Ion channels in renal disease

Response of heterologously expressed pressure sensor-actuator-modulator macromolecule to external mechanical stress

Cells from different organs in the body experience a range of mechanical and osmotic pressures that change in various diseases, including neurological, cardiovascular, ophthalmological, and renal diseases. Here, we demonstrate the use of an engineered Sensor-Actuator-Modulator (SAM) of microbial origin derived from a mechanosensitive channel of large conductance (MscL) for sensing external mechanical stress and modulating activities of mammalian cells. SAM is reliably expressed in the mammalian cell membrane and acts as a tension-activated pressure release valve. Further, the activities of heterologously expressed SAM in mammalian cells could be modulated by osmotic pressure. A comparison of the mechanosensitive activities of SAM-variants from different microbial origins shows differential inward current and dye uptake in response to mechanical stress exerted by hypo-osmotic shock. The use of SAM channels as mechanical stress-activated modulators in mammalian cells could provide new therapeutic approaches for treating disorders related to mechanical or osmotic pressure.

Chloride/Multiple Anion Exchanger SLC26A Family: Systemic Roles of SLC26A4 in Various Organs

Solute carrier family 26 member 4 (SLC26A4) is a member of the SLC26A transporter family and is expressed in various tissues, including the airway epithelium, kidney, thyroid, and tumors. It transports various ions, including bicarbonate, chloride, iodine, and oxalate. As a multiple-ion transporter, SLC26A4 is involved in the maintenance of hearing function, renal function, blood pressure, and hormone and pH regulation. In this review, we have summarized the various functions of SLC26A4 in multiple tissues and organs. Moreover, the relationships between SLC26A4 and other channels, such as cystic fibrosis transmembrane conductance regulator, epithelial sodium channel, and sodium chloride cotransporter, are highlighted. Although the modulation of SLC26A4 is critical for recovery from malfunctions of various organs, development of specific inducers or agonists of SLC26A4 remains challenging. This review contributes to providing a better understanding of the role of SLC26A4 and development of therapeutic approaches for the SLC26A4-associated hearing loss and SLC26A4-related dysfunction of various organs.

Genome mining yields putative disease-associated ROMK variants with distinct defects

Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal, and there is currently no cure. Bartter syndrome type II specifically arises from mutations in KCNJ1, which encodes the renal outer medullary potassium channel, ROMK. Over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified, yet their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined genomic data in both the NIH TOPMed and ClinVar databases with the aid of Rhapsody, a verified computational algorithm that predicts mutation pathogenicity and disease severity. Subsequent phenotypic studies using a yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced cell surface expression. Another mutation (T300R) was ERAD-resistant, but defects in channel activity were apparent based on two-electrode voltage clamp measurements in X. laevis oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies to advance precision medicine.

Genome mining yields new disease-associated ROMK variants with distinct defects

Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal. Although there is no cure for this disease, specific genes that lead to different Bartter syndrome subtypes have been identified. Bartter syndrome type II specifically arises from mutations in the KCNJ1 gene, which encodes the renal outer medullary potassium channel, ROMK. To date, over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified. Yet, their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined ROMK genomic data in both the NIH TOPMed and ClinVar databases with the aid of a computational algorithm that predicts protein misfolding and disease severity. Subsequent phenotypic studies using a high throughput yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced protein expression at the cell surface. Another ERAD-targeted ROMK mutant (L320P) was found in only one of the screens. In contrast, another mutation (T300R) was ERAD-resistant, but defects in ROMK activity were apparent after expression and two-electrode voltage clamp measurements in Xenopus oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies.

Author Summary

Bartter syndrome is a rare genetic disorder characterized by defective renal electrolyte handing, leading to debilitating symptoms and, in some patients, death in infancy. Currently, there is no cure for this disease. Bartter syndrome is divided into five types based on the causative gene. Bartter syndrome type II results from genetic variants in the gene encoding the ROMK protein, which is expressed in the kidney and assists in regulating sodium, potassium, and water homeostasis. Prior work established that some disease-associated ROMK mutants misfold and are destroyed soon after their synthesis in the endoplasmic reticulum (ER). Because a growing number of drugs have been identified that correct defective protein folding, we wished to identify an expanded cohort of similarly misshapen and unstable disease-associated ROMK variants. To this end, we developed a pipeline that employs computational analyses of human genome databases with genetic and biochemical assays. Next, we both confirmed the identity of known variants and uncovered previously uncharacterized ROMK variants associated with Bartter syndrome type II. Further analyses indicated that select mutants are targeted for ER-associated degradation, while another mutant compromises ROMK function. This work sets-the-stage for continued mining for ROMK loss of function alleles as well as other potassium channels, and positions select Bartter syndrome mutations for correction using emerging pharmaceuticals.

Transcriptome analysis reveals the high temperature induced damage is a significant factor affecting the osmotic function of gill tissue in Siberian sturgeon (Acipenser baerii)

BACKGROUND

Maintaining osmotic equilibrium plays an important role in the survival of cold-water fishes. Heat stress has been proven to reduce the activity of Na⁺/K⁺-ATPase in the gill tissue, leading to destruction of the osmotic equilibrium. However, the mechanism of megatemperature affecting gill osmoregulation has not been fully elucidated.

RESULTS

In this study, Siberian sturgeon (Acipenser baerii) was used to analyze histopathological change, plasma ion level, and transcriptome of gill tissue subjected to 20℃, 24℃and 28℃. The results showed that ROS level and damage were increased in gill tissue with the increasing of heat stress temperature. Plasma Cl^- level at 28℃ was distinctly lower than that at 20℃ and 24℃, while no significant difference was found in Na⁺ and K⁺ ion levels among different groups. Transcriptome analysis displayed that osmoregulation-, DNA-repair- and apoptosis-related terms or pathways were enriched in GO and KEGG analysis. Moreover, 194 osmoregulation-related genes were identified. Amongst, the expression of genes limiting ion outflow, occluding (OCLN), and ion absorption, solute carrier family 4, member 2 (AE2) solute carrier family 9, member 3 (NHE3) chloride channel 2 (CLC-2) were increased, while Na⁺/K⁺-ATPase alpha (NKA-a) expression was decreased after heat stress.

CONCLUSIONS

This study reveals for the first time that the effect of heat stress on damage and osmotic regulation in gill tissue of cold-water fishes. Heat stress increases the permeability of fish's gill tissue, and induces the gill tissue to keep ion balance through active ion absorption and passive ion outflow. Our study will contribute to research of global-warming-caused effects on cold-water fishes.

The Post-Translational Modification Networking in WNK-Centric Hypertension Regulation and Electrolyte Homeostasis

The with-no-lysine (WNK) kinase family, comprising four serine-threonine protein kinases (WNK1-4), were first linked to hypertension due to their mutations in association with pseudohypoaldosteronism type II (PHAII). WNK kinases regulate crucial blood pressure regulators, SPAK/OSR1, to mediate the post-translational modifications (PTMs) of their downstream ion channel substrates, such as sodium chloride co-transporter (NCC), epithelial sodium chloride (ENaC), renal outer medullary potassium channel (ROMK), and Na/K/2Cl co-transporters (NKCCs). In this review, we summarize the molecular pathways dysregulating the WNKs and their downstream target renal ion transporters. We summarize each of the genetic variants of WNK kinases and the small molecule inhibitors that have been discovered to regulate blood pressure via WNK-triggered PTM cascades.

Association of prolonged nightly fasting with cardiovascular, renal, inflammation, and nutritional status biomarkers in community-dwelling older adults

BACKGROUND

Prolonged fasting as a dietary strategy has been linked to metabolic benefits; however, data supporting these benefits corresponded to studies in very small samples of young participants in controlled environments, with few cardiovascular risk markers, who were studied for short periods of time.

OBJECTIVES

We sought to assess the association of habitual prolonged nightly fasting with a wide array of cardiovascular, renal, inflammation, and nutritional status biomarkers among community-dwelling older adults.

METHODS

Cross-sectional analysis of data were obtained from 1047 adults aged ≥65 y from the Seniors Study on Nutrition and Cardiovascular Risk in Spain 2 (Seniors-ENRICA-2) cohort. Habitual diet was assessed through a validated diet history. Fasting time was classified into the following categories: <10, 10 to <12, and 2 h/d, the latter being considered prolonged nightly fasting. Adjusted geometric means of biomarker concentrations in blood and serum were estimated using linear regression models, by categories of fasting time. Main confounders included overall diet quality, defined as adherence to a Mediterranean diet score, and BMI (in kg/m2).

RESULTS

Longer fasting time was associated with: lower concentration of HDL cholesterol (difference between the longest and shortest fasting category: -2.94 mg/dL; 95% CI: -4.80, -1.09; P-trend: 0.01); higher potassium concentration (0.11 mEq/L; 95% CI: 0.03, 0.19; P-trend: 0.01); and lower concentration of chloride (-0.50 mEq/L; 95% CI: -0.91, -0.09; P-trend: 0.03). These results were slightly attenuated after additional adjustment for BMI.

CONCLUSIONS

Habitual prolonged nightly fasting did not show beneficial associations with the examined biomarkers. By contrast, some modest detrimental associations were found suggesting that extended periods of time between meals may not be beneficial for older adults.

Impact of Membrane Voltage on Formation and Stability of Human Renal Proximal Tubules in Vitro

More than 15% of adults in the United States suffer from some form of chronic kidney disease (CKD). Current strategies for CKD consist of dialysis or kidney transplant, which, however, can take several years. In this light, tissue engineering and regenerative medicine approaches are the key to improving people's living conditions by advancing previous tissue engineering approaches and seeking new targets as intervention methods for kidney repair or replacement. The membrane voltage (V_m) dynamics of a cell have been associated with cell migration, cell cycle progression, differentiation, and pattern formation. Furthermore, bioelectrical stimuli have been used as a means in the treatment of diseases and wound healing. Here, we investigated the role of V_m as a novel target to guide and manipulate in vitro renal tissue models. Human-immortalized renal proximal tubule epithelial cells (RPTECs-TERT1) were cultured on Matrigel to support the formation of 3D proximal tubular-like structures with the incorporation of a voltage-sensitive dye indicator─bis-(1,3-dibutylbarbituric acid)timethine oxonol (DiBAC). The results demonstrated a correlation between the depolarization and the reorganization of human renal proximal tubule cells, indicating V_m as a candidate variable to control these events. Accordingly, V_m was pharmacologically manipulated using glibenclamide and pinacidil, K_ATP channel modulators, and proximal tubule formation and tubule stability over 21 days were assessed. Chronic manipulation of K_ATP channels induced changes in the tubular network topology without affecting lumen formation. Thus, a relationship was found between the preluminal tubulogenesis phase and K_ATP channels. This relationship may provide future options as a control point during kidney tissue development, treatment, and regeneration goals.

Exosomal and Plasma Non-Coding RNA Signature Associated with Urinary Albumin Excretion in Hypertension

Non-coding RNA (ncRNA), released into circulation or packaged into exosomes, plays important roles in many biological processes in the kidney. The purpose of the present study is to identify a common ncRNA signature associated with early renal damage and its related molecular pathways. Three individual libraries (plasma and urinary exosomes, and total plasma) were prepared from each hypertensive patient (with or without albuminuria) for ncRNA sequencing analysis. Next, an RNA-based transcriptional regulatory network was constructed. The three RNA biotypes with the greatest number of differentially expressed transcripts were long-ncRNA (lncRNA), microRNA (miRNA) and piwi-interacting RNA (piRNAs). We identified a common 24 ncRNA molecular signature related to hypertension-associated urinary albumin excretion, of which lncRNAs were the most representative. In addition, the transcriptional regulatory network showed five lncRNAs (LINC02614, BAALC-AS1, FAM230B, LOC100505824 and LINC01484) and the miR-301a-3p to play a significant role in network organization and targeting critical pathways regulating filtration barrier integrity and tubule reabsorption. Our study found an ncRNA profile associated with albuminuria, independent of biofluid origin (urine or plasma, circulating or in exosomes) that identifies a handful of potential targets, which may be utilized to study mechanisms of albuminuria and cardiovascular damage.

Two functional epithelial sodium channel isoforms are present in rodents despite pronounced evolutionary pseudogenisation and exon fusion

The epithelial sodium channel (ENaC) plays a key role in salt and water homeostasis in tetrapod vertebrates. There are four ENaC subunits (α, β, γ, δ), forming heterotrimeric αβγ- or δβγ-ENaCs. Although the physiology of αβγ-ENaC is well understood, for decades the field has stalled with respect to δβγ-ENaC due to the lack of mammalian model organisms. The SCNN1D gene coding for δ-ENaC was previously believed to be absent in rodents, hindering studies using standard laboratory animals. We analyzed all currently available rodent genomes and discovered that SCNN1D is present in rodents but was independently lost in five rodent lineages, including the Muridae (mice and rats). The independent loss of SCNN1D in rodent lineages may be constrained by phylogeny and taxon-specific adaptation to dry habitats, however habitat aridity does not provide a selection pressure for maintenance of SCNN1D across Rodentia. A fusion of two exons coding for a structurally flexible region in the extracellular domain of δ-ENaC appeared in the Hystricognathi (a group that includes guinea pigs). This conserved pattern evolved at least 41 Ma and represents a new autapomorphic feature for this clade. Exon fusion does not impair functionality of guinea pig (Cavia porcellus) δβγ-ENaC expressed in Xenopus oocytes. Electrophysiological characterization at the whole-cell and single-channel level revealed conserved biophysical features and mechanisms controlling guinea pig αβγ- and δβγ-ENaC function as compared with human orthologs. Guinea pigs therefore represent commercially available mammalian model animals that will help shed light on the physiological function of δ-ENaC.

Blood Pressure Regulation Evolved from Basic Homeostatic Components

Blood pressure (BP) is determined by several physiological factors that are regulated by a range of complex neural, endocrine, and paracrine mechanisms. This study examined a collection of 198 human genes related to BP regulation, in the biological processes and functional prisms, as well as gene expression in organs and tissues. This was made in conjunction with an orthology analysis performed in 19 target organisms along the phylogenetic tree. We have demonstrated that transport and signaling, as well as homeostasis in general, are the most prevalent biological processes associated with BP gene orthologs across the examined species. We showed that these genes and their orthologs are expressed primarily in the kidney and adrenals of complex organisms (e.g., high order vertebrates) and in the nervous system of low complexity organisms (e.g., flies, nematodes). Furthermore, we have determined that basic functions such as ion transport are ancient and appear in all organisms, while more complex regulatory functions, such as control of extracellular volume emerged in high order organisms. Thus, we conclude that the complex system of BP regulation evolved from simpler components that were utilized to maintain specific homeostatic functions that play key roles in existence and survival of organisms.

Exploring the Root Cause for Chronic Kidney Disease of Unknown Etiology (CKDu) via Analysis of Metal Ion and Counterion Contaminants in Drinking Water: A Study in Sri Lanka

The introduction of elevated amounts of foreign ions into the blood may lead to impairment of the filtration membrane of kidneys and chronic kidney damage. In order to assess the risk of consumption of drinking water (dug well water) in chronic kidney disease of unknown etiology (CKDu), affected areas in Sri Lanka, trace metals, and other counterions in water samples obtained from dug wells were analyzed and compared with a reference area. Drinking water could be the major source that is responsible for entering nephrotoxic ion contaminants into the human body. To achieve the objective, drinking water samples were collected from dug wells in two CKDu endemic areas and a reference area where no CKDu patients were found in a dry season. In the Wewelketiya area (one of the endemic areas), Cd concentrations in 60% of water samples and Pb concentrations in 40% of water samples have exceeded the maximum limit given by Sri Lanka water quality standards. Fluoride concentrations also have exceeded the permissible limits of more than 80% of collected water samples in both CKDu endemic areas. However, none of the water samples in reference areas has reported that Cd, Pb, and fluoride are beyond their maximum permissible limits. Hence, people in the particular CKDu endemic areas are at risk of kidney tissue damage due to long-term exposure to drinking water with elevated levels of some metal ions and counterions.

Transport Properties of Gramicidin A Ion Channel in a Free-Standing Lipid Bilayer Filled With Oil Inclusions

Ion channels are key proteins in mammalian cell membranes. They have a central role in the physiology of excitable cells such as neurons, muscle, and heart cells. They also play a crucial role in kidney physiology. The gramicidin ion channel is one of the most studied ion channels, in particular it was intensively employed to investigate the lipid–protein interactions in model cell membranes. For example, even though the sequence of gramicidin is extremely hydrophobic, its motion is impaired in membrane bilayer, i.e., it does not rapidly flip to the other membrane leaflet, and low channel activity were observed when gramicidin is added asymmetrically to only one leaflet of a model cell membrane. In this article, we study the transport properties of gramicidin channel in a heterogeneous model membrane. Using microfluidics, we are forming freestanding bilayers as model cell membranes including heterogeneous domains that are created by oil inclusions. The presence of oil inclusions is then demonstrated by measuring the bilayer capacity via a patch-clamp amplifier and fluorescent confocal inspection. Based on electrophysiological and optical measurements Gramicidin A (gA) ion channels are dispersed into the buffer phases on both side of the formed lipid bilayer and insert spontaneously into the bilayer upon formation. The presence of functional Gramicidin A is then demonstrated by measuring conductivity signals. Based on electrophysiological and optical measurements, we explore the consequence of the presence of these oil inclusions on the functionality of incorporated gA ion channels. For low oil concentration, we measure a decrease of gA transport properties due to the reduction of the bilayer tension. For large oil concentration, we measure a saturation of gA transport properties due to an increase of the bilayer thickness.

Macrocyclic Transmembrane Anion Transporters via a One-Pot Condensation Reaction

Synthetic chloride transporters are potential therapeutic agents for cystic fibrosis and cancer. Reported herein are macrocyclic transmembrane chloride transporters prepared by a one-pot condensation reaction. The most efficient macrocycle possesses a fine balance of hydrophobicity for membrane permeation and hydrophilicity for ion recognition. The macrocycle transports chloride ions by forming channels in the membrane. Hydrogen bonds and anion-π interactions assist chloride transport.

Mechanisms and regulation of chloride transport in the Malpighian tubules of the larval cabbage looper Trichoplusia ni

Malpighian tubules (MTs) and the hindgut together constitute the excretory system of insects. Larvae of lepidopterans (butterflies and moths) demonstrate the so-called cryptonephric arrangement, where the distal blind end of each MT is embedded into the rectal complex. The rest of the free tubule is modified into several distinct regions that differ greatly in the transport of cations and water. However, relatively little is known about the transport of counter-anions (e.g., Cl^- and HCO₃^-) by the MTs of lepidopteran larvae. In the current study we used ion-selective microelectrodes to characterize Cl^- transport in the distinct regions of the free MT of the larval Trichoplusia ni. Firstly, we note that Cl^- transport in the MTs is sensitive to the Cl^- concentration of the bathing saline, and several regions of the MTs are capable of either secreting or reabsorbing Cl^-. In the distal ileac plexus (DIP), a region previously characterized by cellular heterogeneity and its ability to switch between cation secretion and reabsorption, principal cells (PCs) toggled between Cl^- reabsorption (in high-Cl^- saline) and Cl^- secretion (in low-Cl^- saline). In contrast, secondary cells (SCs) in the DIP secreted Cl^- regardless of saline Cl^- concentration. Mechanistically, we have detected a number of 'leak' and ligand-gated Cl^- channels (ClC) and demonstrated that Cl^- channels are involved in Cl^- secretion. Additionally, we demonstrated that the lumen-positive transepithelial potential increased in response to glycine. Using the scanning ion-selective electrode technique we demonstrated that glycine stimulated Cl^- secretion by SCs, but not by PCs. In contrast, when MTs were deprived of glycine, a decrease in Cl^- secretion, coupled with a decrease in the TEP, was observed. In contrast to the effects of glycine, an active dose of helicokinin reduced Cl^- secretion by PCs, but not by SCs. Lastly, we detected expression of chloride-bicarbonate exchangers (CBE) in all regions of the free tubule. Scans of H⁺ transport across the tubule indicated that base equivalents are likely reabsorbed across the ileac plexus. Blocking ClC or CBE led to secretion of a more basic fluid, indicating lack of base reabsorption. We suggest that the transport of Cl^- in the MTs of larval lepidopterans (i) may be correlated with the reabsorption of base, (ii) may be sensitive to Cl^- concentration in the haemolymph, and (iii) could be regulated by helicokinin and glycine.

Activities of Ca2+-related ion channels during the formation of kidney stones in an infection-induced urolithiasis rat model

Bacterial infection has long been recognized to contribute to struvite urinary stone deposition; however, its contribution to the development of chronic kidney stones has not been extensively investigated. In the present study, we hypothesized another possible method of bacteria contributing to the formation of calcium oxalate (CaOx) that accounts for the biggest part of the kidney stone. Bacteria may play important roles by influencing renal Ca²⁺-related ion channel activities, resulting in chronic inflammation of the kidney along with rapid aggregation of stones. We examined the correlation among infection-promoted CaOx kidney stones and alterations in Ca²⁺-related ion channels in an animal model with experimentally induced Proteus mirabilis and foreign body infection. After the bladder was infected for 7 days, the data demonstrated that stones were presented and induced severe renal tubular breakage as well as altered levels of monocyte chemoattractant protein-1, cyclooxygenase-2, osteopontin, and transient receptor potential vanilloid member 5 expression, reflecting responses of kidney ion channels. Monocyte chemoattractant protein-1, osteopontin, and transient receptor potential vanilloid member 5 expression was significantly downregulated over time, indicating the chronic inflammation phase of the kidney and accelerated aggregation of CaOx crystals, respectively, whereas cyclooxygenase-2 exhibited no differences. These results indicated that bacterial infection is considerably correlated with an alteration in renal Ca²⁺-related ion channels and might support specific and targeted Ca²⁺-related ion channel-based therapeutics for urolithiasis and related inflammatory renal damage.

Mapping genes for calcium signaling and their associated human genetic disorders

Motivation

Signal transduction via calcium ions (Ca²⁺) represents a fundamental signaling pathway in all eukaryotic cells. A large portion of the human genome encodes proteins used to assemble signaling systems that can transduce signals with diverse spatial and temporal dynamics.

Results

Here, we provide a map of all of the genes involved in Ca²⁺ signaling and link these genes to human genetic disorders. Using Gene Ontology terms and genome databases, 1805 genes were identified as regulators or targets of intracellular Ca²⁺ signals. Associating these 1805 genes with human genetic disorders uncovered 1470 diseases with mutated ‘Ca²⁺ genes’. A network with scale-free properties appeared when the Ca²⁺ genes were mapped to their associated genetic disorders.

Availability and Implementation

The Ca²⁺ genome database is freely available at http://cagedb.uhlenlab.org and will foster studies of gene functions and genetic disorders associated with Ca²⁺ signaling.

Supplementary information

Supplementary data are available at Bioinformatics online.

Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry

We use atomistic nonequilibrium molecular dynamics simulations to demonstrate how specific ionic flux in peptide nanotubes can be regulated by tailoring the lumen chemistry through single amino acid substitutions. By varying the size and polarity of the functional group inserted into the nanotube interior, we are able to adjust the Na(+) flux by over an order of magnitude. Cl(-) is consistently denied passage. Bulky, nonpolar groups encourage interactions between the Na(+) and the peptide backbone carbonyl groups, disrupting the Na(+) solvation shell and slowing the transport of Na(+). Small groups have the opposite effect and accelerate flow. These results suggest that relative ion flux and selectivity can be precisely regulated in subnanometer pores by molecularly defining the lumen according to biological principles.

Cyst formation following disruption of intracellular calcium signaling

Mutations in polycystin 1 and 2 (PC1 and PC2) cause the common genetic kidney disorder autosomal dominant polycystic kidney disease (ADPKD). It is unknown how these mutations result in renal cysts, but dysregulation of calcium (Ca(2+)) signaling is a known consequence of PC2 mutations. PC2 functions as a Ca(2+)-activated Ca(2+) channel of the endoplasmic reticulum. We hypothesize that Ca(2+) signaling through PC2, or other intracellular Ca(2+) channels such as the inositol 1,4,5-trisphosphate receptor (InsP3R), is necessary to maintain renal epithelial cell function and that disruption of the Ca(2+) signaling leads to renal cyst development. The cell line LLC-PK1 has traditionally been used for studying PKD-causing mutations and Ca(2+) signaling in 2D culture systems. We demonstrate that this cell line can be used in long-term (8 wk) 3D tissue culture systems. In 2D systems, knockdown of InsP3R results in decreased Ca(2+) transient signals that are rescued by overexpression of PC2. In 3D systems, knockdown of either PC2 or InsP3R leads to cyst formation, but knockdown of InsP3R type 1 (InsP3R1) generated the largest cysts. InsP3R1 and InsP3R3 are differentially localized in both mouse and human kidney, suggesting that regional disruption of Ca(2+) signaling contributes to cystogenesis. All cysts had intact cilia 2 wk after starting 3D culture, but the cells with InsP3R1 knockdown lost cilia as the cysts grew. Studies combining 2D and 3D cell culture systems will assist in understanding how mutations in PC2 that confer altered Ca(2+) signaling lead to ADPKD cysts.

The number and location of EF hand motifs dictates the calcium dependence of polycystin-2 function

Polycystin 2 (PC2) is a calcium-dependent calcium channel, and mutations to human PC2 (hPC2) are associated with polycystic kidney disease. The C-terminal tail of hPC2 contains 2 EF hand motifs, but only the second binds calcium. Here, we investigate whether these EF hand motifs serve as a calcium sensor responsible for the calcium dependence of PC2 function. Using NMR and bioinformatics, we show that the overall fold is highly conserved, but in evolutionarily earlier species, both EF hands bind calcium. To test whether the EF hand motif is truly a calcium sensor controlling PC2 channel function, we altered the number of calcium binding sites in hPC2. NMR studies confirmed that modified hPC2 binds an additional calcium ion. Single-channel recordings demonstrated a leftward shift in the calcium dependence, and imaging studies in cells showed that calcium transients were enhanced compared with wild-type hPC2. However, biophysics and functional studies showed that the first EF hand can only bind calcium and be functionally active if the second (native) calcium-binding EF hand is intact. These results suggest that the number and location of calcium-binding sites in the EF hand senses the concentration of calcium required for PC2 channel activity and cellular function.