetic disorders. The CLC exchangers, unlike canonical 'ping-pong' antiporters, simultaneously bind and translocate substrates through partially congruent pathways. How ions of opposite charge bypass each other while moving through a shared pathway remains unknown. Here, we use MD simulations, biochemical and electrophysiological measurements to identify two conserved phenylalanine residues that form an aromatic pathway whose dynamic rearrangements enable H+ movement outside the Cl- pore. These residues are important for H+ transport and voltage-dependent gating in the CLC exchangers. The aromatic pathway residues are evolutionarily conserved in CLC channels where their electrostatic properties and conformational flexibility determine gating. We propose that Cl- and H+ move through physically distinct and evolutionarily conserved routes through the CLC channels and transporters and suggest a unifying mechanism that describes the gating mechanism of both CLC subtypes.

Molecular Basis of CLC Antiporter Inhibition by Fluoride

CLC channels and transporters conduct or transport various kinds of anions, with the exception of fluoride, which acts as an effective inhibitor. Here, we performed sub-nanosecond DFT-based QM/MM simulations of the E. coli anion/proton exchanger ClC-ec1 and observed that fluoride binds incoming protons within the selectivity filter, with excess protons shared with the gating glutamate E148. Depending on E148 conformation, the competition for the proton can involve either a direct F^-/E148 interaction or the modulation of water molecules bridging the two anions. The direct interaction locks E148 in a conformation that does not allow for proton transport, and thus inhibits protein function.

Thirteen novel CLCNKB variants and genotype/phenotype association study in 42 Chinese patients with Bartter syndrome type 3

PURPOSE

Analyze the genotype of 42 Chinese patients with Bartter syndrome type 3 (BS3) and investigate their correlation between genotype and phenotype.

METHODS

Identify CLCNKB gene variants by the next-generation sequencing and the multiplex ligation-dependent probe amplification (MLPA), and then evaluate their mutation effects according to 2015 American College of Medical Genetics and Genomics (ACMG) standards and guidelines.

RESULTS

Thirty-six different variants in CLCNKB gene, including 13 novel ones, were found. The whole gene deletion of CLCNKB gene was the most frequent mutation (40%), and the rate of large deletions is up to 55%. Among 36 variants, six (c.1244T>A, c.1468G>A, c.849_851delCTT, c.359G>T, c.1052G>T, and c.1309G>A) and three (c.228A>C, c.1294_1295TA>CT, and c.1333T>G) variants were classified as "likely pathogenic variants" and "variants with uncertain significance (VUS)," respectively. The other 27 variants were classified as "pathogenic variants". The most common symptoms included: growth retardation (38/42), polydipsia and polyuria (35/42), constipation (31/42), and vomiting (27/42). All patients presented with hypokalemia, hypochloremia, and metabolic alkalosis. The genotype and phenotype association study revealed that who had mutations probably resulting in complete loss of function of both alleles might have severer phenotype. After the treatment that based on indomethacin and potassium chloride, most patients could achieve obvious recovery of growth rate and restoration of hypokalemia.

CONCLUSIONS

The present study have found 36 variants of CLCNKB gene, including 13 novel ones, which enrich the human gene mutation database and provide valuable references to diagnosis, treatment, and the genetic counseling of Chinese population.

Local conformational dynamics regulating transport properties of a Cl- /H+ antiporter

ClC-ec1 is a Cl- /H+ antiporter that exchanges Cl- and H+ ions across the membrane. Experiments have demonstrated that several mutations, including I109F, decrease the Cl- and H+ transport rates by an order of magnitude. Using reactive molecular dynamics simulations of explicit proton transport across the central region in the I109F mutant, a two-dimensional free energy profile has been constructed that is consistent with the experimental transport rates. The importance of a phenylalanine gate formed by F109 and F357 and its influence on hydration connectivity through the central proton transport pathway is revealed. This work demonstrates how seemingly subtle changes in local conformational dynamics can dictate hydration changes and thus transport properties. © 2019 Wiley Periodicals, Inc.

Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration

CLC chloride/proton exchangers may support acidification of endolysosomes and raise their luminal Cl⁻ concentration. Disruption of endosomal ClC‐3 causes severe neurodegeneration. To assess the importance of ClC‐3 Cl⁻/H⁺ exchange, we now generate Clcn3^unc/unc mice in which ClC‐3 is converted into a Cl⁻ channel. Unlike Clcn3^−/− mice, Clcn3^unc/unc mice appear normal owing to compensation by ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced in Clcn3^−/−, but not in Clcn3^unc/unc mice because ClC‐3^unc binds and stabilizes ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence in Clcn3^unc/unc/Clcn4^−/− mice entails even stronger neurodegeneration than observed in Clcn3^−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3^unc/unc or Clcn3^−/− mice before neurodegeneration sets in. Both, Cl⁻/H⁺‐exchange activity and the stabilizing effect on ClC‐4, are central to the biological function of ClC‐3.

Learning Physiology From Inherited Kidney Disorders

The identification of genes causing inherited kidney diseases yielded crucial insights in the molecular basis of disease and improved our understanding of physiological processes that operate in the kidney. Monogenic kidney disorders are caused by mutations in genes coding for a large variety of proteins including receptors, channels and transporters, enzymes, transcription factors, and structural components, operating in specialized cell types that perform highly regulated homeostatic functions. Common variants in some of these genes are also associated with complex traits, as evidenced by genome-wide association studies in the general population. In this review, we discuss how the molecular genetics of inherited disorders affecting different tubular segments of the nephron improved our understanding of various transport processes and of their involvement in homeostasis, while providing novel therapeutic targets. These include inherited disorders causing a dysfunction of the proximal tubule (renal Fanconi syndrome), with emphasis on epithelial differentiation and receptor-mediated endocytosis, or affecting the reabsorption of glucose, the handling of uric acid, and the reabsorption of sodium, calcium, and magnesium along the kidney tubule.

Molecular cloning and characterisation of SaCLCa1, a novel protein of the chloride channel (CLC) family from the halophyte Suaeda altissima (L.) Pall

The SaCLCa1 gene, a putative orthologue of AtCLCa, the Arabidopsis thaliana gene encoding a NO₃-/H⁺ antiporter, was cloned from the halophyte Suaeda altissima. It belonged to the CLC family, comprising anionic channels and anion/H⁺ antiporters. SaCLCa1 ion specificity was studied by heterologous expression of this gene in Saccharomyces cerevisiae GEF1 disrupted strain, Δgef1, where GEF1 encoded the only CLC family protein, the Cl- transporter Gef1p, in undisrupted strains of this organism. For comparison, the function of another recently identified S. altissima CLC family gene, SaCLCc1, was also characterised. Expression of SaCLCc1 in Δgef1 cells restored their ability to grow on selective media. This supported the chloride specificity of this transporter. By contrast, expression of SaCLCa1 did not complement the growth defect phenotype of Δgef1 cells. However, growth of the Δgef1 mutant on the selective media was partially restored when it was transformed with SaCLCa1(C562 T), encoding the modified protein SaCLCa1(P188S), in which proline responsible for NO₃- selectivity in selective filter was replaced by serine providing chloride selectivity. Quantitative real-time polymerase chain reactions (qRT-PCR) showed that significant induction of SaCLCa1 occurred in the roots of S. altissima when plants were grown on nitrate-deficient medium, while SaCLCc1 activation was observed in S. altissima leaves of plants grown in increasing Cl- concentrations of nutrient solution. These results suggested that SaCLCa1 and SaCLCc1 function as anionic transporters with nitrate and chloride specificities, respectively.

Characterizing chloride-dependent acidification in brain clathrin-coated vesicles 1

Endocytic organelles maintain their acidic pH using the V-type ATPase proton pump. However, proton accumulation across the membrane generates a voltage and requires the movement of an additional ion, known as a counterion, to dissipate charge buildup. The role of counterion movement in endosomes is not clear, but a subpopulation of early endosomes, clathrin-coated vesicles (CCVs), has previously been shown to use external chloride (Cl-) to allow V-ATPase-dependent acidification. We aimed to determine the identity and function of this presumed Cl- transporting protein. Our sample of highly enriched bovine brain CCVs exhibited V-type ATPase-facilitated acidification in the presence of external Cl-, independent of the monovalent cations present. While unsuccessful at identifying the mechanism of anion transport, we used glutamate-facilitated acidification, density gradients, and mass spectrometry to show that most brain CCVs are synaptic vesicles, complementing results from earlier studies that argued similarity only on the basis on protein content. The source of Cl--dependent acidification in brain CCVs may be vGLUT1, a synaptic vesicle glutamate transporter with known Cl- permeability, although CCVs in other tissues are likely to utilize different proteins to facilitate acidification.

Investigation into the presence and functional significance of proinsulin C-peptide in the female germline†

Diabetes is associated with poor oocyte quality and the dysregulation of ovarian function and is thus a leading contributor to the increasing prevalence of female reproductive pathologies. Accordingly, it is well-established that insulin fulfills a key role in the regulation of several facets of female reproduction. What remains less certain is whether proinsulin C-peptide, which has recently been implicated in cellular signaling cascades, holds a functional role in the female germline. In the present study, we examined the expression of insulin, C-peptide, and its purported receptor; GPR146, within the mouse ovary and oocyte. Our data establish the presence of abundant C-peptide within follicular fluid and raise the prospect that this bioactive peptide is internalized by oocytes in a G-protein coupled receptor-dependent manner. Further, our data reveal that internalized C-peptide undergoes pronounced subcellular relocalization from the ooplasm to the pronuclei postfertilization. The application of immunoprecipitation analysis and mass spectrometry identified breast cancer type 2 susceptibility protein (BRCA2), the meiotic resumption/DNA repair protein, as a primary binding partner for C-peptide within the oocyte. Collectively, these findings establish a novel accumulation profile for C-peptide in the female germline and provide the first evidence for an interaction between C-peptide and BRCA2. This interaction is particularly intriguing when considering the propensity for oocytes from diabetic women to experience aberrant meiotic resumption and perturbation of traditional DNA repair processes. This therefore provides a clear imperative for further investigation of the implications of dysregulated C-peptide production in these individuals.

A C-Terminal Fragment of Chlorotoxin Retains Bioactivity and Inhibits Cell Migration

Chlorotoxin was originally isolated from the venom of the Israeli scorpion Leiurus quinquestriatus, and has potential as a tumor imaging agent based on its selective binding to tumor cells. Several targets have been suggested for chlorotoxin including voltage-gated chloride channels, and it has been shown to have anti-angiogenic activity and inhibit cell migration. The structure of chlorotoxin is stabilized by four disulfide bonds and contains β-sheet and helical structure. Interestingly, the reduced form has previously been shown to inhibit cell migration to the same extent as the wild type, but structural analysis indicates that the reduced form of the peptide does not maintain the native secondary structure and appears unstructured in solution. This lack of structure suggests that a short stretch of amino acids might be responsible for the bioactivity. To explore this hypothesis, we have synthesized fragments of chlorotoxin without disulfide bonds. As expected for such small peptides, NMR analysis indicated that the peptides were unstructured in solution. However, the peptide corresponding to the eight C-terminal residues inhibited cell migration, in contrast to the other fragments. Our results suggest that the C-terminal region plays a critical role in the bioactivity of chlorotoxin.

Knockdown of CLC-3 in the hippocampal CA1 impairs contextual fear memory

Previous studies support a critical role of hippocampus in contextual fear memory. Structural and functional alterations of hippocampus occur frequently in posttraumatic stress disorders (PTSD). Recent reports reveal that knockout of CLC-3, a member of the CLC family of anion channels and transporters, leads to neuronal degeneration and loss of hippocampus. However, the role of CLC-3 in contextual fear memory remains unknown. Using adenovirus and adeno-associated virus gene transfer to knockdown CLC-3 in hippocampal CA1, we investigate the role of CLC-3 in contextual fear memory. CLC-3 expression is increased in hippocampal CA1 after formation of long-term contextual fear memory. Knockdown of CLC-3 by adenovirus infusion in hippocampal CA1 significantly attenuates the contextual fear memory, reduces spine density, induces defects of excitatory synaptic ultrastructure showed by the decreased PSD length, PSD thickness and active zone length, and impairs L-LTP induction and maintenance. Knockdown of CLC-3 also induces the synaptic NMDAR subunit composition to an increased GluN2A/GluN2B ratio pattern and reduces the activity of CaMKII-α. Furthermore, selectively knockdown of CLC-3 in excitatory neurons by adeno-associated virus driven from CaMKII-α promoter is sufficient to impair long-term contextual fear memory. These findings highlight that CLC-3 in hippocampal CA1 is necessary for contextual fear memory.

Genome-scale characterization of the vacuole nitrate transporter Chloride Channel (CLC) genes and their transcriptional responses to diverse nutrient stresses in allotetraploid rapeseed

The Chloride Channel (CLC) gene family is reported to be involved in vacuolar nitrate (NO₃^-) transport. Nitrate distribution to the cytoplasm is beneficial for enhancing NO₃^- assimilation and plays an important role in the regulation of nitrogen (N) use efficiency (NUE). In this study, genomic information, high-throughput transcriptional profiles, and gene co-expression analysis were integrated to identify the CLCs (BnaCLCs) in Brassica napus. The decreased NO₃^- concentration in the clca-2 mutant up-regulated the activities of nitrate reductase and glutamine synthetase, contributing to increase N assimilation and higher NUE in Arabidopsis thaliana. The genome-wide identification of 22BnaCLC genes experienced strong purifying selection. Segmental duplication was the major driving force in the expansion of the BnaCLC gene family. The most abundant cis-acting regulatory elements in the gene promoters, including DNA-binding One Zinc Finger, W-box, MYB, and GATA-box, might be involved in the transcriptional regulation of BnaCLCs expression. High-throughput transcriptional profiles and quantitative real-time PCR results showed that BnaCLCs responded differentially to distinct NO₃^- regimes. Transcriptomics-assisted gene co-expression network analysis identified BnaA7.CLCa-3 as the core member of the BnaCLC family, and this gene might play a central role in vacuolar NO₃^- transport in crops. The BnaCLC members also showed distinct expression patterns under phosphate depletion and cadmium toxicity. Taken together, our results provide comprehensive insights into the vacuolar BnaCLCs and establish baseline information for future studies on BnaCLCs-mediated vacuolar NO₃^- storage and its effect on NUE.

Identification and analysis of the chloride channel gene family members in tobacco (Nicotiana tabacum)

The chloride channel (CLC) protein family, which includes both chloride (Cl-) channels and chloride/proton (Cl-/H+) antiporters, is present in all domains of life, from prokaryotes to eukaryotes. However, there are no reported studies about this gene family in tobacco, an economically important global crop plant. In this study, we identified seventeen CLC genes in the genome of Nicotiana tabacum. A multiple sequence alignment showed that all of the predicted proteins shared a high sequence similarity and had a highly conserved GKxGPxxH motif. A gene structure analysis revealed that the NtCLC genes had highly divergent intron-exon patterns. A phylogenetic and conserved motif analysis revealed that the NtCLC family was divided into two clades, in a manner similar to other plants. We also evaluated the expression patterns of these NtCLC genes in different tissues and in plants treated with salt stress. The NtCLC genes had highly variable expression patterns, for example, the largely stem- and bud-specific expression patterns of NtCLC6 and NtCLC8, respectively. Salt stress treatment (300 mM NaCl) induced the expression of NtCLC2, NtCLC3, and NtCLC12, suggesting that these genes might play a role in tobacco responses to salt stress. Furthermore, the concentration of Cl- in the NtCLC2- and NtCLC13-silenced plants showed an obvious lower and higher level, respectively, than the control plants. Thus, we indicated that NtCLC2 or NtCLC13 might play an important role in chloride transport or metabolism in tobacco. Together, these findings establish an empirical foundation for the further functional characterization of the NtCLC genes in tobacco.

CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease

CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl−channels, whereas ClC-3 through ClC-7 are 2Cl−/H+-exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl−channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.

Plant Endomembrane Dynamics: Studies of K+/H+ Antiporters Provide Insights on the Effects of pH and Ion Homeostasis

Plants remodel their cells through the dynamic endomembrane system. Intracellular pH is important for membrane trafficking, but the determinants of pH homeostasis are poorly defined in plants. Electrogenic proton (H⁺) pumps depend on counter-ion fluxes to establish transmembrane pH gradients at the plasma membrane and endomembranes. Vacuolar-type H⁺-ATPase-mediated acidification of the trans-Golgi network is crucial for secretion and membrane recycling. Pump and counter-ion fluxes are unlikely to fine-tune pH; rather, alkali cation/H⁺ antiporters, which can alter pH and/or cation homeostasis locally and transiently, are prime candidates. Plants have a large family of predicted cation/H⁺ exchangers (CHX) of obscure function, in addition to the well-studied K⁺(Na⁺)/H⁺ exchangers (NHX). Here, we review the regulation of cytosolic and vacuolar pH, highlighting the similarities and distinctions of NHX and CHX members. In planta, alkalinization of the trans-Golgi network or vacuole by NHXs promotes membrane trafficking, endocytosis, cell expansion, and growth. CHXs localize to endomembranes and/or the plasma membrane and contribute to male fertility, pollen tube guidance, pollen wall construction, stomatal opening, and, in soybean (Glycine max), tolerance to salt stress. Three-dimensional structural models and mutagenesis of Arabidopsis (Arabidopsis thaliana) genes have allowed us to infer that AtCHX17 and AtNHX1 share a global architecture and a translocation core like bacterial Na⁺/H⁺ antiporters. Yet, the presence of distinct residues suggests that some CHXs differ from NHXs in pH sensing and electrogenicity. How H⁺ pumps, counter-ion fluxes, and cation/H⁺ antiporters are linked with signaling and membrane trafficking to remodel membranes and cell walls awaits further investigation.

Chloride Homeostasis in Neurons With Special Emphasis on the Olivocerebellar System: Differential Roles for Transporters and Channels

The intraneuronal ionic composition is an important determinant of brain functioning. There is growing evidence that aberrant homeostasis of the intracellular concentration of Cl- ([Cl-]i) evokes, in addition to that of Na+ and Ca2+, robust impairments of neuronal excitability and neurotransmission and thereby neurological conditions. More specifically, understanding the mechanisms underlying regulation of [Cl-]i is crucial for deciphering the variability in GABAergic and glycinergic signaling of neurons, in both health and disease. The homeostatic level of [Cl-]i is determined by various regulatory mechanisms, including those mediated by plasma membrane Cl- channels and transporters. This review focuses on the latest advances in identification, regulation and characterization of Cl- channels and transporters that modulate neuronal excitability and cell volume. By putting special emphasis on neurons of the olivocerebellar system, we establish that Cl- channels and transporters play an indispensable role in determining their [Cl-]i and thereby their function in sensorimotor coordination.

A selective class of inhibitors for the CLC-Ka chloride ion channel

CLC proteins are a ubiquitously expressed family of chloride-selective ion channels and transporters. A dearth of pharmacological tools for modulating CLC gating and ion conduction limits investigations aimed at understanding CLC structure/function and physiology. Herein, we describe the design, synthesis, and evaluation of a collection of N-arylated benzimidazole derivatives (BIMs), one of which (BIM1) shows unparalleled (>20-fold) selectivity for CLC-Ka over CLC-Kb, the two most closely related human CLC homologs. Computational docking to a CLC-Ka homology model has identified a BIM1 binding site on the extracellular face of the protein near the chloride permeation pathway in a region previously identified as a binding site for other less selective inhibitors. Results from site-directed mutagenesis experiments are consistent with predictions of this docking model. The residue at position 68 is 1 of only ∼20 extracellular residues that differ between CLC-Ka and CLC-Kb. Mutation of this residue in CLC-Ka and CLC-Kb (N68D and D68N, respectively) reverses the preference of BIM1 for CLC-Ka over CLC-Kb, thus showing the critical role of residue 68 in establishing BIM1 selectivity. Molecular docking studies together with results from structure-activity relationship studies with 19 BIM derivatives give insight into the increased selectivity of BIM1 compared with other inhibitors and identify strategies for further developing this class of compounds.

ATP increases [Ca2+ ]i and activates a Ca2+ -dependent Cl- current in rat ventricular fibroblasts

NEW FINDINGS

What is the central question of this study? Although electrophysiological and biophysical characteristics of heart fibroblasts have been studied in detail, their responses to prominent paracrine agents in the myocardium have not been addressed adequately. Our experiments characterize changes in cellular electrophysiology and intracellular calcium in response to ATP. What is the main finding and its importance? In rat ventricular fibroblasts maintained in cell culture, we find that ATP activates a specific subset of Ca²⁺ -activated Cl^- channels as a consequence of binding to P2Y purinoceptors and then activating phospholipase C. This response is not dependent on [Ca²⁺ ]_o but requires an increase in [Ca²⁺ ]_i and is modulated by the type of nucleotide that is the purinergic agonist.

ABSTRACT

Effects of ATP on enzymatically isolated rat ventricular fibroblasts maintained in short-term (36-72 h) cell culture were examined. Immunocytochemical staining of these cells revealed that a fibroblast, as opposed to a myofibroblast, phenotype was predominant. ATP, ADP or uridine 5'-triphosphate (UTP) all produced large increases in [Ca²⁺ ]_i . Voltage-clamp studies (amphotericin-perforated patch) showed that ATP (1-100 μm) activated an outwardly rectifying current, with a reversal potential very close to the Nernst potential for Cl^- . In contrast, ADP was much less effective, and UTP produced no detectable current. The non-selective Cl^- channel blockers niflumic acid, DIDS and NPPB (each at 100 μm), blocked the responses to 100 μm ATP. An agonist for P2Y purinoceptors, 2-MTATP, activated a very similar outwardly rectifying C1^- current. The P2Y receptor antagonists, suramin and PPADS (100 μm each), significantly inhibited the Cl^- current produced by 100 μm ATP. ATP was able to activate this Cl^- current when [Ca²⁺ ]_o was removed, but not when [Ca²⁺ ]_i was buffered with BAPTA-AM. In the presence of the phospholipase C inhibitor U73122, this Cl^- current could not be activated. PCR analysis revealed strong signals for a number of P2Y purinoceptors and for the Ca²⁺ -activated Cl^- channel, TMEM16F (also denoted ANO6). In summary, these results demonstrate that activation of P2Y receptors by ATP causes a phospholipase C-dependent increase in [Ca²⁺ ]_i , followed by activation of a Ca²⁺ -dependent Cl^- current in rat ventricular fibroblasts.

Unfolding of a ClC chloride transporter retains memory of its evolutionary history

ClC chloride channels and transporters are important for chloride homeostasis in species from bacteria to human. Mutations in ClC proteins cause genetically inherited diseases, some of which are likely to have folding defects. The ClC proteins present a challenging and unusual biological folding problem because they are large membrane proteins possessing a complex architecture with many re-entrant helices that go only part way through membrane and loop back out. Here we were able to examine the unfolding of the E. coli ClC transporter, ClC-ec1, using single-molecule forced unfolding methods. We find that the protein can be separated into two stable halves that unfold independently. The independence of the two domains is consistent with an evolutionary model in which the two halves arose from independent folding subunits that later fused together. Maintaining smaller folding domains of lesser complexity within large membrane proteins may be an advantageous strategy to avoid misfolding traps.

Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study

We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl^- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl^-/H⁺ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl^-. Moving the anion into the external binding site (S_ext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl^- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl^- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl^- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl^- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl^- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl^- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl^- transport.

The murine choroid plexus epithelium expresses the 2Cl-/H+ exchanger ClC-7 and Na+/H+ exchanger NHE6 in the luminal membrane domain

The choroid plexus epithelium within the brain ventricles secretes the majority of the cerebrospinal fluid (CSF). The luminal Na⁺-K⁺-ATPase acts in concert with a host of other transport proteins to mediate efficient fluid secretion across the epithelium. The CSF contains little protein buffer, but the pH value seems nonetheless maintained within narrow limits, even when faced with acid-base challenges. The involvement of choroid plexus acid-base transporters in CSF pH regulation is highlighted by the expression of several acid-base transporters in the epithelium. The aim of the present study was to identify novel acid-base transporters expressed in the luminal membrane of the choroid plexus epithelium to pave the way for systematic investigations of each candidate transporter in the regulation of CSF pH. Mass spectrometry analysis of proteins from epithelial cells isolated by fluorescence-activated cell sorting identified the Cl^-/H⁺ exchangers ClC-3, -4, -5, and -7 in addition to known choroid plexus acid-base transporters. RT-PCR on FACS isolated epithelial cells confirmed the expression of the corresponding mRNAs, as well as Na⁺/H⁺ exchanger NHE6 mRNA. Both NHE6 and ClC-7 were immunolocalized to the luminal plasma membrane domain of the choroid plexus epithelial cells. Dynamic imaging of intracellular pH and membrane potential changes in isolated choroid plexus epithelial cells demonstrated Cl^- gradient-driven changes in intracellular pH and membrane potential that are consistent with Cl^-/H⁺ exchange. In conclusion, we have detected for the first time NHE6 and ClC-7 in the choroid plexus, which are potentially involved in pH regulation of the CSF.