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Niu Y, Gu Y, Zhang J, Sun B, Wu L, Mao X, Liu Z, Zhang Y, Li K, Zhang Y. Characteristics of saltiness-enhancing peptides derived from yeast proteins and elucidation of their mechanism of action by molecular docking. Food Chem 2024; 449:139216. [PMID: 38604031 DOI: 10.1016/j.foodchem.2024.139216] [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] [Received: 01/30/2024] [Revised: 03/22/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
This study aimed to identify saltiness-enhancing peptides from yeast protein and elucidate their mechanisms by molecular docking. Yeast protein hydrolysates with optimal saltiness-enhancing effects were prepared under conditions determined using an orthogonal test. Ten saltiness-enhancing peptide candidates were screened using an integrated virtual screening strategy. Sensory evaluation demonstrated that these peptides exhibited diverse taste characteristics (detection thresholds: 0.13-0.50 mmol/L). Peptides NKF, LGLR, WDL, NMKF, FDSL and FDGK synergistically or additively enhanced the saltiness of a 0.30% NaCl solution. Molecular docking revealed that these peptides predominantly interacted with TMC4 by hydrogen bonding, with hydrophilic amino acids from both peptides and TMC4 playing a pivotal role in their binding. Furthermore, Leu217, Gln377, Glu378, Pro474 and Cys475 were postulated as the key binding sites of TMC4. These findings establish a robust theoretical foundation for salt reduction strategies in food and provide novel insights into the potential applications of yeast proteins.
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Affiliation(s)
- Yajie Niu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Yuxiang Gu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China
| | - Jingcheng Zhang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China
| | - Baoguo Sun
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Zunying Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yan Zhang
- National Key Laboratory of Agricultural Microbiology, Wuhan 430070, China
| | - Ku Li
- National Key Laboratory of Agricultural Microbiology, Wuhan 430070, China
| | - Yuyu Zhang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China.
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2
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Cox CD, Poole K, Martinac B. Re-evaluating TRP channel mechanosensitivity. Trends Biochem Sci 2024; 49:693-702. [PMID: 38851904 DOI: 10.1016/j.tibs.2024.05.004] [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] [Received: 01/17/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/10/2024]
Abstract
Transient receptor potential (TRP) channels are implicated in a wide array of mechanotransduction processes. However, a question remains whether TRP channels directly sense mechanical force, thus acting as primary mechanotransducers. We use several recent examples to demonstrate the difficulty in definitively ascribing mechanosensitivity to TRP channel subfamilies. Ultimately, despite being implicated in an ever-growing list of mechanosignalling events in most cases limited robust or reproducible evidence supports the contention that TRP channels act as primary transducers of mechanical forces. They either (i) possess unique and as yet unspecified structural or local requirements for mechanosensitivity; or (ii) act as mechanoamplifiers responding downstream of the activation of a primary mechanotransducer that could include Ca2+-permeable mechanosensitive (MS) channels or other potentially unidentified mechanosensors.
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Affiliation(s)
- Charles D Cox
- School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia; Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, NSW, 2010, Australia
| | - Kate Poole
- School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia.
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, NSW, 2010, Australia.
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3
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Arango AS, Park H, Tajkhorshid E. Topological Learning Approach to Characterizing Biological Membranes. J Chem Inf Model 2024; 64:5242-5252. [PMID: 38912752 DOI: 10.1021/acs.jcim.4c00552] [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: 06/25/2024]
Abstract
Biological membranes play key roles in cellular compartmentalization, structure, and its signaling pathways. At varying temperatures, individual membrane lipids sample from different configurations, a process that frequently leads to higher-order phase behavior and phenomena. Here, we present a persistent homology (PH)-based method for quantifying the structural features of individual and bulk lipids, providing local and contextual information on lipid tail organization. Our method leverages the mathematical machinery of algebraic topology and machine learning to infer temperature-dependent structural information on lipids from static coordinates. To train our model, we generated multiple molecular dynamics trajectories of dipalmitoyl-phosphatidylcholine membranes at varying temperatures. A fingerprint was then constructed for each set of lipid coordinates by PH filtration, in which interaction spheres were grown around the lipid atoms while tracking their intersections. The sphere filtration formed a simplicial complex that captures enduring key topological features of the configuration landscape using homology, yielding persistence data. Following fingerprint extraction for physiologically relevant temperatures, the persistence data were used to train an attention-based neural network for assignment of effective temperature values to selected membrane regions. Our persistence homology-based method captures the local structural effects, via effective temperature, of lipids adjacent to other membrane constituents, e.g., sterols and proteins. This topological learning approach can predict lipid effective temperatures from static coordinates across multiple spatial resolutions. The tool, called MembTDA, can be accessed at https://github.com/hyunp2/Memb-TDA.
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Affiliation(s)
- Andres S Arango
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hyun Park
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Giese APJ, Weng WH, Kindt KS, Chang HHV, Montgomery JS, Ratzan EM, Beirl AJ, Rivera RA, Lotthammer JM, Walujkar S, Foster MP, Zobeiri OA, Holt JR, Riazuddin S, Cullen KE, Sotomayor M, Ahmed ZM. Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.26.542533. [PMID: 37398045 PMCID: PMC10312449 DOI: 10.1101/2023.05.26.542533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Calcium and integrin-binding protein 2 (CIB2) and CIB3 bind to transmembrane channel-like 1 (TMC1) and TMC2, the pore-forming subunits of the inner-ear mechano-electrical transduction (MET) apparatus. These interactions have been proposed to be functionally relevant across mechanosensory organs and vertebrate species. Here we show that both CIB2 and CIB3 can form heteromeric complexes with TMC1 and TMC2 and are integral for MET function in mouse cochlea and vestibular end organs as well as in zebrafish inner ear and lateral line. Our AlphaFold 2 models suggest that vertebrate CIB proteins can simultaneously interact with at least two cytoplasmic domains of TMC1 and TMC2 as validated using nuclear magnetic resonance spectroscopy of TMC1 fragments interacting with CIB2 and CIB3. Molecular dynamics simulations of TMC1/2 complexes with CIB2/3 predict that TMCs are structurally stabilized by CIB proteins to form cation channels. Overall, our work demonstrates that intact CIB2/3 and TMC1/2 complexes are integral to hair-cell MET function in vertebrate mechanosensory epithelia.
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Affiliation(s)
- Arnaud P J Giese
- Department of Otorhinolaryngology - Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wei-Hsiang Weng
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Katie S Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | | | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Evan M Ratzan
- Departments of Otolaryngology and Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alisha J Beirl
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Roberto Aponte Rivera
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey M Lotthammer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Sanket Walujkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Omid A Zobeiri
- Department of Biomedical Engineering, McGill University, Montreal, QC, Canada
| | - Jeffrey R Holt
- Departments of Otolaryngology and Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology - Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kathleen E Cullen
- Departments of Biomedical Engineering, Neuroscience, and Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology - Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology and Visual Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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5
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Jiang Q, Zou W, Li S, Qiu X, Zhu L, Kang L, Müller U. Sequence variations and accessory proteins adapt TMC functions to distinct sensory modalities. Neuron 2024:S0896-6273(24)00448-3. [PMID: 38986620 DOI: 10.1016/j.neuron.2024.06.013] [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: 11/28/2023] [Revised: 05/10/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
Abstract
Transmembrane channel-like (TMC) proteins are expressed throughout the animal kingdom and are thought to encode components of ion channels. Mammals express eight TMCs (mTMC1-8), two of which (mTMC1 and mTMC2) are subunits of mechanotransduction channels. C. elegans expresses two TMCs (TMC-1 and TMC-2), which mediate mechanosensation, egg laying, and alkaline sensing. The mechanisms by which nematode TMCs contribute to such diverse physiological processes and their functional relationship to mammalian mTMCs is unclear. Here, we show that association with accessory proteins tunes nematode TMC-1 to divergent sensory functions. In addition, distinct TMC-1 domains enable touch and alkaline sensing. Strikingly, these domains are segregated in mammals between mTMC1 and mTMC3. Consistent with these findings, mammalian mTMC1 can mediate mechanosensation in nematodes, while mTMC3 can mediate alkaline sensation. We conclude that sequence diversification and association with accessory proteins has led to the emergence of TMC protein complexes with diverse properties and physiological functions.
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Affiliation(s)
- Qiang Jiang
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wenjuan Zou
- Department of Neurosurgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310053, Zhejiang, China
| | - Shitian Li
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xufeng Qiu
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Linhui Zhu
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Lijun Kang
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Yiwu 322000, China.
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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6
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Feng Z, Di Zanni E, Alvarenga O, Chakraborty S, Rychlik N, Accardi A. In or out of the groove? Mechanisms of lipid scrambling by TMEM16 proteins. Cell Calcium 2024; 121:102896. [PMID: 38749289 PMCID: PMC11178363 DOI: 10.1016/j.ceca.2024.102896] [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: 03/20/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 06/13/2024]
Abstract
Phospholipid scramblases mediate the rapid movement of lipids between membrane leaflets, a key step in establishing and maintaining membrane homeostasis of the membranes of all eukaryotic cells and their organelles. Thus, impairment of lipid scrambling can lead to a variety of pathologies. How scramblases catalyzed the transbilayer movement of lipids remains poorly understood. Despite the availability of direct structural information on three unrelated families of scramblases, the TMEM16s, the Xkrs, and ATG-9, a unifying mechanism has failed to emerge thus far. Among these, the most extensively studied and best understood are the Ca2+ activated TMEM16s, which comprise ion channels and/or scramblases. Early work supported the view that these proteins provided a hydrophilic, membrane-exposed groove through which the lipid headgroups could permeate. However, structural, and functional experiments have since challenged this mechanism, leading to the proposal that the TMEM16s distort and thin the membrane near the groove to facilitate lipid scrambling. Here, we review our understanding of the structural and mechanistic underpinnings of lipid scrambling by the TMEM16s and discuss how the different proposals account for the various experimental observations.
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Affiliation(s)
- Zhang Feng
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Eleonora Di Zanni
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Omar Alvarenga
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Sayan Chakraborty
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Nicole Rychlik
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Institute of Physiology I, University of Münster, Robert-Koch-Str. 27a, D-48149 Münster, Germany
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States.
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7
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Kermani AA. Applications of fluorescent protein tagging in structural studies of membrane proteins. FEBS J 2024; 291:2719-2732. [PMID: 37470714 DOI: 10.1111/febs.16910] [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] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Generating active, pure, and monodisperse protein remains a major bottleneck for structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM). The current methodology heavily relies on overexpressing the recombinant protein fused with a histidine tag in conventional expression systems and evaluating the quality and stability of purified protein using size exclusion chromatography (SEC). This requires a large amount of protein and can be highly laborious and time consuming. Therefore, this approach is not suitable for high-throughput screening and low-expressing macromolecules, particularly eukaryotic membrane proteins. Using fluorescent proteins fused to the target protein (applicable to both soluble and membrane proteins) enables rapid and efficient screening of expression level and monodispersity of tens of unpurified constructs using fluorescence-based size exclusion chromatography (FSEC). Moreover, FSEC proves valuable for screening multiple detergents to identify the most stabilizing agent in the case of membrane proteins. Additionally, FSEC can facilitate nanodisc reconstitution by determining the optimal ratio of membrane scaffold protein (MSP), lipids, and target protein. The distinct advantages offered by FSEC indicate that fluorescent proteins can serve as a viable alternative to commonly used affinity tags for both characterization and purification purposes. In this review, I will summarize the advantages of this technique using examples from my own work. It should be noted that this article is not intended to provide an exhaustive review of all available literature, but rather to offer representative examples of FSEC applications.
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Affiliation(s)
- Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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8
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Zhang C, Tong F, Zhou B, He M, Liu S, Zhou X, Ma Q, Feng T, Du WJ, Yang H, Xu H, Xiao L, Xu ZZ, Zhu C, Wu R, Wang YQ, Han Q. TMC6 functions as a GPCR-like receptor to sense noxious heat via Gαq signaling. Cell Discov 2024; 10:66. [PMID: 38886367 PMCID: PMC11183229 DOI: 10.1038/s41421-024-00678-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/08/2024] [Indexed: 06/20/2024] Open
Abstract
Thermosensation is vital for the survival, propagation, and adaption of all organisms, but its mechanism is not fully understood yet. Here, we find that TMC6, a membrane protein of unknown function, is highly expressed in dorsal root ganglion (DRG) neurons and functions as a Gαq-coupled G protein-coupled receptor (GPCR)-like receptor to sense noxious heat. TMC6-deficient mice display a substantial impairment in noxious heat sensation while maintaining normal perception of cold, warmth, touch, and mechanical pain. Further studies show that TMC6 interacts with Gαq via its intracellular C-terminal region spanning Ser780 to Pro810. Specifically disrupting such interaction using polypeptide in DRG neurons, genetically ablating Gαq, or pharmacologically blocking Gαq-coupled GPCR signaling can replicate the phenotype of TMC6 deficient mice regarding noxious heat sensation. Noxious heat stimulation triggers intracellular calcium release from the endoplasmic reticulum (ER) of TMC6- but not control vector-transfected HEK293T cell, which can be significantly inhibited by blocking PLC or IP3R. Consistently, noxious heat-induced intracellular Ca2+ release from ER and action potentials of DRG neurons largely reduced when ablating TMC6 or blocking Gαq/PLC/IP3R signaling pathway as well. In summary, our findings indicate that TMC6 can directly function as a Gαq-coupled GPCR-like receptor sensing noxious heat.
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Affiliation(s)
- Chen Zhang
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Fang Tong
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Bin Zhou
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Mingdong He
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Shuai Liu
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Xiaomeng Zhou
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Qiang Ma
- School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianyu Feng
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Wan-Jie Du
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Huan Yang
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Hao Xu
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Lei Xiao
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Zhen-Zhong Xu
- School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruiqi Wu
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Yan-Qing Wang
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Qingjian Han
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China.
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9
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Holt JR, Fettiplace R, Müller U. Sensory transduction in auditory hair cells-PIEZOs can't touch this. J Gen Physiol 2024; 156:e202413585. [PMID: 38727631 PMCID: PMC11090049 DOI: 10.1085/jgp.202413585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024] Open
Abstract
In this Viewpoint, Holt, Fettiplace, and Müller weigh the evidence supporting a role for PIEZO and TMC channels in mechanosensory transduction in inner ear hair cells.
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Affiliation(s)
- Jeffrey R. Holt
- Departments of Otolaryngology and Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert Fettiplace
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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10
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Wu X, Shang T, Lü X, Luo D, Yang D. A monomeric structure of human TMEM63A protein. Proteins 2024; 92:750-756. [PMID: 38217391 DOI: 10.1002/prot.26660] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/10/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
OSCA/TMEM63 is a newly identified family of mechanically activated (MA) ion channels in plants and animals, respectively, which convert physical forces into electrical signals or trigger intracellular cascades and are essential for eukaryotic physiology. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. However, the molecular architecture of the mammalian TMEM63 proteins remains unclear. Here we elucidate the structure of human TMEM63A in the presence of calcium by single particle cryo-EM, revealing a distinct monomeric architecture containing eleven transmembrane helices. It has structural similarity to the single subunit of the Arabidopsis thaliana OSCA proteins. We locate the ion permeation pathway within the monomeric configuration and observe a nonprotein density resembling lipid. These results lay a foundation for understanding the structural organization of OSCA/TMEM63A family proteins.
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Affiliation(s)
- Xuening Wu
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Tiantian Shang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Xinyi Lü
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Deyi Luo
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Dongxue Yang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
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11
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De-la-Torre P, Martínez-García C, Gratias P, Mun M, Santana P, Akyuz N, González W, Indzhykulian AA, Ramírez D. Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583611. [PMID: 38826329 PMCID: PMC11142246 DOI: 10.1101/2024.03.05.583611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Our ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. Despite extensive research on otoprotective compounds targeting MET channels, our understanding of how small molecule modulators interact with these channels remains limited, hampering the discovery of novel compounds. Here, we propose a structure-based screening approach, integrating 3D-pharmacophore modeling, molecular simulations, and experimental validation. Our pipeline successfully identified several novel compounds and FDA-approved drugs that reduced dye uptake in cultured cochlear explants, indicating MET modulation activity. Molecular docking and free-energy estimations for binding allowed us to identify three potential drug binding sites within the channel pore, phospholipids, and key amino acids involved in modulator interactions. We also identified shared ligand-binding features between TMC and structurally related TMEM16 protein families, providing novel insights into their distinct inhibition, while potentially guiding the rational design of MET-channel-specific modulators. Our pipeline offers a broad application to discover small molecule modulators for a wide spectrum of mechanosensitive ion channels.
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Affiliation(s)
- Pedro De-la-Torre
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | | | - Paul Gratias
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | - Matthew Mun
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | - Paula Santana
- Facultad de Ingeniería, Instituto de Ciencias Químicas Aplicadas, Universidad Autónoma de Chile, Santiago, Chile
| | - Nurunisa Akyuz
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), University of Talca, Talca 3460000, Chile
| | - Artur A. Indzhykulian
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | - David Ramírez
- Department of Pharmacology, Faculty of Biological Sciences, University of Concepción, Chile
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12
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Zhang J, He W, Liang L, Sun B, Zhang Y. Study on the saltiness-enhancing mechanism of chicken-derived umami peptides by sensory evaluation and molecular docking to transmembrane channel-like protein 4 (TMC4). Food Res Int 2024; 182:114139. [PMID: 38519171 DOI: 10.1016/j.foodres.2024.114139] [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] [Received: 12/27/2023] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
The previously obtained chicken-derived umami peptides in the laboratory were evaluated for their saltiness-enhancing effect by sensory evaluation and S-curve, and the results revealed that peptides TPPKID, PKESEKPN, TEDWGR, LPLQDAH, NEFGYSNR, and LPLQD had significant saltiness-enhancing effects. In the binary solution system with salt, the ratio of the experimental detection threshold (129.17 mg/L) to the theoretical detection threshold (274.43 mg/L) of NEFGYSNR was 0.47, which had a synergistic saltiness-enhancing effect with salt. The model of transmembrane channel-like protein 4 (TMC4) channel protein was constructed by homology modeling, which had a 10-fold transmembrane structure and was well evaluated. Molecular docking and frontier molecular orbitals showed that the main active sites of TMC4 were Lys 471, Met 379, Cys 475, Gln 377, and Pro 380, and the main active sites of NEFGYSNR were Tyr, Ser and Asn. This study may provide a theoretical reference for low-sodium diets.
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Affiliation(s)
- Jingcheng Zhang
- China Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, 100048, China
| | - Wei He
- China Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, 100048, China
| | - Li Liang
- China Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, 100048, China
| | - Baoguo Sun
- China Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, 100048, China
| | - Yuyu Zhang
- China Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, 100048, China.
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13
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Han Y, Zhou Z, Jin R, Dai F, Ge Y, Ju X, Ma X, He S, Yuan L, Wang Y, Yang W, Yue X, Chen Z, Sun Y, Corry B, Cox CD, Zhang Y. Mechanical activation opens a lipid-lined pore in OSCA ion channels. Nature 2024; 628:910-918. [PMID: 38570680 DOI: 10.1038/s41586-024-07256-9] [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: 06/26/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
OSCA/TMEM63 channels are the largest known family of mechanosensitive channels1-3, playing critical roles in plant4-7 and mammalian8,9 mechanotransduction. Here we determined 44 cryogenic electron microscopy structures of OSCA/TMEM63 channels in different environments to investigate the molecular basis of OSCA/TMEM63 channel mechanosensitivity. In nanodiscs, we mimicked increased membrane tension and observed a dilated pore with membrane access in one of the OSCA1.2 subunits. In liposomes, we captured the fully open structure of OSCA1.2 in the inside-in orientation, in which the pore shows a large lateral opening to the membrane. Unusually for ion channels, structural, functional and computational evidence supports the existence of a 'proteo-lipidic pore' in which lipids act as a wall of the ion permeation pathway. In the less tension-sensitive homologue OSCA3.1, we identified an 'interlocking' lipid tightly bound in the central cleft, keeping the channel closed. Mutation of the lipid-coordinating residues induced OSCA3.1 activation, revealing a conserved open conformation of OSCA channels. Our structures provide a global picture of the OSCA channel gating cycle, uncover the importance of bound lipids and show that each subunit can open independently. This expands both our understanding of channel-mediated mechanotransduction and channel pore formation, with important mechanistic implications for the TMEM16 and TMC protein families.
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Affiliation(s)
- Yaoyao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Zijing Zhou
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruitao Jin
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Fei Dai
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Yifan Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Xisan Ju
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Xiaonuo Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Sitong He
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Ling Yuan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yingying Wang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Yang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaomin Yue
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongwen Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ben Corry
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia.
| | - Charles D Cox
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia.
- School of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
| | - Yixiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Key Laboratory of Aging Studies, Shanghai, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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14
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Clark S, Jeong H, Posert R, Goehring A, Gouaux E. The structure of the Caenorhabditis elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction. Proc Natl Acad Sci U S A 2024; 121:e2314096121. [PMID: 38354260 PMCID: PMC10895266 DOI: 10.1073/pnas.2314096121] [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: 08/15/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily conserved family of membrane proteins whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila. TMC1 and TMC2 are components of ion channel complexes, but the molecular features that tune these complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here, we present the single-particle cryo-electron microscopy structure of the native TMC-2 complex isolated from C. elegans. The complex is composed of two copies of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the C. elegans TMC-1 complex highlights conserved protein-lipid interactions, as well as a π-helical structural motif in the pore-forming helices, that together suggest a mechanism for TMC-mediated mechanosensory transduction.
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Affiliation(s)
- Sarah Clark
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - Hanbin Jeong
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - Rich Posert
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - April Goehring
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
- HHMI, Oregon Health and Science University, Portland, OR97239
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
- HHMI, Oregon Health and Science University, Portland, OR97239
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15
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Lowry AJ, Liang P, Wan YCS, Pei ZM, Yang H, Zhang Y. TMEM16 and TMEM63/OSCA proteins share a conserved potential to permeate ions and phospholipids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578431. [PMID: 38370744 PMCID: PMC10871192 DOI: 10.1101/2024.02.04.578431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The calcium-activated TMEM16 proteins and the mechanosensitive/osmolarity-activated OSCA/TMEM63 proteins belong to the Transmembrane Channel/Scramblase (TCS) superfamily. Within the superfamily, OSCA/TMEM63 proteins, as well as TMEM16A and TMEM16B, likely function solely as ion channels. However, the remaining TMEM16 members, including TMEM16F, maintain an additional function as scramblases, rapidly exchanging phospholipids between leaflets of the membrane. Although recent studies have advanced our understanding of TCS structure-function relationships, the molecular determinants of TCS ion and lipid permeation remain unclear. Here we show that single lysine mutations in transmembrane helix (TM) 4 allow non-scrambling TCS members to permeate phospholipids. This study highlights the key role of TM 4 in controlling TCS ion and lipid permeation and offers novel insights into the evolution of the TCS superfamily, suggesting that, like TMEM16s, the OSCA/TMEM63 family maintains a conserved potential to permeate ions and phospholipids.
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Affiliation(s)
- Augustus J Lowry
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pengfei Liang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Y C Serena Wan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhen-Ming Pei
- Department of Biology, Duke University, Durham, NC 27710, USA
| | - Huanghe Yang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yang Zhang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Current address: Shenzhen Bay Laboratory, Guangdong 518106, China
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16
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Lee JH, Perez-Flores MC, Park S, Kim HJ, Chen Y, Kang M, Kersigo J, Choi J, Thai PN, Woltz RL, Perez-Flores DC, Perkins G, Sihn CR, Trinh P, Zhang XD, Sirish P, Dong Y, Feng WW, Pessah IN, Dixon RE, Sokolowski B, Fritzsch B, Chiamvimonvat N, Yamoah EN. The Piezo channel is a mechano-sensitive complex component in the mammalian inner ear hair cell. Nat Commun 2024; 15:526. [PMID: 38228630 PMCID: PMC10791687 DOI: 10.1038/s41467-023-44230-x] [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: 07/02/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024] Open
Abstract
The inner ear is the hub where hair cells (HCs) transduce sound, gravity, and head acceleration stimuli to the brain. Hearing and balance rely on mechanosensation, the fastest sensory signals transmitted to the brain. The mechanoelectrical transducer (MET) channel is the entryway for the sound-balance-brain interface, but the channel-complex composition is not entirely known. Here, we report that the mouse utilizes Piezo1 (Pz1) and Piezo2 (Pz2) isoforms as MET-complex components. The Pz channels, expressed in HC stereocilia, and cell lines are co-localized and co-assembled with MET complex partners. Mice expressing non-functional Pz1 and Pz2 at the ROSA26 locus have impaired auditory and vestibular traits that can only be explained if the Pzs are integral to the MET complex. We suggest that Pz subunits constitute part of the MET complex and that interactions with other MET complex components yield functional MET units to generate HC MET currents.
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Affiliation(s)
- Jeong Han Lee
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Maria C Perez-Flores
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Seojin Park
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
- Prestige Biopharma, 11-12F, 44, Myongjigukje7-ro, Gangseo-gu, Busan, 67264, South Korea
| | - Hyo Jeong Kim
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Yingying Chen
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Mincheol Kang
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
- Prestige Biopharma, 11-12F, 44, Myongjigukje7-ro, Gangseo-gu, Busan, 67264, South Korea
| | | | - Jinsil Choi
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Phung N Thai
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Ryan L Woltz
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | | | - Guy Perkins
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Choong-Ryoul Sihn
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Pauline Trinh
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Xiao-Dong Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Yao Dong
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, 1089 VM3B, Davis, CA, 95616, USA
| | - Wayne Wei Feng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, 1089 VM3B, Davis, CA, 95616, USA
| | - Isaac N Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, 1089 VM3B, Davis, CA, 95616, USA
| | - Rose E Dixon
- Department of Physiology & Membrane Biology, Tupper Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Bernd Sokolowski
- Department of Otolaryngology-Head and Neck Surgery, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Bernd Fritzsch
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
- VA Northern California Healthcare System, Sacramento, USA
| | - Ebenezer N Yamoah
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA.
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17
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Beurg M, Schwalbach ET, Fettiplace R. LHFPL5 is a key element in force transmission from the tip link to the hair cell mechanotransducer channel. Proc Natl Acad Sci U S A 2024; 121:e2318270121. [PMID: 38194445 PMCID: PMC10801851 DOI: 10.1073/pnas.2318270121] [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: 10/19/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024] Open
Abstract
During auditory transduction, sound-evoked vibrations of the hair cell stereociliary bundles open mechanotransducer (MET) ion channels via tip links extending from one stereocilium to its neighbor. How tension in the tip link is delivered to the channel is not fully understood. The MET channel comprises a pore-forming subunit, transmembrane channel-like protein (TMC1 or TMC2), aided by several accessory proteins, including LHFPL5 (lipoma HMGIC fusion partner-like 5). We investigated the role of LHFPL5 in transduction by comparing MET channel activation in outer hair cells of Lhfpl5-/- knockout mice with those in Lhfpl5+/- heterozygotes. The 10 to 90 percent working range of transduction in Tmc1+/+; Lhfpl5+/- was 52 nm, from which the single-channel gating force, Z, was evaluated as 0.34 pN. However, in Tmc1+/+; Lhfpl5-/- mice, the working range increased to 123 nm and Z more than halved to 0.13 pN, indicating reduced sensitivity. Tip link tension is thought to activate the channel via a gating spring, whose stiffness is inferred from the stiffness change on tip link destruction. The gating stiffness was ~40 percent of the total bundle stiffness in wild type but was virtually abolished in Lhfpl5-/-, implicating LHFPL5 as a principal component of the gating spring. The mutation Tmc1 p.D569N reduced the LHFPL5 immunolabeling in the stereocilia and like Lhfpl5-/- doubled the MET working range, but other deafness mutations had no effect on the dynamic range. We conclude that tip-link tension is transmitted to the channel primarily via LHFPL5; residual activation without LHFPL5 may occur by direct interaction between PCDH15 and TMC1.
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Affiliation(s)
- Maryline Beurg
- Department of Neuroscience, University of WisconsinSchool of Medicine and Public Health, Madison, WI53706
| | - Evan Travis Schwalbach
- Department of Neuroscience, University of WisconsinSchool of Medicine and Public Health, Madison, WI53706
| | - Robert Fettiplace
- Department of Neuroscience, University of WisconsinSchool of Medicine and Public Health, Madison, WI53706
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18
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Sun P, Smith E, Nicolson T. Transmembrane Channel-Like (Tmc) Subunits Contribute to Frequency Sensitivity in the Zebrafish Utricle. J Neurosci 2024; 44:e1298232023. [PMID: 37952940 PMCID: PMC10851681 DOI: 10.1523/jneurosci.1298-23.2023] [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: 07/12/2023] [Revised: 08/25/2023] [Accepted: 09/16/2023] [Indexed: 11/14/2023] Open
Abstract
Information about dynamic head motion is conveyed by a central "striolar" zone of vestibular hair cells and afferent neurons in the inner ear. How vestibular hair cells are tuned to transduce dynamic stimuli at the molecular level is not well understood. Here we take advantage of the differential expression pattern of tmc1, tmc2a, and tmc2b, which encode channel subunits of the mechanotransduction complex in zebrafish vestibular hair cells. To test the role of various combinations of Tmc subunits in transducing dynamic head movements, we measured reflexive eye movements induced by high-frequency stimuli in single versus double tmc mutants. We found that Tmc2a function correlates with the broadest range of frequency sensitivity, whereas Tmc2b mainly contributes to lower-frequency responses. Tmc1, which is largely excluded from the striolar zone, plays a minor role in sensing lower-frequency stimuli. Our study suggests that the Tmc subunits impart functional differences to the mechanotransduction of dynamic stimuli.Significance Statement Information about dynamic head movements is transmitted by sensory receptors, known as hair cells, in the labyrinth of the inner ear. The sensitivity of hair cells to fast or slow movements of the head differs according to cell type. Whether the mechanotransduction complex that converts mechanical stimuli into electrical signals in hair cells participates in conveying frequency information is not clear. Here we find that the transmembrane channel-like 1/2 genes, which encode a central component of the complex, are differentially expressed in the utricle and contribute to frequency sensitivity in zebrafish.
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Affiliation(s)
- Peng Sun
- Department of Otolaryngology, Stanford University, Stanford, California 94304
| | - Eliot Smith
- Department of Otolaryngology, Stanford University, Stanford, California 94304
| | - Teresa Nicolson
- Department of Otolaryngology, Stanford University, Stanford, California 94304
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19
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Hsieh CY, Tsai CY, Chou YF, Hsu CJ, Wu HP, Wu CC. Otoprotection against aminoglycoside- and cisplatin-induced ototoxicity focusing on the upstream drug uptake pathway. J Chin Med Assoc 2024; 87:17-24. [PMID: 37962398 DOI: 10.1097/jcma.0000000000001023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2023] Open
Abstract
Aminoglycoside- and cisplatin-induced ototoxicity, which is a significant issue owing to the widespread use of these drugs in clinical practice, involves the entry of aminoglycosides and cisplatin into the endolymph and hair cells via specific channels or transporters, followed by reactive oxygen species (ROS) generation and hair cells apoptosis. Current strategies focalize primarily on interference with downstream ROS effects; however, recent evidence has demonstrated that inhibiting the uptake of aminoglycosides and cisplatin by hair cells is another promising strategy for tackling the upstream drug uptake pathway. With advances in structural biology, the conformations of certain aminoglycoside and cisplatin channels and transporters, such as the mechanoelectrical transduction channel and organic cation transporter-2, have been largely elucidated. These channels and transporters may become potential targets for the introduction of new otoprotective strategies. This review focuses on the strategies for inhibiting ototoxic drugs uptake by auditory hair cells and provides potential targets for recent developments in the field of otoprotection. Molecular dynamics (MD) simulations of these proteins could help identify the molecules that inhibit the uptake of aminoglycosides and cisplatin by hair cells. Integrating upstream drug uptake pathway targets and MD simulations may help dissect molecular mechanisms and develop novel otoprotective strategies for aminoglycoside- and cisplatin-induced ototoxicity.
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Affiliation(s)
- Cheng-Yu Hsieh
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Cheng-Yu Tsai
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Yi-Fan Chou
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Chuan-Jen Hsu
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Hung-Pin Wu
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan, ROC
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan, ROC
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20
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Clark S, Mitra J, Elferich J, Goehring A, Ge J, Ha T, Gouaux E. Single molecule studies of the native hair cell mechanosensory transduction complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571162. [PMID: 38168376 PMCID: PMC10760052 DOI: 10.1101/2023.12.11.571162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Hearing and balance rely on the conversion of a mechanical stimulus into an electrical signal, a process known as mechanosensory transduction (MT). In vertebrates, this process is accomplished by an MT complex that is located in hair cells of the inner ear. While the past three decades of research have identified many subunits that are important for MT and revealed interactions between these subunits, the composition and organization of a functional complex remains unknown. The major challenge associated with studying the MT complex is its extremely low abundance in hair cells; current estimates of MT complex quantity range from 3-60 attomoles per cochlea or utricle, well below the detection limit of most biochemical assays that are used to characterize macromolecular complexes. Here we describe the optimization of two single molecule assays, single molecule pull-down (SiMPull) and single molecule array (SiMoA), to study the composition and quantity of native mouse MT complexes. We demonstrate that these assays are capable of detecting and quantifying low attomoles of the native MT subunits protocadherin-15 (PCDH15) and lipoma HMGIC fusion partner-like protein 5 (LHFPL5). Our results illuminate the stoichiometry of PCDH15- and LHFPL5-containing complexes and establish SiMPull and SiMoA as productive methods for probing the abundance, composition, and arrangement of subunits in the native MT complex.
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Affiliation(s)
- Sarah Clark
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Present address: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Jaba Mitra
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, IL 61801, USA
- Present address: Pacific Biosciences, Menlo Park, CA 94025, USA
| | - Johannes Elferich
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Present address: UMass Chan Medical School, Worcester, MA 01655, USA
| | - April Goehring
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Jingpeng Ge
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Present address: School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, 201210, China
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21215, USA
- Present address: Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Present address: Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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21
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Lam AKM, Dutzler R. Mechanistic basis of ligand efficacy in the calcium-activated chloride channel TMEM16A. EMBO J 2023; 42:e115030. [PMID: 37984335 PMCID: PMC10711664 DOI: 10.15252/embj.2023115030] [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: 07/19/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Agonist binding in ligand-gated ion channels is coupled to structural rearrangements around the binding site, followed by the opening of the channel pore. In this process, agonist efficacy describes the equilibrium between open and closed conformations in a fully ligand-bound state. Calcium-activated chloride channels in the TMEM16 family are important sensors of intracellular calcium signals and are targets for pharmacological modulators, yet a mechanistic understanding of agonist efficacy has remained elusive. Using a combination of cryo-electron microscopy, electrophysiology, and autocorrelation analysis, we now show that agonist efficacy in the ligand-gated channel TMEM16A is dictated by the conformation of the pore-lining helix α6 around the Ca2+ -binding site. The closure of the binding site, which involves the formation of a π-helix below a hinge region in α6, appears to be coupled to the opening of the inner pore gate, thereby governing the channel's open probability and conductance. Our results provide a mechanism for agonist binding and efficacy and a structural basis for the design of potentiators and partial agonists in the TMEM16 family.
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Affiliation(s)
- Andy KM Lam
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Raimund Dutzler
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
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22
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Cho SH, Yun Y, Lee DH, Cha JH, Lee SM, Lee J, Suh MH, Lee JH, Oh SH, Park MK, Lee SY. Novel autosomal dominant TMC1 variants linked to hearing loss: insight into protein-lipid interactions. BMC Med Genomics 2023; 16:320. [PMID: 38066485 PMCID: PMC10704677 DOI: 10.1186/s12920-023-01766-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND TMC1, which encodes transmembrane channel-like protein 1, forms the mechanoelectrical transduction (MET) channel in auditory hair cells, necessary for auditory function. TMC1 variants are known to cause autosomal dominant (DFNA36) and autosomal recessive (DFNB7/11) non-syndromic hearing loss, but only a handful of TMC1 variants underlying DFNA36 have been reported, hampering analysis of genotype-phenotype correlations. METHODS In this study, we retrospectively reviewed 338 probands in an in-house database of genetic hearing loss, evaluating the clinical phenotypes and genotypes of novel TMC1 variants associated with DFNA36. To analyze the structural impact of these variants, we generated two structural models of human TMC1, utilizing the Cryo-EM structure of C. elegans TMC1 as a template and AlphaFold protein structure database. Specifically, the lipid bilayer-embedded protein database was used to construct membrane-embedded models of TMC1. We then examined the effect of TMC1 variants on intramolecular interactions and predicted their potential pathogenicity. RESULTS We identified two novel TMC1 variants related to DFNA36 (c.1256T > C:p.Phe419Ser and c.1444T > C:p.Trp482Arg). The affected subjects had bilateral, moderate, late-onset, progressive sensorineural hearing loss with a down-sloping configuration. The Phe419 residue located in the transmembrane domain 4 of TMC1 faces outward towards the channel pore and is in close proximity to the hydrophobic tail of the lipid bilayer. The non-polar-to-polar variant (p.Phe419Ser) alters the hydrophobicity in the membrane, compromising protein-lipid interactions. On the other hand, the Trp482 residue located in the extracellular linker region between transmembrane domains 5 and 6 is anchored to the membrane interfaces via its aromatic rings, mediating several molecular interactions that stabilize the structure of TMC1. This type of aromatic ring-based anchoring is also observed in homologous transmembrane proteins such as OSCA1.2. Conversely, the substitution of Trp with Arg (Trp482Arg) disrupts the cation-π interaction with phospholipids located in the outer leaflet of the phospholipid bilayer, destabilizing protein-lipid interactions. Additionally, Trp482Arg collapses the CH-π interaction between Trp482 and Pro511, possibly reducing the overall stability of the protein. In parallel with the molecular modeling, the two mutants degraded significantly faster compared to the wild-type protein, compromising protein stability. CONCLUSIONS This results expand the genetic spectrum of disease-causing TMC1 variants related to DFNA36 and provide insight into TMC1 transmembrane protein-lipid interactions.
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Affiliation(s)
- Sung Ho Cho
- Seoul National University College of Medicine, Seoul, South Korea
| | - Yejin Yun
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - Dae Hee Lee
- CTCELLS, Inc, 21, Yuseong-daero, 1205beon-gil, Yuseong-gu, Daejeon, Republic of Korea
| | - Joo Hyun Cha
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - So Min Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - Jehyun Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - Myung Hwan Suh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea.
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea.
- Department of Genomic Medicine, Precision Medicine & Rare Disease Center, Seoul, South Korea.
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23
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Arango AS, Park H, Tajkhorshid E. Topological Learning Approach to Characterizing Biological Membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569053. [PMID: 38076911 PMCID: PMC10705453 DOI: 10.1101/2023.11.28.569053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Biological membranes play key roles in cellular compartmentalization, structure, and its signaling pathways. At varying temperatures, individual membrane lipids sample from different configurations, a process that frequently leads to higher-order phase behavior and phenomena. Here we present a persistent homology-based method for quantifying the structural features of individual and bulk lipids, providing local and contextual information on lipid tail organization. Our method leverages the mathematical machinery of algebraic topology and machine learning to infer temperature-dependent structural information of lipids from static coordinates. To train our model, we generated multiple molecular dynamics trajectories of DPPC membranes at varying temperatures. A fingerprint was then constructed for each set of lipid coordinates by a persistent homology filtration, in which interactions spheres were grown around the lipid atoms while tracking their intersections. The sphere filtration formed a simplicial complex that captures enduring key topological features of the configuration landscape, using homology, yielding persistence data. Following fingerprint extraction for physiologically relevant temperatures, the persistence data were used to train an attention-based neural network for assignment of effective temperature values to selected membrane regions. Our persistence homology-based method captures the local structural effects, via effective temperature, of lipids adjacent to other membrane constituents, e.g. sterols and proteins. This topological learning approach can predict lipid effective temperatures from static coordinates across multiple spatial resolutions. The tool, called MembTDA, can be accessed at https://github.com/hyunp2/Memb-TDA.
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Affiliation(s)
- Andres S Arango
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hyun Park
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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24
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Smith ET, Sun P, Yu SK, Raible DW, Nicolson T. Differential expression of mechanotransduction complex genes in auditory/vestibular hair cells in zebrafish. Front Mol Neurosci 2023; 16:1274822. [PMID: 38035267 PMCID: PMC10682102 DOI: 10.3389/fnmol.2023.1274822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Ciliated sensory cells such as photo- and olfactory receptors employ multiple types of opsins or hundreds of unique olfactory G-protein coupled receptors to respond to various wavelengths of light or odorants. With respect to hearing and balance, the mechanotransduction machinery involves fewer variants; however, emerging evidence suggests that specialization occurs at the molecular level. To address how the mechanotransduction complex varies in the inner ear, we characterized the expression of paralogous genes that encode components required for mechanotransduction in zebrafish hair cells using RNA-FISH and bioinformatic analysis. Our data indicate striking zonal differences in the expression of two components of the mechanotransduction complex which are known to physically interact, the transmembrane channel-like 1 and 2 (tmc1/2) family members and the calcium and integrin binding 2 and 3 (cib2/3) paralogues. tmc1, tmc2b, and cib3 are largely expressed in peripheral or extrastriolar hair cells, whereas tmc2a and cib2 are enriched in central or striolar hair cells. In addition, a gene implicated in deaf-blindness, ush1c, is highly enriched in a subset of extrastriolar hair cells. These results indicate that specific combinations of these components may optimize responses to mechanical stimuli in subtypes of sensory receptors within the inner ear.
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Affiliation(s)
- Eliot T. Smith
- Department of Otolaryngology-HNS, Stanford University, Stanford, CA, United States
| | - Peng Sun
- Department of Otolaryngology-HNS, Stanford University, Stanford, CA, United States
| | - Shengyang Kevin Yu
- Department of Otolaryngology-HNS and Biological Structure, Viginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, WA, United States
| | - David W. Raible
- Department of Otolaryngology-HNS and Biological Structure, Viginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, WA, United States
| | - Teresa Nicolson
- Department of Otolaryngology-HNS, Stanford University, Stanford, CA, United States
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25
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Qin Y, Yu D, Wu D, Dong J, Li WT, Ye C, Cheung KC, Zhang Y, Xu Y, Wang Y, Shi YS, Dang S. Cryo-EM structure of TMEM63C suggests it functions as a monomer. Nat Commun 2023; 14:7265. [PMID: 37945568 PMCID: PMC10636204 DOI: 10.1038/s41467-023-42956-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. Deficiency of these channels would cause many diseases including hearing loss. However, their structures and physiological roles are not yet well understood. In this study, we determine the cryo-electron microscopy (cryo-EM) structure of the mouse TMEM63C at 3.56 Å, and revealed structural differences compared to TMEM63A, TMEM63B, and the plant orthologues OSCAs. Further structural guided mutagenesis and calcium imaging demonstrated the important roles of the coupling of TM0 and TM6 in channel activity. Additionally, we confirm that TMEM63C exists primarily as a monomer under physiological conditions, in contrast, TMEM63B is a mix of monomer and dimer in cells, suggesting that oligomerization is a regulatory mechanism for TMEM63 proteins.
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Affiliation(s)
- Yuqi Qin
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Dan Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - Jiangqing Dong
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - William Thomas Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Chang Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - Kai Chit Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yingyi Zhang
- Biological Cryo-EM Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - YongQiang Wang
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94158, USA.
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China.
- Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, 519031, China.
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- HKUST-Shenzhen Research Institute, Nanshan, Shenzhen, 518057, China.
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26
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Zhang N, Häring M, Wolf F, Großhans J, Kong D. Dynamics and functions of E-cadherin complexes in epithelial cell and tissue morphogenesis. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:585-601. [PMID: 38045551 PMCID: PMC10689684 DOI: 10.1007/s42995-023-00206-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Cell-cell adhesion is at the center of structure and dynamics of epithelial tissue. E-cadherin-catenin complexes mediate Ca2+-dependent trans-homodimerization and constitute the kernel of adherens junctions. Beyond the basic function of cell-cell adhesion, recent progress sheds light the dynamics and interwind interactions of individual E-cadherin-catenin complex with E-cadherin superclusters, contractile actomyosin and mechanics of the cortex and adhesion. The nanoscale architecture of E-cadherin complexes together with cis-interactions and interactions with cortical actomyosin adjust to junctional tension and mechano-transduction by reinforcement or weakening of specific features of the interactions. Although post-translational modifications such as phosphorylation and glycosylation have been implicated, their role for specific aspects of in E-cadherin function has remained unclear. Here, we provide an overview of the E-cadherin complex in epithelial cell and tissue morphogenesis focusing on nanoscale architectures by super-resolution approaches and post-translational modifications from recent, in particular in vivo, studies. Furthermore, we review the computational modelling in E-cadherin complexes and highlight how computational modelling has contributed to a deeper understanding of the E-cadherin complexes.
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Affiliation(s)
- Na Zhang
- Department of Biology, Philipps University, 35043 Marburg, Germany
| | - Matthias Häring
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
| | - Fred Wolf
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
| | - Jörg Großhans
- Department of Biology, Philipps University, 35043 Marburg, Germany
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
| | - Deqing Kong
- Department of Biology, Philipps University, 35043 Marburg, Germany
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
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27
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Guo W, Chen L. Force opens a monomeric channel pore. Neuron 2023; 111:3135-3137. [PMID: 37857087 DOI: 10.1016/j.neuron.2023.08.029] [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: 08/29/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023]
Abstract
In this issue of Neuron, Zheng et al.1 report the monomeric architecture of mechanosensitive ion channels TMEM63A and TMEM63B. They show that these high-threshold channels function as monomers on the plasma membrane.
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Affiliation(s)
- Wenjun Guo
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China
| | - Lei Chen
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China.
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28
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Zheng W, Rawson S, Shen Z, Tamilselvan E, Smith HE, Halford J, Shen C, Murthy SE, Ulbrich MH, Sotomayor M, Fu TM, Holt JR. TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels. Neuron 2023; 111:3195-3210.e7. [PMID: 37543036 PMCID: PMC10592209 DOI: 10.1016/j.neuron.2023.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/12/2023] [Accepted: 07/08/2023] [Indexed: 08/07/2023]
Abstract
OSCA/TMEM63s form mechanically activated (MA) ion channels in plants and animals, respectively. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. Here, we uncover an unanticipated monomeric configuration of TMEM63 proteins. Structures of TMEM63A and TMEM63B (referred to as TMEM63s) revealed a single highly restricted pore. Functional analyses demonstrated that TMEM63s are bona fide mechanosensitive ion channels, characterized by small conductance and high thresholds. TMEM63s possess evolutionary variations in the intracellular linker IL2, which mediates dimerization in OSCAs. Replacement of OSCA1.2 IL2 with TMEM63A IL2 or mutations to key variable residues resulted in monomeric OSCA1.2 and MA currents with significantly higher thresholds. Structural analyses revealed substantial conformational differences in the mechano-sensing domain IL2 and gating helix TM6 between TMEM63s and OSCA1.2. Our studies reveal that mechanosensitivity in OSCA/TMEM63 channels is affected by oligomerization and suggest gating mechanisms that may be shared by OSCA/TMEM63, TMEM16, and TMC channels.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Harper E Smith
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Halford
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Chen Shen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Swetha E Murthy
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maximilian H Ulbrich
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Internal Medicine IV, University of Freiburg Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.
| | - Jeffrey R Holt
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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29
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Derudas M, O’Reilly M, Kirkwood NK, Kenyon EJ, Grimsey S, Kitcher SR, Workman S, Bull JC, Ward SE, Kros CJ, Richardson GP. Charge and lipophilicity are required for effective block of the hair-cell mechano-electrical transducer channel by FM1-43 and its derivatives. Front Cell Dev Biol 2023; 11:1247324. [PMID: 37900280 PMCID: PMC10601989 DOI: 10.3389/fcell.2023.1247324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023] Open
Abstract
The styryl dye FM1-43 is widely used to study endocytosis but behaves as a permeant blocker of the mechano-electrical transducer (MET) channel in sensory hair cells, loading rapidly and specifically into the cytoplasm of hair cells in a MET channel-dependent manner. Patch clamp recordings of mouse outer hair cells (OHCs) were used to determine how a series of structural modifications of FM1-43 affect MET channel block. Fluorescence microscopy was used to assess how the modifications influence hair-cell loading in mouse cochlear cultures and zebrafish neuromasts. Cochlear cultures were also used to evaluate otoprotective potential of the modified FM1-43 derivatives. Structure-activity relationships reveal that the lipophilic tail and the cationic head group of FM1-43 are both required for MET channel block in mouse cochlear OHCs; neither moiety alone is sufficient. The extent of MET channel block is augmented by increasing the lipophilicity/bulkiness of the tail, by reducing the number of positive charges in the head group from two to one, or by increasing the distance between the two charged head groups. Loading assays with zebrafish neuromasts and mouse cochlear cultures are broadly in accordance with these observations but reveal a loss of hair-cell specific labelling with increasing lipophilicity. Although FM1-43 and many of its derivatives are generally cytotoxic when tested on cochlear cultures in the presence of an equimolar concentration of the ototoxic antibiotic gentamicin (5 µM), at a 10-fold lower concentration (0.5 µM), two of the derivatives protect OHCs from cell death caused by 48 h-exposure to 5 µM gentamicin.
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Affiliation(s)
- Marco Derudas
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Molly O’Reilly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- Department of Experimental Cardiology, Academic Medical Center, Amsterdam, Netherlands
| | - Nerissa K. Kirkwood
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Emma J. Kenyon
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- School of Medicine, Institute of Life Sciences, Swansea University, Swansea, United Kingdom
| | - Sybil Grimsey
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Siân R. Kitcher
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- Section on Neuronal Circuitry, National Institute on Deafness and Other Communication Disorders NIH, Bethesda, MD, United States
| | - Shawna Workman
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - James C. Bull
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Simon E. Ward
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- Medicines Discovery Institute, Cardiff University, Cardiff, United Kingdom
| | - Corné J. Kros
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Guy P. Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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30
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Sun C, Zhu H, Clark S, Gouaux E. Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology. Nature 2023; 622:195-201. [PMID: 37730991 PMCID: PMC10550821 DOI: 10.1038/s41586-023-06556-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023]
Abstract
Type A γ-aminobutyric acid receptors (GABAARs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants1-3. However, our understanding of GABAAR pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits4 and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABAAR assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABAARs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABAAR assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.
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Affiliation(s)
- Chang Sun
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Sarah Clark
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR, USA.
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31
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Dai G. Signaling by Ion Channels: Pathways, Dynamics and Channelopathies. MISSOURI MEDICINE 2023; 120:367-373. [PMID: 37841571 PMCID: PMC10569386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Charged ions and ion channels play a critical role in regulating the electrical activities of excitable cells. This review discusses the principles of ion channel regulation in the time domain, as well as the diseases that can arise from channel dysfunction and disturbances in ionic balance. Ion channel signaling is a dynamic process that is essential for various physiological functions, including pain sensation, motor control, and the body's response to stress, such as fight-or-flight response.
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Affiliation(s)
- Gucan Dai
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
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32
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Clark S, Jeong H, Goehring A, Kang Y, Gouaux E. Large-scale growth of C. elegans and isolation of membrane protein complexes. Nat Protoc 2023; 18:2699-2716. [PMID: 37495753 DOI: 10.1038/s41596-023-00852-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/02/2023] [Indexed: 07/28/2023]
Abstract
Purification of membrane proteins for biochemical and structural studies is commonly achieved by recombinant overexpression in heterologous cell lines. However, many membrane proteins do not form a functional complex in a heterologous system, and few methods exist to purify sufficient protein from a native source for use in biochemical, biophysical and structural studies. Here, we provide a detailed protocol for the isolation of membrane protein complexes from transgenic Caenorhabditis elegans. We describe how to grow a genetically modified C. elegans line in abundance using standard laboratory equipment, and how to optimize purification conditions on a small scale using fluorescence-detection size-exclusion chromatography. Optimized conditions can then be applied to a large-scale preparation, enabling the purification of adequate quantities of a target protein for structural, biochemical and biophysical studies. Large-scale worm growth can be accomplished in ~9 d, and each optimization experiment can be completed in less than 1 d. We have used these methods to isolate the transmembrane channel-like protein 1 complex, as well as three additional protein complexes (transmembrane-like channel 2, lipid transfer protein and 'Protein S'), from transgenic C. elegans, demonstrating the utility of this approach in purifying challenging, low-abundance membrane protein complexes.
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Affiliation(s)
- Sarah Clark
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Hanbin Jeong
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - April Goehring
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yunsik Kang
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR, USA.
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33
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Park J, Bird JE. The actin cytoskeleton in hair bundle development and hearing loss. Hear Res 2023; 436:108817. [PMID: 37300948 PMCID: PMC10408727 DOI: 10.1016/j.heares.2023.108817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Inner ear hair cells assemble mechanosensitive hair bundles on their apical surface that transduce sounds and accelerations. Each hair bundle is comprised of ∼ 100 individual stereocilia that are arranged into rows of increasing height and width; their specific and precise architecture being necessary for mechanoelectrical transduction (MET). The actin cytoskeleton is fundamental to establishing this architecture, not only by forming the structural scaffold shaping each stereocilium, but also by composing rootlets and the cuticular plate that together provide a stable foundation supporting each stereocilium. In concert with the actin cytoskeleton, a large assortment of actin-binding proteins (ABPs) function to cross-link actin filaments into specific topologies, as well as control actin filament growth, severing, and capping. These processes are individually critical for sensory transduction and are all disrupted in hereditary forms of human hearing loss. In this review, we provide an overview of actin-based structures in the hair bundle and the molecules contributing to their assembly and functional properties. We also highlight recent advances in mechanisms driving stereocilia elongation and how these processes are tuned by MET.
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Affiliation(s)
- Jinho Park
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, United States; Myology Institute, University of Florida, Gainesville, FL 32610, United States
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, United States; Myology Institute, University of Florida, Gainesville, FL 32610, United States.
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34
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Clark S, Jeong H, Posert R, Goehring A, Gouaux E. Structure of C. elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553618. [PMID: 37645790 PMCID: PMC10462014 DOI: 10.1101/2023.08.16.553618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily-conserved family of ion channels whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila. The molecular features that tune homologous TMC ion channel complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here we present the single particle cryo-electron microscopy structure of the native TMC-2 complex isolated from C. elegans. The complex is composed of two copies each of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the C. elegans TMC-1 complex reveals differences in subunit composition and highlights conserved protein-lipid interactions, as well as other structural features, that together suggest a mechanism for TMC-mediated mechanosensory transduction.
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Affiliation(s)
- Sarah Clark
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Hanbin Jeong
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Rich Posert
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - April Goehring
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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35
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Di X, Gao X, Peng L, Ai J, Jin X, Qi S, Li H, Wang K, Luo D. Cellular mechanotransduction in health and diseases: from molecular mechanism to therapeutic targets. Signal Transduct Target Ther 2023; 8:282. [PMID: 37518181 PMCID: PMC10387486 DOI: 10.1038/s41392-023-01501-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 08/01/2023] Open
Abstract
Cellular mechanotransduction, a critical regulator of numerous biological processes, is the conversion from mechanical signals to biochemical signals regarding cell activities and metabolism. Typical mechanical cues in organisms include hydrostatic pressure, fluid shear stress, tensile force, extracellular matrix stiffness or tissue elasticity, and extracellular fluid viscosity. Mechanotransduction has been expected to trigger multiple biological processes, such as embryonic development, tissue repair and regeneration. However, prolonged excessive mechanical stimulation can result in pathological processes, such as multi-organ fibrosis, tumorigenesis, and cancer immunotherapy resistance. Although the associations between mechanical cues and normal tissue homeostasis or diseases have been identified, the regulatory mechanisms among different mechanical cues are not yet comprehensively illustrated, and no effective therapies are currently available targeting mechanical cue-related signaling. This review systematically summarizes the characteristics and regulatory mechanisms of typical mechanical cues in normal conditions and diseases with the updated evidence. The key effectors responding to mechanical stimulations are listed, such as Piezo channels, integrins, Yes-associated protein (YAP) /transcriptional coactivator with PDZ-binding motif (TAZ), and transient receptor potential vanilloid 4 (TRPV4). We also reviewed the key signaling pathways, therapeutic targets and cutting-edge clinical applications of diseases related to mechanical cues.
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Affiliation(s)
- Xingpeng Di
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaoshuai Gao
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Liao Peng
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Jianzhong Ai
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xi Jin
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Shiqian Qi
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Hong Li
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Kunjie Wang
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China.
| | - Deyi Luo
- Department of Urology and Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, P.R. China.
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36
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Chen GL, Li J, Zhang J, Zeng B. To Be or Not to Be an Ion Channel: Cryo-EM Structures Have a Say. Cells 2023; 12:1870. [PMID: 37508534 PMCID: PMC10378246 DOI: 10.3390/cells12141870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
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.
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Affiliation(s)
- Gui-Lan Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Bo Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
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37
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Aristizábal-Ramírez I, Dragich AK, Giese APJ, Sofia Zuluaga-Osorio K, Watkins J, Davies GK, Hadi SE, Riazuddin S, Vander Kooi CW, Ahmed ZM, Frolenkov GI. Calcium and Integrin-binding protein 2 (CIB2) controls force sensitivity of the mechanotransducer channels in cochlear outer hair cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.545606. [PMID: 37461484 PMCID: PMC10350036 DOI: 10.1101/2023.07.09.545606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Calcium and Integrin-Binding Protein 2 (CIB2) is an essential subunit of the mechano-electrical transduction (MET) complex in mammalian auditory hair cells. CIB2 binds to pore-forming subunits of the MET channel, TMC1/2 and is required for their transport and/or retention at the tips of mechanosensory stereocilia. Since genetic ablation of CIB2 results in complete loss of MET currents, the exact role of CIB2 in the MET complex remains elusive. Here, we generated a new mouse strain with deafness-causing p.R186W mutation in Cib2 and recorded small but still measurable MET currents in the cochlear outer hair cells. We found that R186W variant causes increase of the resting open probability of MET channels, steeper MET current dependence on hair bundle deflection (I-X curve), loss of fast adaptation, and increased leftward shifts of I-X curves upon hair cell depolarization. Combined with AlphaFold2 prediction that R186W disrupts one of the multiple interacting sites between CIB2 and TMC1/2, our data suggest that CIB2 mechanically constraints TMC1/2 conformations to ensure proper force sensitivity and dynamic range of the MET channels. Using a custom piezo-driven stiff probe deflecting the hair bundles in less than 10 µs, we also found that R186W variant slows down the activation of MET channels. This phenomenon, however, is unlikely to be due to direct effect on MET channels, since we also observed R186W-evoked disruption of the electron-dense material at the tips of mechanotransducing stereocilia and the loss of membrane-shaping BAIAP2L2 protein from the same location. We concluded that R186W variant of CIB2 disrupts force sensitivity of the MET channels and force transmission to these channels.
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38
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Zhang M, Shan Y, Cox CD, Pei D. A mechanical-coupling mechanism in OSCA/TMEM63 channel mechanosensitivity. Nat Commun 2023; 14:3943. [PMID: 37402734 DOI: 10.1038/s41467-023-39688-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Mechanosensitive (MS) ion channels are a ubiquitous type of molecular force sensor sensing forces from the surrounding bilayer. The profound structural diversity in these channels suggests that the molecular mechanisms of force sensing follow unique structural blueprints. Here we determine the structures of plant and mammalian OSCA/TMEM63 proteins, allowing us to identify essential elements for mechanotransduction and propose roles for putative bound lipids in OSCA/TMEM63 mechanosensation. Briefly, the central cavity created by the dimer interface couples each subunit and modulates dimeric OSCA/TMEM63 channel mechanosensitivity through the modulating lipids while the cytosolic side of the pore is gated by a plug lipid that prevents the ion permeation. Our results suggest that the gating mechanism of OSCA/TMEM63 channels may combine structural aspects of the 'lipid-gated' mechanism of MscS and TRAAK channels and the calcium-induced gating mechanism of the TMEM16 family, which may provide insights into the structural rearrangements of TMEM16/TMC superfamilies.
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Affiliation(s)
- Mingfeng Zhang
- Fudan University, Shanghai, 200433, China.
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310000, China.
| | - Yuanyue Shan
- Fudan University, Shanghai, 200433, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310000, China
| | - Charles D Cox
- Victor Chang Cardiac Research Institute, Sydney, 2010, Australia.
- School of Biomedical Sciences, Faculty of Medicine & Health, UNSW Sydney, Kensington, New South Wales, 2052, Australia.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310000, China.
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39
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Wang X, Liu S, Cheng Q, Qu C, Ren R, Du H, Li N, Yan K, Wang Y, Xiong W, Xu Z. CIB2 and CIB3 Regulate Stereocilia Maintenance and Mechanoelectrical Transduction in Mouse Vestibular Hair Cells. J Neurosci 2023; 43:3219-3231. [PMID: 37001993 PMCID: PMC10162464 DOI: 10.1523/jneurosci.1807-22.2023] [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: 09/22/2022] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
The mechanoelectrical transduction (MET) protein complex in the inner-ear hair cells is essential for hearing and balance perception. Calcium and integrin-binding protein 2 (CIB2) has been reported to be a component of MET complex, and loss of CIB2 completely abolishes MET currents in auditory hair cells, causing profound congenital hearing loss. However, loss of CIB2 does not affect MET currents in vestibular hair cells (VHCs) as well as general balance function. Here, we show that CIB2 and CIB3 act redundantly to regulate MET in VHCs, as MET currents are completely abolished in the VHCs of Cib2/Cib3 double knock-out mice of either sex. Furthermore, we show that Cib2 and Cib3 transcripts have complementary expression patterns in the vestibular maculae, and that they play different roles in stereocilia maintenance in VHCs. Cib2 transcripts are highly expressed in the striolar region, and knock-out of Cib2 affects stereocilia maintenance in striolar VHCs. In contrast, Cib3 transcripts are highly expressed in the extrastriolar region, and knock-out of Cib3 mainly affects stereocilia maintenance in extrastriolar VHCs. Simultaneous knock-out of Cib2 and Cib3 affects stereocilia maintenance in all VHCs and leads to severe balance deficits. Taken together, our present work reveals that CIB2 and CIB3 are important for stereocilia maintenance as well as MET in mouse VHCs.SIGNIFICANCE STATEMENT Calcium and integrin-binding protein 2 (CIB2) is an important component of mechanoelectrical transduction (MET) complex, and loss of CIB2 completely abolishes MET in auditory hair cells. However, MET is unaffected in Cib2 knock-out vestibular hair cells (VHCs). In the present work, we show that CIB3 could compensate for the loss of CIB2 in VHCs, and Cib2/Cib3 double knock-out completely abolishes MET in VHCs. Interestingly, CIB2 and CIB3 could also regulate VHC stereocilia maintenance in a nonredundant way. Cib2 and Cib3 transcripts are highly expressed in the striolar and extrastriolar regions, respectively. Stereocilia maintenance and balance function are differently affected in Cib2 or Cib3 knock-out mice. In conclusion, our data suggest that CIB2 and CIB3 are important for stereocilia maintenance and MET in mouse VHCs.
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Affiliation(s)
- Xiaoying Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Shuang Liu
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, People's Republic of China
- Chinese Institute for Brain Research, Beijing 102206, People's Republic of China
| | - Qi Cheng
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Chengli Qu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Rui Ren
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Haibo Du
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Nana Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Keji Yan
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Yanfei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Wei Xiong
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, People's Republic of China
- Chinese Institute for Brain Research, Beijing 102206, People's Republic of China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People's Republic of China
- Shandong Provincial Collaborative Innovation Center of Cell Biology, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
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40
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Sakuragi T, Nagata S. Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases. Nat Rev Mol Cell Biol 2023:10.1038/s41580-023-00604-z. [PMID: 37106071 PMCID: PMC10134735 DOI: 10.1038/s41580-023-00604-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/29/2023]
Abstract
Cellular membranes function as permeability barriers that separate cells from the external environment or partition cells into distinct compartments. These membranes are lipid bilayers composed of glycerophospholipids, sphingolipids and cholesterol, in which proteins are embedded. Glycerophospholipids and sphingolipids freely move laterally, whereas transverse movement between lipid bilayers is limited. Phospholipids are asymmetrically distributed between membrane leaflets but change their location in biological processes, serving as signalling molecules or enzyme activators. Designated proteins - flippases and scramblases - mediate this lipid movement between the bilayers. Flippases mediate the confined localization of specific phospholipids (phosphatidylserine (PtdSer) and phosphatidylethanolamine) to the cytoplasmic leaflet. Scramblases randomly scramble phospholipids between leaflets and facilitate the exposure of PtdSer on the cell surface, which serves as an important signalling molecule and as an 'eat me' signal for phagocytes. Defects in flippases and scramblases cause various human diseases. We herein review the recent research on the structure of flippases and scramblases and their physiological roles. Although still poorly understood, we address the mechanisms by which they translocate phospholipids between lipid bilayers and how defects cause human diseases.
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Affiliation(s)
- Takaharu Sakuragi
- Biochemistry & Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Shigekazu Nagata
- Biochemistry & Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.
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41
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Krey JF, Chatterjee P, Halford J, Cunningham CL, Perrin BJ, Barr-Gillespie PG. Control of stereocilia length during development of hair bundles. PLoS Biol 2023; 21:e3001964. [PMID: 37011103 PMCID: PMC10101650 DOI: 10.1371/journal.pbio.3001964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/13/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Assembly of the hair bundle, the sensory organelle of the inner ear, depends on differential growth of actin-based stereocilia. Separate rows of stereocilia, labeled 1 through 3 from tallest to shortest, lengthen or shorten during discrete time intervals during development. We used lattice structured illumination microscopy and surface rendering to measure dimensions of stereocilia from mouse apical inner hair cells during early postnatal development; these measurements revealed a sharp transition at postnatal day 8 between stage III (row 1 and 2 widening; row 2 shortening) and stage IV (final row 1 lengthening and widening). Tip proteins that determine row 1 lengthening did not accumulate simultaneously during stages III and IV; while the actin-bundling protein EPS8 peaked at the end of stage III, GNAI3 peaked several days later-in early stage IV-and GPSM2 peaked near the end of stage IV. To establish the contributions of key macromolecular assemblies to bundle structure, we examined mouse mutants that eliminated tip links (Cdh23v2J or Pcdh15av3J), transduction channels (TmieKO), or the row 1 tip complex (Myo15ash2). Cdh23v2J/v2J and Pcdh15av3J/av3J bundles had adjacent stereocilia in the same row that were not matched in length, revealing that a major role of these cadherins is to synchronize lengths of side-by-side stereocilia. Use of the tip-link mutants also allowed us to distinguish the role of transduction from effects of transduction proteins themselves. While levels of GNAI3 and GPSM2, which stimulate stereocilia elongation, were greatly attenuated at the tips of TmieKO/KO row 1 stereocilia, they accumulated normally in Cdh23v2J/v2J and Pcdh15av3J/av3J stereocilia. These results reinforced the suggestion that the transduction proteins themselves facilitate localization of proteins in the row 1 complex. By contrast, EPS8 concentrates at tips of all TmieKO/KO, Cdh23v2J/v2J, and Pcdh15av3J/av3J stereocilia, correlating with the less polarized distribution of stereocilia lengths in these bundles. These latter results indicated that in wild-type hair cells, the transduction complex prevents accumulation of EPS8 at the tips of shorter stereocilia, causing them to shrink (rows 2 and 3) or disappear (row 4 and microvilli). Reduced rhodamine-actin labeling at row 2 stereocilia tips of tip-link and transduction mutants suggests that transduction's role is to destabilize actin filaments there. These results suggest that regulation of stereocilia length occurs through EPS8 and that CDH23 and PCDH15 regulate stereocilia lengthening beyond their role in gating mechanotransduction channels.
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Affiliation(s)
- Jocelyn F. Krey
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Paroma Chatterjee
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Julia Halford
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Christopher L. Cunningham
- Pittsburgh Hearing Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin J. Perrin
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Peter G. Barr-Gillespie
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
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Jung J, Müller U. Mechanoelectrical transduction-related genetic forms of hearing loss. CURRENT OPINION IN PHYSIOLOGY 2023; 32:100632. [PMID: 36936795 PMCID: PMC10022594 DOI: 10.1016/j.cophys.2023.100632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hair cells of the mammalian cochlea are specialized mechanosensory cells that convert mechanical stimuli into electrical signals to initiate the neuronal responses that lead to the perception of sound. The mechanoelectrical transduction (MET) machinery of cochlear hair cells is a multimeric protein complex that consists of the pore forming subunits of the MET channel and several essential accessory subunits that are crucial to regulate channel function and render the channel mechanically sensitive. Mutations have been discovered in the genes that encode all known components of the MET machinery. These mutations cause hearing loss with or without vestibular dysfunction. Some mutations also affect other tissues such as the retina. In this brief review, we will summarize gene mutations that affect the MET machinery of hair cells and how the study of the affected genes has illuminated our understanding of the physiological role of the encoded proteins.
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Affiliation(s)
- Jinsei Jung
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Rao P, Gouaux E. Purification and biochemical analysis of native AMPA receptors from three different mammalian species. PLoS One 2023; 18:e0275351. [PMID: 36930594 PMCID: PMC10022779 DOI: 10.1371/journal.pone.0275351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/29/2022] [Indexed: 03/18/2023] Open
Abstract
The majority of fast, excitatory synaptic transmission in the central nervous system (CNS) is mediated by α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), which are glutamate-activated ion channels integral to synaptic plasticity, motor coordination, learning, and memory. Native AMPARs are multiprotein assemblies comprised of a tetrameric receptor core that co-assembles with a broad range of peripheral auxiliary proteins which shape subcellular localization and signaling properties of the resulting complexes. Structure determination of AMPARs has traditionally relied on recombinant expression systems; however, these methods are not well suited to elucidate the diverse array of AMPAR assemblies that are differentially expressed in mammalian brains. While recent studies of native receptor complexes have advanced our understanding of endogenous assemblies, receptors thus far have only been isolated from rodent brain tissue. Here, we employed an immunoaffinity purification strategy to isolate native AMPARs from the brains of three different mammals-pigs, sheep, and cows. Compared to rodents, pigs, sheep, and cows are ungulate mammals, animals with closer genomic identity with humans. Here we determined the molecular size, overall yield, and purity of native AMPARs isolated from these three mammals, thereby demonstrating that structural determination and biochemical analysis is possible from a clade of mammals evolutionarily distinct from rodents.
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Affiliation(s)
- Prashant Rao
- Vollum Institute, Oregon Health & Science University, Portland, OR, United States of America
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, United States of America
- Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR, United States of America
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44
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The tetraspan LHFPL5 is critical to establish maximal force sensitivity of the mechanotransduction channel of cochlear hair cells. Cell Rep 2023; 42:112245. [PMID: 36917610 DOI: 10.1016/j.celrep.2023.112245] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/28/2023] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
The mechanoelectrical transduction (MET) channel of cochlear hair cells is gated by the tip link, but the mechanisms that establish the exquisite force sensitivity of this MET channel are not known. Here, we show that the tetraspan lipoma HMGIC fusion partner-like 5 (LHFPL5) directly couples the tip link to the MET channel. Disruption of these interactions severely perturbs MET. Notably, the N-terminal cytoplasmic domain of LHFPL5 binds to an amphipathic helix in TMC1, a critical gating domain conserved between different MET channels. Mutations in the amphipathic helix of TMC1 or in the N-terminus of LHFPL5 that perturb interactions of LHFPL5 with the amphipathic helix affect channel responses to mechanical force. We conclude that LHFPL5 couples the tip link to the MET channel and that channel gating depends on a structural element in TMC1 that is evolutionarily conserved between MET channels. Overall, our findings support a tether model for transduction channel gating by the tip link.
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Goodman MB, Haswell ES, Vásquez V. Mechanosensitive membrane proteins: Usual and unusual suspects in mediating mechanotransduction. J Gen Physiol 2023; 155:e202213248. [PMID: 36696153 PMCID: PMC9930137 DOI: 10.1085/jgp.202213248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This Viewpoint, which accompanies a Special Issue focusing on membrane mechanosensors, discusses unifying and unique features of both established and emerging mechanosensitive (MS) membrane proteins, their distribution across protein families and phyla, and current and future challenges in the study of these important proteins and their partners. MS membrane proteins are essential for tissue development, cellular motion, osmotic homeostasis, and sensing external and self-generated mechanical cues like those responsible for touch and proprioception. Though researchers' attention and this Viewpoint focus on a few famous ion channels that are considered the usual suspects as MS mechanosensors, we also discuss some of the more unusual suspects, such as G-protein coupled receptors. As the field continues to grow, so too will the list of proteins suspected to function as mechanosensors and the diversity of known MS membrane proteins.
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Affiliation(s)
- Miriam B. Goodman
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Elizabeth S. Haswell
- Department of Biology, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Valeria Vásquez
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
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Karska J, Kowalski S, Saczko J, Moisescu MG, Kulbacka J. Mechanosensitive Ion Channels and Their Role in Cancer Cells. MEMBRANES 2023; 13:167. [PMID: 36837670 PMCID: PMC9965697 DOI: 10.3390/membranes13020167] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Mechanical forces are an inherent element in the world around us. The effects of their action can be observed both on the macro and molecular levels. They can also play a prominent role in the tissues and cells of animals due to the presence of mechanosensitive ion channels (MIChs) such as the Piezo and TRP families. They are essential in many physiological processes in the human body. However, their role in pathology has also been observed. Recent discoveries have highlighted the relationship between these channels and the development of malignant tumors. Multiple studies have shown that MIChs mediate the proliferation, migration, and invasion of various cancer cells via various mechanisms. This could show MIChs as new potential biomarkers in cancer detection and prognosis and interesting therapeutic targets in modern oncology. Our paper is a review of the latest literature on the role of the Piezo1 and TRP families in the molecular mechanisms of carcinogenesis in different types of cancer.
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Affiliation(s)
- Julia Karska
- Faculty of Medicine, Wroclaw Medical University, 50-345 Wroclaw, Poland
| | - Szymon Kowalski
- Faculty of Medicine, Wroclaw Medical University, 50-345 Wroclaw, Poland
| | - Jolanta Saczko
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Mihaela G. Moisescu
- Department of Biophysics and Cellular Biotechnology, Research Center of Excellence in Biophysics and Cellular Biotechnology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Julita Kulbacka
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
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Barrallo-Gimeno A, Llorens J. Hair cell toxicology: With the help of a little fish. Front Cell Dev Biol 2022; 10:1085225. [PMID: 36582469 PMCID: PMC9793777 DOI: 10.3389/fcell.2022.1085225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Hearing or balance loss are disabling conditions that have a serious impact in those suffering them, especially when they appear in children. Their ultimate cause is frequently the loss of function of mechanosensory hair cells in the inner ear. Hair cells can be damaged by environmental insults, like noise or chemical agents, known as ototoxins. Two of the most common ototoxins are life-saving medications: cisplatin against solid tumors, and aminoglycoside antibiotics to treat infections. However, due to their localization inside the temporal bone, hair cells are difficult to study in mammals. As an alternative animal model, zebrafish larvae have hair cells similar to those in mammals, some of which are located in a fish specific organ on the surface of the skin, the lateral line. This makes them easy to observe in vivo and readily accessible for ototoxins or otoprotective substances. These features have made possible advances in the study of the mechanisms mediating ototoxicity or identifying new potential ototoxins. Most importantly, the small size of the zebrafish larvae has allowed screening thousands of molecules searching for otoprotective agents in a scale that would be highly impractical in rodent models. The positive hits found can then start the long road to reach clinical settings to prevent hearing or balance loss.
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Affiliation(s)
- Alejandro Barrallo-Gimeno
- Department de Ciències Fisiològiques, Facultat de Medicina i Ciències de la Salut, Campus de Bellvitge, Universitat de Barcelona, L’Hospitalet de Llobregat, Spain,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain,Institut D'Investigació Biomèdica de Bellvitge, IDIBELL, L’Hospitalet de Llobregat, Spain,*Correspondence: Alejandro Barrallo-Gimeno,
| | - Jordi Llorens
- Department de Ciències Fisiològiques, Facultat de Medicina i Ciències de la Salut, Campus de Bellvitge, Universitat de Barcelona, L’Hospitalet de Llobregat, Spain,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain,Institut D'Investigació Biomèdica de Bellvitge, IDIBELL, L’Hospitalet de Llobregat, Spain
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Qiu X, Müller U. Sensing sound: Cellular specializations and molecular force sensors. Neuron 2022; 110:3667-3687. [PMID: 36223766 PMCID: PMC9671866 DOI: 10.1016/j.neuron.2022.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/03/2022] [Accepted: 09/14/2022] [Indexed: 11/08/2022]
Abstract
Organisms of all phyla express mechanosensitive ion channels with a wide range of physiological functions. In recent years, several classes of mechanically gated ion channels have been identified. Some of these ion channels are intrinsically mechanosensitive. Others depend on accessory proteins to regulate their response to mechanical force. The mechanotransduction machinery of cochlear hair cells provides a particularly striking example of a complex force-sensing machine. This molecular ensemble is embedded into a specialized cellular compartment that is crucial for its function. Notably, mechanotransduction channels of cochlear hair cells are not only critical for auditory perception. They also shape their cellular environment and regulate the development of auditory circuitry. Here, we summarize recent discoveries that have shed light on the composition of the mechanotransduction machinery of cochlear hair cells and how this machinery contributes to the development and function of the auditory system.
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Affiliation(s)
- Xufeng Qiu
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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