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Hu M, Feng X, Liu Q, Liu S, Huang F, Xu H. The ion channels of endomembranes. Physiol Rev 2024; 104:1335-1385. [PMID: 38451235 DOI: 10.1152/physrev.00025.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The endomembrane system consists of organellar membranes in the biosynthetic pathway [endoplasmic reticulum (ER), Golgi apparatus, and secretory vesicles] as well as those in the degradative pathway (early endosomes, macropinosomes, phagosomes, autophagosomes, late endosomes, and lysosomes). These endomembrane organelles/vesicles work together to synthesize, modify, package, transport, and degrade proteins, carbohydrates, and lipids, regulating the balance between cellular anabolism and catabolism. Large ion concentration gradients exist across endomembranes: Ca2+ gradients for most endomembrane organelles and H+ gradients for the acidic compartments. Ion (Na+, K+, H+, Ca2+, and Cl-) channels on the organellar membranes control ion flux in response to cellular cues, allowing rapid informational exchange between the cytosol and organelle lumen. Recent advances in organelle proteomics, organellar electrophysiology, and luminal and juxtaorganellar ion imaging have led to molecular identification and functional characterization of about two dozen endomembrane ion channels. For example, whereas IP3R1-3 channels mediate Ca2+ release from the ER in response to neurotransmitter and hormone stimulation, TRPML1-3 and TMEM175 channels mediate lysosomal Ca2+ and H+ release, respectively, in response to nutritional and trafficking cues. This review aims to summarize the current understanding of these endomembrane channels, with a focus on their subcellular localizations, ion permeation properties, gating mechanisms, cell biological functions, and disease relevance.
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Affiliation(s)
- Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xinghua Feng
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiang Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Siyu Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Fangqian Huang
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States
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2
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Greene D, Shiferaw Y. A structure-based computational model of IP 3R1 incorporating Ca and IP3 regulation. Biophys J 2024; 123:1274-1288. [PMID: 38627970 PMCID: PMC11140470 DOI: 10.1016/j.bpj.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/20/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
The inositol 1,4,5-triphosphate receptor (IP3R) mediates Ca release in many cell types and is pivotal to a wide range of cellular processes. High-resolution cryoelectron microscopy studies have provided new structural details of IP3R type 1 (IP3R1), showing that channel function is determined by the movement of various domains within and between each of its four subunits. Channel properties are regulated by ligands, such as Ca and IP3, which bind at specific sites and control the interactions between these domains. However, it is not known how the various ligand-binding sites on IP3R1 interact to control the opening of the channel. In this study, we present a coarse-grained model of IP3R1 that accounts for the channel architecture and the location of specific Ca- and IP3-binding sites. This computational model accounts for the domain-domain interactions within and between the four subunits that form IP3R1, and it also describes how ligand binding regulates these interactions. Using a kinetic model, we explore how two Ca-binding sites on the cytosolic side of the channel interact with the IP3-binding site to regulate the channel open probability. Our primary finding is that the bell-shaped open probability of IP3R1 provides constraints on the relative strength of these regulatory binding sites. In particular, we argue that a specific Ca-binding site, whose function has not yet been established, is very likely a channel antagonist. Additionally, we apply our model to show that domain-domain interactions between neighboring subunits exert control over channel cooperativity and dictate the nonlinear response of the channel to Ca concentration. This suggests that specific domain-domain interactions play a pivotal role in maintaining the channel's stability, and a disruption of these interactions may underlie disease states associated with Ca dysregulation.
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Affiliation(s)
- D'Artagnan Greene
- Department of Physics & Astronomy, California State University, Northridge, California
| | - Yohannes Shiferaw
- Department of Physics & Astronomy, California State University, Northridge, California.
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3
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Mughal A, Sackheim AM, Koide M, Bonson G, Ebner G, Hennig G, Lockette W, Nelson MT, Freeman K. Pathogenic soluble tau peptide disrupts endothelial calcium signaling and vasodilation in the brain microvasculature. J Cereb Blood Flow Metab 2024; 44:680-688. [PMID: 38420777 PMCID: PMC11197144 DOI: 10.1177/0271678x241235790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/27/2024] [Indexed: 03/02/2024]
Abstract
The accumulation of the microtubule-associated tau protein in and around blood vessels contributes to brain microvascular dysfunction through mechanisms that are incompletely understood. Delivery of nutrients to active neurons in the brain relies on capillary calcium (Ca2+) signals to direct blood flow. The initiation and amplification of endothelial cell Ca2+ signals require an intact microtubule cytoskeleton. Since tau accumulation in endothelial cells disrupts native microtubule stability, we reasoned that tau-induced microtubule destabilization would impair endothelial Ca2+ signaling. We tested the hypothesis that tau disrupts the regulation of local cerebral blood flow by reducing endothelial cell Ca2+ signals and endothelial-dependent vasodilation. We used a pathogenic soluble tau peptide (T-peptide) model of tau aggregation and mice with genetically encoded endothelial Ca2+ sensors to measure cerebrovascular endothelial responses to tau exposure. T-peptide significantly attenuated endothelial Ca2+ activity and cortical capillary blood flow in vivo. Further, T-peptide application constricted pressurized cerebral arteries and inhibited endothelium-dependent vasodilation. This study demonstrates that pathogenic tau alters cerebrovascular function through direct attenuation of endothelial Ca2+ signaling and endothelium-dependent vasodilation.
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Affiliation(s)
- Amreen Mughal
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Adrian M Sackheim
- Department of Emergency Medicine, University of Vermont, Burlington, VT, USA
| | - Masayo Koide
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Grace Bonson
- Department of Emergency Medicine, University of Vermont, Burlington, VT, USA
| | - Grace Ebner
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Grant Hennig
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Warren Lockette
- Division of Endocrinology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Mark T Nelson
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - Kalev Freeman
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
- Department of Emergency Medicine, University of Vermont, Burlington, VT, USA
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4
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Davis MJ, Zawieja SD. Pacemaking in the lymphatic system. J Physiol 2024. [PMID: 38520402 DOI: 10.1113/jp284752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/25/2024] Open
Abstract
Lymphatic collecting vessels exhibit spontaneous phasic contractions that are critical for lymph propulsion and tissue fluid homeostasis. This rhythmic activity is driven by action potentials conducted across the lymphatic muscle cell (LMC) layer to produce entrained contractions. The contraction frequency of a lymphatic collecting vessel displays exquisite mechanosensitivity, with a dynamic range from <1 to >20 contractions per minute. A myogenic pacemaker mechanism intrinsic to the LMCs was initially postulated to account for pressure-dependent chronotropy. Further interrogation into the cellular constituents of the lymphatic vessel wall identified non-muscle cell populations that shared some characteristics with interstitial cells of Cajal, which have pacemaker functions in the gastrointestinal and lower urinary tracts, thus raising the possibility of a non-muscle cell pacemaker. However, recent genetic knockout studies in mice support LMCs and a myogenic origin of the pacemaker activity. LMCs exhibit stochastic, but pressure-sensitive, sarcoplasmic reticulum calcium release (puffs and waves) from IP3R1 receptors, which couple to the calcium-activated chloride channel Anoctamin 1, causing depolarisation. The resulting electrical activity integrates across the highly coupled lymphatic muscle electrical syncytia through connexin 45 to modulate diastolic depolarisation. However, multiple other cation channels may also contribute to the ionic pacemaking cycle. Upon reaching threshold, a voltage-gated calcium channel-dependent action potential fires, resulting in a nearly synchronous calcium global calcium flash within the LMC layer to drive an entrained contraction. This review summarizes the key ion channels potentially responsible for the pressure-dependent chronotropy of lymphatic collecting vessels and various mechanisms of IP3R1 regulation that could contribute to frequency tuning.
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Affiliation(s)
- Michael J Davis
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Scott D Zawieja
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO, USA
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5
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Engevik KA, Scribano FJ, Gebert JT, Perry JL, Crawford SE, Hyser JM. Distribution of P2Y and P2X purinergic receptor expression within the intestine. Am J Physiol Gastrointest Liver Physiol 2024; 326:G107-G119. [PMID: 37987757 PMCID: PMC11208031 DOI: 10.1152/ajpgi.00108.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Nucleotides are potent extracellular signaling molecules during homeostasis, infection, and injury due to their ability to activate purinergic receptors. The nucleotide ATP activates P2X receptors (P2RXs), whereas the nucleotides ADP, ATP, UTP, and UDP-glucose selectively activate different P2Y receptors (P2RYs). Several studies have established crucial roles for P2 receptors during intestinal inflammatory and infectious diseases, yet the most extensive characterization of purinergic signaling has focused on immune cells and the central and enteric nervous systems. As epithelial cells serve as the first barrier against irritants and infection, we hypothesized that the gut epithelium may express multiple purinergic receptors that respond to extracellular nucleotide signals. Using the Human Protein Atlas and Gut Cell Survey, we queried single-cell RNA sequencing (RNAseq) data for the P2 purinergic receptors in the small and large intestines. In silico analysis reveals robust mRNA expression of P2RY1, P2RY2, P2RY11, and P2RX4 throughout the gastrointestinal tract. Human intestinal organoids exhibited a similar expression pattern with a prominent expression of P2RY1, P2RY2, and P2RX4, but this purinergic receptor repertoire was not conserved in T84, Caco2, and HT29 intestinal epithelial cell lines. Finally, P2YR1 and P2YR2 agonists elicited robust calcium responses in human intestinal organoids, but calcium responses were weaker or absent in the cell lines. These findings suggest that the gastrointestinal epithelia respond to extracellular purinergic signaling via P2RY1, P2RY2, P2RY11, and P2RX4 receptors and highlight the benefit of using intestinal organoids as a model of intestinal purinergic signaling.NEW & NOTEWORTHY Several studies have revealed crucial roles for P2 receptors during inflammatory and infectious diseases, however, these have largely been demonstrated in immune cells and the enteric nervous system. Although epithelial cells serve as the first barrier against infection and inflammation, the role of purinergic signaling within the gastrointestinal tract remains largely unknown. This work expands our knowledge of purinergic receptor distribution and relative expression along the intestine.
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Affiliation(s)
- Kristen A Engevik
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
| | - Francesca J Scribano
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
| | - J Thomas Gebert
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
| | - Jacob L Perry
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
| | - Sue E Crawford
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
| | - Joseph M Hyser
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States
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Yuan Y, Arige V, Saito R, Mu Q, Brailoiu GC, Pereira GJS, Bolsover SR, Keller M, Bracher F, Grimm C, Brailoiu E, Marchant JS, Yule DI, Patel S. Two-pore channel-2 and inositol trisphosphate receptors coordinate Ca 2+ signals between lysosomes and the endoplasmic reticulum. Cell Rep 2024; 43:113628. [PMID: 38160394 PMCID: PMC10931537 DOI: 10.1016/j.celrep.2023.113628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Lysosomes and the endoplasmic reticulum (ER) are Ca2+ stores mobilized by the second messengers NAADP and IP3, respectively. Here, we establish Ca2+ signals between the two sources as fundamental building blocks that couple local release to global changes in Ca2+. Cell-wide Ca2+ signals evoked by activation of endogenous NAADP-sensitive channels on lysosomes comprise both local and global components and exhibit a major dependence on ER Ca2+ despite their lysosomal origin. Knockout of ER IP3 receptor channels delays these signals, whereas expression of lysosomal TPC2 channels accelerates them. High-resolution Ca2+ imaging reveals elementary events upon TPC2 opening and signals coupled to IP3 receptors. Biasing TPC2 activation to a Ca2+-permeable state sensitizes local Ca2+ signals to IP3. This increases the potency of a physiological agonist to evoke global Ca2+ signals and activate a downstream target. Our data provide a conceptual framework to understand how Ca2+ release from physically separated stores is coordinated.
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Affiliation(s)
- Yu Yuan
- Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Vikas Arige
- Department of Pharmacology and Physiology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Ryo Saito
- Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, UK; Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Qianru Mu
- Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Gabriela C Brailoiu
- Department of Pharmaceutical Sciences, Jefferson College of Pharmacy, Thomas Jefferson University, 901 Walnut Street, Philadelphia, PA 19107, USA
| | - Gustavo J S Pereira
- Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, UK; Department of Pharmacology, Federal University of São Paulo (UNIFESP), São Paulo 04044-020, Brazil
| | - Stephen R Bolsover
- Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Marco Keller
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilian University, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Franz Bracher
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilian University, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Christian Grimm
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilian University, Nussbaumstrasse 26, 80336 Munich, Germany; Immunology, Infection and Pandemic Research IIP, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596 Frankfurt, Germany
| | - Eugen Brailoiu
- Department of Neural Sciences and Center for Substance Abuse Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Jonathan S Marchant
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, UK.
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7
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Lemos FO, de Ridder I, Bootman MD, Bultynck G, Parys JB. The Complex Effects of PKM2 and PKM2:IP 3R Disruption on Intracellular Ca 2+ Handling and Cellular Functions. Cells 2023; 12:2527. [PMID: 37947604 PMCID: PMC10647343 DOI: 10.3390/cells12212527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pyruvate kinase M (PKM) 2 was described to interact with the inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) and suppress its activity. To further investigate the physiological importance of the PKM2:IP3R interaction, we developed and characterized HeLa PKM2 knockout (KO) cells. In the HeLa PKM2 KO cells, the release of Ca2+ to the cytosol appears to be more sensitive to low agonist concentrations than in HeLa wild-type (WT) cells. However, upon an identical IP3-induced Ca2+ release, Ca2+ uptake in the mitochondria is decreased in HeLa PKM2 KO cells, which may be explained by the smaller number of contact sites between the ER and the mitochondria. Furthermore, in HeLa PKM2 KO cells, mitochondria are more numerous, though they are smaller and less branched and have a hyperpolarized membrane potential. TAT-D5SD, a cell-permeable peptide representing a sequence derived from IP3R1 that can disrupt the PKM2:IP3R interaction, induces Ca2+ release into the cytosol and Ca2+ uptake into mitochondria in both HeLa WT and PKM2 KO cells. Moreover, TAT-D5SD induced apoptosis in HeLa WT and PKM2 KO cells but not in HeLa cells completely devoid of IP3Rs. These results indicate that PKM2 separately regulates cytosolic and mitochondrial Ca2+ handling and that the cytotoxic effect of TAT-D5SD depends on IP3R activity but not on PKM2. However, the tyrosine kinase Lck, which also interacts with the D5SD sequence, is expressed neither in HeLa WT nor PKM2 KO cells, and we can also exclude a role for PKM1, which is upregulated in HeLa PKM2 KO cells, indicating that the TAT-D5SD peptide has a more complex mode of action than anticipated.
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Affiliation(s)
- Fernanda O. Lemos
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
| | - Ian de Ridder
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
| | - Martin D. Bootman
- School of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK;
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
| | - Jan B. Parys
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
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8
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Rönkkö J, Rodriguez Y, Rasila T, Torregrosa-Muñumer R, Pennonen J, Kvist J, Kuuluvainen E, Bosch LVD, Hietakangas V, Bultynck G, Tyynismaa H, Ylikallio E. Human IP 3 receptor triple knockout stem cells remain pluripotent despite altered mitochondrial metabolism. Cell Calcium 2023; 114:102782. [PMID: 37481871 DOI: 10.1016/j.ceca.2023.102782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/14/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ER Ca2+-release channels that control a broad set of cellular processes. Animal models lacking IP3Rs in different combinations display severe developmental phenotypes. Given the importance of IP3Rs in human diseases, we investigated their role in human induced pluripotent stem cells (hiPSC) by developing single IP3R and triple IP3R knockouts (TKO). Genome edited TKO-hiPSC lacking all three IP3R isoforms, IP3R1, IP3R2, IP3R3, failed to generate Ca2+ signals in response to agonists activating GPCRs, but retained stemness and pluripotency. Steady state metabolite profiling and flux analysis of TKO-hiPSC indicated distinct alterations in tricarboxylic acid cycle metabolites consistent with a deficiency in their pyruvate utilization via pyruvate dehydrogenase, shifting towards pyruvate carboxylase pathway. These results demonstrate that IP3Rs are not essential for hiPSC identity and pluripotency but regulate mitochondrial metabolism. This set of knockout hiPSC is a valuable resource for investigating IP3Rs in human cell types of interest.
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Affiliation(s)
- Julius Rönkkö
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Yago Rodriguez
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Tiina Rasila
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Rubén Torregrosa-Muñumer
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Jana Pennonen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Emilia Kuuluvainen
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00790, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00790, Finland
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute, KU Leuven - University of Leuven, 3000, Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Ville Hietakangas
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00790, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00790, Finland
| | - Geert Bultynck
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, Leuven, 3000, Belgium
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland; Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland.
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9
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Baker MR, Fan G, Arige V, Yule DI, Serysheva II. Understanding IP 3R channels: From structural underpinnings to ligand-dependent conformational landscape. Cell Calcium 2023; 114:102770. [PMID: 37393815 PMCID: PMC10529787 DOI: 10.1016/j.ceca.2023.102770] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed large-conductance Ca2+-permeable channels predominantly localized to the endoplasmic reticulum (ER) membranes of virtually all eukaryotic cell types. IP3Rs work as Ca2+ signaling hubs through which diverse extracellular stimuli and intracellular inputs are processed and then integrated to result in delivery of Ca2+ from the ER lumen to generate cytosolic Ca2+ signals with precise temporal and spatial properties. IP3R-mediated Ca2+ signals control a vast repertoire of cellular functions ranging from gene transcription and secretion to the more enigmatic brain activities such as learning and memory. IP3Rs open and release Ca2+ when they bind both IP3 and Ca2+, the primary channel agonists. Despite overwhelming evidence supporting functional interplay between IP3 and Ca2+ in activation and inhibition of IP3Rs, the mechanistic understanding of how IP3R channels convey their gating through the interplay of two primary agonists remains one of the major puzzles in the field. The last decade has seen much progress in the use of cryogenic electron microscopy to elucidate the molecular mechanisms of ligand binding, ion permeation, ion selectivity and gating of the IP3R channels. The results of these studies, summarized in this review, provide a prospective view of what the future holds in structural and functional research of IP3Rs.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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10
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Smith HA, Thillaiappan NB, Rossi AM. IP 3 receptors: An "elementary" journey from structure to signals. Cell Calcium 2023; 113:102761. [PMID: 37271052 DOI: 10.1016/j.ceca.2023.102761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are large tetrameric channels which sit mostly in the membrane of the endoplasmic reticulum (ER) and mediate Ca2+ release from intracellular stores in response to extracellular stimuli in almost all cells. Dual regulation of IP3Rs by IP3 and Ca2+ itself, upstream "licensing", and the arrangement of IP3Rs into small clusters in the ER membrane, allow IP3Rs to generate spatially and temporally diverse Ca2+ signals. The characteristic biphasic regulation of IP3Rs by cytosolic Ca2+ concentration underpins regenerative Ca2+ signals by Ca2+-induced Ca2+-release, while also preventing uncontrolled explosive Ca2+ release. In this way, cells can harness a simple ion such as Ca2+ as a near-universal intracellular messenger to regulate diverse cellular functions, including those with conflicting outcomes such as cell survival and cell death. High-resolution structures of the IP3R bound to IP3 and Ca2+ in different combinations have together started to unravel the workings of this giant channel. Here we discuss, in the context of recently published structures, how the tight regulation of IP3Rs and their cellular geography lead to generation of "elementary" local Ca2+ signals known as Ca2+ "puffs", which form the fundamental bottleneck through which all IP3-mediated cytosolic Ca2+ signals must first pass.
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Affiliation(s)
- Holly A Smith
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | | | - Ana M Rossi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom.
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Lunko O, Foskett JK. Viewing Ca 2+-binding sites in the inositol trisphosphate receptor. Cell Calcium 2023; 110:102697. [PMID: 36736164 PMCID: PMC10173365 DOI: 10.1016/j.ceca.2023.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
Ca2+ is a major ligand of the inositol 1,4,5-trisphosphate receptor (IP3R) Ca2+-release channel. Fan et al. [1] recently solved additional cryo-electron microscopy (cryo-EM) structures of the IP3R in different ligand-binding states, revealing new Ca2+ binding sites.
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Affiliation(s)
- Olesia Lunko
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 700D Clinical Research Building, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - J Kevin Foskett
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 700D Clinical Research Building, 415 Curie Blvd, Philadelphia, PA 19104, USA.
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12
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Fan G, Baker MR, Terry LE, Arige V, Chen M, Seryshev AB, Baker ML, Ludtke SJ, Yule DI, Serysheva II. Conformational motions and ligand-binding underlying gating and regulation in IP 3R channel. Nat Commun 2022; 13:6942. [PMID: 36376291 PMCID: PMC9663519 DOI: 10.1038/s41467-022-34574-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP3R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP3R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
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Affiliation(s)
- Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Lara E Terry
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander B Seryshev
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA.
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13
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Kuo IY, Ehrlich BE. Location, location, and activation of a channel by calcium. Proc Natl Acad Sci U S A 2022; 119:e2214826119. [PMID: 36215521 PMCID: PMC9618095 DOI: 10.1073/pnas.2214826119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ivana Y. Kuo
- aDepartment of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153
| | - Barbara E. Ehrlich
- bDepartment of Pharmacology, Yale University, New Haven, CT 06511
- cDepartment of Pathology, New York University School of Medicine, New York, NY 10016
- 1To whom correspondence may be addressed.
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