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Irie K. [Analysis of the Divalent Cation Blocking in Ion Channels by Crystal Structure and Molecular Dynamics Simulations]. YAKUGAKU ZASSHI 2024; 144:521-526. [PMID: 38692927 DOI: 10.1248/yakushi.23-00178-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Neural activity generates essential responses, such as thinking, memory formation, and muscle contraction. It is controlled by the well-coordinated activity of various cation-selective channels of the cell membrane. The divalent cation block plays an essential role in various tetrameric ion channels. For example, N-methyl-D-aspartic acid receptors, which are tetrameric ion channels involved in memory formation, are inhibited by magnesium ions. Divalent cations are thought to bind in the ion pathway of the ion channel and as a consequence block the channel current, however, direct observation of such a block has not been reported yet. As a consequence, the behavior of these blocking divalent cations remains poorly understood. NavAb, a similar tetrameric sodium channel cloned from Arcobacter butzleri, is one of the most structurally analyzed tetrameric channels that is not inhibited by divalent cations. In this study, we elucidated the molecular mechanism of the divalent cation block by reproducing the divalent cation block in NavAb. The X-ray crystal structure of divalent-cation-block mutants show electron density in the ion transmission pathway of the divalent cation blocked mutants, indicating that the mutations increasing the hydrophilicity of the inner vestibule of the pore domain enable a divalent cation to stack into the ion pathway. In molecular dynamics simulations, the stacked calcium ion repels the sodium ions near the channel lumen's entrance at the selective filter's bottom. These results suggest the primary process of the divalent cation block mechanism in tetrameric cation channels and suggest a process of functional acquisition in ion channel evolution.
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Affiliation(s)
- Katsumasa Irie
- Department of Biophysical Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University
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2
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Spafford JD. A governance of ion selectivity based on the occupancy of the "beacon" in one- and four-domain calcium and sodium channels. Channels (Austin) 2023; 17:2191773. [PMID: 37075164 PMCID: PMC10120453 DOI: 10.1080/19336950.2023.2191773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
One of nature's exceptions was discovered when a Cav3 T-type channel was observed to switch phenotype from a calcium channel into a sodium channel by neutralizing an aspartate residue in the high field strength (HFS) +1 position within the ion selectivity filter. The HFS+1 site is dubbed a "beacon" for its location at the entryway just above the constricted, minimum radius of the HFS site's electronegative ring. A classification is proposed based on the occupancy of the HFS+1 "beacon" which correlates with the calcium- or sodium-selectivity phenotype. If the beacon is a glycine, or neutral, non-glycine residue, then the cation channel is calcium-selective or sodium-permeable, respectively (Class I). Occupancy of a beacon aspartate are calcium-selective channels (Class II) or possessing a strong calcium block (Class III). A residue lacking in position of the sequence alignment for the beacon are sodium channels (Class IV). The extent to which animal channels are sodium-selective is dictated in the occupancy of the HFS site with a lysine residue (Class III/IV). Governance involving the beacon solves the quandary the HFS site as a basis for ion selectivity, where an electronegative ring of glutamates at the HFS site generates a sodium-selective channel in one-domain channels but generates a calcium-selective channel in four-domain channels. Discovery of a splice variant in an exceptional channel revealed nature's exploits, highlighting the "beacon" as a principal determinant for calcium and sodium selectivity, encompassing known ion channels composed of one and four domains, from bacteria to animals.
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Affiliation(s)
- J David Spafford
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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3
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Sylvain-Bonfanti L, Page J, Arbelet-Bonnin D, Meimoun P, Grésillon É, Bouteau F, Laurenti P. [Anaesthesia, a process common to all living organisms]. Med Sci (Paris) 2023; 39:738-743. [PMID: 37943134 DOI: 10.1051/medsci/2023123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
Because of their interest in medicine, most studies of anaesthesia focus on the nervous system of metazoans, and the fact that any life form can be anaesthetised is often underlooked. If electrical signalling is an essential phenomenon for the success of animals, it appears to be widespread beyond metazoans. Indeed, anaesthesia targets Na+/Ca2+ voltage-gated channels that exist in a wide variety of species and originate from ancestral channels that predate eukaryotes in the course of evolution. The fact that the anaesthetic capacity that leads to loss of sensitivity is common to all phyla may lead to two hypotheses: to be investigated is the evolutionary maintenance of the ability to be anaesthetised due to an adaptive advantage or to a simple intrinsic defect in ion channels? The study of anaesthesia in organisms phylogenetically distant from animals opens up promising prospects for the discovery of new anaesthetic treatments. Moreover, it should also lead to a better understanding of a still poorly understood phenomenon that yet unifies all living organisms. We hope that this new understanding of the unity of life will help humans to assume their responsibilities towards all species, at a time when we are threatening biodiversity with mass extinction.
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Affiliation(s)
- Lucia Sylvain-Bonfanti
- Université Paris-Cité, laboratoire interdisciplinaire des énergies de demain (LIED UMR 8236), Paris, France - Université Paris-Cité, laboratoire dynamiques sociales et recomposition des espaces (LADYSS UMR 7533), Paris, France
| | - Julien Page
- Université Paris-Cité, laboratoire interdisciplinaire des énergies de demain (LIED UMR 8236), Paris, France
| | - Delphine Arbelet-Bonnin
- Université Paris-Cité, laboratoire interdisciplinaire des énergies de demain (LIED UMR 8236), Paris, France
| | - Patrice Meimoun
- Université Paris-Cité, laboratoire interdisciplinaire des énergies de demain (LIED UMR 8236), Paris, France - Sorbonne université, Paris, France
| | - Étienne Grésillon
- Université Paris-Cité, laboratoire dynamiques sociales et recomposition des espaces (LADYSS UMR 7533), Paris, France
| | - François Bouteau
- Université Paris-Cité, laboratoire interdisciplinaire des énergies de demain (LIED UMR 8236), Paris, France
| | - Patrick Laurenti
- Université Paris-Cité, laboratoire interdisciplinaire des énergies de demain (LIED UMR 8236), Paris, France
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4
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Enck JR, Olson EC. Calcium Signaling during Cortical Apical Dendrite Initiation: A Role for Cajal-Retzius Neurons. Int J Mol Sci 2023; 24:12965. [PMID: 37629145 PMCID: PMC10455361 DOI: 10.3390/ijms241612965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The apical dendrite of a cortical projection neuron (CPN) is generated from the leading process of the migrating neuron as the neuron completes migration. This transformation occurs in the cortical marginal zone (MZ), a layer that contains the Cajal-Retzius neurons and their axonal projections. Cajal-Retzius neurons (CRNs) are well known for their critical role in secreting Reelin, a glycoprotein that controls dendritogenesis and cell positioning in many regions of the developing brain. In this study, we examine the possibility that CRNs in the MZ may provide additional signals to arriving CPNs, that may promote the maturation of CPNs and thus shape the development of the cortex. We use whole embryonic hemisphere explants and multiphoton microscopy to confirm that CRNs display intracellular calcium transients of <1-min duration and high amplitude during early corticogenesis. In contrast, developing CPNs do not show high-amplitude calcium transients, but instead show a steady increase in intracellular calcium that begins at the time of dendritic initiation, when the leading process of the migrating CPN is encountering the MZ. The possible existence of CRN to CPN communication was revealed by the application of veratridine, a sodium channel activator, which has been shown to preferentially stimulate more mature cells in the MZ at an early developmental time. Surprisingly, veratridine application also triggers large calcium transients in CPNs, which can be partially blocked by a cocktail of antagonists that block glutamate and glycine receptor activation. These findings outline a model in which CRN spontaneous activity triggers the release of glutamate and glycine, neurotransmitters that can trigger intracellular calcium elevations in CPNs. These elevations begin as CPNs initiate dendritogenesis and continue as waves in the post-migratory cells. Moreover, we show that the pharmacological blockade of glutamatergic signaling disrupts migration, while forced expression of a bacterial voltage-gated calcium channel (CavMr) in the migrating neurons promotes dendritic growth and migration arrest. The identification of CRN to CPN signaling during early development provides insight into the observation that many autism-linked genes encode synaptic proteins that, paradoxically, are expressed in the developing cortex well before the appearance of synapses and the establishment of functional circuits.
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Affiliation(s)
| | - Eric C. Olson
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, 505 Irving Ave., Syracuse, NY 13210, USA;
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Irie K, Oda Y, Sumikama T, Oshima A, Fujiyoshi Y. The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat Commun 2023; 14:4236. [PMID: 37454189 PMCID: PMC10349818 DOI: 10.1038/s41467-023-39987-0] [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: 12/01/2022] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Divalent cation block is observed in various tetrameric ion channels. For blocking, a divalent cation is thought to bind in the ion pathway of the channel, but such block has not yet been directly observed. So, the behaviour of these blocking divalent cations remains still uncertain. Here, we elucidated the mechanism of the divalent cation block by reproducing the blocking effect into NavAb, a well-studied tetrameric sodium channel. Our crystal structures of NavAb mutants show that the mutations increasing the hydrophilicity of the inner vestibule of the pore domain enable a divalent cation to stack on the ion pathway. Furthermore, non-equilibrium molecular dynamics simulation showed that the stacking calcium ion repel sodium ion at the bottom of the selectivity filter. These results suggest the primary process of the divalent cation block mechanism in tetrameric cation channels.
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Affiliation(s)
- Katsumasa Irie
- Department of Biophysical Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1, Shichibancho, Wakayama, 640-8156, Japan.
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan.
| | - Yoshinori Oda
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
| | - Takashi Sumikama
- PRESTO, JST, Kawaguchi, 332-0012, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, 501-11193, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory (CeSPL), Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan
- CeSPIA Inc., 2-1-1, Otemachi, Chiyoda, Tokyo, 100-0004, Japan
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Chaves G, Jardin C, Derst C, Musset B. Voltage-Gated Proton Channels in the Tree of Life. Biomolecules 2023; 13:1035. [PMID: 37509071 PMCID: PMC10377628 DOI: 10.3390/biom13071035] [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: 05/14/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
With a single gene encoding HV1 channel, proton channel diversity is particularly low in mammals compared to other members of the superfamily of voltage-gated ion channels. Nonetheless, mammalian HV1 channels are expressed in many different tissues and cell types where they exert various functions. In the first part of this review, we regard novel aspects of the functional expression of HV1 channels in mammals by differentially comparing their involvement in (1) close conjunction with the NADPH oxidase complex responsible for the respiratory burst of phagocytes, and (2) in respiratory burst independent functions such as pH homeostasis or acid extrusion. In the second part, we dissect expression of HV channels within the eukaryotic tree of life, revealing the immense diversity of the channel in other phylae, such as mollusks or dinoflagellates, where several genes encoding HV channels can be found within a single species. In the last part, a comprehensive overview of the biophysical properties of a set of twenty different HV channels characterized electrophysiologically, from Mammalia to unicellular protists, is given.
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Affiliation(s)
- Gustavo Chaves
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Christophe Jardin
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Christian Derst
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
| | - Boris Musset
- Center of Physiology, Pathophysiology and Biophysics, The Nuremberg Location, Paracelsus Medical University, 90419 Nuremberg, Germany
- Center of Physiology, Pathophysiology and Biophysics, The Salzburg Location, Paracelsus Medical University, 5020 Salzburg, Austria
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7
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Li X, Jin Z, Xiong L, Tong L, Zhu H, Zhang X, Qin G. Effects of Land Reclamation on Soil Bacterial Community and Potential Functions in Bauxite Mining Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16921. [PMID: 36554801 PMCID: PMC9778865 DOI: 10.3390/ijerph192416921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Studying the characteristics of microorganisms in mine reclamation sites can provide a scientific reference basis for mine land reclamation. Soils in the plough layer (0-20 cm) of the bauxite mine plots in Pingguo city, Guangxi Zhuang Autonomous Region, China, with different reclamation years were used as the research objects. The community structure of soil bacteria was analyzed with high-throughput sequencing technology. The results show the following: (1) Reclamation significantly increased the contents of soil nutrients (p < 0.05). (2) The relative abundances of Proteobacteria were high (22.90~41.56%) in all plots, and reclamation significantly reduced the relative abundances of Firmicutes (3.42-10.77%) compared to that in the control plot (24.74%) (p < 0.05). The relative abundances of α-proteobacteria generally increased while the reclamation year increased. The relative abundances of α-proteobacteria and γ-proteobacteria showed significant positive correlations with soil carbon, nitrogen, and phosphorus nutrients (p < 0.01). The relative abundance of Acidobacteria Group 6 showed significant positive correlations with soil exchangeable Ca and Mg (p < 0.01). (3) Bacterial co-occurrence network showed more Copresence interactions in all plots (50.81-58.39%). The reclaimed plots had more nodes, higher modularity, and longer characteristic path length than the control plot, and the keystone taxa changed in different plots. (4) The chemoheterotrophy and aerobic chemoheterotrophy were the most abundant functional groups in all plots (35.66-48.26%), while reclamation reduced the relative abundance of fermentation groups (1.75-11.21%). The above findings indicated that reclamation improved soil nutrients, changed the bacterial community structure and potential functions, and accelerated the microbial stabilization of the reclaimed soil.
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Affiliation(s)
- Xuesong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Zhenjiang Jin
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin 541004, China
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Liyuan Xiong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Lingchen Tong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Hongying Zhu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Xiaowen Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Guangfa Qin
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
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8
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Modulation of L-type calcium channels in Alzheimer's disease: A potential therapeutic target. Comput Struct Biotechnol J 2022; 21:11-20. [PMID: 36514335 PMCID: PMC9719069 DOI: 10.1016/j.csbj.2022.11.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/28/2022] Open
Abstract
Calcium plays a fundamental role in various signaling pathways and cellular processes in the human organism. In the nervous system, voltage-gated calcium channels such as L-type calcium channels (LTCCs) are critical elements in mediating neurotransmitter release, synaptic integration and plasticity. Dysfunction of LTCCs has been implicated in both aging and Alzheimer's Disease (AD), constituting a key component of calcium hypothesis of AD. As such, LTCCs are a promising drug target in AD. However, due to their structural and functional complexity, the mechanisms by which LTCCs contribute to AD are still unclear. In this review, we briefly summarize the structure, function, and modulation of LTCCs that are the backbone for understanding pathological processes involving LTCCs. We suggest targeting molecular pathways up-regulating LTCCs in AD may be a more promising approach, given the diverse physiological functions of LTCCs and the ineffectiveness of LTCC blockers in clinical studies.
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Key Words
- AC, adenylyl cyclase
- AD, Alzheimer’s Disease
- AHP, afterhyperpolarization
- AR, adrenoceptor
- Aging
- Alzheimer’s disease
- Aβ, β-amyloid
- BIN1, bridging integrator 1
- BTZs, benzothiazepines
- CDF, calcium-dependent facilitation
- CDI, calcium-dependent inactivation
- CaMKII, calmodulin-dependent protein kinase II
- DHP, dihydropyridine
- L-type calcium channel
- LTCC, L-type calcium channels
- LTD, long-term depression
- LTP, long-term potentiation
- NFT, neurofibrillary tangles
- NMDAR, N-methyl-D-aspartate receptor
- PAA, phenylalkylamines
- PKA, protein kinase A
- PKC, protein kinase C
- PKG, protein kinase G
- SFK, Src family kinase
- Tau
- VSD, voltage sensing domain
- β-Amyloid
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9
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Guan W, Orellana KG, Stephens RF, Zhorov BS, Spafford JD. A lysine residue from an extracellular turret switches the ion preference in a Cav3 T-Type channel from calcium to sodium ions. J Biol Chem 2022; 298:102621. [PMID: 36272643 PMCID: PMC9694082 DOI: 10.1016/j.jbc.2022.102621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/19/2022] Open
Abstract
Cav3 T-type calcium channels from great pond snail Lymnaea stagnalis have a selectivity-filter ring of five acidic residues, EE(D)DD. Splice variants with exons 12b or 12a spanning the extracellular loop between the outer helix IIS5 and membrane-descending pore helix IIP1 (IIS5-P1) in Domain II of the pore module possess calcium selectivity or dominant sodium permeability, respectively. Here, we use AlphaFold2 neural network software to predict that a lysine residue in exon 12a is salt-bridged to the aspartate residue immediately C terminal to the second-domain glutamate in the selectivity filter. Exon 12b has a similar folding but with an alanine residue in place of lysine in exon 12a. We express LCav3 channels with mutated exons Ala-12b-Lys and Lys-12a-Ala and demonstrate that they switch the ion preference to high sodium permeability and calcium selectivity, respectively. We propose that in the calcium-selective variants, a calcium ion chelated between Domain II selectivity-filter glutamate and aspartate is knocked-out by the incoming calcium ion in the process of calcium permeation, whereas sodium ions are repelled. The aspartate is neutralized by the lysine residue in the sodium-permeant variants, allowing for sodium permeation through the selectivity-filter ring of four negatively charged residues akin to the prokaryotic sodium channels with four glutamates in the selectivity filter. The evolutionary adaptation in invertebrate LCav3 channels highlight the involvement of a key, ubiquitous aspartate, "a calcium beacon" of sorts in the outer pore of Domain II, as determinative for the calcium ion preference over sodium ions through eukaryotic Cav1, Cav2, and Cav3 channels.
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Affiliation(s)
- Wendy Guan
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kaidy G. Orellana
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Robert F. Stephens
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Boris S. Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada,Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia,Almazov National Medical Research Centre, St. Petersburg, Russia
| | - J. David Spafford
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada,For correspondence: J. David Spafford
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Naranjo D. A scenario for the origin of life: Volume regulation by bacteriorhodopsin required extremely voltage sensitive Na‐channels and very selective K‐channels. Bioessays 2022; 44:e2100210. [DOI: 10.1002/bies.202100210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/25/2022]
Affiliation(s)
- David Naranjo
- Instituto de Neurociencia, Facultad de Ciencias Universidad de Valparaíso Playa Ancha Valparaíso Chile
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11
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Nagayama K, Patel T, Nakamura H, Berliner L, Hall D. Editors’ Roundup: June 2022. Biophys Rev 2022; 14:619-623. [DOI: 10.1007/s12551-022-00970-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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12
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Irie K. The insights into calcium ion selectivity provided by ancestral prokaryotic ion channels. Biophys Physicobiol 2022; 18:274-283. [PMID: 35004101 PMCID: PMC8677417 DOI: 10.2142/biophysico.bppb-v18.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/16/2021] [Indexed: 12/01/2022] Open
Abstract
Prokaryotic channels play an important role in the structural biology of ion channels. At the end of the 20th century, the first structure of a prokaryotic ion channel was revealed. Subsequently, the reporting of structures of various prokaryotic ion channels have provided fundamental insights into the structure of ion channels of higher organisms. Voltage-dependent Ca2+ channels (Cavs) are indispensable for coupling action potentials with Ca2+ signaling. Similar to other proteins, Cavs were predicted to have a prokaryotic counterpart; however, it has taken more than 20 years for one to be identified. The homotetrameric channel obtained from Meiothermus ruber generates the calcium ion specific current, so it is named as CavMr. Its selectivity filter contains a smaller number of negatively charged residues than mutant Cavs generated from other prokaryotic channels. CavMr belonged to a different cluster of phylogenetic trees than canonical prokaryotic cation channels. The glycine residue of the CavMr selectivity filter is a determinant for calcium selectivity. This glycine residue is conserved among eukaryotic Cavs, suggesting that there is a universal mechanism for calcium selectivity. A family of homotetrameric channels has also been identified from eukaryotic unicellular algae, and the investigation of these channels can help to understand the mechanism for ion selection that is conserved from prokaryotes to eukaryotes.
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Affiliation(s)
- Katsumasa Irie
- Department of Biophysical Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan.,Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Nagoya, Aichi 464-8601, Japan
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13
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Haschka D, Grander M, Eibensteiner J, Dichtl S, Koppelstätter S, Weiss G. Nifedipine Potentiates Susceptibility of Salmonella Typhimurium to Different Classes of Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10101200. [PMID: 34680781 PMCID: PMC8532624 DOI: 10.3390/antibiotics10101200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The calcium channel blocker nifedipine induces cellular iron export, thereby limiting the availability of the essential nutrient iron for intracellular pathogens, resulting in bacteriostatic activity. To study if nifedipine may exert a synergistic anti-microbial activity when combined with antibiotics, we used the mouse macrophage cell line RAW267.4, infected with the intracellular bacterium Salmonella Typhimurium, and exposed the cells to varying concentrations of nifedipine and/or ampicillin, azithromycin and ceftriaxone. We observed a significant additive effect of nifedipine in combination with various antibiotics, which was not observed when using Salmonella, with defects in iron uptake. Of interest, increasing intracellular iron levels increased the bacterial resistance to treatment with antibiotics or nifedipine or their combination. We further showed that nifedipine increases the expression of the siderophore-binding peptide lipocalin-2 and promotes iron storage within ferritin, where the metal is less accessible for bacteria. Our data provide evidence for an additive effect of nifedipine with conventional antibiotics against Salmonella, which is partly linked to reduced bacterial access to iron.
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Abstract
Calcium (Ca2+) is a unique mineral that serves as both a nutrient and a signal in all eukaryotes. To maintain Ca2+ homeostasis for both nutrition and signaling purposes, the toolkit for Ca2+ transport has expanded across kingdoms of eukaryotes to encode specific Ca2+ signals referred to as Ca2+ signatures. In parallel, a large array of Ca2+-binding proteins has evolved as specific sensors to decode Ca2+ signatures. By comparing these coding and decoding mechanisms in fungi, animals, and plants, both unified and divergent themes have emerged, and the underlying complexity will challenge researchers for years to come. Considering the scale and breadth of the subject, instead of a literature survey, in this review we focus on a conceptual framework that aims to introduce to readers to the principles and mechanisms of Ca2+ signaling. We finish with several examples of Ca2+-signaling pathways, including polarized cell growth, immunity and symbiosis, and systemic signaling, to piece together specific coding and decoding mechanisms in plants versus animals. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Chao Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
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Abstract
Bacteria are electrically powered organisms; cells maintain an electrical potential across their plasma membrane as a source of free energy to drive essential processes. In recent years, however, bacterial membrane potential has been increasingly recognized as dynamic. Those dynamics have been implicated in diverse physiological functions and behaviors, including cell division and cell-to-cell signaling. In eukaryotic cells, such dynamics play major roles in coupling bioelectrical stimuli to changes in internal cell states. Neuroscientists and physiologists have established detailed molecular pathways that transduce eukaryotic membrane potential dynamics to physiological and gene expression responses. We are only just beginning to explore these intracellular responses to bioelectrical activity in bacteria. In this review, we summarize progress in this area, including evidence of gene expression responses to stimuli from electrodes and mechanically induced membrane potential spikes. We argue that the combination of provocative results, missing molecular detail, and emerging tools makes the investigation of bioelectrically induced long-term intracellular responses an important and rewarding effort in the future of microbiology.
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Affiliation(s)
- Joshua M Jones
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Joseph W Larkin
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
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16
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Machine Learning Establishes Single-Cell Calcium Dynamics as an Early Indicator of Antibiotic Response. Microorganisms 2021; 9:microorganisms9051000. [PMID: 34063175 PMCID: PMC8148219 DOI: 10.3390/microorganisms9051000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022] Open
Abstract
Changes in bacterial physiology necessarily precede cell death in response to antibiotics. Herein we investigate the early disruption of Ca2+ homeostasis as a marker for antibiotic response. Using a machine learning framework, we quantify the temporal information encoded in single-cell Ca2+ dynamics. We find Ca2+ dynamics distinguish kanamycin sensitive and resistant cells before changes in gross cell phenotypes such as cell growth or protein stability. The onset time (pharmacokinetics) and probability (pharmacodynamics) of these aberrant Ca2+ dynamics are dose and time-dependent, even at the resolution of single-cells. Of the compounds profiled, we find Ca2+ dynamics are also an indicator of Polymyxin B activity. In Polymyxin B treated cells, we find aberrant Ca2+ dynamics precedes the entry of propidium iodide marking membrane permeabilization. Additionally, we find modifying membrane voltage and external Ca2+ concentration alters the time between these aberrant dynamics and membrane breakdown suggesting a previously unappreciated role of Ca2+ in the membrane destabilization during Polymyxin B treatment. In conclusion, leveraging live, single-cell, Ca2+ imaging coupled with machine learning, we have demonstrated the discriminative capacity of Ca2+ dynamics in identifying antibiotic-resistant bacteria.
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17
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Roudaire T, Héloir MC, Wendehenne D, Zadoroznyj A, Dubrez L, Poinssot B. Cross Kingdom Immunity: The Role of Immune Receptors and Downstream Signaling in Animal and Plant Cell Death. Front Immunol 2021; 11:612452. [PMID: 33763054 PMCID: PMC7982415 DOI: 10.3389/fimmu.2020.612452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Both plants and animals are endowed with sophisticated innate immune systems to combat microbial attack. In these multicellular eukaryotes, innate immunity implies the presence of cell surface receptors and intracellular receptors able to detect danger signal referred as damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs). Membrane-associated pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), C-type lectin receptors (CLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are employed by these organisms for sensing different invasion patterns before triggering antimicrobial defenses that can be associated with a form of regulated cell death. Intracellularly, animals nucleotide-binding and oligomerization domain (NOD)-like receptors or plants nucleotide-binding domain (NBD)-containing leucine rich repeats (NLRs) immune receptors likely detect effectors injected into the host cell by the pathogen to hijack the immune signaling cascade. Interestingly, during the co-evolution between the hosts and their invaders, key cross-kingdom cell death-signaling macromolecular NLR-complexes have been selected, such as the inflammasome in mammals and the recently discovered resistosome in plants. In both cases, a regulated cell death located at the site of infection constitutes a very effective mean for blocking the pathogen spread and protecting the whole organism from invasion. This review aims to describe the immune mechanisms in animals and plants, mainly focusing on cell death signaling pathways, in order to highlight recent advances that could be used on one side or the other to identify the missing signaling elements between the perception of the invasion pattern by immune receptors, the induction of defenses or the transmission of danger signals to other cells. Although knowledge of plant immunity is less advanced, these organisms have certain advantages allowing easier identification of signaling events, regulators and executors of cell death, which could then be exploited directly for crop protection purposes or by analogy for medical research.
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Affiliation(s)
- Thibault Roudaire
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Marie-Claire Héloir
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Aymeric Zadoroznyj
- Institut National de la Santé et de la Recherche Médicale (Inserm), LNC UMR1231, Dijon, France.,LNC UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laurence Dubrez
- Institut National de la Santé et de la Recherche Médicale (Inserm), LNC UMR1231, Dijon, France.,LNC UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Benoit Poinssot
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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18
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Yates P, Koester JA, Taylor AR. Brevetoxin and Conotoxin Interactions with Single-Domain Voltage-Gated Sodium Channels from a Diatom and Coccolithophore. Mar Drugs 2021; 19:md19030140. [PMID: 33801270 PMCID: PMC8002053 DOI: 10.3390/md19030140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 01/16/2023] Open
Abstract
The recently characterized single-domain voltage-gated ion channels from eukaryotic protists (EukCats) provide an array of novel channel proteins upon which to test the pharmacology of both clinically and environmentally relevant marine toxins. Here, we examined the effects of the hydrophilic µ-CTx PIIIA and the lipophilic brevetoxins PbTx-2 and PbTx-3 on heterologously expressed EukCat ion channels from a marine diatom and coccolithophore. Surprisingly, none of the toxins inhibited the peak currents evoked by the two EukCats tested. The lack of homology in the outer pore elements of the channel may disrupt the binding of µ-CTx PIIIA, while major structural differences between mammalian sodium channels and the C-terminal domains of the EukCats may diminish interactions with the brevetoxins. However, all three toxins produced significant negative shifts in the voltage dependence of activation and steady state inactivation, suggesting alternative and state-dependent binding conformations that potentially lead to changes in the excitability of the phytoplankton themselves.
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19
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Xu L, Sun L, Xie L, Mou S, Zhang D, Zhu J, Xu P. Advances in L-Type Calcium Channel Structures, Functions and Molecular Modeling. Curr Med Chem 2021; 28:514-524. [PMID: 32664834 DOI: 10.2174/0929867327666200714154059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/14/2020] [Accepted: 06/19/2020] [Indexed: 11/22/2022]
Abstract
L-type Calcium Channels (LTCCs), also termed as Cav1, belong to voltage-gated calcium channels (VGCCs/Cavs), which play a critical role in a wide spectrum of physiological processes, including neurotransmission, cell cycle, muscular contraction, cardiac action potential and gene expression. Aberrant regulation of calcium channels is involved in neurological, cardiovascular, muscular and psychiatric disorders. Accordingly, LTCCs have been regarded as important drug targets, and a number of LTCC drugs are in clinical use. In this review, the recent development of structures and biological functions of LTCCs are introduced. Moreover, the representative modulators and ligand binding sites of LTCCs are discussed. Finally, molecular modeling and Computer-aided Drug Design (CADD) methods for understanding structure-function relations of LTCCs are summarized.
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Affiliation(s)
- Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Lilei Sun
- Department of Radiology, Weifang Second People's Hospital, Weifang 261041, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Shanzhi Mou
- School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001, China
| | - Dawei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Jingyu Zhu
- School of Medicine and Pharmaceutics, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Department of Orthopedics, Second Military Medical University Affiliated Changzheng Hospital, Shanghai 200003, China
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20
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Are antibacterial effects of non-antibiotic drugs random or purposeful because of a common evolutionary origin of bacterial and mammalian targets? Infection 2020; 49:569-589. [PMID: 33325009 PMCID: PMC7737717 DOI: 10.1007/s15010-020-01547-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/28/2020] [Indexed: 01/09/2023]
Abstract
Purpose Advances in structural biology, genetics, bioinformatics, etc. resulted in the availability of an enormous pool of information enabling the analysis of the ancestry of pro- and eukaryotic genes and proteins. Methods This review summarizes findings of structural and/or functional homologies of pro- and eukaryotic enzymes catalysing analogous biological reactions because of their highly conserved active centres so that non-antibiotics interacted with bacterial targets. Results Protease inhibitors such as staurosporine or camostat inhibited bacterial serine/threonine or serine/tyrosine protein kinases, serine/threonine phosphatases, and serine/threonine kinases, to which penicillin-binding-proteins are linked, so that these drugs synergized with β-lactams, reverted aminoglycoside-resistance and attenuated bacterial virulence. Calcium antagonists such as nitrendipine or verapamil blocked not only prokaryotic ion channels but interacted with negatively charged bacterial cell membranes thus disrupting membrane energetics and inducing membrane stress response resulting in inhibition of P-glycoprotein such as bacterial pumps thus improving anti-mycobacterial activities of rifampicin, tetracycline, fluoroquinolones, bedaquilin and imipenem-activity against Acinetobacter spp. Ciclosporine and tacrolimus attenuated bacterial virulence. ACE-inhibitors like captopril interacted with metallo-β-lactamases thus reverting carbapenem-resistance; prokaryotic carbonic anhydrases were inhibited as well resulting in growth impairment. In general, non-antibiotics exerted weak antibacterial activities on their own but synergized with antibiotics, and/or reverted resistance and/or attenuated virulence. Conclusions Data summarized in this review support the theory that prokaryotic proteins represent targets for non-antibiotics because of a common evolutionary origin of bacterial- and mammalian targets resulting in highly conserved active centres of both, pro- and eukaryotic proteins with which the non-antibiotics interact and exert antibacterial actions.
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21
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Abstract
A native calcium ion channel has been identified in bacteria for the first time.
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Affiliation(s)
| | - León D Islas
- Department of Physiology, School of Medicine, UNAMMéxico CityMexico
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