Cryo-EM structure of the calcium homeostasis modulator 1 channel

A mechanism of CALHM1 ion channel gating

The calcium homeostasis modulator (CALHM) proteins comprise a family of six genes, some of which have been demonstrated to function as ion channels. CALHM1, the founding member, is an extracellular Ca2+- and voltage-gated large-pore nonselective ion channel. The mechanisms by which Ca2+ and voltage regulate CALHM1 channel gating are unknown. Cryo-electron microscopic structures of CALHM1 and its paralogs have provided little insight into these features, although they have suggested that the amino-termini, including an amino-terminal helix (NTH) and the first transmembrane helix (TM1), may possess significant flexibility. Here, we investigated the role of the amino-terminus in the gating regulation of human CALHM1 channels expressed in Xenopus oocytes. Deletion of the NTH and the proximal end of TM1 markedly reduced the voltage dependence of channel gating, whereas extracellular Ca2+ retained the ability to close the channel, indicating that the amino-terminus is not the Ca2+-regulated gate. Furthermore, inhibition of channel currents by ruthenium red was independent of the presence of the amino-terminus and was mediated by effects on channel gating rather than pore block. The introduction of a cysteine residue into the proximal end of TM1 enabled complete inhibition of the channel by a cross-linking reagent under conditions in which the channel was in a closed state. Our findings indicate that although the NTH plays a role in voltage-dependent gating, it does not act as the gate itself. Instead, our results suggest that the gate in CALHM1 is formed by proximal regions of the first transmembrane domain.NEW & NOTEWORTHY CALHM1 is a voltage- and extracellular Ca2+-regulated large-pore ion channel that plays an essential role in taste perception. The mechanisms that regulate the opening and the closing of the channel are unknown. Here we explored the role of the amino-terminal region of the channel in gating regulation. Our data define the roles of the amino-terminus in channel gating, establishing components essential for the opening and closing of the CALHM1 channel gate.

Activated human Orai1 channel in lipid biolayer may exist as a pentamer

The human Orai1 (hOrai1) channel plays a crucial role in extracellular Ca2+ influx and has emerged as an attractive drug target for various diseases. However, the activated structure of the hOrai1 channel assembly within a lipid bilayer remains unknown. In this study, we expressed and purified the hOrai1 channel covalently linked to two SOAR tandems (HOSS). Patch-clamp experiments in whole-cell configuration showed that HOSS is constitutively active. Biochemical characterization confirmed that the purified HOSS channels were successfully incorporated into MSP1E3D1 nanodiscs. Negative staining revealed that the HOSS channels resemble a mushroom, with the body representing the hOrai1 channel and the leg representing the SOAR domain. Surprisingly, 2D analysis of cryo-EM data demonstrated a pentameric assembly of HOSS in a lipid bilayer. Our findings suggest that the hOrai1 channel may assemble into different oligomeric states in response to varying membrane environments.

Oligomeric rearrangement may regulate channel activity

Channels are typically gated by several factors, including voltage, ligand and mechanical force. Most members of the calcium homeostasis modulator (CALHM) protein family, large-pore ATP release channels, exist in different oligomeric states. Dynamic conversions between CALHM1 heptamers and octamers to gate the channel were proposed. Meanwhile, the latest study observed that the transient receptor potential vanilloid 3 (TRPV3) channel adopts a dynamic transition between pentamers and canonical tetramers in response to small molecule treatment. These results suggest that oligomeric rearrangement may add a new layer to regulate the channel activities.

Biology, function and structure of the calcium homeostasis modulator family

Calcium homeostasis modulators (CALHMs) are the most recently discovered members of the large-pore channel family. They mediate the conductance of ions and larger molecules, such as ATP, and play critical roles in pathways related to Alzheimer's disease, neuroinflammation, neuromodulation, taste perception and innate immune responses. Since the inaugural report on CALHM1 in 2008, significant breakthroughs have revealed their biological roles, ion and ATP channel functions, and structures, positioning the field for further advancements. In this review, we discuss the overall progress and recent developments in understanding the biological roles, functions and molecular structures of CALHM proteins.

Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs

The CALHM proteins constitute a family of large pore channels that contains six closely related paralogs in humans. Two family members, CALHM1 and 3, have been associated with the release of ATP during taste sensation. Both proteins form heteromeric channels that activate at positive potential and decreased extracellular Ca2+ concentration. Although the structures of several family members displayed large oligomeric organizations of different size, their function has in most cases remained elusive. Our previous study has identified the paralogs CALHM2, 4 and, 6 to be highly expressed in the placenta and defined their structural properties as membrane proteins exhibiting features of large pore channels with unknown activation properties (Drożdżyk et al., 2020). Here, we investigated whether these placental paralogs would form heteromers and characterized heteromeric complexes consisting of CALHM2 and CALHM4 subunits using specific binders as fiducial markers. Both proteins assemble with different stoichiometries with the largest population containing CALHM2 as the predominant component. In these oligomers, the subunits segregate and reside in their preferred conformation found in homomeric channels. Our study has thus revealed the properties that govern the formation of CALHM heteromers in a process of potential relevance in a cellular context.

Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes

Genetic and genomic analyses of longitudinal traits related to milk production efficiency are paramount for optimizing water buffaloes breeding schemes. Therefore, this study aimed to (1) compare single-trait random regression models under a single-step genomic BLUP setting based on alternative covariance functions (i.e., Wood, Wilmink, and Ali and Schaeffer) to describe milk (MY), fat (FY), protein (PY), and mozzarella (MZY) yields, fat-to-protein ratio (FPR), somatic cell score (SCS), lactation length (LL), and lactation persistency (LP) in Murrah dairy buffaloes (Bubalus bubalis); (2) combine the best functions for each trait under a multiple-trait framework; (3) estimate time-dependent SNP effects for all the studied longitudinal traits; and (4) identify the most likely candidate genes associated with the traits. A total of 323,140 test-day records from the first lactation of 4,588 Murrah buffaloes were made available for the study. The model included the average curve of the population nested within herd-year-season of calving, systematic effects of number of milkings per day, and age at first calving as linear and quadratic covariates, and additive genetic, permanent environment, and residual as random effects. The Wood model had the best goodness of fit based on the deviance information criterion and posterior model probabilities for all traits. Moderate heritabilities were estimated over time for most traits (0.30 ± 0.02 for MY; 0.26 ± 0.03 for FY; 0.45 ± 0.04 for PY; 0.28 ± 0.05 for MZY; 0.13 ± 0.02 for FPR; and 0.15 ± 0.03 for SCS). The heritability estimates for LP ranged from 0.38 ± 0.02 to 0.65 ± 0.03 depending on the trait definition used. Similarly, heritabilities estimated for LL ranged from 0.10 ± 0.01 to 0.14 ± 0.03. The genetic correlation estimates across days in milk (DIM) for all traits ranged from -0.06 (186-215 DIM for MY-SCS) to 0.78 (66-95 DIM for PY-MZY). The SNP effects calculated for the random regression model coefficients were used to estimate the SNP effects throughout the lactation curve (from 5 to 305 d). Numerous relevant genomic regions and candidate genes were identified for all traits, confirming their polygenic nature. The candidate genes identified contribute to a better understanding of the genetic background of milk-related traits in Murrah buffaloes and reinforce the value of incorporating genomic information in their breeding programs.

The multifaceted role of extracellular ATP in sperm function: From spermatogenesis to fertilization

Extracellular adenosine 5'-triphosphate (ATP) is a vital signaling molecule involved in various physiological processes within the body. In recent years, studies have revealed its significant role in male reproduction, particularly in sperm function. This review explores the multifaceted role of extracellular ATP in sperm function, from spermatogenesis to fertilization. We discuss the impact of extracellular ATP on spermatogenesis, sperm maturation and sperm-egg fusion, highlighting the complex regulatory mechanisms and potential clinical applications in the context of male infertility. By examining the latest research, we emphasize the crucial role of extracellular ATP in sperm function and propose future research directions to further.

CALHM2 V136G polymorphism reduces astrocytic ATP release and is associated with depressive symptoms and Alzheimer's disease risk

INTRODUCTION

Depression is considered a prodromal state of Alzheimer's disease (AD), yet the underlying mechanism(s) by which depression increases the risk of AD are not known.

METHODS

Single-nucleotide polymorphism (SNP) analysis was used to determine the CALHM2 variants in AD patients. Cellular and molecular experiments were conducted to investigate the function of CALHM2 V136G mutation. We generated a new genetically engineered Calhm2 V136G mouse model and performed behavioral tests with these mice.

RESULTS

CALHM2 V136G mutation (rs232660) is significantly associated with AD. V136G mutation resulted in loss of the CALHM2 ATP-release function in astrocytes and impaired synaptic plasticity. Mice homozygous for the Calhm2 V136G allele displayed depressive-like behaviors that were rescued by administration of exogenous ATP. Moreover, Calhm2 V136G mutation predisposed mice to cognitive decline in old age.

DISCUSSION

CALHM2 dysfunction is a biologically relevant mechanism that may contribute to the observed clinical correlation between depression and AD.

To Be or Not to Be an Ion Channel: Cryo-EM Structures Have a Say

Ion channels are the second largest class of drug targets after G protein-coupled receptors. In addition to well-recognized ones like voltage-gated Na/K/Ca channels in the heart and neurons, novel ion channels are continuously discovered in both excitable and non-excitable cells and demonstrated to play important roles in many physiological processes and diseases such as developmental disorders, neurodegenerative diseases, and cancer. However, in the field of ion channel discovery, there are an unignorable number of published studies that are unsolid and misleading. Despite being the gold standard of a functional assay for ion channels, electrophysiological recordings are often accompanied by electrical noise, leak conductance, and background currents of the membrane system. These unwanted signals, if not treated properly, lead to the mischaracterization of proteins with seemingly unusual ion-conducting properties. In the recent ten years, the technical revolution of cryo-electron microscopy (cryo-EM) has greatly advanced our understanding of the structures and gating mechanisms of various ion channels and also raised concerns about the pore-forming ability of some previously identified channel proteins. In this review, we summarize cryo-EM findings on ion channels with molecular identities recognized or disputed in recent ten years and discuss current knowledge of proposed channel proteins awaiting cryo-EM analyses. We also present a classification of ion channels according to their architectures and evolutionary relationships and discuss the possibility and strategy of identifying more ion channels by analyzing structures of transmembrane proteins of unknown function. We propose that cross-validation by electrophysiological and structural analyses should be essentially required for determining molecular identities of novel ion channels.

Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red

Calcium homeostasis modulator 1 (CALHM1) is a voltage-dependent channel involved in neuromodulation and gustatory signaling. Despite recent progress in the structural biology of CALHM1, insights into functional regulation, pore architecture, and channel blockade remain limited. Here we present the cryo-EM structure of human CALHM1, revealing an octameric assembly pattern similar to the non-mammalian CALHM1s and the lipid-binding pocket conserved across species. We demonstrate by MD simulations that this pocket preferentially binds a phospholipid over cholesterol to stabilize its structure and regulate the channel activities. Finally, we show that residues in the amino-terminal helix form the channel pore that ruthenium red binds and blocks.

Bidirectional sensitivity of CALHM1 channel to protons from both sides of plasma membrane

Calcium homeostasis modulator 1 (CALHM1), a newly discovered voltage-dependent nonselective ion channel, has drawn attention for its role in neuronal activity and taste sensation. Its sluggish voltage-dependent activation is facilitated by lowering extracellular Ca²⁺ concentration ([Ca²⁺]_e). Here, we investigated the effects of extracellular and intracellular pH (pH_e and pH_i) on human CALHM1. When normalized to the amplitude of the CALHM1 current (I_CALHM1) under whole cell patch clamp at symmetrical pH 7.4, I_CALHM1 decreased at acidic pH_e or pH_i, whereas it sharply increased at alkaline pH_e or pH_i. The effects of pH were preserved in the inside-out configuration. The voltage dependence of I_CALHM1 showed leftward and rightward shifts at alkaline and acidic pH_e and pH_i, respectively. Site-directed mutagenesis of the water-accessible charged residues of the pore and nearby domains revealed that E17, K229, E233, D257, and E259 are nonadditively responsible for facilitation at alkaline pH_i. Identification of the pH_e-sensing residue was not possible because mutation of putative residues impaired membrane expression, resulting in undetectable I_CALHM1. Alkaline pH_e-dependent facilitation appeared gradually with depolarization, suggesting that the sensitivity to pH_e might be due to H⁺ diffusion through the open-state CALHM1. At pH_e 6.2, decreased [Ca²⁺]_e could not recover the inhibited I_CALHM1 but further augmented the increased I_CALHM1 at pH_e 8.6, suggesting that unidentified common residues might contribute to the [Ca²⁺]_e and acidic pH_e. This study is the first, to our knowledge, to demonstrate the remarkable pH sensitivity of CALHM1, which might contribute to the pH-dependent modulation of neuronal excitability or taste sensation.

Dark-Field Imaging Monitoring of Adenosine Triphosphate in Live Cells by Au NBPs@ZIF-8 Nanoprobes

Monitoring the fluctuation of adenosine triphosphate (ATP) level in living cells could promote the understanding of metabolic pathways and cell biology. Here, we proposed a highly sensitive, selective, and biocompatible nanoprobe with core-shell structure, namely Au NBPs@ZIF-8 composed by gold nanobipyramids (Au NBPs) and zeolitic imidazolate framework-8 (ZIF-8), for monitoring intracellular ATP level fluctuation in living cells. Because the coordination between ATP and Zn²⁺ (the metal node of ZIF-8) was much stronger than that between 2-methylimidazole and Zn²⁺, which caused the decomposition of the ZIF-8 shell and the exposure of Au NBPs in the presence of ATP, it led to the change of the localized surface plasmon resonance scattering properties of nanoprobes under dark-field microscopy. Tricolor (RGB) analysis showed that R/G value had a good linear relationship with the ATP concentrations in the range of 10 μM to 4 mM (R² = 0.999) with a detection limit of 5.28 μM. This ATP sensing platform also exhibited excellent selectivity in complex intracellular interfering substances. Besides, we realized intracellular ATP real-time imaging in HeLa cells and observed the ATP level fluctuation under dark-field microscopy. The method mentioned here could be further applied for delivery of therapeutics for biomedical applications.

Cryo-EM structure of the heptameric calcium homeostasis modulator 1 channel

Calcium homeostasis modulator 1 (CALHM1) is a voltage- and Ca²⁺-gated ATP channel that plays an important role in neuronal signaling. However, as the previously reported CALHM structures are all in the ATP-conducting state, the gating mechanism of ATP permeation is still elusive. Here, we report cryo-EM reconstructions of two Danio rerio CALHM1 heptamers with ordered or flexible long C-terminal helices at resolutions of 3.2 Å and 2.9 Å, respectively, and one D. rerio CALHM1 octamer with flexible long C-terminal helices at a resolution of 3.5 Å. Structural analysis shows that the heptameric CALHM1s are in an ATP-nonconducting state with a central pore diameter of approximately 6.6 Å. Compared with those inside the octameric CALHM1, the N-helix inside the heptameric CALHM1 is in the “down” position to avoid steric clashing with the adjacent TM1 helix. Molecular dynamics simulations show that as the N-helix moves from the “down” position to the “up” position, the pore size of ATP molecule permeation increases significantly. Our results provide important information for elucidating the mechanism of ATP molecule permeation in the CALHM1 channel.

Intramolecular Disulfide Bonds for Biogenesis of CALHM1 Ion Channel Are Dispensable for Voltage-Dependent Activation

Calcium homeostasis modulator 1 (CALHM1) is a membrane protein with four transmembrane helices that form an octameric ion channel with voltage-dependent activation. There are four conserved cysteine (Cys) residues in the extracellular domain that form two intramolecular disulfide bonds. We investigated the roles of C42-C127 and C44-C161 in human CALHM1 channel biogenesis and the ionic current (ICALHM1). Replacing Cys with Ser or Ala abolished the membrane trafficking as well as ICALHM1. Immunoblotting analysis revealed dithiothreitol-sensitive multimeric CALHM1, which was markedly reduced in C44S and C161S, but preserved in C42S and C127S. The mixed expression of C42S and wild-type did not show a dominant-negative effect. While the heteromeric assembly of CALHM1 and CALHM3 formed active ion channels, the co-expression of C42S and CALHM3 did not produce functional channels. Despite the critical structural role of the extracellular cysteine residues, a treatment with the membrane-impermeable reducing agent tris(2-carboxyethyl) phosphine (TCEP, 2 mM) did not affect ICALHM1 for up to 30 min. Interestingly, incubation with TCEP (2 mM) for 2-6 h reduced both ICALHM1 and the surface expression of CALHM1 in a time-dependent manner. We propose that the intramolecular disulfide bonds are essential for folding, oligomerization, trafficking and maintenance of CALHM1 in the plasma membrane, but dispensable for the voltage-dependent activation once expressed on the plasma membrane.

On the molecular nature of large-pore channels

Membrane transport is a fundamental means to control basic cellular processes such as apoptosis, inflammation, and neurodegeneration and is mediated by a number of transporters, pumps, and channels. Accumulating evidence over the last half century has shown that a type of so-called "large-pore channel" exists in various tissues and organs in gap-junctional and non-gap-junctional forms in order to flow not only ions but also metabolites such as ATP. They are formed by a number of protein families with little or no evolutionary linkages including connexin, innexin, pannexin, leucine-rich repeat-containing 8 (LRRC8), and calcium homeostasis modulator (CALHM). This review summarizes the history and concept of large-pore channels starting from connexin gap junction channels to the more recent developments in innexin, pannexin, LRRC8, and CALHM. We describe structural and functional features of large-pore channels that are crucial for their diverse functions on the basis of available structures.

Upregulation of Calcium Homeostasis Modulators in Contractile-To-Proliferative Phenotypical Transition of Pulmonary Arterial Smooth Muscle Cells

Excessive pulmonary artery (PA) smooth muscle cell (PASMC) proliferation and migration are implicated in the development of pathogenic pulmonary vascular remodeling characterized by concentric arterial wall thickening and arteriole muscularization in patients with pulmonary arterial hypertension (PAH). Pulmonary artery smooth muscle cell contractile-to-proliferative phenotypical transition is a process that promotes pulmonary vascular remodeling. A rise in cytosolic Ca2+ concentration [(Ca2+) cyt ] in PASMCs is a trigger for pulmonary vasoconstriction and a stimulus for pulmonary vascular remodeling. Here, we report that the calcium homeostasis modulator (CALHM), a Ca2+ (and ATP) channel that is allosterically regulated by voltage and extracellular Ca2+, is upregulated during the PASMC contractile-to-proliferative phenotypical transition. Protein expression of CALHM1/2 in primary cultured PASMCs in media containing serum and growth factors (proliferative PASMC) was significantly greater than in freshly isolated PA (contractile PASMC) from the same rat. Upregulated CALHM1/2 in proliferative PASMCs were associated with an increased ratio of pAKT/AKT and pmTOR/mTOR and an increased expression of the cell proliferation marker PCNA, whereas serum starvation and rapamycin significantly downregulated CALHM1/2. Furthermore, CALHM1/2 were upregulated in freshly isolated PA from rats with monocrotaline (MCT)-induced PH and in primary cultured PASMC from patients with PAH in comparison to normal controls. Intraperitoneal injection of CGP 37157 (0.6 mg/kg, q8H), a non-selective blocker of CALHM channels, partially reversed established experimental PH. These data suggest that CALHM upregulation is involved in PASMC contractile-to-proliferative phenotypical transition. Ca2+ influx through upregulated CALHM1/2 may play an important role in the transition of sustained vasoconstriction to excessive vascular remodeling in PAH or precapillary PH. Calcium homeostasis modulator could potentially be a target to develop novel therapies for PAH.

Posttranslational regulation of CALHM1/3 channel: N-linked glycosylation and S-palmitoylation

Among calcium homeostasis modulator (CALHM) family members, CALHM1 and 3 together form a voltage-gated large-pore ion channel called CALHM1/3. CALHM1/3 plays an essential role in taste perception by mediating neurotransmitter release at channel synapses of taste bud cells. However, it is poorly understood how CALHM1/3 is regulated. Biochemical analyses of the two subunits following site-directed mutagenesis and pharmacological treatments established that both CALHM1 and 3 were N-glycosylated at single Asn residues in their second extracellular loops. Biochemical and electrophysiological studies revealed that N-glycan acquisition on CALHM1 and 3, respectively, controls the biosynthesis and gating kinetics of the CALHM1/3 channel. Furthermore, failure in subsequent remodeling of N-glycans decelerated the gating kinetics. Thus, the acquisition of N-glycans on both subunits and their remodeling differentially contribute to the functional expression of CALHM1/3. Meanwhile, metabolic labeling and acyl-biotin exchange assays combined with genetic modification demonstrated that CALHM3 was reversibly palmitoylated at three intracellular Cys residues. Screening of the DHHC protein acyltransferases identified DHHC3 and 15 as CALHM3 palmitoylating enzymes. The palmitoylation-deficient mutant CALHM3 showed a normal degradation rate and interaction with CALHM1. However, the same mutation markedly attenuated the channel activity but not surface localization of CALHM1/3, suggesting that CALHM3 palmitoylation is a critical determinant of CALHM1/3 activity but not its formation or forward trafficking. Overall, this study characterized N-glycosylation and S-palmitoylation of CALHM1/3 subunits and clarified their differential contributions to its functional expression, providing insights into the fine control of the CALHM1/3 channel and associated physiological processes.

Taste transduction and channel synapses in taste buds

The variety of taste sensations, including sweet, umami, bitter, sour, and salty, arises from diverse taste cells, each of which expresses specific taste sensor molecules and associated components for downstream signal transduction cascades. Recent years have witnessed major advances in our understanding of the molecular mechanisms underlying transduction of basic tastes in taste buds, including the identification of the bona fide sour sensor H⁺ channel OTOP1, and elucidation of transduction of the amiloride-sensitive component of salty taste (the taste of sodium) and the TAS1R-independent component of sweet taste (the taste of sugar). Studies have also discovered an unconventional chemical synapse termed "channel synapse" which employs an action potential-activated CALHM1/3 ion channel instead of exocytosis of synaptic vesicles as the conduit for neurotransmitter release that links taste cells to afferent neurons. New images of the channel synapse and determinations of the structures of CALHM channels have provided structural and functional insights into this unique synapse. In this review, we discuss the current view of taste transduction and neurotransmission with emphasis on recent advances in the field.