1
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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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2
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Schreiber R, Ousingsawat J, Kunzelmann K. The anoctamins: Structure and function. Cell Calcium 2024; 120:102885. [PMID: 38642428 DOI: 10.1016/j.ceca.2024.102885] [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: 02/21/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/22/2024]
Abstract
When activated by increase in intracellular Ca2+, anoctamins (TMEM16 proteins) operate as phospholipid scramblases and as ion channels. Anoctamin 1 (ANO1) is the Ca2+-activated epithelial anion-selective channel that is coexpressed together with the abundant scramblase ANO6 and additional intracellular anoctamins. In salivary and pancreatic glands, ANO1 is tightly packed in the apical membrane and secretes Cl-. Epithelia of airways and gut use cystic fibrosis transmembrane conductance regulator (CFTR) as an apical Cl- exit pathway while ANO1 supports Cl- secretion mainly by facilitating activation of luminal CFTR and basolateral K+ channels. Under healthy conditions ANO1 modulates intracellular Ca2+ signals by tethering the endoplasmic reticulum, and except of glands its direct secretory contribution as Cl- channel might be small, compared to CFTR. In the kidneys ANO1 supports proximal tubular acid secretion and protein reabsorption and probably helps to excrete HCO3-in the collecting duct epithelium. However, under pathological conditions as in polycystic kidney disease, ANO1 is strongly upregulated and may cause enhanced proliferation and cyst growth. Under pathological condition, ANO1 and ANO6 are upregulated and operate as secretory channel/phospholipid scramblases, partly by supporting Ca2+-dependent processes. Much less is known about the role of other epithelial anoctamins whose potential functions are discussed in this review.
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Affiliation(s)
- Rainer Schreiber
- Physiological Institute, University of Regensburg, University street 31, D-93053 Regensburg, Germany
| | - Jiraporn Ousingsawat
- Physiological Institute, University of Regensburg, University street 31, D-93053 Regensburg, Germany
| | - Karl Kunzelmann
- Physiological Institute, University of Regensburg, University street 31, D-93053 Regensburg, Germany.
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3
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Ando J, Murai K, Mori M, Michiyuki T, Iida T, Makino A, Shinoda H, Watanabe R. Exploring fluoropolymers for fabrication of femtoliter chamber arrays used in digital bioanalysis. Sci Rep 2024; 14:11442. [PMID: 38769440 PMCID: PMC11106263 DOI: 10.1038/s41598-024-61726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/08/2024] [Indexed: 05/22/2024] Open
Abstract
The global supply of fluoropolymers and fluorinated solvents is decreasing due to environmental concerns regarding polyfluoroalkyl substances. CYTOP has been used for decades primarily as a component of a femtoliter chamber array for digital bioanalysis; however, its supply has recently become scarce, increasing the urgency of fabricating a femtoliter chamber array using alternative materials. In this study, we investigated the feasibility of fabricating a femtoliter chamber array using four types of fluoropolymers in stable supply as candidate substitutes and verified their applicability for digital bioanalysis. Among these candidates, Fluorine Sealant emerged as a viable option for fabricating femtoliter chamber arrays using a conventional photolithography process. To validate its efficacy, we performed various digital bioanalysis using FP-A-based chamber arrays with model enzymes such as CRISPR-Cas, horseradish peroxidase, and β-galactosidase. The results demonstrated the similar performance to that of CYTOP, highlighting the broader utility of FP-A in digital bioanalysis. Our findings underscore the potential of FP-A to enhance the versatility of digital bioanalysis and foster the ongoing advancement of innovative diagnostic technologies.
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Affiliation(s)
- Jun Ando
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.
| | - Kazue Murai
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Makiko Mori
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Tomoe Michiyuki
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Tatsuya Iida
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Asami Makino
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Hajime Shinoda
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.
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4
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. Proc Natl Acad Sci U S A 2024; 121:e2319476121. [PMID: 38621120 PMCID: PMC11047089 DOI: 10.1073/pnas.2319476121] [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: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 04/17/2024] Open
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Cristian Rocha-Roa
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
| | - Matthew A. Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Stefano Vanni
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
- Swiss National Center for Competence in Research Bio-Inspired Materials, University of Fribourg, FribourgCH-1700, Switzerland
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5
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Miao S, Fourgeaud L, Burrola PG, Stern S, Zhang Y, Happonen KE, Novak SW, Gage FH, Lemke G. Tyro3 promotes the maturation of glutamatergic synapses. Front Neurosci 2024; 18:1327423. [PMID: 38410160 PMCID: PMC10894971 DOI: 10.3389/fnins.2024.1327423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
The receptor tyrosine kinase Tyro3 is abundantly expressed in neurons of the neocortex, hippocampus, and striatum, but its role in these cells is unknown. We found that neuronal expression of this receptor was markedly up-regulated in the postnatal mouse neocortex immediately prior to the final development of glutamatergic synapses. In the absence of Tyro3, cortical and hippocampal synapses never completed end-stage differentiation and remained electrophysiologically and ultrastructurally immature. Tyro3-/- cortical neurons also exhibited diminished plasma membrane expression of the GluA2 subunits of AMPA-type glutamate receptors, which are essential to mature synaptic function. Correspondingly, GluA2 membrane insertion in wild-type neurons was stimulated by Gas6, a Tyro3 ligand widely expressed in the postnatal brain. Behaviorally, Tyro3-/- mice displayed learning enhancements in spatial recognition and fear-conditioning assays. Together, these results demonstrate that Tyro3 promotes the functional maturation of glutamatergic synapses by driving plasma membrane translocation of GluA2 AMPA receptor subunits.
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Affiliation(s)
- Sheng Miao
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Lawrence Fourgeaud
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Patrick G Burrola
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Shani Stern
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Yuhan Zhang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kaisa E Happonen
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Sammy Weiser Novak
- Waitt Advanced Biophotonics Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Greg Lemke
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
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6
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Kim E, Bang J, Sung JH, Lee J, Shin DH, Kim S, Lee BC. Generation of human TMEM16F-specific affibodies using purified TMEM16F. Front Mol Biosci 2024; 10:1319251. [PMID: 38274091 PMCID: PMC10808743 DOI: 10.3389/fmolb.2023.1319251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction: TMEM16 family proteins are involved in a variety of functions, including ion transport, phospholipid scrambling, and the regulation of membrane proteins. Among them, TMEM16F has dual functions as a phospholipid scramblase and a nonselective ion channel. TMEM16F is widely expressed and functions in platelet activation during blood clotting, bone formation, and T cell activation. Despite the functional importance of TMEM16F, the modulators of TMEM16F function have not been sufficiently studied. Method: In this study, we generated TMEM16F-specific affibodies by performing phage display with brain-specific TMEM16F (hTMEM16F) variant 1 purified from GnTi- cells expressing this variant in the presence of digitonin as a detergent. Purified human TMEM16F protein, which was proficient in transporting phospholipids in a Ca2+-dependent manner in proteoliposomes, was coated onto plates and then the phage library was added to fish out TMEM16F-binding affibodies. For the validation of interaction between affibodies and TMEM16F proteins, ELISA, bio-layer interferometry, and size exclusion chromatography were conducted. Results and Discussion: As a result, the full sequences of 38 candidates were acquired from 98 binding candidates. Then, we selected 10 candidates and purified seven of them from E. coli expressing these candidates. Using various assays, we confirmed that two affibodies bound to human TMEM16F with high affinity. These affibodies can be useful for therapeutical and diagnostic applications of TMEM16F-related cancer and neurodegenerative diseases. Future studies will be required to investigate the effects of these affibodies on TMEM16F function.
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Affiliation(s)
- Eunyoung Kim
- Korea Brain Research Institute, Neurovascular Unit Research Group, Daegu, Republic of Korea
| | - Jinho Bang
- Korea Institute of Ceramic Engineering and Technology, Bio-Healthcare Materials Center, Cheongju, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Republic of Korea
| | - Ji Hye Sung
- Korea Brain Research Institute, Neurovascular Unit Research Group, Daegu, Republic of Korea
| | - Jonghwan Lee
- Korea Institute of Ceramic Engineering and Technology, Bio-Healthcare Materials Center, Cheongju, Republic of Korea
| | - Dae Hwan Shin
- College of Pharmacy, Chungbuk National University, Cheongju, Republic of Korea
| | - Sunghyun Kim
- Korea Institute of Ceramic Engineering and Technology, Bio-Healthcare Materials Center, Cheongju, Republic of Korea
| | - Byoung-Cheol Lee
- Korea Brain Research Institute, Neurovascular Unit Research Group, Daegu, Republic of Korea
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7
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Li Q, Liu H, Jin Y, Yu Y, Wang Y, Wu D, Guo Y, Xi L, Ye D, Pan Y, Zhang X, Li J. Analysis of a new therapeutic target and construction of a prognostic model for breast cancer based on ferroptosis genes. Comput Biol Med 2023; 165:107370. [PMID: 37643511 DOI: 10.1016/j.compbiomed.2023.107370] [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: 04/05/2023] [Revised: 07/09/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
Breast cancer, which is the most common malignant tumor among women worldwide and an important cause of death in women. The existing prognostic model for patients with breast cancer is not accurate as breast cancer is resistant to commonly used antitumor drugs. Ferroptosis is a novel mechanism of programmed cell death that depends on iron accumulation and lipid peroxidation. Various studies have confirmed the role of ferroptosis in tumor regulation and ferroptosis is now considered to play an important role in breast cancer development. At present, the association between breast cancer prognosis and ferroptosis-related gene expression remains unclear. Further exploration of this research area may optimize the evaluation and prediction of prognosis of patients with breast cancer and finding of new therapeutic targets. In this study, clinical factors and the expression of multiple genes were evaluated in breast cancer samples from the Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database database. Eleven prognostication-related genes (TP63, IFNG, MT3, ANO6, FLT3, PTGS2, SLC1A4, JUN, SLC7A5, CHAC1, and TF) were identified from differentially expressed genes to construct a survival prediction model, which showed a good prediction ability. KEGG pathway analysis revealed that immune-related pathways were the primary pathways. ssGSEA analysis showed significant differences in the distribution of certain immune-related cell subsets, such as CD8+T cells and B cells, and in the expression of multiple immune genes, including type II IFN response and APC coinhibition. In addition, 10 immune targets related to ferroptosis in breast cancer were found: CD276, CD80, HHLA2, LILRA2, NCR3LG1, NECTIN3, PVR, SLAMF9,TNFSF4, and BTN1A1. Using TCGA, new ferroptosis genes related to breast cancer prognosis were identified, a new reliable and accurate prognosis model was developed, and 10 new potential therapeutic targets different from the traditional targeted drugs were identified to provide a reference for improving the poor prognosis of patients with breast cancer.
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Affiliation(s)
- Qi Li
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Hengchen Liu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Yun Jin
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Yuanquan Yu
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Yihang Wang
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Di Wu
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Yinghao Guo
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Longfu Xi
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Dan Ye
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Yanzhi Pan
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Xiaoxiao Zhang
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
| | - Jiangtao Li
- Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
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8
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Ali H, Naseem A, Siddiqui ZI. SARS-CoV-2 Syncytium under the Radar: Molecular Insights of the Spike-Induced Syncytia and Potential Strategies to Limit SARS-CoV-2 Replication. J Clin Med 2023; 12:6079. [PMID: 37763019 PMCID: PMC10531702 DOI: 10.3390/jcm12186079] [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: 08/04/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 infection induces non-physiological syncytia when its spike fusogenic protein on the surface of the host cells interacts with the ACE2 receptor on adjacent cells. Spike-induced syncytia are beneficial for virus replication, transmission, and immune evasion, and contribute to the progression of COVID-19. In this review, we highlight the properties of viral fusion proteins, mainly the SARS-CoV-2 spike, and the involvement of the host factors in the fusion process. We also highlight the possible use of anti-fusogenic factors as an antiviral for the development of therapeutics against newly emerging SARS-CoV-2 variants and how the fusogenic property of the spike could be exploited for biomedical applications.
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Affiliation(s)
- Hashim Ali
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Asma Naseem
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Zaheenul Islam Siddiqui
- Diabetes and Obesity Research Center, NYU Grossman Long Island School of Medicine, New York, NY 11501, USA
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9
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Herrera SA, Günther Pomorski T. Reconstitution of ATP-dependent lipid transporters: gaining insight into molecular characteristics, regulation, and mechanisms. Biosci Rep 2023; 43:BSR20221268. [PMID: 37417269 PMCID: PMC10412526 DOI: 10.1042/bsr20221268] [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: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023] Open
Abstract
Lipid transporters play a crucial role in supporting essential cellular processes such as organelle assembly, vesicular trafficking, and lipid homeostasis by driving lipid transport across membranes. Cryo-electron microscopy has recently resolved the structures of several ATP-dependent lipid transporters, but functional characterization remains a major challenge. Although studies of detergent-purified proteins have advanced our understanding of these transporters, in vitro evidence for lipid transport is still limited to a few ATP-dependent lipid transporters. Reconstitution into model membranes, such as liposomes, is a suitable approach to study lipid transporters in vitro and to investigate their key molecular features. In this review, we discuss the current approaches for reconstituting ATP-driven lipid transporters into large liposomes and common techniques used to study lipid transport in proteoliposomes. We also highlight the existing knowledge on the regulatory mechanisms that modulate the activity of lipid transporters, and finally, we address the limitations of the current approaches and future perspectives in this field.
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Affiliation(s)
- Sara Abad Herrera
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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10
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Feng S, Puchades C, Ko J, Wu H, Chen Y, Figueroa EE, Gu S, Han TW, Ho B, Cheng T, Li J, Shoichet B, Jan YN, Cheng Y, Jan LY. Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase. Nat Commun 2023; 14:4874. [PMID: 37573365 PMCID: PMC10423226 DOI: 10.1038/s41467-023-40410-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 07/23/2023] [Indexed: 08/14/2023] Open
Abstract
The dual functions of TMEM16F as Ca2+-activated ion channel and lipid scramblase raise intriguing questions regarding their molecular basis. Intrigued by the ability of the FDA-approved drug niclosamide to inhibit TMEM16F-dependent syncytia formation induced by SARS-CoV-2, we examined cryo-EM structures of TMEM16F with or without bound niclosamide or 1PBC, a known blocker of TMEM16A Ca2+-activated Cl- channel. Here, we report evidence for a lipid scrambling pathway along a groove harboring a lipid trail outside the ion permeation pore. This groove contains the binding pocket for niclosamide and 1PBC. Mutations of two residues in this groove specifically affect lipid scrambling. Whereas mutations of some residues in the binding pocket of niclosamide and 1PBC reduce their inhibition of TMEM16F-mediated Ca2+ influx and PS exposure, other mutations preferentially affect the ability of niclosamide and/or 1PBC to inhibit TMEM16F-mediated PS exposure, providing further support for separate pathways for ion permeation and lipid scrambling.
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Affiliation(s)
- Shengjie Feng
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Cristina Puchades
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Juyeon Ko
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Yifei Chen
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA
| | - Eric E Figueroa
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Shuo Gu
- BioDuro-Sundia Inc., Irvine, CA, USA
| | - Tina W Han
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Brandon Ho
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Tong Cheng
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA
| | - Junrui Li
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Brian Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF) School of Pharmacy, San Francisco, CA, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA.
| | - Lily Yeh Jan
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA.
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11
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Montalbo RCK, Tu HL. Micropatterning of functional lipid bilayer assays for quantitative bioanalysis. BIOMICROFLUIDICS 2023; 17:031302. [PMID: 37179590 PMCID: PMC10171888 DOI: 10.1063/5.0145997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Interactions of the cell with its environment are mediated by the cell membrane and membrane-localized molecules. Supported lipid bilayers have enabled the recapitulation of the basic properties of cell membranes and have been broadly used to further our understanding of cellular behavior. Coupled with micropatterning techniques, lipid bilayer platforms have allowed for high throughput assays capable of performing quantitative analysis at a high spatiotemporal resolution. Here, an overview of the current methods of the lipid membrane patterning is presented. The fabrication and pattern characteristics are briefly described to present an idea of the quality and notable features of the methods, their utilizations for quantitative bioanalysis, as well as to highlight possible directions for the advanced micropatterning lipid membrane assays.
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12
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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: 25] [Impact Index Per Article: 25.0] [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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13
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Chua GL, Tan BC, Loke RYJ, He M, Chin CF, Wong BH, Kuk ACY, Ding M, Wenk MR, Guan L, Torta F, Silver DL. Mfsd2a utilizes a flippase mechanism to mediate omega-3 fatty acid lysolipid transport. Proc Natl Acad Sci U S A 2023; 120:e2215290120. [PMID: 36848557 PMCID: PMC10013850 DOI: 10.1073/pnas.2215290120] [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: 09/07/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
Major Facilitator Superfamily Domain containing 2a (Mfsd2a) is a sodium-dependent lysophosphatidylcholine (LPC) transporter expressed at the blood-brain barrier that constitutes the main pathway by which the brain obtains omega-3 fatty acids, such as docosahexanoic acid. Mfsd2a deficiency in humans results in severe microcephaly, underscoring the importance of LPC transport by Mfsd2a for brain development. Biochemical studies and recent cryo-electron microscopy (cryo-EM) structures of Mfsd2a bound to LPC suggest that Mfsd2a transports LPC via an alternating access mechanism between outward-facing and inward-facing conformational states in which the LPC inverts during transport between the outer and inner leaflet of a membrane. However, direct biochemical evidence of flippase activity by Mfsd2a has not been demonstrated and it is not understood how Mfsd2a could invert LPC between the outer and inner leaflet of the membrane in a sodium-dependent manner. Here, we established a unique in vitro assay using recombinant Mfsd2a reconstituted in liposomes that exploits the ability of Mfsd2a to transport lysophosphatidylserine (LPS) coupled with a small molecule LPS binding fluorophore that allowed for monitoring of directional flipping of the LPS headgroup from the outer to the inner liposome membrane. Using this assay, we demonstrate that Mfsd2a flips LPS from the outer to the inner leaflet of a membrane bilayer in a sodium-dependent manner. Furthermore, using cryo-EM structures as guides together with mutagenesis and a cell-based transport assay, we identify amino acid residues important for Mfsd2a activity that likely constitute substrate interaction domains. These studies provide direct biochemical evidence that Mfsd2a functions as a lysolipid flippase.
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Affiliation(s)
- Geok-Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Bryan C. Tan
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Randy Y. J. Loke
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Menglan He
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Cheen-Fei Chin
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Bernice H. Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Alvin C. Y. Kuk
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Mei Ding
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117596, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117596, Singapore
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117596, Singapore
| | - David L. Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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14
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Iida T, Ando J, Shinoda H, Makino A, Yoshimura M, Murai K, Mori M, Takeuchi H, Noda T, Nishimasu H, Watanabe R. Compact wide-field femtoliter-chamber imaging system for high-speed and accurate digital bioanalysis. LAB ON A CHIP 2023; 23:684-691. [PMID: 36255223 DOI: 10.1039/d2lc00741j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The femtoliter-chamber array is a bioanalytical platform that enables highly sensitive and quantitative analysis of biological reactions at the single-molecule level. This feature has been considered a key technology for "digital bioanalysis" in the biomedical field; however, its versatility is limited by the need for a large and expensive setup such as a fluorescence microscope, which requires a long time to acquire the entire image of a femtoliter-chamber array. To address these issues, we developed a compact and inexpensive wide-field imaging system (COWFISH) that can acquire fluorescence images with a large field of view (11.8 mm × 7.9 mm) and a high spatial resolution of ∼ 3 μm, enabling high-speed analysis of sub-million femtoliter chambers in 20 s. Using COWFISH, we demonstrated a CRISPR-Cas13a-based digital detection of viral RNA of SARS-CoV-2 with an equivalent detection sensitivity (limit of detection: 480 aM) and a 10-fold reduction in total imaging time, as compared to confocal fluorescence microscopy. In addition, we demonstrated the feasibility of COWFISH to discriminate between SARS-CoV-2-positive and -negative clinical specimens with 95% accuracy, showing its application in COVID-19 diagnosis. Therefore, COWFISH can serve as a compact and inexpensive imaging system for high-speed and accurate digital bioanalysis, paving a way for various biomedical applications, such as diagnosis of viral infections.
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Affiliation(s)
| | - Jun Ando
- Cluster for Pioneering Research, RIKEN, Japan.
| | | | | | | | - Kazue Murai
- Cluster for Pioneering Research, RIKEN, Japan.
| | - Makiko Mori
- Cluster for Pioneering Research, RIKEN, Japan.
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University, Japan
| | - Takeshi Noda
- Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Japan
- RCAST, The University of Tokyo, Japan
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15
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Tanimoto Y, Yoshimura Y, Hayashi F, Morigaki K. Retarded Diffusion and Confinement of Membrane-Bound Molecules in a Patterned Hybrid Membrane of Phospholipid Bilayers and Monolayers. J Phys Chem B 2023; 127:520-527. [PMID: 36598865 DOI: 10.1021/acs.jpcb.2c06053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The biological membrane is a complex two-dimensional fluid, in which various molecular interactions regulate the lateral diffusion of membrane-associated molecules. Pinning of membrane proteins or lipids by extra-membrane proteins impedes the diffusion. In addition, coupling between two monolayer leaflets within a phospholipid bilayer via interdigitation plays important roles, though this effect remains elusive. Here, we fabricate a substrate-supported model membrane with patterned bilayer/monolayer regions to explore the influences of interleaflet coupling. A patterned monolayer of polymerized diacetylene phospholipid, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (DiynePC), was lithographically generated and used to form patterned lipid bilayers and monolayers. A phospholipid monolayer was formed on top of the polymerized monolayer. The bilayer/monolayer hybrid membrane was continuous and fluid, but lateral diffusion in the monolayer region was significantly retarded, suggesting the influences of interleaflet coupling. We reconstituted photoreceptor rhodopsin (Rh) and G-protein transducin (Gt) as model transmembrane and peripheral proteins. Rh diffused laterally only in the bilayer region, whereas Gt diffused in both bilayer and monolayer regions. The patterned hybrid bilayer/monolayer membrane reproduces the retarded diffusion and confinement of membrane-bound molecules in a controlled manner and provides insight into the physicochemical and functional roles of semipermeable corrals in the cell membrane.
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Affiliation(s)
- Yasushi Tanimoto
- Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan.,Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi, Osaka558-8585, Japan
| | - Yu Yoshimura
- Graduate School of Agricultural Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan
| | - Kenichi Morigaki
- Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan.,Graduate School of Agricultural Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan
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16
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Arndt M, Alvadia C, Straub MS, Clerico Mosina V, Paulino C, Dutzler R. Structural basis for the activation of the lipid scramblase TMEM16F. Nat Commun 2022; 13:6692. [PMID: 36335104 PMCID: PMC9637102 DOI: 10.1038/s41467-022-34497-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
TMEM16F, a member of the conserved TMEM16 family, plays a central role in the initiation of blood coagulation and the fusion of trophoblasts. The protein mediates passive ion and lipid transport in response to an increase in intracellular Ca2+. However, the mechanism of how the protein facilitates both processes has remained elusive. Here we investigate the basis for TMEM16F activation. In a screen of residues lining the proposed site of conduction, we identify mutants with strongly activating phenotype. Structures of these mutants determined herein by cryo-electron microscopy show major rearrangements leading to the exposure of hydrophilic patches to the membrane, whose distortion facilitates lipid diffusion. The concomitant opening of a pore promotes ion conduction in the same protein conformation. Our work has revealed a mechanism that is distinct for this branch of the family and that will aid the development of a specific pharmacology for a promising drug target.
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Affiliation(s)
- Melanie Arndt
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Carolina Alvadia
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Monique S. Straub
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Vanessa Clerico Mosina
- grid.4830.f0000 0004 0407 1981Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Cristina Paulino
- grid.4830.f0000 0004 0407 1981Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Raimund Dutzler
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
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17
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Jia Z, Huang J, Chen J. Activation of TMEM16F by inner gate charged mutations and possible lipid/ion permeation mechanisms. Biophys J 2022; 121:3445-3457. [PMID: 35978550 PMCID: PMC9515230 DOI: 10.1016/j.bpj.2022.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/24/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Transmembrane protein 16F (TMEM16F) is a ubiquitously expressed Ca2+-activated phospholipid scramblase that also functions as a largely non-selective ion channel. Though recent structural studies have revealed the closed and intermediate conformations of mammalian TMEM16F (mTMEM16F), the open and conductive state remains elusive. Instead, it has been proposed that an open hydrophilic pathway may not be required for lipid scrambling. We previously identified an inner activation gate, consisting of F518, Y563, and I612, and showed that charged mutations of the inner gate residues led to constitutively active mTMEM16F scrambling. Herein, atomistic simulations show that lysine substitution of F518 and Y563 can indeed lead to spontaneous opening of the permeation pore in the Ca2+-bound state of mTMEM16F. Dilation of the pore exposes hydrophilic patches in the upper pore region, greatly increases the pore hydration level, and enables lipid scrambling. The putative open state of mTMEM16F resembles the active state of fungal scramblases and is a meta-stable state for the wild-type protein in the Ca2+-bound state. Therefore, mTMEM16F may be capable of supporting the canonical in-groove scrambling mechanism in addition to the out-of-groove one. Further analysis reveals that the in-groove phospholipid and ion transduction pathways of mTMEM16F overlap from the intracellular side up to the inner gate but diverge from each other with different exits to the extracellular side of membrane.
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Affiliation(s)
- Zhiguang Jia
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts
| | - Jian Huang
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts.
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18
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Noji H, Minagawa Y, Ueno H. Enzyme-based digital bioassay technology - key strategies and future perspectives. LAB ON A CHIP 2022; 22:3092-3109. [PMID: 35861036 DOI: 10.1039/d2lc00223j] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Digital bioassays based on single-molecule enzyme reactions represent a new class of bioanalytical methods that enable the highly sensitive detection of biomolecules in a quantitative manner. Since the first reports of these methods in the 2000s, there has been significant growth in this new bioanalytical strategy. The principal strategy of this method is to compartmentalize target molecules in micron-sized reactors at the single-molecule level and count the number of microreactors showing positive signals originating from the target molecule. A representative application of digital bioassay is the digital enzyme-linked immunosorbent assay (ELISA). Owing to their versatility, various types of digital ELISAs have been actively developed. In addition, some disease markers and viruses possess catalytic activity, and digital bioassays for such enzymes and viruses have, thus, been developed. Currently, with the emergence of new microreactor technologies, the targets of this methodology are expanding from simple enzymes to more complex systems, such as membrane transporters and cell-free gene expression. In addition, multiplex or multiparametric digital bioassays have been developed to assess precisely the heterogeneities in sample molecules/systems that are obscured by ensemble measurements. In this review, we first introduce the basic concepts of digital bioassays and introduce a range of digital bioassays. Finally, we discuss the perspectives of new classes of digital bioassays and emerging fields based on digital bioassay technology.
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Affiliation(s)
- Hiroyuki Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Hiroshi Ueno
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
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19
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Falzone ME, Feng Z, Alvarenga OE, Pan Y, Lee B, Cheng X, Fortea E, Scheuring S, Accardi A. TMEM16 scramblases thin the membrane to enable lipid scrambling. Nat Commun 2022; 13:2604. [PMID: 35562175 PMCID: PMC9095706 DOI: 10.1038/s41467-022-30300-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Abstract
TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets through a membrane-spanning hydrophilic groove. Direct information on lipid-groove interactions is lacking. We report the 2.3 Å resolution cryogenic electron microscopy structure of the nanodisc-reconstituted Ca2+-bound afTMEM16 scramblase showing how rearrangement of individual lipids at the open pathway results in pronounced membrane thinning. Only the groove's intracellular vestibule contacts lipids, and mutagenesis suggests scrambling does not require specific protein-lipid interactions with the extracellular vestibule. We find scrambling can occur outside a closed groove in thinner membranes and is inhibited in thicker membranes, despite an open pathway. Our results show afTMEM16 thins the membrane to enable scrambling and that an open hydrophilic pathway is not a structural requirement to allow rapid transbilayer movement of lipids. This mechanism could be extended to other scramblases lacking a hydrophilic groove.
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Affiliation(s)
- Maria E Falzone
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Omar E Alvarenga
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - ByoungCheol Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Eva Fortea
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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20
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Tamura N, Goto S, Yokota H, Goto S. Contributing Role of Mitochondrial Energy Metabolism on Platelet Adhesion, Activation and Thrombus Formation under Blood Flow Conditions. Platelets 2022; 33:1083-1089. [PMID: 35348041 DOI: 10.1080/09537104.2022.2046722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Platelets have an active energy metabolism mediated by mitochondria. However, the role of mitochondria in platelet adhesion, activation, and thrombus formation under blood flow conditions remains to be elucidated. Blood specimens were obtained from healthy adult volunteers. The consumption of glucose molecules by platelets was measured after 24 hours. Platelet adhesion, activation, and thrombus formation on collagen fibrils and immobilized von Willebrand factor (VWF) at a wall shear rate of 1,500 s-1 were detected by fluorescence microscopy with an ultrafast laser confocal unit in the presence or absence of mitochondrial functional inhibitors of carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), antimycin A, and oligomycin. Consumption of glucose molecules within the first 24 h of 4.21 × 10-15 ± 4.46 x 10-15 (n = 6) increased to 13.82 × 10-15 ± 3.46 x 10-15 (n = 4) in the presence of FCCP, 12.11 × 10-15 ± 2.33 x 10-15 (n = 4) in the presence of antimycin A, and 11.87 × 10-15 ± 3.56 x 10-15 (n = 4) in the presence of oligomycin (p < .05). These mitochondrial functional blockers did not influence both surface area coverage by platelets and the 3-dimensional size of platelet thrombi formed on the collagen fibrils. However, a rapid increase in the intracellular calcium ion concentration ([Ca2+]i) upon adhering on immobilized VWF decreased significantly from 405.5 ± 86.2 nM in control to 198.0 ± 79.2 nM in the presence of FCCP (p < .005). A similar decrease in the rapid increase in ([Ca2+]i) was observed in the presence of antimycin A and oligomycin. Mitochondrial function is necessary for platelet activation represented by a rapid increase in [Ca2+]i after platelet adhesion on VWF. However, the influence could not be detected as changes in platelet adhesion or 3-dimensional growth of platelet thrombi on collagen fibrils.
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Affiliation(s)
- Noriko Tamura
- Department of Health and Nutrition, Faculty of Health Sciences, Niigata University of Health and Welfare, Niigata, Japan
| | - Shinichi Goto
- Department of Medicine (Cardiology), Tokai University School of Medicine, Isehara, Japan
| | - Hideo Yokota
- Image Processing Research Team, Center for Advanced Photonics, Riken, Wako, Japan
| | - Shinya Goto
- Department of Medicine (Cardiology), Tokai University School of Medicine, Isehara, Japan
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21
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Cheng Y, Feng S, Puchades C, Ko J, Figueroa E, Chen Y, Wu H, Gu S, Han T, Li J, Ho B, Shoichet B, Jan YN, Jan L. Identification of a conserved drug binding pocket in TMEM16 proteins. RESEARCH SQUARE 2022:rs.3.rs-1296933. [PMID: 35169791 PMCID: PMC8845511 DOI: 10.21203/rs.3.rs-1296933/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The TMEM16 family of calcium-activated membrane proteins includes ten mammalian paralogs (TMEM16A-K) playing distinct physiological roles with some implicated in cancer and airway diseases. Their modulators with therapeutic potential include 1PBC, a potent inhibitor with anti-tumoral properties, and the FDA-approved drug niclosamide that targets TMEM16F to inhibit syncytia formation induced by SARS-CoV-2 infection. Here, we report cryo-EM structures of TMEM16F associated with 1PBC and niclosamide, revealing that both molecules bind the same drug binding pocket. We functionally and computationally validate this binding pocket in TMEM16A as well as TMEM16F, thereby showing that drug modulation also involves residues that are not conserved between TMEM16A and TMEM16F. This study establishes a much-needed structural framework for the development of more potent and more specific drug molecules targeting TMEM16 proteins.
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Affiliation(s)
| | | | | | | | | | | | - Hao Wu
- University of California San Francisco
| | | | | | | | | | | | | | - Lily Jan
- University of California, San Francisco
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22
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Polymodal Control of TMEM16x Channels and Scramblases. Int J Mol Sci 2022; 23:ijms23031580. [PMID: 35163502 PMCID: PMC8835819 DOI: 10.3390/ijms23031580] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The TMEM16A/anoctamin-1 calcium-activated chloride channel (CaCC) contributes to a range of vital functions, such as the control of vascular tone and epithelial ion transport. The channel is a founding member of a family of 10 proteins (TMEM16x) with varied functions; some members (i.e., TMEM16A and TMEM16B) serve as CaCCs, while others are lipid scramblases, combine channel and scramblase function, or perform additional cellular roles. TMEM16x proteins are typically activated by agonist-induced Ca2+ release evoked by Gq-protein-coupled receptor (GqPCR) activation; thus, TMEM16x proteins link Ca2+-signalling with cell electrical activity and/or lipid transport. Recent studies demonstrate that a range of other cellular factors—including plasmalemmal lipids, pH, hypoxia, ATP and auxiliary proteins—also control the activity of the TMEM16A channel and its paralogues, suggesting that the TMEM16x proteins are effectively polymodal sensors of cellular homeostasis. Here, we review the molecular pathophysiology, structural biology, and mechanisms of regulation of TMEM16x proteins by multiple cellular factors.
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23
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Le SC, Liang P, Lowry AJ, Yang H. Gating and Regulatory Mechanisms of TMEM16 Ion Channels and Scramblases. Front Physiol 2021; 12:787773. [PMID: 34867487 PMCID: PMC8640346 DOI: 10.3389/fphys.2021.787773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
The transmembrane protein 16 (TMEM16) family consists of Ca2+-activated ion channels and Ca2+-activated phospholipid scramblases (CaPLSases) that passively flip-flop phospholipids between the two leaflets of the membrane bilayer. Owing to their diverse functions, TMEM16 proteins have been implicated in various human diseases, including asthma, cancer, bleeding disorders, muscular dystrophy, arthritis, epilepsy, dystonia, ataxia, and viral infection. To understand TMEM16 proteins in health and disease, it is critical to decipher their molecular mechanisms of activation gating and regulation. Structural, biophysical, and computational characterizations over the past decade have greatly advanced the molecular understanding of TMEM16 proteins. In this review, we summarize major structural features of the TMEM16 proteins with a focus on regulatory mechanisms and gating.
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Affiliation(s)
- Son C. Le
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Pengfei Liang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Augustus J. Lowry
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Huanghe Yang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
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Xie L, Xu DM, Cai XJ, Zhang ZW, Yu WJ, Qiu JF, Xu CW, He CL, Xu XR, Yin J. Apoptosis in platelets from adult patients with chronic idiopathic thrombocytopenic purpura. Blood Coagul Fibrinolysis 2021; 32:434-442. [PMID: 34102655 DOI: 10.1097/mbc.0000000000001054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Adult chronic idiopathic thrombocytopenic purpura (cITP) is a chronic and usually life-long haemorrhagic disorder in which enhanced platelet destruction and weakened platelet production lead to thrombocytopenia. Platelets were isolated from blood samples collected from 40 adult patients with cITP and 40 healthy volunteers. Mitochondrial membrane potential (ΔΨm) and plasma membrane phosphatidylserine externalization were determined by flow cytometry, and activation of caspase-3 and expressions of Bax, Bak and Bcl-xL were analysed by western blotting. Flow cytometry showed increased mitochondrial depolarization and lower ΔΨm in platelets from adult patients with cITP. In addition, plasma membrane phosphatidylserine externalization was observed on platelets from adult patients with cITP, but rarely from healthy volunteers. Western blot analysis of platelet proteins revealed that, in adult cITP patients, caspase-3 was activated, which cleaved gelsolin and to release a 47-kDa fragment. Moreover, the expressions of Bax and Bak were elevated, and Bcl-xL was decreased markedly in platelets from adult patients with cITP. Our findings reveal, based on loss of mitochondrial membrane potential (Δψm), phosphatidylserine exposure, caspase-3 activation, enhanced expression of Bax and Bak, and attenuated expression of Bcl-xL, that platelet death in the pathogenesis of thrombocytopenia in chronic ITP in adults is apoptotic.
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Affiliation(s)
- Long Xie
- Department of Clinical Laboratory Medicine
| | | | | | | | | | | | | | | | - Xian-Ru Xu
- Division of Inventional Ultrasonic Therapeutics, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jun Yin
- Department of Clinical Laboratory Medicine
- Division of Hematology
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25
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Millington-Burgess SL, Harper MT. Epigallocatechin gallate inhibits release of extracellular vesicles from platelets without inhibiting phosphatidylserine exposure. Sci Rep 2021; 11:17678. [PMID: 34480042 PMCID: PMC8417220 DOI: 10.1038/s41598-021-97212-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/12/2021] [Indexed: 02/03/2023] Open
Abstract
Arterial thrombosis triggers myocardial infarction and is a leading cause of death worldwide. Procoagulant platelets, a subpopulation of activated platelets that expose phosphatidylserine (PS), promote coagulation and occlusive thrombosis. Procoagulant platelets may therefore be a therapeutic target. PS exposure in procoagulant platelets requires TMEM16F, a phospholipid scramblase. Epigallocatechin gallate (EGCG) has been reported to inhibit TMEM16F but this has been challenged. We investigated whether EGCG inhibits PS exposure in procoagulant platelets. PS exposure is often measured using fluorophore-conjugated annexin V. EGCG quenched annexin V-FITC fluorescence, which gives the appearance of inhibition of PS exposure. However, EGCG did not quench annexin V-APC fluorescence. Using this fluorophore, we show that EGCG does not inhibit annexin V binding to procoagulant platelets. We confirmed this by using NBD-labelled PS to monitor PS scrambling. EGCG did not quench NBD fluorescence and did not inhibit PS scrambling. Procoagulant platelets also release PS-exposing extracellular vesicles (EVs) that further propagate coagulation. Surprisingly, EGCG inhibited EV release. This inhibition required the gallate group of EGCG. In conclusion, EGCG does not inhibit PS exposure in procoagulant platelets but does inhibit the EV release. Future investigation of this inhibition may help us further understand how EVs are released by procoagulant platelets.
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Affiliation(s)
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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Diederichs T, Tampé R. Membrane-Suspended Nanopores in Microchip Arrays for Stochastic Transport Recording and Sensing. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.703673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transport of nutrients, xenobiotics, and signaling molecules across biological membranes is essential for life. As gatekeepers of cells, membrane proteins and nanopores are key targets in pharmaceutical research and industry. Multiple techniques help in elucidating, utilizing, or mimicking the function of biological membrane-embedded nanodevices. In particular, the use of DNA origami to construct simple nanopores based on the predictable folding of nucleotides provides a promising direction for innovative sensing and sequencing approaches. Knowledge of translocation characteristics is crucial to link structural design with function. Here, we summarize recent developments and compare features of membrane-embedded nanopores with solid-state analogues. We also describe how their translocation properties are characterized by microchip systems. The recently developed silicon chips, comprising solid-state nanopores of 80 nm connecting femtoliter cavities in combination with vesicle spreading and formation of nanopore-suspended membranes, will pave the way to characterize translocation properties of nanopores and membrane proteins in high-throughput and at single-transporter resolution.
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Abstract
CRISPR-based nucleic-acid detection is an emerging technology for molecular diagnostics. However, these methods generally require several hours and could cause amplification errors, due to the pre-amplification of target nucleic acids to enhance the detection sensitivity. Here, we developed a platform that allows “CRISPR-based amplification-free digital RNA detection (SATORI)”, by combining CRISPR-Cas13-based RNA detection and microchamber-array technologies. SATORI detected single-stranded RNA targets with maximal sensitivity of ~10 fM in <5 min, with high specificity. Furthermore, the simultaneous use of multiple different guide RNAs enhanced the sensitivity, thereby enabling the detection of the SARS-CoV-2 N-gene RNA at ~5 fM levels. Therefore, we hope SATORI will serve as a powerful class of accurate and rapid diagnostics. The authors develop a platform (SATORI) that enables accurate and rapid detection of single-stranded RNA at a single-molecule level without a pre-amplification step. As a proof-of-concept, they demonstrate its utility in detecting the SARS-CoV-2 N gene at a minimum concentration of ~5 fM, which is much lower than other amplification-free CRISPR-Cas-based methods.
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The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction. J Mol Biol 2021; 433:166941. [PMID: 33741412 DOI: 10.1016/j.jmb.2021.166941] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022]
Abstract
The TMEM16 family of membrane proteins displays a remarkable functional dichotomy - while some family members function as Ca2+-activated anion channels, the majority of characterized TMEM16 homologs are Ca2+-activated lipid scramblases, which catalyze the exchange of phospholipids between the two membrane leaflets. Furthermore, some TMEM16 scramblases can also function as channels. Due to their involvement in important physiological processes, the family has been actively studied ever since their molecular identity was unraveled. In this review, we will summarize the recent advances in the field and how they influenced our view of TMEM16 family function and evolution. Structural, functional and computational studies reveal how relatively small rearrangements in the permeation pathway are responsible for the observed functional duality: while TMEM16 scramblases can adopt both ion- and lipid conductive conformations, TMEM16 channels can only populate the former. Recent data further provides the molecular details of a stepwise activation mechanism, which is initiated by Ca2+ binding and modulated by various cellular factors, including lipids. TMEM16 function and the surrounding membrane properties are inextricably intertwined, with the protein inducing bilayer deformations associated with scrambling, while the surrounding lipids modulate TMEM16 conformation and activity.
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Abstract
Platelets are the major cellular contributor to arterial thrombosis. However, activated platelets form two distinct subpopulations during thrombosis. Pro-aggregatory platelets aggregate to form the main body of the thrombus. In contrast, procoagulant platelets expose phosphatidylserine on their outer surface and promote thrombin generation. This apparently all-or-nothing segregation into subpopulations indicates that, during activation, platelets commit to becoming procoagulant or pro-aggregatory. Although the signaling pathways that control this commitment are not understood, distinct cytosolic and mitochondrial Ca2+ signals in different subpopulations are likely to be central. In this review, we discuss how these Ca2+ signals control procoagulant platelet formation and whether this process can be targeted pharmacologically to prevent arterial thrombosis.
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Affiliation(s)
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge Cambridge, UK
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30
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The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes. Nat Struct Mol Biol 2021; 28:825-834. [PMID: 34625749 PMCID: PMC8500837 DOI: 10.1038/s41594-021-00665-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 08/19/2021] [Indexed: 02/04/2023]
Abstract
Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3.8 Å. Its membrane-spanning region carrying 22 charged amino acids adopts a cuboid-like structure stabilized by salt bridges between hydrophilic residues in transmembrane helices. Phosphatidylcholine binding was observed in a hydrophobic cleft on the surface exposed to the outer leaflet of the plasma membrane. Six charged residues placed from top to bottom inside the molecule were essential for scrambling phospholipids in inward and outward directions, apparently providing a pathway for their translocation. A tryptophan residue was present between the head group of phosphatidylcholine and the extracellular end of the path. Its mutation to alanine made the Xkr8-Basigin complex constitutively active, indicating that it plays a vital role in regulating its scramblase activity. The structure of Xkr8-Basigin provides insights into the molecular mechanisms underlying phospholipid scrambling.
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31
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Le SC, Yang H. Structure-Function of TMEM16 Ion Channels and Lipid Scramblases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1349:87-109. [PMID: 35138612 PMCID: PMC11020148 DOI: 10.1007/978-981-16-4254-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The TMEM16 protein family comprises two novel classes of structurally conserved but functionally distinct membrane transporters that function as Ca2+-dependent Cl- channels (CaCCs) or dual functional Ca2+-dependent ion channels and phospholipid scramblases. Extensive functional and structural studies have advanced our understanding of TMEM16 molecular mechanisms and physiological functions. TMEM16A and TMEM16B CaCCs control transepithelial fluid transport, smooth muscle contraction, and neuronal excitability, whereas TMEM16 phospholipid scramblases mediate the flip-flop of phospholipids across the membrane to allow phosphatidylserine externalization, which is essential in a plethora of important processes such as blood coagulation, bone development, and viral and cell fusion. In this chapter, we summarize the major methods in studying TMEM16 ion channels and scramblases and then focus on the current mechanistic understanding of TMEM16 Ca2+- and voltage-dependent channel gating as well as their ion and phospholipid permeation.
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Affiliation(s)
- Son C Le
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Huanghe Yang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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32
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Yasuhara K, Morigaki K. New lipid membrane technologies for reconstitution, analysis, and utilization of 'living' membrane proteins. Biophys Physicobiol 2020; 17:125-129. [PMID: 33240738 PMCID: PMC7671742 DOI: 10.2142/biophysico.bsj-2020021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022] Open
Affiliation(s)
- Kazuma Yasuhara
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kenichi Morigaki
- Biosignal Research Center, Kobe University, Kobe, Hyogo 657-8501, Japan.,Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo 657-8501, Japan
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33
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Clarke R, Hossain K, Cao K. Physiological roles of transverse lipid asymmetry of animal membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183382. [DOI: 10.1016/j.bbamem.2020.183382] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
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34
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Feng S, Dang S, Han TW, Ye W, Jin P, Cheng T, Li J, Jan YN, Jan LY, Cheng Y. Cryo-EM Studies of TMEM16F Calcium-Activated Ion Channel Suggest Features Important for Lipid Scrambling. Cell Rep 2020; 28:567-579.e4. [PMID: 31291589 PMCID: PMC6684876 DOI: 10.1016/j.celrep.2019.06.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/03/2019] [Accepted: 06/05/2019] [Indexed: 12/25/2022] Open
Abstract
As a Ca2+-activated lipid scramblase and ion channel that mediates Ca2+ influx, TMEM16F relies on both functions to facilitate extracellular vesicle generation, blood coagulation, and bone formation. How a bona fide ion channel scrambles lipids remains elusive. Our structural analyses revealed the coexistence of an intact channel pore and PIP2-dependent protein conformation changes leading to membrane distortion. Correlated to the extent of membrane distortion, many tightly bound lipids are slanted. Structure-based mutagenesis studies further reveal that neutralization of some lipid-binding residues or those near membrane distortion specifically alters the onset of lipid scrambling, but not Ca2+ influx, thus identifying features outside of channel pore that are important for lipid scrambling. Together, our studies demonstrate that membrane distortion does not require open hydrophilic grooves facing the membrane interior and provide further evidence to suggest separate pathways for lipid scrambling and ion permeation. TMEM16F is a calcium-activated ion channel and lipid scramblase linked to the bleeding disorder Scott syndrome. Feng et al. examine cryo-EM structures of TMEM16F with or without Ca2+ ions and PIP2 nanodisc supplementation and identify structural features for lipid binding and membrane distortion critical for lipid scrambling activity.
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Affiliation(s)
- Shengjie Feng
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shangyu Dang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tina Wei Han
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wenlei Ye
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peng Jin
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tong Cheng
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Junrui Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lily Yeh Jan
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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35
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Soga N, Ota A, Nakajima K, Watanabe R, Ueno H, Noji H. Monodisperse Liposomes with Femtoliter Volume Enable Quantitative Digital Bioassays of Membrane Transporters and Cell-Free Gene Expression. ACS NANO 2020; 14:11700-11711. [PMID: 32864949 DOI: 10.1021/acsnano.0c04354] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Digital bioassays have emerged as a new category of bioanalysis. However, digital bioassays for membrane transporter proteins have not been well established yet despite high demands in molecular physiology and molecular pharmacology due to the lack of biologically functional monodisperse liposomes with femtoliter volumes. Here, we established a simple and robust method to produce femtoliter-sized liposomes (femto-liposomes). We prepared 106 monodispersed water-in-oil droplets stabilized by a lipid monolayer using a polyethylene glycol-coated femtoliter reactor array device. Droplets were subjected to the optimized emulsion transfer process for femto-liposome production. Liposomes were monodispersed (coefficient of variation = 5-15%) and had suitable diameter (0.6-5.3 μm) and uniform volumes of subfemtoliter or a few femtoliters; thus, they were termed uniform femto-liposomes. The unilamellarity of uniform femto-liposomes allowed quantitative single-molecule analysis of passive and active transporter proteins: α-hemolysin and FoF1-ATPase. Digital gene expression in uniform femto-liposomes (cell-free transcription and translation from single DNA molecules) was also demonstrated, showing the versatility of digital assays for membrane transporter proteins and cell-free synthetic biology.
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Affiliation(s)
- Naoki Soga
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Ota
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kota Nakajima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rikiya Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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36
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Nagata S, Segawa K. Sensing and clearance of apoptotic cells. Curr Opin Immunol 2020; 68:1-8. [PMID: 32853880 DOI: 10.1016/j.coi.2020.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/07/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Macrophages specifically engulf apoptotic cells but not healthy cells. Phosphatidylserine (PtdSer) is localized at the inner leaflet of plasma membranes as a result of the action of flippases (ATP11A and 11C). When cells undergo apoptosis, caspase 3 cleaves and inactivates the flippases, while simultaneously cleaving XKR8 to activate its phospholipid scramblase activity. PtdSer is thus swiftly and irreversibly exposed to the cell surface as an 'eat me' signal. Tissue resident macrophages recognize the apoptotic cells using a PtdSer-receptor TIM4 and engulf them with TAM tyrosine-kinase receptors, and integrins. The PtdSer 'eat me' signal appears to override 'don't eat me' signals in most cases.
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Affiliation(s)
- Shigekazu Nagata
- Laboratory of Biochemistry & Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Katsumori Segawa
- Laboratory of Biochemistry & Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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37
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Le T, Le SC, Zhang Y, Liang P, Yang H. Evidence that polyphenols do not inhibit the phospholipid scramblase TMEM16F. J Biol Chem 2020; 295:12537-12544. [PMID: 32709749 DOI: 10.1074/jbc.ac120.014872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/23/2020] [Indexed: 01/06/2023] Open
Abstract
TMEM16 Ca2+-activated phospholipid scramblases (CaPLSases) mediate rapid transmembrane phospholipid flip-flop and as such play essential roles in various physiological and pathological processes such as blood coagulation, skeletal development, viral infection, cell-cell fusion, and ataxia. Pharmacological tools specifically targeting TMEM16 CaPLSases are urgently needed to understand these novel membrane transporters and their contributions to health and disease. Tannic acid (TA) and epigallocatechin gallate (EGCG) were recently reported as promising TMEM16F CaPLSase inhibitors. However, our present study shows that TA and EGCG do not inhibit the phospholipid-scrambling or ion conduction activities of the dual-functional TMEM16F. Instead, we found that TA and EGCG mainly acted as fluorescence quenchers that rapidly suppress the fluorophores conjugated to annexin V, a phosphatidylserine-binding probe commonly used to report on TMEM16 CaPLSase activity. These data demonstrate the false positive effects of TA and EGCG on inhibiting TMEM16F phospholipid scrambling and discourage the use of these polyphenols as CaPLSase inhibitors. Appropriate controls as well as a combination of both fluorescence imaging and electrophysiological validation are necessary in future endeavors to develop TMEM16 CaPLSase inhibitors.
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Affiliation(s)
- Trieu Le
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Son C Le
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Yang Zhang
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Pengfei Liang
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Huanghe Yang
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA .,Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
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38
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Öhlinger T, Müllner EW, Fritz M, Sauer T, Werning M, Baron DM, Salzer U. Lysophosphatidic acid-induced pro-thrombotic phosphatidylserine exposure and ionophore-induced microvesiculation is mediated by the scramblase TMEM16F in erythrocytes. Blood Cells Mol Dis 2020; 83:102426. [PMID: 32222693 DOI: 10.1016/j.bcmd.2020.102426] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 12/31/2022]
Abstract
Recent studies indicate that erythrocytes actively modulate blood clotting and thrombus formation. The lipid mediator lysophosphatidic acid (LPA) is produced by activated platelets, and triggers a signaling process in erythrocytes. This results in cellular calcium uptake and exposure of phosphatidylserine (PS) at the cell surface, thereby generating activated membrane binding sites for factors of the clotting cascade. Moreover, erythrocytes of patients with a bleeding disorder and mutations in the scramblase TMEM16F show impaired PS exposure and microvesiculation upon treatment with calcium ionophore. We report that TMEM16F inhibitors tannic acid (TA) and epigallocatechin-3-gallate (EGCG) inhibit LPA-induced PS exposure and calcium uptake at low micromolar concentrations; fluoxetine, an antidepressant and a known activator of TMEM16F, enhances these processes. These effectors likewise modulate erythrocyte PS exposure and microvesicle shedding induced by calcium ionophore treatment. Further, LPA-treated erythrocytes triggered thrombin generation in platelet-free plasma which was partially impaired in the presence of TA and EGCG. Thus, this study suggests that LPA activates the scramblase TMEM16F in erythrocytes, thereby possibly mediating a pro-thrombotic function in these cells. EGCG as well as fluoxetine, substances with potentially high plasma concentrations due to alimentation or medical treatment, should be considered as potential effectors of systemic hemostatic regulation.
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Affiliation(s)
- Thomas Öhlinger
- Center for Medical Biochemistry, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria; Department of Anaesthesia, Intensive Care Medicine and Pain Medicine, Medical University of Vienna, Vienna, Austria
| | - Ernst W Müllner
- Center for Medical Biochemistry, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Magdalena Fritz
- Center for Medical Biochemistry, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Thomas Sauer
- Center for Medical Biochemistry, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Maike Werning
- Center for Medical Biochemistry, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - David M Baron
- Department of Anaesthesia, Intensive Care Medicine and Pain Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Salzer
- Center for Medical Biochemistry, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria.
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39
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Zhang Y, Le T, Grabau R, Mohseni Z, Kim H, Natale DR, Feng L, Pan H, Yang H. TMEM16F phospholipid scramblase mediates trophoblast fusion and placental development. SCIENCE ADVANCES 2020; 6:eaba0310. [PMID: 32494719 PMCID: PMC7202889 DOI: 10.1126/sciadv.aba0310] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/19/2020] [Indexed: 05/12/2023]
Abstract
Cell-cell fusion or syncytialization is fundamental to the reproduction, development, and homeostasis of multicellular organisms. In addition to various cell type-specific fusogenic proteins, cell surface externalization of phosphatidylserine (PS), a universal eat-me signal in apoptotic cells, has been observed in different cell fusion events. Nevertheless, the molecular underpinnings of PS externalization and cellular mechanisms of PS-facilitated cell-cell fusion are unclear. Here, we report that TMEM16F, a Ca2+-activated phospholipid scramblase (CaPLSase), plays an essential role in placental trophoblast fusion by translocating PS to cell surface independent of apoptosis. The placentas from the TMEM16F knockout mice exhibit deficiency in trophoblast syncytialization and placental development, which lead to perinatal lethality. We thus identified a new biological function of TMEM16F CaPLSase in trophoblast fusion and placental development. Our findings provide insight into understanding cell-cell fusion mechanism of other cell types and on mitigating pregnancy complications such as miscarriage, intrauterine growth restriction, and preeclampsia.
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Affiliation(s)
- Yang Zhang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Trieu Le
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Ryan Grabau
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA
| | - Zahra Mohseni
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Hoejeong Kim
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - David R. Natale
- Departments of Obstetrics and Gynaecology and Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Liping Feng
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Jiao Tong University School of Medicine, Shanghai, China
| | - Hua Pan
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA
| | - Huanghe Yang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Corresponding author.
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40
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Reddy EC, Rand ML. Procoagulant Phosphatidylserine-Exposing Platelets in vitro and in vivo. Front Cardiovasc Med 2020; 7:15. [PMID: 32195268 PMCID: PMC7062866 DOI: 10.3389/fcvm.2020.00015] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
The physiological heterogeneity of platelets leads to diverse responses and the formation of discrete subpopulations upon platelet stimulation. Procoagulant platelets are an example of such subpopulations, a key characteristic of which is exposure either of the anionic aminophospholipid phosphatidylserine (PS) or of tissue factor on the activated platelet surface. This review focuses on the former, in which PS exposure on a subpopulation of platelets facilitates assembly of the intrinsic tenase and prothrombinase complexes, thereby accelerating thrombin generation on the activated platelet surface, contributing importantly to the hemostatic process. Mechanisms involved in platelet PS exposure, and accompanying events, induced by physiologically relevant agonists are considered then contrasted with PS exposure resulting from intrinsic pathway-mediated apoptosis in platelets. Pathologies of PS exposure, both inherited and acquired, are described. A consideration of platelet PS exposure as an antithrombotic target concludes the review.
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Affiliation(s)
- Emily C Reddy
- Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Margaret L Rand
- Division of Haematology/Oncology, Translational Medicine, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.,Departments of Laboratory Medicine & Pathobiology, Biochemistry, and Paediatrics, University of Toronto, Toronto, ON, Canada
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41
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Galle JN, Hegemann JH. Exofacial phospholipids at the plasma membrane: ill-defined targets for early infection processes. Biol Chem 2020; 400:1323-1334. [PMID: 31408428 DOI: 10.1515/hsz-2019-0187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/06/2019] [Indexed: 02/04/2023]
Abstract
The eukaryotic plasma membrane (PM) consists largely of phospholipids and proteins, and separates the intracellular compartments from the extracellular space. It also serves as a signaling platform for cell-to-cell communication and an interaction platform for the molecular crosstalk between pathogens and their target cells. Much research has been done to elucidate the interactions between pathogens and host membrane proteins. However, little is known about the interactions between pathogens and membrane phospholipids, although reports have described a contribution of phospholipids to cell recognition and/or invasion during early infection by diverse pathogens. Thus, during adhesion to the host cell, the obligate intracellular bacterial pathogens Chlamydia spp., the facultative intracellular pathogen Helicobacter pylori and the facultative aerobic pathogen Vibrio parahaemolyticus, interact with exofacial phospholipids. This review focuses on several prominent instances of pathogen interaction with host-cell phospholipids.
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Affiliation(s)
- Jan N Galle
- Lehrstuhl für Funktionelle Genomforschung der Mikroorganismen, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Johannes H Hegemann
- Lehrstuhl für Funktionelle Genomforschung der Mikroorganismen, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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42
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Komatsu T, Urano Y. Chemical toolbox for 'live' biochemistry to understand enzymatic functions in living systems. J Biochem 2020; 167:139-149. [PMID: 31553443 DOI: 10.1093/jb/mvz074] [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: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 11/12/2022] Open
Abstract
In this review, we present an overview of the recent advances in chemical toolboxes that are used to provide insights into 'live' protein functions in living systems. Protein functions are mediated by various factors inside of cells, such as protein-protein interactions, posttranslational modifications, and they are also subject to environmental factors such as pH, redox states and crowding conditions. Obtaining a true understanding of protein functions in living systems is therefore a considerably difficult task. Recent advances in research tools have allowed us to consider 'live' biochemistry as a valid approach to precisely understand how proteins function in a live cell context.
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Affiliation(s)
- Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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43
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Nagata S, Sakuragi T, Segawa K. Flippase and scramblase for phosphatidylserine exposure. Curr Opin Immunol 2020; 62:31-38. [DOI: 10.1016/j.coi.2019.11.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/25/2019] [Indexed: 01/30/2023]
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44
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Yang X, Cheng X, Tang Y, Qiu X, Wang Y, Kang H, Wu J, Wang Z, Liu Y, Chen F, Xiao X, Mackman N, Billiar TR, Han J, Lu B. Bacterial Endotoxin Activates the Coagulation Cascade through Gasdermin D-Dependent Phosphatidylserine Exposure. Immunity 2019; 51:983-996.e6. [PMID: 31836429 DOI: 10.1016/j.immuni.2019.11.005] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/11/2019] [Accepted: 11/08/2019] [Indexed: 01/09/2023]
Abstract
Excessive activation of the coagulation system leads to life-threatening disseminated intravascular coagulation (DIC). Here, we examined the mechanisms underlying the activation of coagulation by lipopolysaccharide (LPS), the major cell-wall component of Gram-negative bacteria. We found that caspase-11, a cytosolic LPS receptor, activated the coagulation cascade. Caspase-11 enhanced the activation of tissue factor (TF), an initiator of coagulation, through triggering the formation of gasdermin D (GSDMD) pores and subsequent phosphatidylserine exposure, in a manner independent of cell death. GSDMD pores mediated calcium influx, which induced phosphatidylserine exposure through transmembrane protein 16F, a calcium-dependent phospholipid scramblase. Deletion of Casp11, ablation of Gsdmd, or neutralization of phosphatidylserine or TF prevented LPS-induced DIC. In septic patients, plasma concentrations of interleukin (IL)-1α and IL-1β, biomarkers of GSDMD activation, correlated with phosphatidylserine exposure in peripheral leukocytes and DIC scores. Our findings mechanistically link immune recognition of LPS to coagulation, with implications for the treatment of DIC.
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Affiliation(s)
- Xinyu Yang
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China
| | - Xiaoye Cheng
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China
| | - Yiting Tang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410000, P.R. China
| | - Xianhui Qiu
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China
| | - Yupeng Wang
- National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Haixia Kang
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine Shanghai 200025, P.R. China
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhongtai Wang
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China
| | - Yukun Liu
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China
| | - Fangping Chen
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China
| | - Xianzhong Xiao
- Department of Pathophysiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410000, P.R. China; Key Laboratory of Sepsis Translational Medicine of Hunan, Central South University, Changsha, Hunan Province 410000, P.R. China
| | - Nigel Mackman
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ben Lu
- Department of Hematology and Critical Care Medicine, The 3rd Xiangya Hospital, Central South University, Changsha 410000, P.R. China; Department of Pathophysiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410000, P.R. China; Key Laboratory of Sepsis Translational Medicine of Hunan, Central South University, Changsha, Hunan Province 410000, P.R. China.
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45
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Synthetic protein-conductive membrane nanopores built with DNA. Nat Commun 2019; 10:5018. [PMID: 31685824 PMCID: PMC6828756 DOI: 10.1038/s41467-019-12639-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2019] [Indexed: 11/08/2022] Open
Abstract
AbstractNanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.
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46
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Abstract
Tissue macrophages rapidly recognize and engulf apoptotic cells. These events require the display of so-called eat-me signals on the apoptotic cell surface, the most fundamental of which is phosphatidylserine (PtdSer). Externalization of this phospholipid is catalysed by scramblase enzymes, several of which are activated by caspase cleavage. PtdSer is detected both by macrophage receptors that bind to this phospholipid directly and by receptors that bind to a soluble bridging protein that is independently bound to PtdSer. Prominent among the latter receptors are the MER and AXL receptor tyrosine kinases. Eat-me signals also trigger macrophages to engulf virus-infected or metabolically traumatized, but still living, cells, and this 'murder by phagocytosis' may be a common phenomenon. Finally, the localized presentation of PtdSer and other eat-me signals on delimited cell surface domains may enable the phagocytic pruning of these 'locally dead' domains by macrophages, most notably by microglia of the central nervous system.
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Affiliation(s)
- Greg Lemke
- Molecular Neurobiology Laboratory, Immunobiology and Microbial Pathogenesis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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47
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Minagawa Y, Ueno H, Tabata KV, Noji H. Mobile imaging platform for digital influenza virus counting. LAB ON A CHIP 2019; 19:2678-2687. [PMID: 31312832 DOI: 10.1039/c9lc00370c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Droplet-based digital bioassays enable highly sensitive and quantitative analysis of biomolecules, and are thought to be suitable for point-of-care diagnosis. However, digital bioassays generally require fluorescence microscopy for detection, which is too large for point-of-care testing. Here, we developed a simple smartphone-based mobile imaging platform for digital bioassays. The size of the mobile imaging platform was 23 × 10 × 7 cm (length × width × height). With this platform, a digital enzyme assay of bovine alkaline phosphatase was successfully completed. Digital influenza virus counting-based on a fluorogenic assay for neuraminidase activity of the virus-was also demonstrated. Distinct fluorescence spots derived from single virus particles were observed with the mobile imaging platform. The number of detected fluorescence spots showed good linearity against the virus titer, suggesting that high sensitivity and quantification were achieved, although the imaging with the mobile platform detected 60% of influenza virus particles that were identified with conventional fluorescence microscopy. The lower detection efficiency is due to its relatively lower signal-to-noise ratio than that found with conventional microscopes, and unavoidable intrinsic heterogeneity of neuraminidase activity among virus particles. Digital influenza virus counting with the mobile imaging platform still showed 100 times greater sensitivity than that with a commercial rapid influenza test kit. Virus detection of clinical samples was also successfully demonstrated, suggesting the potential to realize a highly sensitive point-of-care system for influenza virus detection with smartphones.
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Affiliation(s)
- Yoshihiro Minagawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
| | - Hiroshi Ueno
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
| | - Kazuhito V Tabata
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
| | - Hiroyuki Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
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48
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Ye W, Han TW, He M, Jan YN, Jan LY. Dynamic change of electrostatic field in TMEM16F permeation pathway shifts its ion selectivity. eLife 2019; 8:e45187. [PMID: 31318330 PMCID: PMC6690719 DOI: 10.7554/elife.45187] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022] Open
Abstract
TMEM16F is activated by elevated intracellular Ca2+, and functions as a small-conductance ion channel and as a phospholipid scramblase. In contrast to its paralogs, the TMEM16A/B calcium-activated chloride channels, mouse TMEM16F has been reported as a cation-, anion-, or non-selective ion channel, without a definite conclusion. Starting with the Q559K mutant that shows no current rundown and less outward rectification in excised patch, we found that the channel shifted its ion selectivity in response to the change of intracellular Ca2+ concentration, with an increased permeability ratio of Cl- to Na+ (PCl-/PNa+) at a higher Ca2+ level. The gradual shift of relative ion permeability did not correlate with the channel activation state. Instead, it was indicative of an alteration of electrostatic field in the permeation pathway. The dynamic change of ion selectivity suggests a charge-screening mechanism for TMEM16F ion conduction, and it provides hints to further studies of TMEM16F physiological functions.
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Affiliation(s)
- Wenlei Ye
- Department of PhysiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Tina W Han
- Department of PhysiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Mu He
- Department of PhysiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Yuh Nung Jan
- Department of PhysiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Lily Yeh Jan
- Department of PhysiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
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49
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Chandra G, Defour A, Mamchoui K, Pandey K, Mishra S, Mouly V, Sreetama S, Mahad Ahmad M, Mahjneh I, Morizono H, Pattabiraman N, Menon AK, Jaiswal JK. Dysregulated calcium homeostasis prevents plasma membrane repair in Anoctamin 5/TMEM16E-deficient patient muscle cells. Cell Death Discov 2019; 5:118. [PMID: 31341644 PMCID: PMC6639303 DOI: 10.1038/s41420-019-0197-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 01/30/2023] Open
Abstract
Autosomal recessive mutations in Anoctamin 5 (ANO5/TMEM16E), a member of the transmembrane 16 (TMEM16) family of Ca2+-activated ion channels and phospholipid scramblases, cause adult-onset muscular dystrophies (limb girdle muscular dystrophy 2L (LGMD2L) and Miyoshi Muscular Dystrophy (MMD3). However, the molecular role of ANO5 is unclear and ANO5 knockout mouse models show conflicting requirements of ANO5 in muscle. To study the role of ANO5 in human muscle cells we generated a myoblast line from a MMD3-patient carrying the c.2272C>T mutation, which we find causes the mutant protein to be degraded. The patient myoblasts exhibit normal myogenesis, but are compromised in their plasma membrane repair (PMR) ability. The repair deficit is linked to the poor ability of the endoplasmic reticulum (ER) to clear cytosolic Ca2+ increase caused by focal plasma membrane injury. Expression of wild-type ANO5 or pharmacological prevention of injury-triggered cytosolic Ca2+ overload enable injured patient muscle cells to repair. A homology model of ANO5 shows that several of the known LGMD2L/MMD3 patient mutations line the transmembrane region of the protein implicated in its channel activity. These results point to a role of cytosolic Ca2+ homeostasis in PMR, indicate a role for ANO5 in ER-mediated cytosolic Ca2+ uptake and identify normalization of cytosolic Ca2+ homeostasis as a potential therapeutic approach to treat muscular dystrophies caused by ANO5 deficit.
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Affiliation(s)
- Goutam Chandra
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Aurelia Defour
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA.,7Present Address: Aix Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, 13385 Marseille, France
| | - Kamel Mamchoui
- 2Center for Research in Myology, Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Kalpana Pandey
- 3Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 USA
| | - Soumya Mishra
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Vincent Mouly
- 2Center for Research in Myology, Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - SenChandra Sreetama
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Mohammad Mahad Ahmad
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Ibrahim Mahjneh
- 4Department of Neurology, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Hiroki Morizono
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA.,5Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20037 USA
| | | | - Anant K Menon
- 3Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 USA
| | - Jyoti K Jaiswal
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA.,5Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20037 USA
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50
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Ousingsawat J, Schreiber R, Kunzelmann K. TMEM16F/Anoctamin 6 in Ferroptotic Cell Death. Cancers (Basel) 2019; 11:E625. [PMID: 31060306 PMCID: PMC6562394 DOI: 10.3390/cancers11050625] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022] Open
Abstract
Ca2+ activated Cl- channels (TMEM16A; ANO1) support cell proliferation and cancer growth. Expression of TMEM16A is strongly enhanced in different types of malignomas. In contrast, TMEM16F (ANO6) operates as a Ca2+ activated chloride/nonselective ion channel and scrambles membrane phospholipids to expose phosphatidylserine at the cell surface. Both phospholipid scrambling and cell swelling induced through activation of nonselective ion currents appear to destabilize the plasma membrane thereby causing cell death. There is growing evidence that activation of TMEM16F contributes to various forms of regulated cell death. In the present study, we demonstrate that ferroptotic cell death, occurring during peroxidation of plasma membrane phospholipids activates TMEM16F. Ferroptosis was induced by erastin, an inhibitor of the cystine-glutamate antiporter and RSL3, an inhibitor of glutathione peroxidase 4 (GPX4). Cell death was largely reduced in the intestinal epithelium, and in peritoneal macrophages isolated from mice with tissue-specific knockout of TMEM16F. We show that TMEM16F is activated during erastin and RSL3-induced ferroptosis. In contrast, inhibition of ferroptosis by ferrostatin-1 and by inhibitors of TMEM16F block TMEM16F currents and inhibit cell death. We conclude that activation of TMEM16F is a crucial component during ferroptotic cell death, a finding that may be useful to induce cell death in cancer cells.
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Affiliation(s)
- Jiraporn Ousingsawat
- Institut für Physiologie, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Rainer Schreiber
- Institut für Physiologie, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Karl Kunzelmann
- Institut für Physiologie, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
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